Query psy6519
Match_columns 208
No_of_seqs 218 out of 783
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 20:06:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6519.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6519hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0217 Uncharacterized conser 100.0 5.9E-55 1.3E-59 380.8 14.0 153 27-186 1-167 (241)
2 PRK00110 hypothetical protein; 100.0 1.1E-51 2.4E-56 361.7 13.9 150 27-185 1-164 (245)
3 TIGR01033 DNA-binding regulato 100.0 2.2E-51 4.8E-56 358.3 13.9 154 27-187 1-168 (238)
4 PRK12378 hypothetical protein; 100.0 5.3E-49 1.1E-53 343.1 13.8 148 28-185 1-163 (235)
5 PF01709 Transcrip_reg: Transc 100.0 9.1E-47 2E-51 328.0 7.2 148 31-185 1-162 (234)
6 KOG2972|consensus 100.0 5.2E-39 1.1E-43 282.3 10.5 165 12-187 15-194 (276)
7 PRK07562 ribonucleotide-diphos 98.9 3.1E-09 6.6E-14 110.2 6.2 70 33-103 296-371 (1220)
8 PF00392 GntR: Bacterial regul 50.1 73 0.0016 21.7 5.8 49 50-101 1-49 (64)
9 PF08671 SinI: Anti-repressor 45.8 31 0.00067 21.6 3.0 25 75-99 4-28 (30)
10 COG3636 Predicted transcriptio 39.4 49 0.0011 26.2 3.9 39 44-88 45-90 (100)
11 smart00497 IENR1 Intron encode 33.9 84 0.0018 20.2 3.9 34 69-102 8-43 (53)
12 smart00685 DM14 Repeats in fly 33.3 72 0.0016 22.8 3.6 27 38-64 17-43 (59)
13 PF00488 MutS_V: MutS domain V 32.0 39 0.00084 29.4 2.5 22 78-99 207-228 (235)
14 COG0217 Uncharacterized conser 31.6 11 0.00025 33.9 -0.9 39 109-157 81-122 (241)
15 cd03285 ABC_MSH2_euk MutS2 hom 29.6 44 0.00096 28.6 2.4 25 77-101 195-219 (222)
16 PHA03188 UL14 tegument protein 29.1 3.1E+02 0.0068 24.2 7.5 66 27-98 1-66 (199)
17 PF05225 HTH_psq: helix-turn-h 26.1 64 0.0014 21.3 2.2 22 79-100 19-40 (45)
18 smart00534 MUTSac ATPase domai 25.9 69 0.0015 26.3 2.9 22 77-98 162-183 (185)
19 PHA03103 double-strand RNA-bin 24.1 1.2E+02 0.0027 26.2 4.1 43 52-103 12-54 (183)
20 cd03284 ABC_MutS1 MutS1 homolo 23.0 72 0.0016 27.2 2.5 22 77-98 193-214 (216)
21 PF05902 4_1_CTD: 4.1 protein 22.6 51 0.0011 26.7 1.4 20 68-87 79-98 (114)
22 PF07592 DDE_Tnp_ISAZ013: Rhod 21.1 33 0.00071 32.0 0.1 15 26-40 222-236 (311)
23 PLN02350 phosphogluconate dehy 20.8 86 0.0019 30.7 2.9 75 52-138 380-468 (493)
24 PF09682 Holin_LLH: Phage holi 20.2 4.1E+02 0.0089 20.4 6.8 57 45-101 39-101 (108)
No 1
>COG0217 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=5.9e-55 Score=380.78 Aligned_cols=153 Identities=30% Similarity=0.424 Sum_probs=136.8
Q ss_pred cccchHHHhHHHHHHhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCccchhHHHHHHhcCCCHHHHHHHHHhcCCCCC-
Q psy6519 27 YAGHSKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKSSMPMTTIENAIKSCNVPEN- 105 (208)
Q Consensus 27 maGHsKW~nIkh~K~a~Da~ksk~fsKl~keI~vA~K~GG~~DP~~N~rL~~aI~~AK~~nmPkd~IErAIkka~~~~~- 105 (208)
|+|||||+||||+|+++|++|+|+|+||+|||++|||.|| +||+.||+||.||++||++|||||+|||||+||+|+.+
T Consensus 1 MaGHsKw~nIkhrK~a~Dakr~Kif~Kl~keI~vAaK~Gg-~dP~~NprLr~aI~kAk~~nmPkd~IerAI~ka~G~~d~ 79 (241)
T COG0217 1 MAGHSKWANIKHRKAAQDAKRSKIFTKLIKEITVAAKQGG-PDPESNPRLRTAIEKAKAANMPKDNIERAIKKASGGKDG 79 (241)
T ss_pred CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCccCHHHHHHHHHHHHcCCCHHHHHHHHHhccCCCCc
Confidence 8999999999999999999999999999999999999999 99999999999999999999999999999999987433
Q ss_pred -cc--eEEE----------EEEecCCCCchhhhhhhhcchhhHhhhCccccCCCCcchhhccccceeecCchhhhhhhhh
Q psy6519 106 -IY--GYLE----------LSCLPWKPTLSIARLVSLEGSACLVSAMSRVRFPPSANFISNRLGLFLECSEPITRMKQAS 172 (208)
Q Consensus 106 -~~--~~yE----------ve~~Tdn~nRT~~~vR~~fgka~~~k~gg~l~~sGSVsfmF~r~G~i~~~S~p~t~~~~a~ 172 (208)
+| ++|| |||||||+|||+++|| ++|.|+||+||.+|||+|||+|+|+|.+......+.++ .
