Query 018680
Match_columns 352
No_of_seqs 124 out of 148
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 03:07:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018680.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018680hhsearch_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 3E-113 5E-118 823.4 28.0 261 86-349 1-263 (299)
2 TIGR02239 recomb_RAD51 DNA rep 90.2 0.35 7.6E-06 47.7 4.2 48 264-316 13-60 (316)
3 TIGR02238 recomb_DMC1 meiotic 88.2 0.59 1.3E-05 46.1 4.3 49 263-316 12-60 (313)
4 PLN03186 DNA repair protein RA 87.6 0.68 1.5E-05 46.4 4.3 60 252-316 28-87 (342)
5 PRK04301 radA DNA repair and r 84.9 0.71 1.5E-05 44.9 2.8 56 252-314 8-63 (317)
6 PLN03187 meiotic recombination 83.7 1 2.2E-05 45.3 3.4 60 251-315 30-89 (344)
7 PRK03609 umuC DNA polymerase V 79.3 1.4 3.1E-05 44.6 2.7 51 251-311 180-230 (422)
8 PF14520 HHH_5: Helix-hairpin- 78.3 2 4.4E-05 32.1 2.6 50 255-311 10-59 (60)
9 PTZ00035 Rad51 protein; Provis 77.4 3 6.5E-05 41.6 4.2 60 251-315 22-81 (337)
10 TIGR02236 recomb_radA DNA repa 73.7 2.8 6.1E-05 40.4 2.9 50 255-311 4-53 (310)
11 PRK02406 DNA polymerase IV; Va 72.8 3.4 7.5E-05 40.4 3.3 52 251-312 169-220 (343)
12 PRK03352 DNA polymerase IV; Va 68.3 2.3 5E-05 41.7 1.0 41 251-296 178-218 (346)
13 PF14229 DUF4332: Domain of un 68.3 8.5 0.00018 33.1 4.4 48 264-313 7-56 (122)
14 PRK03858 DNA polymerase IV; Va 66.8 3 6.4E-05 41.6 1.4 41 251-296 174-214 (396)
15 PRK02794 DNA polymerase IV; Pr 64.1 5.2 0.00011 40.6 2.6 55 251-315 210-264 (419)
16 PRK03348 DNA polymerase IV; Pr 63.2 4.3 9.3E-05 42.0 1.9 53 251-312 181-233 (454)
17 cd01700 PolY_Pol_V_umuC umuC s 62.1 6.1 0.00013 38.7 2.6 51 251-311 177-227 (344)
18 PRK14133 DNA polymerase IV; Pr 62.1 7.5 0.00016 38.2 3.2 51 251-311 174-224 (347)
19 PRK01810 DNA polymerase IV; Va 60.2 7.3 0.00016 39.1 2.9 51 251-311 180-230 (407)
20 cd03586 PolY_Pol_IV_kappa DNA 59.5 7.7 0.00017 37.4 2.8 52 251-312 172-223 (334)
21 PRK01172 ski2-like helicase; P 58.3 10 0.00023 40.6 3.8 51 255-312 617-667 (674)
22 PRK03103 DNA polymerase IV; Re 58.2 8 0.00017 38.9 2.7 52 251-312 182-233 (409)
23 PF10691 DUF2497: Protein of u 57.3 28 0.00061 28.0 5.2 41 24-64 33-73 (73)
24 PRK01216 DNA polymerase IV; Va 56.9 11 0.00024 37.7 3.5 52 251-311 179-230 (351)
25 cd01701 PolY_Rev1 DNA polymera 54.3 11 0.00024 38.2 3.0 54 251-311 223-276 (404)
26 PF03118 RNA_pol_A_CTD: Bacter 50.6 11 0.00024 29.3 1.8 37 265-306 24-60 (66)
27 cd00424 PolY Y-family of DNA p 50.5 11 0.00025 36.9 2.4 55 251-315 174-229 (343)
28 PF04994 TfoX_C: TfoX C-termin 49.4 6.1 0.00013 31.9 0.2 30 253-284 6-35 (81)
29 cd01702 PolY_Pol_eta DNA Polym 48.6 8.2 0.00018 38.8 1.0 56 251-313 183-239 (359)
30 cd01703 PolY_Pol_iota DNA Poly 47.5 10 0.00023 38.4 1.6 59 251-315 173-243 (379)
31 PF11754 Velvet: Velvet factor 47.4 2.3E+02 0.0049 26.4 10.3 59 171-235 97-172 (203)
32 COG3743 Uncharacterized conser 46.8 23 0.00049 31.8 3.4 60 249-312 66-126 (133)
33 PF02889 Sec63: Sec63 Brl doma 45.4 18 0.0004 34.5 2.8 54 251-311 149-202 (314)
34 KOG1520 Predicted alkaloid syn 44.1 89 0.0019 32.4 7.6 118 162-294 150-303 (376)
35 PF14229 DUF4332: Domain of un 42.9 14 0.00031 31.7 1.5 38 252-294 55-92 (122)
36 TIGR02979 phageshock_pspD phag 37.4 42 0.00091 26.2 3.1 14 42-55 40-53 (59)
37 cd07978 TAF13 The TATA Binding 36.8 53 0.0011 27.3 3.9 35 270-312 52-89 (92)
38 PF09584 Phageshock_PspD: Phag 35.4 45 0.00097 26.7 3.1 15 42-56 45-59 (66)
39 KOG4233 DNA-bridging protein B 34.2 44 0.00094 27.9 2.9 56 246-313 15-78 (90)
40 cd03468 PolY_like DNA Polymera 32.4 40 0.00087 32.5 2.9 35 257-296 177-211 (335)
41 TIGR01954 nusA_Cterm_rpt trans 31.9 70 0.0015 22.3 3.4 42 265-311 6-47 (50)
42 PRK10917 ATP-dependent DNA hel 31.0 21 0.00046 38.8 0.9 39 246-286 5-43 (681)
43 PRK10497 peripheral inner memb 30.9 61 0.0013 26.4 3.2 15 42-56 52-66 (73)
44 COG4766 EutQ Ethanolamine util 30.2 1.4E+02 0.0029 27.9 5.7 92 29-120 13-107 (176)
45 PF09816 EAF: RNA polymerase I 30.2 1.5E+02 0.0033 24.8 5.7 67 69-138 31-103 (109)
46 PRK15457 ethanolamine utilizat 29.5 1.1E+02 0.0024 29.8 5.3 17 45-61 89-105 (233)
47 PRK07758 hypothetical protein; 27.9 93 0.002 26.4 4.0 37 266-307 48-84 (95)
48 PF06594 HCBP_related: Haemoly 27.1 38 0.00082 23.8 1.3 18 186-203 24-41 (43)
49 PRK05256 condesin subunit E; P 25.0 97 0.0021 30.2 4.0 50 266-315 107-160 (238)
50 KOG1104 Nuclear cap-binding co 23.4 89 0.0019 35.1 3.9 41 275-315 224-268 (759)
51 PF00853 Runt: Runt domain; I 23.3 1.8E+02 0.0039 26.2 5.0 34 179-214 74-107 (135)
52 PTZ00205 DNA polymerase kappa; 23.0 72 0.0016 34.7 3.0 53 251-305 310-367 (571)
53 PRK14973 DNA topoisomerase I; 22.9 68 0.0015 36.8 3.0 54 252-312 879-932 (936)
54 PF12645 HTH_16: Helix-turn-he 22.0 1.1E+02 0.0025 23.6 3.2 26 28-53 2-29 (65)
55 COG5340 Predicted transcriptio 21.1 61 0.0013 31.9 1.9 42 268-310 25-66 (269)
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=2.5e-113 Score=823.41 Aligned_cols=261 Identities=59% Similarity=1.000 Sum_probs=256.9
Q ss_pred ceEEEEccCCCCCcccCCceeecCCCCeEEEEEEcCCCCeeecCCCCCcceEEEEEecCCCCCCCCCCCCHHHHhccccc
Q 018680 86 SLKLIFSQKLSLPIFTGSKITDVENNPLQIVVVDTRSNGLIAPASLPQPIKIELVVLDGDFPPGDRDHWTPEEFESNIVK 165 (352)
Q Consensus 86 ~~~L~F~n~l~~pifT~~~I~a~~g~~I~V~l~D~~t~n~iv~~g~~ss~kvEIvVLdGDF~~~~~e~WT~eeF~~~IV~ 165 (352)
+|||+|+|+|++|+|||++|+|+||+||+|+|+|++|+ |++||+||+|||||||||||+.+++++||+|||++|||+
T Consensus 1 ~~~L~F~n~l~~pifT~~~i~a~~g~~i~V~l~d~~~~---v~~g~lss~kieIvvLdGdF~~~~~~~wT~eeF~~~iv~ 77 (299)
