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HH Suite

HH Suite

The HHsearch/HHblits software package is distributed under Gnu Public License, Version 3.

Prerequisites

Below is a list of prerequisites for using HH Suite:

To load HH Suite type the following:

$ module load gcc blast psipred hhsuite

The uniprot20 and nr20 databases can be found in /share/apps/databases. To save typing you may want to alias the datbase you will be referencing.

alias hhbits='hhbits -d /share/apps/databases/uniprot20

The HH Suite userguide may be found on farm.caes.ucdavis.edu:/share/apps/hhsuite-2.0.9/hhsuite-userguide.pdf

Test Run

qlogin
module load gcc blast psipred hhsuite

Module GCC 4.5.0 Loaded. Module blast 2.2.22 loaded. Module psipred 3.21 loaded. Module hhsuite 2.0.9 loaded.

hhsearch -cpu 4 -i $HHSUITE_HOME/data/query.a3m -d /share/apps/databases/uniprot20_02Sep11_hhm_db -o ~/outputfile
/share/apps/hhsuite-2.0.9/data/query.a3m is in A2M, A3M or FASTA format
Read /share/apps/hhsuite-2.0.9/data/query.a3m with 59 sequences
Alignment in /share/apps/hhsuite-2.0.9/data/query.a3m contains 431 match states
59 out of 59 sequences passed filter (90% max pairwise sequence identity)
Effective number of sequences exp(entropy) = 4.3 
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Realigning 120 database HMMs using HMM-HMM Maximum Accuracy algorithm
...........
Query         sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3
Match_columns 431
No_of_seqs    59 out of 59
Neff          4.3 
Searched_HMMs 44750
Date          Wed Feb  1 16:19:26 2012
Command       hhsearch -cpu 4 -i /share/apps/hhsuite-2.0.9/data/query.a3m -d /share/apps/databases/uniprot20_02Sep11_hhm_db -o /home/bill/query.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 cl|ROYGENIBA|169|236 GD18431;   95.7 0.00043 9.7E-09   67.5   0.0   98  204-317    69-170 (236)
  2 cl|KICNORIBA|151|232 Kinase-li  95.7 0.00047   1E-08   67.4   0.0   99  203-316    70-172 (232)
  3 cl|KORXODABE|156|871 G-type le  95.4 0.00088   2E-08   75.5   0.0   81  218-315   565-649 (871)
  4 cl|PUDQUTIBE|168|219 Protein k  95.0  0.0017 3.9E-08   62.9   0.0   89  216-316    59-152 (219)
  5 cl|COMBOSIBA|57|221 Protein ki  94.7  0.0027 6.1E-08   61.6   0.0   97  204-317    47-148 (221)
  6 cl|XULDOKEBE|67|360 Probable r  94.3  0.0042 9.5E-08   64.2   0.0   97  204-316    99-199 (360)
  7 cl|BEZRAFABE|157|878 G-type le  94.3  0.0046   1E-07   70.0   0.0   83  219-318   572-660 (878)
  8 cl|LEBNORIBE|70|230 STK-type p  93.8  0.0078 1.7E-07   58.7   0.0   98  204-316    37-138 (230)
  9 cl|KADXIQEBE|63|366 Pto kinase  93.6  0.0094 2.1E-07   61.7   0.0   96  205-316   100-199 (366)
 10 cl|REVWOCABE|52|1081 Probable   92.6    0.02 4.6E-07   66.0   0.0   78  218-310   799-880 (1081)
