Query 016573
Match_columns 387
No_of_seqs 127 out of 146
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 08:04:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016573.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016573hhsearch_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 1E-121 3E-126 890.0 29.4 287 93-382 1-287 (299)
2 TIGR02239 recomb_RAD51 DNA rep 89.2 0.49 1.1E-05 47.3 4.5 48 270-322 13-60 (316)
3 TIGR02238 recomb_DMC1 meiotic 87.2 0.69 1.5E-05 46.3 4.1 49 269-322 12-60 (313)
4 PLN03186 DNA repair protein RA 87.2 0.69 1.5E-05 47.0 4.1 61 258-323 28-88 (342)
5 PRK04301 radA DNA repair and r 83.8 0.84 1.8E-05 45.0 2.8 57 257-320 7-63 (317)
6 PLN03187 meiotic recombination 81.7 1.3 2.9E-05 45.0 3.4 60 257-321 30-89 (344)
7 PF14520 HHH_5: Helix-hairpin- 81.5 0.58 1.3E-05 35.5 0.6 50 261-317 10-59 (60)
8 PTZ00035 Rad51 protein; Provis 75.6 3.3 7.1E-05 41.9 4.0 60 257-321 22-81 (337)
9 PF14229 DUF4332: Domain of un 73.8 3.7 8E-05 35.8 3.4 50 270-321 7-58 (122)
10 PRK03609 umuC DNA polymerase V 72.4 3.2 6.9E-05 42.6 3.1 51 257-317 180-230 (422)
11 TIGR02236 recomb_radA DNA repa 71.4 3.2 6.9E-05 40.5 2.7 50 261-317 4-53 (310)
12 PRK02406 DNA polymerase IV; Va 69.1 4.6 0.0001 40.1 3.3 52 257-318 169-220 (343)
13 PRK01172 ski2-like helicase; P 60.5 9.5 0.00021 41.5 4.0 51 261-318 617-667 (674)
14 PRK03352 DNA polymerase IV; Va 60.4 4 8.6E-05 40.6 1.0 41 257-302 178-218 (346)
15 PF10691 DUF2497: Protein of u 60.2 22 0.00047 29.0 5.0 39 32-71 34-73 (73)
16 PRK03858 DNA polymerase IV; Va 58.1 5.2 0.00011 40.5 1.4 48 257-309 174-221 (396)
17 PRK03348 DNA polymerase IV; Pr 56.7 6.3 0.00014 41.3 1.8 48 257-309 181-228 (454)
18 PRK14133 DNA polymerase IV; Pr 56.0 12 0.00026 37.3 3.5 51 257-317 174-224 (347)
19 cd01700 PolY_Pol_V_umuC umuC s 54.5 10 0.00022 37.6 2.8 51 257-317 177-227 (344)
20 PRK02794 DNA polymerase IV; Pr 54.5 11 0.00023 38.8 3.0 55 257-321 210-264 (419)
21 PF04994 TfoX_C: TfoX C-termin 52.4 6.8 0.00015 32.1 1.0 30 258-289 5-34 (81)
22 cd03586 PolY_Pol_IV_kappa DNA 51.1 15 0.00032 36.0 3.2 52 257-318 172-223 (334)
23 PRK03103 DNA polymerase IV; Re 47.5 16 0.00035 37.2 3.0 52 257-318 182-233 (409)
24 PRK01810 DNA polymerase IV; Va 47.4 16 0.00036 37.1 3.0 51 257-317 180-230 (407)
25 COG3743 Uncharacterized conser 45.8 27 0.00059 31.7 3.8 59 256-318 67-126 (133)
26 PF02889 Sec63: Sec63 Brl doma 45.6 18 0.0004 34.9 2.9 54 257-317 149-202 (314)
27 cd00424 PolY Y-family of DNA p 43.7 20 0.00044 35.6 2.9 55 257-321 174-229 (343)
28 cd01701 PolY_Rev1 DNA polymera 41.0 13 0.00029 38.1 1.2 54 257-317 223-276 (404)
29 PRK01216 DNA polymerase IV; Va 40.7 13 0.00028 37.8 1.1 51 257-316 179-229 (351)
30 PF03118 RNA_pol_A_CTD: Bacter 40.0 14 0.0003 29.1 0.9 36 271-311 24-59 (66)
31 COG1200 RecG RecG-like helicas 39.3 13 0.00029 41.4 0.9 41 257-299 11-51 (677)
32 cd01702 PolY_Pol_eta DNA Polym 38.2 17 0.00036 37.1 1.4 55 257-318 183-238 (359)
33 PF14229 DUF4332: Domain of un 37.0 23 0.00049 30.9 1.9 39 258-301 55-93 (122)
34 cd01703 PolY_Pol_iota DNA Poly 35.9 19 0.00042 37.0 1.4 57 258-320 174-242 (379)
35 KOG1520 Predicted alkaloid syn 34.0 1.7E+02 0.0037 30.8 7.9 47 169-221 151-197 (376)
36 KOG4233 DNA-bridging protein B 33.8 49 0.0011 28.0 3.2 60 252-319 15-78 (90)
37 TIGR02979 phageshock_pspD phag 33.2 48 0.001 26.3 2.9 25 34-62 29-53 (59)
38 PF06594 HCBP_related: Haemoly 31.0 30 0.00065 24.7 1.4 18 192-209 24-41 (43)
39 PF09584 Phageshock_PspD: Phag 29.5 57 0.0012 26.5 2.8 14 49-62 45-58 (66)
40 PRK10917 ATP-dependent DNA hel 29.2 25 0.00053 38.8 1.0 38 252-291 5-42 (681)
41 PRK15457 ethanolamine utilizat 28.9 83 0.0018 31.1 4.4 74 52-126 89-163 (233)
42 TIGR01954 nusA_Cterm_rpt trans 28.8 78 0.0017 22.4 3.3 42 271-317 6-47 (50)
43 PRK05256 condesin subunit E; P 27.6 93 0.002 30.8 4.4 74 272-345 107-186 (238)
44 cd03468 PolY_like DNA Polymera 27.5 35 0.00077 33.3 1.7 35 263-302 177-211 (335)
45 PRK10497 peripheral inner memb 26.4 73 0.0016 26.3 3.0 14 49-62 52-65 (73)
46 PRK07758 hypothetical protein; 25.5 1E+02 0.0023 26.5 3.9 37 272-313 48-84 (95)
47 cd07978 TAF13 The TATA Binding 25.5 1.2E+02 0.0025 25.6 4.2 35 276-318 52-89 (92)
48 PF11754 Velvet: Velvet factor 24.2 1.5E+02 0.0032 28.0 5.1 62 177-241 97-172 (203)
49 PF04270 Strep_his_triad: Stre 23.7 56 0.0012 25.3 1.8 21 355-375 32-52 (53)
50 COG5340 Predicted transcriptio 22.5 60 0.0013 32.4 2.1 41 273-314 24-64 (269)
51 COG4766 EutQ Ethanolamine util 21.7 3E+02 0.0066 26.0 6.4 92 35-128 12-108 (176)
52 PF00853 Runt: Runt domain; I 20.8 1.7E+02 0.0037 26.7 4.4 35 185-221 74-108 (135)
53 COG3827 Uncharacterized protei 20.6 1.9E+02 0.0041 28.6 5.0 39 32-71 189-228 (231)
54 smart00611 SEC63 Domain of unk 20.4 1.3E+02 0.0029 29.1 4.1 52 258-316 153-204 (312)
55 PRK14973 DNA topoisomerase I; 20.3 80 0.0017 36.7 2.9 54 258-318 879-932 (936)
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=1.5e-121 Score=890.05 Aligned_cols=287 Identities=64% Similarity=1.067 Sum_probs=282.7
Q ss_pred ceEEEecCCCCCCcccCCccccCCCCceEEEEEeCCCCCeeccCCCCcceEEEEEeeCCCCCCCCCCCCHHHHhcccccc
Q 016573 93 NLQLHYKTRMPPHLFTGGKVEGDQGAAIHVVLIDMNTGDVVQTGPESSAKLNVVVLEGDFNEEEDDNWTKEHFESHEVKE 172 (387)
Q Consensus 93 ~~~L~F~n~l~~pifT~~kI~a~~g~~I~V~L~D~~t~~~V~~Gplss~kveIvVLdGDF~~~~~e~WT~eEF~~~IV~~ 172 (387)
+|||+|+|+|++|||||++|+|+||+||+|+|+|++|+ |++||+||+|||||||||||+++++++||+|||++|||++
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 CCCCccccccceEEEeccceeecCCceeecCCccccccceeEEEEecCCCCCCcceeeeeecCeEeeecCCCccccCCCC
