Query 009611
Match_columns 531
No_of_seqs 140 out of 165
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 15:12:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009611.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009611hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07887 Calmodulin_bind: Calm 100.0 2E-123 5E-128 934.1 30.1 299 17-318 1-299 (299)
2 TIGR02239 recomb_RAD51 DNA rep 87.0 0.73 1.6E-05 47.9 4.3 48 194-246 13-60 (316)
3 TIGR02238 recomb_DMC1 meiotic 84.6 1 2.2E-05 47.0 3.9 49 193-246 12-60 (313)
4 PLN03186 DNA repair protein RA 84.5 0.78 1.7E-05 48.5 3.1 61 182-247 28-88 (342)
5 PRK04301 radA DNA repair and r 80.9 1.2 2.6E-05 45.8 2.7 57 181-244 7-63 (317)
6 PLN03187 meiotic recombination 78.6 1.8 4E-05 45.9 3.3 61 181-246 30-90 (344)
7 PF14520 HHH_5: Helix-hairpin- 75.9 1.1 2.3E-05 35.5 0.5 51 184-241 9-59 (60)
8 PTZ00035 Rad51 protein; Provis 70.8 3.9 8.5E-05 43.1 3.4 60 181-245 22-81 (337)
9 PF14229 DUF4332: Domain of un 70.6 4.6 9.9E-05 36.8 3.3 52 194-247 7-60 (122)
10 PRK03609 umuC DNA polymerase V 69.7 3.9 8.4E-05 43.8 3.1 52 181-242 180-231 (422)
11 TIGR02236 recomb_radA DNA repa 67.2 4.2 9.1E-05 41.4 2.6 51 185-242 4-54 (310)
12 PRK02406 DNA polymerase IV; Va 66.2 5.5 0.00012 41.3 3.3 52 181-242 169-220 (343)
13 PRK03352 DNA polymerase IV; Va 55.2 5.3 0.00011 41.4 0.9 41 181-226 178-218 (346)
14 PRK03858 DNA polymerase IV; Va 53.8 6.5 0.00014 41.5 1.3 41 181-226 174-214 (396)
15 PRK01172 ski2-like helicase; P 53.3 14 0.0003 41.9 3.9 45 193-242 623-667 (674)
16 PRK03348 DNA polymerase IV; Pr 53.0 7.5 0.00016 42.5 1.7 53 181-242 181-233 (454)
17 PRK14133 DNA polymerase IV; Pr 52.9 14 0.0003 38.4 3.5 51 181-241 174-224 (347)
18 PRK02794 DNA polymerase IV; Pr 51.0 13 0.00027 39.9 3.0 55 181-245 210-264 (419)
19 cd01700 PolY_Pol_V_umuC umuC s 50.7 12 0.00027 38.7 2.8 51 181-241 177-227 (344)
20 cd03586 PolY_Pol_IV_kappa DNA 47.8 17 0.00037 37.1 3.2 52 181-242 172-223 (334)
21 PF04994 TfoX_C: TfoX C-termin 47.2 9.4 0.0002 32.7 1.1 74 181-294 4-78 (81)
22 PRK01810 DNA polymerase IV; Va 45.0 18 0.0004 38.4 3.0 51 181-241 180-230 (407)
23 PRK03103 DNA polymerase IV; Re 44.4 19 0.00041 38.3 3.0 52 181-242 182-233 (409)
24 cd00424 PolY Y-family of DNA p 41.2 23 0.00049 36.8 3.0 55 181-245 174-229 (343)
25 PF14229 DUF4332: Domain of un 39.5 21 0.00046 32.5 2.2 39 182-225 55-93 (122)
26 COG3743 Uncharacterized conser 38.1 38 0.00082 32.1 3.6 59 180-242 67-126 (133)
27 PF02889 Sec63: Sec63 Brl doma 37.6 28 0.00061 35.2 2.9 55 180-241 148-202 (314)
28 cd01701 PolY_Rev1 DNA polymera 36.5 17 0.00036 39.0 1.2 54 181-241 223-276 (404)
29 PRK01216 DNA polymerase IV; Va 36.2 16 0.00035 38.7 1.0 51 181-240 179-229 (351)
30 cd01702 PolY_Pol_eta DNA Polym 33.1 22 0.00048 37.8 1.4 55 181-242 183-238 (359)
31 cd07978 TAF13 The TATA Binding 30.8 78 0.0017 27.9 4.2 35 200-242 52-89 (92)
32 cd01703 PolY_Pol_iota DNA Poly 29.8 26 0.00057 37.6 1.3 58 181-244 173-242 (379)
33 KOG4233 DNA-bridging protein B 28.8 57 0.0012 28.8 2.9 60 176-243 15-78 (90)
34 PF03118 RNA_pol_A_CTD: Bacter 28.0 27 0.00059 28.7 0.8 27 195-224 24-50 (66)
35 PF11754 Velvet: Velvet factor 27.9 1.1E+02 0.0024 30.1 5.2 62 101-165 97-172 (203)
36 COG3355 Predicted transcriptio 25.8 2.2E+02 0.0048 26.8 6.4 57 192-255 31-91 (126)
37 PRK10917 ATP-dependent DNA hel 25.4 32 0.00069 39.6 1.1 38 176-215 5-42 (681)
38 PF11033 ComJ: Competence prot 25.2 2.5E+02 0.0054 26.5 6.6 26 68-94 9-34 (125)
39 PF06594 HCBP_related: Haemoly 25.0 46 0.00099 24.9 1.5 18 116-133 24-41 (43)
40 cd03468 PolY_like DNA Polymera 20.9 56 0.0012 33.3 1.7 35 187-226 177-211 (335)
41 TIGR01954 nusA_Cterm_rpt trans 20.7 1.2E+02 0.0027 22.4 3.1 42 195-241 6-47 (50)
42 COG0540 PyrB Aspartate carbamo 20.6 54 0.0012 35.1 1.5 75 82-168 14-113 (316)
No 1
>PF07887 Calmodulin_bind: Calmodulin binding protein-like; InterPro: IPR012416 The members of this family are putative or actual calmodulin binding proteins expressed by various plant species. Some members (for example, Q8H6T7 from SWISSPROT), are known to be involved in the induction of plant defence responses []. However, their precise function in this regard is as yet unknown.
