Query psy16786
Match_columns 211
No_of_seqs 201 out of 276
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 22:03:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16786.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16786hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1189|consensus 100.0 2.3E-59 4.9E-64 456.1 7.9 145 57-211 544-688 (960)
2 COG5406 Nucleosome binding fac 100.0 6.8E-47 1.5E-51 364.8 9.6 143 59-211 592-736 (1001)
3 PF08644 SPT16: FACT complex s 100.0 1.8E-32 3.8E-37 226.7 8.6 91 58-158 61-152 (152)
4 PF08644 SPT16: FACT complex s 99.9 1E-23 2.2E-28 174.7 3.3 83 6-88 66-151 (152)
5 KOG1189|consensus 99.7 5.3E-18 1.2E-22 167.3 4.1 83 6-88 550-634 (960)
6 COG5406 Nucleosome binding fac 99.4 2.1E-13 4.5E-18 133.7 3.7 80 9-88 599-680 (1001)
7 PF03531 SSrecog: Structure-sp 58.8 20 0.00044 31.8 5.1 56 148-204 152-207 (222)
8 PF08206 OB_RNB: Ribonuclease 49.4 15 0.00033 25.3 2.2 31 147-177 1-33 (58)
9 PF08567 TFIIH_BTF_p62_N: TFII 41.7 46 0.00099 24.7 3.9 54 143-197 10-68 (79)
10 PRK00153 hypothetical protein; 31.4 57 0.0012 25.1 3.1 55 86-140 4-59 (104)
11 PF03852 Vsr: DNA mismatch end 29.6 21 0.00046 26.9 0.4 29 151-179 31-62 (75)
12 KOG4540|consensus 26.7 36 0.00079 32.4 1.5 48 154-201 293-345 (425)
13 COG5153 CVT17 Putative lipase 26.7 36 0.00079 32.4 1.5 48 154-201 293-345 (425)
14 PRK09993 C-lysozyme inhibitor; 24.0 26 0.00057 29.7 0.1 22 138-159 127-153 (153)
15 KOG2187|consensus 22.9 78 0.0017 31.8 3.0 42 62-105 263-305 (534)
16 PRK00153 hypothetical protein; 21.3 3.8E+02 0.0082 20.5 7.8 57 18-74 3-60 (104)
17 smart00357 CSP Cold shock prot 20.2 1.9E+02 0.0041 18.7 3.7 25 146-170 1-25 (64)
No 1
>KOG1189|consensus
Probab=100.00 E-value=2.3e-59 Score=456.07 Aligned_cols=145 Identities=68% Similarity=1.074 Sum_probs=140.7
Q ss_pred cCCCCccceeeeeecCCCCCCCCCCCCCccHHHHHHHHHHHHHHHHhHHHHHHhhhccccccceeeccCCCCCccccccc
Q psy16786 57 RSKGNPKLKDLTYRSSNQREPGQPSTPSTNLNTVFRLIKEVQKKFRSREAEEKEKEDLVKQDKLEESRSKGNPKLKDLYM 136 (211)
Q Consensus 57 k~~~~~~LkeL~~Rp~~~r~~G~le~h~n~l~~~~~~Ikel~K~~~~re~e~~e~~~~v~Q~~L~~~~~~~~~~L~dv~i 136 (211)
.++.+.||+++++|++++ ++++++|++||+|+|++++||+|++|++++|+||+|++++++++|+|+||||
T Consensus 544 ~~~~a~flkeit~rs~~~----------~~~s~~f~~ik~l~k~~~~re~e~~eke~~v~qdkL~~~kn~~~p~L~dlyi 613 (960)
T KOG1189|consen 544 ENPGAQFLKEITFRSSNG----------KRSSEAFRQIKELQKRFKSREAERKEKEDLVKQDKLIESKNKSNPKLKDLYI 613 (960)
T ss_pred CCchhhhhhheeeeecCC----------cchHHHHHHHHHHHHHHHHHHhhhhhhhchhhhhHHHHhhccCCCchhheEe
Confidence 346778999999999998 4789999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCcccceEEEeecceeeeccCCCeeeEeecccceecccCCCCceEEEEEeeeccceeecccccccccccC
Q psy16786 137 RPNIVMKRMTGSLEAHVNGFRYTSVRGDKVDILYNNIKHAFFQPCDGELVILLHFHLKNAIMFGKKKHVDVQFYT 211 (211)