Q 016573 173 REGKRPILTGDLLVTLKEGFGTLGDLTFTDNSSWIRSRKFRLGLKVSPGYCDGIRVREAKTEGFAVKDHRGELYKKHYPP 252 (387)
Q Consensus 173 R~Gk~pLL~Gdl~v~L~~Gva~l~di~FtDnSs~~rsrKFRLgarv~~~~~~g~RI~EAvse~FvVkd~Rge~~kKh~pP 252 (387)
|+||+|||+|+++|+|+||+|+|+||+|||||||+|||||||||||+++++.|+|||||+||||+|||||||+|||||||
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 CCCCcceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhccccCCCeeEEEEecC
Q 016573 253 ALHDEVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVLGGKLYVYYADG 332 (387)
Q Consensus 253 ~L~DeVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAktCvl~~k~~~y~~~~ 332 (387)
+|+|||||||+|||||+|||+|+.+||+||+|||+++++||++||+|||+|||++||++||+|||||++++++|+|| .+
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 CCcEEEEEcccceeeeeeeCCeEeecCCCChhhhhhhhhhHHHhHhhccc
Q 016573 333 TQNTGVVFNNIYELRGLIDDGQFVSLESLTHSQKTLPDSGLHEHVFAFRY 382 (387)
Q Consensus 333 ~~nv~l~FN~i~~lvG~~~~g~y~~~~~L~~~qk~~V~~L~~qa~~~~~~ 382 (387)
++|++|+|||||+||||+|+|+|+|.|+||+.||++|++|+++||..|+.
T Consensus 238 ~~nv~l~FN~i~~lvga~~~g~y~s~d~L~~~qK~~v~~Lv~~AY~n~~~ 287 (299)
T PF07887_consen 238 EQNVGLFFNCIYELVGAIFGGQYVSLDNLSSAQKAYVDKLVKQAYENWDN 287 (299)
T ss_pred CCceEEEEcchhhEEeEEECCEEEehHHcCHHHHHHHHHHHHHHHHhhhh
Confidence 68999999999999999999999999999999999999999999999974
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=89.21 E-value=0.49 Score=47.27 Aligned_cols=48 Identities=27% Similarity=0.213 Sum_probs=42.7
Q ss_pred hhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhccccCC
Q 016573 270 LHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVLG 322 (387)
Q Consensus 270 ~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAktCvl~ 322 (387)
--++|+++||.||+||+. .+|..|.+++ |+|...++.+..||.+|...
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 89999999999999988653
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=87.22 E-value=0.69 Score=46.27 Aligned_cols=49 Identities=29% Similarity=0.249 Sum_probs=42.8
Q ss_pred hhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhccccCC
Q 016573 269 ALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVLG 322 (387)
Q Consensus 269 ~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAktCvl~ 322 (387)
..-++|+++||.||+||+. .++..|.++. |+|...++.+++.|+.+...
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 4899999997 89999999999999988654
No 4
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=87.18 E-value=0.69 Score=47.01 Aligned_cols=61 Identities=30% Similarity=0.230 Sum_probs=47.5
Q ss_pred ceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhccccCCC
Q 016573 258 VWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVLGG 323 (387)
Q Consensus 258 VwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAktCvl~~ 323 (387)
+-.|..-|-.-.--++|.++||.||+||+.+ ++..|.++. |+|....+.+++||.+|....
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 4444443333334599999999999998764 789999998 899999999999998886543
No 5
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=83.77 E-value=0.84 Score=45.01 Aligned_cols=57 Identities=21% Similarity=0.278 Sum_probs=45.1
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhcccc
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCV 320 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAktCv 320 (387)
++-.|..||+. ..++|.++||+|++|++. .|++.|.+++ |++.+.++.+.+-|+.+.
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 34455566654 459999999999999965 5999999998 788889998888887644
No 6
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=81.74 E-value=1.3 Score=45.04 Aligned_cols=60 Identities=22% Similarity=0.221 Sum_probs=47.0
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhccccC
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVL 321 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAktCvl 321 (387)
++..|+.-|-.-.--++|.++||+||+|++. .++..|-++. |+|....+.+++.|+..+.
T Consensus 30 ~~~~l~~~g~~~~~~~kL~~~g~~tv~~~~~---~~~~~L~~~~--g~s~~~~~ki~~~a~~~~~ 89 (344)
T PLN03187 30 SIDKLISQGINAGDVKKLQDAGIYTCNGLMM---HTKKNLTGIK--GLSEAKVDKICEAAEKLLN 89 (344)
T ss_pred CHHHHhhCCCCHHHHHHHHHcCCCcHHHHHh---CCHHHHHHhc--CCCHHHHHHHHHHHHHhhc
Confidence 3556655333344559999999999999876 4788899986 8999999999999887653
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=81.55 E-value=0.58 Score=35.45 Aligned_cols=50 Identities=34% Similarity=0.528 Sum_probs=40.2
Q ss_pred eeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhc
Q 016573 261 LDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 317 (387)
Q Consensus 261 LekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAk 317 (387)
+.+||+.-+ ++|.++||.|++|+.. -+++.|.++= |++.+.=+.+++.|+
T Consensus 10 I~Gig~~~a--~~L~~~G~~t~~~l~~---a~~~~L~~i~--Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 10 IPGIGPKRA--EKLYEAGIKTLEDLAN---ADPEELAEIP--GIGEKTAEKIIEAAR 59 (60)
T ss_dssp STTCHHHHH--HHHHHTTCSSHHHHHT---SHHHHHHTST--TSSHHHHHHHHHHHH
T ss_pred CCCCCHHHH--HHHHhcCCCcHHHHHc---CCHHHHhcCC--CCCHHHHHHHHHHHh
Confidence 455666544 8999999999999866 4888899885 789999999998886
No 8
>PTZ00035 Rad51 protein; Provisional
Probab=75.62 E-value=3.3 Score=41.89 Aligned_cols=60 Identities=33% Similarity=0.297 Sum_probs=46.1
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhccccC
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVL 321 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAktCvl 321 (387)
++-.|+.-|-.-.--++|.++||+||+||+. .++..|.++. |+|...=+.+++.|+.++.