Probab=100.00 E-value=2.4e-123 Score=934.10 Aligned_cols=299 Identities=66% Similarity=1.116 Sum_probs=295.0
Q ss_pred ceEEEecCCCCCCcccCCccccCCCCceEEEEEeCCCCceeccCCCCcceEEEEEeeCCCCCCCCCCCCHHHHhcccccc
Q 009611 17 NLQLHYKTRMPPHLFTGGKVEGDQGAAIHVVLIDMNTGDVVQTGPESSAKLNVVVLEGDFNEEEDDNWTKEHFESHEVKE 96 (531)
Q Consensus 17 ~~qL~F~n~L~~pifTg~kI~ae~g~~I~V~L~D~~tg~iVtsGplSs~kiEIvVLdGDF~~~~~e~WT~eEF~~~IVk~ 96 (531)
+|||+|+|+|++|||||++|+|+||+||+|+|+|++|+ |++||+|++|||||||||||+.+++++||+|||++|||++
T Consensus 1 ~~~L~F~n~l~~pifT~~~i~a~~g~~i~V~l~d~~~~--v~~g~lss~kieIvvLdGdF~~~~~~~wT~eeF~~~iv~~ 78 (299)
T PF07887_consen 1 NLQLRFLNKLSLPIFTGSKIEAEDGAPIKVALVDANTG--VTSGPLSSAKIEIVVLDGDFNDEDCEDWTEEEFNSHIVKE 78 (299)
T ss_pred CeEEEecCCCCCCcccCCceEecCCCcEEEEEEECCCC--ccCCCCCCcEEEEEEEccccCCCccCCCCHHHHhhcEeec
Confidence 58999999999999999999999999999999999988 9999999999999999999999999999999999999999
Q ss_pred CCCCccceeccEEEEeccceeeccCeeeecCCcccccccceEEEEecCCCCCCcceeeeeecceEeeeCCccccccCCCC
Q 009611 97 REGKRPILTGDLLVTLKEGFGTLGDLTFTDNSSWIRSRKFRLGLKVSPGYCDGIRVREAKTEGFAVKDHRGELYKKHYPP 176 (531)
Q Consensus 97 ReGk~pLL~Gdl~v~L~~Gva~l~di~FTDnSsw~rSrKFRLgaRv~~~~~~g~RI~EAvsE~FvVkDhRge~ykKh~pP 176 (531)
|+||+|||+|+++|+|+||+|+|+||+|||||||+|||||||||||+++++.|+|||||+||||+|||||||+|||||||
T Consensus 79 r~gk~pLL~G~~~v~L~~G~a~l~di~FtdnSs~~rsrKFRLgarv~~~~~~~~rI~Eavse~FvVkd~Rge~~kKh~pP 158 (299)
T PF07887_consen 79 REGKRPLLTGDLQVTLKNGVATLGDISFTDNSSWIRSRKFRLGARVVSGSCDGVRIREAVSEPFVVKDHRGELYKKHYPP 158 (299)
T ss_pred CCCCCCCCCccEEEEecCCEEEccccEEecCcccccCCcEEEEEEEccCCCCCceeEEeeecCEEEEecccccccCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhcccccCCceEEEEecC
Q 009611 177 ALHDEVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVLGGKLYVYYADG 256 (531)
Q Consensus 177 ~L~DeVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~k~y~y~~~~ 256 (531)
+|+|||||||||||||+|||+|+.+||+||+|||+++++||++||+|||+|||++||++||+|||||++++++|+|| .+
T Consensus 159 ~L~DeVwRLe~Igk~G~~hk~L~~~~I~tV~dFl~l~~~d~~~Lr~ilg~~ms~k~We~~v~HA~tCvl~~~~y~y~-~~ 237 (299)
T PF07887_consen 159 SLDDEVWRLEKIGKDGAFHKRLKKNGINTVEDFLKLLNKDPQKLREILGSGMSNKMWETTVEHAKTCVLGDKLYVYY-DE 237 (299)
T ss_pred CCCCchhhhhhccccCHHHHHHHHcCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHHHHHHHHhcCCCCcEEEEE-ec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999 55
Q ss_pred CccEEEEEcccceeeeeecCCeeeeCCCCChHhHHHHHHHHHHHHHhcccccccCcccccCc
Q 009611 257 TQNTGVVFNNIYELRGLIDDGQFVSLESLTHSQKISVDSLVKRAYDNWHQVLEYDGKFLSSL 318 (531)
Q Consensus 257 ~~nv~l~FN~i~~lvG~~~~g~y~s~d~L~~~qk~~V~~Lk~~AY~nw~~~~e~d~~~~~n~ 318 (531)
++|++|+|||||+||||+|+|+|++.|+||+.||++|++||++||+||++|++||++|++||
T Consensus 238 ~~nv~l~FN~i~~lvga~~~g~y~s~d~L~~~qK~~v~~Lv~~AY~n~~~l~e~d~~~~~n~ 299 (299)
T PF07887_consen 238 EQNVGLFFNCIYELVGAIFGGQYVSLDNLSSAQKAYVDKLVKQAYENWDNLEEYDGKMLNNY 299 (299)
T ss_pred CCceEEEEcchhhEEeEEECCEEEehHHcCHHHHHHHHHHHHHHHHhhhhheecccchhccC
Confidence 78999999999999999999999999999999999999999999999999999999999986
No 2
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=87.03 E-value=0.73 Score=47.95 Aligned_cols=48 Identities=27% Similarity=0.213 Sum_probs=42.7
Q ss_pred hhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhcccccC
Q 009611 194 LHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVLG 246 (531)
Q Consensus 194 ~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 246 (531)
--++|+++||.||+||+. .+|..|.+++ |+|....+.+..||.+|...
T Consensus 13 ~~~~l~~~g~~t~~~~~~---~~~~~L~~i~--~ls~~~~~~~~~~~~~~~~~ 60 (316)
T TIGR02239 13 DIKKLQEAGLHTVESVAY---APKKQLLEIK--GISEAKADKILAEAAKLVPM 60 (316)
T ss_pred HHHHHHHcCCCcHHHHHh---CCHHHHHHHh--CCCHHHHHHHHHHHHHhccc
Confidence 448999999999999986 4899999998 79999999999999998654
No 3
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=84.61 E-value=1 Score=46.95 Aligned_cols=49 Identities=29% Similarity=0.249 Sum_probs=42.8
Q ss_pred hhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhcccccC
Q 009611 193 ALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVLG 246 (531)
Q Consensus 193 ~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 246 (531)
.--++|+++||.||+||+. .++..|.++. |+|...++.+++.|+.+...
T Consensus 12 ~~~~~L~~~g~~t~~~~~~---~~~~~L~~~~--gls~~~~~~i~~~~~~~~~~ 60 (313)
T TIGR02238 12 ADIKKLKSAGICTVNGVIM---TTRRALCKIK--GLSEAKVDKIKEAASKIINP 60 (313)
T ss_pred HHHHHHHHcCCCcHHHHHh---CCHHHHHHhc--CCCHHHHHHHHHHHHhhhcc
Confidence 3458999999999999876 4889999997 79999999999999988655
No 4
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=84.50 E-value=0.78 Score=48.52 Aligned_cols=61 Identities=30% Similarity=0.230 Sum_probs=47.5
Q ss_pred ceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhcccccCC
Q 009611 182 VWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVLGG 247 (531)
Q Consensus 182 VwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~ 247 (531)
+-+|+.-|-.-.--++|+++||.||+||+.+ ++..|.++. |+|....+.+++||.+|....