T PF07887_consen 1 NLQLRFLNKLSLPIFTGSKIEAEDGAPIKVALVDANTG---VTSGPLSSAKIEIVVLDGDFNDEDCEDWTEEEFNSHIVK 77 (299)
T ss_pred CeEEEecCCCCCCcccCCceEecCCCcEEEEEEECCCC---ccCCCCCCcEEEEEEEccccCCCccCCCCHHHHhhcEee
Confidence 58999999999999999999999999999999999886 999999999999999999999999999999999999999
Q ss_pred cCCCCCCcccccEEEEecCceeecCCeEEecCCccccCCceEEEEEeecCCCCceeeeeeeecceEEeecCCcccccCCC
Q 018680 166 ERTGKRPLLTGDVNVTARDGVAPIGDIEFTDNSSWIRSRKFRIGAKVARGSYQGVRICEAITDAFVVKDHRGELYKKHHP 245 (352)
Q Consensus 166 ~R~Gk~pLL~Gdl~v~L~~Gva~l~di~FtDnSs~~rSrkFRLgaRv~~~~~~g~RI~EAvse~FvVkd~Rge~~kKh~p 245 (352)
+|+||+|||+|+++|+|+||+|+|+||+|||||||+|||||||||||+++++.|+|||||+||||+|||||||+||||||
T Consensus 78 ~r~gk~pLL~G~~~v~L~~G~a~l~di~FtdnSs~~rsrKFRLgarv~~~~~~~~rI~Eavse~FvVkd~Rge~~kKh~p 157 (299)
T PF07887_consen 78 EREGKRPLLTGDLQVTLKNGVATLGDISFTDNSSWIRSRKFRLGARVVSGSCDGVRIREAVSEPFVVKDHRGELYKKHYP 157 (299)
T ss_pred cCCCCCCCCCccEEEEecCCEEEccccEEecCcccccCCcEEEEEEEccCCCCCceeEEeeecCEEEEecccccccCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhccccCCCceEEEe--
Q 018680 246 PMLEDEVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVMGNKLYIFR-- 323 (352)
Q Consensus 246 P~L~DeVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAktCvl~~k~y~y~-- 323 (352)
|+|+|||||||+|||+|+|||+|+++||+||+|||+++++||++||+|||+|||++||++|++|||||++++++|+|+
T Consensus 158 P~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 158 PSLDDEVWRLEKIGKDGAFHKRLKKNGINTVEDFLKLLNKDPQKLREILGSGMSNKMWETTVEHAKTCVLGDKLYVYYDE 237 (299)
T ss_pred CCCCCchhhhhhccccCHHHHHHHHcCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHHHHHHHHhcCCCCcEEEEEec
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeEEEEcccceEeeeEECCeeeec
Q 018680 324 GHNCIILLNPICQVVRAVINNQTLIS 349 (352)
Q Consensus 324 ~~~~~l~FN~i~~lvg~~f~g~~~~~ 349 (352)
++|++|+|||||+||||+|+|||++.
T Consensus 238 ~~nv~l~FN~i~~lvga~~~g~y~s~ 263 (299)
T PF07887_consen 238 EQNVGLFFNCIYELVGAIFGGQYVSL 263 (299)
T ss_pred CCceEEEEcchhhEEeEEECCEEEeh
Confidence 68999999999999999999999984
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=90.17 E-value=0.35 Score=47.67 Aligned_cols=48 Identities=31% Similarity=0.284 Sum_probs=42.5
Q ss_pred hhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhccccCC
Q 018680 264 FHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVMG 316 (352)
Q Consensus 264 ~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAktCvl~ 316 (352)
.-++|+++||.||+||+.. +|..|.+++ ++|...++.+..||.+|...
T Consensus 13 ~~~~l~~~g~~t~~~~~~~---~~~~L~~i~--~ls~~~~~~~~~~~~~~~~~ 60 (316)
T TIGR02239 13 DIKKLQEAGLHTVESVAYA---PKKQLLEIK--GISEAKADKILAEAAKLVPM 60 (316)
T ss_pred HHHHHHHcCCCcHHHHHhC---CHHHHHHHh--CCCHHHHHHHHHHHHHhccc
Confidence 3488999999999999875 899999998 68999999999999988653
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=88.22 E-value=0.59 Score=46.13 Aligned_cols=49 Identities=35% Similarity=0.311 Sum_probs=42.8
Q ss_pred hhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhccccCC
Q 018680 263 AFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVMG 316 (352)
Q Consensus 263 ~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAktCvl~ 316 (352)
..-++|+++||.||+||+.. ++..|.++. |+|...++.+++.|+.+...
T Consensus 12 ~~~~~L~~~g~~t~~~~~~~---~~~~L~~~~--gls~~~~~~i~~~~~~~~~~ 60 (313)
T TIGR02238 12 ADIKKLKSAGICTVNGVIMT---TRRALCKIK--GLSEAKVDKIKEAASKIINP 60 (313)
T ss_pred HHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHhhhcc
Confidence 34589999999999998765 799999998 69999999999999988654
No 4
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=87.63 E-value=0.68 Score=46.42 Aligned_cols=60 Identities=32% Similarity=0.287 Sum_probs=46.8
Q ss_pred eeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhccccCC
Q 018680 252 VWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVMG 316 (352)
Q Consensus 252 VwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAktCvl~ 316 (352)
+-.|+.-|-.-..-++|+++||.||+||+.. ++..|.+++ ++|....+.+++||.+|...
T Consensus 28 ~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~---~~~~L~~i~--~is~~~~~~~~~~~~~~~~~ 87 (342)
T PLN03186 28 IEQLQASGIAALDIKKLKDAGIHTVESLAYA---PKKDLLQIK--GISEAKVEKILEAASKLVPL 87 (342)
T ss_pred HHHHHhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHHhccc
Confidence 4444442333234488999999999999875 789999998 68999999999999888654
No 5
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=84.91 E-value=0.71 Score=44.94 Aligned_cols=56 Identities=25% Similarity=0.356 Sum_probs=44.7
Q ss_pred eeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhcccc
Q 018680 252 VWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCV 314 (352)
Q Consensus 252 VwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAktCv 314 (352)
+..|.+||+. .-++|.++||.|++|++. .+++.|.+++ |++.+.++.+.+-|+.+.
T Consensus 8 l~~l~gIg~~--~a~~L~~~Gi~t~~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~a~~~~ 63 (317)
T PRK04301 8 LEDLPGVGPA--TAEKLREAGYDTVEAIAV---ASPKELSEAA--GIGESTAAKIIEAAREAA 63 (317)
T ss_pred HhhcCCCCHH--HHHHHHHcCCCCHHHHHc---CCHHHHHHhc--CCCHHHHHHHHHHHHHhh
Confidence 4455566644 458999999999999965 4899999999 578889999998887644
No 6
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=83.72 E-value=1 Score=45.32 Aligned_cols=60 Identities=27% Similarity=0.271 Sum_probs=47.3
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhccccC
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVM 315 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAktCvl 315 (352)
++..|+.-|-.-..-++|.++||+||+|++.. ++..|-++. |+|...++.+++.|+..+.