Q Consensus 137 RP~~~~kr~~G~LE~H~NG~Ry~s~r~~~vDilf~NIKHafFQp~~~E~ivliHfhLk~pImiGkKkt~DVQFy~ 211 (211)
||+|.|||++|+||||+|||||+|.|+++|||||+||||||||||++|||+|||||||||||+||||++|||||+
T Consensus 614 Rp~i~~Kr~~G~lEaH~NGfRy~s~R~~~vdiLfsNIKhafFqpc~~Emi~llHfHLknpIm~GkkK~~dVQFY~ 688 (960)
T KOG1189|consen 614 RPNIDTKRIPGSLEAHENGFRYQSLRDERVDILFSNIKHAFFQPCEGEMIILLHFHLKNPIMVGKKKTKDVQFYR 688 (960)
T ss_pred cCCccccccccceeeecCceeeeeccccchhhhhhhhhhhhcCccccceeeEeeehhccceeecccceeeeeeee
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999996
No 2
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=100.00 E-value=6.8e-47 Score=364.81 Aligned_cols=143 Identities=43% Similarity=0.721 Sum_probs=137.7
Q ss_pred CCCccceeeeeecCCCCCCCCCCCCCccHHHHHHHHHHHHHHHHhHHHHHHhhhccccccceeeccCCCCCccccccccc
Q psy16786 59 KGNPKLKDLTYRSSNQREPGQPSTPSTNLNTVFRLIKEVQKKFRSREAEEKEKEDLVKQDKLEESRSKGNPKLKDLYMRP 138 (211)
Q Consensus 59 ~~~~~LkeL~~Rp~~~r~~G~le~h~n~l~~~~~~Ikel~K~~~~re~e~~e~~~~v~Q~~L~~~~~~~~~~L~dv~iRP 138 (211)
++..||+.+++||.++ ++|.++|++|.+|+|.+.+||+|++|-+|+++|++|++++.+++.++.+++|||
T Consensus 592 ~~~qF~rsit~rS~~g----------~rms~~fk~I~dlKK~atkrEterke~adv~eqdKlie~k~~rt~~~~~~~vRp 661 (1001)
T COG5406 592 RGEQFLRSITSRSIRG----------NRMSDLFKEINDLKKGATKRETERKEDADVLEQDKLIERKLSRTDVYMKTDVRP 661 (1001)
T ss_pred cchhhhhheeeeeccC----------ccHHHHHHHHHHHHhhhhhhhhhhHHHHHHHhhhhhhhccccccchhhhccccc
Confidence 5567999999999987 799999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcccceEEEeecceeeecc-CCC-eeeEeecccceecccCCCCceEEEEEeeeccceeecccccccccccC
Q psy16786 139 NIVMKRMTGSLEAHVNGFRYTSV-RGD-KVDILYNNIKHAFFQPCDGELVILLHFHLKNAIMFGKKKHVDVQFYT 211 (211)
Q Consensus 139 ~~~~kr~~G~LE~H~NG~Ry~s~-r~~-~vDilf~NIKHafFQp~~~E~ivliHfhLk~pImiGkKkt~DVQFy~ 211 (211)
+++|||.+|+||+|+||+||+|+ |.| +|||||+||||+|||||.+|+|||||||||+|||+||||++|||||+
T Consensus 662 ~~d~KR~pg~~eiHeNGiRfqsplrsds~idiLFSNikhlfFq~c~gEliviiH~HLk~PIl~GkrKvqdVQFYR 736 (1001)
T COG5406 662 GSDGKRKPGNLEIHENGIRFQSPLRSDSHIDILFSNIKHLFFQECNGELIVIIHFHLKSPILTGKRKVQDVQFYR 736 (1001)
T ss_pred CCCcCccCccEEEecCceeecCCcccCceeEEeeccchhheeccCCceEEEEEEEeecCceecCCceeeeeeeee
Confidence 99999999999999999999997 754 89999999999999999999999999999999999999999999997
No 3
>PF08644 SPT16: FACT complex subunit (SPT16/CDC68); InterPro: IPR013953 Proteins in this entry are subunits the FACT complex; the FACT complex is a stable heterodimer in Saccharomyces cerevisiae (Baker's yeast) comprising Spt16p and Pob3p. The complex plays a role in transcription initiation and promotes binding of TATA-binding protein (TBP) to a TATA box in chromatin []; it also facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilising and then reassembling nucleosome structure [, ]. The proteins in this entry are non-peptidase homologues belonging to MEROPS peptidase family M24 (clan MG).
