Query 043314
Match_columns 273
No_of_seqs 112 out of 140
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 03:45:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043314.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043314hhsearch_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-111 5E-116 784.1 24.1 258 13-273 1-283 (299)
2 TIGR02239 recomb_RAD51 DNA rep 87.6 0.42 9E-06 45.4 2.6 47 175-226 13-60 (316)
3 TIGR02238 recomb_DMC1 meiotic 85.1 0.62 1.3E-05 44.3 2.4 48 174-226 12-60 (313)
4 PLN03186 DNA repair protein RA 84.9 0.7 1.5E-05 44.7 2.7 59 163-226 28-87 (342)
5 PRK04301 radA DNA repair and r 77.6 0.87 1.9E-05 42.6 0.5 55 163-224 8-63 (317)
6 PLN03187 meiotic recombination 77.3 1.2 2.5E-05 43.3 1.3 59 162-225 30-89 (344)
7 PF14520 HHH_5: Helix-hairpin- 77.1 0.99 2.1E-05 32.5 0.6 49 166-221 10-59 (60)
8 PTZ00035 Rad51 protein; Provis 71.1 3.2 7E-05 39.8 2.6 59 162-225 22-81 (337)
9 PRK03609 umuC DNA polymerase V 66.4 2.6 5.7E-05 41.1 1.0 50 162-221 180-230 (422)
10 PRK02406 DNA polymerase IV; Va 63.6 3.7 8E-05 38.7 1.3 50 162-221 169-219 (343)
11 TIGR02236 recomb_radA DNA repa 58.5 3.9 8.5E-05 37.9 0.6 49 166-221 4-53 (310)
12 PRK03352 DNA polymerase IV; Va 57.8 2.5 5.4E-05 39.9 -0.9 41 162-207 178-218 (346)
13 PRK03858 DNA polymerase IV; Va 57.5 2.9 6.2E-05 40.1 -0.5 48 162-214 174-221 (396)
14 PF14229 DUF4332: Domain of un 57.0 9.5 0.00021 31.6 2.5 47 175-223 7-56 (122)
15 PRK03348 DNA polymerase IV; Pr 53.2 4.1 8.8E-05 40.6 -0.3 48 162-214 181-228 (454)
16 COG3743 Uncharacterized conser 51.4 11 0.00025 32.4 2.2 58 161-222 67-126 (133)
17 PRK01172 ski2-like helicase; P 50.1 9.6 0.00021 39.4 1.8 50 166-222 617-667 (674)
18 PRK14133 DNA polymerase IV; Pr 49.1 9.7 0.00021 36.0 1.6 50 162-221 174-224 (347)
19 PRK02794 DNA polymerase IV; Pr 48.9 7.7 0.00017 37.8 0.9 52 163-224 211-263 (419)
20 PF03118 RNA_pol_A_CTD: Bacter 46.8 6.4 0.00014 29.4 -0.0 26 177-205 25-50 (66)
21 cd01700 PolY_Pol_V_umuC umuC s 45.7 9.2 0.0002 36.1 0.9 49 163-221 178-227 (344)
22 PF04994 TfoX_C: TfoX C-termin 44.8 13 0.00028 28.9 1.4 29 165-195 7-35 (81)
23 PRK01216 DNA polymerase IV; Va 43.2 12 0.00026 36.1 1.3 40 162-206 179-218 (351)
24 cd03586 PolY_Pol_IV_kappa DNA 42.5 13 0.00028 34.5 1.3 50 162-221 172-222 (334)
25 PF00853 Runt: Runt domain; I 42.1 72 0.0016 27.6 5.6 35 89-125 73-107 (135)
26 cd01701 PolY_Rev1 DNA polymera 41.6 12 0.00026 36.6 0.9 43 162-207 223-265 (404)
27 PF14229 DUF4332: Domain of un 40.6 12 0.00027 30.9 0.8 39 163-206 55-93 (122)
28 PRK03103 DNA polymerase IV; Re 40.5 16 0.00034 35.4 1.5 40 162-206 182-221 (409)
