Query 013185
Match_columns 448
No_of_seqs 130 out of 158
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 01:16:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013185.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013185hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07887 Calmodulin_bind: Calm 100.0 2E-125 5E-130 931.6 30.1 299 92-393 1-299 (299)
2 TIGR02239 recomb_RAD51 DNA rep 88.8 0.49 1.1E-05 48.2 4.2 49 268-321 12-60 (316)
3 TIGR02238 recomb_DMC1 meiotic 87.0 0.64 1.4E-05 47.4 3.8 49 268-321 12-60 (313)
4 PLN03186 DNA repair protein RA 86.8 0.5 1.1E-05 48.9 2.9 62 256-322 27-88 (342)
5 PRK04301 radA DNA repair and r 82.0 0.92 2E-05 45.6 2.3 57 256-319 7-63 (317)
6 PLN03187 meiotic recombination 81.9 1.2 2.5E-05 46.4 3.1 60 256-320 30-89 (344)
7 PF14520 HHH_5: Helix-hairpin- 76.4 0.53 1.1E-05 36.4 -1.1 51 259-316 9-59 (60)
8 PTZ00035 Rad51 protein; Provis 75.3 2.5 5.5E-05 43.5 3.2 60 256-320 22-81 (337)
9 TIGR02236 recomb_radA DNA repa 71.0 2.8 6.1E-05 41.7 2.3 50 260-316 4-53 (310)
10 PRK03609 umuC DNA polymerase V 70.6 3.3 7.1E-05 43.4 2.8 52 256-317 180-231 (422)
11 PRK02406 DNA polymerase IV; Va 67.6 4.6 0.0001 40.9 3.0 52 256-317 169-220 (343)
12 PF14229 DUF4332: Domain of un 63.0 9.7 0.00021 33.9 3.8 52 269-322 7-60 (122)
13 PRK01172 ski2-like helicase; P 58.1 8.7 0.00019 42.6 3.2 51 260-317 617-667 (674)
14 PRK03352 DNA polymerase IV; Va 58.0 4 8.8E-05 41.3 0.6 41 256-301 178-218 (346)
15 PRK03858 DNA polymerase IV; Va 56.3 5.1 0.00011 41.3 1.0 48 256-308 174-221 (396)
16 PRK14133 DNA polymerase IV; Pr 54.7 11 0.00025 38.2 3.2 51 256-316 174-224 (347)
17 PRK03348 DNA polymerase IV; Pr 54.6 6.4 0.00014 42.1 1.4 49 256-309 181-229 (454)
18 PRK02794 DNA polymerase IV; Pr 53.1 10 0.00023 39.7 2.7 55 256-320 210-264 (419)
19 PF10691 DUF2497: Protein of u 52.2 31 0.00068 28.7 4.8 41 30-70 33-73 (73)
20 cd01700 PolY_Pol_V_umuC umuC s 51.6 11 0.00023 38.3 2.4 51 256-316 177-227 (344)
21 cd03586 PolY_Pol_IV_kappa DNA 49.8 14 0.00031 36.8 2.9 52 256-317 172-223 (334)
22 PRK01810 DNA polymerase IV; Va 47.2 15 0.00032 38.2 2.7 51 256-316 180-230 (407)
23 PRK03103 DNA polymerase IV; Re 46.8 14 0.00031 38.4 2.5 52 256-317 182-233 (409)
24 COG4766 EutQ Ethanolamine util 44.8 70 0.0015 30.7 6.4 93 34-127 12-108 (176)
25 PF04994 TfoX_C: TfoX C-termin 44.6 9 0.0002 32.0 0.5 74 257-370 5-79 (81)
26 COG3743 Uncharacterized conser 44.2 28 0.00061 32.2 3.7 59 255-317 67-126 (133)
27 TIGR01954 nusA_Cterm_rpt trans 43.6 26 0.00056 25.5 2.8 42 270-316 6-47 (50)
28 cd00424 PolY Y-family of DNA p 41.7 20 0.00043 36.4 2.6 56 256-321 174-230 (343)
29 PF02889 Sec63: Sec63 Brl doma 39.9 21 0.00046 35.2 2.4 54 256-316 149-202 (314)
30 cd01701 PolY_Rev1 DNA polymera 38.7 14 0.0003 38.8 0.9 54 256-316 223-276 (404)
31 PRK01216 DNA polymerase IV; Va 38.5 13 0.00029 38.5 0.7 51 256-315 179-229 (351)
32 cd01702 PolY_Pol_eta DNA Polym 36.0 17 0.00036 37.8 1.0 55 256-317 183-238 (359)
33 PF03118 RNA_pol_A_CTD: Bacter 35.5 16 0.00035 29.4 0.6 36 270-310 24-59 (66)
34 cd01703 PolY_Pol_iota DNA Poly 32.3 21 0.00045 37.5 1.0 58 256-319 173-242 (379)
35 KOG1520 Predicted alkaloid syn 30.7 1.5E+02 0.0033 31.8 7.0 46 168-219 151-196 (376)
36 cd07978 TAF13 The TATA Binding 30.3 83 0.0018 27.1 4.2 35 275-317 52-89 (92)
37 PRK07758 hypothetical protein; 28.7 65 0.0014 28.4 3.3 37 271-312 48-84 (95)
38 PRK15457 ethanolamine utilizat 27.9 95 0.0021 31.3 4.7 73 52-125 90-163 (233)
39 PF07340 Herpes_IE1: Cytomegal 27.6 85 0.0018 33.7 4.5 26 6-31 1-27 (392)
40 PF14229 DUF4332: Domain of un 27.5 34 0.00073 30.5 1.4 39 257-300 55-93 (122)
41 PF06594 HCBP_related: Haemoly 27.3 37 0.0008 24.8 1.3 18 191-208 24-41 (43)
42 PF13957 YafO_toxin: Toxin Yaf 27.0 28 0.00061 30.6 0.8 88 263-378 14-105 (109)
43 KOG4233 DNA-bridging protein B 27.0 66 0.0014 27.8 2.9 60 251-318 15-78 (90)
44 TIGR02979 phageshock_pspD phag 26.8 75 0.0016 25.8 3.0 25 33-61 29-53 (59)
45 PRK05256 condesin subunit E; P 26.6 94 0.002 31.3 4.4 74 271-344 107-186 (238)
46 COG3355 Predicted transcriptio 24.1 2.2E+02 0.0049 26.1 6.0 40 267-306 31-74 (126)
47 PRK10917 ATP-dependent DNA hel 23.8 32 0.00068 38.7 0.6 39 250-290 4-42 (681)
48 PF09584 Phageshock_PspD: Phag 23.1 91 0.002 25.8 3.0 15 48-62 45-59 (66)
49 cd03468 PolY_like DNA Polymera 22.5 44 0.00095 33.3 1.3 35 262-301 177-211 (335)
50 PF10148 SCHIP-1: Schwannomin- 21.7 1.3E+02 0.0029 30.4 4.4 16 88-103 45-60 (238)
51 PRK10497 peripheral inner memb 20.9 1.1E+02 0.0024 25.8 3.1 15 48-62 52-66 (73)
52 PF08806 Sep15_SelM: Sep15/Sel 20.1 62 0.0013 27.0 1.5 36 97-133 21-56 (78)
53 PF04270 Strep_his_triad: Stre 20.1 92 0.002 24.7 2.3 22 353-374 31-52 (53)
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=2.3e-125 Score=931.57 Aligned_cols=299 Identities=69% Similarity=1.159 Sum_probs=294.9
Q ss_pred ceEEEEcCCCCCCcccCCceeccCCCceEEEEEeCCCCceeccCCCccceEEEEEeeCCCCCCCCCCCCHHHHhhccccc
