Query psy13391
Match_columns 146
No_of_seqs 161 out of 1091
Neff 8.6
Searched_HMMs 46136
Date Fri Aug 16 18:17:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13391.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13391hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05399 DNA mismatch repair p 99.9 3.7E-21 8E-26 165.7 15.5 133 1-143 307-441 (854)
2 TIGR01070 mutS1 DNA mismatch r 99.9 5.8E-21 1.3E-25 164.0 15.9 133 1-143 293-427 (840)
3 COG0249 MutS Mismatch repair A 99.8 4.1E-20 8.9E-25 158.1 12.5 138 1-143 305-442 (843)
4 smart00533 MUTSd DNA-binding d 99.8 1.1E-17 2.4E-22 128.9 15.4 135 1-143 24-159 (308)
5 KOG0219|consensus 99.7 5.7E-17 1.2E-21 135.3 11.5 137 1-144 335-471 (902)
6 KOG0221|consensus 99.7 2.5E-16 5.3E-21 128.5 13.9 137 1-144 289-428 (849)
7 PF05192 MutS_III: MutS domain 99.6 3.7E-15 8E-20 108.3 10.3 110 1-117 42-151 (204)
8 KOG0217|consensus 99.4 4.2E-12 9.1E-17 108.6 13.4 141 1-142 583-724 (1125)
9 PRK00409 recombination and DNA 99.4 1.4E-11 3.1E-16 105.8 13.1 128 2-143 34-162 (782)
10 TIGR01069 mutS2 MutS2 family p 99.1 9.8E-10 2.1E-14 94.5 12.6 122 2-143 34-157 (771)
11 KOG0220|consensus 98.9 2.2E-08 4.8E-13 83.7 11.9 133 1-142 303-454 (867)
12 KOG0218|consensus 98.6 2.9E-07 6.3E-12 77.5 10.0 70 1-71 503-576 (1070)
13 COG1193 Mismatch repair ATPase 96.3 0.041 8.8E-07 47.9 9.8 121 2-141 32-153 (753)
14 PF05952 ComX: Bacillus compet 78.9 2.8 6E-05 24.5 2.7 19 15-33 3-21 (57)
15 PF12290 DUF3802: Protein of u 59.3 22 0.00048 23.6 4.0 48 21-68 51-102 (113)
16 PF10589 NADH_4Fe-4S: NADH-ubi 58.1 11 0.00024 20.7 2.2 24 36-59 23-46 (46)
17 PF11690 DUF3287: Protein of u 54.8 24 0.00052 23.4 3.6 58 15-76 41-99 (109)
18 PTZ00473 Plasmodium Vir superf 53.7 56 0.0012 26.7 6.2 24 56-79 137-160 (420)
19 PF07319 DnaI_N: Primosomal pr 41.6 28 0.0006 22.2 2.4 65 57-134 19-83 (94)
20 PRK01026 tetrahydromethanopter 38.1 42 0.0009 20.8 2.6 21 4-24 13-33 (77)
21 PHA03080 putative virion core 37.3 2.2E+02 0.0048 22.9 7.7 42 39-80 69-113 (366)
22 COG4064 MtrG Tetrahydromethano 36.2 58 0.0013 19.8 2.9 30 4-33 13-44 (75)
23 PHA01735 hypothetical protein 35.5 82 0.0018 19.1 3.5 26 43-68 19-44 (76)
24 TIGR01149 mtrG N5-methyltetrah 35.5 52 0.0011 19.9 2.7 22 3-24 9-30 (70)
25 PF04210 MtrG: Tetrahydrometha 35.4 51 0.0011 20.0 2.6 21 4-24 10-30 (70)
26 PF05503 Pox_G7: Poxvirus G7-l 29.4 3E+02 0.0066 22.1 7.7 40 40-79 69-111 (363)
27 PF06569 DUF1128: Protein of u 28.3 1.1E+02 0.0023 18.7 3.2 56 8-68 13-68 (71)
28 PF02609 Exonuc_VII_S: Exonucl 26.5 1.3E+02 0.0027 16.8 5.6 23 42-64 8-30 (53)
29 TIGR01399 hrcV type III secret 24.6 1.7E+02 0.0036 25.9 4.9 45 24-70 504-548 (677)
30 PRK00965 tetrahydromethanopter 24.3 1.3E+02 0.0027 19.5 3.2 27 91-117 32-58 (96)
31 PF15173 FAM180: FAM180 family 24.2 1.8E+02 0.0038 20.1 4.0 41 37-77 72-115 (137)
32 PRK14066 exodeoxyribonuclease 22.6 2E+02 0.0042 17.6 5.6 23 41-63 12-34 (75)
33 PRK14063 exodeoxyribonuclease 22.5 2E+02 0.0043 17.6 5.7 22 42-63 14-35 (76)
34 PRK00578 prfB peptide chain re 22.1 4.3E+02 0.0094 21.4 8.2 6 125-130 129-134 (367)
35 PRK15337 type III secretion sy 21.4 2.3E+02 0.0049 25.1 5.1 45 24-70 514-558 (686)
36 PF05440 MtrB: Tetrahydrometha 21.2 1.5E+02 0.0033 19.2 3.1 27 91-117 31-57 (97)
No 1
>PRK05399 DNA mismatch repair protein MutS; Provisional
Probab=99.87 E-value=3.7e-21 Score=165.65 Aligned_cols=133 Identities=26% Similarity=0.382 Sum_probs=118.5
Q ss_pred CCCCCCChHHHHHHHHHHHHHHhCHHHHHHHHHHhhCCCCCHHHHHHHHhcCCCCHHHHHHHHHHHhhHHHHHHHHHhhh
Q psy13391 1 MKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRVYEGVSQLPKLISILESLV 80 (146)
Q Consensus 1 l~~Pl~d~~~I~~R~d~Ve~f~~~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~~~~~dl~~l~~~l~~~~~i~~~l~~~~ 80 (146)
|++|++|+++|++|||+|++|.+++.++..++. .|++++|++|+++|+..|+++++||..+++++..++.+++.+....
T Consensus 307 l~~Pl~d~~~I~~R~d~Ve~l~~~~~~~~~l~~-~L~~i~Dlerll~ri~~~~~~~~dl~~l~~~l~~~~~l~~~l~~~~ 385 (854)
T PRK05399 307 LHRPLRDREAIEARLDAVEELLEDPLLREDLRE-LLKGVYDLERLLSRIALGRANPRDLAALRDSLEALPELKELLAELD 385 (854)
T ss_pred HhCcCCCHHHHHHHHHHHHHHHhCHHHHHHHHH-HHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 579999999999999999999999999999999 9999999999999999999999999999999999999999987643
Q ss_pred hhhhhhhHHHHHHHHHHhhhhHHHHHHHHHhhhccccc--cccCcceeCCCCCHhHHHHHHHhcc
Q psy13391 81 QNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERF--HSEREFFIRPSFDEDLQGKAIKSNL 143 (146)
Q Consensus 81 ~~~~~~l~~~~l~~l~~~~~~~~~l~~~I~~~id~~~~--~~~~~~~Ik~g~d~~Ld~lr~~~~~ 143 (146)
...+..+...+..+.++.+.|+++|+++++ ..+| ++|++|||++||++|+.++.
T Consensus 386 --------~~~l~~l~~~l~~~~~l~~~i~~~i~~~~~~~~~~~-~~i~~g~~~~Ld~lr~~~~~ 441 (854)
T PRK05399 386 --------SPLLAELAEQLDPLEELADLLERAIVEEPPLLIRDG-GVIADGYDAELDELRALSDN 441 (854)
T ss_pred --------cHHHHHHHhhcccHHHHHHHHHHHHccCCchhcccC-CEECCCCCHHHHHHHHHHHH
Confidence 345666666677899999999999998864 2324 59999999999999998764
No 2
>TIGR01070 mutS1 DNA mismatch repair protein MutS.
