Query psy5543
Match_columns 60
No_of_seqs 49 out of 51
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 20:14:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5543.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5543hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3988|consensus 99.9 1.6E-26 3.4E-31 174.4 2.8 53 7-59 273-327 (378)
2 PF00685 Sulfotransfer_1: Sulf 58.6 9.9 0.00022 24.3 2.3 35 24-58 232-267 (267)
3 PF14261 DUF4351: Domain of un 50.1 10 0.00022 21.9 1.2 21 30-50 14-34 (59)
4 PF04736 Eclosion: Eclosion ho 41.9 15 0.00032 22.5 1.0 26 30-57 36-62 (62)
5 TIGR03495 phage_LysB phage lys 36.4 21 0.00047 24.0 1.3 17 29-45 91-108 (135)
6 smart00833 CobW_C Cobalamin sy 31.5 12 0.00026 21.2 -0.5 20 24-43 9-28 (92)
7 PF07683 CobW_C: Cobalamin syn 30.9 8.7 0.00019 22.1 -1.2 22 23-44 8-29 (94)
8 PF12490 BCAS3: Breast carcino 30.1 26 0.00057 25.0 0.9 14 1-14 203-216 (251)
9 KOG2182|consensus 28.1 12 0.00027 30.4 -1.1 30 29-58 182-212 (514)
10 PF09921 DUF2153: Uncharacteri 27.8 39 0.00084 23.0 1.4 21 29-49 46-72 (126)
11 PF12460 MMS19_C: RNAPII trans 26.4 25 0.00054 26.1 0.3 41 14-55 330-371 (415)
12 COG4755 Uncharacterized protei 26.3 43 0.00093 23.5 1.4 21 29-49 64-90 (151)
13 PF14549 P22_Cro: DNA-binding 26.2 48 0.001 19.2 1.4 24 27-50 21-44 (60)
14 PF09494 Slx4: Slx4 endonuclea 22.5 40 0.00086 19.3 0.6 13 25-37 23-35 (64)
15 PF01618 MotA_ExbB: MotA/TolQ/ 21.7 40 0.00086 21.4 0.5 18 41-58 55-72 (139)
16 KOG4415|consensus 20.8 35 0.00077 25.4 0.2 10 1-10 47-56 (247)
No 1
>KOG3988|consensus
Probab=99.92 E-value=1.6e-26 Score=174.38 Aligned_cols=53 Identities=64% Similarity=0.881 Sum_probs=51.9
Q ss_pred ccc--cCCCCCcccccchhccccchhhhhhhcCCCChHHHhchHhhhhHhhcCCC
Q psy5543 7 FKT--YTPPPRVERSSDQVIKPVNLEALTKWVGKIPEDVMKDMDEIAPMLASGNG 59 (60)
Q Consensus 7 i~~--~vsLSk~E~STdQVvkpvn~eaLskW~g~iP~dv~~dm~~iaPmL~~l~~ 59 (60)
||+ +|||||+|||||||+||||++||+||+|+||+||++||++|||||++||-
T Consensus 273 Igk~~gVsLskvErSsdQVikpVNl~AlskWvg~ip~dvvrdma~iAPmL~~LGY 327 (378)
T KOG3988|consen 273 IGKPGGVSLSKVERSSDQVIKPVNLEALSKWVGCIPEDVVRDMADIAPMLAILGY 327 (378)
T ss_pred cCCCCCCChhhhhccHhhhhccccHHHHHHHhccCCHHHHHHHHHHHHHHHHhCC
Confidence 888 99999999999999999999999999999999999999999999999995
No 2
>PF00685 Sulfotransfer_1: Sulfotransferase domain; InterPro: IPR000863 This family includes a range of sulphotransferase proteins including flavonyl 3-sulphotransferase, aryl sulphotransferase, alcohol sulphotransferase, oestrogen sulphotransferase and phenol-sulphating phenol sulphotransferase. These enzymes are responsible for the transfer of sulphate groups to specific compounds.; GO: 0008146 sulfotransferase activity; PDB: 3MGC_A 3MGB_A 3MG9_A 1G3M_B 1HY3_B 2QP4_A 3F3Y_C 1EFH_A 1OV4_A 1J99_A ....