Q 013185 92 NLQLHFRTRLSLPLFTGGKVEGEQGTAIHIVLIDANTGHVVTTGPESLVKLDVVVLEGDFNNEDDDNWTQEEFVSHVVKE 171 (448)
Q Consensus 92 ~~~L~F~n~l~~pifTg~kI~a~~g~~I~V~L~D~~t~~iVt~Gplss~kvEIvVLdGDF~~~~~e~WT~eEF~~~IV~~ 171 (448)
+|||+|+|+|++|||||++|+|+||+||+|+|+|++|+ |++||+|++|||||||||||+++++++||+|||++|||++
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 CCCCCcccceeeEEEecCceeeccCceeecCCccccccccEEEEEeecCCCCcceeeeeeccceEEeecCCcccccCCCC
Q 013185 172 REGKRPLLSGDLQVTLKEGVGTLGDLTFTDNSSWIRSRKFRLGLKVASGYCEGIRIREAKTDAFTVKDHRGELYKKHYPP 251 (448)
Q Consensus 172 ReGk~pLL~Gdl~v~L~~Gva~l~di~FTDnSsw~rSrKFRLgaRv~~~~~~g~RI~EAvsE~FvVkDhRge~ykKh~pP 251 (448)
|+||+|||+|+++|+|+||+|+|+||+|||||||+|||||||||||+++++.|+|||||+||||+|||||||+|||||||
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 CCCccceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhcccccCCceEEEecCC
Q 013185 252 ALNDEVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCVLSGKLYVYYPDD 331 (448)
Q Consensus 252 ~L~DeVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~k~y~y~~~~ 331 (448)
+|+|||||||||||||+|||+|+++||+||+|||+|+++||++||+|||+|||++||++||+|||||++++++|+|| .+
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 CCcEEEEEccccceeeeeeCCeeecCCCCChHhHHHHHHHHHHHHhhccceeeecccccCCC
Q 013185 332 PRNVGVVFNNIYEFCGLIADGQYHSADSLSESQKVHVDTLVKKAYDNWMHVIEYDGKSLLGF 393 (448)
Q Consensus 332 ~~nv~l~FN~i~~lvG~~~~g~y~~~d~L~~~qk~~V~~Lk~~AY~~~~~~~~~d~~~~~~~ 393 (448)
++|++|+|||||+||||.|+|+|++.|+||+.||++|++||++||+||++|++||++|++|+
T Consensus 238 ~~nv~l~FN~i~~lvga~~~g~y~s~d~L~~~qK~~v~~Lv~~AY~n~~~l~e~d~~~~~n~ 299 (299)
T PF07887_consen 238 EQNVGLFFNCIYELVGAIFGGQYVSLDNLSSAQKAYVDKLVKQAYENWDNLEEYDGKMLNNY 299 (299)
T ss_pred CCceEEEEcchhhEEeEEECCEEEehHHcCHHHHHHHHHHHHHHHHhhhhheecccchhccC
Confidence 78999999999999999999999999999999999999999999999999999999999986
No 2
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=88.76 E-value=0.49 Score=48.18 Aligned_cols=49 Identities=29% Similarity=0.312 Sum_probs=43.3
Q ss_pred hhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhcccccC
Q 013185 268 SFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCVLS 321 (448)
Q Consensus 268 ~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 321 (448)
.--++|+++||.||+||+.. +|..|.+++ |+|...++.+..||.+|...
T Consensus 12 ~~~~~l~~~g~~t~~~~~~~---~~~~L~~i~--~ls~~~~~~~~~~~~~~~~~ 60 (316)
T TIGR02239 12 ADIKKLQEAGLHTVESVAYA---PKKQLLEIK--GISEAKADKILAEAAKLVPM 60 (316)
T ss_pred HHHHHHHHcCCCcHHHHHhC---CHHHHHHHh--CCCHHHHHHHHHHHHHhccc
Confidence 34579999999999999876 899999998 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=87.00 E-value=0.64 Score=47.39 Aligned_cols=49 Identities=27% Similarity=0.311 Sum_probs=43.3
Q ss_pred hhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhcccccC
Q 013185 268 SFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCVLS 321 (448)
Q Consensus 268 ~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 321 (448)
.--++|+++||.||+||+.. ++..|.++. |+|...++.+++.|+.+...
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 45589999999999999876 899999997 89999999999999988654
No 4
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=86.80 E-value=0.5 Score=48.90 Aligned_cols=62 Identities=27% Similarity=0.314 Sum_probs=49.1
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhcccccCC
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCVLSG 322 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~ 322 (448)
++-+|+.-|-.-.--++|.++||.||+||+.+ ++..|.+++ |+|....+.+++||.+|....
T Consensus 27 ~~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~---~~~~L~~i~--~is~~~~~~~~~~~~~~~~~~ 88 (342)
T PLN03186 27 PIEQLQASGIAALDIKKLKDAGIHTVESLAYA---PKKDLLQIK--GISEAKVEKILEAASKLVPLG 88 (342)
T ss_pred cHHHHHhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHHhcccc
Confidence 34455443344445679999999999999876 889999998 899999999999998886543
No 5
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=81.96 E-value=0.92 Score=45.57 Aligned_cols=57 Identities=19% Similarity=0.304 Sum_probs=45.4
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhcccc
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCV 319 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAktCv 319 (448)
++-.|.+||+ ...++|.++||.|++|++.+ +++.|.+++ |++.+.++.+++-|+.++
T Consensus 7 ~l~~l~gIg~--~~a~~L~~~Gi~t~~dl~~~---~~~~L~~~~--g~~~~~a~~l~~~a~~~~ 63 (317)
T PRK04301 7 DLEDLPGVGP--ATAEKLREAGYDTVEAIAVA---SPKELSEAA--GIGESTAAKIIEAAREAA 63 (317)
T ss_pred cHhhcCCCCH--HHHHHHHHcCCCCHHHHHcC---CHHHHHHhc--CCCHHHHHHHHHHHHHhh
Confidence 3445556664 45589999999999999664 999999998 778889999988887644
No 6
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=81.86 E-value=1.2 Score=46.36 Aligned_cols=60 Identities=23% Similarity=0.335 Sum_probs=47.9
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhccccc
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCVL 320 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 320 (448)
++..|+.-|-.-.--++|.++||+||+|++.. ++..|-++. |+|...++.+++.|+..+.