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 4555654233334459999999999999876 4888999997 8999988999998887664
No 9
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=73.83 E-value=3.7 Score=35.78 Aligned_cols=50 Identities=28% Similarity=0.209 Sum_probs=37.1
Q ss_pred hhhhhhhCCCccHHHHHHHHhcChHH--HHHHHcCCCChhhHHHHHHhhccccC
Q 016573 270 LHKKLMKADIVTVEDFLRILVRDPQK--LRNILGSGMSNRMWENTVEHAKTCVL 321 (387)
Q Consensus 270 ~hkrL~~~gI~tV~dFL~l~~~d~~k--LR~iLg~gms~k~We~~v~HAktCvl 321 (387)
.-.+|...||+|++|||..-.....+ |-+-+ |++.+-=...+.+|.=|..
T Consensus 7 ~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~--~i~~~~l~~w~~~AdL~ri 58 (122)
T PF14229_consen 7 EAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKL--GISERNLLKWVNQADLMRI 58 (122)
T ss_pred HHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhc--CCCHHHHHHHHhHHHhhhc
Confidence 44899999999999999987665544 55554 6888777777777765543
No 10
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=72.43 E-value=3.2 Score=42.64 Aligned_cols=51 Identities=22% Similarity=0.233 Sum_probs=40.2
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhc
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 317 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAk 317 (387)
+|..|-+||+. ..++|...||+|++|+.++ ++..|++.||. .+..+..||.
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 45555577774 4499999999999999885 88999999963 5777777775
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=71.39 E-value=3.2 Score=40.53 Aligned_cols=50 Identities=24% Similarity=0.317 Sum_probs=38.0
Q ss_pred eeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhc
Q 016573 261 LDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 317 (387)
Q Consensus 261 LekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAk 317 (387)
|.+||+. .-++|.++||.|++|++. .|++.|.+++ |++.+..+.+.+-|.
T Consensus 4 i~gig~~--~~~~L~~~Gi~ti~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 4 LPGVGPA--TAEKLREAGYDTFEAIAV---ASPKELSEIA--GISEGTAAKIIQAAR 53 (310)
T ss_pred cCCCCHH--HHHHHHHcCCCCHHHHHc---CCHHHHHhcc--CCCHHHHHHHHHHHH
Confidence 4455543 448999999999999877 4889999998 567777666666665
No 12
>PRK02406 DNA polymerase IV; Validated
Probab=69.09 E-value=4.6 Score=40.06 Aligned_cols=52 Identities=23% Similarity=0.247 Sum_probs=39.5
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhcc
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAkt 318 (387)
+|..|-+||+. .-++|...||+|++|+.++ ++..|++.||. .+..+.+||.-
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 46666667764 3488999999999999885 78899999974 45666667653
No 13
>PRK01172 ski2-like helicase; Provisional
Probab=60.53 E-value=9.5 Score=41.48 Aligned_cols=51 Identities=24% Similarity=0.509 Sum_probs=41.6
Q ss_pred eeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhcc
Q 016573 261 LDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (387)
Q Consensus 261 LekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAkt 318 (387)
|.++++ ...++|.++||.||.|+.. .|+++|-+|+ |++++.=+.++++|+.
T Consensus 617 ip~~~~--~~a~~l~~~g~~~~~di~~---~~~~~~~~i~--~~~~~~~~~i~~~~~~ 667 (674)
T PRK01172 617 IPKVGR--VRARRLYDAGFKTVDDIAR---SSPERIKKIY--GFSDTLANAIVNRAMK 667 (674)
T ss_pred CCCCCH--HHHHHHHHcCCCCHHHHHh---CCHHHHHHHh--ccCHHHHHHHHHHHHH
Confidence 344444 4669999999999999877 7888898898 6889999999999875
No 14
>PRK03352 DNA polymerase IV; Validated
Probab=60.41 E-value=4 Score=40.58 Aligned_cols=41 Identities=27% Similarity=0.324 Sum_probs=33.2
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcC
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGS 302 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~ 302 (387)
+|..|-+||+.. .++|...||+|++|++++ ++..|.+.||.
T Consensus 178 pl~~l~gig~~~--~~~L~~~Gi~ti~dl~~l---~~~~L~~~fG~ 218 (346)
T PRK03352 178 PTDALWGVGPKT--AKRLAALGITTVADLAAA---DPAELAATFGP 218 (346)
T ss_pred CHHHcCCCCHHH--HHHHHHcCCccHHHHhcC---CHHHHHHHhCh
Confidence 466666777744 488999999999999885 78889999975
No 15
>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=60.17 E-value=22 Score=29.03 Aligned_cols=39 Identities=33% Similarity=0.496 Sum_probs=29.9
Q ss_pred chHHHHHHHHHHhHHHH-HHHhhhhHHHHHhHHHHHHHHHh
Q 016573 32 ALASVIVEALKMDSLQR-LCSSLEPLLRRIVSEEVERALTK 71 (387)
Q Consensus 32 ~~~svi~e~~~~~~~q~-~~~~lEp~lrrvV~EEve~~l~~ 71 (387)
++-.+++|+|+-- |+. |=..|=.|+.|+|++||+|..+|
T Consensus 34 TlE~lvremLRPm-LkeWLD~nLP~lVErlVr~EIeRi~rr 73 (73)
T PF10691_consen 34 TLEDLVREMLRPM-LKEWLDENLPGLVERLVREEIERIARR 73 (73)
T ss_pred cHHHHHHHHHHHH-HHHHHHhccHHHHHHHHHHHHHHHhcC
Confidence 5778888888764 333 55578889999999999997654
No 16
>PRK03858 DNA polymerase IV; Validated
Probab=58.13 E-value=5.2 Score=40.47 Aligned_cols=48 Identities=27% Similarity=0.269 Sum_probs=35.3
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhH
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMW 309 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~W 309 (387)
+|..|-+||+.-. ++|.+.||+|++|+.+ .++..|++.||..+-...|
T Consensus 174 pl~~l~Gig~~~~--~~L~~~Gi~t~~dl~~---l~~~~L~~~fG~~~~~~l~ 221 (396)
T PRK03858 174 PVRRLWGVGPVTA--AKLRAHGITTVGDVAE---LPESALVSLLGPAAGRHLH 221 (396)
T ss_pred ChhhcCCCCHHHH--HHHHHhCCCcHHHHhc---CCHHHHHHHhCcHHHHHHH
Confidence 3555557777544 8999999999999986 5888999999753333333
No 17
>PRK03348 DNA polymerase IV; Provisional
Probab=56.72 E-value=6.3 Score=41.30 Aligned_cols=48 Identities=25% Similarity=0.341 Sum_probs=37.1
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhH
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMW 309 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~W 309 (387)
.|..|-+||+... ++|...||+|++||.++ ++..|++.||..+-..-|
T Consensus 181 Pv~~L~GIG~~t~--~~L~~lGI~TigDLa~l---~~~~L~~~fG~~~g~~L~ 228 (454)
T PRK03348 181 PVRRLWGIGPVTE--EKLHRLGIETIGDLAAL---SEAEVANLLGATVGPALH 228 (454)
T ss_pred CccccCCCCHHHH--HHHHHcCCccHHHHhcC---CHHHHHHHHCHHHHHHHH
Confidence 5778888887644 88999999999999874 788999999743333333
No 18
>PRK14133 DNA polymerase IV; Provisional
Probab=56.01 E-value=12 Score=37.29 Aligned_cols=51 Identities=24% Similarity=0.367 Sum_probs=39.0
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhc
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 317 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAk 317 (387)
+|..|-+||+... ++|...||+|++|++++ +...|+..||. .|..+.++|.