T Consensus 30 ~~~~l~~~g~~~~~~~kL~~~g~~tv~~~~~~---~~~~L~~~~--g~s~~~~~ki~~~a~~~~~ 89 (344)
T PLN03187 30 SIDKLISQGINAGDVKKLQDAGIYTCNGLMMH---TKKNLTGIK--GLSEAKVDKICEAAEKLLN 89 (344)
T ss_pred CHHHHhhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHHhhc
Confidence 35566553333345589999999999998764 788899987 7899999999999987654
No 7
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=79.28 E-value=1.4 Score=44.61 Aligned_cols=51 Identities=31% Similarity=0.384 Sum_probs=41.3
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhc
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAk 311 (352)
+|..|-+||+. .-++|.+.||+|++|+.++ ++..|++.||. .+..+..||.
T Consensus 180 Pv~~l~GiG~~--~~~~L~~lGi~TigdL~~~---~~~~L~~~fG~-----~~~~l~~~a~ 230 (422)
T PRK03609 180 PVEEVWGVGRR--ISKKLNAMGIKTALDLADT---NIRFIRKHFNV-----VLERTVRELR 230 (422)
T ss_pred ChhhcCCccHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHCH-----HHHHHHHHhC
Confidence 46667778875 4489999999999999986 78899999973 5777777775
No 8
>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=78.30 E-value=2 Score=32.05 Aligned_cols=50 Identities=38% Similarity=0.561 Sum_probs=39.8
Q ss_pred eeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhc
Q 018680 255 LEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (352)
Q Consensus 255 Le~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAk 311 (352)
+.+||+. ..++|.++||.|++|+..+ +++.|.++= |++.+.=+.+++.|+
T Consensus 10 I~Gig~~--~a~~L~~~G~~t~~~l~~a---~~~~L~~i~--Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 10 IPGIGPK--RAEKLYEAGIKTLEDLANA---DPEELAEIP--GIGEKTAEKIIEAAR 59 (60)
T ss_dssp STTCHHH--HHHHHHHTTCSSHHHHHTS---HHHHHHTST--TSSHHHHHHHHHHHH
T ss_pred CCCCCHH--HHHHHHhcCCCcHHHHHcC---CHHHHhcCC--CCCHHHHHHHHHHHh
Confidence 4455555 3388999999999998764 888999985 689999999998886
No 9
>PTZ00035 Rad51 protein; Provisional
Probab=77.39 E-value=3 Score=41.60 Aligned_cols=60 Identities=35% Similarity=0.327 Sum_probs=46.2
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhccccC
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVM 315 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAktCvl 315 (352)
++..|+.-|-.-..-++|+++||+||+||+.. ++..|.++. |+|...=+.+++.|+.++.
T Consensus 22 ~~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~~---~~~~L~~~~--gis~~~~~~i~~~~~~~~~ 81 (337)
T PTZ00035 22 EIEKLQSAGINAADIKKLKEAGICTVESVAYA---TKKDLCNIK--GISEAKVEKIKEAASKLVP 81 (337)
T ss_pred cHHHHhcCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhh--CCCHHHHHHHHHHHHHhcc
Confidence 45566542333334489999999999998764 888999998 6899999999999887764
No 10
>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=73.66 E-value=2.8 Score=40.41 Aligned_cols=50 Identities=32% Similarity=0.417 Sum_probs=38.3
Q ss_pred eeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhc
Q 018680 255 LEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (352)
Q Consensus 255 Le~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAk 311 (352)
|.+||+. .-++|.++||.|++|++.+ +++.|.+++ |++.+..+.+.+-|.
T Consensus 4 i~gig~~--~~~~L~~~Gi~ti~dl~~~---~~~~L~~~~--g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 4 LPGVGPA--TAEKLREAGYDTFEAIAVA---SPKELSEIA--GISEGTAAKIIQAAR 53 (310)
T ss_pred cCCCCHH--HHHHHHHcCCCCHHHHHcC---CHHHHHhcc--CCCHHHHHHHHHHHH
Confidence 4455544 3488999999999998874 899999999 467777777766665
No 11
>PRK02406 DNA polymerase IV; Validated
Probab=72.81 E-value=3.4 Score=40.44 Aligned_cols=52 Identities=29% Similarity=0.332 Sum_probs=40.2
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhcc
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARK 312 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAkt 312 (352)
+|..|-+||+. .-++|...||+|++|+.++ +...|++.||. .+..+..||.-
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 56777777754 4478999999999999885 78899999973 46666667753
No 12
>PRK03352 DNA polymerase IV; Validated
Probab=68.33 E-value=2.3 Score=41.69 Aligned_cols=41 Identities=34% Similarity=0.493 Sum_probs=33.8
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCC
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGP 296 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~ 296 (352)
+|..|-+||+. ..++|.+.||+|++|++++ ++..|.+.||.
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 56777778875 4478999999999999986 78889999974
No 13
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=68.29 E-value=8.5 Score=33.08 Aligned_cols=48 Identities=38% Similarity=0.337 Sum_probs=35.4
Q ss_pred hhhhhhhcCCccHHHHHHhhccChHH--HHHHhCCCCChhhHHHHHHhhccc
Q 018680 264 FHKKLSAAGIKTVQDFLKLSIVEPQR--LRKILGPGMSEKMWEVTMQHARKC 313 (352)
Q Consensus 264 ~hk~L~~~~I~tV~dFLkl~~~d~~k--Lr~iLg~~ms~k~We~~v~HAktC 313 (352)
+-.+|...||+|++|||..-.....+ |-+-+ |++.+-=...+.+|.=|
T Consensus 7 ~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~--~i~~~~l~~w~~~AdL~ 56 (122)
T PF14229_consen 7 EAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKL--GISERNLLKWVNQADLM 56 (122)
T ss_pred HHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhc--CCCHHHHHHHHhHHHhh
Confidence 44789999999999999987765555 66655 56777666666666544
No 14
>PRK03858 DNA polymerase IV; Validated
Probab=66.81 E-value=3 Score=41.65 Aligned_cols=41 Identities=39% Similarity=0.497 Sum_probs=33.4
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCC
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGP 296 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~ 296 (352)
+|..|-+||+.- -++|.+.||+|++|+.. .++..|++.||.
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 466666788754 48899999999999986 488899999984
No 15
>PRK02794 DNA polymerase IV; Provisional
Probab=64.12 E-value=5.2 Score=40.57 Aligned_cols=55 Identities=22% Similarity=0.219 Sum_probs=42.8
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhccccC
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVM 315 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAktCvl 315 (352)
+|..|.+||+. .-++|...||+|++|+..+ +...|++.||. .|..+..+|.--+.
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 45556667754 4588999999999998875 78899999973 58888888875554
No 16
>PRK03348 DNA polymerase IV; Provisional
Probab=63.23 E-value=4.3 Score=41.98 Aligned_cols=53 Identities=30% Similarity=0.364 Sum_probs=39.7
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhcc
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARK 312 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAkt 312 (352)
+|..|-+||+.. -++|.+.||+|++||.++ +...|++.||..+ ...+..+|.-
T Consensus 181 Pv~~L~GIG~~t--~~~L~~lGI~TigDLa~l---~~~~L~~~fG~~~----g~~L~~~a~G 233 (454)
T PRK03348 181 PVRRLWGIGPVT--EEKLHRLGIETIGDLAAL---SEAEVANLLGATV----GPALHRLARG 233 (454)
T ss_pred CccccCCCCHHH--HHHHHHcCCccHHHHhcC---CHHHHHHHHCHHH----HHHHHHHHcC
Confidence 688888888764 478999999999999875 7889999997323 3334455543
No 17
>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=62.15 E-value=6.1 Score=38.72 Aligned_cols=51 Identities=33% Similarity=0.411 Sum_probs=39.4
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhc
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAk 311 (352)
+|..|-+||+. .-++|...||+|++|+.++ +.+.|.+.||. .|.....+|.
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 45666677774 4478999999999999986 78889999973 4666777775
No 18
>PRK14133 DNA polymerase IV; Provisional
Probab=62.07 E-value=7.5 Score=38.24 Aligned_cols=51 Identities=31% Similarity=0.463 Sum_probs=39.6
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhc
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAk 311 (352)
+|..|.+||+.-. ++|.+.||+|++|++++ +...|++.|| +.|..+.++|.