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 35666554444456689999999999999876 788899986 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=76.41 E-value=0.53 Score=36.43 Aligned_cols=51 Identities=29% Similarity=0.484 Sum_probs=40.3
Q ss_pred eeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhc
Q 013185 259 RLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAK 316 (448)
Q Consensus 259 RLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAk 316 (448)
.+.+||+. ..++|.++||.|++|+..+ +++.|.++= |++.+.=+.+++.|+
T Consensus 9 ~I~Gig~~--~a~~L~~~G~~t~~~l~~a---~~~~L~~i~--Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 9 SIPGIGPK--RAEKLYEAGIKTLEDLANA---DPEELAEIP--GIGEKTAEKIIEAAR 59 (60)
T ss_dssp TSTTCHHH--HHHHHHHTTCSSHHHHHTS---HHHHHHTST--TSSHHHHHHHHHHHH
T ss_pred cCCCCCHH--HHHHHHhcCCCcHHHHHcC---CHHHHhcCC--CCCHHHHHHHHHHHh
Confidence 34556554 3488999999999998765 888899985 789999999998886
No 8
>PTZ00035 Rad51 protein; Provisional
Probab=75.27 E-value=2.5 Score=43.47 Aligned_cols=60 Identities=30% Similarity=0.360 Sum_probs=47.1
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhccccc
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCVL 320 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 320 (448)
++-.|+.-|-.-.--++|.++||+||+||+.. ++..|-++. |+|...=+.+++.|+.++.
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 45566553333345689999999999998866 888999997 7899999999998887764
No 9
>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=71.00 E-value=2.8 Score=41.70 Aligned_cols=50 Identities=24% Similarity=0.345 Sum_probs=38.6
Q ss_pred eeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhc
Q 013185 260 LEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAK 316 (448)
Q Consensus 260 LekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAk 316 (448)
|.+||+ ..-++|.++||.|++|++.+ +++.|.+++ |++.+..+.+.+-|+
T Consensus 4 i~gig~--~~~~~L~~~Gi~ti~dl~~~---~~~~L~~~~--g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 4 LPGVGP--ATAEKLREAGYDTFEAIAVA---SPKELSEIA--GISEGTAAKIIQAAR 53 (310)
T ss_pred cCCCCH--HHHHHHHHcCCCCHHHHHcC---CHHHHHhcc--CCCHHHHHHHHHHHH
Confidence 445554 34589999999999998876 899999998 567777777766665
No 10
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=70.57 E-value=3.3 Score=43.38 Aligned_cols=52 Identities=21% Similarity=0.273 Sum_probs=41.3
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhcc
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKT 317 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 317 (448)
+|..|-+||+. ..++|.+.||+|++|+.++ ++..|++.||. .+..+..||.-
T Consensus 180 Pv~~l~GiG~~--~~~~L~~lGi~TigdL~~~---~~~~L~~~fG~-----~~~~l~~~a~G 231 (422)
T PRK03609 180 PVEEVWGVGRR--ISKKLNAMGIKTALDLADT---NIRFIRKHFNV-----VLERTVRELRG 231 (422)
T ss_pred ChhhcCCccHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHCH-----HHHHHHHHhCC
Confidence 45566677774 4589999999999999987 88999999963 57777778753
No 11
>PRK02406 DNA polymerase IV; Validated
Probab=67.65 E-value=4.6 Score=40.87 Aligned_cols=52 Identities=25% Similarity=0.384 Sum_probs=40.4
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhcc
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKT 317 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 317 (448)
+|..|-+||+. .-++|...||+|++|+.++ +...|++.||. .+..+.+||.-
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 4478999999999999886 78899999974 46666677654
No 12
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=62.97 E-value=9.7 Score=33.87 Aligned_cols=52 Identities=29% Similarity=0.289 Sum_probs=37.3
Q ss_pred hhhhhhhcCCccHHHHHHHHhhChHH--HHHHHcCCCCchhHHHHHHhhcccccCC
Q 013185 269 FHKRLNKAGIFTVEDFLRLVVRDSQR--LRNILGSGMSNKMWDVLVDHAKTCVLSG 322 (448)
Q Consensus 269 ~hkrL~~~~I~tV~dFL~l~~~d~~k--LR~iLg~gmS~k~We~~v~HAktCvl~~ 322 (448)
...+|+..||+|++|||..-.....+ |-+-+ |++.+-=...+.+|.=|...+
T Consensus 7 ~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~--~i~~~~l~~w~~~AdL~ri~g 60 (122)
T PF14229_consen 7 EAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKL--GISERNLLKWVNQADLMRIPG 60 (122)
T ss_pred HHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhc--CCCHHHHHHHHhHHHhhhcCC
Confidence 45799999999999999986554444 55544 678877777777776554433
No 13
>PRK01172 ski2-like helicase; Provisional
Probab=58.09 E-value=8.7 Score=42.58 Aligned_cols=51 Identities=31% Similarity=0.586 Sum_probs=41.8
Q ss_pred eeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhcc
Q 013185 260 LEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKT 317 (448)
Q Consensus 260 LekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 317 (448)
|.++++ ...++|.++||.||.|+.. .|+++|-+|+ |++++.=+.++++|+.
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 4668999999999999887 4888898898 6899999999999875
No 14
>PRK03352 DNA polymerase IV; Validated
Probab=58.00 E-value=4 Score=41.32 Aligned_cols=41 Identities=32% Similarity=0.357 Sum_probs=33.8
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcC
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGS 301 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~ 301 (448)
+|..|-+||+. ..++|...||+|++||+++ ++..|++.||.
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 56666677774 4478999999999999986 78899999975
No 15
>PRK03858 DNA polymerase IV; Validated
Probab=56.26 E-value=5.1 Score=41.30 Aligned_cols=48 Identities=29% Similarity=0.381 Sum_probs=35.9
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhH
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMW 308 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~W 308 (448)
+|..|-+||+.- -++|.+.||+|++|+.++ ++..|++.||..+-...|
T Consensus 174 pl~~l~Gig~~~--~~~L~~~Gi~t~~dl~~l---~~~~L~~~fG~~~~~~l~ 221 (396)
T PRK03858 174 PVRRLWGVGPVT--AAKLRAHGITTVGDVAEL---PESALVSLLGPAAGRHLH 221 (396)
T ss_pred ChhhcCCCCHHH--HHHHHHhCCCcHHHHhcC---CHHHHHHHhCcHHHHHHH
Confidence 466666787754 489999999999999864 888999999753333333
No 16
>PRK14133 DNA polymerase IV; Provisional
Probab=54.71 E-value=11 Score=38.17 Aligned_cols=51 Identities=27% Similarity=0.522 Sum_probs=39.6
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhc
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAK 316 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAk 316 (448)
+|..|-+||+... ++|..-||+|++|++++ +...|+..||. .|..+.++|.