T Consensus 80 ~~~~ei~YEGygP~GvaiiVe~LTDN~NRTas~vR-----~~F~K~GG~lg~~GSV~~mF~~kGvi~~~~~~~~ed~l-~ 153 (241)
T COG0217 80 ANYEEIRYEGYGPGGVAIIVEALTDNRNRTASNVR-----SAFNKNGGNLGEPGSVSYMFDRKGVIVVEKNEIDEDEL-L 153 (241)
T ss_pred cceEEEEEEeECCCceEEEEEeccCCcchhHHHHH-----HHHHhcCCccCCCceEEEEEeccEEEEECCCCCCHHHH-H
Confidence 55 9999 9999999999999999 66666999999999999999999999998665333322 3
Q ss_pred hHHHHhhccccccC
Q psy6519 173 VLLATALAHNVFPV 186 (208)
Q Consensus 173 ~s~a~A~A~~V~p~ 186 (208)
..+-.|.|.+|...
T Consensus 154 e~~ieagaeDv~~~ 167 (241)
T COG0217 154 EAAIEAGAEDVEED 167 (241)
T ss_pred HHHHHCCchhhhcC
Confidence 33445678888776
No 2
>PRK00110 hypothetical protein; Validated
Probab=100.00 E-value=1.1e-51 Score=361.73 Aligned_cols=150 Identities=29% Similarity=0.368 Sum_probs=133.3
Q ss_pred cccchHHHhHHHHHHhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCccchhHHHHHHhcCCCHHHHHHHHHhcCCC--C
Q psy6519 27 YAGHSKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKSSMPMTTIENAIKSCNVP--E 104 (208)
Q Consensus 27 maGHsKW~nIkh~K~a~Da~ksk~fsKl~keI~vA~K~GG~~DP~~N~rL~~aI~~AK~~nmPkd~IErAIkka~~~--~ 104 (208)
|+|||||+||||+|+++|++|+|+|+||+|||++|||+|| |||+.|++||++|++||++|||||+|||||+|+++. .
T Consensus 1 maGHskW~~Ikh~K~~~D~kksk~f~kl~reI~vAak~GG-~DP~~N~~Lr~aI~~Ak~~nmPkd~IerAIkk~~g~~~~ 79 (245)
T PRK00110 1 MAGHSKWANIKHRKGAQDAKRGKIFTKLIREITVAAKLGG-GDPEGNPRLRLAIDKAKAANMPKDNIERAIKKGTGELDG 79 (245)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC-CCCccCHHHHHHHHHHHHhCCCHHHHHHHHHHhcCCCCc
Confidence 8999999999999999999999999999999999999999 999999999999999999999999999999999875 2
Q ss_pred Ccc--eEEE----------EEEecCCCCchhhhhhhhcchhhHhhhCccccCCCCcchhhccccceeecCchhhhhhhhh
Q psy6519 105 NIY--GYLE----------LSCLPWKPTLSIARLVSLEGSACLVSAMSRVRFPPSANFISNRLGLFLECSEPITRMKQAS 172 (208)
Q Consensus 105 ~~~--~~yE----------ve~~Tdn~nRT~~~vR~~fgka~~~k~gg~l~~sGSVsfmF~r~G~i~~~S~p~t~~~~a~ 172 (208)
.+| ++|| |||+|||+|||+++|| ++|+|+||+|+.+|||.|||+|+|+|.+... ... -..
T Consensus 80 ~~~~e~~YEg~gP~GvaiiVe~lTDN~nRt~~~vR-----~~f~K~gG~l~~~Gsv~~~Fe~kG~i~~~~~--~~d-~~~ 151 (245)
T PRK00110 80 ANYEEIRYEGYGPGGVAIIVEALTDNRNRTAAEVR-----HAFSKNGGNLGETGSVSYMFDRKGVIVIEPL--DED-ELM 151 (245)
T ss_pred cceEEEEEEEEcCCCeEEEEEEecCCHHHHHHHHH-----HHHHhcCceeCCCcceEEEeccceEEEeCCC--CHH-HHH
Confidence 344 9999 9999999999999999 6677799999999999999999999999743 111 222
Q ss_pred hHHHHhhcccccc
Q psy6519 173 VLLATALAHNVFP 185 (208)
Q Consensus 173 ~s~a~A~A~~V~p 185 (208)
..+-.|.|.+|..
T Consensus 152 e~aieaGaeDv~~ 164 (245)
T PRK00110 152 EAALEAGAEDVET 164 (245)
T ss_pred HHHHhCCCCEeec
Confidence 3334577988864
No 3
>TIGR01033 DNA-binding regulatory protein, YebC/PmpR family. This model describes a minimally characterized protein family, restricted to bacteria excepting for some eukaryotic sequences that have possible transit peptides. YebC from E. coli is crystallized, and PA0964 from Pseudomonas aeruginosa has been shown to be a sequence-specific DNA-binding regulatory protein.
Probab=100.00 E-value=2.2e-51 Score=358.31 Aligned_cols=154 Identities=29% Similarity=0.397 Sum_probs=135.5
Q ss_pred cccchHHHhHHHHHHhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCccchhHHHHHHhcCCCHHHHHHHHHhcCCC--C
Q psy6519 27 YAGHSKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKSSMPMTTIENAIKSCNVP--E 104 (208)
Q Consensus 27 maGHsKW~nIkh~K~a~Da~ksk~fsKl~keI~vA~K~GG~~DP~~N~rL~~aI~~AK~~nmPkd~IErAIkka~~~--~ 104 (208)
|+|||||+||||+|+++|++|+|+|+||+|+|++|||+|| +||+.|++||++|++||++|||||+|||||+|+++. .