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 77999999999999885 7788999997 25777777774
No 19
>PRK01810 DNA polymerase IV; Validated
Probab=60.24 E-value=7.3 Score=39.14 Aligned_cols=51 Identities=29% Similarity=0.335 Sum_probs=39.0
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhc
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAk 311 (352)
+|..|-+||+.- -++|...||+|++|+.++ +...|++.||. .+..+.++|.
T Consensus 180 pv~~l~giG~~~--~~~L~~~Gi~tigdL~~~---~~~~L~~rfG~-----~g~~l~~~a~ 230 (407)
T PRK01810 180 PVGEMHGIGEKT--AEKLKDIGIQTIGDLAKA---DEHILRAKLGI-----NGVRLQRRAN 230 (407)
T ss_pred CHhhcCCcCHHH--HHHHHHcCCCcHHHHHhC---CHHHHHHHHhH-----HHHHHHHHhc
Confidence 466666777643 488999999999998774 77889999973 4666777776
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=59.49 E-value=7.7 Score=37.45 Aligned_cols=52 Identities=35% Similarity=0.468 Sum_probs=40.7
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhcc
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARK 312 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAkt 312 (352)
+|..|-+||+. .-.+|...||+|++|+..+ ++..|.+.+| +.|....+||+-
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 45666667754 4588999999999999875 7888999886 478888888864
No 21
>PRK01172 ski2-like helicase; Provisional
Probab=58.31 E-value=10 Score=40.63 Aligned_cols=51 Identities=33% Similarity=0.595 Sum_probs=41.5
Q ss_pred eeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhcc
Q 018680 255 LEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARK 312 (352)
Q Consensus 255 Le~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAkt 312 (352)
|.++++. ..++|.++||.||.|+.. .++++|-+|+ |++++.=+.++++|+.
T Consensus 617 ip~~~~~--~a~~l~~~g~~~~~di~~---~~~~~~~~i~--~~~~~~~~~i~~~~~~ 667 (674)
T PRK01172 617 IPKVGRV--RARRLYDAGFKTVDDIAR---SSPERIKKIY--GFSDTLANAIVNRAMK 667 (674)
T ss_pred CCCCCHH--HHHHHHHcCCCCHHHHHh---CCHHHHHHHh--ccCHHHHHHHHHHHHH
Confidence 3444444 558899999999999877 6888898998 5899999999999875
No 22
>PRK03103 DNA polymerase IV; Reviewed
Probab=58.24 E-value=8 Score=38.90 Aligned_cols=52 Identities=29% Similarity=0.358 Sum_probs=39.7
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhcc
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARK 312 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAkt 312 (352)
.|..|-+||+. .-++|.+.||+|++|+.++ ++..|++.||. .|..+.++|.-
T Consensus 182 pi~~l~gig~~--~~~~L~~~Gi~tigdl~~~---~~~~L~~~fG~-----~~~~l~~~a~G 233 (409)
T PRK03103 182 PVRKLFGVGSR--MEKHLRRMGIRTIGQLANT---PLERLKKRWGI-----NGEVLWRTANG 233 (409)
T ss_pred CHhhcCCccHH--HHHHHHHcCCCCHHHHhcC---CHHHHHHHHCH-----HHHHHHHHhcC
Confidence 56666678875 5578999999999998874 68889999973 46666677653
No 23
>PF10691 DUF2497: Protein of unknown function (DUF2497) ; InterPro: IPR019632 Members of this family belong to the Alphaproteobacteria. The function of the family is not known.
Probab=57.35 E-value=28 Score=27.99 Aligned_cols=41 Identities=20% Similarity=0.239 Sum_probs=28.5
Q ss_pred CchhHHHHHHHHhhhHHHHHHhhhHHHHHHHHHHHHHHhhh
Q 018680 24 PSFASVIGEAVMVNSFQNFFSALEPLLRRVVNEEVQRGVSK 64 (352)
Q Consensus 24 p~~~~vi~e~~~~~s~q~~~~~lEp~lrrvV~EEve~~l~~ 64 (352)
.++-.+++|.++-+--+=|=..|=.++.|+|++||+|..++
T Consensus 33 ~TlE~lvremLRPmLkeWLD~nLP~lVErlVr~EIeRi~rr 73 (73)
T PF10691_consen 33 RTLEDLVREMLRPMLKEWLDENLPGLVERLVREEIERIARR 73 (73)
T ss_pred ccHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhcC
Confidence 35666666766666333344467778889999999997653
No 24
>PRK01216 DNA polymerase IV; Validated
Probab=56.93 E-value=11 Score=37.72 Aligned_cols=52 Identities=25% Similarity=0.368 Sum_probs=38.5
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhc
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAk 311 (352)
+|..|.+||+. ...+|...||+|++|+.++ +...|++.||. ..+..+-.+|.
T Consensus 179 Pi~~l~giG~~--~~~~L~~~Gi~TigdL~~~---~~~~L~~rfG~----~~~~~L~~~a~ 230 (351)
T PRK01216 179 DIADIPGIGDI--TAEKLKKLGVNKLVDTLRI---EFDELKGIIGE----AKAKYLFSLAR 230 (351)
T ss_pred CcccccCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHCH----HHHHHHHHHhC
Confidence 57777788865 4489999999999998865 67889999972 23444555553
No 25
>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=54.33 E-value=11 Score=38.17 Aligned_cols=54 Identities=28% Similarity=0.276 Sum_probs=39.6
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhc
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAk 311 (352)
+|..|.+||+. .-++|.+.||.|++|+..+- .++..|++.||. +.+..+..+|.
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 67777788865 45999999999999998762 137889999973 34555555554
No 26
>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=50.63 E-value=11 Score=29.26 Aligned_cols=37 Identities=35% Similarity=0.391 Sum_probs=23.6
Q ss_pred hhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHH
Q 018680 265 HKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVT 306 (352)
Q Consensus 265 hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~ 306 (352)
...|..+||+||+|++++ +++.|.++= |+..+.-+.+
T Consensus 24 ~n~L~~~~I~tv~dL~~~---s~~~L~~i~--n~G~ksl~EI 60 (66)
T PF03118_consen 24 YNCLKRAGIHTVGDLVKY---SEEDLLKIK--NFGKKSLEEI 60 (66)
T ss_dssp HHHHHCTT--BHHHHHCS----HHHHHTST--TSHHHHHHHH
T ss_pred HHHHHHhCCcCHHHHHhC---CHHHHHhCC--CCCHhHHHHH
Confidence 356999999999997765 677888875 3445544443
No 27
>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=50.55 E-value=11 Score=36.88 Aligned_cols=55 Identities=25% Similarity=0.144 Sum_probs=40.8
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccC-hHHHHHHhCCCCChhhHHHHHHhhccccC
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVE-PQRLRKILGPGMSEKMWEVTMQHARKCVM 315 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d-~~kLr~iLg~~ms~k~We~~v~HAktCvl 315 (352)
+|..|-+||+. .-++|.+.||+|++|++++ + ...|+..+| +.+..+.++|.--+.
T Consensus 174 pi~~l~giG~~--~~~~L~~~Gi~ti~dl~~~---~~~~~l~~~fg-----~~~~~l~~~a~G~d~ 229 (343)
T cd00424 174 PLTDLPGIGAV--TAKRLEAVGINPIGDLLAA---SPDALLALWGG-----VSGERLWYALRGIDD 229 (343)
T ss_pred ChhhcCCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHhh-----HHHHHHHHHhCCcCC
Confidence 46777778875 4488999999999998865 5 556777775 357777788875544
No 28
>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=49.38 E-value=6.1 Score=31.91 Aligned_cols=30 Identities=33% Similarity=0.477 Sum_probs=18.1
Q ss_pred eeeeeecccchhhhhhhhcCCccHHHHHHhhc
Q 018680 253 WRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSI 284 (352)
Q Consensus 253 wRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~ 284 (352)
..|-+||.. .-+.|.+.||+||+||..+=.