Probab=99.87 E-value=5.8e-21 Score=163.95 Aligned_cols=133 Identities=26% Similarity=0.397 Sum_probs=117.8
Q ss_pred CCCCCCChHHHHHHHHHHHHHHhCHHHHHHHHHHhhCCCCCHHHHHHHHhcCCCCHHHHHHHHHHHhhHHHHHHHHHhhh
Q psy13391 1 MKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRVYEGVSQLPKLISILESLV 80 (146)
Q Consensus 1 l~~Pl~d~~~I~~R~d~Ve~f~~~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~~~~~dl~~l~~~l~~~~~i~~~l~~~~ 80 (146)
|++|++|+++|++|||+|++|.++..++..++. .|++++|++|+++|+..|+++|+||..+++++..++.+++.+....
T Consensus 293 l~~Pl~d~~~I~~Rld~Ve~l~~~~~l~~~l~~-~L~~i~Dlerll~ri~~~~~~~~dl~~l~~~l~~~~~l~~~l~~~~ 371 (840)
T TIGR01070 293 LHRPLRDREVLEARQDTVEVLLRHFFLREGLRP-LLKEVGDLERLAARVALGNARPRDLARLRTSLEQLPELRALLEELE 371 (840)
T ss_pred hhCCCCCHHHHHHHHHHHHHHHhCHHHHHHHHH-HhccCcCHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 579999999999999999999999999999999 9999999999999999999999999999999999999999987643
Q ss_pred hhhhhhhHHHHHHHHHHhhhhHHHHHHHHHhhhccccc--cccCcceeCCCCCHhHHHHHHHhcc
Q psy13391 81 QNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERF--HSEREFFIRPSFDEDLQGKAIKSNL 143 (146)
Q Consensus 81 ~~~~~~l~~~~l~~l~~~~~~~~~l~~~I~~~id~~~~--~~~~~~~Ik~g~d~~Ld~lr~~~~~ 143 (146)
...+..+...+..+..+.+.|+++|+++++ .++| +.|++|||++||++|+.++.
T Consensus 372 --------~~~l~~l~~~l~~~~~l~~~i~~~i~~~~~~~~~~~-~~I~~g~~~~Ld~lr~~~~~ 427 (840)
T TIGR01070 372 --------GPTLQALAAQIDDFSELLELLEAALIENPPLVVRDG-GLIREGYDEELDELRAASRE 427 (840)
T ss_pred --------cHHHHHHHHhcccHHHHHHHHHHHHhcCCccccccC-CeeCCCCCHHHHHHHHHHHH
Confidence 345566666777889999999999998764 2335 59999999999999998753
No 3
>COG0249 MutS Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=99.83 E-value=4.1e-20 Score=158.06 Aligned_cols=138 Identities=28% Similarity=0.409 Sum_probs=114.8
Q ss_pred CCCCCCChHHHHHHHHHHHHHHhCHHHHHHHHHHhhCCCCCHHHHHHHHhcCCCCHHHHHHHHHHHhhHHHHHHHHHhhh
Q psy13391 1 MKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRVYEGVSQLPKLISILESLV 80 (146)
Q Consensus 1 l~~Pl~d~~~I~~R~d~Ve~f~~~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~~~~~dl~~l~~~l~~~~~i~~~l~~~~ 80 (146)
|.+|++|.++|+.|||+|++|.++..+++.|+. .|++++|++|+++|+..|+++|+||..+++++..++.+.+.+....
T Consensus 305 l~~PL~~~~~I~~Rld~Ve~l~~~~~l~~~L~~-~L~~v~DleRl~~Rl~~~~~~~rDl~~l~~~l~~~~~i~~~l~~~~ 383 (843)
T COG0249 305 LLQPLLDKEEIEERLDAVEELKDNPELREKLRE-MLKKVPDLERLLSRLSLGRASPRDLLRLRDSLEKIPEIFKLLSSLK 383 (843)
T ss_pred hhCcccCHHHHHHHHHHHHHHHhhhHHHHHHHH-HHhcCcCHHHHHHHHHcCCCChhhHHHHHHHHHHHHHHHHHHhccc
Confidence 579999999999999999999999999999999 9999999999999999999999999999999999999999998754
Q ss_pred hhhhhhhHHHHHHHHHHhhhhHHHHHHHHHhhhccccccccCcceeCCCCCHhHHHHHHHhcc
Q psy13391 81 QNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHSEREFFIRPSFDEDLQGKAIKSNL 143 (146)
Q Consensus 81 ~~~~~~l~~~~l~~l~~~~~~~~~l~~~I~~~id~~~~~~~~~~~Ik~g~d~~Ld~lr~~~~~ 143 (146)
. +..+ ......+. .++.+.++..+++.+|.++++..-..++|+.||+++||++|..++.
T Consensus 384 ~--~~~l-~~~~~~i~-~~~~~~e~~~ll~~~i~~~~~~~~~~~ii~~g~~~eLd~lr~~~~~ 442 (843)
T COG0249 384 S--ESDL-LLLLEDIE-SLDYLAELLELLETAINEDPPLAVRDGIIKEGYNIELDELRDLLNN 442 (843)
T ss_pred c--chhh-hHHhhhhh-ccccHHHHHHHHHHHhhhcchhhcchhHHhcchhHHHHHHHHHHHH
Confidence 2 0101 12222222 3344668999999999999863212269999999999999998763
No 4
>smart00533 MUTSd DNA-binding domain of DNA mismatch repair MUTS family.
Probab=99.78 E-value=1.1e-17 Score=128.93 Aligned_cols=135 Identities=31% Similarity=0.430 Sum_probs=100.5
Q ss_pred CCCCCCChHHHHHHHHHHHHHHhCHHHHHHHHHHhhCCCCCHHHHHHHHhcCCCCHHHHHHHHHHHhhHHHHHHHHHhhh
Q psy13391 1 MKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRVYEGVSQLPKLISILESLV 80 (146)
Q Consensus 1 l~~Pl~d~~~I~~R~d~Ve~f~~~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~~~~~dl~~l~~~l~~~~~i~~~l~~~~ 80 (146)
+++|++|.++|++||++|++|.++..++..++. .|++++|++|++.|+..|++++.||..++.++..+..+.+.+....
T Consensus 24 l~~Pl~~~~~I~~R~~~v~~~~~~~~l~~~l~~-~L~~~~Di~~~l~~~~~~~~~~~el~~l~~~l~~~~~l~~~l~~~~ 102 (308)
T smart00533 24 LLQPLLDLKEINERLDAVEELVENPELRQKLRQ-LLKRIPDLERLLSRIERGRASPRDLLRLYDSLEGLKEIRQLLESLD 102 (308)
T ss_pred HHhhCCCHHHHHHHHHHHHHHHhChHHHHHHHH-HHccCCcHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 468999999999999999999999999999999 9999999999999999999999999999999999999999997643
Q ss_pred hhhhhhhHHHHHHHHHHhhhhHHHHHHHHHh-hhccccccccCcceeCCCCCHhHHHHHHHhcc
Q psy13391 81 QNVEASNLNTILSSLQSLSNDLAKFQEMIET-TIDIERFHSEREFFIRPSFDEDLQGKAIKSNL 143 (146)
Q Consensus 81 ~~~~~~l~~~~l~~l~~~~~~~~~l~~~I~~-~id~~~~~~~~~~~Ik~g~d~~Ld~lr~~~~~ 143 (146)
.. .....+..+. ..+......+.. ..+.+....+.++.|++|+|++||++|+.++.
T Consensus 103 ~~----~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~~~~~~i~~~~s~~Ld~lr~~~~~ 159 (308)
T smart00533 103 GP----LLGLLLKVIL---EPLLELLELLLELLNDDDPLEVNDGGLIKDGFDPELDELREKLEE 159 (308)
T ss_pred cH----HHHHHHHhhc---cchHHHHHHHHHHhccCCcccccCCCeeCCCCCHHHHHHHHHHHH
Confidence 10 0011111111 111112222222 22333322213369999999999999998864
No 5
>KOG0219|consensus
Probab=99.72 E-value=5.7e-17 Score=135.25 Aligned_cols=137 Identities=39% Similarity=0.596 Sum_probs=121.1
Q ss_pred CCCCCCChHHHHHHHHHHHHHHhCHHHHHHHHHHhhCCCCCHHHHHHHHhcCCCCHHHHHHHHHHHhhHHHHHHHHHhhh
Q psy13391 1 MKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRVYEGVSQLPKLISILESLV 80 (146)
Q Consensus 1 l~~Pl~d~~~I~~R~d~Ve~f~~~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~~~~~dl~~l~~~l~~~~~i~~~l~~~~ 80 (146)
+.+|+++++.|++|||.|+.++++...+..++.+.|..+||+.|++.|+. +++..|..++|+....++++..+|.+..