T Consensus 174 pv~~l~gig~~~~--~~L~~~Gi~ti~dl~~l---~~~~L~~rfG~-----~g~~l~~~a~ 224 (347)
T PRK14133 174 PISKVHGIGKKSV--EKLNNIGIYTIEDLLKL---SREFLIEYFGK-----FGVEIYERIR 224 (347)
T ss_pred CccccCCCCHHHH--HHHHHcCCccHHHHhhC---CHHHHHHHHhH-----HHHHHHHHhC
Confidence 4566666766544 78999999999999874 78889999963 4677777774
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=54.50 E-value=10 Score=37.63 Aligned_cols=51 Identities=31% Similarity=0.326 Sum_probs=38.8
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhc
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 317 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAk 317 (387)
+|..|-+||+... ++|...||+|++|+.++ +.+.|.+.||. .|....++|+
T Consensus 177 pl~~l~gig~~~~--~~L~~~Gi~ti~dL~~~---~~~~L~~rfG~-----~~~~l~~~a~ 227 (344)
T cd01700 177 PVGDVWGIGRRTA--KKLNAMGIHTAGDLAQA---DPDLLRKKFGV-----VGERLVRELN 227 (344)
T ss_pred ChhhcCccCHHHH--HHHHHcCCCcHHHHhcC---CHHHHHHHHHH-----HHHHHHHHhC
Confidence 3555556777444 78999999999999885 78889999974 4666667765
No 20
>PRK02794 DNA polymerase IV; Provisional
Probab=54.49 E-value=11 Score=38.83 Aligned_cols=55 Identities=24% Similarity=0.149 Sum_probs=41.7
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhccccC
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVL 321 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAktCvl 321 (387)
+|..|-+||+ ..-++|...||+|++|+.++ +...|++.||. +|..+..+|.--+.
T Consensus 210 Pl~~L~GiG~--~~~~~L~~~GI~tigdL~~l---~~~~L~~rfG~-----~g~~l~~~a~G~d~ 264 (419)
T PRK02794 210 PVGIIWGVGP--ATAARLARDGIRTIGDLQRA---DEADLMRRFGS-----MGLRLWRLARGIDD 264 (419)
T ss_pred ChhhhCCCCH--HHHHHHHHhccchHHHHhhC---CHHHHHHHHhH-----HHHHHHHHhCCCCC
Confidence 3455556665 44589999999999998874 88899999964 57888888875543
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=52.44 E-value=6.8 Score=32.07 Aligned_cols=30 Identities=30% Similarity=0.303 Sum_probs=18.8
Q ss_pred ceeeeeecccchhhhhhhhCCCccHHHHHHHH
Q 016573 258 VWRLDRIAKDGALHKKLMKADIVTVEDFLRIL 289 (387)
Q Consensus 258 VwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~ 289 (387)
+..|-+||.. .-+.|.+.||+||+||..+=
T Consensus 5 l~~LpNig~~--~e~~L~~vGI~t~~~L~~~G 34 (81)
T PF04994_consen 5 LKDLPNIGPK--SERMLAKVGIHTVEDLRELG 34 (81)
T ss_dssp GCGSTT--HH--HHHHHHHTT--SHHHHHHHH
T ss_pred hhhCCCCCHH--HHHHHHHcCCCCHHHHHHhC
Confidence 4445566654 33899999999999998753
No 22
>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=51.13 E-value=15 Score=35.97 Aligned_cols=52 Identities=23% Similarity=0.353 Sum_probs=39.7
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhcc
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAkt 318 (387)
+|..|-.||+. .-.+|...||+|++|+.++ ++..|++.+| ..|....+||+-
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 35555566654 4489999999999999874 7888999885 468888888863
No 23
>PRK03103 DNA polymerase IV; Reviewed
Probab=47.53 E-value=16 Score=37.21 Aligned_cols=52 Identities=19% Similarity=0.194 Sum_probs=38.6
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhcc
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAkt 318 (387)
.|..|-+||+. .-++|...||+|++|+.+ .++..|++.||. .+..+.++|.-
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 45566677774 448899999999999876 478889999963 35666666653
No 24
>PRK01810 DNA polymerase IV; Validated
Probab=47.36 E-value=16 Score=37.14 Aligned_cols=51 Identities=27% Similarity=0.281 Sum_probs=37.9
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhc
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 317 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAk 317 (387)
+|..|-+||+.-. ++|...||+|++|+.+ .+...|++.||. .+..+.+||.
T Consensus 180 pv~~l~giG~~~~--~~L~~~Gi~tigdL~~---~~~~~L~~rfG~-----~g~~l~~~a~ 230 (407)
T PRK01810 180 PVGEMHGIGEKTA--EKLKDIGIQTIGDLAK---ADEHILRAKLGI-----NGVRLQRRAN 230 (407)
T ss_pred CHhhcCCcCHHHH--HHHHHcCCCcHHHHHh---CCHHHHHHHHhH-----HHHHHHHHhc
Confidence 4555556776444 8899999999999876 478889999964 3556667776
No 25
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=45.83 E-value=27 Score=31.68 Aligned_cols=59 Identities=22% Similarity=0.267 Sum_probs=42.6
Q ss_pred CcceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHH-HHHhhcc
Q 016573 256 DEVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWEN-TVEHAKT 318 (387)
Q Consensus 256 DeVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~-~v~HAkt 318 (387)
|+.-+|.+||. ++-+.|+..||+|-.|.-.+-..|-..+-..| +..-+.|.. -|+.|+.