T Consensus 28 ~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~---~~~~L~~i~--~is~~~~~~~~~~~~~~~~~~ 88 (342)
T PLN03186 28 IEQLQASGIAALDIKKLKDAGIHTVESLAYA---PKKDLLQIK--GISEAKVEKILEAASKLVPLG 88 (342)
T ss_pred HHHHHhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHHhcccc
Confidence 4444442333334599999999999998764 788999998 789999999999998886543
No 5
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=80.90 E-value=1.2 Score=45.81 Aligned_cols=57 Identities=21% Similarity=0.278 Sum_probs=45.7
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhcccc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCV 244 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCv 244 (531)
++-.|.+||+. ..++|.++||+|++|++. .++..|.+++ |++.+.++.+++-|+.++
T Consensus 7 ~l~~l~gIg~~--~a~~L~~~Gi~t~~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~a~~~~ 63 (317)
T PRK04301 7 DLEDLPGVGPA--TAEKLREAGYDTVEAIAV---ASPKELSEAA--GIGESTAAKIIEAAREAA 63 (317)
T ss_pred cHhhcCCCCHH--HHHHHHHcCCCCHHHHHc---CCHHHHHHhc--CCCHHHHHHHHHHHHHhh
Confidence 34556667654 559999999999999965 5999999998 678889999998887644
No 6
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=78.56 E-value=1.8 Score=45.91 Aligned_cols=61 Identities=21% Similarity=0.212 Sum_probs=47.4
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhcccccC
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVLG 246 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 246 (531)
++..|+.-|-.-.--++|.++||+||+|++. .++..|-++. |+|....+.+++.|+..+..
T Consensus 30 ~~~~l~~~g~~~~~~~kL~~~g~~tv~~~~~---~~~~~L~~~~--g~s~~~~~ki~~~a~~~~~~ 90 (344)
T PLN03187 30 SIDKLISQGINAGDVKKLQDAGIYTCNGLMM---HTKKNLTGIK--GLSEAKVDKICEAAEKLLNQ 90 (344)
T ss_pred CHHHHhhCCCCHHHHHHHHHcCCCcHHHHHh---CCHHHHHHhc--CCCHHHHHHHHHHHHHhhcc
Confidence 3566655333334569999999999999876 4788899986 79999999999999876543
No 7
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=75.90 E-value=1.1 Score=35.52 Aligned_cols=51 Identities=31% Similarity=0.496 Sum_probs=40.7
Q ss_pred eeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhc
Q 009611 184 RLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 241 (531)
Q Consensus 184 RLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 241 (531)
.+.+||+.- .++|.+.||.|++|+.. -+++.|.++= |++.+.=+.+++.|+
T Consensus 9 ~I~Gig~~~--a~~L~~~G~~t~~~l~~---a~~~~L~~i~--Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 9 SIPGIGPKR--AEKLYEAGIKTLEDLAN---ADPEELAEIP--GIGEKTAEKIIEAAR 59 (60)
T ss_dssp TSTTCHHHH--HHHHHHTTCSSHHHHHT---SHHHHHHTST--TSSHHHHHHHHHHHH
T ss_pred cCCCCCHHH--HHHHHhcCCCcHHHHHc---CCHHHHhcCC--CCCHHHHHHHHHHHh
Confidence 355666653 48999999999999866 4788899874 789999999998886
No 8
>PTZ00035 Rad51 protein; Provisional
Probab=70.79 E-value=3.9 Score=43.07 Aligned_cols=60 Identities=33% Similarity=0.297 Sum_probs=46.3
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhccccc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVL 245 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 245 (531)
++-.|+.-|-.-.--++|+++||+||+||+. .++..|-++. |+|...=+.+++.|+.++.
T Consensus 22 ~~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~---~~~~~L~~~~--gis~~~~~~i~~~~~~~~~ 81 (337)
T PTZ00035 22 EIEKLQSAGINAADIKKLKEAGICTVESVAY---ATKKDLCNIK--GISEAKVEKIKEAASKLVP 81 (337)
T ss_pred cHHHHhcCCCCHHHHHHHHHcCCCcHHHHHh---CCHHHHHHhh--CCCHHHHHHHHHHHHHhcc
Confidence 4556654222233459999999999999876 4888999997 7899999999999987764
No 9
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=70.60 E-value=4.6 Score=36.76 Aligned_cols=52 Identities=29% Similarity=0.233 Sum_probs=37.6
Q ss_pred hhhhhhhCCcccHHHHHHHHhcChHH--HHHHHcCCCCchhHHHHHHhhcccccCC
Q 009611 194 LHKKLMKADIVTVEDFLRILVRDPQK--LRNILGSGMSNRMWENTVEHAKTCVLGG 247 (531)
Q Consensus 194 ~hkrL~~~gI~tV~dFLrl~~~d~~k--LR~iLg~gmS~k~We~~v~HAktCvl~~ 247 (531)
.-++|+..||+|++|||..-.....+ |-+-+ |++.+-=...+.+|.=|...+
T Consensus 7 ~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~--~i~~~~l~~w~~~AdL~ri~g 60 (122)
T PF14229_consen 7 EAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKL--GISERNLLKWVNQADLMRIPG 60 (122)
T ss_pred HHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhc--CCCHHHHHHHHhHHHhhhcCC
Confidence 45899999999999999986655444 55554 678877667777776554433
No 10
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=69.74 E-value=3.9 Score=43.81 Aligned_cols=52 Identities=21% Similarity=0.222 Sum_probs=41.6
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhcc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 242 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 242 (531)
+|..|-+||+. ..++|.+.||+|++|+.++ ++..|++.||. .+..+..||.-
T Consensus 180 Pv~~l~GiG~~--~~~~L~~lGi~TigdL~~~---~~~~L~~~fG~-----~~~~l~~~a~G 231 (422)
T PRK03609 180 PVEEVWGVGRR--ISKKLNAMGIKTALDLADT---NIRFIRKHFNV-----VLERTVRELRG 231 (422)
T ss_pred ChhhcCCccHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHCH-----HHHHHHHHhCC
Confidence 45556677774 4499999999999999985 88999999973 57788888853
No 11
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=67.20 E-value=4.2 Score=41.43 Aligned_cols=51 Identities=24% Similarity=0.312 Sum_probs=39.2
Q ss_pred eeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhcc
Q 009611 185 LDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 242 (531)
Q Consensus 185 LekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 242 (531)
|.+||+. .-++|.++||.|++|++. .+++.|.+++ |++.+..+.+.+-|+.