Probab=99.97 E-value=1.8e-32 Score=226.74 Aligned_cols=91 Identities=53% Similarity=0.841 Sum_probs=87.6
Q ss_pred CCCCccceeeeeecCCCCCCCCCCCCCccHHHHHHHHHHHHHHHHhHHHHHHhhhccccccceeeccCCCCCcccccccc
Q psy16786 58 SKGNPKLKDLTYRSSNQREPGQPSTPSTNLNTVFRLIKEVQKKFRSREAEEKEKEDLVKQDKLEESRSKGNPKLKDLYMR 137 (211)
Q Consensus 58 ~~~~~~LkeL~~Rp~~~r~~G~le~h~n~l~~~~~~Ikel~K~~~~re~e~~e~~~~v~Q~~L~~~~~~~~~~L~dv~iR 137 (211)
.+.+.|||||+||+++.+ +|++++++||||||++++||+|++|++++|+||+|++++++++|+|+|||||
T Consensus 61 ~~~~~fiKeltfRs~d~~----------~~~~v~~~Ikel~k~~~~re~E~~e~~~~v~QekL~~~~~~~~~~L~dl~iR 130 (152)
T PF08644_consen 61 DPDAIFIKELTFRSKDSR----------HLQEVFRQIKELQKRVKQREQERREKADLVEQEKLILSKNRRPPRLKDLYIR 130 (152)
T ss_pred CCCCeEEEEEEEEeCCch----------HHHHHHHHHHHHHHHHHHHHHHHHHhcccccccceEEccCCCCCccCCceEC
Confidence 467899999999999984 6999999999999999999999999999999999999998999999999999
Q ss_pred cCCCC-CcccceEEEeecceee
Q psy16786 138 PNIVM-KRMTGSLEAHVNGFRY 158 (211)
Q Consensus 138 P~~~~-kr~~G~LE~H~NG~Ry 158 (211)
|+++| ||++|+||||+|||||
T Consensus 131 P~~~g~kr~~G~LEaH~NGfRy 152 (152)
T PF08644_consen 131 PAIGGRKRVPGTLEAHTNGFRY 152 (152)
T ss_pred CCCccccccCceEEEecCcccC
Confidence 99999 9999999999999999
No 4
>PF08644 SPT16: FACT complex subunit (SPT16/CDC68); InterPro: IPR013953 Proteins in this entry are subunits the FACT complex; the FACT complex is a stable heterodimer in Saccharomyces cerevisiae (Baker's yeast) comprising Spt16p and Pob3p. The complex plays a role in transcription initiation and promotes binding of TATA-binding protein (TBP) to a TATA box in chromatin []; it also facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilising and then reassembling nucleosome structure [, ]. The proteins in this entry are non-peptidase homologues belonging to MEROPS peptidase family M24 (clan MG).