T Consensus 1 maGHskw~~Ikh~K~~~D~~ksk~f~kl~r~I~vA~k~GG-~DP~~N~~L~~ai~~Ak~~~~Pkd~IerAIkr~~g~~~~ 79 (238)
T TIGR01033 1 MAGHSKWANIKHRKAAQDAKRGKIFTKLIKEIIVAAKLGG-GDPESNPRLRTAIEKAKAANMPKDNIERAIKKGAGELDG 79 (238)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC-CCCccCHHHHHHHHHHHHhCCCHHHHHHHHHHhcCCCCc
Confidence 7999999999999999999999999999999999999999 999999999999999999999999999999999874 3
Q ss_pred Ccc--eEEE----------EEEecCCCCchhhhhhhhcchhhHhhhCccccCCCCcchhhccccceeecCchhhhhhhhh
Q psy6519 105 NIY--GYLE----------LSCLPWKPTLSIARLVSLEGSACLVSAMSRVRFPPSANFISNRLGLFLECSEPITRMKQAS 172 (208)
Q Consensus 105 ~~~--~~yE----------ve~~Tdn~nRT~~~vR~~fgka~~~k~gg~l~~sGSVsfmF~r~G~i~~~S~p~t~~~~a~ 172 (208)
.+| ++|| |||+|||+|||+++|| .+|.|+||+|+.+|||.|||+|+|+|.+........ -..
T Consensus 80 ~~~~~~~YEg~gP~GvaiiVe~lTDN~nRt~~~ir-----~~f~K~gg~l~~~gsv~~~Fe~kG~i~~~~~~~~~d-~~~ 153 (238)
T TIGR01033 80 SNYEEITYEGYAPGGVAIIVECLTDNKNRTASEVR-----SAFNKNGGSLGEPGSVSYLFSRKGVIEVPKNEVDEE-DLM 153 (238)
T ss_pred cceEEEEEEEEcCCceEEEEEEecCCHHhHHHHHH-----HHHHHcCCeeCCCCceeeeeecceEEEECCCCCCHH-HHH
Confidence 344 9999 9999999999999999 777779999999999999999999999974322222 223
Q ss_pred hHHHHhhccccccCC
Q psy6519 173 VLLATALAHNVFPVP 187 (208)
Q Consensus 173 ~s~a~A~A~~V~p~P 187 (208)
..+..|.|.+|.+..
T Consensus 154 e~aieaGAedv~~~~ 168 (238)
T TIGR01033 154 EAAIEAGAEDIDVDD 168 (238)
T ss_pred HHHHhCCCceeeccC
Confidence 334567799986543
No 4
>PRK12378 hypothetical protein; Provisional
Probab=100.00 E-value=5.3e-49 Score=343.14 Aligned_cols=148 Identities=28% Similarity=0.396 Sum_probs=129.2
Q ss_pred ccchHHHhHHHHHHhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCccchhHHHHHHhcCCCHHHHHHHHHhcCCCC-Cc
Q psy6519 28 AGHSKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKSSMPMTTIENAIKSCNVPE-NI 106 (208)
Q Consensus 28 aGHsKW~nIkh~K~a~Da~ksk~fsKl~keI~vA~K~GG~~DP~~N~rL~~aI~~AK~~nmPkd~IErAIkka~~~~-~~ 106 (208)
+|| ||+||||+|+++|++|+|+|+||+|||++|||+|| +||+.|++||.+|++||++|||||+|||||||+++.+ .+
T Consensus 1 ~g~-kW~~Ikh~K~~~Da~ksk~f~kl~reI~vA~k~GG-~dP~~N~~Lr~aI~~Ak~~nmPkd~IerAIkk~~g~~~~~ 78 (235)
T PRK12378 1 MGR-AWENIKAKKAKKDGAKSKIFAKLGKEIYVAAKQGG-PDPESNPALRFVIERAKKANVPKDVIERAIKKAKGGGGED 78 (235)
T ss_pred CCc-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC-CCCccCHHHHHHHHHHHHhCCCHHHHHHHHHhccCCCCCc
Confidence 477 99999999999999999999999999999999999 9999999999999999999999999999999998753 34
Q ss_pred c--eEEE----------EEEecCCCCchhhhhhhhcchhhHhhhCccccCCCCcchhhccccceeecCchhhhhhhhhhH
Q psy6519 107 Y--GYLE----------LSCLPWKPTLSIARLVSLEGSACLVSAMSRVRFPPSANFISNRLGLFLECSEPITRMKQASVL 174 (208)
Q Consensus 107 ~--~~yE----------ve~~Tdn~nRT~~~vR~~fgka~~~k~gg~l~~sGSVsfmF~r~G~i~~~S~p~t~~~~a~~s 174 (208)
| ++|| |||+|||+|||+++|| ++|.|+||+|+.+|||+|||+|+|+|.+... + ..-....
T Consensus 79 ~~e~~YEgygPgGvaiiVe~lTDN~nRt~~~vr-----~~f~K~gg~l~~~gsv~~~Fe~kG~i~i~~~--~-~d~~~e~ 150 (235)
T PRK12378 79 YEEVRYEGFGPNGVMVIVECLTDNVNRTVANVR-----SAFNKNGGNLGTSGSVAFMFDHKGVFVFEGD--D-EDELLEA 150 (235)
T ss_pred eEEEEEEEEcCCCcEEEEEECCCCHHHHHHHHH-----HHHhhcCCeECCCCceeeeeecceEEEeCCC--C-HHHHHHH
Confidence 4 9999 9999999999999999 6677799999999999999999999999754 2 2222333
Q ss_pred HHHhhc--ccccc
Q psy6519 175 LATALA--HNVFP 185 (208)
Q Consensus 175 ~a~A~A--~~V~p 185 (208)
+-.|.| .+|..