T Consensus 335 ~~qpL~~~~ri~~r~d~v~~l~~~~~~rq~L~~~lL~~~pdi~rl~~~l~--~~~L~d~~r~yq~~~~l~~~~~~l~~~~ 412 (902)
T KOG0219|consen 335 LKQPLRDIDRINERHDLVEALVEDAEIRQKLRDDLLRRIPDISRLARRLM--KANLQDVNRIYQAAKLLPTVVQVLISLS 412 (902)
T ss_pred hhcchHHHHHHHHHhhhHHHHHhhhHHHHHHHHHHhhcChhHHHhhhhhh--hcchHHHHHHHHHHHHhHHHHHHHHhhh
Confidence 46899999999999999999999999999999989999999999999999 8899999999999999999999998754
Q ss_pred hhhhhhhHHHHHHHHHHhhhhHHHHHHHHHhhhccccccccCcceeCCCCCHhHHHHHHHhccc
Q psy13391 81 QNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHSEREFFIRPSFDEDLQGKAIKSNLK 144 (146)
Q Consensus 81 ~~~~~~l~~~~l~~l~~~~~~~~~l~~~I~~~id~~~~~~~~~~~Ik~g~d~~Ld~lr~~~~~~ 144 (146)
.++..+ ...++......+.++..++++++|+++..+ +.|+||+.||++|.++|+.++.+
T Consensus 413 ~~~~~l----l~~~l~~~~~~~~kf~~~ve~t~D~da~ee-~ey~VR~eFdeeL~eLrq~LdeL 471 (902)
T KOG0219|consen 413 ESHNRL----LKSPLTEHLKKLEKFQEMVETTVDLDAEEE-NEYRVRVDFDEELQELREKLDEL 471 (902)
T ss_pred hhhhhh----hhhhhhhhhhhHHHHHHHHHHHhhHhHHhc-CcEEEecccCHHHHHHHHHHHHH
Confidence 322222 333666666788999999999999999877 78999999999999999998865
No 6
>KOG0221|consensus
Probab=99.71 E-value=2.5e-16 Score=128.49 Aligned_cols=137 Identities=20% Similarity=0.286 Sum_probs=120.5
Q ss_pred CCCCCCChHHHHHHHHHHHHHHh--CHHHHHHHHHHhhCCCCCHHHHHHHHhcCCCCHHHHHHHHHHHhhHHHHHHHHHh
Q psy13391 1 MKQPLKDLDAIVERHAAVNILVN--NTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRVYEGVSQLPKLISILES 78 (146)
Q Consensus 1 l~~Pl~d~~~I~~R~d~Ve~f~~--~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~~~~~dl~~l~~~l~~~~~i~~~l~~ 78 (146)
+.+|++|.++|..|+++|.+|+. |.+....|.+ .|++++|+.-+++|+..|+++..+|-.+++++++...|.+++.+
T Consensus 289 f~nPttd~~~l~sR~~~i~~fl~~qNa~~~~~Ls~-~lgr~k~~~~~~~~~~sg~t~l~~W~~~~stv~~~~~i~~~~rs 367 (849)
T KOG0221|consen 289 FTNPTTDLGELSSRLDVIQFFLLPQNADMAQMLSR-LLGRIKNVPLILKRMKSGHTKLSDWQVLYSTVYSALGIRDACRS 367 (849)
T ss_pred hcCCCCcHHHHHHHHHHHHHHhcchhhHHHHHHHH-HHhhcccHHHHHHHHhcCCceechHHHHHHHHHHHHHHHHHHHh
Confidence 35899999999999999999996 7788999999 99999999999999999999999999999999999999999988
Q ss_pred hhhhhhhhhHHHHHHHHHH-hhhhHHHHHHHHHhhhccccccccCcceeCCCCCHhHHHHHHHhccc
Q psy13391 79 LVQNVEASNLNTILSSLQS-LSNDLAKFQEMIETTIDIERFHSEREFFIRPSFDEDLQGKAIKSNLK 144 (146)
Q Consensus 79 ~~~~~~~~l~~~~l~~l~~-~~~~~~~l~~~I~~~id~~~~~~~~~~~Ik~g~d~~Ld~lr~~~~~~ 144 (146)
.+. ...+...+.+ .+.++.+++.++.++||++.+..+|.+.|.+|+|++|||.|..|+-|
T Consensus 368 lp~------s~~~~~~~~~~~~~~l~eia~~~g~vIdF~~S~~~~r~Tv~~giD~elDE~r~~y~~l 428 (849)
T KOG0221|consen 368 LPQ------SIQLFRDIAQEFSDDLHEIASLIGKVIDFEGSLAENRFTVLPGIDPELDEKRRRYMGL 428 (849)
T ss_pred Ccc------chhhhhHHHHHHHHHHHHHHHHhhheeccccccccceEEecCCCChHHHHHHHHHccc
Confidence 762 1334444433 34678999999999999998766688999999999999999999865
No 7
>PF05192 MutS_III: MutS domain III C-terminus.; InterPro: IPR007696 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the core domain (domain 3) found in proteins of the MutS family. The core domain of MutS adopts a multi-helical structure comprised of two subdomains, which are interrupted by the clamp domain. Two of the helices in the core domain comprise the levers that extend towards the DNA. This domain is found associated with Pfam:PF00488, Pfam:PF05188, Pfam:PF01624 and Pfam:PF05190. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterised in [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2O8F_A 3THW_A 3THX_A 2O8C_A 3THY_A 2O8E_A 2O8B_A 3THZ_A 2O8D_A 1FW6_A ....
Probab=99.62 E-value=3.7e-15 Score=108.32 Aligned_cols=110 Identities=26% Similarity=0.487 Sum_probs=92.7
Q ss_pred CCCCCCChHHHHHHHHHHHHHHhCHHHHHHHHHHhhCCCCCHHHHHHHHhcCCCCHHHHHHHHHHHhhHHHHHHHHHhhh
Q psy13391 1 MKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRVYEGVSQLPKLISILESLV 80 (146)
Q Consensus 1 l~~Pl~d~~~I~~R~d~Ve~f~~~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~~~~~dl~~l~~~l~~~~~i~~~l~~~~ 80 (146)
+++|++|+++|++||++|++|.+|+.++..++. .|++++|+++++.|+..|++++.+|..++.++..+..+.+.+...-
T Consensus 42 l~~P~~d~~~I~~R~~~v~~~~~n~~~~~~~~~-~l~~~~di~~~l~~l~~~~~~~~~~~~l~~~l~~~~~i~~~~~~~~ 120 (204)
T PF05192_consen 42 LLQPLTDIEEIEKRQDAVEEFLQNEELREELRS-ILKKIPDIERILKRLRSGRASPQDLLKLYKTLRSIIEIKKLLSERL 120 (204)
T ss_dssp HHS-BS-HHHHHHHHHHHHHHHHTHHHHHHHHH-HHTTC-SHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHCTS
T ss_pred HhCccchHHHHHHHHHHHHHHHHhhhHhhhhhh-hhhccchHHHHHHHHHHhhcChHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 368999999999999999999999999999999 9999999999999999999999999999999999999998865432
Q ss_pred hhhhhhhHHHHHHHHHHhhhhHHHHHHHHHhhhcccc
Q psy13391 81 QNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIER 117 (146)
Q Consensus 81 ~~~~~~l~~~~l~~l~~~~~~~~~l~~~I~~~id~~~ 117 (146)
.. .+.+..+.+.++++..+.+.|+.++|++.