Probab=99.88 E-value=1e-23 Score=174.65 Aligned_cols=83 Identities=40% Similarity=0.544 Sum_probs=79.1
Q ss_pred CCCCCCCCCCCCCcHHHHHHHHHHHHHHHhhhHHHHHHHhccccccccccccCCCCccceeeeeecCCC---CCCCCCCC
Q psy16786 6 NQREPGQPSTPSTNLNTVFRLIKEVQKKFRSREAEEKEKEDLVKQDKLEESRSKGNPKLKDLTYRSSNQ---REPGQPST 82 (211)
Q Consensus 6 ~~k~~~~rS~d~~~l~~v~r~IKeL~K~~k~RE~E~ke~adlV~QdkLi~~k~~~~~~LkeL~~Rp~~~---r~~G~le~ 82 (211)
-.||.+|||.|++||++++++||||||++++||+|++|++|+|+||+|+++++++++.|++||+||+.+ |.+|+||+
T Consensus 66 fiKeltfRs~d~~~~~~v~~~Ikel~k~~~~re~E~~e~~~~v~QekL~~~~~~~~~~L~dl~iRP~~~g~kr~~G~LEa 145 (152)
T PF08644_consen 66 FIKELTFRSKDSRHLQEVFRQIKELQKRVKQREQERREKADLVEQEKLILSKNRRPPRLKDLYIRPAIGGRKRVPGTLEA 145 (152)
T ss_pred EEEEEEEEeCCchHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccceEEccCCCCCccCCceECCCCccccccCceEEE
Confidence 368899999999999999999999999999999999999999999999999989999999999999996 68999999
Q ss_pred CCccHH
Q psy16786 83 PSTNLN 88 (211)
Q Consensus 83 h~n~l~ 88 (211)
|+|||.
T Consensus 146 H~NGfR 151 (152)
T PF08644_consen 146 HTNGFR 151 (152)
T ss_pred ecCccc
Confidence 999984
No 5
>KOG1189|consensus
Probab=99.70 E-value=5.3e-18 Score=167.28 Aligned_cols=83 Identities=49% Similarity=0.634 Sum_probs=79.3
Q ss_pred CCCCCCCCCCCCCcHHHHHHHHHHHHHHHhhhHHHHHHHhccccccccccccCCCCccceeeeeecCCC--CCCCCCCCC
Q psy16786 6 NQREPGQPSTPSTNLNTVFRLIKEVQKKFRSREAEEKEKEDLVKQDKLEESRSKGNPKLKDLTYRSSNQ--REPGQPSTP 83 (211)
Q Consensus 6 ~~k~~~~rS~d~~~l~~v~r~IKeL~K~~k~RE~E~ke~adlV~QdkLi~~k~~~~~~LkeL~~Rp~~~--r~~G~le~h 83 (211)
=.|+.+|||.|++|++++||+||+|+|++++||+|++|+|++|+||+|++++++.++.|++||+||.+. |.||+||+|
T Consensus 550 flkeit~rs~~~~~~s~~f~~ik~l~k~~~~re~e~~eke~~v~qdkL~~~kn~~~p~L~dlyiRp~i~~Kr~~G~lEaH 629 (960)
T KOG1189|consen 550 FLKEITFRSSNGKRSSEAFRQIKELQKRFKSREAERKEKEDLVKQDKLIESKNKSNPKLKDLYIRPNIDTKRIPGSLEAH 629 (960)
T ss_pred hhhheeeeecCCcchHHHHHHHHHHHHHHHHHHhhhhhhhchhhhhHHHHhhccCCCchhheEecCCccccccccceeee
Confidence 357889999999999999999999999999999999999999999999999999999999999999997 999999999
Q ss_pred CccHH
Q psy16786 84 STNLN 88 (211)
Q Consensus 84 ~n~l~ 88 (211)
+||+.
T Consensus 630 ~NGfR 634 (960)
T KOG1189|consen 630 ENGFR 634 (960)
T ss_pred cCcee
Confidence 99974
No 6
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=99.38 E-value=2.1e-13 Score=133.66 Aligned_cols=80 Identities=24% Similarity=0.371 Sum_probs=76.3
Q ss_pred CCCCCCCCCCcHHHHHHHHHHHHHHHhhhHHHHHHHhccccccccccccCCCCccceeeeeecCCC--CCCCCCCCCCcc
Q psy16786 9 EPGQPSTPSTNLNTVFRLIKEVQKKFRSREAEEKEKEDLVKQDKLEESRSKGNPKLKDLTYRSSNQ--REPGQPSTPSTN 86 (211)
Q Consensus 9 ~~~~rS~d~~~l~~v~r~IKeL~K~~k~RE~E~ke~adlV~QdkLi~~k~~~~~~LkeL~~Rp~~~--r~~G~le~h~n~ 86 (211)
.-++||.++.+|.++|++|.+|+|.+++||+|++|.||+++|||||+++..+...+..+++||..+ |.||.||+|+||
T Consensus 599 sit~rS~~g~rms~~fk~I~dlKK~atkrEterke~adv~eqdKlie~k~~rt~~~~~~~vRp~~d~KR~pg~~eiHeNG 678 (1001)
T COG5406 599 SITSRSIRGNRMSDLFKEINDLKKGATKRETERKEDADVLEQDKLIERKLSRTDVYMKTDVRPGSDGKRKPGNLEIHENG 678 (1001)
T ss_pred heeeeeccCccHHHHHHHHHHHHhhhhhhhhhhHHHHHHHhhhhhhhccccccchhhhcccccCCCcCccCccEEEecCc
Confidence 357899999999999999999999999999999999999999999999999999999999999997 899999999999
Q ss_pred HH
Q psy16786 87 LN 88 (211)
Q Consensus 87 l~ 88 (211)
+.