T Consensus 6 ~~LpNig~~--~e~~L~~vGI~t~~~L~~~Ga 35 (81)
T PF04994_consen 6 KDLPNIGPK--SERMLAKVGIHTVEDLRELGA 35 (81)
T ss_dssp CGSTT--HH--HHHHHHHTT--SHHHHHHHHH
T ss_pred hhCCCCCHH--HHHHHHHcCCCCHHHHHHhCH
Confidence 334455544 237799999999999987643
No 29
>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=48.61 E-value=8.2 Score=38.78 Aligned_cols=56 Identities=16% Similarity=0.235 Sum_probs=39.0
Q ss_pred ceeeeeeecccchhhhh-hhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhccc
Q 018680 251 EVWRLEKIGKDGAFHKK-LSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKC 313 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~-L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAktC 313 (352)
+|..|-+||+. .-++ |...||.|++|+.++. .++..|++.||. +.++.+..+|.--
T Consensus 183 pv~~l~GiG~~--~~~~ll~~~Gi~ti~dl~~~~-~~~~~L~~~fG~----~~g~~l~~~a~G~ 239 (359)
T cd01702 183 PITSIRGLGGK--LGEEIIDLLGLPTEGDVAGFR-SSESDLQEHFGE----KLGEWLYNLLRGI 239 (359)
T ss_pred cHHHhCCcCHH--HHHHHHHHcCCcCHHHHHhcc-CCHHHHHHHHHH----HHHHHHHHHhCCC
Confidence 47777778743 2244 6889999999998765 578899999973 3455555566543
No 30
>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=47.46 E-value=10 Score=38.42 Aligned_cols=59 Identities=24% Similarity=0.245 Sum_probs=41.5
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhc------------cChHHHHHHhCCCCChhhHHHHHHhhccccC
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSI------------VEPQRLRKILGPGMSEKMWEVTMQHARKCVM 315 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~------------~d~~kLr~iLg~~ms~k~We~~v~HAktCvl 315 (352)
+|..|-+||+.-. ++|.+.||.|++|+..+-+ .+.+.|++.||. +.+..+.++|.--+.
T Consensus 173 pv~~l~GiG~~~~--~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~----~~g~~l~~~a~G~d~ 243 (379)
T cd01703 173 DLRKIPGIGYKTA--AKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGE----GIGQRIWKLLFGRDT 243 (379)
T ss_pred CccccCCcCHHHH--HHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHCH----HHHHHHHHHHCCCCC
Confidence 4556667887754 8999999999999987641 127789999973 345556666665443
No 31
>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=47.38 E-value=2.3e+02 Score=26.42 Aligned_cols=59 Identities=20% Similarity=0.274 Sum_probs=38.2
Q ss_pred CCcccccEEEEe-----cCce--e---ecCCeEEecCCccccCCceEEEEEeecCCC-------CceeeeeeeecceEEe
Q 018680 171 RPLLTGDVNVTA-----RDGV--A---PIGDIEFTDNSSWIRSRKFRIGAKVARGSY-------QGVRICEAITDAFVVK 233 (352)
Q Consensus 171 ~pLL~Gdl~v~L-----~~Gv--a---~l~di~FtDnSs~~rSrkFRLgaRv~~~~~-------~g~RI~EAvse~FvVk 233 (352)
.+.|.|.+...+ .+|. | .++||++. .-+.|||-.++..=.. ...-+-|+.|+||.|-
T Consensus 97 ~r~L~Gs~vss~~~l~d~~~~~~g~fFvF~DLsVR------~eG~frLrf~l~~i~~~~~~~~~~~~~la~~~S~~F~V~ 170 (203)
T PF11754_consen 97 TRNLVGSLVSSAFRLKDPDGKEPGGFFVFPDLSVR------TEGRFRLRFSLFDIGPSPGQGGGSSPVLAEVFSDPFTVY 170 (203)
T ss_pred cccCcccEeeeeEEecCCCCCeEEEEEEeCCceEC------cCCEEEEEEEEEEecCCccccCCCCcEEEEEECcCEEEE
Confidence 368888876443 2343 2 23555443 2578999999886322 2356889999999996
Q ss_pred ec
Q 018680 234 DH 235 (352)
Q Consensus 234 d~ 235 (352)
..
T Consensus 171 s~ 172 (203)
T PF11754_consen 171 SA 172 (203)
T ss_pred CH
Confidence 54
No 32
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=46.80 E-value=23 Score=31.75 Aligned_cols=60 Identities=18% Similarity=0.277 Sum_probs=41.7
Q ss_pred CCceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHH-HHHhhcc
Q 018680 249 EDEVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEV-TMQHARK 312 (352)
Q Consensus 249 ~DeVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~-~v~HAkt 312 (352)
.|+.-+|.+||.. +-+.|+..||+|-.|.-.+-..|-..+-..| +..-+-|.. -|+.|+.
T Consensus 66 ~DDLt~I~GIGPk--~e~~Ln~~GI~tfaQIAAwt~~di~~id~~l--~f~GRi~RDdWi~QAk~ 126 (133)
T COG3743 66 KDDLTRISGIGPK--LEKVLNELGIFTFAQIAAWTRADIAWIDDYL--NFDGRIERDDWIAQAKA 126 (133)
T ss_pred cccchhhcccCHH--HHHHHHHcCCccHHHHHhcCHHHHHHHHhhc--CCcchhHHHHHHHHHHH
Confidence 3999999999986 6699999999996665443333333344445 677777765 6666653
No 33
>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=45.44 E-value=18 Score=34.47 Aligned_cols=54 Identities=31% Similarity=0.501 Sum_probs=37.3
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhc
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAk 311 (352)
...-|.+|+.+.+ ++|..+||.|+++|+++ +++++..+| +......+.+.+.|.
T Consensus 149 ~L~Qlp~i~~~~~--~~l~~~~i~~l~~l~~~---~~~e~~~ll--~~~~~~~~~i~~~~~ 202 (314)
T PF02889_consen 149 PLLQLPHIGEESL--KKLEKRGIKTLQDLRDL---SPEELEELL--NRNPPFGKEILEVAS 202 (314)
T ss_dssp GGGGSTT--HHHH--HHHHHTT--SHHHHHHS----HHHHHHHH---S-HHHHHHHHHHHC
T ss_pred hhhcCCCCCHHHH--HHHhccCCCcHHHHhhC---CHHHHHHHH--hhhhhhHHHHHHHHH
Confidence 3455667777654 88999999999999965 899999999 456688888888875
No 34
>KOG1520 consensus Predicted alkaloid synthase/Surface mucin Hemomucin [General function prediction only]
Probab=44.09 E-value=89 Score=32.43 Aligned_cols=118 Identities=22% Similarity=0.302 Sum_probs=65.8
Q ss_pred cccccCCCCCCcccccEEEEecCceeecCCeEEecCCccccCCceEEEEEeecCCCC----------------ceee---
Q 018680 162 NIVKERTGKRPLLTGDVNVTARDGVAPIGDIEFTDNSSWIRSRKFRIGAKVARGSYQ----------------GVRI--- 222 (352)
Q Consensus 162 ~IV~~R~Gk~pLL~Gdl~v~L~~Gva~l~di~FtDnSs~~rSrkFRLgaRv~~~~~~----------------g~RI--- 222 (352)
.++-+=+|+...++.++.|.= +| .+-|||+||.---|.|.+++---++++. +.+.
T Consensus 150 ~l~~~~~G~~~kf~N~ldI~~-~g-----~vyFTDSSsk~~~rd~~~a~l~g~~~GRl~~YD~~tK~~~VLld~L~F~NG 223 (376)
T KOG1520|consen 150 LLADEAEGKPFKFLNDLDIDP-EG-----VVYFTDSSSKYDRRDFVFAALEGDPTGRLFRYDPSTKVTKVLLDGLYFPNG 223 (376)
T ss_pred eccccccCeeeeecCceeEcC-CC-----eEEEeccccccchhheEEeeecCCCccceEEecCcccchhhhhhccccccc
Confidence 334445777777777766654 54 4789999997666888888765533220 1111
Q ss_pred -eeeeecceEEeecCCc-------ccccCC---------CCCCCCceeeeeeecccchhhhhhhhcCCccHHHHHHhhcc
Q 018680 223 -CEAITDAFVVKDHRGE-------LYKKHH---------PPMLEDEVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIV 285 (352)
Q Consensus 223 -~EAvse~FvVkd~Rge-------~~kKh~---------pP~L~DeVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~ 285 (352)
+=-..+.|++--.=+- ....+. -|-.-|.+-+= .+|.|.=.|....=. |.+++..