T Consensus 67 DDLt~I~GIGP--k~e~~Ln~~GI~tfaQIAAwt~~di~~id~~l--~f~GRi~RDdWi~QAk~ 126 (133)
T COG3743 67 DDLTRISGIGP--KLEKVLNELGIFTFAQIAAWTRADIAWIDDYL--NFDGRIERDDWIAQAKA 126 (133)
T ss_pred ccchhhcccCH--HHHHHHHHcCCccHHHHHhcCHHHHHHHHhhc--CCcchhHHHHHHHHHHH
Confidence 99999999998 46799999999997665554444444444445 677777765 6666653
No 26
>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=45.64 E-value=18 Score=34.90 Aligned_cols=54 Identities=26% Similarity=0.408 Sum_probs=37.5
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhc
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 317 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAk 317 (387)
...-|.+|+.+.+ ++|...||.|+++|+++ +++++..+| +......+.+.+.|.
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 3455668887665 89999999999999854 899999999 556688888888876
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=43.70 E-value=20 Score=35.64 Aligned_cols=55 Identities=20% Similarity=0.023 Sum_probs=40.1
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcC-hHHHHHHHcCCCChhhHHHHHHhhccccC
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRD-PQKLRNILGSGMSNRMWENTVEHAKTCVL 321 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d-~~kLR~iLg~gms~k~We~~v~HAktCvl 321 (387)
+|..|-+||+.-. ++|...||+|++|+.++ + ..-|+..+| +.+..+.++|.--+.
T Consensus 174 pi~~l~giG~~~~--~~L~~~Gi~ti~dl~~~---~~~~~l~~~fg-----~~~~~l~~~a~G~d~ 229 (343)
T cd00424 174 PLTDLPGIGAVTA--KRLEAVGINPIGDLLAA---SPDALLALWGG-----VSGERLWYALRGIDD 229 (343)
T ss_pred ChhhcCCCCHHHH--HHHHHcCCCcHHHHhcC---CHHHHHHHHhh-----HHHHHHHHHhCCcCC
Confidence 4666667777544 89999999999998764 6 566777775 357777788875443
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=40.95 E-value=13 Score=38.11 Aligned_cols=54 Identities=22% Similarity=0.221 Sum_probs=38.8
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhc
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 317 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAk 317 (387)
.|..|-+||+. .-++|...||.|+.|+..+- .++..|++.||. +.+..+..+|.
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 56677777764 45999999999999998761 127889999974 24455555554
No 29
>PRK01216 DNA polymerase IV; Validated
Probab=40.74 E-value=13 Score=37.79 Aligned_cols=51 Identities=24% Similarity=0.282 Sum_probs=37.4
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhh
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHA 316 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HA 316 (387)
+|..|-.||+.. ..+|...||+|++|+.++ +...|++.||. ..+..+-.+|
T Consensus 179 Pi~~l~giG~~~--~~~L~~~Gi~TigdL~~~---~~~~L~~rfG~----~~~~~L~~~a 229 (351)
T PRK01216 179 DIADIPGIGDIT--AEKLKKLGVNKLVDTLRI---EFDELKGIIGE----AKAKYLFSLA 229 (351)
T ss_pred CcccccCCCHHH--HHHHHHcCCCcHHHHhcC---CHHHHHHHHCH----HHHHHHHHHh
Confidence 467777888644 489999999999998764 77889999973 2344444555
No 30
>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=40.01 E-value=14 Score=29.07 Aligned_cols=36 Identities=25% Similarity=0.337 Sum_probs=22.5
Q ss_pred hhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHH
Q 016573 271 HKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWEN 311 (387)
Q Consensus 271 hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~ 311 (387)
...|..+||+||+|++++ +++.|.++= |+..+.=+.
T Consensus 24 ~n~L~~~~I~tv~dL~~~---s~~~L~~i~--n~G~ksl~E 59 (66)
T PF03118_consen 24 YNCLKRAGIHTVGDLVKY---SEEDLLKIK--NFGKKSLEE 59 (66)
T ss_dssp HHHHHCTT--BHHHHHCS----HHHHHTST--TSHHHHHHH
T ss_pred HHHHHHhCCcCHHHHHhC---CHHHHHhCC--CCCHhHHHH
Confidence 368999999999997664 667777774 344444333
No 31
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=39.31 E-value=13 Score=41.43 Aligned_cols=41 Identities=32% Similarity=0.299 Sum_probs=33.9
Q ss_pred cceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHH
Q 016573 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNI 299 (387)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~i 299 (387)
++..|.+||...+ ++|++-||+||+|.|-++=.+=+..+.+
T Consensus 11 ~l~~l~gig~~~a--~~l~~Lgi~tv~DLL~~~P~~YeD~~~~ 51 (677)
T COG1200 11 PLSTLKGIGPKTA--EKLKKLGIHTVQDLLLYLPRRYEDRTLL 51 (677)
T ss_pred chhhhcCcCHHHH--HHHHHcCCCcHHHHHHhCccchhhcccc
Confidence 5899999999888 8999999999999998887665544444
No 32
>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=38.24 E-value=17 Score=37.05 Aligned_cols=55 Identities=11% Similarity=0.117 Sum_probs=37.0
Q ss_pred cceeeeeecccchhhhh-hhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhcc
Q 016573 257 EVWRLDRIAKDGALHKK-LMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (387)
Q Consensus 257 eVwRLekIgKdG~~hkr-L~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAkt 318 (387)
+|..|-.||+. .-++ |...||.|++|+.++. .++..|++.||. +.+..+.++|+-
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 46667777742 2244 5889999999998754 478889999864 234444455543
No 33
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=37.00 E-value=23 Score=30.88 Aligned_cols=39 Identities=33% Similarity=0.490 Sum_probs=29.4
Q ss_pred ceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHc
Q 016573 258 VWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILG 301 (387)
Q Consensus 258 VwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg 301 (387)
..|..+||. .|..-|..+||.||+++- ..+|++|.+.++
T Consensus 55 L~ri~gi~~--~~a~LL~~AGv~Tv~~LA---~~~p~~L~~~l~ 93 (122)
T PF14229_consen 55 LMRIPGIGP--QYAELLEHAGVDTVEELA---QRNPQNLHQKLG 93 (122)
T ss_pred hhhcCCCCH--HHHHHHHHhCcCcHHHHH---hCCHHHHHHHHH
Confidence 345666655 466899999999999974 478988887653
No 34
>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=35.85 E-value=19 Score=37.01 Aligned_cols=57 Identities=14% Similarity=0.058 Sum_probs=38.3
Q ss_pred ceeeeeecccchhhhhhhhCCCccHHHHHHHHh------------cChHHHHHHHcCCCChhhHHHHHHhhcccc
Q 016573 258 VWRLDRIAKDGALHKKLMKADIVTVEDFLRILV------------RDPQKLRNILGSGMSNRMWENTVEHAKTCV 320 (387)
Q Consensus 258 VwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~------------~d~~kLR~iLg~gms~k~We~~v~HAktCv 320 (387)
|-.|-+||+... ++|...||.|++|+..+-+ .+++.|++.||. +.+..+.++|.--+
T Consensus 174 v~~l~GiG~~~~--~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~----~~g~~l~~~a~G~d 242 (379)
T cd01703 174 LRKIPGIGYKTA--AKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGE----GIGQRIWKLLFGRD 242 (379)
T ss_pred ccccCCcCHHHH--HHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHCH----HHHHHHHHHHCCCC
Confidence 444446777654 8999999999999986541 117789999864 23444555665433
No 35
>KOG1520 consensus Predicted alkaloid synthase/Surface mucin Hemomucin [General function prediction only]
Probab=33.99 E-value=1.7e+02 Score=30.82 Aligned_cols=47 Identities=32% Similarity=0.297 Sum_probs=31.5
Q ss_pred ccccCCCCccccccceEEEeccceeecCCceeecCCccccccceeEEEEecCC
Q 016573 169 EVKEREGKRPILTGDLLVTLKEGFGTLGDLTFTDNSSWIRSRKFRLGLKVSPG 221 (387)
Q Consensus 169 IV~~R~Gk~pLL~Gdl~v~L~~Gva~l~di~FtDnSs~~rsrKFRLgarv~~~ 221 (387)
++-+=+|+...++.++.|.= +| .|-|||+||.--.|.|-+++--.+.