T Consensus 679 iR 680 (1001)
T COG5406 679 IR 680 (1001)
T ss_pred ee
Confidence 64
No 7
>PF03531 SSrecog: Structure-specific recognition protein (SSRP1); InterPro: IPR000969 Human structure-specific recognition protein, SSRP1, [] binds specifically to DNA modified with the anti-cancer drug cisplatin. An 81kDa protein is predicted, containing several highly-charged domains and a stretch of 75 residues that share 47% identity with a portion of the high mobility group (HMG) protein HMG1. This HMG box probably constitutes the structure recognition element for cisplatin-modified DNA, the probable recognition motif being the local duplex unwinding and bending that occurs on formation of intra-strand cross-links []. SSRP1 is the human homologue of a recently identified mouse protein that binds to recombination signal sequences []. These sequences have been postulated to form stem-loop structures, further implicating local bends and unwinding in DNA as a recognition target for HMG-box proteins. A Drosophila melanogaster cDNA encoding an HMG-box-containing protein has also been isolated [, ]. This protein shares 50% sequence identity with human SSRP1. In vitro binding studies using Drosophila SSRP showed that the protein binds to single-stranded DNA and RNA, with highest affinity for nucleotides G and U. Comparison of the predicted amino acid sequences among SSRP family members reveals 48% identity, with structural conservation in the C terminus of the HMG box, as well as domains of highly charged residues. The most highly conserved regions lie in the poorly understood N terminus, suggesting that this portion of the protein is critical for its function []. This entry contains Pob3 Q04636 from SWISSPROT, which is a subunit of the heterodimeric yeast FACT complex (Spt16p (IPR013953 from INTERPRO)-Pob3p) []. The FACT complex facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilising and then reassembling nucleosome structure [, ].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 3F5R_A 2GCL_B 2GCJ_D.
Probab=58.82 E-value=20 Score=31.79 Aligned_cols=56 Identities=18% Similarity=0.254 Sum_probs=41.9
Q ss_pred eEEEeecceeeeccCCCeeeEeecccceecccCCCCceEEEEEeeeccceeeccccc
Q psy16786 148 SLEAHVNGFRYTSVRGDKVDILYNNIKHAFFQPCDGELVILLHFHLKNAIMFGKKKH 204 (211)
Q Consensus 148 ~LE~H~NG~Ry~s~r~~~vDilf~NIKHafFQp~~~E~ivliHfhLk~pImiGkKkt 204 (211)
.+|.|.+-||.... .-..-|.|+||..+|.=|-..+.-+.+=+.|-.||-=|.-+.