T Consensus 4 i~gig~~--~~~~L~~~Gi~ti~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~~~~ 54 (310)
T TIGR02236 4 LPGVGPA--TAEKLREAGYDTFEAIAV---ASPKELSEIA--GISEGTAAKIIQAARK 54 (310)
T ss_pred cCCCCHH--HHHHHHHcCCCCHHHHHc---CCHHHHHhcc--CCCHHHHHHHHHHHHH
Confidence 4455554 448999999999999877 4899999998 5677777777766663
No 12
>PRK02406 DNA polymerase IV; Validated
Probab=66.24 E-value=5.5 Score=41.26 Aligned_cols=52 Identities=23% Similarity=0.247 Sum_probs=40.1
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhcc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 242 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 242 (531)
+|..|-+||+. .-++|...||+|++|+.++ +...|++.||. .+..+.+||+-
T Consensus 169 pi~~l~giG~~--~~~~L~~~Gi~ti~dl~~l---~~~~L~~~fG~-----~~~~l~~~a~G 220 (343)
T PRK02406 169 PVEKIPGVGKV--TAEKLHALGIYTCADLQKY---DLAELIRHFGK-----FGRRLYERARG 220 (343)
T ss_pred CcchhcCCCHH--HHHHHHHcCCCcHHHHHhC---CHHHHHHHHhH-----HHHHHHHHhCC
Confidence 56667677764 4488999999999999885 78899999973 46666677653
No 13
>PRK03352 DNA polymerase IV; Validated
Probab=55.24 E-value=5.3 Score=41.41 Aligned_cols=41 Identities=27% Similarity=0.322 Sum_probs=33.5
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcC
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGS 226 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~ 226 (531)
+|..|-+||+. ..++|...||+|++|++++ ++..|++.||.
T Consensus 178 pl~~l~gig~~--~~~~L~~~Gi~ti~dl~~l---~~~~L~~~fG~ 218 (346)
T PRK03352 178 PTDALWGVGPK--TAKRLAALGITTVADLAAA---DPAELAATFGP 218 (346)
T ss_pred CHHHcCCCCHH--HHHHHHHcCCccHHHHhcC---CHHHHHHHhCh
Confidence 56666677775 4488999999999999985 78899999975
No 14
>PRK03858 DNA polymerase IV; Validated
Probab=53.83 E-value=6.5 Score=41.47 Aligned_cols=41 Identities=29% Similarity=0.264 Sum_probs=33.3
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcC
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGS 226 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~ 226 (531)
+|..|-+||+.- -++|.+.||+|++|+.+ .++..|++.||.
T Consensus 174 pl~~l~Gig~~~--~~~L~~~Gi~t~~dl~~---l~~~~L~~~fG~ 214 (396)
T PRK03858 174 PVRRLWGVGPVT--AAKLRAHGITTVGDVAE---LPESALVSLLGP 214 (396)
T ss_pred ChhhcCCCCHHH--HHHHHHhCCCcHHHHhc---CCHHHHHHHhCc
Confidence 455666787754 48999999999999986 588899999975
No 15
>PRK01172 ski2-like helicase; Provisional
Probab=53.33 E-value=14 Score=41.95 Aligned_cols=45 Identities=27% Similarity=0.494 Sum_probs=38.7
Q ss_pred hhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhcc
Q 009611 193 ALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 242 (531)
Q Consensus 193 ~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 242 (531)
...++|.++||.||.|+.. .|+++|-+|+ |++++.=+.++++|+.
T Consensus 623 ~~a~~l~~~g~~~~~di~~---~~~~~~~~i~--~~~~~~~~~i~~~~~~ 667 (674)
T PRK01172 623 VRARRLYDAGFKTVDDIAR---SSPERIKKIY--GFSDTLANAIVNRAMK 667 (674)
T ss_pred HHHHHHHHcCCCCHHHHHh---CCHHHHHHHh--ccCHHHHHHHHHHHHH
Confidence 3669999999999999877 7888898888 6889999999999875
No 16
>PRK03348 DNA polymerase IV; Provisional
Probab=53.02 E-value=7.5 Score=42.47 Aligned_cols=53 Identities=25% Similarity=0.268 Sum_probs=39.6
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhcc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 242 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 242 (531)
.|.+|-+||+... ++|...||+|++||.++ +...|++.||..+ ...+..+|+-
T Consensus 181 Pv~~L~GIG~~t~--~~L~~lGI~TigDLa~l---~~~~L~~~fG~~~----g~~L~~~a~G 233 (454)
T PRK03348 181 PVRRLWGIGPVTE--EKLHRLGIETIGDLAAL---SEAEVANLLGATV----GPALHRLARG 233 (454)
T ss_pred CccccCCCCHHHH--HHHHHcCCccHHHHhcC---CHHHHHHHHCHHH----HHHHHHHHcC
Confidence 6788888887644 88999999999999874 7889999997433 3334445543
No 17
>PRK14133 DNA polymerase IV; Provisional
Probab=52.86 E-value=14 Score=38.44 Aligned_cols=51 Identities=24% Similarity=0.384 Sum_probs=39.6
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 241 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 241 (531)
+|..|-+||+.-. ++|...||+|++|++++ +...|++.|| +.|..+.++|.
T Consensus 174 pv~~l~gig~~~~--~~L~~~Gi~ti~dl~~l---~~~~L~~rfG-----~~g~~l~~~a~ 224 (347)
T PRK14133 174 PISKVHGIGKKSV--EKLNNIGIYTIEDLLKL---SREFLIEYFG-----KFGVEIYERIR 224 (347)
T ss_pred CccccCCCCHHHH--HHHHHcCCccHHHHhhC---CHHHHHHHHh-----HHHHHHHHHhC
Confidence 4666667766544 78999999999999874 7888999997 35777777775
No 18
>PRK02794 DNA polymerase IV; Provisional
Probab=51.02 E-value=13 Score=39.94 Aligned_cols=55 Identities=22% Similarity=0.132 Sum_probs=42.4
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhccccc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVL 245 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 245 (531)
+|..|-+||+. .-++|...||+|++|+.++ +...|++.||. .+..+.++|.--+.
