Query 027357
Match_columns 224
No_of_seqs 53 out of 55
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 08:45:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027357.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027357hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10330 Stb3: Putative Sin3 b 65.1 2 4.3E-05 34.0 -0.1 40 79-118 34-74 (92)
2 COG2932 Predicted transcriptio 64.2 42 0.00091 28.7 7.8 46 133-186 124-169 (214)
3 cd06529 S24_LexA-like Peptidas 45.9 1E+02 0.0022 21.4 7.7 62 134-211 2-63 (81)
4 PF03799 FtsQ: Cell division p 32.8 34 0.00073 25.4 2.0 14 167-180 4-17 (117)
5 TIGR02449 conserved hypothetic 27.6 69 0.0015 23.8 2.8 22 14-41 35-56 (65)
6 COG1722 XseB Exonuclease VII s 27.6 1.2E+02 0.0025 23.3 4.2 33 11-43 31-68 (81)
7 PRK10276 DNA polymerase V subu 27.5 2.3E+02 0.005 22.7 6.1 51 127-186 47-97 (139)
8 PRK14063 exodeoxyribonuclease 26.6 1.6E+02 0.0036 22.0 4.8 33 12-44 27-64 (76)
9 cd06462 Peptidase_S24_S26 The 26.3 1.4E+02 0.0031 20.5 4.2 29 157-186 19-47 (84)
10 TIGR00498 lexA SOS regulatory 22.1 3E+02 0.0065 23.0 6.1 25 17-41 28-52 (199)
No 1
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=65.13 E-value=2 Score=33.99 Aligned_cols=40 Identities=25% Similarity=0.299 Sum_probs=29.5
Q ss_pred eeeccCcccccchhcCCcceeccccceEEEeeC-CeeeEEE
Q 027357 79 LPVCRAEEKENNVLEAPWECKSEGDFGVVVAEK-GWTRWVV 118 (224)
Q Consensus 79 lPV~g~~~l~~~~~~a~~~~~~~g~FgvV~~~~-g~~~WVa 118 (224)
+|-...++.+++-=.-+..++..+.=|-|.|+| ||++|-|
T Consensus 34 vPgF~~ls~sKqRRLi~~ALE~gd~~~~VvFEKvGWGrW~a 74 (92)
T PF10330_consen 34 VPGFSDLSPSKQRRLIMAALEGGDKDGDVVFEKVGWGRWDA 74 (92)
T ss_pred CCCcccCCHHHHHHHHHHHHhcCCCCCCEEEEEeccceeee
Confidence 566777777776433444455788888999999 9999985
No 2
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=64.18 E-value=42 Score=28.67 Aligned_cols=46 Identities=17% Similarity=0.256 Sum_probs=37.1
Q ss_pred EEEEecCCCcCCCcCCCCcccceEEEEEeCCCcccccCCcEEEEEcCCCeEEEe
Q 027357 133 VVVAFSDARVLPWRANRWYYEEAILVVADRSRKEVAVDDGFYLVVGDGGELKVE 186 (224)
Q Consensus 133 VaI~~~~~~~LP~~~~~~~k~E~vLvV~DR~~~e~~~~d~yyLV~~~g~~L~l~ 186 (224)
+||.+.-|.-.|.-.++ .+ ++||.+.+.. .+|..|++..+| .+-++
T Consensus 124 ~~i~V~GDSMeP~~~~G-----d~-ilVd~~~~~~-~gd~v~v~~~g~-~~~VK 169 (214)
T COG2932 124 FALRVTGDSMEPTYEDG-----DT-LLVDPGVNTR-RGDRVYVETDGG-ELYVK 169 (214)
T ss_pred EEEEEeCCcccccccCC-----CE-EEECCCCcee-eCCEEEEEEeCC-eEEEE
Confidence 78888888867776666 33 8999999999 888899998887 77666
No 3
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=45.87 E-value=1e+02 Score=21.45 Aligned_cols=62 Identities=27% Similarity=0.377 Sum_probs=40.7
Q ss_pred EEEecCCCcCCCcCCCCcccceEEEEEeCCCcccccCCcEEEEEcCCCeEEEeecccccccCccccceeEEEEEcCCC
Q 027357 134 VVAFSDARVLPWRANRWYYEEAILVVADRSRKEVAVDDGFYLVVGDGGELKVERGSMLKERGVEESLGTVALVVRPPK 211 (224)
Q Consensus 134 aI~~~~~~~LP~~~~~~~k~E~vLvV~DR~~~e~~~~d~yyLV~~~g~~L~l~~G~~l~e~~~~~~LG~VilvvRPpk 211 (224)
++.+.++.-.|.-.++ - +|++|+..+ . ..+.+|++..++ +..+. .+...+. |.+.|..--|.