T Consensus 152 di~~y~~~lrl~Gk-tyDykI~y~~I~rlflLpk~d~~~~~~Vi~LdpPiRQGQT~Y 207 (222)
T PF03531_consen 152 DIEMYPTFLRLHGK-TYDYKIQYSSISRLFLLPKPDDRHVFFVISLDPPIRQGQTRY 207 (222)
T ss_dssp EEEE-SSEEEEEES-SBEEEEEGGGEEEEEEEE-TTSSEEEEEEEEEEEEEETTEEE
T ss_pred cccccccccccccc-cccccccccccccccccccccccccccccccccccccccccc
Confidence 57888888888642 123558999999999999877777777788999998886543
No 8
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=49.37 E-value=15 Score=25.34 Aligned_cols=31 Identities=29% Similarity=0.525 Sum_probs=19.6
Q ss_pred ceEEEeecceeeeccCCCeeeEee--cccceec
Q psy16786 147 GSLEAHVNGFRYTSVRGDKVDILY--NNIKHAF 177 (211)
Q Consensus 147 G~LE~H~NG~Ry~s~r~~~vDilf--~NIKHaf 177 (211)
|++++|.+||=|..+-+..-||.. .|++.|+
T Consensus 1 G~~~~~~~GfGFv~~~~~~~DifIp~~~l~~A~ 33 (58)
T PF08206_consen 1 GTLKIHPKGFGFVIPDDGGEDIFIPPRNLNGAM 33 (58)
T ss_dssp EEEEE-SSS-EEEEECT-TEEEEE-HHHHTTS-
T ss_pred CEEEEEcCCCEEEEECCCCCCEEECHHHHCCCC
Confidence 899999999999976444566654 4555554
No 9
>PF08567 TFIIH_BTF_p62_N: TFIIH p62 subunit, N-terminal domain; InterPro: IPR013876 The N-terminal region of the TFIIH basal transcription factor complex p62 subunit (BTF2-p62) forms an interaction with the 3' endonuclease XPG, which is essential for activity. The 3' endonuclease XPG is a major component of the nucleotide excision repair machinery. The structure of the N-terminal region reveals that it adopts a pleckstrin homology (PH) fold [, ]. ; PDB: 1Y5O_A 2LOX_A 2GS0_A 2L2I_A 2K2U_A 1PFJ_A 2RNR_B.
Probab=41.73 E-value=46 Score=24.71 Aligned_cols=54 Identities=26% Similarity=0.367 Sum_probs=37.6
Q ss_pred CcccceEEEeecc--eeeecc--CCC-eeeEeecccceecccCCCCceEEEEEeeeccce
Q psy16786 143 KRMTGSLEAHVNG--FRYTSV--RGD-KVDILYNNIKHAFFQPCDGELVILLHFHLKNAI 197 (211)
Q Consensus 143 kr~~G~LE~H~NG--~Ry~s~--r~~-~vDilf~NIKHafFQp~~~E~ivliHfhLk~pI 197 (211)
||..|+|.+...+ +.++.. .+. .|.|.|++|+.+.==|.. ---|+|=.-++++-
T Consensus 10 KK~~G~L~l~~d~~~~~W~~~~~~~~~~v~i~~~~I~~lq~Sp~~-s~Kv~Lki~~~~~~ 68 (79)
T PF08567_consen 10 KKKDGTLTLTEDRKPLEWTPKASDGPSTVSIPLNDIKNLQQSPEG-SPKVMLKIVLKDDS 68 (79)
T ss_dssp TTEEEEEEEETTCSSEEEEECCSSSSSEEEEETTTEEEEEE--TT-SSTEEEEEEETTSC
T ss_pred EcCCcEEEEecCCceEEEeecCCCCCceEEEEHHHhhhhccCCCC-CcceEEEEEEecCC
Confidence 7899999999999 888853 233 399999999997655554 33445555555543
No 10
>PRK00153 hypothetical protein; Validated
Probab=31.39 E-value=57 Score=25.09 Aligned_cols=55 Identities=16% Similarity=0.280 Sum_probs=35.3
Q ss_pred cHHHHHHHHHHHHHHHHhHHHHHHhhhc-cccccceeeccCCCCCcccccccccCC
Q psy16786 86 NLNTVFRLIKEVQKKFRSREAEEKEKED-LVKQDKLEESRSKGNPKLKDLYMRPNI 140 (211)
Q Consensus 86 ~l~~~~~~Ikel~K~~~~re~e~~e~~~-~v~Q~~L~~~~~~~~~~L~dv~iRP~~ 140 (211)
||++++++.+++|+++..-..+-++..- .-+.+-+|...=...-.+.+|.|-|.+
T Consensus 4 ~~~~m~~qaq~~q~~~~~~q~~l~~~~~~~~s~~G~V~V~v~G~~~v~~i~Id~~l 59 (104)
T PRK00153 4 NMQNLMKQAQQMQEKMQKMQEELAQMEVEGEAGGGLVKVTMTGKKEVKRVKIDPSL 59 (104)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhccEEEEEECCCeEEEEEecCceEEEEEECHHH
Confidence 6999999999999999876555444431 223444543321123477788887765
No 11
>PF03852 Vsr: DNA mismatch endonuclease Vsr; InterPro: IPR004603 This entry represents VSR (very short patch repair) endonucleases, which occur in a variety of bacteria. VSR recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine []. GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine []. The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer alpha/beta/alpha topology []. ; GO: 0004519 endonuclease activity, 0006298 mismatch repair; PDB: 1ODG_A 1VSR_A 1CW0_A.