T Consensus 210 Pl~~L~GiG~~--~~~~L~~~GI~tigdL~~l---~~~~L~~rfG~-----~g~~l~~~a~G~d~ 264 (419)
T PRK02794 210 PVGIIWGVGPA--TAARLARDGIRTIGDLQRA---DEADLMRRFGS-----MGLRLWRLARGIDD 264 (419)
T ss_pred ChhhhCCCCHH--HHHHHHHhccchHHHHhhC---CHHHHHHHHhH-----HHHHHHHHhCCCCC
Confidence 35555566654 4589999999999998874 78899999974 58888888875543
No 19
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=50.74 E-value=12 Score=38.66 Aligned_cols=51 Identities=29% Similarity=0.304 Sum_probs=39.2
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 241 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 241 (531)
+|..|-+||+. .-++|...||+|++|+.++ +.+.|.+.||. .+....++|+
T Consensus 177 pl~~l~gig~~--~~~~L~~~Gi~ti~dL~~~---~~~~L~~rfG~-----~~~~l~~~a~ 227 (344)
T cd01700 177 PVGDVWGIGRR--TAKKLNAMGIHTAGDLAQA---DPDLLRKKFGV-----VGERLVRELN 227 (344)
T ss_pred ChhhcCccCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHHH-----HHHHHHHHhC
Confidence 35555667764 4478999999999999985 78899999974 4666777765
No 20
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=47.81 E-value=17 Score=37.07 Aligned_cols=52 Identities=23% Similarity=0.353 Sum_probs=40.5
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhcc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 242 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 242 (531)
+|..|-+||+. .-++|...||+|++|+.++ ++..|++.+| +.|..+.+||+-
T Consensus 172 pl~~l~gig~~--~~~~L~~~Gi~ti~dl~~~---~~~~L~~~~g-----~~~~~l~~~~~G 223 (334)
T cd03586 172 PVRKIPGVGKV--TAEKLKELGIKTIGDLAKL---DVELLKKLFG-----KSGRRLYELARG 223 (334)
T ss_pred CchhhCCcCHH--HHHHHHHcCCcCHHHHHcC---CHHHHHHHHh-----HHHHHHHHHhCC
Confidence 45566667654 4589999999999999874 7888999885 578888888864
No 21
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=47.20 E-value=9.4 Score=32.65 Aligned_cols=74 Identities=26% Similarity=0.340 Sum_probs=43.1
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcCh-HHHHHHHcCCCCchhHHHHHHhhcccccCCceEEEEecCCcc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDP-QKLRNILGSGMSNRMWENTVEHAKTCVLGGKLYVYYADGTQN 259 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~-~kLR~iLg~gmS~k~We~~v~HAktCvl~~k~y~y~~~~~~n 259 (531)
.+..|..||.. .-+.|.+.||+||+||..+=.+.. -+|++. |
T Consensus 4 ~l~~LpNig~~--~e~~L~~vGI~t~~~L~~~Ga~~a~~~Lk~~-~---------------------------------- 46 (81)
T PF04994_consen 4 RLKDLPNIGPK--SERMLAKVGIHTVEDLRELGAVEAYLRLKAS-G---------------------------------- 46 (81)
T ss_dssp -GCGSTT--HH--HHHHHHHTT--SHHHHHHHHHHHHHHHHHHH------------------------------------
T ss_pred chhhCCCCCHH--HHHHHHHcCCCCHHHHHHhCHHHHHHHHHHH-C----------------------------------
Confidence 34455566664 338999999999999998654432 345544 2
Q ss_pred EEEEEcccceeeeeecCCeeeeCCCCChHhHHHHH
Q 009611 260 TGVVFNNIYELRGLIDDGQFVSLESLTHSQKISVD 294 (531)
Q Consensus 260 v~l~FN~i~~lvG~~~~g~y~s~d~L~~~qk~~V~ 294 (531)
..+-+|-+|.|.||+-|-+ ...|++.+|....
T Consensus 47 ~~~~~~~L~aL~gAi~g~~---~~~L~~~~K~~L~ 78 (81)
T PF04994_consen 47 PSVCLNLLYALEGAIQGIH---WADLPDEEKQELL 78 (81)
T ss_dssp TT--HHHHHHHHHHHCTS----GGGS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHcCCC---HHHCCHHHHHHHH
Confidence 2255677899999988744 3466777766554
No 22
>PRK01810 DNA polymerase IV; Validated
Probab=44.98 E-value=18 Score=38.40 Aligned_cols=51 Identities=25% Similarity=0.260 Sum_probs=39.0
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 241 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 241 (531)
+|..|-+||+.- -++|...||+|++|+.+ .+...|++.||. .+..+.+||.
T Consensus 180 pv~~l~giG~~~--~~~L~~~Gi~tigdL~~---~~~~~L~~rfG~-----~g~~l~~~a~ 230 (407)
T PRK01810 180 PVGEMHGIGEKT--AEKLKDIGIQTIGDLAK---ADEHILRAKLGI-----NGVRLQRRAN 230 (407)
T ss_pred CHhhcCCcCHHH--HHHHHHcCCCcHHHHHh---CCHHHHHHHHhH-----HHHHHHHHhc
Confidence 455566677643 48899999999999877 478889999974 4666777776
No 23
>PRK03103 DNA polymerase IV; Reviewed
Probab=44.36 E-value=19 Score=38.32 Aligned_cols=52 Identities=19% Similarity=0.194 Sum_probs=40.2
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhcc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 242 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 242 (531)
.|..|-+||+. .-++|...||+|++|+.+ .++..|++.||. .+..+.++|.-
T Consensus 182 pi~~l~gig~~--~~~~L~~~Gi~tigdl~~---~~~~~L~~~fG~-----~~~~l~~~a~G 233 (409)
T PRK03103 182 PVRKLFGVGSR--MEKHLRRMGIRTIGQLAN---TPLERLKKRWGI-----NGEVLWRTANG 233 (409)
T ss_pred CHhhcCCccHH--HHHHHHHcCCCCHHHHhc---CCHHHHHHHHCH-----HHHHHHHHhcC
Confidence 46666678775 458899999999999886 478899999963 46777777764
No 24
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=41.21 E-value=23 Score=36.84 Aligned_cols=55 Identities=18% Similarity=0.003 Sum_probs=41.1
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcC-hHHHHHHHcCCCCchhHHHHHHhhccccc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRD-PQKLRNILGSGMSNRMWENTVEHAKTCVL 245 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d-~~kLR~iLg~gmS~k~We~~v~HAktCvl 245 (531)
+|..|-+||+.- -++|...||+|++|++++ + ...|+..+| +.+..+.++|+--+.
T Consensus 174 pi~~l~giG~~~--~~~L~~~Gi~ti~dl~~~---~~~~~l~~~fg-----~~~~~l~~~a~G~d~ 229 (343)
T cd00424 174 PLTDLPGIGAVT--AKRLEAVGINPIGDLLAA---SPDALLALWGG-----VSGERLWYALRGIDD 229 (343)
T ss_pred ChhhcCCCCHHH--HHHHHHcCCCcHHHHhcC---CHHHHHHHHhh-----HHHHHHHHHhCCcCC
Confidence 466677788754 489999999999998764 6 566777775 467788888875543
No 25
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=39.53 E-value=21 Score=32.45 Aligned_cols=39 Identities=33% Similarity=0.499 Sum_probs=30.2
Q ss_pred ceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHc
Q 009611 182 VWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILG 225 (531)
Q Consensus 182 VwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg 225 (531)
..|+.+|+.. |..-|..+||.||+++- ..+|++|.+.++
T Consensus 55 L~ri~gi~~~--~a~LL~~AGv~Tv~~LA---~~~p~~L~~~l~ 93 (122)
T PF14229_consen 55 LMRIPGIGPQ--YAELLEHAGVDTVEELA---QRNPQNLHQKLG 93 (122)
T ss_pred hhhcCCCCHH--HHHHHHHhCcCcHHHHH---hCCHHHHHHHHH
Confidence 4466666654 66899999999999974 478988888653
No 26
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=38.10 E-value=38 Score=32.14 Aligned_cols=59 Identities=22% Similarity=0.272 Sum_probs=42.7
Q ss_pred CcceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHH-HHHhhcc
Q 009611 180 DEVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWEN-TVEHAKT 242 (531)
Q Consensus 180 DeVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~-~v~HAkt 242 (531)
|+.-||.+||.. +-+.|+..||+|-.+.-.+-..|-..+-..| +..-+.|.. -|+.|+.