T Consensus 2 ~~~v~g~sM~p~i~~g-----d-~lii~~~~~-~-~~g~i~~~~~~~-~~~ik---r~~~~~~----~~~~L~s~N~~ 63 (81)
T cd06529 2 ALRVKGDSMEPTIPDG-----D-LVLVDPSDT-P-RDGDIVVARLDG-ELTVK---RLQRRGG----GRLRLISDNPA 63 (81)
T ss_pred EEEEECCCcCCccCCC-----C-EEEEcCCCC-C-CCCCEEEEEECC-EEEEE---EEEECCC----CcEEEEeCCCC
Confidence 4555666645653333 3 457898876 6 788899999988 88888 5554433 56666665554
No 4
>PF03799 FtsQ: Cell division protein FtsQ; InterPro: IPR005548 FtsQ is one of several cell division proteins. FtsQ interacts with other Fts proteins, reviewed in []. The precise function of FtsQ is unknown.; PDB: 2VH1_B 2VH2_B 2ALJ_A 1YR1_A.
Probab=32.78 E-value=34 Score=25.38 Aligned_cols=14 Identities=36% Similarity=0.631 Sum_probs=11.7
Q ss_pred cccCCcEEEEEcCC
Q 027357 167 VAVDDGFYLVVGDG 180 (224)
Q Consensus 167 ~~~~d~yyLV~~~g 180 (224)
|...++||+|+++|
T Consensus 4 ~~~~~~~~lvd~~G 17 (117)
T PF03799_consen 4 WQDGGGYYLVDENG 17 (117)
T ss_dssp ECCTTEEEEEETTS
T ss_pred EecCCceEEECCCC
Confidence 54568899999999
No 5
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=27.60 E-value=69 Score=23.75 Aligned_cols=22 Identities=27% Similarity=0.415 Sum_probs=17.6
Q ss_pred HHHHHHHHHhhhhhccHHHHHHHHHHHc
Q 027357 14 EERTAALQLALDVVESEDAKNVITRELE 41 (224)
Q Consensus 14 qeR~rli~kgL~~A~Se~AR~~ie~lL~ 41 (224)
.+|..|++| .+.||++||.+++
T Consensus 35 ~ER~~L~ek------ne~Ar~rvEamI~ 56 (65)
T TIGR02449 35 EERAQLLEK------NEQARQKVEAMIT 56 (65)
T ss_pred HHHHHHHHH------HHHHHHHHHHHHH
Confidence 466666664 7899999999988
No 6
>COG1722 XseB Exonuclease VII small subunit [DNA replication, recombination, and repair]
Probab=27.56 E-value=1.2e+02 Score=23.26 Aligned_cols=33 Identities=18% Similarity=0.292 Sum_probs=27.8
Q ss_pred CchHHHHHHHHHhhhhhcc-----HHHHHHHHHHHccC
Q 027357 11 NPSEERTAALQLALDVVES-----EDAKNVITRELEGG 43 (224)
Q Consensus 11 d~~qeR~rli~kgL~~A~S-----e~AR~~ie~lL~~~ 43 (224)
.||++-.++++||.+.+.. ..|+++|++++...
