Query psy1958
Match_columns 202
No_of_seqs 195 out of 1103
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 20:37:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1958.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1958hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1979|consensus 100.0 1.5E-45 3.3E-50 338.7 12.8 198 2-201 303-525 (694)
2 COG0323 MutL DNA mismatch repa 99.8 2E-19 4.4E-24 171.8 12.8 57 144-200 447-504 (638)
3 PRK00095 mutL DNA mismatch rep 99.6 2.2E-14 4.8E-19 137.1 13.8 58 144-201 426-485 (617)
4 PF08676 MutL_C: MutL C termin 98.9 3.8E-09 8.1E-14 82.8 6.6 53 148-200 2-55 (144)
5 smart00853 MutL_C MutL C termi 98.7 3.2E-08 7E-13 76.5 6.6 53 149-201 2-57 (136)
6 KOG1978|consensus 96.8 0.0058 1.3E-07 59.0 8.6 46 144-189 484-529 (672)
7 PF10872 DUF2740: Protein of u 36.7 32 0.0007 21.6 2.0 25 172-196 8-32 (48)
8 PF14122 YokU: YokU-like prote 33.7 14 0.0003 27.0 0.0 23 165-187 55-77 (87)
9 PF04351 PilP: Pilus assembly 27.9 99 0.0021 24.3 4.0 28 146-173 76-107 (149)
10 COG4318 Uncharacterized protei 25.1 1.8E+02 0.0038 24.5 5.0 55 121-182 38-92 (221)
11 PF14998 Ripply: Transcription 24.2 75 0.0016 23.2 2.4 35 159-195 37-71 (87)
No 1
>KOG1979|consensus
Probab=100.00 E-value=1.5e-45 Score=338.71 Aligned_cols=198 Identities=37% Similarity=0.599 Sum_probs=162.6
Q ss_pred CCCccccCCCCCceeeccchHHHHHHHHHHHHHhccCCCCceeecccccCCCCCCCCCCCCCCCCCCCCCCCCCCccCCC
Q psy1958 2 DQPPVNVHPTKHEVHFLHEDTIIERVQSMLEKTLLGSNTSRVFYTQTKLPSFSTEPPTTKAKPSSTSSNTNNTTTTTTPA 81 (202)
Q Consensus 2 ~~vDvNVHPtK~eV~f~~e~~i~~~i~~~~~~~l~~~~~~~~~~~Q~llp~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~ 81 (202)
++|||||||||+||+|+++++|++.|++.|++.|.+.+.+|+|..|.++|+..+..+. ..+++-. +.+.+.++.|+|+
T Consensus 303 ~~vDVNVHPTK~eV~FL~qEeIie~I~~~ie~~L~~~d~er~~~~q~~iP~~~~~~~e-r~~~~~~-~~~s~~ks~k~~~ 380 (694)
T KOG1979|consen 303 ENVDVNVHPTKREVHFLNQEEIIERICQQIEERLSALDTERTFLKQVMIPGPSTLKSE-RNKPSLK-QSPSAQKSDKRYE 380 (694)
T ss_pred HHcccccCCCcceeEeecHHHHHHHHHHHHHHHHhccCcccchhhhhcccCCcccccc-ccCcccc-ccccccccchhcc
Confidence 4799999999999999999999999999999999999999999999999987655221 1111100 1112336678999
Q ss_pred CCccccCcccccccchhhhhhcccccc--------------cc-cc------cc---cccccee-eecchHHHHHHHHHH
Q psy1958 82 YKLVRTDASEQKLDRFLSKYIADQRAT--------------SK-QT------SN---KKYKRRE-IKLSSVRDLRGEIEK 136 (202)
Q Consensus 82 ~~~VRtD~~~~~l~~f~~~~~~~~~~~--------------~~-~~------~~---~~~~~~~-~~ltSv~~L~~ei~~ 136 (202)
++|||||+++++|++|+++.....+++ ++ .+ .+ ....+++ ++|+||+.||++|..