Probab=29.56 E-value=21 Score=26.85 Aligned_cols=29 Identities=34% Similarity=0.527 Sum_probs=19.6
Q ss_pred Eeecceeeecc-C--CCeeeEeecccceeccc
Q psy16786 151 AHVNGFRYTSV-R--GDKVDILYNNIKHAFFQ 179 (211)
Q Consensus 151 ~H~NG~Ry~s~-r--~~~vDilf~NIKHafFQ 179 (211)
+|..|+||.-. + -.+.||.|..-|-|+|=
T Consensus 31 L~~~G~RyR~~~~~lpG~PDiv~~~~k~aIFV 62 (75)
T PF03852_consen 31 LHALGLRYRLNRKDLPGKPDIVFPKYKIAIFV 62 (75)
T ss_dssp HHHTT--EEES-TTSTT--SEEEGGGTEEEEE
T ss_pred HHhcCCEEEEccCcCCCCCCEEECCCCEEEEE
Confidence 58899999843 2 35899999999999883
No 12
>KOG4540|consensus
Probab=26.72 E-value=36 Score=32.39 Aligned_cols=48 Identities=23% Similarity=0.230 Sum_probs=36.7
Q ss_pred cceeeeccC---CCeeeEeecccceecccCC-CCceEEEEEe-eeccceeecc
Q psy16786 154 NGFRYTSVR---GDKVDILYNNIKHAFFQPC-DGELVILLHF-HLKNAIMFGK 201 (211)
Q Consensus 154 NG~Ry~s~r---~~~vDilf~NIKHafFQp~-~~E~ivliHf-hLk~pImiGk 201 (211)
=|+||--+- ..+=|.+=+|+=|+.|||. -.+|--+.|| |--.||..|+
T Consensus 293 lG~~fglP~VaFesPGd~~aa~rLhLp~ppglpd~~~~iwHfGhnaDpif~G~ 345 (425)
T KOG4540|consen 293 LGIRFGLPVVAFESPGDAYAANRLHLPDPPGLPDNMEGIWHFGHNADPIFRGE 345 (425)
T ss_pred hccccCCceEEecCchhhhhhhccCCCCCCCCCccccceEEeccCCCceEeee
Confidence 367775321 2345778899999999996 5577788999 7889999996
No 13
>COG5153 CVT17 Putative lipase essential for disintegration of autophagic bodies inside the vacuole [Intracellular trafficking and secretion / Lipid metabolism]
Probab=26.72 E-value=36 Score=32.39 Aligned_cols=48 Identities=23% Similarity=0.230 Sum_probs=36.7
Q ss_pred cceeeeccC---CCeeeEeecccceecccCC-CCceEEEEEe-eeccceeecc
Q psy16786 154 NGFRYTSVR---GDKVDILYNNIKHAFFQPC-DGELVILLHF-HLKNAIMFGK 201 (211)
Q Consensus 154 NG~Ry~s~r---~~~vDilf~NIKHafFQp~-~~E~ivliHf-hLk~pImiGk 201 (211)
=|+||--+- ..+=|.+=+|+=|+.|||. -.+|--+.|| |--.||..|+
T Consensus 293 lG~~fglP~VaFesPGd~~aa~rLhLp~ppglpd~~~~iwHfGhnaDpif~G~ 345 (425)
T COG5153 293 LGIRFGLPVVAFESPGDAYAANRLHLPDPPGLPDNMEGIWHFGHNADPIFRGE 345 (425)
T ss_pred hccccCCceEEecCchhhhhhhccCCCCCCCCCccccceEEeccCCCceEeee
Confidence 367775321 2345778899999999996 5577788999 7889999996
No 14
>PRK09993 C-lysozyme inhibitor; Provisional
Probab=24.03 E-value=26 Score=29.70 Aligned_cols=22 Identities=45% Similarity=0.699 Sum_probs=18.3
Q ss_pred cCCCCCc-----ccceEEEeecceeee
Q psy16786 138 PNIVMKR-----MTGSLEAHVNGFRYT 159 (211)
Q Consensus 138 P~~~~kr-----~~G~LE~H~NG~Ry~ 159 (211)
++|+||- .+|+||=|-|+|-|.