T Consensus 67 DDLt~I~GIGPk--~e~~Ln~~GI~tfaQIAAwt~~di~~id~~l--~f~GRi~RDdWi~QAk~ 126 (133)
T COG3743 67 DDLTRISGIGPK--LEKVLNELGIFTFAQIAAWTRADIAWIDDYL--NFDGRIERDDWIAQAKA 126 (133)
T ss_pred ccchhhcccCHH--HHHHHHHcCCccHHHHHhcCHHHHHHHHhhc--CCcchhHHHHHHHHHHH
Confidence 999999999985 7799999999996665544444444444445 677777765 6776664
No 27
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. ; PDB: 3IM2_A 3IM1_A 3HIB_A 2Q0Z_X.
Probab=37.58 E-value=28 Score=35.16 Aligned_cols=55 Identities=25% Similarity=0.404 Sum_probs=37.7
Q ss_pred CcceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhc
Q 009611 180 DEVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 241 (531)
Q Consensus 180 DeVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 241 (531)
....-|.+|+.+.+ ++|.+.||.|+++|+++ ++.+|..+| +......+.+.+.|+
T Consensus 148 ~~L~Qlp~i~~~~~--~~l~~~~i~~l~~l~~~---~~~e~~~ll--~~~~~~~~~i~~~~~ 202 (314)
T PF02889_consen 148 SPLLQLPHIGEESL--KKLEKRGIKTLQDLRDL---SPEELEELL--NRNPPFGKEILEVAS 202 (314)
T ss_dssp -GGGGSTT--HHHH--HHHHHTT--SHHHHHHS----HHHHHHHH---S-HHHHHHHHHHHC
T ss_pred ChhhcCCCCCHHHH--HHHhccCCCcHHHHhhC---CHHHHHHHH--hhhhhhHHHHHHHHH
Confidence 34566778888765 89999999999999854 899999998 456677788887776
No 28
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=36.48 E-value=17 Score=39.02 Aligned_cols=54 Identities=22% Similarity=0.221 Sum_probs=39.7
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 241 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 241 (531)
.|..|-+||+. .-++|...||.|+.|+.++- .++..|++.||. +.+..+.++|+
T Consensus 223 Pv~~l~GIG~~--~~~~L~~~Gi~t~~dl~~~~-~~~~~L~~~fG~----~~g~~L~~~a~ 276 (404)
T cd01701 223 KVGDLPGVGSS--LAEKLVKLFGDTCGGLELRS-KTKEKLQKVLGP----KTGEKLYDYCR 276 (404)
T ss_pred CHhHhCCCCHH--HHHHHHHcCCcchHHHHhCc-ccHHHHHHHHCH----HHHHHHHHHhC
Confidence 57777788765 45999999999999998761 127899999974 34555555554
No 29
>PRK01216 DNA polymerase IV; Validated
Probab=36.17 E-value=16 Score=38.67 Aligned_cols=51 Identities=24% Similarity=0.281 Sum_probs=38.5
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhh
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHA 240 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HA 240 (531)
+|..|.+||+. -.++|...||+|++|+.++ +...|++.||. ..+..+-.+|
T Consensus 179 Pi~~l~giG~~--~~~~L~~~Gi~TigdL~~~---~~~~L~~rfG~----~~~~~L~~~a 229 (351)
T PRK01216 179 DIADIPGIGDI--TAEKLKKLGVNKLVDTLRI---EFDELKGIIGE----AKAKYLFSLA 229 (351)
T ss_pred CcccccCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHCH----HHHHHHHHHh
Confidence 57777788864 4489999999999998764 77889999973 3344555566
No 30
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=33.06 E-value=22 Score=37.76 Aligned_cols=55 Identities=11% Similarity=0.117 Sum_probs=38.2
Q ss_pred cceeeeeecccchhhhh-hhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhcc
Q 009611 181 EVWRLDRIAKDGALHKK-LMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 242 (531)
Q Consensus 181 eVwRLekIgKdG~~hkr-L~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 242 (531)
+|..|-+||+. .-++ |...||.|++|+.++. .++..|++.||. +.++.+.++|+-
T Consensus 183 pv~~l~GiG~~--~~~~ll~~~Gi~ti~dl~~~~-~~~~~L~~~fG~----~~g~~l~~~a~G 238 (359)
T cd01702 183 PITSIRGLGGK--LGEEIIDLLGLPTEGDVAGFR-SSESDLQEHFGE----KLGEWLYNLLRG 238 (359)
T ss_pred cHHHhCCcCHH--HHHHHHHHcCCcCHHHHHhcc-CCHHHHHHHHHH----HHHHHHHHHhCC
Confidence 46777777742 2244 5889999999998754 478889999874 344555555553
No 31
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=30.83 E-value=78 Score=27.90 Aligned_cols=35 Identities=31% Similarity=0.675 Sum_probs=28.1
Q ss_pred hCCcccHHHHHHHHhcChHHH---HHHHcCCCCchhHHHHHHhhcc
Q 009611 200 KADIVTVEDFLRILVRDPQKL---RNILGSGMSNRMWENTVEHAKT 242 (531)
Q Consensus 200 ~~gI~tV~dFLrl~~~d~~kL---R~iLg~gmS~k~We~~v~HAkt 242 (531)
...| +++||+=++-.||.|| +++| .|+..++-||.