T Consensus 381 ~~mVRtDsse~ki~~fl~~~~~~~~s~~~~nes~~~~~s~~~~e~s~~p~dd~r~~~~~~~~rE~~~L~Si~~Lr~eV~~ 460 (694)
T KOG1979|consen 381 NKMVRTDSSERKIDSFLSPLTQVGSSNSTGNESEQGDDSSLSNENSRLPEDDVRFEYTAKTPRERFRLESIKKLRKEVID 460 (694)
T ss_pred cceeeccccccchhhhhCCccccCcccccccccccccccccccccccCccchhhhhhccccchhccchhhHHHHHHHHHh
Confidence 999999999999999997544311100 00 00 00 0112334 999999999999999
Q ss_pred hcChhHHHhccCcEEEEEEcCcEEEEEeCCeEEEEehHHHHHHHHHHHHHHHcCCCceeeecCCC
Q psy1958 137 QKSSQLCEVFRKLSFVGCATPCMCLIQHETKLYIVNVTYVLEELFYQLMLHDFGNFGVFRFEGSF 201 (202)
Q Consensus 137 ~~~~~l~~~~~~~~~VG~v~~~y~LiQ~~~~LyLvd~~~~~ee~~YQ~~l~~fgn~~~~~l~~p~ 201 (202)
++|..++++|++|+|||++|+.++|+||+++||+||+..+++|+|||+++.+|||||.++|++|+
T Consensus 461 ~~h~~l~e~~~n~~yVG~vd~~~alvQh~t~Ly~~d~~~ls~ElfYQi~i~dF~Nfg~~~l~~p~ 525 (694)
T KOG1979|consen 461 SCHVVLTEMFRNLSYVGVVDERTALVQHGTSLYLCDTVSLSKELFYQILITDFGNFGKIRLSEPL 525 (694)
T ss_pred hccHHHHHHHHhcceeeeechhhhhhhcCceEEEechHHHHHHHHHHHHHHHhcccceeecCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999985
No 2
>COG0323 MutL DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]
Probab=99.81 E-value=2e-19 Score=171.80 Aligned_cols=57 Identities=21% Similarity=0.306 Sum_probs=51.1
Q ss_pred HhccCcEEEEEEcCcEEEEEeCCeEEEEehHHHHHHHHHHHHHHHcCCC-ceeeecCC
Q psy1958 144 EVFRKLSFVGCATPCMCLIQHETKLYIVNVTYVLEELFYQLMLHDFGNF-GVFRFEGS 200 (202)
Q Consensus 144 ~~~~~~~~VG~v~~~y~LiQ~~~~LyLvd~~~~~ee~~YQ~~l~~fgn~-~~~~l~~p 200 (202)
+.++.+.++||++++|+|+|++++|||||+|++||+++|+.+...+++. ..+.|.-|
T Consensus 447 ~~~~~~~~i~q~~~~yil~e~~~~L~lvDqhaa~Eri~ye~l~~~~~~~~~~Q~LliP 504 (638)
T COG0323 447 DVFPLGEAIGQVHGTYILAEHEDGLVLVDQHAAHERILYEKLKNELGNVGELQPLLIP 504 (638)
T ss_pred cccccceEEEEecceEEEEEeCCCEEEEEhHHhHHHHHHHHHHHHhcccccccccccC
Confidence 5789999999999999999999999999999999999999999999998 44444444
No 3
>PRK00095 mutL DNA mismatch repair protein; Reviewed
Probab=99.58 E-value=2.2e-14 Score=137.06 Aligned_cols=58 Identities=17% Similarity=0.227 Sum_probs=51.2
Q ss_pred HhccCcEEEEEEcCcEEEEEeCCeEEEEehHHHHHHHHHHHHHHHcCC--CceeeecCCC
Q psy1958 144 EVFRKLSFVGCATPCMCLIQHETKLYIVNVTYVLEELFYQLMLHDFGN--FGVFRFEGSF 201 (202)
Q Consensus 144 ~~~~~~~~VG~v~~~y~LiQ~~~~LyLvd~~~~~ee~~YQ~~l~~fgn--~~~~~l~~p~ 201 (202)
+.++.+.++||++++|+|++.+++|||||+|+||||++|++++..+++ ...+.|..|+
T Consensus 426 ~~~~~~~vigQv~~~YIl~e~~~~L~iIDQHAAhERI~yE~l~~~~~~~~~~~Q~LL~P~ 485 (617)
T PRK00095 426 DSFPLGYALGQLHGTYILAENEDGLYLVDQHAAHERLLYEQLKDKLAEVGLASQPLLIPL 485 (617)
T ss_pred ccCcCceEeEEEcCEEEEEEeCCcEEEEEHHHHHHHHHHHHHHHHhccCCCcccccccCe
Confidence 345667899999999999999999999999999999999999999865 6677777775
No 4
>PF08676 MutL_C: MutL C terminal dimerisation domain; InterPro: IPR014790 MutL and MutS are key components of the DNA repair machinery that corrects replication errors []. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signalling complex for repair. The N-terminal region of MutL contains the ATPase domain and the C-terminal is involved in dimerisation []. ; GO: 0005524 ATP binding, 0006298 mismatch repair; PDB: 3NCV_B 1X9Z_B 3GAB_C 3KDK_A 3KDG_A.