 11 cl|ZELMICABE|219|1160 Receptor  90.6   0.058 1.3E-06   63.1   0.0   86  216-315   866-955 (1160)
 12 cl|FAHZUBABE|135|1206 Probable  90.5   0.061 1.4E-06   63.1   0.0   97  187-310   872-973 (1206)
 13 cl|MUGZEHEBE|86|389 Os08g03353  90.4   0.063 1.4E-06   56.1   0.0   87  216-315    99-189 (389)
 14 cl|RETZECABE|80|1038 Probably   89.7   0.083 1.9E-06   61.2   0.0   84  216-315   748-836 (1038)
 15 cl|RIQDEDABE|53|950 Putative l  89.1     0.1 2.2E-06   60.0   0.0   85  216-315   644-732 (950)
 16 cl|QAWHICABA|55|1090 Leucine-r  88.5    0.12 2.7E-06   60.0   0.0   87  216-315   810-901 (1090)
 17 cl|MEWVIBEBE|65|475 Serine/thr  88.4    0.12 2.8E-06   55.1   0.0   98  204-316   154-255 (475)
 18 cl|CIYHUBEBE|54|437 Probable p  87.8    0.15 3.3E-06   53.9   0.0   95  214-321   171-269 (437)
 19 cl|QUWYACABA|393|1249 LRR rece  87.8    0.15 3.3E-06   60.2   0.0   85  216-315   952-1040(1249)
 20 cl|PIMNELABA|71|641 NFR1a; Nod  87.1    0.18   4E-06   54.9   0.0   79  219-316   390-475 (641)
 21 cl|CEFLIFABE|55|877 Probably i  85.7    0.25 5.5E-06   56.3   0.0   84  218-315   569-657 (877)
 22 cl|NAMHUCABE|97|1142 Leucine-r  83.0    0.41 9.1E-06   56.1   0.0   85  216-315   867-956 (1142)
 23 cl|SIWXOZABE|64|416 Aminoglyco  79.7    0.66 1.5E-05   49.1   0.0   33  203-235   120-160 (416)
 24 cl|YEYMUKABA|120|637 Serine/th  79.1    0.71 1.6E-05   51.3   0.0   93  201-321   358-460 (637)
 25 cl|MOXSUDUBA|183|46 Conserv. [  78.2     0.8 1.8E-05   34.2   0.0   32   12-47      3-37  (46)
 26 cl|MICHIKABE|188|660 Probable   74.8     1.2 2.6E-05   49.9   0.0   44  269-315   130-174 (660)
 27 cl|WAPBADABA|75|1042 Probable   74.6     1.2 2.6E-05   51.1   0.0   88  215-317   687-781 (1042)
 28 cl|ZIWLELABA|105|616 Probable   69.6     1.9 4.2E-05   47.8   0.0   42  273-317   116-157 (616)
 29 cl|GASKAGABA|57|754 Wall-assoc  68.5     2.1 4.6E-05   48.5   0.0  101  201-316   459-567 (754)
 30 cl|GOLZIVABE|79|456 Protein ki  68.4     2.1 4.6E-05   45.4   0.0   50  216-278   179-232 (456)
 31 cl|TUPPILABA|58|592 Protein ki  66.9     2.4 5.3E-05   46.9   0.0   26  296-321   407-432 (592)
 32 cl|FUMWESIBE|159|222 AGAP00429  66.7     2.4 5.3E-05   41.3   0.0   48  155-203   133-180 (222)
 33 cl|RALLIDABE|91|972 Probable r  66.2     2.5 5.6E-05   48.8   0.0   93  203-315   595-695 (972)
 34 cl|SILDUPABA|85|563 Probable s  64.0     2.9 6.5E-05   45.2   0.0  101  218-332   263-389 (563)
 35 cl|VUXQURIBA|56|213 Calcineuri  61.1     3.6   8E-05   40.3   0.0   73  138-212   118-194 (213)
 36 cl|ZAGTETEBA|106|297 Secretago  60.8     3.7 8.2E-05   41.8   0.0   50  169-222   166-219 (297)
 37 cl|NOMRAYIBE|86|181 Calmodulin  58.8     4.2 9.4E-05   38.9   0.0   60  137-201    68-128 (181)
 38 cl|YOTWELIBA|92|233 Calcium-bi  57.4     4.6  0.0001   39.7   0.0   59  137-196   157-216 (233)