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 4666666766443 78999999999999886 78889999963 5777777775
No 17
>PRK03348 DNA polymerase IV; Provisional
Probab=54.59 E-value=6.4 Score=42.07 Aligned_cols=49 Identities=29% Similarity=0.435 Sum_probs=38.0
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHH
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWD 309 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We 309 (448)
+|.+|-+||+.. -++|...||+|++||.++ +...|++.||..+-..-|.
T Consensus 181 Pv~~L~GIG~~t--~~~L~~lGI~TigDLa~l---~~~~L~~~fG~~~g~~L~~ 229 (454)
T PRK03348 181 PVRRLWGIGPVT--EEKLHRLGIETIGDLAAL---SEAEVANLLGATVGPALHR 229 (454)
T ss_pred CccccCCCCHHH--HHHHHHcCCccHHHHhcC---CHHHHHHHHCHHHHHHHHH
Confidence 688888888754 478999999999999886 7889999997534334443
No 18
>PRK02794 DNA polymerase IV; Provisional
Probab=53.12 E-value=10 Score=39.67 Aligned_cols=55 Identities=29% Similarity=0.227 Sum_probs=42.6
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhccccc
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCVL 320 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 320 (448)
+|..|-+||+ ..-++|...||+|++|+..+ +...|++.||. +|..+..+|.--+.
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 4555556665 45589999999999998875 88899999974 58888888875543
No 19
>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=52.20 E-value=31 Score=28.72 Aligned_cols=41 Identities=27% Similarity=0.352 Sum_probs=27.4
Q ss_pred CchhHHHHHHHhhhhHHHHHHhhhHHHHHHhHHHHHHHHHh
Q 013185 30 PALASVIVEALKVDSLQKLCSSLEPILRRVVSEEVERALAK 70 (448)
Q Consensus 30 p~~~svi~ea~~~~~~q~l~~~lEp~lrrvV~EEve~~l~~ 70 (448)
.++-.+++|+|+---=+=|=..|=.++.|+|++||+|..++
T Consensus 33 ~TlE~lvremLRPmLkeWLD~nLP~lVErlVr~EIeRi~rr 73 (73)
T PF10691_consen 33 RTLEDLVREMLRPMLKEWLDENLPGLVERLVREEIERIARR 73 (73)
T ss_pred ccHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhcC
Confidence 46667777776653222233456678899999999997653
No 20
>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=51.62 E-value=11 Score=38.26 Aligned_cols=51 Identities=31% Similarity=0.393 Sum_probs=39.5
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhc
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAK 316 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAk 316 (448)
+|..|-+||+. .-++|...||+|++|+.++ +.+.|.+.||. .|.....+|+
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 45566667764 4478999999999999986 78899999974 4666777765
No 21
>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=49.85 E-value=14 Score=36.82 Aligned_cols=52 Identities=29% Similarity=0.453 Sum_probs=40.6
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhcc
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKT 317 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 317 (448)
+|..|-+||+. .-++|...||+|++|+..+ ++..|++.+| +.|....+||+-
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 45566666654 4578999999999999875 7888999885 478888888864
No 22
>PRK01810 DNA polymerase IV; Validated
Probab=47.19 E-value=15 Score=38.24 Aligned_cols=51 Identities=29% Similarity=0.345 Sum_probs=38.9
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhc
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAK 316 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAk 316 (448)
+|..|-+||+. .-++|...||+|++|+.++ +...|++.||. .+..+.++|.
T Consensus 180 pv~~l~giG~~--~~~~L~~~Gi~tigdL~~~---~~~~L~~rfG~-----~g~~l~~~a~ 230 (407)
T PRK01810 180 PVGEMHGIGEK--TAEKLKDIGIQTIGDLAKA---DEHILRAKLGI-----NGVRLQRRAN 230 (407)
T ss_pred CHhhcCCcCHH--HHHHHHHcCCCcHHHHHhC---CHHHHHHHHhH-----HHHHHHHHhc
Confidence 45556667764 3478999999999998775 78889999964 4666777776
No 23
>PRK03103 DNA polymerase IV; Reviewed
Probab=46.85 E-value=14 Score=38.37 Aligned_cols=52 Identities=27% Similarity=0.342 Sum_probs=40.1
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhcc
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKT 317 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 317 (448)
.|..|-+||+. .-++|...||+|++||.++ ++..|++.||. .|..+.++|.-
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 56666677774 5578999999999998875 78889999963 46677777754
No 24
>COG4766 EutQ Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=44.82 E-value=70 Score=30.72 Aligned_cols=93 Identities=17% Similarity=0.255 Sum_probs=60.8
Q ss_pred HHHHHHHhhhh-HHHHHHh-hhHHHHHHhHHHHHHHHHhcCCCC--CCCCCCCCcccCCCCCceEEEEcCCCCCCcccCC
Q 013185 34 SVIVEALKVDS-LQKLCSS-LEPILRRVVSEEVERALAKLGPAK--LTGRSSPKRIEGPDGRNLQLHFRTRLSLPLFTGG 109 (448)
Q Consensus 34 svi~ea~~~~~-~q~l~~~-lEp~lrrvV~EEve~~l~~~~~~~--~~~rs~p~~i~~~~~~~~~L~F~n~l~~pifTg~ 109 (448)
+-|+|.+..+- .-.+|+. +|-++++|++|+.-....-..+.- ..+||--+ ....+...+.|+|...=+.-+||++
T Consensus 12 ~~i~~si~a~l~~~~~~~~l~~Qlm~kVmkek~s~~~~~~~~~~k~v~~ksgik-vvk~s~vk~~~r~d~gqp~~V~~td 90 (176)
T COG4766 12 QRIRESIIAQLPEGQFTKELVEQLMEKVMKEKQSLECGWMQPSFKSVDGKSGIK-VVKLSSVKFGLRFDTGQPDCVYTTD 90 (176)
T ss_pred HHHHHHHHHhCChhhhhHHHHHHHHHHHHhchhhhhhhhcccceeecccCCcee-EEecccceeEeeecCCCCCeEEeec
Confidence 44666554432 3356765 556999999998765554433211 11222111 2223445788899988778899999
Q ss_pred ceeccCCCceEEEEEeCC
Q 013185 110 KVEGEQGTAIHIVLIDAN 127 (448)
Q Consensus 110 kI~a~~g~~I~V~L~D~~ 127 (448)
-+.-.+|.++-+.+..-.
T Consensus 91 Lvt~~~g~~l~aG~m~~~ 108 (176)
T COG4766 91 LVTEQEGSRLGAGLMEMK 108 (176)
T ss_pred eeecccCCccccceeeec
Confidence 999999999999988754
No 25
>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=44.61 E-value=9 Score=32.01 Aligned_cols=74 Identities=30% Similarity=0.382 Sum_probs=42.7
Q ss_pred ceeeeeecccchhhhhhhhcCCccHHHHHHHHhhCh-HHHHHHHcCCCCchhHHHHHHhhcccccCCceEEEecCCCCcE
Q 013185 257 VWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDS-QRLRNILGSGMSNKMWDVLVDHAKTCVLSGKLYVYYPDDPRNV 335 (448)
Q Consensus 257 VwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~-~kLR~iLg~gmS~k~We~~v~HAktCvl~~k~y~y~~~~~~nv 335 (448)
+..|-+||.. .-+.|.+.||+||+||..+=.+.. -+|++. | .