T Consensus 121 ~~------~~~L~~l~~~l~~~~~l~~~i~~~id~~~ 151 (204)
T PF05192_consen 121 ES------SPLLRKLLSSLPDFSELLDEIESTIDEDK 151 (204)
T ss_dssp SS------THHHHHHHHHHCSHHHHHHHHHHHBHTS-
T ss_pred cc------HHHHHHHHHhcccHHHHHHHHHHHHhcCc
Confidence 10 13566666666678999999999999964
No 8
>KOG0217|consensus
Probab=99.42 E-value=4.2e-12 Score=108.57 Aligned_cols=141 Identities=21% Similarity=0.256 Sum_probs=97.4
Q ss_pred CCCCCCChHHHHHHHHHHHHHHhCHHHHHHHHHHhhCCCCCHHHHHHHHhcCCCC-HHHHHHHHHHHhhHHHHHHHHHhh
Q psy13391 1 MKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAG-LKDCYRVYEGVSQLPKLISILESL 79 (146)
Q Consensus 1 l~~Pl~d~~~I~~R~d~Ve~f~~~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~~~-~~dl~~l~~~l~~~~~i~~~l~~~ 79 (146)
+++|++|.+.|++|||+|++|..++..+..+.. .|+++||+||++.|+..+..+ .+++..+..+|..+..+.+++...
T Consensus 583 l~~Pl~~~~~I~~R~dav~~l~~~~~~~~~~~e-~l~klPDlERlL~Rih~~~~~~~k~i~~f~rvLegfk~~~~~~~~~ 661 (1125)
T KOG0217|consen 583 LMAPLCDKEDIKQRQDAVDSLGKAPMDRTKVGE-TLKKLPDLERLLVRIHNGGEKNKKKIADFIRVLEGFKEINKLLGSL 661 (1125)
T ss_pred hhCcCCCHHHHHHHHHHHHHHhcCchhHHHHHH-HHhhCCcHHHHHHHHHhcCccchhHHHHHHHHHHHHHHHHHHHHHH
Confidence 579999999999999999999999999999999 999999999999999998877 666667766777776666666554
Q ss_pred hhhhhhhhHHHHHHHHHHhhhhHHHHHHHHHhhhccccccccCcceeCCCCCHhHHHHHHHhc
Q psy13391 80 VQNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHSEREFFIRPSFDEDLQGKAIKSN 142 (146)
Q Consensus 80 ~~~~~~~l~~~~l~~l~~~~~~~~~l~~~I~~~id~~~~~~~~~~~Ik~g~d~~Ld~lr~~~~ 142 (146)
.......-....+..+...++++..=......+++.....++|.+....|||.++|+.-+..+
T Consensus 662 ~~v~~~~~~~~~is~~~~~~p~~~~~i~~~~~af~r~~a~~eg~i~P~~Gfd~eyD~a~k~~~ 724 (1125)
T KOG0217|consen 662 INVLKEGEGLRLISELLESMPNLSEEIENWTEAFDRVKAVKEGVIVPLEGFDEEYDEAMKRVD 724 (1125)
T ss_pred HHHHHhhHHHHHHHHHhcCcchhhHHHHHHHHHHHHHHHhhcCccCCCccccHHHHHHhhHHH
Confidence 311000000122222222222333333444556665443333666667899999998766543
No 9
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=99.36 E-value=1.4e-11 Score=105.83 Aligned_cols=128 Identities=16% Similarity=0.184 Sum_probs=105.5
Q ss_pred CCCCCChHHHHHHHHHHHHHHhCHHHHHHHHHHhhCCCCCHHHHHHHHhcCC-CCHHHHHHHHHHHhhHHHHHHHHHhhh
Q psy13391 2 KQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKK-AGLKDCYRVYEGVSQLPKLISILESLV 80 (146)
Q Consensus 2 ~~Pl~d~~~I~~R~d~Ve~f~~~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~-~~~~dl~~l~~~l~~~~~i~~~l~~~~ 80 (146)
++|++|+++|++||+.|+.|.. .+...... .|++++|+++++.|+..|. .+|.|+..+.+++..+..+++.+....
T Consensus 34 l~P~~~~~~i~~~l~~~~e~~~--~~~~~~~~-~l~~~~Di~~~l~r~~~g~~l~~~eL~~i~~~l~~~~~l~~~l~~~~ 110 (782)
T PRK00409 34 LDPETDFEEVEELLEETDEAAK--LLRLKGLP-PFEGVKDIDDALKRAEKGGVLSGDELLEIAKTLRYFRQLKRFIEDLE 110 (782)
T ss_pred CCCCCCHHHHHHHHHHHHHHHH--HHHhcCCC-CCCCCccHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4799999999999999999983 33445566 7999999999999999865 889999999999999999999987531
Q ss_pred hhhhhhhHHHHHHHHHHhhhhHHHHHHHHHhhhccccccccCcceeCCCCCHhHHHHHHHhcc
Q psy13391 81 QNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHSEREFFIRPSFDEDLQGKAIKSNL 143 (146)
Q Consensus 81 ~~~~~~l~~~~l~~l~~~~~~~~~l~~~I~~~id~~~~~~~~~~~Ik~g~d~~Ld~lr~~~~~ 143 (146)
.. . ..+.+..+...+..++.+.+.|..+||++ +.|++|+|++|+.+|+.++.
T Consensus 111 ~~--~--~~~~L~~~~~~l~~~~~l~~~i~~~id~~-------g~i~d~aS~eL~~iR~~~~~ 162 (782)
T PRK00409 111 EE--E--ELPILEEWVAKIRTLPELEQEIHNCIDEE-------GEVKDSASEKLRGIRRQLRR 162 (782)
T ss_pred cc--c--chhHHHHHHHcCcCcHHHHHHHHHHhCCC-------CEECCCCCHHHHHHHHHHHH
Confidence 00 0 03456666666778889999999999874 38999999999999998864
No 10
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=99.13 E-value=9.8e-10 Score=94.48 Aligned_cols=122 Identities=16% Similarity=0.120 Sum_probs=101.9
Q ss_pred CCCCCChHHHHHHHHHHHHHHhCHHHHHHHHHHhhCCCCCHHHHHHHHhcCC-CCHHH-HHHHHHHHhhHHHHHHHHHhh
Q psy13391 2 KQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKK-AGLKD-CYRVYEGVSQLPKLISILESL 79 (146)
Q Consensus 2 ~~Pl~d~~~I~~R~d~Ve~f~~~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~-~~~~d-l~~l~~~l~~~~~i~~~l~~~ 79 (146)
+.|+++.++|++|++.|+.|..... .- .|++++|+.+++.|+..|. +++.+ +..++.++..+..++..+...
T Consensus 34 l~P~~~~~~i~~~l~~~~e~~~~~~-----~~-~l~~~~di~~~l~r~~~g~~l~~~e~l~~i~~~l~~~~~l~~~l~~~ 107 (771)
T TIGR01069 34 LKPPKSVEESKEIIIKLTALGSIEN-----NV-RFFGFEDIRELLKRAELGGIVKGLEYILVIQNALKTVKHLKVLSEHV 107 (771)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHhhc-----cC-CcCCCccHHHHHHHHhcCCcCChHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4799999999999999999987432 44 7999999999999999877 78866 999999999999999988653
Q ss_pred hhhhhhhhHHHHHHHHHHhhhhHHHHHHHHHhhhccccccccCcceeCCCCCHhHHHHHHHhcc
Q psy13391 80 VQNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHSEREFFIRPSFDEDLQGKAIKSNL 143 (146)
Q Consensus 80 ~~~~~~~l~~~~l~~l~~~~~~~~~l~~~I~~~id~~~~~~~~~~~Ik~g~d~~Ld~lr~~~~~ 143 (146)
. . .+.+..+...+..++.+...|.++||++ +.|+++++++|+++|+..+.