T Consensus 151 aieaGa~~edv~~ 163 (235)
T PRK12378 151 LIDADVDVEDVEE 163 (235)
T ss_pred HHhCCCCcccccc
Confidence 334555 66643
No 5
>PF01709 Transcrip_reg: Transcriptional regulator; InterPro: IPR002876 This entry represents the core region of several hypothetical proteins found in bacteria, plants, and yeast proteins. This core region can be subdivided into three domains: a 3-helical bundle domain, and two alpha+beta domains with different folds, where domain 3 (ferredoxin-like fold) is inserted within domain 2. This core region is found in the following hypothetical proteins: YebC from Escherichia coli, HP0162 from Helicobacter pylori (Campylobacter pylori) and aq1575 from Aquifex aeolicus []. The crystal structure of a conserved hypothetical protein, Aq1575, from Aquifex aeolicus has been determined. A structural homology search reveals that this protein has a new fold with no obvious similarity to those of other proteins of known three-dimensional structure. The protein reveals a monomer consisting of three domains arranged along a pseudo threefold symmetry axis. There is a large cleft with approximate dimensions of 10 A x 10 A x 20 A in the centre of the three domains along the symmetry axis. Two possible active sites are suggested based on the structure and multiple sequence alignment. There are several highly conserved residues in these putative active sites [].; PDB: 1LFP_A 1MW7_A 1KON_A.
Probab=100.00 E-value=9.1e-47 Score=327.98 Aligned_cols=148 Identities=33% Similarity=0.444 Sum_probs=121.6
Q ss_pred hHHHhHHHHHHhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCccchhHHHHHHhcCCCHHHHHHHHHhcCCC--CCcc-
Q psy6519 31 SKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKSSMPMTTIENAIKSCNVP--ENIY- 107 (208)
Q Consensus 31 sKW~nIkh~K~a~Da~ksk~fsKl~keI~vA~K~GG~~DP~~N~rL~~aI~~AK~~nmPkd~IErAIkka~~~--~~~~- 107 (208)
|||+||||+|+++|++|+++|+||+|||++|||+|| |||+.|++|+++|++||+.|||||+|||||+|+++. ..++
T Consensus 1 sKW~nIkh~K~~~D~~ksk~f~kl~reI~~Avk~GG-~DP~~N~~L~~ai~~Ak~~nmPk~~IerAIkk~~~~~~~~~~~ 79 (234)
T PF01709_consen 1 SKWSNIKHKKAAQDAKKSKLFTKLSREITVAVKEGG-PDPDMNPRLRSAIEKAKKANMPKDNIERAIKKASGKSDGANYE 79 (234)
T ss_dssp -SCGGTSSSTTTTTTSHHHHHHHHHHHHHHHHHCC--S-GGGSHHHHHHHHHHHHTT--HHHHHHHHHHCCSTSST---E
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC-CCCCcCHHHHHHHHHHHHhCCCHHHHHHHHHhcCcCCCCcCce
Confidence 799999999999999999999999999999999999 999999999999999999999999999999999885 2333
Q ss_pred -eEEE----------EEEecCCCCchhhhhhhhcchhhHhhhCccccCCCCcchhhccccceeecCchhhhhhhhhhHHH
Q psy6519 108 -GYLE----------LSCLPWKPTLSIARLVSLEGSACLVSAMSRVRFPPSANFISNRLGLFLECSEPITRMKQASVLLA 176 (208)
Q Consensus 108 -~~yE----------ve~~Tdn~nRT~~~vR~~fgka~~~k~gg~l~~sGSVsfmF~r~G~i~~~S~p~t~~~~a~~s~a 176 (208)
++|| |||+|||+|||+++|| .+|.|+||+|+.+|||+|||+|+|+|.+......+. -....+-
T Consensus 80 ~~~yEg~gP~Gvaiive~lTDN~nRt~~~ir-----~~~~K~gg~l~~~gsv~~~F~~kG~i~~~~~~~~~d-~~~e~aI 153 (234)
T PF01709_consen 80 EITYEGYGPGGVAIIVECLTDNKNRTVSDIR-----SIFKKNGGSLGPSGSVSFMFERKGVIEVSKKDLDED-ELMEDAI 153 (234)
T ss_dssp EEEEEEEETTTEEEEEEEEES-HHHHHHHHH-----HHHHTTT-EEE-TTSSGGGEEEEEEEEEEHCCS-HH-HHHHHHH
T ss_pred EEEEEEEcCCCcEEEEEEeCCCHhHHHHHHH-----HHHHHcCceeCCCCcceeeeeeeEEEEEEeCCCChH-HHHHHHH
Confidence 9999 9999999999999999 667779999999999999999999999984333333 2233344
Q ss_pred Hhhcccccc
Q psy6519 177 TALAHNVFP 185 (208)
Q Consensus 177 ~A~A~~V~p 185 (208)
.|.|.+|..