 39 cl|PURFICABE|62|1163 Probable   57.1     4.7 0.00011   46.8   0.0  114  204-331   787-925 (1163)
 40 cl|QAKHEWOBA|71|83 EF hand fam  55.9     5.1 0.00011   33.9   0.0   55  134-194     8-63  (83)
 41 cl|ROGVIXIBA|118|185 Calmoduli  54.5     5.5 0.00012   38.2   0.0   61  131-197   113-174 (185)
 42 cl|BAXXUFABE|162|756 Cysteine-  53.9     5.8 0.00013   45.1   0.0   98  203-315   454-555 (756)
 43 cl|LAKBAHABE|153|758 Protein k  53.4     5.9 0.00013   44.3   0.0  114  184-318   381-517 (758)
 44 cl|NOMRAYIBE|86|181 Calmodulin  51.8     6.6 0.00015   37.6   0.0   61  136-197   104-165 (181)
 45 cl|PALWURIBA|58|199 MGC83560 p  51.5     6.7 0.00015   38.1   0.0   65  173-246    70-134 (199)
 46 cl|MOPWOGABE|59|731 Protein ST  50.7       7 0.00016   44.3   0.0  175  202-402   454-677 (731)
 47 cl|BUFCABUBA|74|57 ATP synthas  50.7       7 0.00016   31.0   0.0   15   34-48      9-23  (57)
 48 cl|LIMZOHABA|110|653 Tyrosine-  49.8     7.4 0.00017   43.3   0.0   23  217-239   434-460 (653)
 49 cl|LASYUHEBE|192|368 Acyl-CoA   49.6     7.5 0.00017   40.9   0.0   46  203-249    83-136 (368)
 50 cl|XIXQABABA|98|2855 Spectrin   49.3     7.7 0.00017   47.9   0.0   56  141-196  2678-2757(2855)
 51 cl|NUNMOBOBA|59|188 Calmodulin  49.0     7.8 0.00017   37.2   0.0   60  133-198    97-157 (188)
 52 cl|ZIGBIPABA|121|538 Calcium-d  45.1     9.8 0.00022   41.4   0.0   61  129-196   431-492 (538)
 53 cl|BEDXOLABE|285|643 2-octapre  45.0     9.9 0.00022   42.7   0.0   81  216-321   302-388 (643)
 54 cl|ROSLACABA|102|1239 Protein   44.9      10 0.00022   44.6   0.0  106  185-316   870-1004(1239)
 55 cl|LASYUHEBA|94|376 Acyl-CoA d  44.6      10 0.00023   39.9   0.0   34  203-236    95-136 (376)
 56 cl|DETREQOBA|227|123 Protein S  44.5      10 0.00023   34.3   0.0   53  148-201    37-89  (123)
 57 cl|KICSAZABA|58|413 Probable s  44.2      10 0.00023   40.2   0.0   26  292-317   149-174 (413)
 58 cl|VORBIQOBA|57|104 Exported p  43.6      11 0.00024   33.2   0.0   20   29-48      1-20  (104)
 59 cl|SAHRIVABA|144|474 ABC trans  43.6      11 0.00024   40.9   0.0   55  269-326   278-336 (474)
 60 cl|LATZAKABE|69|689 Probable L  42.1      12 0.00026   42.3   0.0   81  217-312   406-490 (689)
 61 cl|NUNMOBOBA|59|188 Calmodulin  41.9      12 0.00027   36.0   0.0   64  136-205    27-91  (188)
 62 cl|QINFUHABE|105|681 Cysteine-  41.3      12 0.00028   42.1   0.0   98  204-316   406-507 (681)
 63 cl|GISSIHABE|55|729 Receptor-l  40.3      13 0.00029   41.3   0.0  130  155-315   384-529 (729)
 64 cl|GUCTITIBE|97|220 Probable c  39.9      13  0.0003   36.5   0.0   60  137-201   110-170 (220)
 65 cl|GEDBOKOBA|51|145 Curlin gen  38.8      14 0.00032   34.0   0.0   27  325-354    32-58  (145)