T Consensus 224 laLS~d~sfvl~~Et~~~ri~rywi~g~k~gt~EvFa~~LPG~PDNIR~~----~~G~fWVal~~~~~~----~~~~~~~ 295 (376)
T KOG1520|consen 224 LALSPDGSFVLVAETTTARIKRYWIKGPKAGTSEVFAEGLPGYPDNIRRD----STGHFWVALHSKRST----LWRLLMK 295 (376)
T ss_pred ccCCCCCCEEEEEeeccceeeeeEecCCccCchhhHhhcCCCCCcceeEC----CCCCEEEEEecccch----HHHhhhc
Confidence 1123356665433222 122222 46666666443 566665555433222 7777777
Q ss_pred ChHHHHHHh
Q 018680 286 EPQRLRKIL 294 (352)
Q Consensus 286 d~~kLr~iL 294 (352)
.| -+|+++
T Consensus 296 ~p-~vr~~~ 303 (376)
T KOG1520|consen 296 YP-WVRKFI 303 (376)
T ss_pred Ch-HHHHHH
Confidence 76 677764
No 35
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=42.94 E-value=14 Score=31.71 Aligned_cols=38 Identities=32% Similarity=0.589 Sum_probs=28.5
Q ss_pred eeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHh
Q 018680 252 VWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKIL 294 (352)
Q Consensus 252 VwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iL 294 (352)
..|..+||.. |...|...||.||+++-. .+|++|.+-+
T Consensus 55 L~ri~gi~~~--~a~LL~~AGv~Tv~~LA~---~~p~~L~~~l 92 (122)
T PF14229_consen 55 LMRIPGIGPQ--YAELLEHAGVDTVEELAQ---RNPQNLHQKL 92 (122)
T ss_pred hhhcCCCCHH--HHHHHHHhCcCcHHHHHh---CCHHHHHHHH
Confidence 3466666654 668899999999999854 7888887644
No 36
>TIGR02979 phageshock_pspD phage shock protein PspD. Members of this family are phage shock protein PspD, found in a minority of bacteria that carry the defining genes of the phage shock regulon (pspA, pspB, pspC, and pspF). It is found in Escherichia coli, Yersinia pestis, and closely related species, where it is part of the phage shock operon. It is known to be expressed but its function is unknown.
Probab=37.36 E-value=42 Score=26.23 Aligned_cols=14 Identities=50% Similarity=0.802 Sum_probs=11.4
Q ss_pred HHHhhhHHHHHHHH
Q 018680 42 FFSALEPLLRRVVN 55 (352)
Q Consensus 42 ~~~~lEp~lrrvV~ 55 (352)
+.-+|||+|+|..+
T Consensus 40 La~aLEPllkr~~~ 53 (59)
T TIGR02979 40 LAIALEPMLKRAAN 53 (59)
T ss_pred HHHHHHHHHHHHHH
Confidence 45599999999865
No 37
>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=36.81 E-value=53 Score=27.28 Aligned_cols=35 Identities=29% Similarity=0.508 Sum_probs=28.9
Q ss_pred hcCCccHHHHHHhhccChHHH---HHHhCCCCChhhHHHHHHhhcc
Q 018680 270 AAGIKTVQDFLKLSIVEPQRL---RKILGPGMSEKMWEVTMQHARK 312 (352)
Q Consensus 270 ~~~I~tV~dFLkl~~~d~~kL---r~iLg~~ms~k~We~~v~HAkt 312 (352)
...| +++||+=++-.||.|| +++| .|+..++-|+.
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 4566 9999999999999775 5667 79999998875
No 38
>PF09584 Phageshock_PspD: Phage shock protein PspD (Phageshock_PspD); InterPro: IPR014321 Members of this entry are phage shock protein PspD, they are found in a minority of bacteria that carry the defining genes of the phage shock regulon (pspA, pspB, pspC, and pspF). It is found in Escherichia coli, Yersinia pestis, and closely related species, where it is part of the phage shock operon. It is known to be expressed but its function is unknown.
Probab=35.38 E-value=45 Score=26.65 Aligned_cols=15 Identities=60% Similarity=0.802 Sum_probs=12.0
Q ss_pred HHHhhhHHHHHHHHH
Q 018680 42 FFSALEPLLRRVVNE 56 (352)
Q Consensus 42 ~~~~lEp~lrrvV~E 56 (352)
+.-.|||+|||.++-
T Consensus 45 La~~LEPllrr~~~~ 59 (66)
T PF09584_consen 45 LALALEPLLRRGLNK 59 (66)
T ss_pred HHHHHHHHHHHHHHH
Confidence 445899999999764
No 39
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=34.22 E-value=44 Score=27.88 Aligned_cols=56 Identities=32% Similarity=0.499 Sum_probs=39.9
Q ss_pred CCCCCceeeeeeecccchhhhhhhhcCCcc----HHHHHHhhccChHHHH----HHhCCCCChhhHHHHHHhhccc
Q 018680 246 PMLEDEVWRLEKIGKDGAFHKKLSAAGIKT----VQDFLKLSIVEPQRLR----KILGPGMSEKMWEVTMQHARKC 313 (352)
Q Consensus 246 P~L~DeVwRLe~IgKdG~~hk~L~~~~I~t----V~dFLkl~~~d~~kLr----~iLg~~ms~k~We~~v~HAktC 313 (352)
|+=+-+|--|.+||.. +-.+|..+|+.. .++|| ++.+|++-.+ ...| ++-+||++|
T Consensus 15 PmGeK~V~~laGIg~~--lg~~L~~~GfdkAYvllGQfL-llkKdE~lF~~Wlk~~~g---------at~~~a~~~ 78 (90)
T KOG4233|consen 15 PMGEKDVTWLAGIGET--LGIKLVDAGFDKAYVLLGQFL-LLKKDEDLFQEWLKETCG---------ATAKQAQDC 78 (90)
T ss_pred ccCCCcceeeccccHH--hhhhHHhccccHHHHHHHHHH-HhcccHHHHHHHHHHHcC---------ccHHHHHHH
Confidence 6677789999999976 557899999975 46776 4457775544 3444 366777776
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=32.43 E-value=40 Score=32.46 Aligned_cols=35 Identities=20% Similarity=0.389 Sum_probs=28.5
Q ss_pred eecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCC
Q 018680 257 KIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGP 296 (352)
Q Consensus 257 ~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~ 296 (352)
.||+... .+|.+.||+|++||..+ +...|++.||.
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 5676544 88999999999998875 67789999973
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=31.90 E-value=70 Score=22.32 Aligned_cols=42 Identities=29% Similarity=0.344 Sum_probs=31.7
Q ss_pred hhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhc
Q 018680 265 HKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (352)
Q Consensus 265 hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAk 311 (352)
-.+|..+|+.||+++.. .+++.|..+- |++...=+.++.=|+
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 36799999999999765 4677888876 577777666666554
No 42
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=30.95 E-value=21 Score=38.75 Aligned_cols=39 Identities=33% Similarity=0.408 Sum_probs=32.3
Q ss_pred CCCCCceeeeeeecccchhhhhhhhcCCccHHHHHHhhccC
Q 018680 246 PMLEDEVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVE 286 (352)
Q Consensus 246 P~L~DeVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d 286 (352)
+.|++.|..|++||+.-+ +.|++.||+||.|.|..+=+.