Probab=58.55 E-value=9.9 Score=24.33 Aligned_cols=35 Identities=6% Similarity=0.207 Sum_probs=28.9
Q ss_pred ccccchhhhhhhcCCCChHHHhchHhhh-hHhhcCC
Q psy5543 24 IKPVNLEALTKWVGKIPEDVMKDMDEIA-PMLASGN 58 (60)
Q Consensus 24 vkpvn~eaLskW~g~iP~dv~~dm~~ia-PmL~~l~ 58 (60)
-..+......+|...++++.++.+.++| +.|+.||
T Consensus 232 ~~~~~~~~~~~W~~~l~~e~~~~i~~~~~~~m~~~~ 267 (267)
T PF00685_consen 232 SRFFRKGKSGRWKNELSPEQIDRIERICGDAMRELG 267 (267)
T ss_dssp STSSEET-STGGGGTSBHHHHHHHHHHHHHHHTTSS
T ss_pred ceeeeecccCcccccCCHHHHHHHHHHHHHHHccCC
Confidence 4677888889999999999999999887 6777776
No 3
>PF14261 DUF4351: Domain of unknown function (DUF4351)
Probab=50.14 E-value=10 Score=21.89 Aligned_cols=21 Identities=19% Similarity=0.607 Sum_probs=17.4
Q ss_pred hhhhhhcCCCChHHHhchHhh
Q psy5543 30 EALTKWVGKIPEDVMKDMDEI 50 (60)
Q Consensus 30 eaLskW~g~iP~dv~~dm~~i 50 (60)
--|.+.+|.+|+++...+..+
T Consensus 14 RlL~rrFG~lp~~~~~~I~~l 34 (59)
T PF14261_consen 14 RLLTRRFGELPPEIQERIQQL 34 (59)
T ss_pred HHHHHHcCCCCHHHHHHHHcC
Confidence 457899999999998877665
No 4
>PF04736 Eclosion: Eclosion hormone; InterPro: IPR006825 Eclosion hormone is an insect neuropeptide that triggers the performance of ecdysis behaviour, which causes shedding of the old cuticle at the end of a molt [, ].; GO: 0008255 ecdysis-triggering hormone activity, 0007218 neuropeptide signaling pathway, 0018990 ecdysis, chitin-based cuticle
Probab=41.92 E-value=15 Score=22.47 Aligned_cols=26 Identities=46% Similarity=0.767 Sum_probs=18.8
Q ss_pred hhhhhhcCC-CChHHHhchHhhhhHhhcC
Q psy5543 30 EALTKWVGK-IPEDVMKDMDEIAPMLASG 57 (60)
Q Consensus 30 eaLskW~g~-iP~dv~~dm~~iaPmL~~l 57 (60)
|+--|..|+ ||+ -+|.++|+|+|.+|
T Consensus 36 e~C~k~kGk~iPD--Ced~~SI~pFLnkl 62 (62)
T PF04736_consen 36 ESCVKFKGKLIPD--CEDIDSIAPFLNKL 62 (62)
T ss_pred HHHHHhCCCcCCC--ccchhhHHHHHhcC
Confidence 344455666 565 47899999999986
No 5
>TIGR03495 phage_LysB phage lysis regulatory protein, LysB family. Members of this protein family are phage lysis regulatory protein, including the well-studied protein LysB (lysis protein B) of Enterobacteria phage P2. For members of this family, genes are found in phage or in prophage regions of bacterial genomes, typically near a phage lysozyme or phage holin.
Probab=36.41 E-value=21 Score=24.02 Aligned_cols=17 Identities=35% Similarity=0.935 Sum_probs=14.4
Q ss_pred hhhhhhhcCC-CChHHHh
Q psy5543 29 LEALTKWVGK-IPEDVMK 45 (60)
Q Consensus 29 ~eaLskW~g~-iP~dv~~ 45 (60)
-|.|.+|.+. +|++|++
T Consensus 91 Ne~lR~Wa~t~LPd~V~R 108 (135)
T TIGR03495 91 NEDLRRWADTPLPDDVIR 108 (135)
T ss_pred CHHHHHHhcCCCcHHHHH
Confidence 4678999988 9999875
No 6
>smart00833 CobW_C Cobalamin synthesis protein cobW C-terminal domain. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis PUBMED:12869542. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression PUBMED:7765511.
Probab=31.53 E-value=12 Score=21.22 Aligned_cols=20 Identities=25% Similarity=0.456 Sum_probs=16.4
Q ss_pred ccccchhhhhhhcCCCChHH
Q psy5543 24 IKPVNLEALTKWVGKIPEDV 43 (60)
Q Consensus 24 vkpvn~eaLskW~g~iP~dv 43 (60)
-+|++.+.|.+|...+|..+
T Consensus 9 ~~~~~~~~l~~~l~~l~~~i 28 (92)
T smart00833 9 RRPFHPQRLLAALDELPEGV 28 (92)
T ss_pred CCCCCHHHHHHHHHhccCCe
Confidence 37889999999999988543
No 7
>PF07683 CobW_C: Cobalamin synthesis protein cobW C-terminal domain; InterPro: IPR011629 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [].; PDB: 1NIJ_A.