T Consensus 5 l~~LpNig~~--~e~~L~~vGI~t~~~L~~~Ga~~a~~~Lk~~-~----------------------------------~ 47 (81)
T PF04994_consen 5 LKDLPNIGPK--SERMLAKVGIHTVEDLRELGAVEAYLRLKAS-G----------------------------------P 47 (81)
T ss_dssp GCGSTT--HH--HHHHHHHTT--SHHHHHHHHHHHHHHHHHHH------------------------------------T
T ss_pred hhhCCCCCHH--HHHHHHHcCCCCHHHHHHhCHHHHHHHHHHH-C----------------------------------C
Confidence 3445556653 347899999999999998743332 344443 1 2
Q ss_pred EEEEccccceeeeeeCCeeecCCCCChHhHHHHHH
Q 013185 336 GVVFNNIYEFCGLIADGQYHSADSLSESQKVHVDT 370 (448)
Q Consensus 336 ~l~FN~i~~lvG~~~~g~y~~~d~L~~~qk~~V~~ 370 (448)
.+-+|-.|.|.||.-|= ....|++.+|.....
T Consensus 48 ~~~~~~L~aL~gAi~g~---~~~~L~~~~K~~L~~ 79 (81)
T PF04994_consen 48 SVCLNLLYALEGAIQGI---HWADLPDEEKQELLE 79 (81)
T ss_dssp T--HHHHHHHHHHHCTS----GGGS-HHHHHHHHH
T ss_pred CCCHHHHHHHHHHHcCC---CHHHCCHHHHHHHHh
Confidence 35577789999998773 345677777765543
No 26
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=44.17 E-value=28 Score=32.25 Aligned_cols=59 Identities=25% Similarity=0.397 Sum_probs=42.8
Q ss_pred ccceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHH-HHHhhcc
Q 013185 255 DEVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDV-LVDHAKT 317 (448)
Q Consensus 255 DeVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~-~v~HAkt 317 (448)
|+.-+|.+||. ++-+.|+..||+|-.+.-.+-..|-..+-..| +..-+.|.. -|+.|+.
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 47799999999996665555444444444445 677777766 6776653
No 27
>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=43.61 E-value=26 Score=25.48 Aligned_cols=42 Identities=26% Similarity=0.357 Sum_probs=32.4
Q ss_pred hhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhc
Q 013185 270 HKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAK 316 (448)
Q Consensus 270 hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAk 316 (448)
-.+|..+||.||+++..+ +++.|..+- |++...=+.++.=|+
T Consensus 6 ~~~L~~~G~~s~e~la~~---~~~eL~~i~--g~~~e~a~~ii~~a~ 47 (50)
T TIGR01954 6 AQLLVEEGFTTVEDLAYV---PIDELLSIE--GFDEETAKELINRAR 47 (50)
T ss_pred HHHHHHcCCCCHHHHHcc---CHHHHhcCC--CCCHHHHHHHHHHHH
Confidence 357999999999998766 778888875 677777666666554
No 28
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=41.75 E-value=20 Score=36.42 Aligned_cols=56 Identities=23% Similarity=0.115 Sum_probs=41.6
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhC-hHHHHHHHcCCCCchhHHHHHHhhcccccC
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRD-SQRLRNILGSGMSNKMWDVLVDHAKTCVLS 321 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d-~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 321 (448)
+|..|-+||+. .-++|.+.||+|++|+.++ + ...|+..+| +.+..+.++|+--+..
T Consensus 174 pi~~l~giG~~--~~~~L~~~Gi~ti~dl~~~---~~~~~l~~~fg-----~~~~~l~~~a~G~d~~ 230 (343)
T cd00424 174 PLTDLPGIGAV--TAKRLEAVGINPIGDLLAA---SPDALLALWGG-----VSGERLWYALRGIDDE 230 (343)
T ss_pred ChhhcCCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHhh-----HHHHHHHHHhCCcCCC
Confidence 56667777774 4488999999999998875 6 566777775 4677888888765543
No 29
>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=39.85 E-value=21 Score=35.16 Aligned_cols=54 Identities=26% Similarity=0.440 Sum_probs=37.7
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhc
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAK 316 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAk 316 (448)
...-|.+|+.+.+ ++|..+||.|+++|+++ ++++|..+| +......+.+.+.|.
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 4556678887665 88999999999999865 899999999 456677888888776
No 30
>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=38.71 E-value=14 Score=38.80 Aligned_cols=54 Identities=22% Similarity=0.243 Sum_probs=39.9
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhc
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAK 316 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAk 316 (448)
+|..|-+||+. .-++|...||.|++|+..+- .++..|++.||. +.+..+..+|.
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 67777788764 45899999999999998771 127889999974 34555555554
No 31
>PRK01216 DNA polymerase IV; Validated
Probab=38.50 E-value=13 Score=38.49 Aligned_cols=51 Identities=25% Similarity=0.391 Sum_probs=38.5
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhh
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHA 315 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HA 315 (448)
+|..|..||+. -.++|...||+|++|+.++ +...|++.||. ..+..+-.+|
T Consensus 179 Pi~~l~giG~~--~~~~L~~~Gi~TigdL~~~---~~~~L~~rfG~----~~~~~L~~~a 229 (351)
T PRK01216 179 DIADIPGIGDI--TAEKLKKLGVNKLVDTLRI---EFDELKGIIGE----AKAKYLFSLA 229 (351)
T ss_pred CcccccCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHCH----HHHHHHHHHh
Confidence 57777788864 4489999999999998875 77889999974 2344455556
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=35.96 E-value=17 Score=37.84 Aligned_cols=55 Identities=15% Similarity=0.249 Sum_probs=38.1
Q ss_pred cceeeeeecccchhhhh-hhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhcc
Q 013185 256 EVWRLEKIGKDGSFHKR-LNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKT 317 (448)
Q Consensus 256 eVwRLekIgKdG~~hkr-L~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 317 (448)
+|..|-+||+. .-++ |...||.|++|+.++. .++..|++.||. +.++.+..+|+-
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 57777777742 2244 5889999999998764 478889999874 334555555554
No 33
>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=35.46 E-value=16 Score=29.36 Aligned_cols=36 Identities=28% Similarity=0.416 Sum_probs=22.3
Q ss_pred hhhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHH
Q 013185 270 HKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDV 310 (448)
Q Consensus 270 hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~ 310 (448)
...|..+||+||+|++++ +++.|.++= |+..+.-+.