T Consensus 154 e~GaeDve~ 162 (234)
T PF01709_consen 154 EAGAEDVEE 162 (234)
T ss_dssp HHTESEEEE
T ss_pred hCCCcEeee
Confidence 567999973
No 6
>KOG2972|consensus
Probab=100.00 E-value=5.2e-39 Score=282.27 Aligned_cols=165 Identities=27% Similarity=0.376 Sum_probs=134.8
Q ss_pred eecccccCcccch-hccccchHHHhHHHHHHhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCccchhHHHHHHhcCCCH
Q psy6519 12 KVHRLIPDEGYLL-VRYAGHSKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKSSMPM 90 (208)
Q Consensus 12 ~~~r~~~~~~~~s-~~maGHsKW~nIkh~K~a~Da~ksk~fsKl~keI~vA~K~GG~~DP~~N~rL~~aI~~AK~~nmPk 90 (208)
|..|+.+.+. | ..|+|||||+||||+|+|+|++|+|++.||+++|..|||.|| +||+.|.+|+.+++.||+.+|||
T Consensus 15 ~~s~s~sv~~--s~~~~sgH~kwskIk~~Kg~nD~~rsk~~nkl~~~i~~aVk~gg-~np~lN~~LAtlle~ak~~~vpk 91 (276)
T KOG2972|consen 15 HFSRSRSVTT--SGWIMSGHNKWSKIKHKKGANDQARSKQINKLSQGIILAVKQGG-ANPELNMRLATLLESAKKISVPK 91 (276)
T ss_pred hcCchhheec--ccceecccchhhhhcccccccHHHHHHHHHHHHHHHHHHHHhcC-CCchhhhHHHHHHHHHHhcCCCH
Confidence 4555444431 4 469999999999999999999999999999999999999999 99999999999999999999999
Q ss_pred HHHHHHHHhcCCCCC---cceEEE----------EEEecCCCCchhhhhhhhcchhhHhhhCccccCCCCcchhhccccc
Q psy6519 91 TTIENAIKSCNVPEN---IYGYLE----------LSCLPWKPTLSIARLVSLEGSACLVSAMSRVRFPPSANFISNRLGL 157 (208)
Q Consensus 91 d~IErAIkka~~~~~---~~~~yE----------ve~~Tdn~nRT~~~vR~~fgka~~~k~gg~l~~sGSVsfmF~r~G~ 157 (208)
|.||+||+||+++++ .+..|| ||++|||+||++++||++|++ +|| +..+++.|||+++|+
T Consensus 92 d~ien~i~ras~k~~~a~e~~~ye~~gp~GV~liVealTdnknr~~~~iRs~~nk-----~GG--~s~~~~r~~FdkKG~ 164 (276)
T KOG2972|consen 92 DGIENAINRASGKEGSAVEFIEYEAMGPSGVGLIVEALTDNKNRAASSIRSIFNK-----HGG--ASASGVRFLFDKKGV 164 (276)
T ss_pred HHHHHHHHHhccCCCCceEEEEEeeecCCceEEEEEeeeccHhHHHHHHHHHHHH-----cCC--cccccceeEEeccce
Confidence 999999999988543 458899 999999999999999955555 998 456899999999994
Q ss_pred eeecCchhhhhh-hhhhHHHHhhccccccCC
Q psy6519 158 FLECSEPITRMK-QASVLLATALAHNVFPVP 187 (208)
Q Consensus 158 i~~~S~p~t~~~-~a~~s~a~A~A~~V~p~P 187 (208)
+++- .|....| .-....+.|.|.++.--|
T Consensus 165 Vv~V-~~~~~dk~vL~ie~ie~~A~d~~~~~ 194 (276)
T KOG2972|consen 165 VVNV-PPEKRDKDVLNIEAIEAGAEDIVAEP 194 (276)
T ss_pred EEec-ChhhcchhhhhHHHHHhcccccccCc
Confidence 3332 3444444 444444667777665443
No 7
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=98.85 E-value=3.1e-09 Score=110.24 Aligned_cols=70 Identities=21% Similarity=0.213 Sum_probs=64.9
Q ss_pred HHhHHHHHHhhhHHHHHHHHHHHHHHHHHHHhC------CCCCCCcCccchhHHHHHHhcCCCHHHHHHHHHhcCCC
Q psy6519 33 WQNIRHIKAAKDQEKATLFTNLSKKLKLAVKEG------GGTDPNTNYRLASTIDYCKKSSMPMTTIENAIKSCNVP 103 (208)
Q Consensus 33 W~nIkh~K~a~Da~ksk~fsKl~keI~vA~K~G------G~~DP~~N~rL~~aI~~AK~~nmPkd~IErAIkka~~~ 103 (208)
|.+.+..|.+.+..++|+++|+.++|..|+|.| | +||+.|++|+.+|++||+.+||++.|+|+|+++.++
T Consensus 296 ~K~~ee~Kvaalv~gski~~k~lk~I~~A~~~~~G~~~~~-~DP~~NpaLk~aI~~Ak~~~vP~~~I~RvI~~A~qg 371 (1220)
T PRK07562 296 WKVKEEQKVAALVTGSKIVSKHLKAIMKACVNCEGDGDDC-FDPAKNPALKREIKAAKKALVPENYIKRVIQFARQG 371 (1220)
T ss_pred hccchhhhHHhhhhcchHHHHHHHHHHHHHHhcccccccc-CCccccHHHHHHHHHHHhccCCHHHHHHHHHHhhcc
Confidence 445557899999999999999999999999998 5 899999999999999999999999999999998766
No 8
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=50.06 E-value=73 Score=21.71 Aligned_cols=49 Identities=20% Similarity=0.358 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCcCccchhHHHHHHhcCCCHHHHHHHHHhcC
Q psy6519 50 LFTNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKSSMPMTTIENAIKSCN 101 (208)
Q Consensus 50 ~fsKl~keI~vA~K~GG~~DP~~N~rL~~aI~~AK~~nmPkd~IErAIkka~ 101 (208)
++..+..+|...+..|. ...+-+|-+.-+-|+..+++..++.+|++...