T Consensus 5 ~~~~~~~~~l~gvg~~~~--~~l~~lgi~t~~dll~~~P~~ 43 (681)
T PRK10917 5 LLLDAPLTSLKGVGPKTA--EKLAKLGIHTVQDLLLHLPRR 43 (681)
T ss_pred ccccCChhhcCCCCHHHH--HHHHHcCCCCHHHHhhcCCCc
Confidence 457789999999987644 789999999999999887544
No 43
>PRK10497 peripheral inner membrane phage-shock protein; Provisional
Probab=30.91 E-value=61 Score=26.37 Aligned_cols=15 Identities=53% Similarity=0.820 Sum_probs=11.8
Q ss_pred HHHhhhHHHHHHHHH
Q 018680 42 FFSALEPLLRRVVNE 56 (352)
Q Consensus 42 ~~~~lEp~lrrvV~E 56 (352)
+.-.|||+|||.++-
T Consensus 52 L~~~LEPlLkr~~~~ 66 (73)
T PRK10497 52 LAVALEPLLKRAANK 66 (73)
T ss_pred HHHHHHHHHHHHHHH
Confidence 445899999999754
No 44
>COG4766 EutQ Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=30.19 E-value=1.4e+02 Score=27.88 Aligned_cols=92 Identities=18% Similarity=0.300 Sum_probs=59.3
Q ss_pred HHHHHHHhh-hHHHHHHh-hhHHHHHHHHHHHHHHhhhcCCC-CccccCCccccccCCCCceEEEEccCCCCCcccCCce
Q 018680 29 VIGEAVMVN-SFQNFFSA-LEPLLRRVVNEEVQRGVSKYNPC-RSLTRSSSLRIQALEPSSLKLIFSQKLSLPIFTGSKI 105 (352)
Q Consensus 29 vi~e~~~~~-s~q~~~~~-lEp~lrrvV~EEve~~l~~~~~~-~~~~rs~~~~~~~~~~~~~~L~F~n~l~~pifT~~~I 105 (352)
-|+|.+..+ +.-.+|+. +|-++++|++|+.-....-..|. .+..+-+...++......+.|+|...=+.-+||++-+
T Consensus 13 ~i~~si~a~l~~~~~~~~l~~Qlm~kVmkek~s~~~~~~~~~~k~v~~ksgikvvk~s~vk~~~r~d~gqp~~V~~tdLv 92 (176)
T COG4766 13 RIRESIIAQLPEGQFTKELVEQLMEKVMKEKQSLECGWMQPSFKSVDGKSGIKVVKLSSVKFGLRFDTGQPDCVYTTDLV 92 (176)
T ss_pred HHHHHHHHhCChhhhhHHHHHHHHHHHHhchhhhhhhhcccceeecccCCceeEEecccceeEeeecCCCCCeEEeecee
Confidence 455544433 34446663 57789999999977665433221 1223222222332233468889988777889999999
Q ss_pred eecCCCCeEEEEEEc
Q 018680 106 TDVENNPLQIVVVDT 120 (352)
Q Consensus 106 ~a~~g~~I~V~l~D~ 120 (352)
.-.+|.++-+.+..-
T Consensus 93 t~~~g~~l~aG~m~~ 107 (176)
T COG4766 93 TEQEGSRLGAGLMEM 107 (176)
T ss_pred ecccCCccccceeee
Confidence 999999999988764
No 45
>PF09816 EAF: RNA polymerase II transcription elongation factor; InterPro: IPR019194 This entry represents the N-terminal domain of ELL-associated factor (Eaf) proteins, which act as transcriptional transactivators of ELL and ELL2 RNA Polymerase II (Pol II) transcriptional elongation factors [, , , ]. Eaf proteins form a stable heterodimer complex with ELL proteins to facilitate the binding of RNA polymerase II to activate transcription elongation. ELL and EAF1 are components of Cajal bodies, which have a role in leukemogenesis []. EAF1 also has the capacity to interact with ELL1 and ELL2. The N terminus of approx 120 of EAF1 has a region of high serine, aspartic acid, and glutamic acid residues [, ].
Probab=30.15 E-value=1.5e+02 Score=24.83 Aligned_cols=67 Identities=15% Similarity=0.188 Sum_probs=42.0
Q ss_pred CccccCCccccccC-CCCceEEEEcc-CCC----CCcccCCceeecCCCCeEEEEEEcCCCCeeecCCCCCcceEE
Q 018680 69 RSLTRSSSLRIQAL-EPSSLKLIFSQ-KLS----LPIFTGSKITDVENNPLQIVVVDTRSNGLIAPASLPQPIKIE 138 (352)
Q Consensus 69 ~~~~rs~~~~~~~~-~~~~~~L~F~n-~l~----~pifT~~~I~a~~g~~I~V~l~D~~t~n~iv~~g~~ss~kvE 138 (352)
.++..+.+..+... ....++|.|-+ .-. .-+|.|..=. .+.-=.|-|||..++ ..+-..+.+.+++-
T Consensus 31 ~S~d~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~f~G~~~~--~~~~ecVLifD~~~~-~f~LErl~s~~~~n 103 (109)
T PF09816_consen 31 ASVDTSKPGTLYVGSSNDEYTLTLPNPNGSGNNETYVFKGSQRP--SKEKECVLIFDPETG-EFVLERLSSTINLN 103 (109)
T ss_pred CCCCCCCCeEEEecCCCCeEEEEEeCCCCCCCcccEEEEeccCC--CCCcEEEEEEECCCC-EEEEEEcceEEEEE
Confidence 44555544555443 45679999933 221 2589998322 233456888999898 88877777666554
No 46
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=29.47 E-value=1.1e+02 Score=29.84 Aligned_cols=17 Identities=18% Similarity=0.327 Sum_probs=12.8
Q ss_pred hhhHHHHHHHHHHHHHH
Q 018680 45 ALEPLLRRVVNEEVQRG 61 (352)
Q Consensus 45 ~lEp~lrrvV~EEve~~ 61 (352)
-||-++|+|+.|++-..
T Consensus 89 ~i~~lv~~v~~e~~~~~ 105 (233)
T PRK15457 89 LVAQLMEKVMKEKQSLE 105 (233)
T ss_pred HHHHHHHHHHHHHhccc
Confidence 36779999999887543
No 47
>PRK07758 hypothetical protein; Provisional
Probab=27.85 E-value=93 Score=26.45 Aligned_cols=37 Identities=24% Similarity=0.342 Sum_probs=25.0
Q ss_pred hhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHH
Q 018680 266 KKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTM 307 (352)
Q Consensus 266 k~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v 307 (352)
..|..+||+||+|+.+ ++++.|-++= |+..|.-+.+.
T Consensus 48 N~Lk~AGI~TL~dLv~---~te~ELl~ik--nlGkKSL~EIk 84 (95)
T PRK07758 48 RALEHHGIHTVEELSK---YSEKEILKLH--GMGPASLPKLR 84 (95)
T ss_pred HHHHHcCCCcHHHHHc---CCHHHHHHcc--CCCHHHHHHHH
Confidence 5688999999999866 4556666653 34455555544
No 48
>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=27.09 E-value=38 Score=23.84 Aligned_cols=18 Identities=39% Similarity=0.745 Sum_probs=14.9
Q ss_pred eeecCCeEEecCCccccC
Q 018680 186 VAPIGDIEFTDNSSWIRS 203 (352)
Q Consensus 186 va~l~di~FtDnSs~~rS 203 (352)
-..+..+.|-|++.|.+.