Probab=30.90 E-value=8.7 Score=22.08 Aligned_cols=22 Identities=32% Similarity=0.755 Sum_probs=15.7
Q ss_pred hccccchhhhhhhcCCCChHHH
Q psy5543 23 VIKPVNLEALTKWVGKIPEDVM 44 (60)
Q Consensus 23 Vvkpvn~eaLskW~g~iP~dv~ 44 (60)
.-+|++.+.|..|....+.+++
T Consensus 8 ~~~p~~~~~l~~~l~~~~~~vl 29 (94)
T PF07683_consen 8 FDRPFDPERLEAWLQELPGDVL 29 (94)
T ss_dssp ESS-B-HHHHHHHHHHTTTTEE
T ss_pred eCCCCCHHHHHHHHHhCCCCEE
Confidence 3479999999999988776654
No 8
>PF12490 BCAS3: Breast carcinoma amplified sequence 3 ; InterPro: IPR022175 This domain family is found in eukaryotes, and is typically between 229 and 245 amino acids in length. The proteins in this family have been shown to be proto-oncogenes implicated in the development of breast cancer.
Probab=30.08 E-value=26 Score=24.98 Aligned_cols=14 Identities=71% Similarity=1.255 Sum_probs=11.6
Q ss_pred CCCcccccccCCCC
Q psy5543 1 MGPQFSFKTYTPPP 14 (60)
Q Consensus 1 ~~~~~~i~~~vsLS 14 (60)
|||||+|++.-+.+
T Consensus 203 ~gpQf~F~~~~~~~ 216 (251)
T PF12490_consen 203 MGPQFSFKTMSSPS 216 (251)
T ss_pred cCCcEEEEEecCCC
Confidence 79999999886655
No 9
>KOG2182|consensus
Probab=28.07 E-value=12 Score=30.37 Aligned_cols=30 Identities=27% Similarity=0.468 Sum_probs=25.8
Q ss_pred hhhhhhhcCC-CChHHHhchHhhhhHhhcCC
Q psy5543 29 LEALTKWVGK-IPEDVMKDMDEIAPMLASGN 58 (60)
Q Consensus 29 ~eaLskW~g~-iP~dv~~dm~~iaPmL~~l~ 58 (60)
--+|+.|+.. .|+-+..-.++.||.++.+.
T Consensus 182 sGsLsAW~R~~yPel~~GsvASSapv~A~~D 212 (514)
T KOG2182|consen 182 SGSLSAWFREKYPELTVGSVASSAPVLAKVD 212 (514)
T ss_pred hhHHHHHHHHhCchhheeecccccceeEEec
Confidence 4569999976 99999999999999988753
No 10
>PF09921 DUF2153: Uncharacterized protein conserved in archaea (DUF2153); InterPro: IPR014450 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.81 E-value=39 Score=23.03 Aligned_cols=21 Identities=29% Similarity=0.819 Sum_probs=17.1
Q ss_pred hhhhhhhc------CCCChHHHhchHh
Q psy5543 29 LEALTKWV------GKIPEDVMKDMDE 49 (60)
Q Consensus 29 ~eaLskW~------g~iP~dv~~dm~~ 49 (60)
++|.++|. .++|+|++.+.+.
T Consensus 46 lKaFd~WLqdP~ItshMPreML~dv~~ 72 (126)
T PF09921_consen 46 LKAFDQWLQDPMITSHMPREMLEDVWE 72 (126)
T ss_pred HHHHHHHHcCchhHhcCCHHHHHHHHH
Confidence 57889997 5599999988764
No 11
>PF12460 MMS19_C: RNAPII transcription regulator C-terminal; InterPro: IPR024687 This domain, approximately 60 amino acids in length, is found in the N-terminal region of MMS19 proteins. MMS19 is required for both nucleotide excision repair (NER) and RNA polymerase II (RNAP II) transcription [].