T Consensus 1 l~~~i~~~l~~~I~~g~---~~~g~~lps~~~la~~~~vsr~tvr~al~~L~ 49 (64)
T PF00392_consen 1 LYEQIYDQLRQAILSGR---LPPGDRLPSERELAERYGVSRTTVREALRRLE 49 (64)
T ss_dssp HHHHHHHHHHHHHHTTS---S-TTSBE--HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHcCC---CCCCCEeCCHHHHHHHhccCCcHHHHHHHHHH
Confidence 36678888888888875 34456777778889999999999999999854
No 9
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=45.85 E-value=31 Score=21.59 Aligned_cols=25 Identities=16% Similarity=0.186 Sum_probs=19.4
Q ss_pred cchhHHHHHHhcCCCHHHHHHHHHh
Q psy6519 75 RLASTIDYCKKSSMPMTTIENAIKS 99 (208)
Q Consensus 75 rL~~aI~~AK~~nmPkd~IErAIkk 99 (208)
....+|..|++.|+.++-|...++.
T Consensus 4 EW~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 4 EWVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 3567899999999999999988763
No 10
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=39.36 E-value=49 Score=26.23 Aligned_cols=39 Identities=18% Similarity=0.267 Sum_probs=26.2
Q ss_pred hHHHHHHHHHHHHH-------HHHHHHhCCCCCCCcCccchhHHHHHHhcCC
Q psy6519 44 DQEKATLFTNLSKK-------LKLAVKEGGGTDPNTNYRLASTIDYCKKSSM 88 (208)
Q Consensus 44 Da~ksk~fsKl~ke-------I~vA~K~GG~~DP~~N~rL~~aI~~AK~~nm 88 (208)
+.+|++=.++++++ ++.|.+.|| ||++..++.-+|..|+
T Consensus 45 ~var~~GMsqvA~~aGlsRe~LYkaLS~~G------NPtf~Til~V~kAlG~ 90 (100)
T COG3636 45 VVARSRGMSQVARKAGLSREGLYKALSPGG------NPTFDTILAVLKALGL 90 (100)
T ss_pred HHHHhcCHHHHHHHhCccHHHHHHHhCCCC------CCcHHHHHHHHHHcCc
Confidence 45555556666554 566776666 7888888877777765
No 11
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=33.88 E-value=84 Score=20.22 Aligned_cols=34 Identities=15% Similarity=0.198 Sum_probs=26.7
Q ss_pred CCCcCc--cchhHHHHHHhcCCCHHHHHHHHHhcCC
Q psy6519 69 DPNTNY--RLASTIDYCKKSSMPMTTIENAIKSCNV 102 (208)
Q Consensus 69 DP~~N~--rL~~aI~~AK~~nmPkd~IErAIkka~~ 102 (208)
|++.|. ...++-+.|+..++...+|.++++....
T Consensus 8 d~~~~~i~~f~S~~eAa~~lg~~~~~I~~~~~~~~~ 43 (53)
T smart00497 8 DLDGNLIGEFSSIREAAKYLGISHSSISKYLNTGKK 43 (53)
T ss_pred eCCCCEEEEecCHHHHHHHhCCCHHHHHHHHhCCCc
Confidence 344443 4778899999999999999999997443
No 12
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=33.28 E-value=72 Score=22.83 Aligned_cols=27 Identities=33% Similarity=0.399 Sum_probs=22.7
Q ss_pred HHHHhhhHHHHHHHHHHHHHHHHHHHh
Q psy6519 38 HIKAAKDQEKATLFTNLSKKLKLAVKE 64 (208)
Q Consensus 38 h~K~a~Da~ksk~fsKl~keI~vA~K~ 64 (208)
+-|.+.|..+++.|.+++|.+..+++.
T Consensus 17 ~AK~~gd~~kAr~~~R~~K~~~~~I~~ 43 (59)
T smart00685 17 QAKRAGDEEKARRHLRIAKQFDDAIKA 43 (59)
T ss_pred HHHHcCCHHHHHHHHHHHhhHHHHHHH
Confidence 467888999999999999988776654
No 13
>PF00488 MutS_V: MutS domain V C-terminus.; InterPro: IPR000432 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 C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....
Probab=32.00 E-value=39 Score=29.42 Aligned_cols=22 Identities=27% Similarity=0.351 Sum_probs=17.7
Q ss_pred hHHHHHHhcCCCHHHHHHHHHh
Q psy6519 78 STIDYCKKSSMPMTTIENAIKS 99 (208)
Q Consensus 78 ~aI~~AK~~nmPkd~IErAIkk 99 (208)
-+|+-|+..|+|++.|++|-+.
T Consensus 207 ~ai~iA~~~g~p~~II~rA~~i 228 (235)
T PF00488_consen 207 YAIEIAKLAGLPEEIIERAKEI 228 (235)
T ss_dssp CHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHhCcCHHHHHHHHHH
Confidence 4899999999999999999764
No 14
>COG0217 Uncharacterized conserved protein [Function unknown]
Probab=31.61 E-value=11 Score=33.90 Aligned_cols=39 Identities=23% Similarity=0.267 Sum_probs=33.2
Q ss_pred EEE-EEEecCCCCchhhhhhhhcchhhHhhhCcc--ccCCCCcchhhccccc
Q psy6519 109 YLE-LSCLPWKPTLSIARLVSLEGSACLVSAMSR--VRFPPSANFISNRLGL 157 (208)
Q Consensus 109 ~yE-ve~~Tdn~nRT~~~vR~~fgka~~~k~gg~--l~~sGSVsfmF~r~G~ 157 (208)
.|| ++|+++.| .|.+++++++++ -++...|.+.|.+.|=
T Consensus 81 ~~~ei~YEGygP----------~GvaiiVe~LTDN~NRTas~vR~~F~K~GG 122 (241)
T COG0217 81 NYEEIRYEGYGP----------GGVAIIVEALTDNRNRTASNVRSAFNKNGG 122 (241)
T ss_pred ceEEEEEEeECC----------CceEEEEEeccCCcchhHHHHHHHHHhcCC
Confidence 466 99999999 788999999888 4578889999998874
No 15
>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=29.61 E-value=44 Score=28.64 Aligned_cols=25 Identities=20% Similarity=0.197 Sum_probs=22.1
Q ss_pred hhHHHHHHhcCCCHHHHHHHHHhcC
Q psy6519 77 ASTIDYCKKSSMPMTTIENAIKSCN 101 (208)
Q Consensus 77 ~~aI~~AK~~nmPkd~IErAIkka~ 101 (208)
..+|+-|+..++|++.|+||-+.+.