T Consensus 108 ~-~------~~~L~~~~~~l~~~~~l~~~i~~~id~~-------g~i~d~aS~~L~~ir~~~~~ 157 (771)
T TIGR01069 108 L-D------LEILFHLRLNLITLPPLENDIIACIDDD-------GKVKDGASEELDAIRESLKA 157 (771)
T ss_pred c-c------chHHHHHHhcCCCcHHHHHHHHHHhCCC-------CEECCCcCHHHHHHHHHHHH
Confidence 1 0 2445555556677889999999999864 38999999999999998754
No 11
>KOG0220|consensus
Probab=98.91 E-value=2.2e-08 Score=83.75 Aligned_cols=133 Identities=14% Similarity=0.208 Sum_probs=107.2
Q ss_pred CCCCCCChHHHHHHHHHHHHHHhCHHHHHHHHHHhhCCCCCHHHHHHHHhcCC---------CCHHHHHHHHHHHhhHHH
Q psy13391 1 MKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKK---------AGLKDCYRVYEGVSQLPK 71 (146)
Q Consensus 1 l~~Pl~d~~~I~~R~d~Ve~f~~~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~---------~~~~dl~~l~~~l~~~~~ 71 (146)
+.+|++|...|+.|+++++.+..++.+...++. .+|..+|+++.++++..-. +.......|+.++..+..
T Consensus 303 ilqpl~d~~ti~~rleaiqeL~a~~~L~~~Lr~-~~k~~~dld~~~s~~~~~~~~~~i~~~~s~I~~~~~Lk~tL~lv~~ 381 (867)
T KOG0220|consen 303 ILQPLTDIETINMRLEAIQELLADEELFFGLRS-VIKRFLDLDQLLSVLVQIPTQDTVNAAESKINNLIYLKHTLELVDP 381 (867)
T ss_pred hcccccchhhhhHHHHHHHHHhcCchHhhhhHH-HHhhhhhHHHHHHHHHhhhhHHhhhcchhHHHHHHHHHHHHHHHHH
Confidence 479999999999999999999999999999999 9999999999999987532 234567788888888888
Q ss_pred HHHHHHhhhhhhhhhhHHHHHHHHHHhh--hhHHHHHHHHHhhhccccc--------cccCcceeCCCCCHhHHHHHHHh
Q psy13391 72 LISILESLVQNVEASNLNTILSSLQSLS--NDLAKFQEMIETTIDIERF--------HSEREFFIRPSFDEDLQGKAIKS 141 (146)
Q Consensus 72 i~~~l~~~~~~~~~~l~~~~l~~l~~~~--~~~~~l~~~I~~~id~~~~--------~~~~~~~Ik~g~d~~Ld~lr~~~ 141 (146)
++..+.+.. ...+....+.+ +.+..+.+.|.+.|+++.+ ..+++|.+|.+.+..||-.|+.|
T Consensus 382 ~~~al~~~~--------s~~~~e~~~~~~~~r~~~i~~~i~e~I~dd~l~a~~~l~~~~qkcyAvks~i~~~LDiaR~ty 453 (867)
T KOG0220|consen 382 LKIALKNCN--------SNLLREYYGSFKDKRFGIILEKIKEVINDDALYAKGCLNLRTQKCYAVKSNINGFLDIARRTY 453 (867)
T ss_pred HHHHHhhch--------hHHHHHHHHHhcchHHHHHHHHHHHHhhHHHHhccchhhhhccceeeecccccHHHHHHHHHH
Confidence 888776543 23334444433 4578889999999998763 33478999999999999999987
Q ss_pred c
Q psy13391 142 N 142 (146)
Q Consensus 142 ~ 142 (146)
-
T Consensus 454 ~ 454 (867)
T KOG0220|consen 454 T 454 (867)
T ss_pred H
Confidence 4
No 12
>KOG0218|consensus
Probab=98.63 E-value=2.9e-07 Score=77.49 Aligned_cols=70 Identities=24% Similarity=0.287 Sum_probs=59.8
Q ss_pred CCCCCCChHHHHHHHHHHHHHH---hCHHHHHHHHHHhhCCCCCHHHHHHHHhcCCCCH-HHHHHHHHHHhhHHH
Q psy13391 1 MKQPLKDLDAIVERHAAVNILV---NNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGL-KDCYRVYEGVSQLPK 71 (146)
Q Consensus 1 l~~Pl~d~~~I~~R~d~Ve~f~---~~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~~~~-~dl~~l~~~l~~~~~ 71 (146)
+.+||+|...|++|+|+|+++. ++....+.+++ .|.+.||+.|-++||..|+++| +++..+.+++..+..
T Consensus 503 vtkPLvd~~~I~eRLDAVeeitshssnS~vf~si~~-~l~rlpDl~rgL~rIy~~tCtp~~eff~vlk~iy~a~s 576 (1070)
T KOG0218|consen 503 VTKPLVDVHQIEERLDAVEEITSHSSNSIVFESINQ-MLNRLPDLLRGLNRIYYGTCTPRKEFFFVLKQIYSAVS 576 (1070)
T ss_pred HhcccccHHHHHHHHHHHHHHHhcccchHHHHHHHH-HHHhCcHhHhhHHHHhcccCCcHHHHHHHHHHHHHHHH
Confidence 4689999999999999999994 35558999999 9999999999999999999999 777777666655443
No 13
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=96.34 E-value=0.041 Score=47.92 Aligned_cols=121 Identities=17% Similarity=0.191 Sum_probs=95.0
Q ss_pred CCCCCChHHHHHHHHHHHHHHhCHHHHHHHHHHhhCCCCCHHHHHHHHhcC-CCCHHHHHHHHHHHhhHHHHHHHHHhhh
Q psy13391 2 KQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRK-KAGLKDCYRVYEGVSQLPKLISILESLV 80 (146)
Q Consensus 2 ~~Pl~d~~~I~~R~d~Ve~f~~~~~l~~~lr~~~Lk~i~DleRi~~ri~~~-~~~~~dl~~l~~~l~~~~~i~~~l~~~~ 80 (146)
+.|.++.+.|+..++-++.+...... ...- .++++.|+.-.+.|+..| ...+.++..+...+.....++..++...
T Consensus 32 l~p~~~~~~i~~~~~e~~~~~~~~~~-~g~~--~~~~l~~i~~~l~~~e~g~~l~~~el~~i~~~l~~~~~lkr~~~~~e 108 (753)
T COG1193 32 LKPRTDLELIEEELSETAEALDILED-EGLP--PLGGLNDVSEALGRLEKGGRLHVEELLEISDFLRGFRALKRAIKKLE 108 (753)
T ss_pred cCccccHHHHHHHHHHHHHHHHHHhc-cCCC--CchhhhhhHHHHHHHhhcccCCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 46999999999999999988864332 2222 488899999999999854 4789999999999999999999888754
Q ss_pred hhhhhhhHHHHHHHHHHhhhhHHHHHHHHHhhhccccccccCcceeCCCCCHhHHHHHHHh
Q psy13391 81 QNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHSEREFFIRPSFDEDLQGKAIKS 141 (146)
Q Consensus 81 ~~~~~~l~~~~l~~l~~~~~~~~~l~~~I~~~id~~~~~~~~~~~Ik~g~d~~Ld~lr~~~ 141 (146)
. .. ......+..++.+...|..++|.+ ..|.+..+++|+.+|...
T Consensus 109 ~-------~~--~~~~~~~~~~~~l~~~i~~~id~~-------g~i~d~as~~l~~ir~~l 153 (753)
T COG1193 109 R-------IK--RTLALALIELSDLELEINIPIDDD-------GLIKDRASFELDAIRRQL 153 (753)
T ss_pred h-------HH--HHHHHhhhcchHHHHHHhhhhccc-------ccccccccHHHHHHHhhh
Confidence 2 11 333445567888889999888864 388889999999998765
No 14
>PF05952 ComX: Bacillus competence pheromone ComX; InterPro: IPR009233 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment [].