 66 cl|NESNAFOBA|115|157 Calmoduli  38.1      15 0.00033   34.5   0.0   56  137-198    16-72  (157)
 67 cl|VUXTIZABE|155|412 Aminoglyc  38.1      15 0.00033   39.3   0.0   33  203-235   128-168 (412)
 68 cl|REHBIDABE|55|793 Wall-assoc  36.8      16 0.00036   41.8   0.0   87  215-315   510-601 (793)
 69 cl|YADVOSIBA|92|188 Novel prot  36.7      16 0.00036   35.2   0.0   69  171-248    51-119 (188)
 70 cl|GUYDERIBE|100|225 Guanylyl   36.0      17 0.00038   35.9   0.0   86  137-226   105-193 (225)
 71 cl|YUDFEWIBA|88|192 Membrane p  35.5      17 0.00039   34.6   0.0   17   32-48     45-61  (192)
 72 cl|NUTLEDABE|71|818 Probable s  35.4      18 0.00039   41.4   0.0   40  279-319   338-377 (818)
 73 cl|KITBAVIBA|52|176 IscU; SUF   34.2      19 0.00042   34.2   0.0   16   22-38    129-144 (176)
 74 cl|RECLAHABE|100|723 Probable   33.9      19 0.00043   40.9   0.0   44  269-315   154-198 (723)
 75 cl|RIBGOGABE|69|737 L-type lec  33.7      20 0.00044   40.9   0.0   81  218-313   437-521 (737)
 76 cl|GAYNAHABA|55|643 Interleuki  33.0      20 0.00045   39.5   0.0   84  218-315   259-346 (643)
 77 cl|RABYUBUBA|178|55 ATP syntha  32.4      21 0.00047   27.4   0.0   14   36-49      9-22  (55)
 78 cl|DOSHARIBE|84|218 Calmodulin  32.0      22 0.00048   35.1   0.0   58  132-195   143-201 (218)
 79 cl|GAGCAQEBA|123|316 Myelin pr  31.9      22 0.00049   36.2   0.0   26   29-54    168-195 (316)
 80 cl|BILSAYIBE|67|161 Probable c  31.8      22 0.00049   33.4   0.0   58  134-197    92-150 (161)
 81 cl|DAVDACOBA|272|165 Sigma fac  30.9      23 0.00052   33.1   0.0   26  324-352    50-75  (165)
 82 cl|RECLAHABA|133|712 Probable   30.5      24 0.00053   40.1   0.0   42  272-316   124-165 (712)
 83 cl|DOPPOFOBA|128|185 GK25095;   29.5      26 0.00057   33.8   0.0   46  148-198    83-128 (185)
 84 cl|SOKKEGABE|129|768 Probable   29.4      26 0.00057   40.3   0.0   44  269-315   164-208 (768)
 85 cl|ZAGTETEBA|106|297 Secretago  29.3      26 0.00058   35.9   0.0   39  169-209    78-116 (297)
 86 cl|LAVGEQOBA|235|120 Probable   28.8      27  0.0006   31.6   0.0   47    6-52     70-117 (120)
 87 cl|GUBMIVIBA|55|192 Probable r  28.7      27  0.0006   33.6   0.0   18  337-354    24-41  (192)
 88 cl|TIVMEDABE|61|948 Serine/thr  27.9      28 0.00063   40.8   0.0  110  203-324   326-443 (948)
 89 cl|VEHTEMIBA|57|229 Calcium an  27.8      29 0.00064   34.3   0.0   28  170-197   184-211 (229)
 90 cl|MUWVICUBA|156|55 ATP syntha  27.6      29 0.00065   27.3   0.0   14   36-49      9-22  (55)
 91 cl|FEHYUHABE|284|670 Serine/th  27.2      30 0.00066   39.2   0.0   68  228-316    96-164 (670)
 92 cl|VUXYABUBA|3511|72 ATP synth  27.1      30 0.00067   28.7   0.0   14   35-48     20-33  (72)
 93 cl|VITCIQIBA|77|188 Calcium an  26.8      31 0.00069   33.4   0.0   50  148-198   120-169 (188)