T Consensus 195 s~a~~~a~~~g~p~~vi~~A~~~~~ 219 (222)
T cd03285 195 SFGIHVAELANFPKEVIEMAKQKAL 219 (222)
T ss_pred cHHHHHHHHhCcCHHHHHHHHHHHH
Confidence 5699999999999999999987654
No 16
>PHA03188 UL14 tegument protein; Provisional
Probab=29.14 E-value=3.1e+02 Score=24.18 Aligned_cols=66 Identities=18% Similarity=0.269 Sum_probs=37.5
Q ss_pred cccchHHHhHHHHHHhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCccchhHHHHHHhcCCCHHHHHHHHH
Q psy6519 27 YAGHSKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKSSMPMTTIENAIK 98 (208)
Q Consensus 27 maGHsKW~nIkh~K~a~Da~ksk~fsKl~keI~vA~K~GG~~DP~~N~rL~~aI~~AK~~nmPkd~IErAIk 98 (208)
|+||..++- .++.-..-..-.-....+=|+=++=.=.+| -|++ +|.+..+.-.||++ -..+++.|.
T Consensus 1 ~~~~~~~~~-~~RrrR~~L~Ea~~Re~iyK~RTLdLir~G-Vd~~-dP~FV~AFTsAK~A---~~dl~rqLr 66 (199)
T PHA03188 1 MSGHTPLSA-AHRRNRVHLLEAHHRAGLFKERTLDLIRGG-ASTQ-DPAFVHAFTAAKDA---CADLNNNIR 66 (199)
T ss_pred CCCCCcchH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHcC-CCCC-ChHHHHHHHHHHHH---HHHHHHHHH
Confidence 788877743 344333333333333333333333333456 6654 89999999999998 445555553
No 17
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=26.13 E-value=64 Score=21.28 Aligned_cols=22 Identities=18% Similarity=0.277 Sum_probs=16.6
Q ss_pred HHHHHHhcCCCHHHHHHHHHhc
Q psy6519 79 TIDYCKKSSMPMTTIENAIKSC 100 (208)
Q Consensus 79 aI~~AK~~nmPkd~IErAIkka 100 (208)
.-+.|+..|||+.+|.+-++..
T Consensus 19 ~r~AA~~ygVp~sTL~~r~~g~ 40 (45)
T PF05225_consen 19 IRKAAKKYGVPRSTLRRRLRGK 40 (45)
T ss_dssp HHHHHHHHT--HHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHcCC
Confidence 5567999999999999888753
No 18
>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family.
Probab=25.86 E-value=69 Score=26.26 Aligned_cols=22 Identities=27% Similarity=0.382 Sum_probs=19.7
Q ss_pred hhHHHHHHhcCCCHHHHHHHHH
Q psy6519 77 ASTIDYCKKSSMPMTTIENAIK 98 (208)
Q Consensus 77 ~~aI~~AK~~nmPkd~IErAIk 98 (208)
.-+++-|+..++|.+.|++|-+
T Consensus 162 s~a~~~a~~~g~~~~i~~~a~~ 183 (185)
T smart00534 162 SYGIEVAKLAGLPKEVIERAKE 183 (185)
T ss_pred cHHHHHHHHhCCCHHHHHHHHH
Confidence 3689999999999999999965
No 19
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=24.10 E-value=1.2e+02 Score=26.21 Aligned_cols=43 Identities=14% Similarity=0.136 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHhCCCCCCCcCccchhHHHHHHhcCCCHHHHHHHHHhcCCC
Q psy6519 52 TNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKSSMPMTTIENAIKSCNVP 103 (208)
Q Consensus 52 sKl~keI~vA~K~GG~~DP~~N~rL~~aI~~AK~~nmPkd~IErAIkka~~~ 103 (208)
..|.++|..-...|+ .- .|++-||+.|++|..|.|.+=+-+..
T Consensus 12 ~~lv~~~~~~l~~~~-~~--------~a~~i~~~l~~~k~~vNr~LY~l~~~ 54 (183)
T PHA03103 12 YELVKKEVKNLGLGE-GI--------TAIEISRKLNIEKSEVNKQLYKLQRE 54 (183)
T ss_pred HHHHHHHHHHhccCC-Cc--------cHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence 356667777777766 33 38999999999999999999886544
No 20
>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam
Probab=23.04 E-value=72 Score=27.17 Aligned_cols=22 Identities=23% Similarity=0.360 Sum_probs=19.3
Q ss_pred hhHHHHHHhcCCCHHHHHHHHH
Q psy6519 77 ASTIDYCKKSSMPMTTIENAIK 98 (208)
Q Consensus 77 ~~aI~~AK~~nmPkd~IErAIk 98 (208)
.-+++-|+..++|++.|+||-.