Probab=98.89 E-value=3.8e-09 Score=82.81 Aligned_cols=53 Identities=17% Similarity=0.213 Sum_probs=45.9
Q ss_pred CcEEEEEEcCcEEEEEeCCeEEEEehHHHHHHHHHHHHHHHcCCC-ceeeecCC
Q psy1958 148 KLSFVGCATPCMCLIQHETKLYIVNVTYVLEELFYQLMLHDFGNF-GVFRFEGS 200 (202)
Q Consensus 148 ~~~~VG~v~~~y~LiQ~~~~LyLvd~~~~~ee~~YQ~~l~~fgn~-~~~~l~~p 200 (202)
-..++|+++++|+|++.+++|||||+|+||||+.|++++.++.+- .++.|..|
T Consensus 2 ~~~vlgq~~~~yil~~~~~~L~liDqHAAhERi~~E~l~~~~~~~~~~q~Ll~P 55 (144)
T PF08676_consen 2 LLKVLGQLDNKYILAESEDGLYLIDQHAAHERILYEKLLKQLEEGEQSQPLLFP 55 (144)
T ss_dssp T-EEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHCCHCS-EEEEEEE
T ss_pred ceeeHhHhCCEEEEEEeCCCEEEEEHHHHHHHHHHHHHHHhhccCCCceecCCC
Confidence 468999999999999999999999999999999999999999654 66666555
No 5
>smart00853 MutL_C MutL C terminal dimerisation domain. MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation.
Probab=98.72 E-value=3.2e-08 Score=76.49 Aligned_cols=53 Identities=11% Similarity=0.126 Sum_probs=45.2
Q ss_pred cEEEEEEcCcEEEEEeCCeEEEEehHHHHHHHHHHHHHHHcCC--C-ceeeecCCC
Q psy1958 149 LSFVGCATPCMCLIQHETKLYIVNVTYVLEELFYQLMLHDFGN--F-GVFRFEGSF 201 (202)
Q Consensus 149 ~~~VG~v~~~y~LiQ~~~~LyLvd~~~~~ee~~YQ~~l~~fgn--~-~~~~l~~p~ 201 (202)
+.++|+++++|++++.+++||+||+|+||||+.|++++..+.. . ..+.|-.|+
T Consensus 2 ~~~l~qv~~~yil~~~~~~l~liDqhaA~ERi~~e~l~~~~~~~~~~~~Q~Ll~P~ 57 (136)
T smart00853 2 GRVLGQVHGTYILAESEDGLVLIDQHAAHERILYEQLKAKLQAGLLEKSQPLLIPV 57 (136)
T ss_pred ccEEEEEcCEEEEEEcCCCEEEEEhHHHHHHHHHHHHHHHHhcCCCccccccCCCE
Confidence 5689999999999999999999999999999999999998733 3 256666654
No 6
>KOG1978|consensus
Probab=96.81 E-value=0.0058 Score=58.98 Aligned_cols=46 Identities=15% Similarity=0.252 Sum_probs=42.6
Q ss_pred HhccCcEEEEEEcCcEEEEEeCCeEEEEehHHHHHHHHHHHHHHHc
Q psy1958 144 EVFRKLSFVGCATPCMCLIQHETKLYIVNVTYVLEELFYQLMLHDF 189 (202)
Q Consensus 144 ~~~~~~~~VG~v~~~y~LiQ~~~~LyLvd~~~~~ee~~YQ~~l~~f 189 (202)
..|..+..+||.+.-++++-.+.+|++||+||+-|.+.|+.++..+
T Consensus 484 ~df~~meiigqfNlgFIi~~l~~dlfIvdqha~dEk~Nfe~l~~~~ 529 (672)
T KOG1978|consen 484 ADFSRMEIIGQFNLGFIIVKLEKDLFIVDQHASDEKRNFERLQSTT 529 (672)
T ss_pred cchhhcceeeeccccceeeeccCceEEeccchhhhhhhHHHHHHhc
Confidence 3678888999999999999999999999999999999999999876
No 7
>PF10872 DUF2740: Protein of unknown function (DUF2740); InterPro: IPR022626 This entry is represented by Bacteriophage P22, Orf48. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family of proteins with unknown function has a highly conserved sequence. They are found in Enterobacteria and Enterobacteria phages.