T Consensus 151 l~~~~~G~~~kf~N~ldI~~-~g-----~vyFTDSSsk~~~rd~~~a~l~g~~ 197 (376)
T KOG1520|consen 151 LADEAEGKPFKFLNDLDIDP-EG-----VVYFTDSSSKYDRRDFVFAALEGDP 197 (376)
T ss_pred ccccccCeeeeecCceeEcC-CC-----eEEEeccccccchhheEEeeecCCC
Confidence 33444777677776666544 44 5789999996655888887765543
No 36
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=33.78 E-value=49 Score=27.98 Aligned_cols=60 Identities=27% Similarity=0.404 Sum_probs=40.4
Q ss_pred CCCCCcceeeeeecccchhhhhhhhCCCcc----HHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhccc
Q 016573 252 PALHDEVWRLDRIAKDGALHKKLMKADIVT----VEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTC 319 (387)
Q Consensus 252 P~L~DeVwRLekIgKdG~~hkrL~~~gI~t----V~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAktC 319 (387)
|+=+-+|--|.+||.. +-.+|..+|+.. .++|| ++.+|++-.+.-| ...--++-+||++|
T Consensus 15 PmGeK~V~~laGIg~~--lg~~L~~~GfdkAYvllGQfL-llkKdE~lF~~Wl-----k~~~gat~~~a~~~ 78 (90)
T KOG4233|consen 15 PMGEKDVTWLAGIGET--LGIKLVDAGFDKAYVLLGQFL-LLKKDEDLFQEWL-----KETCGATAKQAQDC 78 (90)
T ss_pred ccCCCcceeeccccHH--hhhhHHhccccHHHHHHHHHH-HhcccHHHHHHHH-----HHHcCccHHHHHHH
Confidence 6667789999999874 558999999975 46776 4567876554433 11111266777776
No 37
>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=33.21 E-value=48 Score=26.31 Aligned_cols=25 Identities=44% Similarity=0.587 Sum_probs=16.4
Q ss_pred HHHHHHHHHHhHHHHHHHhhhhHHHHHhH
Q 016573 34 ASVIVEALKMDSLQRLCSSLEPLLRRIVS 62 (387)
Q Consensus 34 ~svi~e~~~~~~~q~~~~~lEp~lrrvV~ 62 (387)
.||=+.=+++- |.-.|||+|+|...
T Consensus 29 KsVsrkPLr~l----La~aLEPllkr~~~ 53 (59)
T TIGR02979 29 KSVARRPLKML----LAIALEPMLKRAAN 53 (59)
T ss_pred HHHhhccHHHH----HHHHHHHHHHHHHH
Confidence 34444445552 56699999999743
No 38
>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=31.04 E-value=30 Score=24.72 Aligned_cols=18 Identities=22% Similarity=0.578 Sum_probs=15.1
Q ss_pred eeecCCceeecCCccccc
Q 016573 192 FGTLGDLTFTDNSSWIRS 209 (387)
Q Consensus 192 va~l~di~FtDnSs~~rs 209 (387)
-..+..+.|-|++.|++.
T Consensus 24 ~~~Ie~i~FaDGt~w~~~ 41 (43)
T PF06594_consen 24 SYRIEQIEFADGTVWTRA 41 (43)
T ss_pred CCcEeEEEEcCCCEecHH
Confidence 566889999999999863
No 39
>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=29.55 E-value=57 Score=26.46 Aligned_cols=14 Identities=57% Similarity=0.816 Sum_probs=11.5
Q ss_pred HHHhhhhHHHHHhH
Q 016573 49 LCSSLEPLLRRIVS 62 (387)
Q Consensus 49 ~~~~lEp~lrrvV~ 62 (387)
|.-.|||+|||.++
T Consensus 45 La~~LEPllrr~~~ 58 (66)
T PF09584_consen 45 LALALEPLLRRGLN 58 (66)
T ss_pred HHHHHHHHHHHHHH
Confidence 55689999999854
No 40
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=29.20 E-value=25 Score=38.81 Aligned_cols=38 Identities=34% Similarity=0.344 Sum_probs=31.7
Q ss_pred CCCCCcceeeeeecccchhhhhhhhCCCccHHHHHHHHhc
Q 016573 252 PALHDEVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVR 291 (387)
Q Consensus 252 P~L~DeVwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~ 291 (387)
+.|++.|-.|++||+.-+ +.|++.||+||.|.|..+=+
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 41
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=28.92 E-value=83 Score=31.07 Aligned_cols=74 Identities=11% Similarity=0.190 Sum_probs=36.6
Q ss_pred hhhhHHHHHhHHHHHHHHHhccccccCCCCCCCCccCCCCCceEE-EecCCCCCCcccCCccccCCCCceEEEEEe
Q 016573 52 SLEPLLRRIVSEEVERALTKFGHAKLAARSPPPRIHGPGEKNLQL-HYKTRMPPHLFTGGKVEGDQGAAIHVVLID 126 (387)
Q Consensus 52 ~lEp~lrrvV~EEve~~l~~~~~~~~~~rs~~~~~~~~~~~~~~L-~F~n~l~~pifT~~kI~a~~g~~I~V~L~D 126 (387)
-||-++|+|+.|++-....-..+ .+..-..|.++-...++.+++ .|..+.+..+|+.+-+..++|+.+-..++.