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 357899999999997766 667777774 344444333
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=32.33 E-value=21 Score=37.49 Aligned_cols=58 Identities=14% Similarity=0.151 Sum_probs=39.6
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHh------------hChHHHHHHHcCCCCchhHHHHHHhhcccc
Q 013185 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVV------------RDSQRLRNILGSGMSNKMWDVLVDHAKTCV 319 (448)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~------------~d~~kLR~iLg~gmS~k~We~~v~HAktCv 319 (448)
+|-.|-+||+... ++|.+.||.|++|+..+-+ .+...|++.||. +.+..+.++|+--+
T Consensus 173 pv~~l~GiG~~~~--~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~----~~g~~l~~~a~G~d 242 (379)
T cd01703 173 DLRKIPGIGYKTA--AKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGE----GIGQRIWKLLFGRD 242 (379)
T ss_pred CccccCCcCHHHH--HHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHCH----HHHHHHHHHHCCCC
Confidence 3444446777544 8999999999999986631 117789999864 34555666666544
No 35
>KOG1520 consensus Predicted alkaloid synthase/Surface mucin Hemomucin [General function prediction only]
Probab=30.72 E-value=1.5e+02 Score=31.78 Aligned_cols=46 Identities=33% Similarity=0.387 Sum_probs=30.9
Q ss_pred ccccCCCCCcccceeeEEEecCceeeccCceeecCCccccccccEEEEEeec
Q 013185 168 VVKEREGKRPLLSGDLQVTLKEGVGTLGDLTFTDNSSWIRSRKFRLGLKVAS 219 (448)
Q Consensus 168 IV~~ReGk~pLL~Gdl~v~L~~Gva~l~di~FTDnSsw~rSrKFRLgaRv~~ 219 (448)
++-+=+|+...++.++.|.= +| .|-|||+||.--.|.|-+++--.+
T Consensus 151 l~~~~~G~~~kf~N~ldI~~-~g-----~vyFTDSSsk~~~rd~~~a~l~g~ 196 (376)
T KOG1520|consen 151 LADEAEGKPFKFLNDLDIDP-EG-----VVYFTDSSSKYDRRDFVFAALEGD 196 (376)
T ss_pred ccccccCeeeeecCceeEcC-CC-----eEEEeccccccchhheEEeeecCC
Confidence 33444777666666665543 44 578999999766688888776554
No 36
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=30.31 E-value=83 Score=27.08 Aligned_cols=35 Identities=23% Similarity=0.439 Sum_probs=28.0
Q ss_pred hcCCccHHHHHHHHhhChHHHH---HHHcCCCCchhHHHHHHhhcc
Q 013185 275 KAGIFTVEDFLRLVVRDSQRLR---NILGSGMSNKMWDVLVDHAKT 317 (448)
Q Consensus 275 ~~~I~tV~dFL~l~~~d~~kLR---~iLg~gmS~k~We~~v~HAkt 317 (448)
...| +++||+=++-.||.||- ++| .|+..++-|+.
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 3567 99999999999997654 455 68888888875
No 37
>PRK07758 hypothetical protein; Provisional
Probab=28.66 E-value=65 Score=28.36 Aligned_cols=37 Identities=24% Similarity=0.402 Sum_probs=24.9
Q ss_pred hhhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHHHHH
Q 013185 271 KRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLV 312 (448)
Q Consensus 271 krL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v 312 (448)
..|..+||+||+|+.++ +++.|-+|= |+..+.-+.+.
T Consensus 48 N~Lk~AGI~TL~dLv~~---te~ELl~ik--nlGkKSL~EIk 84 (95)
T PRK07758 48 RALEHHGIHTVEELSKY---SEKEILKLH--GMGPASLPKLR 84 (95)
T ss_pred HHHHHcCCCcHHHHHcC---CHHHHHHcc--CCCHHHHHHHH
Confidence 46889999999998765 555566653 44455555443
No 38
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=27.95 E-value=95 Score=31.28 Aligned_cols=73 Identities=14% Similarity=0.267 Sum_probs=36.0
Q ss_pred hhHHHHHHhHHHHHHHHHhcCCCCCCCCCCCCcccCCCCCceEE-EEcCCCCCCcccCCceeccCCCceEEEEEe
Q 013185 52 LEPILRRVVSEEVERALAKLGPAKLTGRSSPKRIEGPDGRNLQL-HFRTRLSLPLFTGGKVEGEQGTAIHIVLID 125 (448)
Q Consensus 52 lEp~lrrvV~EEve~~l~~~~~~~~~~rs~p~~i~~~~~~~~~L-~F~n~l~~pifTg~kI~a~~g~~I~V~L~D 125 (448)
||-++|+|+.|++-....-..+. ...-..|.++.--.++.+++ +|..+.+..+|+.+-+..++|..+-..++.
T Consensus 90 i~~lv~~v~~e~~~~~~~~~~~~-~~~~~~~~Gi~vVrg~svk~~~fdg~~~~~v~~~d~~~~~d~s~m~aGf~~ 163 (233)
T PRK15457 90 VAQLMEKVMKEKQSLEQGAMQPS-FKSVTGKGGIKVIDGSSVKFGRFDGAEPHCVGLTDLVTGDDGSSMAAGFMQ 163 (233)
T ss_pred HHHHHHHHHHHHhcccccccCCC-ccceeCCCceEEEECCeEEEeecCCCCcccEEeeeeeccCCCCceeeEEEE
Confidence 67799999888764332110000 00011123332233445665 555455555666666666666655555443
No 39
>PF07340 Herpes_IE1: Cytomegalovirus IE1 protein; InterPro: IPR010855 Expression from a human cytomegalovirus early promoter (E1.7) has been shown to be activated in trans by the IE2 gene product. Although the IE1 gene product alone had no effect on this early viral promoter, maximal early promoter activity was detected when both IE1 and IE2 gene products were present []. The IE1 protein from cytomegalovirus is also known as UL123.; GO: 0050792 regulation of viral reproduction, 0042025 host cell nucleus
Probab=27.57 E-value=85 Score=33.74 Aligned_cols=26 Identities=38% Similarity=0.606 Sum_probs=19.6
Q ss_pred cccccCcCCCCCCCCCC-CCCCCCCCc
Q 013185 6 MERSNSKRGLDSSSAEE-GQPDRKRPA 31 (448)
Q Consensus 6 ~~~~~~kr~~~~~~~~~-~~~~~~rp~ 31 (448)
||++.+||.+|+.+.+. |.||..||-
T Consensus 1 ~~~~~~kr~~d~~~p~~gps~k~pr~e 27 (392)
T PF07340_consen 1 MESSAGKRKMDSAGPDPGPSPKMPRPE 27 (392)
T ss_pred CCCcccCCCCCCCCCCCCCCCCCCCCC
Confidence 68888999999876543 567777754
No 40
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=27.47 E-value=34 Score=30.47 Aligned_cols=39 Identities=36% Similarity=0.615 Sum_probs=29.6
Q ss_pred ceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHc
Q 013185 257 VWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILG 300 (448)
Q Consensus 257 VwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg 300 (448)
.+|..+||. .|..-|..+||.||+++-. .+|++|.+.++
T Consensus 55 L~ri~gi~~--~~a~LL~~AGv~Tv~~LA~---~~p~~L~~~l~ 93 (122)
T PF14229_consen 55 LMRIPGIGP--QYAELLEHAGVDTVEELAQ---RNPQNLHQKLG 93 (122)
T ss_pred hhhcCCCCH--HHHHHHHHhCcCcHHHHHh---CCHHHHHHHHH
Confidence 345566655 4678999999999999854 68998888653
No 41
>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=27.31 E-value=37 Score=24.77 Aligned_cols=18 Identities=22% Similarity=0.612 Sum_probs=15.2
Q ss_pred eeeccCceeecCCccccc
Q 013185 191 VGTLGDLTFTDNSSWIRS 208 (448)
Q Consensus 191 va~l~di~FTDnSsw~rS 208 (448)
-..+..+.|-|++.|++.