T Consensus 52 ~~k~-~~eD~~FliR~D~~Kl~Rl~~lL-------~~k~~~k~ark 89 (92)
T cd07978 52 RGKV-KVEDLIFLLRKDPKKLARLRELL-------SMKDELKKARK 89 (92)
T ss_pred CCCC-CHHHHHHHHhcCHHHHHHHHHHH-------HHHHHHHHHHh
Confidence 4567 9999999999999655 5556 68888888875
No 32
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=29.80 E-value=26 Score=37.55 Aligned_cols=58 Identities=14% Similarity=0.072 Sum_probs=40.1
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHh------------cChHHHHHHHcCCCCchhHHHHHHhhcccc
Q 009611 181 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILV------------RDPQKLRNILGSGMSNRMWENTVEHAKTCV 244 (531)
Q Consensus 181 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~------------~d~~kLR~iLg~gmS~k~We~~v~HAktCv 244 (531)
+|-.|-+||+... ++|.+.||.|++|+.++-+ .+...|++.||. +....+.++|+--+
T Consensus 173 pv~~l~GiG~~~~--~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~----~~g~~l~~~a~G~d 242 (379)
T cd01703 173 DLRKIPGIGYKTA--AKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGE----GIGQRIWKLLFGRD 242 (379)
T ss_pred CccccCCcCHHHH--HHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHCH----HHHHHHHHHHCCCC
Confidence 3455557777654 8999999999999986541 117789999864 34556666776444
No 33
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=28.83 E-value=57 Score=28.79 Aligned_cols=60 Identities=27% Similarity=0.393 Sum_probs=40.0
Q ss_pred CCCCCcceeeeeecccchhhhhhhhCCccc----HHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhccc
Q 009611 176 PALHDEVWRLDRIAKDGALHKKLMKADIVT----VEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTC 243 (531)
Q Consensus 176 P~L~DeVwRLekIgKdG~~hkrL~~~gI~t----V~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktC 243 (531)
|+=+-+|--|.+||.. +-.+|..+|+.. .++|| ++.+|++-.+.-|. ..--++-+||++|
T Consensus 15 PmGeK~V~~laGIg~~--lg~~L~~~GfdkAYvllGQfL-llkKdE~lF~~Wlk-----~~~gat~~~a~~~ 78 (90)
T KOG4233|consen 15 PMGEKDVTWLAGIGET--LGIKLVDAGFDKAYVLLGQFL-LLKKDEDLFQEWLK-----ETCGATAKQAQDC 78 (90)
T ss_pred ccCCCcceeeccccHH--hhhhHHhccccHHHHHHHHHH-HhcccHHHHHHHHH-----HHcCccHHHHHHH
Confidence 5666789999999985 668999999975 36676 45678765555431 1112355677766
No 34
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=28.00 E-value=27 Score=28.73 Aligned_cols=27 Identities=30% Similarity=0.346 Sum_probs=18.6
Q ss_pred hhhhhhCCcccHHHHHHHHhcChHHHHHHH
Q 009611 195 HKKLMKADIVTVEDFLRILVRDPQKLRNIL 224 (531)
Q Consensus 195 hkrL~~~gI~tV~dFLrl~~~d~~kLR~iL 224 (531)
...|..+||+||+|++++ +++.|.++=
T Consensus 24 ~n~L~~~~I~tv~dL~~~---s~~~L~~i~ 50 (66)
T PF03118_consen 24 YNCLKRAGIHTVGDLVKY---SEEDLLKIK 50 (66)
T ss_dssp HHHHHCTT--BHHHHHCS----HHHHHTST
T ss_pred HHHHHHhCCcCHHHHHhC---CHHHHHhCC
Confidence 368999999999997664 667777774
No 35
>PF11754 Velvet: Velvet factor; InterPro: IPR021740 The velvet factor is conserved in many fungal species and is found to have gained different roles depending on the organism's need, expanding the conserved role in developmental programmes []. The velvet factor orthologues can be adapted to the fungal-specific life cycle and may be involved in diverse functions such as sclerotia formation and toxin production, as in Aspergillus parasiticus [], nutrition-dependent sporulation, as in A. fumigatus [], or the microconidia-to-macroconidia ratio and cell wall formation, as in the heterothallic fungus Gibberella moniliformis (Fusarium verticillioides).
Probab=27.86 E-value=1.1e+02 Score=30.14 Aligned_cols=62 Identities=26% Similarity=0.324 Sum_probs=37.1
Q ss_pred ccceeccEEEE---ec--cce--eeccCeeeecCCcccccccceEEEEecCCC-------CCCcceeeeeecceEeeeC
Q 009611 101 RPILTGDLLVT---LK--EGF--GTLGDLTFTDNSSWIRSRKFRLGLKVSPGY-------CDGIRVREAKTEGFAVKDH 165 (531)
Q Consensus 101 ~pLL~Gdl~v~---L~--~Gv--a~l~di~FTDnSsw~rSrKFRLgaRv~~~~-------~~g~RI~EAvsE~FvVkDh 165 (531)
...|.|.+... |+ +|. |.. ..|.|=|-. .-+.|||-.++..=. ....-+-|+.|+||.|-..
T Consensus 97 ~r~L~Gs~vss~~~l~d~~~~~~g~f--FvF~DLsVR-~eG~frLrf~l~~i~~~~~~~~~~~~~la~~~S~~F~V~s~ 172 (203)
T PF11754_consen 97 TRNLVGSLVSSAFRLKDPDGKEPGGF--FVFPDLSVR-TEGRFRLRFSLFDIGPSPGQGGGSSPVLAEVFSDPFTVYSA 172 (203)
T ss_pred cccCcccEeeeeEEecCCCCCeEEEE--EEeCCceEC-cCCEEEEEEEEEEecCCccccCCCCcEEEEEECcCEEEECH
Confidence 46788886554 33 333 211 234444432 246899988876422 1235689999999999653
No 36
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=25.83 E-value=2.2e+02 Score=26.76 Aligned_cols=57 Identities=28% Similarity=0.388 Sum_probs=39.2
Q ss_pred chhhhhhhhCCcccHHHHHHHHhcCh----HHHHHHHcCCCCchhHHHHHHhhcccccCCceEEEEec
Q 009611 192 GALHKKLMKADIVTVEDFLRILVRDP----QKLRNILGSGMSNRMWENTVEHAKTCVLGGKLYVYYAD 255 (531)
Q Consensus 192 G~~hkrL~~~gI~tV~dFLrl~~~d~----~kLR~iLg~gmS~k~We~~v~HAktCvl~~k~y~y~~~ 255 (531)
.+|+..|+.+|=.||+|.-..++++. ..|++++-.||=.+-=..+ .-|+-.|+|.+.