T Consensus 89 ~i~~lv~~v~~e~~~~~~~~~~~-~~~~~~~~~Gi~vVrg~svk~~~fdg~~~~~v~~~d~~~~~d~s~m~aGf~~ 163 (233)
T PRK15457 89 LVAQLMEKVMKEKQSLEQGAMQP-SFKSVTGKGGIKVIDGSSVKFGRFDGAEPHCVGLTDLVTGDDGSSMAAGFMQ 163 (233)
T ss_pred HHHHHHHHHHHHHhcccccccCC-CccceeCCCceEEEECCeEEEeecCCCCcccEEeeeeeccCCCCceeeEEEE
Confidence 36678999988886433211000 010111223333333455665 555455555666666666666655555443
No 42
>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=28.80 E-value=78 Score=22.39 Aligned_cols=42 Identities=21% Similarity=0.293 Sum_probs=31.7
Q ss_pred hhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhc
Q 016573 271 HKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 317 (387)
Q Consensus 271 hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAk 317 (387)
-.+|..+||.||+++.. .+++.|..+- |++...=+.++.=|+
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 5677787875 677777666666554
No 43
>PRK05256 condesin subunit E; Provisional
Probab=27.56 E-value=93 Score=30.76 Aligned_cols=74 Identities=16% Similarity=0.205 Sum_probs=51.0
Q ss_pred hhhhhCCCccHHHHHHHHh--cChHHHHHHHc--CCCChhhHHHHHHhhccccC--CCeeEEEEecCCCcEEEEEcccce
Q 016573 272 KKLMKADIVTVEDFLRILV--RDPQKLRNILG--SGMSNRMWENTVEHAKTCVL--GGKLYVYYADGTQNTGVVFNNIYE 345 (387)
Q Consensus 272 krL~~~gI~tV~dFL~l~~--~d~~kLR~iLg--~gms~k~We~~v~HAktCvl--~~k~~~y~~~~~~nv~l~FN~i~~ 345 (387)
++|++.||.|+++.+.-+. .|+++|.+.++ .+-|+-+=+++.+-.++|-- ..-=.++...+..+...+=++||-
T Consensus 107 erLa~~gift~qeL~deL~~ladE~kllklvn~R~~GsDlD~~Kl~ekvr~sLrrLrRlgmI~~l~~d~~kF~iteAvfR 186 (238)
T PRK05256 107 ERLAHEGIFTQQELYDELLTLADEAKLLKLVNNRSTGSDLDKQKLQEKVRTSLNRLRRLGMVWFMGHDSSKFRITESVFR 186 (238)
T ss_pred HHHhcCCceeHHHHHHHHHHhhcHHHHHHHhcCCCCcchhhHHHHHHHHHHHHHHHHhccceeeecCCCceEEecHHHHh
Confidence 7999999999999886544 48999999985 23377778888899999863 333335544433344444455554
No 44
>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=27.46 E-value=35 Score=33.28 Aligned_cols=35 Identities=17% Similarity=0.307 Sum_probs=28.9
Q ss_pred eecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcC
Q 016573 263 RIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGS 302 (387)
Q Consensus 263 kIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~ 302 (387)
.||+... .+|.+.||+|++||..+ +...|++.||.
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 89999999999988774 78889999975
No 45
>PRK10497 peripheral inner membrane phage-shock protein; Provisional
Probab=26.36 E-value=73 Score=26.31 Aligned_cols=14 Identities=50% Similarity=0.842 Sum_probs=11.4
Q ss_pred HHHhhhhHHHHHhH
Q 016573 49 LCSSLEPLLRRIVS 62 (387)
Q Consensus 49 ~~~~lEp~lrrvV~ 62 (387)
|.-.|||+|||.++
T Consensus 52 L~~~LEPlLkr~~~ 65 (73)
T PRK10497 52 LAVALEPLLKRAAN 65 (73)
T ss_pred HHHHHHHHHHHHHH
Confidence 55699999999854
No 46
>PRK07758 hypothetical protein; Provisional
Probab=25.49 E-value=1e+02 Score=26.55 Aligned_cols=37 Identities=19% Similarity=0.262 Sum_probs=24.9
Q ss_pred hhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHH
Q 016573 272 KKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTV 313 (387)
Q Consensus 272 krL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v 313 (387)
..|..+||+||+|+.+ ++++.|-++= |+..+.-+.+.
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 6788999999999865 4555566653 44455555443
No 47
>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=25.48 E-value=1.2e+02 Score=25.60 Aligned_cols=35 Identities=29% Similarity=0.619 Sum_probs=27.7
Q ss_pred hCCCccHHHHHHHHhcChHHHHH---HHcCCCChhhHHHHHHhhcc
Q 016573 276 KADIVTVEDFLRILVRDPQKLRN---ILGSGMSNRMWENTVEHAKT 318 (387)
Q Consensus 276 ~~gI~tV~dFL~l~~~d~~kLR~---iLg~gms~k~We~~v~HAkt 318 (387)
...| +++||+=++-.||.||-. +| .|+..++-|+.
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 999999999999976655 45 58888888875
No 48
>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=24.15 E-value=1.5e+02 Score=28.00 Aligned_cols=62 Identities=24% Similarity=0.294 Sum_probs=38.0
Q ss_pred ccccccceEEEe---c--cce--eecCCceeecCCccccccceeEEEEecCCC-------CCCcceeeeeecCeEeeec
Q 016573 177 RPILTGDLLVTL---K--EGF--GTLGDLTFTDNSSWIRSRKFRLGLKVSPGY-------CDGIRVREAKTEGFAVKDH 241 (387)
Q Consensus 177 ~pLL~Gdl~v~L---~--~Gv--a~l~di~FtDnSs~~rsrKFRLgarv~~~~-------~~g~RI~EAvse~FvVkd~ 241 (387)
.+.|.|.+...+ + +|. |.. ..|.|=|-.+ -+.|||-.++..=. ....-+-|+.|+||.|-..
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--FVFPDLSVRT-EGRFRLRFSLFDIGPSPGQGGGSSPVLAEVFSDPFTVYSA 172 (203)
T ss_pred cccCcccEeeeeEEecCCCCCeEEEE--EEeCCceECc-CCEEEEEEEEEEecCCccccCCCCcEEEEEECcCEEEECH
Confidence 467888765433 3 333 211 2344444422 57899998877532 2235689999999999654
No 49
>PF04270 Strep_his_triad: Streptococcal histidine triad protein ; InterPro: IPR006270 This entry represents a repeated sequence region that includes a His-X-X-His-X-His (histidine triad) motif, which is found in family of Streptococcal proteins. Members of the family are suggested to cleave human complement component 3, and family member PhpA has been shown in vaccine studies to be a protective antigen in mice []. ; PDB: 2CS7_C.
Probab=23.72 E-value=56 Score=25.30 Aligned_cols=21 Identities=14% Similarity=0.213 Sum_probs=16.7
Q ss_pred EeecCCCChhhhhhhhhhHHH
Q 016573 355 FVSLESLTHSQKTLPDSGLHE 375 (387)
Q Consensus 355 y~~~~~L~~~qk~~V~~L~~q 375 (387)
|++..+||+.|..+++...++
T Consensus 32 yI~k~dLs~~E~~aA~~~~~~ 52 (53)
T PF04270_consen 32 YIPKSDLSASELKAAQAYLAG 52 (53)
T ss_dssp EEEGGGS-HHHHHHHHHHHH-
T ss_pred CCchhhCCHHHHHHHHHHHhc
Confidence 999999999999988877654
No 50
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=22.48 E-value=60 Score=32.35 Aligned_cols=41 Identities=20% Similarity=0.379 Sum_probs=34.4
Q ss_pred hhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHH
Q 016573 273 KLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVE 314 (387)
Q Consensus 273 rL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~ 314 (387)
.-+.++|.|+.|--.+...+|+.||.+++. +.+|.|=.=|.