Probab=36.74 E-value=32 Score=21.63 Aligned_cols=25 Identities=20% Similarity=0.328 Sum_probs=21.8
Q ss_pred ehHHHHHHHHHHHHHHHcCCCceee
Q psy1958 172 NVTYVLEELFYQLMLHDFGNFGVFR 196 (202)
Q Consensus 172 d~~~~~ee~~YQ~~l~~fgn~~~~~ 196 (202)
++..+|..++-++++..|..-|+++
T Consensus 8 ~qdk~hk~ilrdrflssfkqpgrfr 32 (48)
T PF10872_consen 8 YQDKIHKHILRDRFLSSFKQPGRFR 32 (48)
T ss_pred cHHHHHHHHHHHHHHHHhcCcchHH
Confidence 5789999999999999998877654
No 8
>PF14122 YokU: YokU-like protein
Probab=33.68 E-value=14 Score=26.97 Aligned_cols=23 Identities=13% Similarity=0.508 Sum_probs=20.4
Q ss_pred CCeEEEEehHHHHHHHHHHHHHH
Q psy1958 165 ETKLYIVNVTYVLEELFYQLMLH 187 (202)
Q Consensus 165 ~~~LyLvd~~~~~ee~~YQ~~l~ 187 (202)
++.|+|||..++-+.+-|++++.
T Consensus 55 Edql~Lidtk~l~~sity~~LM~ 77 (87)
T PF14122_consen 55 EDQLFLIDTKKLPNSITYEELMN 77 (87)
T ss_pred hhheEEEecccCCccccHHHHhh
Confidence 45899999999999999999875
No 9
>PF04351 PilP: Pilus assembly protein, PilP; InterPro: IPR007446 The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [].; PDB: 2Y4Y_B 2Y4X_A 2IVW_A 2LC4_A.
Probab=27.90 E-value=99 Score=24.29 Aligned_cols=28 Identities=32% Similarity=0.551 Sum_probs=23.3
Q ss_pred ccCcEEEEEEcCc---EEEEEe-CCeEEEEeh
Q psy1958 146 FRKLSFVGCATPC---MCLIQH-ETKLYIVNV 173 (202)
Q Consensus 146 ~~~~~~VG~v~~~---y~LiQ~-~~~LyLvd~ 173 (202)
|..+++||.+... |+|+|. +..+|.|-.
T Consensus 76 Ld~LklvG~l~~~~~~~ALv~~pdg~v~~V~~ 107 (149)
T PF04351_consen 76 LDQLKLVGTLSQGGQPWALVQDPDGKVYRVKV 107 (149)
T ss_dssp CCCEEEEEEEEETTEEEEEEEE-TTEEEEEET
T ss_pred hhHeEEEEEEeeCCEEEEEEEeCCCCEEEecC
Confidence 6889999999743 999998 778998864
No 10
>COG4318 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.07 E-value=1.8e+02 Score=24.52 Aligned_cols=55 Identities=11% Similarity=0.136 Sum_probs=41.6
Q ss_pred eeecchHHHHHHHHHHhcChhHHHhccCcEEEEEEcCcEEEEEeCCeEEEEehHHHHHHHHH
Q psy1958 121 EIKLSSVRDLRGEIEKQKSSQLCEVFRKLSFVGCATPCMCLIQHETKLYIVNVTYVLEELFY 182 (202)
Q Consensus 121 ~~~ltSv~~L~~ei~~~~~~~l~~~~~~~~~VG~v~~~y~LiQ~~~~LyLvd~~~~~ee~~Y 182 (202)
.+-+-.|+..++++.+...++...++.+|..--++ --++.+||.|+|-+...+.-
T Consensus 38 tVGm~eVe~kr~~la~~kpk~~~~fl~kh~iPvVl-------GPggr~YltDhHHL~~Al~~ 92 (221)
T COG4318 38 TVGMREVELKRAKLAEKKPKDGEAFLGKHEIPVVL-------GPGGRFYLTDHHHLSRALLR 92 (221)
T ss_pred ehhhhHHHHHHHHHHhhCcchHHHHhhcCCCCeEe-------CCCCceeeechHHHHHHHHH
Confidence 35666778888888888888888888888654333 34678999999988876653
No 11
>PF14998 Ripply: Transcription Regulator
Probab=24.20 E-value=75 Score=23.23 Aligned_cols=35 Identities=23% Similarity=0.226 Sum_probs=29.5
Q ss_pred EEEEEeCCeEEEEehHHHHHHHHHHHHHHHcCCCcee
Q psy1958 159 MCLIQHETKLYIVNVTYVLEELFYQLMLHDFGNFGVF 195 (202)
Q Consensus 159 y~LiQ~~~~LyLvd~~~~~ee~~YQ~~l~~fgn~~~~ 195 (202)
-.-+||-.+||+ ...=+++++||.+-.=+.||+.+
T Consensus 37 ~~~FqHPVRL~w--PkSk~~dYLy~~gE~lL~nFPVQ 71 (87)
T PF14998_consen 37 LSGFQHPVRLYW--PKSKCYDYLYSEGEKLLANFPVQ 71 (87)
T ss_pred ccccCCceEeec--cchHHHHHHHHHHHHHHHcCCce
Confidence 456899999999 77779999999988888888854
Done!