Probab=78.89 E-value=2.8 Score=24.50 Aligned_cols=19 Identities=42% Similarity=0.482 Sum_probs=16.7
Q ss_pred HHHHHHHHhCHHHHHHHHH
Q psy13391 15 HAAVNILVNNTEARMNLHE 33 (146)
Q Consensus 15 ~d~Ve~f~~~~~l~~~lr~ 33 (146)
|++|.+|++||++...+.+
T Consensus 3 Q~iV~YLv~nPevl~kl~~ 21 (57)
T PF05952_consen 3 QEIVNYLVQNPEVLEKLKE 21 (57)
T ss_pred HHHHHHHHHChHHHHHHHc
Confidence 7899999999998887776
No 15
>PF12290 DUF3802: Protein of unknown function (DUF3802); InterPro: IPR020979 This family of proteins is found in bacteria and are typically between 114 and 143 amino acids in length. There is a conserved KNLFD sequence motif. The annotation with this family suggests that it may be the B subunit of bacterial type IIA DNA topoisomerase but there is no evidence to support this annotation.
Probab=59.34 E-value=22 Score=23.64 Aligned_cols=48 Identities=15% Similarity=0.088 Sum_probs=29.8
Q ss_pred HHhCHHHHHHHHHHhhCC----CCCHHHHHHHHhcCCCCHHHHHHHHHHHhh
Q psy13391 21 LVNNTEARMNLHEYALRG----LPDMQSLAMRIGRKKAGLKDCYRVYEGVSQ 68 (146)
Q Consensus 21 f~~~~~l~~~lr~~~Lk~----i~DleRi~~ri~~~~~~~~dl~~l~~~l~~ 68 (146)
|-+|+++-...|...++. ++|++.+++++-..++++....-|-+...-
T Consensus 51 c~Qnp~L~~~~R~~iirE~Daiv~DLeEVLa~V~~~~aT~eQ~~Fi~Ef~~L 102 (113)
T PF12290_consen 51 CEQNPELEFSQRFQIIREADAIVYDLEEVLASVWNQKATNEQIAFIEEFIGL 102 (113)
T ss_pred HccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 334666655555533443 578888888888888887765555444433
No 16
>PF10589 NADH_4Fe-4S: NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; InterPro: IPR019575 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the F subunit of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoF. This family does not have any members in chloroplast or cyanobacteria, where the quinone may be plastoquinone and NADH may be replaced by NADPH, nor in Methanosarcina, where NADH is replaced by F420H2. This entry represents the iron-sulphur binding domain of the F subunit.; GO: 0055114 oxidation-reduction process; PDB: 3IAS_S 2FUG_A 3I9V_A 3M9S_1 3IAM_A 2YBB_1.
Probab=58.10 E-value=11 Score=20.72 Aligned_cols=24 Identities=17% Similarity=0.219 Sum_probs=17.3
Q ss_pred hCCCCCHHHHHHHHhcCCCCHHHH
Q psy13391 36 LRGLPDMQSLAMRIGRKKAGLKDC 59 (146)
Q Consensus 36 Lk~i~DleRi~~ri~~~~~~~~dl 59 (146)
=-+.+=+..++.++..|++++.|+
T Consensus 23 R~Gt~~l~~~l~~i~~G~~~~~Dl 46 (46)
T PF10589_consen 23 REGTRQLAEILEKIVRGEGTPEDL 46 (46)
T ss_dssp HCCCCHHHHHHHHHTBT---HHHH
T ss_pred HhHHHHHHHHHHHHHcCCCCcccC
Confidence 345677889999999999999886
No 17
>PF11690 DUF3287: Protein of unknown function (DUF3287); InterPro: IPR021704 This eukaryotic family of proteins has no known function.
Probab=54.77 E-value=24 Score=23.39 Aligned_cols=58 Identities=9% Similarity=0.094 Sum_probs=35.7
Q ss_pred HHHHHHHHh-CHHHHHHHHHHhhCCCCCHHHHHHHHhcCCCCHHHHHHHHHHHhhHHHHHHHH
Q psy13391 15 HAAVNILVN-NTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRVYEGVSQLPKLISIL 76 (146)
Q Consensus 15 ~d~Ve~f~~-~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~~~~~dl~~l~~~l~~~~~i~~~l 76 (146)
.+.++.... +..++..-+. ..+++.|| ++-+++..=...|.||.... +..+..|-..|
T Consensus 41 ~~F~~kV~~qH~~~~~e~r~-L~kKi~~l-~veRkmr~Les~p~~W~~~g--f~~~a~iP~~l 99 (109)
T PF11690_consen 41 YDFIDKVVDQHQRYCDERRK-LRKKIQDL-RVERKMRALESHPFDWERRG--FDKVAPIPDML 99 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHHHH-HHHHHHHhccCChHHHHHhc--hHHhccccHHH
Confidence 333333333 5567778887 88889998 55555555567999997653 33443443333
No 18
>PTZ00473 Plasmodium Vir superfamily; Provisional
Probab=53.65 E-value=56 Score=26.71 Aligned_cols=24 Identities=13% Similarity=0.257 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHhhHHHHHHHHHhh
Q psy13391 56 LKDCYRVYEGVSQLPKLISILESL 79 (146)
Q Consensus 56 ~~dl~~l~~~l~~~~~i~~~l~~~ 79 (146)
++++.+|.-....+..|+.++...
T Consensus 137 ~e~ImKL~yFteNig~Ik~lm~~~ 160 (420)
T PTZ00473 137 LEDIMKLFYFTENVGDIKSLMGAP 160 (420)
T ss_pred HHHHHHHHHHHhhhHHHHHHhcCC
Confidence 788999999999999999888754
No 19
>PF07319 DnaI_N: Primosomal protein DnaI N-terminus; InterPro: IPR009928 This entry represents the N terminus (approximately 120 residues) of bacterial primosomal DnaI proteins, although one family member appears to be of viral origin. DnaI is one of the components of the Bacillus subtilis replication restart primosome, and is required for the DnaB75-dependent loading of the DnaC helicase [].; PDB: 2K7R_A.
Probab=41.64 E-value=28 Score=22.16 Aligned_cols=65 Identities=14% Similarity=0.177 Sum_probs=32.7
Q ss_pred HHHHHHHHHHhhHHHHHHHHHhhhhhhhhhhHHHHHHHHHHhhhhHHHHHHHHHhhhccccccccCcceeCCCCCHhH
Q psy13391 57 KDCYRVYEGVSQLPKLISILESLVQNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHSEREFFIRPSFDEDL 134 (146)
Q Consensus 57 ~dl~~l~~~l~~~~~i~~~l~~~~~~~~~~l~~~~l~~l~~~~~~~~~l~~~I~~~id~~~~~~~~~~~Ik~g~d~~L 134 (146)
...-.+.+-+.+=+.++.++..+..+ +....+. .++..|.+.+...=.... +++-.+-+||-|.|
T Consensus 19 ~~~~~l~~~vl~dp~V~~Fl~~h~~e----Lt~~~i~------rsl~kLyEy~~e~~~~~~---~~~~~~~~Gy~P~L 83 (94)
T PF07319_consen 19 ERYEQLKQEVLSDPEVQAFLQEHQPE----LTQEMIE------RSLSKLYEYVSERKKCQN---EGCPNIAKGYQPKL 83 (94)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHSTTT------HHHHH------HTHHHHHHHHHS-SS-TT---TTS--SSTTEEEEE
T ss_pred HHHHHHHHHHHcCHHHHHHHHHhHHh----cCHHHHH------HHHHHHHHHHHHHHHHhh---cCCCCcCCCCCCeE
Confidence 34567777788888888888877311 1121111 134455555443221111 25567888887765
No 20
>PRK01026 tetrahydromethanopterin S-methyltransferase subunit G; Provisional
Probab=38.07 E-value=42 Score=20.80 Aligned_cols=21 Identities=24% Similarity=0.224 Sum_probs=17.5
Q ss_pred CCCChHHHHHHHHHHHHHHhC
Q psy13391 4 PLKDLDAIVERHAAVNILVNN 24 (146)
Q Consensus 4 Pl~d~~~I~~R~d~Ve~f~~~ 24 (146)
|-.|.+++.+|+|-+|.=+++
T Consensus 13 ~~~d~~~i~~rLD~iEeKVEf 33 (77)
T PRK01026 13 DPKDFKEIQKRLDEIEEKVEF 33 (77)
T ss_pred CHHHHHHHHHHHHHHHHHHHH
Confidence 556788999999999988874
No 21
>PHA03080 putative virion core protein; Provisional
Probab=37.32 E-value=2.2e+02 Score=22.93 Aligned_cols=42 Identities=10% Similarity=0.334 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHhcCC---CCHHHHHHHHHHHhhHHHHHHHHHhhh
Q psy13391 39 LPDMQSLAMRIGRKK---AGLKDCYRVYEGVSQLPKLISILESLV 80 (146)
Q Consensus 39 i~DleRi~~ri~~~~---~~~~dl~~l~~~l~~~~~i~~~l~~~~ 80 (146)
+.|+-+++.|+.... ++..||++|+.+|..+..-+.++....