T Consensus 24 ~~~Ie~i~FaDGt~w~~~ 41 (43)
T PF06594_consen 24 SYRIEQIEFADGTVWTRA 41 (43)
T ss_pred CCcEeEEEEcCCCEecHH
Confidence 567889999999999863
No 42
>PF13957 YafO_toxin: Toxin YafO, type II toxin-antitoxin system
Probab=26.98 E-value=28 Score=30.64 Aligned_cols=88 Identities=19% Similarity=0.269 Sum_probs=51.9
Q ss_pred ecccchhhh--hhhhcCCccHHHHHHHHhhChHHHHHHHcCCCCchhHH-HHHHhhcccccCCceEEEecCCCCcEEEEE
Q 013185 263 IGKDGSFHK--RLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWD-VLVDHAKTCVLSGKLYVYYPDDPRNVGVVF 339 (448)
Q Consensus 263 IgKdG~~hk--rL~~~~I~tV~dFL~l~~~d~~kLR~iLg~gmS~k~We-~~v~HAktCvl~~k~y~y~~~~~~nv~l~F 339 (448)
+||||.|+. .+..++|..|- +. +.+.+-..+.|. ....+.+|++ ..-||.. +++.
T Consensus 14 fGkD~~~~~p~~~~~~~l~hiH-------i~------~~~~~~~~~~w~~~~~q~~rTSD---~~LVY~~------~~~~ 71 (109)
T PF13957_consen 14 FGKDGPFERPPEAVDSGLRHIH-------IR------KSGTPNDEDPWPRKKPQFNRTSD---NYLVYAQ------HFFD 71 (109)
T ss_pred CcCCcCccCCHhHHhcCcEEEE-------Ee------cccCCcccccCcccccCCCCCCC---cEEEEec------CccC
Confidence 599999887 33333333221 11 234556788998 4455555554 4444543 3566
Q ss_pred ccccceeeeeeC-CeeecCCCCChHhHHHHHHHHHHHHhh
Q 013185 340 NNIYEFCGLIAD-GQYHSADSLSESQKVHVDTLVKKAYDN 378 (448)
Q Consensus 340 N~i~~lvG~~~~-g~y~~~d~L~~~qk~~V~~Lk~~AY~~ 378 (448)
+.-|.|++++-. .+-.+ ....++..|.+-|.+-
T Consensus 72 ~~~y~liaii~p~AH~~~------~~~~~m~~l~~~Ae~F 105 (109)
T PF13957_consen 72 PNHYLLIAIIDPDAHEKA------EDTSLMSELAKIAEEF 105 (109)
T ss_pred CCcEEEEEEeCchHHHhh------hhHHHHHHHHHHHHHH
Confidence 777888888755 23333 3355688888887654
No 43
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=26.96 E-value=66 Score=27.78 Aligned_cols=60 Identities=25% Similarity=0.408 Sum_probs=39.6
Q ss_pred CCCCccceeeeeecccchhhhhhhhcCCcc----HHHHHHHHhhChHHHHHHHcCCCCchhHHHHHHhhccc
Q 013185 251 PALNDEVWRLEKIGKDGSFHKRLNKAGIFT----VEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTC 318 (448)
Q Consensus 251 P~L~DeVwRLekIgKdG~~hkrL~~~~I~t----V~dFL~l~~~d~~kLR~iLg~gmS~k~We~~v~HAktC 318 (448)
|+=+-+|--|.+||.. +-.+|..+|+.. .++|| ++.+|++-.+.-|. ..--++-+||++|
T Consensus 15 PmGeK~V~~laGIg~~--lg~~L~~~GfdkAYvllGQfL-llkKdE~lF~~Wlk-----~~~gat~~~a~~~ 78 (90)
T KOG4233|consen 15 PMGEKDVTWLAGIGET--LGIKLVDAGFDKAYVLLGQFL-LLKKDEDLFQEWLK-----ETCGATAKQAQDC 78 (90)
T ss_pred ccCCCcceeeccccHH--hhhhHHhccccHHHHHHHHHH-HhcccHHHHHHHHH-----HHcCccHHHHHHH
Confidence 5666788899999874 557999999976 46776 44678765555331 1112355677766
No 44
>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=26.76 E-value=75 Score=25.78 Aligned_cols=25 Identities=44% Similarity=0.666 Sum_probs=16.0
Q ss_pred hHHHHHHHhhhhHHHHHHhhhHHHHHHhH
Q 013185 33 ASVIVEALKVDSLQKLCSSLEPILRRVVS 61 (448)
Q Consensus 33 ~svi~ea~~~~~~q~l~~~lEp~lrrvV~ 61 (448)
+||=+.=+++ + |.-.|||+|||...