T Consensus 24 aae~hkiiTirdvae~~ev~~n~lr~lasr-LekkG~LeRi~ 64 (269)
T COG5340 24 AAEGHKIITIRDVAETLEVAPNTLRELASR-LEKKGWLERIL 64 (269)
T ss_pred HHHhCceEEeHHhhhhccCCHHHHHHHHhh-hhhcchhhhhc
Confidence 345679999999999999999999999976 88889965443
No 51
>COG4766 EutQ Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=21.74 E-value=3e+02 Score=26.01 Aligned_cols=92 Identities=15% Similarity=0.249 Sum_probs=59.9
Q ss_pred HHHHHHHHHh-HHHHHHHh-hhhHHHHHhHHHHHHHHHhccccccC---CCCCCCCccCCCCCceEEEecCCCCCCcccC
Q 016573 35 SVIVEALKMD-SLQRLCSS-LEPLLRRIVSEEVERALTKFGHAKLA---ARSPPPRIHGPGEKNLQLHYKTRMPPHLFTG 109 (387)
Q Consensus 35 svi~e~~~~~-~~q~~~~~-lEp~lrrvV~EEve~~l~~~~~~~~~---~rs~~~~~~~~~~~~~~L~F~n~l~~pifT~ 109 (387)
+-|+|++..+ +.-++|+. +|-++++|++|+.-....-..+ .+. +||--+ ...-..-.+.|+|...=+.-+||+
T Consensus 12 ~~i~~si~a~l~~~~~~~~l~~Qlm~kVmkek~s~~~~~~~~-~~k~v~~ksgik-vvk~s~vk~~~r~d~gqp~~V~~t 89 (176)
T COG4766 12 QRIRESIIAQLPEGQFTKELVEQLMEKVMKEKQSLECGWMQP-SFKSVDGKSGIK-VVKLSSVKFGLRFDTGQPDCVYTT 89 (176)
T ss_pred HHHHHHHHHhCChhhhhHHHHHHHHHHHHhchhhhhhhhccc-ceeecccCCcee-EEecccceeEeeecCCCCCeEEee
Confidence 4566665543 34556765 4678899999987665543322 111 223111 112223467889998877889999
Q ss_pred CccccCCCCceEEEEEeCC
Q 016573 110 GKVEGDQGAAIHVVLIDMN 128 (387)
Q Consensus 110 ~kI~a~~g~~I~V~L~D~~ 128 (387)
+=++-.+|.++-+.+..-.
T Consensus 90 dLvt~~~g~~l~aG~m~~~ 108 (176)
T COG4766 90 DLVTEQEGSRLGAGLMEMK 108 (176)
T ss_pred ceeecccCCccccceeeec
Confidence 9999999999999987753
No 52
>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=20.82 E-value=1.7e+02 Score=26.68 Aligned_cols=35 Identities=26% Similarity=0.454 Sum_probs=26.9
Q ss_pred EEEeccceeecCCceeecCCccccccceeEEEEecCC
Q 016573 185 LVTLKEGFGTLGDLTFTDNSSWIRSRKFRLGLKVSPG 221 (387)
Q Consensus 185 ~v~L~~Gva~l~di~FtDnSs~~rsrKFRLgarv~~~ 221 (387)
.-.|+|++|-+.|+.|---|. |.+.|-|-.-+...
T Consensus 74 tavmknqvA~FnDLRFvGRSG--RGKsFtltItv~t~ 108 (135)
T PF00853_consen 74 TAVMKNQVARFNDLRFVGRSG--RGKSFTLTITVFTN 108 (135)
T ss_dssp EEEEETTEEEESS-EECST-T--TTSEEEEEEEE-SS
T ss_pred hhhhhcccccccccccccccC--CccceEEEEEEeCC
Confidence 688999999999999998776 55679998877754
No 53
>COG3827 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.64 E-value=1.9e+02 Score=28.56 Aligned_cols=39 Identities=33% Similarity=0.474 Sum_probs=28.4
Q ss_pred chHHHHHHHHHHhHHHHHH-HhhhhHHHHHhHHHHHHHHHh
Q 016573 32 ALASVIVEALKMDSLQRLC-SSLEPLLRRIVSEEVERALTK 71 (387)
Q Consensus 32 ~~~svi~e~~~~~~~q~~~-~~lEp~lrrvV~EEve~~l~~ 71 (387)
+|-.+..|+|+-- ||.-+ -.|=-++.|+|+|||||-.+.
T Consensus 189 sleE~a~eMLRPm-LqdWLDkNLPtLVErLVrEEIeRv~RG 228 (231)
T COG3827 189 SLEEMAAEMLRPM-LQDWLDKNLPTLVERLVREEIERVVRG 228 (231)
T ss_pred cHHHHHHHHHHHH-HHHHHHccchHHHHHHHHHHHHHHHcc
Confidence 5777777777653 55533 367778899999999997653
No 54
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=20.35 E-value=1.3e+02 Score=29.08 Aligned_cols=52 Identities=19% Similarity=0.372 Sum_probs=37.2
Q ss_pred ceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhh
Q 016573 258 VWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHA 316 (387)
Q Consensus 258 VwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HA 316 (387)
..-|.+|+.+-+ ++|.++||.|.+|+..+ +++++..++ |+..+.=+.+.+.+
T Consensus 153 L~Qlp~i~~~~~--~~l~~~~i~s~~~l~~~---~~~~~~~ll--~~~~~~~~~i~~~~ 204 (312)
T smart00611 153 LLQLPHLPEEIL--KRLEKKKVLSLEDLLEL---EDEERGELL--GLLDAEGERVYKVL 204 (312)
T ss_pred cccCCCCCHHHH--HHHHhCCCCCHHHHHhc---CHHHHHHHH--cCCHHHHHHHHHHH
Confidence 455677777544 78999999999998764 788899998 45555555555554
No 55
>PRK14973 DNA topoisomerase I; Provisional
Probab=20.30 E-value=80 Score=36.71 Aligned_cols=54 Identities=20% Similarity=0.316 Sum_probs=43.5
Q ss_pred ceeeeeecccchhhhhhhhCCCccHHHHHHHHhcChHHHHHHHcCCCChhhHHHHHHhhcc
Q 016573 258 VWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (387)
Q Consensus 258 VwRLekIgKdG~~hkrL~~~gI~tV~dFL~l~~~d~~kLR~iLg~gms~k~We~~v~HAkt 318 (387)
.=.++++|-+.. .+|..+||.||+|+++. |+.+|-..- |++.+.-..+..+|+.
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 334567788777 89999999999999987 888887764 7888888888877763
Done!