T Consensus 69 ~~~l~~iL~~Lr~~~~yV~n~~EF~rLynsL~RfTH~~SFF~tC~ 113 (366)
T PHA03080 69 IEHLKKILDNLRRHSVYVCNSTEFWRLYNSLYRFTHCKSFFNTCM 113 (366)
T ss_pred HHHHHHHHHHhcccceeecChHHHHHHHHHHHHHhhhHHHHHHhH
Confidence 345556677776433 678899999999999888777776543
No 22
>COG4064 MtrG Tetrahydromethanopterin S-methyltransferase, subunit G [Coenzyme metabolism]
Probab=36.15 E-value=58 Score=19.77 Aligned_cols=30 Identities=17% Similarity=0.171 Sum_probs=20.9
Q ss_pred CCCChHHHHHHHHHHHHHHhC--HHHHHHHHH
Q psy13391 4 PLKDLDAIVERHAAVNILVNN--TEARMNLHE 33 (146)
Q Consensus 4 Pl~d~~~I~~R~d~Ve~f~~~--~~l~~~lr~ 33 (146)
|-.|.+++++|+|-+|.=+++ .++.+.+-+
T Consensus 13 ~~~dfne~~kRLdeieekvef~~~Ev~Qr~Gk 44 (75)
T COG4064 13 DPDDFNEIHKRLDEIEEKVEFVNGEVYQRIGK 44 (75)
T ss_pred CHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence 346788999999999987773 444444443
No 23
>PHA01735 hypothetical protein
Probab=35.55 E-value=82 Score=19.14 Aligned_cols=26 Identities=19% Similarity=0.138 Sum_probs=20.9
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHHhh
Q psy13391 43 QSLAMRIGRKKAGLKDCYRVYEGVSQ 68 (146)
Q Consensus 43 eRi~~ri~~~~~~~~dl~~l~~~l~~ 68 (146)
+.+++|+..|.++-.|+..-.+.|+.
T Consensus 19 ~El~~RiksgeATtaDL~AA~d~Lk~ 44 (76)
T PHA01735 19 NELLSRIKSGEATTADLRAACDWLKS 44 (76)
T ss_pred HHHHHHHhcCcccHHHHHHHHHHHHH
Confidence 46788999999999998887666643
No 24
>TIGR01149 mtrG N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit G. coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.
Probab=35.47 E-value=52 Score=19.94 Aligned_cols=22 Identities=9% Similarity=0.182 Sum_probs=18.1
Q ss_pred CCCCChHHHHHHHHHHHHHHhC
Q psy13391 3 QPLKDLDAIVERHAAVNILVNN 24 (146)
Q Consensus 3 ~Pl~d~~~I~~R~d~Ve~f~~~ 24 (146)
-|-.|.+++.+|+|-+|.=+++
T Consensus 9 v~~~d~~~i~~rLd~iEeKVEf 30 (70)
T TIGR01149 9 VEPDEFNEVMKRLDEIEEKVEF 30 (70)
T ss_pred cCHHHHHHHHHHHHHHHHHHHH
Confidence 3557889999999999988874
No 25
>PF04210 MtrG: Tetrahydromethanopterin S-methyltransferase, subunit G ; InterPro: IPR005866 This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane
Probab=35.40 E-value=51 Score=20.01 Aligned_cols=21 Identities=19% Similarity=0.257 Sum_probs=17.5
Q ss_pred CCCChHHHHHHHHHHHHHHhC
Q psy13391 4 PLKDLDAIVERHAAVNILVNN 24 (146)
Q Consensus 4 Pl~d~~~I~~R~d~Ve~f~~~ 24 (146)
|-.+.+++.+|+|.+|.=+++
T Consensus 10 ~~~~~~~i~~rLd~iEeKvEf 30 (70)
T PF04210_consen 10 DPDDFNEIMKRLDEIEEKVEF 30 (70)
T ss_pred CHHHHHHHHHHHHHHHHHHHh
Confidence 446788999999999998874
No 26
>PF05503 Pox_G7: Poxvirus G7-like ; InterPro: IPR008787 This family of proteins which include vaccinia virus G7L and fowlpox virus FPV120 are associated with the intracellualar mature virus particle. The function of this family of proteins is not known.
Probab=29.38 E-value=3e+02 Score=22.12 Aligned_cols=40 Identities=13% Similarity=0.309 Sum_probs=29.1
Q ss_pred CCHHHHHHHHhcCC---CCHHHHHHHHHHHhhHHHHHHHHHhh
Q psy13391 40 PDMQSLAMRIGRKK---AGLKDCYRVYEGVSQLPKLISILESL 79 (146)
Q Consensus 40 ~DleRi~~ri~~~~---~~~~dl~~l~~~l~~~~~i~~~l~~~ 79 (146)
.|+-.++.|+.... ++-.||++|+.+|..+..-..++...
T Consensus 69 ~~L~~iL~~Lr~~s~yV~n~~EF~rLynsL~RfTH~~SFF~tC 111 (363)
T PF05503_consen 69 EHLKSILDNLRRYSVYVCNSSEFWRLYNSLYRFTHCKSFFNTC 111 (363)
T ss_pred HHHHHHHHhhcccceeecChHHHHHHHHHHHHHhhhHHHHHHh
Confidence 34455666666433 67789999999999988877777654
No 27
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=28.33 E-value=1.1e+02 Score=18.72 Aligned_cols=56 Identities=16% Similarity=0.152 Sum_probs=25.1
Q ss_pred hHHHHHHHHHHHHHHhCHHHHHHHHHHhhCCCCCHHHHHHHHhcCCCCHHHHHHHHHHHhh
Q psy13391 8 LDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRVYEGVSQ 68 (146)
Q Consensus 8 ~~~I~~R~d~Ve~f~~~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~~~~~dl~~l~~~l~~ 68 (146)
+++|.+++.+|..=.=+++-+..-..+-|+.++|+- . ..++-+|.+.-.+.+-|.+
T Consensus 13 Ie~Ik~KL~mvN~~~i~~~~f~~~~yedl~diy~~V---~--~K~~fS~sEm~aI~~ELG~ 68 (71)
T PF06569_consen 13 IEEIKQKLNMVNAGAIKPEDFSEEKYEDLKDIYEMV---M--SKDSFSPSEMQAIAEELGQ 68 (71)
T ss_pred HHHHHHHHHHhhHHhCCHHhCChhhHHHHHHHHHHH---H--hccCCCHHHHHHHHHHHHh
Confidence 566777777776544332212111111222222221 1 1334566666666655544
No 28
>PF02609 Exonuc_VII_S: Exonuclease VII small subunit; InterPro: IPR003761 Exonuclease VII is composed of two non-identical subunits; one large subunit and 4 small ones []. This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield nucleoside 5'-phosphates.; GO: 0008855 exodeoxyribonuclease VII activity, 0006308 DNA catabolic process, 0009318 exodeoxyribonuclease VII complex; PDB: 1VP7_F.
Probab=26.51 E-value=1.3e+02 Score=16.82 Aligned_cols=23 Identities=13% Similarity=0.473 Sum_probs=16.0
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHH
Q psy13391 42 MQSLAMRIGRKKAGLKDCYRVYE 64 (146)
Q Consensus 42 leRi~~ri~~~~~~~~dl~~l~~ 64 (146)
++.|+.++..|..+..+...+|.