Probab=26.37 E-value=25 Score=26.06 Aligned_cols=41 Identities=24% Similarity=0.512 Sum_probs=32.4
Q ss_pred CCcccccchhccccchhhhhhhcCCCChHHH-hchHhhhhHhh
Q psy5543 14 PRVERSSDQVIKPVNLEALTKWVGKIPEDVM-KDMDEIAPMLA 55 (60)
Q Consensus 14 Sk~E~STdQVvkpvn~eaLskW~g~iP~dv~-~dm~~iaPmL~ 55 (60)
++++.+.+. +|+.++.||+.=..++|..++ .++..+-|+|-
T Consensus 330 ~~~~~~~~~-~k~~yL~ALs~ll~~vP~~vl~~~l~~LlPLLl 371 (415)
T PF12460_consen 330 EGFKEADDE-IKSNYLTALSHLLKNVPKSVLLPELPTLLPLLL 371 (415)
T ss_pred HHHhhcChh-hHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHH
Confidence 344555555 799999999999999999876 56888888874
No 12
>COG4755 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.31 E-value=43 Score=23.47 Aligned_cols=21 Identities=24% Similarity=0.833 Sum_probs=17.5
Q ss_pred hhhhhhhcC------CCChHHHhchHh
Q psy5543 29 LEALTKWVG------KIPEDVMKDMDE 49 (60)
Q Consensus 29 ~eaLskW~g------~iP~dv~~dm~~ 49 (60)
+.|.++|.. ++|+++++|..+
T Consensus 64 LKaFd~WLqdP~v~s~mPremL~dv~~ 90 (151)
T COG4755 64 LKAFDSWLQDPVVTSVMPREMLRDVES 90 (151)
T ss_pred HHHHHHHHhCchHhhhCcHHHHHHHHH
Confidence 678999984 499999998765
No 13
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=26.19 E-value=48 Score=19.24 Aligned_cols=24 Identities=21% Similarity=0.602 Sum_probs=15.3
Q ss_pred cchhhhhhhcCCCChHHHhchHhh
Q psy5543 27 VNLEALTKWVGKIPEDVMKDMDEI 50 (60)
Q Consensus 27 vn~eaLskW~g~iP~dv~~dm~~i 50 (60)
|...|++.|.+.||.+-.-.+..+
T Consensus 21 Vs~~aVs~W~~~IP~~ra~~Ie~~ 44 (60)
T PF14549_consen 21 VSPQAVSQWGERIPAERAYQIEKL 44 (60)
T ss_dssp S-HHHHHHHHTS--HHHHHHHHHH
T ss_pred CCHHHHHHhcCccCHHHHHHHHHH
Confidence 455688999888999876665554
No 14
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=22.52 E-value=40 Score=19.28 Aligned_cols=13 Identities=46% Similarity=1.063 Sum_probs=11.8
Q ss_pred cccchhhhhhhcC
Q psy5543 25 KPVNLEALTKWVG 37 (60)
Q Consensus 25 kpvn~eaLskW~g 37 (60)
.||+++.|.+|..
T Consensus 23 ePI~L~el~~~L~ 35 (64)
T PF09494_consen 23 EPINLEELHAWLK 35 (64)
T ss_pred CCccHHHHHHHHH
Confidence 5999999999986
No 15
>PF01618 MotA_ExbB: MotA/TolQ/ExbB proton channel family MotA family only; InterPro: IPR002898 This family groups together integral membrane proteins that appear to be involved in translocation of proteins across a membrane. These proteins are probably proton channels. MotA is an essential component of the flagellar motor that uses a proton gradient to generate rotational motion in the flagellar []. ExbB is part of the TonB-dependent transduction complex. The TonB complex uses the proton gradient across the inner bacterial membrane to transport large molecules across the outer bacterial membrane.; GO: 0008565 protein transporter activity, 0006810 transport, 0016020 membrane
Probab=21.66 E-value=40 Score=21.36 Aligned_cols=18 Identities=22% Similarity=0.444 Sum_probs=14.0
Q ss_pred hHHHhchHhhhhHhhcCC
Q psy5543 41 EDVMKDMDEIAPMLASGN 58 (60)
Q Consensus 41 ~dv~~dm~~iaPmL~~l~ 58 (60)
-.++..+..+||||.-||
T Consensus 55 ~~~l~~i~~~aP~lGLlG 72 (139)
T PF01618_consen 55 LSILRTIASIAPLLGLLG 72 (139)
T ss_pred hHHHHHHHHHHHHHHHHH
Confidence 456778888999988776
No 16
>KOG4415|consensus
Probab=20.85 E-value=35 Score=25.43 Aligned_cols=10 Identities=60% Similarity=1.042 Sum_probs=7.8
Q ss_pred CCCccccccc
Q psy5543 1 MGPQFSFKTY 10 (60)
Q Consensus 1 ~~~~~~i~~~ 10 (60)
|||||.+.+.
T Consensus 47 mGPQFef~ei 56 (247)
T KOG4415|consen 47 MGPQFEFFEI 56 (247)
T ss_pred ecCceeEEEe
Confidence 7999988653
Done!