T Consensus 193 s~a~~~a~~~g~~~~ii~rA~~ 214 (216)
T cd03284 193 SYGIEVARLAGLPEEVIERARE 214 (216)
T ss_pred cHHHHHHHHhCcCHHHHHHHHH
Confidence 4589999999999999999853
No 21
>PF05902 4_1_CTD: 4.1 protein C-terminal domain (CTD); InterPro: IPR008379 There is a unique sequence domain at the C terminus of all known 4.1 proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24 kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates [].; GO: 0003779 actin binding, 0005198 structural molecule activity, 0005856 cytoskeleton
Probab=22.57 E-value=51 Score=26.67 Aligned_cols=20 Identities=25% Similarity=0.308 Sum_probs=17.7
Q ss_pred CCCCcCccchhHHHHHHhcC
Q psy6519 68 TDPNTNYRLASTIDYCKKSS 87 (208)
Q Consensus 68 ~DP~~N~rL~~aI~~AK~~n 87 (208)
+|-+....|+.||.+||.+|
T Consensus 79 ~DIDhDqaLa~aI~eAk~q~ 98 (114)
T PF05902_consen 79 ADIDHDQALAQAIKEAKEQH 98 (114)
T ss_pred CCcchHHHHHHHHHHHHHhC
Confidence 78778899999999999876
No 22
>PF07592 DDE_Tnp_ISAZ013: Rhodopirellula transposase DDE domain; InterPro: IPR011518 These transposases are found in the planctomycete Rhodopirellula baltica, the cyanobacterium Nostoc, and the Gram-positive bacterium Streptomyces. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.10 E-value=33 Score=32.03 Aligned_cols=15 Identities=40% Similarity=0.600 Sum_probs=12.7
Q ss_pred ccccchHHHhHHHHH
Q psy6519 26 RYAGHSKWQNIRHIK 40 (208)
Q Consensus 26 ~maGHsKW~nIkh~K 40 (208)
..-|||||.+|-||-
T Consensus 222 yPP~tSKwN~IEHRl 236 (311)
T PF07592_consen 222 YPPGTSKWNPIEHRL 236 (311)
T ss_pred cCCCcccccchhhhH
Confidence 367999999999973
No 23
>PLN02350 phosphogluconate dehydrogenase (decarboxylating)
Probab=20.81 E-value=86 Score=30.73 Aligned_cols=75 Identities=7% Similarity=0.049 Sum_probs=52.3
Q ss_pred HHHHHHHHHHHHhCCCCCC--------------CcCccchhHHHHHHhcCCCHHHHHHHHHhcCCCCCcceEEEEEEecC
Q psy6519 52 TNLSKKLKLAVKEGGGTDP--------------NTNYRLASTIDYCKKSSMPMTTIENAIKSCNVPENIYGYLELSCLPW 117 (208)
Q Consensus 52 sKl~keI~vA~K~GG~~DP--------------~~N~rL~~aI~~AK~~nmPkd~IErAIkka~~~~~~~~~yEve~~Td 117 (208)
+.|...|..|.+.. ||. +..+.||.+++.|-+.++|--.|-.|+.+-..- -..+
T Consensus 380 s~lL~~i~~a~~~~--~~l~~l~~~~~~~~~~~~~~~~~r~~V~~a~~~gip~P~ls~aL~y~~s~----------~~~~ 447 (493)
T PLN02350 380 AVFLDRIKKAYDRN--PDLASLLVDPEFAKEMVERQAAWRRVVSLAINAGISTPGMSASLAYFDTY----------RRAR 447 (493)
T ss_pred HhHHHHHHHHHHcC--CChhhhcCCHHHHHHHHHhhhHHHHHHHHHHHcCCCHHHHHHHHHHHHhh----------ccCC
Confidence 44566777777753 332 223457888999999999999999999853321 1224
Q ss_pred CCCchhhhhhhhcchhhHhhh
Q psy6519 118 KPTLSIARLVSLEGSACLVSA 138 (208)
Q Consensus 118 n~nRT~~~vR~~fgka~~~k~ 138 (208)
-+.+-++-.|.+||.|.+...
T Consensus 448 ~~~nliqaqRd~FGaH~~~r~ 468 (493)
T PLN02350 448 LPANLVQAQRDYFGAHTYERV 468 (493)
T ss_pred ccHHHHHHHHHHhCCCceeeC
Confidence 467789999999999666543
No 24
>PF09682 Holin_LLH: Phage holin protein (Holin_LLH); InterPro: IPR010026 This entry represents the Bacteriophage LL-H, Orf107, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=20.17 E-value=4.1e+02 Score=20.41 Aligned_cols=57 Identities=18% Similarity=0.210 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCCCcCccchhHHHHHHhc------CCCHHHHHHHHHhcC
Q psy6519 45 QEKATLFTNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKS------SMPMTTIENAIKSCN 101 (208)
Q Consensus 45 a~ksk~fsKl~keI~vA~K~GG~~DP~~N~rL~~aI~~AK~~------nmPkd~IErAIkka~ 101 (208)
.+..+++.-+++.-..||=+=...+.+..-++..|++..++. +++.+.|+.+|+.|-
T Consensus 39 e~~~~~~~~vak~Av~aveq~~~~~~~G~~K~~~A~~~v~~~L~~~gi~~t~~~i~~~IEaAV 101 (108)
T PF09682_consen 39 EKLVKILEIVAKIAVNAVEQVAKEGGKGEEKKAEAVQYVKERLKKKGIKVTDEQIEGAIEAAV 101 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 334444554666655554332112225556777776665554 788999999998763
Done!