T Consensus 29 KsVsrkPLr~--l--La~aLEPllkr~~~ 53 (59)
T TIGR02979 29 KSVARRPLKM--L--LAIALEPMLKRAAN 53 (59)
T ss_pred HHHhhccHHH--H--HHHHHHHHHHHHHH
Confidence 3444444444 2 45589999999854
No 45
>PRK05256 condesin subunit E; Provisional
Probab=26.59 E-value=94 Score=31.34 Aligned_cols=74 Identities=19% Similarity=0.294 Sum_probs=50.8
Q ss_pred hhhhhcCCccHHHHHHHHh--hChHHHHHHHc--CCCCchhHHHHHHhhcccc--cCCceEEEecCCCCcEEEEEccccc
Q 013185 271 KRLNKAGIFTVEDFLRLVV--RDSQRLRNILG--SGMSNKMWDVLVDHAKTCV--LSGKLYVYYPDDPRNVGVVFNNIYE 344 (448)
Q Consensus 271 krL~~~~I~tV~dFL~l~~--~d~~kLR~iLg--~gmS~k~We~~v~HAktCv--l~~k~y~y~~~~~~nv~l~FN~i~~ 344 (448)
++|++.||.|+++.+.-+. .|++||.+.++ .+-|+-+-+++.+-.++|- +..-=.++...+..+...+=++||-
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 7999999999999876544 48999999985 3337778888999999986 3333344544322344444455544
No 46
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=24.14 E-value=2.2e+02 Score=26.12 Aligned_cols=40 Identities=23% Similarity=0.523 Sum_probs=31.4
Q ss_pred chhhhhhhhcCCccHHHHHHHHhhCh----HHHHHHHcCCCCch
Q 013185 267 GSFHKRLNKAGIFTVEDFLRLVVRDS----QRLRNILGSGMSNK 306 (448)
Q Consensus 267 G~~hkrL~~~~I~tV~dFL~l~~~d~----~kLR~iLg~gmS~k 306 (448)
.+|+..|+.+|=.||+|.-.-++++. ..|++++-.||=.+
T Consensus 31 ~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~R 74 (126)
T COG3355 31 EVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVER 74 (126)
T ss_pred HHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeee
Confidence 46888888999999999999999985 46777765665443
No 47
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=23.81 E-value=32 Score=38.73 Aligned_cols=39 Identities=31% Similarity=0.416 Sum_probs=31.7
Q ss_pred CCCCCccceeeeeecccchhhhhhhhcCCccHHHHHHHHhh
Q 013185 250 PPALNDEVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVR 290 (448)
Q Consensus 250 pP~L~DeVwRLekIgKdG~~hkrL~~~~I~tV~dFL~l~~~ 290 (448)
...|++.|-.|++||+.- .+.|++-||+||.|.|..+=+
T Consensus 4 ~~~~~~~~~~l~gvg~~~--~~~l~~lgi~t~~dll~~~P~ 42 (681)
T PRK10917 4 LLLLDAPLTSLKGVGPKT--AEKLAKLGIHTVQDLLLHLPR 42 (681)
T ss_pred cccccCChhhcCCCCHHH--HHHHHHcCCCCHHHHhhcCCC
Confidence 345778999999998754 378999999999999988654
No 48
>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=23.12 E-value=91 Score=25.85 Aligned_cols=15 Identities=47% Similarity=0.789 Sum_probs=12.1
Q ss_pred HHHhhhHHHHHHhHH
Q 013185 48 LCSSLEPILRRVVSE 62 (448)
Q Consensus 48 l~~~lEp~lrrvV~E 62 (448)
|.-.|||+|||.++.
T Consensus 45 La~~LEPllrr~~~~ 59 (66)
T PF09584_consen 45 LALALEPLLRRGLNK 59 (66)
T ss_pred HHHHHHHHHHHHHHH
Confidence 455899999999764
No 49
>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=22.48 E-value=44 Score=33.29 Aligned_cols=35 Identities=20% Similarity=0.323 Sum_probs=28.9
Q ss_pred eecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcC
Q 013185 262 KIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGS 301 (448)
Q Consensus 262 kIgKdG~~hkrL~~~~I~tV~dFL~l~~~d~~kLR~iLg~ 301 (448)
.||+... .+|.+.||+|++||..+ +...|++.||.
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 89999999999998876 78889999975
No 50
>PF10148 SCHIP-1: Schwannomin-interacting protein 1; InterPro: IPR015649 SCHIP-1 is a coiled-coil protein that specifically associates with schwannomin in vitro and in vivo. The product of the neurofibromatosis type 2 (NF2) tumour suppressor gene, known as schwannomin or merlin, is involved in NF2-associated and sporadic schwannomas and meningiomas. It is closely related to the ezrin-radixin-moesin family members, which link membrane proteins to the cytoskeleton. Association with SCHIP-1 can be observed only with some naturally occurring mutants of schwannomin, or a schwannomin spliced isoform lacking exons 2 and 3, but not with the schwannomin isoform exhibiting growth-suppressive activity []. This entry consists of mammalian SCHIP-1 proteins from Mus musculus (Mouse) and Homo sapiens (Human).
Probab=21.66 E-value=1.3e+02 Score=30.40 Aligned_cols=16 Identities=38% Similarity=0.443 Sum_probs=13.4
Q ss_pred CCCCceEEEEcCCCCC
Q 013185 88 PDGRNLQLHFRTRLSL 103 (448)
Q Consensus 88 ~~~~~~~L~F~n~l~~ 103 (448)
+.+.++|.||+|.++.
T Consensus 45 qsgmNLQVCFmNE~~s 60 (238)
T PF10148_consen 45 QSGMNLQVCFMNETSS 60 (238)
T ss_pred CCCceeeEEeecCCCC
Confidence 4578999999999854
No 51
>PRK10497 peripheral inner membrane phage-shock protein; Provisional
Probab=20.87 E-value=1.1e+02 Score=25.78 Aligned_cols=15 Identities=40% Similarity=0.806 Sum_probs=11.9
Q ss_pred HHHhhhHHHHHHhHH
Q 013185 48 LCSSLEPILRRVVSE 62 (448)
Q Consensus 48 l~~~lEp~lrrvV~E 62 (448)
|.-.|||+|||.++-
T Consensus 52 L~~~LEPlLkr~~~~ 66 (73)
T PRK10497 52 LAVALEPLLKRAANK 66 (73)
T ss_pred HHHHHHHHHHHHHHH
Confidence 445899999999764
No 52
>PF08806 Sep15_SelM: Sep15/SelM redox domain; InterPro: IPR014912 Sep15 and SelM are eukaryotic selenoproteins that have a thioredoxin-like domain and a surface accessible active site redox motif []. This suggests that they function as thiol-disulphide isomerases involved in disulphide bond formation in the endoplasmic reticulum []. ; PDB: 2A4H_A 2A2P_A.
Probab=20.14 E-value=62 Score=27.05 Aligned_cols=36 Identities=28% Similarity=0.405 Sum_probs=23.8
Q ss_pred EcCCCCCCcccCCceeccCCCceEEEEEeCCCCceec
Q 013185 97 FRTRLSLPLFTGGKVEGEQGTAIHIVLIDANTGHVVT 133 (448)
Q Consensus 97 F~n~l~~pifTg~kI~a~~g~~I~V~L~D~~t~~iVt 133 (448)
|.+.=..+.|.+-.|+-.-|++=.+.|+|.+ |+.+.
T Consensus 21 Fi~~~~~~~y~~v~vk~i~G~~P~L~l~d~~-g~~~E 56 (78)
T PF08806_consen 21 FIKSDVPPLYPNVEVKYIPGAPPELVLLDED-GEEVE 56 (78)
T ss_dssp HCCCCCGHHBTTEEEEEESS---EEEEE-SS-S--SE
T ss_pred HHhccchhccCceEEEEeCCCCCEEEEEcCC-CCEEE
Confidence 6665446889999999999999999999974 66554
No 53
>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=20.11 E-value=92 Score=24.69 Aligned_cols=22 Identities=18% Similarity=0.232 Sum_probs=17.4
Q ss_pred eeecCCCCChHhHHHHHHHHHH
Q 013185 353 QYHSADSLSESQKVHVDTLVKK 374 (448)
Q Consensus 353 ~y~~~d~L~~~qk~~V~~Lk~~ 374 (448)
+||++.+|++.|..+++.+.++
T Consensus 31 HyI~k~dLs~~E~~aA~~~~~~ 52 (53)
T PF04270_consen 31 HYIPKSDLSASELKAAQAYLAG 52 (53)
T ss_dssp EEEEGGGS-HHHHHHHHHHHH-
T ss_pred cCCchhhCCHHHHHHHHHHHhc
Confidence 4999999999999998877653
Done!