T Consensus 127 ~sidg~tvl~aaltgsl~nhp~~fn~~ 153 (153)
T PRK09993 127 LSIDGKTVLFAALTGSLENHPDGFNFK 153 (153)
T ss_pred cccccceeeHHhhhCchhcCccccCcC
Confidence 4678873 799999999999883
No 15
>KOG2187|consensus
Probab=22.85 E-value=78 Score=31.79 Aligned_cols=42 Identities=24% Similarity=0.196 Sum_probs=30.4
Q ss_pred ccceeeeeecCCCC-CCCCCCCCCccHHHHHHHHHHHHHHHHhHH
Q psy16786 62 PKLKDLTYRSSNQR-EPGQPSTPSTNLNTVFRLIKEVQKKFRSRE 105 (211)
Q Consensus 62 ~~LkeL~~Rp~~~r-~~G~le~h~n~l~~~~~~Ikel~K~~~~re 105 (211)
=|.+.|++|-...+ .-+.+++|..-++. ..+.|+++.++++=
T Consensus 263 G~wk~LtVRt~~~~~~~~il~i~~~~l~~--e~l~e~~~ki~~~f 305 (534)
T KOG2187|consen 263 GFWKQLTVRTEFRGGAMAILTIHPCKLAT--EELTELKKKIEQRF 305 (534)
T ss_pred CceeeeEEEecccCceEEEEEEEeecccH--HHHHHHHHHHHHHH
Confidence 38999999955543 34778888777664 45688888887763
No 16
>PRK00153 hypothetical protein; Validated
Probab=21.33 E-value=3.8e+02 Score=20.47 Aligned_cols=57 Identities=16% Similarity=0.214 Sum_probs=41.4
Q ss_pred CcHHHHHHHHHHHHHHHhhhHHHHHHHh-ccccccccccccCCCCccceeeeeecCCC
Q psy16786 18 TNLNTVFRLIKEVQKKFRSREAEEKEKE-DLVKQDKLEESRSKGNPKLKDLTYRSSNQ 74 (211)
Q Consensus 18 ~~l~~v~r~IKeL~K~~k~RE~E~ke~a-dlV~QdkLi~~k~~~~~~LkeL~~Rp~~~ 74 (211)
.+|++++++.+++|+++.+-+.|-+++. +.-..+-+|...-...-.|.+|.|-|..-
T Consensus 3 ~~~~~m~~qaq~~q~~~~~~q~~l~~~~~~~~s~~G~V~V~v~G~~~v~~i~Id~~ll 60 (104)
T PRK00153 3 GNMQNLMKQAQQMQEKMQKMQEELAQMEVEGEAGGGLVKVTMTGKKEVKRVKIDPSLV 60 (104)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhccEEEEEECCCeEEEEEecCceEEEEEECHHHc
Confidence 3799999999999999988766655553 23355667665444556899999988653
No 17
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=20.20 E-value=1.9e+02 Score=18.68 Aligned_cols=25 Identities=20% Similarity=0.360 Sum_probs=15.2
Q ss_pred cceEEEeecceeeeccCCCeeeEee
Q psy16786 146 TGSLEAHVNGFRYTSVRGDKVDILY 170 (211)
Q Consensus 146 ~G~LE~H~NG~Ry~s~r~~~vDilf 170 (211)
.|+++.+..|+-|-...++.-||.+
T Consensus 1 ~G~i~~~~~g~gfv~~~~~~~~i~v 25 (64)
T smart00357 1 TGVVKWFNKGFGFIRPDDGGKDVFV 25 (64)
T ss_pred CeEEEEEcCCeeEEecCCCCccEEE
Confidence 3777777777777654322236666
Done!