T Consensus 24 ~~~Ie~i~FaDGt~w~~~ 41 (43)
T PF06594_consen 24 SYRIEQIEFADGTVWTRA 41 (43)
T ss_pred CCcEeEEEEcCCCEecHH
Confidence 566889999999999753
No 49
>PRK05256 condesin subunit E; Provisional
Probab=25.01 E-value=97 Score=30.24 Aligned_cols=50 Identities=18% Similarity=0.227 Sum_probs=39.6
Q ss_pred hhhhhcCCccHHHHHHhhc--cChHHHHHHhC--CCCChhhHHHHHHhhccccC
Q 018680 266 KKLSAAGIKTVQDFLKLSI--VEPQRLRKILG--PGMSEKMWEVTMQHARKCVM 315 (352)
Q Consensus 266 k~L~~~~I~tV~dFLkl~~--~d~~kLr~iLg--~~ms~k~We~~v~HAktCvl 315 (352)
++|++.||+|+++.+.-+. .|+++|.+.++ ..-|+-+-+++-+-.++|--
T Consensus 107 erLa~~gift~qeL~deL~~ladE~kllklvn~R~~GsDlD~~Kl~ekvr~sLr 160 (238)
T PRK05256 107 ERLAHEGIFTQQELYDELLTLADEAKLLKLVNNRSTGSDLDKQKLQEKVRTSLN 160 (238)
T ss_pred HHHhcCCceeHHHHHHHHHHhhcHHHHHHHhcCCCCcchhhHHHHHHHHHHHHH
Confidence 7899999999999887654 58999999884 22367777788888888853
No 50
>KOG1104 consensus Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]
Probab=23.42 E-value=89 Score=35.07 Aligned_cols=41 Identities=22% Similarity=0.233 Sum_probs=21.9
Q ss_pred cHHHHHHhhccChHHHHHH-hC---CCCChhhHHHHHHhhccccC
Q 018680 275 TVQDFLKLSIVEPQRLRKI-LG---PGMSEKMWEVTMQHARKCVM 315 (352)
Q Consensus 275 tV~dFLkl~~~d~~kLr~i-Lg---~~ms~k~We~~v~HAktCvl 315 (352)
.-+|||.++-..-++||+- +. +--.-+..+.+.-||..=.+
T Consensus 224 ~qeeyle~L~~qI~~lr~n~w~e~hIprPy~~Fes~L~~~~~h~L 268 (759)
T KOG1104|consen 224 PQEEYLELLWAQIQKLRQNDWAENHIPRPYLGFESTLVHALQHNL 268 (759)
T ss_pred hHHHHHHHHHHHHHHHHhcCcccccCCCchhhHHHHHHHhcccCC
Confidence 3467777766555566541 00 01233456777777765444
No 51
>PF00853 Runt: Runt domain; InterPro: IPR013524 The AML1 gene is rearranged by the t(8;21) translocation in acute myeloid leukemia []. The gene is highly similar to the Drosophila melanogaster segmentation gene runt and to the mouse transcription factor PEBP2 alpha subunit gene []. The region of shared similarity, known as the Runt domain, is responsible for DNA-binding and protein-protein interaction. In addition to the highly-conserved Runt domain, the AML-1 gene product carries a putative ATP-binding site (GRSGRGKS), and has a C-terminal region rich in proline and serine residues. The protein (known as acute myeloid leukemia 1 protein, oncogene AML-1, core-binding factor (CBF), alpha-B subunit, etc.) binds to the core site, 5'-pygpyggt-3', of a number of enhancers and promoters. The protein is a heterodimer of alpha- and beta-subunits. The alpha-subunit binds DNA as a monomer, and appears to have a role in the development of normal hematopoiesis. CBF is a nuclear protein expressed in numerous tissue types, except brain and heart; highest levels have been found to occur in thymus, bone marrow and peripheral blood. This domain occurs towards the N terminus of the proteins in this entry.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1E50_E 1LJM_A 1CO1_A 1H9D_C 1CMO_A 1EAO_B 1HJC_D 1HJB_F 2J6W_B 1EAN_A ....
Probab=23.26 E-value=1.8e+02 Score=26.17 Aligned_cols=34 Identities=24% Similarity=0.438 Sum_probs=25.7
Q ss_pred EEEecCceeecCCeEEecCCccccCCceEEEEEeec
Q 018680 179 NVTARDGVAPIGDIEFTDNSSWIRSRKFRIGAKVAR 214 (352)
Q Consensus 179 ~v~L~~Gva~l~di~FtDnSs~~rSrkFRLgaRv~~ 214 (352)
.-.|+|++|-..|+.|..-|. |.+.|-|-.-+..
T Consensus 74 tavmknqvA~FnDLRFvGRSG--RGKsFtltItv~t 107 (135)
T PF00853_consen 74 TAVMKNQVARFNDLRFVGRSG--RGKSFTLTITVFT 107 (135)
T ss_dssp EEEEETTEEEESS-EECST-T--TTSEEEEEEEE-S
T ss_pred hhhhhcccccccccccccccC--CccceEEEEEEeC
Confidence 578999999999999998776 3556999887764
No 52
>PTZ00205 DNA polymerase kappa; Provisional
Probab=22.98 E-value=72 Score=34.75 Aligned_cols=53 Identities=23% Similarity=0.369 Sum_probs=36.9
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHhh-----ccChHHHHHHhCCCCChhhHHH
Q 018680 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLS-----IVEPQRLRKILGPGMSEKMWEV 305 (352)
Q Consensus 251 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~-----~~d~~kLr~iLg~~ms~k~We~ 305 (352)
.|-+|-+||+... ++|...||+|++|+.+.- ...+..|+.+||..+--..|..
T Consensus 310 pV~ki~GIG~~t~--~~L~~~GI~TigDLa~~~~~l~~~f~~k~l~~llG~~~G~~l~~~ 367 (571)
T PTZ00205 310 GLRSVPGVGKVTE--ALLKGLGITTLSDIYNRRVELCYILHNNLFRFLLGASIGIMQWPD 367 (571)
T ss_pred CcceeCCcCHHHH--HHHHHcCCCcHHHHhcCCHHHHHHhHHHHHHHHhCchhhHHHHHH
Confidence 5778889988865 899999999999997642 1223457788874333344544
No 53
>PRK14973 DNA topoisomerase I; Provisional
Probab=22.93 E-value=68 Score=36.77 Aligned_cols=54 Identities=24% Similarity=0.372 Sum_probs=44.0
Q ss_pred eeeeeeecccchhhhhhhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhhcc
Q 018680 252 VWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARK 312 (352)
Q Consensus 252 VwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HAkt 312 (352)
.=.++++|-+.. .+|..+||.||+|+++. |+.+|-..- |++.|.-..+..+|+.
T Consensus 879 l~~vkg~ge~t~--~~l~~ag~~~~e~l~~~---d~~~la~~~--~i~~k~~~~~~~~~~~ 932 (936)
T PRK14973 879 LLSVPGLGETTL--EKLYLAGVYDGDLLVSA---DPKKLAKVT--GIDEKKLRNLQAYAKK 932 (936)
T ss_pred hhhccCCCHHHH--HHHHHcCCCCHHHhccC---CHHHHhhhc--CCCHHHHHHHHHHHhh
Confidence 335567777777 88999999999999987 888998876 6788888888887763
No 54
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=22.01 E-value=1.1e+02 Score=23.64 Aligned_cols=26 Identities=19% Similarity=0.399 Sum_probs=20.1
Q ss_pred HHHHHHHHhh--hHHHHHHhhhHHHHHH
Q 018680 28 SVIGEAVMVN--SFQNFFSALEPLLRRV 53 (352)
Q Consensus 28 ~vi~e~~~~~--s~q~~~~~lEp~lrrv 53 (352)
+||..|...+ .|+.++...||+|++.
T Consensus 2 ~vI~~A~~GD~~A~~~IL~~y~~yI~kl 29 (65)
T PF12645_consen 2 EVIKAAKQGDPEAMEEILKHYEPYISKL 29 (65)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence 4666666654 4889999999999973
No 55
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=21.06 E-value=61 Score=31.85 Aligned_cols=42 Identities=21% Similarity=0.342 Sum_probs=35.3
Q ss_pred hhhcCCccHHHHHHhhccChHHHHHHhCCCCChhhHHHHHHhh
Q 018680 268 LSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHA 310 (352)
Q Consensus 268 L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~We~~v~HA 310 (352)
-+.++|.|+.|--.+...+|+.||++++ -+.+|.|=.=|.--
T Consensus 25 ae~hkiiTirdvae~~ev~~n~lr~las-rLekkG~LeRi~rG 66 (269)
T COG5340 25 AEGHKIITIRDVAETLEVAPNTLRELAS-RLEKKGWLERILRG 66 (269)
T ss_pred HHhCceEEeHHhhhhccCCHHHHHHHHh-hhhhcchhhhhcCc
Confidence 3457999999999999999999999997 68899997655443
Done!