T Consensus 8 Le~Iv~~Le~~~~sLdes~~lye 30 (53)
T PF02609_consen 8 LEEIVEKLESGELSLDESLKLYE 30 (53)
T ss_dssp HHHHHHHHHTT-S-HHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHHH
Confidence 67788888888888877777653
No 29
>TIGR01399 hrcV type III secretion protein, HrcV family. Members of this family are closely homologous to the flagellar biosynthesis protein FlhA (TIGR01398) and should all participate in type III secretion systems. Examples include InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc. Type III secretion systems resemble flagellar biogenesis systems, and may share the property of translocating special classes of peptides through the membrane.
Probab=24.57 E-value=1.7e+02 Score=25.87 Aligned_cols=45 Identities=9% Similarity=0.157 Sum_probs=37.6
Q ss_pred CHHHHHHHHHHhhCCCCCHHHHHHHHhcCCCCHHHHHHHHHHHhhHH
Q psy13391 24 NTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRVYEGVSQLP 70 (146)
Q Consensus 24 ~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~~~~~dl~~l~~~l~~~~ 70 (146)
++.+.+++. ..-.+..+.++++++-.-+.+.+|+..+.+++....
T Consensus 504 ~p~Lv~Elp--~~~~l~~i~~VLq~LL~E~VsIRdl~~IlEtLad~~ 548 (677)
T TIGR01399 504 YPELVKEVQ--RVLPLQRIAEVLQRLVSEQVSIRNLRLILETLIEWA 548 (677)
T ss_pred HHHHHHHHh--ccCCHHHHHHHHHHHHhCCCccccHHHHHHHHHHHh
Confidence 677888884 355688999999999999999999999988887653
No 30
>PRK00965 tetrahydromethanopterin S-methyltransferase subunit B; Provisional
Probab=24.33 E-value=1.3e+02 Score=19.54 Aligned_cols=27 Identities=15% Similarity=0.291 Sum_probs=22.4
Q ss_pred HHHHHHHhhhhHHHHHHHHHhhhcccc
Q psy13391 91 ILSSLQSLSNDLAKFQEMIETTIDIER 117 (146)
Q Consensus 91 ~l~~l~~~~~~~~~l~~~I~~~id~~~ 117 (146)
-+.++.+.+..++.+++-+.+++|++.
T Consensus 32 s~~pi~E~i~kLe~~addL~nsLdP~~ 58 (96)
T PRK00965 32 DMDPIEEEINKLEALADDLENSLDPRN 58 (96)
T ss_pred echHHHHHHHHHHHHHHHHHhccCCCC
Confidence 356777778889999999999999875
No 31
>PF15173 FAM180: FAM180 family
Probab=24.18 E-value=1.8e+02 Score=20.12 Aligned_cols=41 Identities=22% Similarity=0.289 Sum_probs=27.7
Q ss_pred CCCCCHHHHHHHHhc--CCCCHHHHHHHH-HHHhhHHHHHHHHH
Q psy13391 37 RGLPDMQSLAMRIGR--KKAGLKDCYRVY-EGVSQLPKLISILE 77 (146)
Q Consensus 37 k~i~DleRi~~ri~~--~~~~~~dl~~l~-~~l~~~~~i~~~l~ 77 (146)
|.++|++|.++.++. |..++.|+-... ..++++..+....+
T Consensus 72 k~l~di~rl~~~ls~~~g~L~~~DFErtlLTlvy~ayr~~~s~~ 115 (137)
T PF15173_consen 72 KSLPDIRRLSAQLSQHRGPLSPEDFERTLLTLVYTAYRLANSSE 115 (137)
T ss_pred CcHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHHhhh
Confidence 667899999999985 556788887654 44445555554433
No 32
>PRK14066 exodeoxyribonuclease VII small subunit; Provisional
Probab=22.58 E-value=2e+02 Score=17.62 Aligned_cols=23 Identities=9% Similarity=0.377 Sum_probs=18.1
Q ss_pred CHHHHHHHHhcCCCCHHHHHHHH
Q psy13391 41 DMQSLAMRIGRKKAGLKDCYRVY 63 (146)
Q Consensus 41 DleRi~~ri~~~~~~~~dl~~l~ 63 (146)
-++.|++++-.|..+..+.+.+|
T Consensus 12 ~LE~IV~~LE~g~l~Leesl~ly 34 (75)
T PRK14066 12 KLEEVVKKLEGGELSLDDSLKAF 34 (75)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHH
Confidence 36788888888888888777765
No 33
>PRK14063 exodeoxyribonuclease VII small subunit; Provisional
Probab=22.45 E-value=2e+02 Score=17.62 Aligned_cols=22 Identities=9% Similarity=0.344 Sum_probs=17.4
Q ss_pred HHHHHHHHhcCCCCHHHHHHHH
Q psy13391 42 MQSLAMRIGRKKAGLKDCYRVY 63 (146)
Q Consensus 42 leRi~~ri~~~~~~~~dl~~l~ 63 (146)
++.|++++..|..+..+...+|
T Consensus 14 LE~Iv~~LE~~~l~Leesl~ly 35 (76)
T PRK14063 14 LEHLVSKLEQGDVPLEEAISYF 35 (76)
T ss_pred HHHHHHHHHCCCCCHHHHHHHH
Confidence 6778888888888887776665
No 34
>PRK00578 prfB peptide chain release factor 2; Validated
Probab=22.10 E-value=4.3e+02 Score=21.41 Aligned_cols=6 Identities=17% Similarity=0.047 Sum_probs=2.7
Q ss_pred eeCCCC
Q psy13391 125 FIRPSF 130 (146)
Q Consensus 125 ~Ik~g~ 130 (146)
.|++|.
T Consensus 129 eI~aG~ 134 (367)
T PRK00578 129 TIHAGA 134 (367)
T ss_pred EEecCC
Confidence 345544
No 35
>PRK15337 type III secretion system protein InvA; Provisional
Probab=21.39 E-value=2.3e+02 Score=25.10 Aligned_cols=45 Identities=4% Similarity=0.110 Sum_probs=37.4
Q ss_pred CHHHHHHHHHHhhCCCCCHHHHHHHHhcCCCCHHHHHHHHHHHhhHH
Q psy13391 24 NTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRVYEGVSQLP 70 (146)
Q Consensus 24 ~~~l~~~lr~~~Lk~i~DleRi~~ri~~~~~~~~dl~~l~~~l~~~~ 70 (146)
++.+.+++.. .-.+..+.++++++-.-+.+.+|+..+.+++.-..
T Consensus 514 ~p~Lv~elp~--~l~l~~i~~VLq~LL~E~VsIRdl~~IlE~l~d~~ 558 (686)
T PRK15337 514 YPDLLKEVYR--HATVQRISEVLQRLLSERISIRNMKLIMEALALWA 558 (686)
T ss_pred CHHHHHHHhc--cCCHHHHHHHHHHHHhcCCccccHHHHHHHHHHHh
Confidence 6788888844 44588999999999999999999999988886543
No 36
>PF05440 MtrB: Tetrahydromethanopterin S-methyltransferase subunit B; InterPro: IPR008690 The N5-methyltetrahydromethanopterin: coenzyme M (2.1.1.86 from EC) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump [].; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane
Probab=21.17 E-value=1.5e+02 Score=19.19 Aligned_cols=27 Identities=11% Similarity=0.215 Sum_probs=22.6
Q ss_pred HHHHHHHhhhhHHHHHHHHHhhhcccc
Q psy13391 91 ILSSLQSLSNDLAKFQEMIETTIDIER 117 (146)
Q Consensus 91 ~l~~l~~~~~~~~~l~~~I~~~id~~~ 117 (146)
-+.++.+.+..++.+++-+.+++|++.
T Consensus 31 s~~pi~eqi~kLe~~addl~nsLdP~~ 57 (97)
T PF05440_consen 31 SMDPINEQIDKLEKAADDLVNSLDPRT 57 (97)
T ss_pred echHHHHHHHHHHHHHHHHHhccCCCC
Confidence 366777788889999999999999875
Done!