T Consensus 31 l~Le~sl~~~erG~~L~k~c~~~L~~Ae~~v~~l~~~~ 68 (81)
T COG1722 31 LPLEEALKEFERGMALYKECQEKLQQAEQRVEKLLEED 68 (81)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3589999999999988765 68999999999844
No 7
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=27.46 E-value=2.3e+02 Score=22.69 Aligned_cols=51 Identities=16% Similarity=0.181 Sum_probs=32.3
Q ss_pred ccccceEEEEecCCCcCCCcCCCCcccceEEEEEeCCCcccccCCcEEEEEcCCCeEEEe
Q 027357 127 GLRNGGVVVAFSDARVLPWRANRWYYEEAILVVADRSRKEVAVDDGFYLVVGDGGELKVE 186 (224)
Q Consensus 127 ~a~d~PVaI~~~~~~~LP~~~~~~~k~E~vLvV~DR~~~e~~~~d~yyLV~~~g~~L~l~ 186 (224)
...+ -+++-+.++.-.|... +..- +|++|++.+ . .++..|++..+| ++.+.
T Consensus 47 ~~~~-~f~l~V~GdSM~~~~I----~~GD-~liVd~~~~-~-~~Gdivv~~~~g-~~~vK 97 (139)
T PRK10276 47 HPSA-TYFVKASGDSMIDAGI----SDGD-LLIVDSAIT-A-SHGDIVIAAVDG-EFTVK 97 (139)
T ss_pred CCCC-EEEEEEecCCCCCCCC----CCCC-EEEEECCCC-C-CCCCEEEEEECC-EEEEE
Confidence 4544 7888888888334322 2223 556898864 5 556678877777 77666
No 8
>PRK14063 exodeoxyribonuclease VII small subunit; Provisional
Probab=26.59 E-value=1.6e+02 Score=22.03 Aligned_cols=33 Identities=12% Similarity=0.217 Sum_probs=26.2
Q ss_pred chHHHHHHHHHhhhhhcc-----HHHHHHHHHHHccCC
Q 027357 12 PSEERTAALQLALDVVES-----EDAKNVITRELEGGR 44 (224)
Q Consensus 12 ~~qeR~rli~kgL~~A~S-----e~AR~~ie~lL~~~~ 44 (224)
||++-.+++++|.+.+.. +.|+++|..++...+
T Consensus 27 ~Leesl~lyeeG~~L~k~C~~~L~~aE~ki~~l~~~~~ 64 (76)
T PRK14063 27 PLEEAISYFKEGMELSKLCDEKLKNVQEQMAVILGEDG 64 (76)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 488999999999887654 678899998887443
No 9
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=26.29 E-value=1.4e+02 Score=20.52 Aligned_cols=29 Identities=34% Similarity=0.424 Sum_probs=22.1
Q ss_pred EEEEeCCCcccccCCcEEEEEcCCCeEEEe
Q 027357 157 LVVADRSRKEVAVDDGFYLVVGDGGELKVE 186 (224)
Q Consensus 157 LvV~DR~~~e~~~~d~yyLV~~~g~~L~l~ 186 (224)
+|++|+..+.. .++.+|++..+++.+.+.
T Consensus 19 ~v~i~~~~~~~-~~G~iv~~~~~~~~~~ik 47 (84)
T cd06462 19 LVLVDKSSYEP-KRGDIVVFRLPGGELTVK 47 (84)
T ss_pred EEEEEecCCCC-cCCEEEEEEcCCCcEEEE
Confidence 67888888767 778888888765467766
No 10
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=22.05 E-value=3e+02 Score=22.95 Aligned_cols=25 Identities=8% Similarity=0.048 Sum_probs=18.5
Q ss_pred HHHHHHhhhhhccHHHHHHHHHHHc
Q 027357 17 TAALQLALDVVESEDAKNVITRELE 41 (224)
Q Consensus 17 ~rli~kgL~~A~Se~AR~~ie~lL~ 41 (224)
.+.|++.|.+.-+.+....|.+|-.
T Consensus 28 ~~ela~~~~~~s~~tv~~~l~~L~~ 52 (199)
T TIGR00498 28 IREIARAVGLRSPSAAEEHLKALER 52 (199)
T ss_pred HHHHHHHhCCCChHHHHHHHHHHHH
Confidence 6789999988745667777777755
Done!