 94 cl|QUKSULABE|178|661 Calcium-d  26.7      31 0.00069   38.9   0.0   53  137-196   513-566 (661)
 95 cl|MUBBOHOBA|315|155 Cytochrom  25.7      33 0.00074   32.1   0.0   42    6-47     86-128 (155)
 96 cl|MATRIRABE|75|531 Calcium-de  25.4      34 0.00075   37.8   0.0   55  136-197   445-500 (531)
 97 cl|CONGUVIBE|570|185 Myosin, e  25.1      34 0.00077   32.7   0.0   62  130-197   105-167 (185)
 98 cl|NAWKAGIBA|174|202 Neurocalc  24.3      36 0.00081   33.2   0.0   73  137-212   105-185 (202)
 99 cl|QUPVITIBE|69|200 Squidulin;  23.9      37 0.00084   33.1   0.0   62  133-200   113-175 (200)
100 cl|BUGLAGIBE|91|256 Chromosome  23.8      38 0.00085   34.0   0.0   69  137-211   131-200 (256)
101 cl|GESWEYIBA|114|181 Calmoduli  23.7      38 0.00085   32.6   0.0   60  132-197   106-166 (181)
102 cl|DOPPOFOBA|128|185 GK25095;   23.6      38 0.00086   32.6   0.0   58  134-197   105-163 (185)
103 cl|VUXTIZABA|105|377 Aminoglyc  23.5      39 0.00087   35.8   0.0   43  203-245    93-143 (377)
104 cl|HICLIVABA|72|474 Serine-thr  23.4      39 0.00087   34.8   0.0   27  291-317   134-160 (474)
105 cl|GUCTITIBE|97|220 Probable c  23.4      39 0.00087   33.4   0.0   58  133-196   143-201 (220)
106 cl|YOCSEBOBA|54|165 Calcium-bi  23.3      39 0.00088   31.9   0.0   38  168-213    19-56  (165)
107 cl|TOLPENABA|72|515 AKT kinase  22.9      40  0.0009   36.2   0.0   66  229-316   243-310 (515)
108 cl|RAWXANABA|453|589 Paraquat-  21.8      44 0.00098   37.3   0.0   28   27-54     43-74  (589)
109 cl|HAPLEWIBE|267|170 Myosin-ID  21.7      44 0.00099   31.6   0.0   48  147-199    81-128 (170)
110 cl|HIZDEHABE|169|739 L-type le  21.6      45   0.001   38.0   0.0   68  218-308   416-495 (739)
111 cl|DEWYUKABA|74|628 Os01g01171  20.8      48  0.0011   36.5   0.0   85  218-315   371-461 (628)
112 cl|QIRCEVIBE|145|202 Protein d  20.7      48  0.0011   32.4   0.0   60  212-287    49-109 (202)
113 cl|LIVDELIBA|65|254 MGC115522   20.7      48  0.0011   33.3   0.0   55  139-195   161-221 (254)
114 cl|BILSAYIBE|67|161 Probable c  20.7      48  0.0011   31.2   0.0   60  139-202    59-119 (161)
115 cl|CUTCIKABE|87|651 Protein ty  20.7      48  0.0011   37.0   0.0   36  290-325   130-167 (651)
116 cl|XITGEHABA|117|732 Probable   20.4      49  0.0011   37.8   0.0   72  228-315   453-528 (732)
117 cl|LEDHIBABE|102|1757 Dual oxi  20.2      50  0.0011   40.6   0.0   51  141-197   857-908 (1757)
118 cl|CONGUVIBE|570|185 Myosin, e  20.2      50  0.0011   31.6   0.0   49  148-201    87-135 (185)
119 cl|QUCPAVIBE|146|188 Troponin   20.2      50  0.0011   31.9   0.0   19  177-195   153-171 (188)
120 cl|ZUDQISIBA|145|204 Hydrolase  20.1      50  0.0011   32.3   0.0   26  299-324   113-140 (204)


Done
support/hpc/software/hhsuite.txt · Last modified: 2012/02/01 16:20 by tlknight