T Consensus 31 ~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~-------~~Ggy~yiY~~i 91 (126)
T COG3355 31 EVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNL-------KGGGYYYLYKPI 91 (126)
T ss_pred HHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeecc-------CCCceeEEEecC
Confidence 57888888999999999999999995 4677776555544322221 334456667554
No 37
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=25.39 E-value=32 Score=39.57 Aligned_cols=38 Identities=34% Similarity=0.344 Sum_probs=31.7
Q ss_pred CCCCCcceeeeeecccchhhhhhhhCCcccHHHHHHHHhc
Q 009611 176 PALHDEVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVR 215 (531)
Q Consensus 176 P~L~DeVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~ 215 (531)
..|++.|-.|++||+.-+ ++|++.||+||+|.|..+=+
T Consensus 5 ~~~~~~~~~l~gvg~~~~--~~l~~lgi~t~~dll~~~P~ 42 (681)
T PRK10917 5 LLLDAPLTSLKGVGPKTA--EKLAKLGIHTVQDLLLHLPR 42 (681)
T ss_pred ccccCChhhcCCCCHHHH--HHHHHcCCCCHHHHhhcCCC
Confidence 457789999999987544 88999999999999988654
No 38
>PF11033 ComJ: Competence protein J (ComJ); InterPro: IPR020354 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. The proteins in this entry play a role in the competence of cells to be transformed. They inhibit the activity of the DNA-entry nuclease. DNA-entry nuclease inhibitor is a subunit of a 75 kDa protein complex, which governs binding and entry of donor DNA. The complex is a tetramer of two subunits of the DNA-entry nuclease and two subunits of a competence-specific protein ComJ. Only the complex is able to bind ds- and ss-DNA []. It is found in the plasma membrane.
Probab=25.17 E-value=2.5e+02 Score=26.51 Aligned_cols=26 Identities=23% Similarity=0.337 Sum_probs=19.2
Q ss_pred EEEEeeCCCCCCCCCCCCHHHHhcccc
Q 009611 68 NVVVLEGDFNEEEDDNWTKEHFESHEV 94 (531)
Q Consensus 68 EIvVLdGDF~~~~~e~WT~eEF~~~IV 94 (531)
+|.|-.+||.... .+||.|+|..--+
T Consensus 9 Qi~v~~~~~~~p~-~dWtde~i~qG~a 34 (125)
T PF11033_consen 9 QITVFNRDGEPPY-IDWTDEDIEQGYA 34 (125)
T ss_pred eEEEEccCCCCcc-cccCHhHHhCcce
Confidence 5677788887642 4899999987544
No 39
>PF06594 HCBP_related: Haemolysin-type calcium binding protein related domain; InterPro: IPR010566 This family consists of a number of bacteria specific domains, which are found in haemolysin-type calcium binding proteins. This family is found in conjunction with IPR001343 from INTERPRO and is often found in multiple copies.
Probab=25.02 E-value=46 Score=24.90 Aligned_cols=18 Identities=22% Similarity=0.578 Sum_probs=15.1
Q ss_pred eeeccCeeeecCCccccc
Q 009611 116 FGTLGDLTFTDNSSWIRS 133 (531)
Q Consensus 116 va~l~di~FTDnSsw~rS 133 (531)
-..|..+.|-|++.|.+.
T Consensus 24 ~~~Ie~i~FaDGt~w~~~ 41 (43)
T PF06594_consen 24 SYRIEQIEFADGTVWTRA 41 (43)
T ss_pred CCcEeEEEEcCCCEecHH
Confidence 567889999999999753
No 40
>cd03468 PolY_like DNA Polymerase Y-family. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.
Probab=20.94 E-value=56 Score=33.31 Aligned_cols=35 Identities=17% Similarity=0.307 Sum_probs=29.0
Q ss_pred eecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcC
Q 009611 187 RIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGS 226 (531)
Q Consensus 187 kIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~ 226 (531)
+||+... .+|.+.||+|++||..+ +...|++.||.
T Consensus 177 gig~~~~--~~L~~~Gi~t~~dl~~~---~~~~l~~rfG~ 211 (335)
T cd03468 177 RLPPETV--ELLARLGLRTLGDLAAL---PRAELARRFGL 211 (335)
T ss_pred CCCHHHH--HHHHHhCcccHHHHHhC---ChHHHHhhcCH
Confidence 5776544 89999999999998874 78889999975
No 41
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=20.74 E-value=1.2e+02 Score=22.41 Aligned_cols=42 Identities=21% Similarity=0.293 Sum_probs=31.3
Q ss_pred hhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhc
Q 009611 195 HKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 241 (531)
Q Consensus 195 hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 241 (531)
-.+|..+||.||+++.. .+++.|..+- |++...=+.++.=|+
T Consensus 6 ~~~L~~~G~~s~e~la~---~~~~eL~~i~--g~~~e~a~~ii~~a~ 47 (50)
T TIGR01954 6 AQLLVEEGFTTVEDLAY---VPIDELLSIE--GFDEETAKELINRAR 47 (50)
T ss_pred HHHHHHcCCCCHHHHHc---cCHHHHhcCC--CCCHHHHHHHHHHHH
Confidence 36899999999999765 5677777775 577776666666554
No 42
>COG0540 PyrB Aspartate carbamoyltransferase, catalytic chain [Nucleotide transport and metabolism]
Probab=20.58 E-value=54 Score=35.09 Aligned_cols=75 Identities=25% Similarity=0.351 Sum_probs=50.1
Q ss_pred CCCCHHHHhccc-----c---ccCCCCccceeccEEEEeccceeeccCeeeecCCcccccc----cceEEEEecC-----
Q 009611 82 DNWTKEHFESHE-----V---KEREGKRPILTGDLLVTLKEGFGTLGDLTFTDNSSWIRSR----KFRLGLKVSP----- 144 (531)
Q Consensus 82 e~WT~eEF~~~I-----V---k~ReGk~pLL~Gdl~v~L~~Gva~l~di~FTDnSsw~rSr----KFRLgaRv~~----- 144 (531)
++||.||+..-. . ....++.++|.|.+..+| |=+||-.||+- -=|||+.|+.
T Consensus 14 ~dls~~ei~~ll~~A~~~~~~~~~~~~~~~l~gk~v~~l-----------FFEpSTRTr~SFE~A~krLG~~Vv~~~~~~ 82 (316)
T COG0540 14 EDLSREELELLLDTADEFKAVARAEKKLDLLKGKVVANL-----------FFEPSTRTRLSFETAMKRLGADVVNFSDSE 82 (316)
T ss_pred HhCCHHHHHHHHHHHHHHHHhhhccCCcchhcCcEEEEE-----------EecCCCchhhhHHHHHHHcCCcEEeecCCc
Confidence 467777754211 1 235778889999877665 88999888766 4689999862
Q ss_pred -CCCCCc------ceeeee-ecceEeeeCCcc
Q 009611 145 -GYCDGI------RVREAK-TEGFAVKDHRGE 168 (531)
Q Consensus 145 -~~~~g~------RI~EAv-sE~FvVkDhRge 168 (531)
+...|+ |.-+|. .+.||++ |+-+
T Consensus 83 sSs~KGEtL~DT~~tl~ayg~D~iViR-H~~e 113 (316)
T COG0540 83 SSSKKGETLADTIRTLSAYGVDAIVIR-HPEE 113 (316)
T ss_pred ccccccccHHHHHHHHHhhCCCEEEEe-Cccc
Confidence 112343 678888 7888776 4433
Done!