29 PF06594 HCBP_related: Haemoly 40.0 17 0.00038 24.6 1.3 18 97-114 24-41 (43)
30 cd00424 PolY Y-family of DNA p 34.0 18 0.00038 34.2 0.8 51 162-222 174-226 (343)
31 PRK01810 DNA polymerase IV; Va 33.6 18 0.0004 34.9 0.8 50 162-221 180-230 (407)
32 KOG4233 DNA-bridging protein B 32.1 47 0.001 26.7 2.7 59 157-223 15-78 (90)
33 cd01702 PolY_Pol_eta DNA Polym 30.3 12 0.00027 36.1 -1.0 42 162-206 183-225 (359)
34 cd01703 PolY_Pol_iota DNA Poly 29.8 15 0.00032 36.0 -0.5 42 163-206 174-227 (379)
35 PRK10917 ATP-dependent DNA hel 29.6 17 0.00038 38.0 -0.1 38 157-196 5-42 (681)
36 PF04717 Phage_base_V: Phage-r 29.5 1E+02 0.0022 23.0 4.2 38 130-167 12-54 (79)
37 KOG1520 Predicted alkaloid syn 28.7 1.5E+02 0.0032 29.8 6.1 160 30-205 108-303 (376)
38 PF05224 NDT80_PhoG: NDT80 / P 27.9 1.3E+02 0.0028 26.6 5.2 51 96-146 118-178 (186)
39 smart00198 SCP SCP / Tpx-1 / A 27.8 84 0.0018 25.2 3.7 43 199-241 11-68 (144)
40 KOG1690 emp24/gp25L/p24 family 26.5 1.7E+02 0.0037 27.2 5.7 95 16-127 31-129 (215)
41 cd07978 TAF13 The TATA Binding 25.8 86 0.0019 25.1 3.3 34 181-222 52-89 (92)
42 PRK05256 condesin subunit E; P 24.3 83 0.0018 29.6 3.3 49 177-225 107-160 (238)
43 COG0540 PyrB Aspartate carbamo 23.7 40 0.00086 33.0 1.2 69 68-150 29-114 (316)
44 PF05643 DUF799: Putative bact 23.4 65 0.0014 29.9 2.4 74 107-207 26-106 (215)
45 PF11754 Velvet: Velvet factor 23.0 1.1E+02 0.0025 27.3 3.9 62 82-146 97-172 (203)
46 cd03468 PolY_like DNA Polymera 22.8 54 0.0012 30.3 1.9 34 168-206 177-210 (335)
47 PF10657 RC-P840_PscD: Photosy 20.0 1.2E+02 0.0025 26.4 3.1 28 235-262 115-142 (144)
No 1
>PF07887 Calmodulin_bind: Calmodulin binding protein-like; InterPro: IPR012416 The members of this family are putative or actual calmodulin binding proteins expressed by various plant species. Some members (for example, Q8H6T7 from SWISSPROT), are known to be involved in the induction of plant defence responses []. However, their precise function in this regard is as yet unknown.
Probab=100.00 E-value=2.4e-111 Score=784.09 Aligned_cols=258 Identities=55% Similarity=0.888 Sum_probs=251.8
Q ss_pred ceEEEEccCCCCCcccCCceeecCCCceEEEEEEcCCCCceecCCCCCceEEeeh----------------Hhhhhcccc
Q 043314 13 SLKLNFSKKLSLPIFTGSKITNIESDHLQIVVVKTRSGSRIAPANLSQPIKILMV----------------EEFESNIVK 76 (273)
Q Consensus 13 ~~~L~F~n~l~~pifT~~~I~a~~g~~i~V~L~D~~~~~~iv~~g~~ss~kieIv----------------eeF~~~Iv~ 76 (273)
++||+|+|+|++|||||++|+|+||+||+|+|+|++ |+ |++||+||+||||| |||+++||+
T Consensus 1 ~~~L~F~n~l~~pifT~~~i~a~~g~~i~V~l~d~~-~~--v~~g~lss~kieIvvLdGdF~~~~~~~wT~eeF~~~iv~ 77 (299)
T PF07887_consen 1 NLQLRFLNKLSLPIFTGSKIEAEDGAPIKVALVDAN-TG--VTSGPLSSAKIEIVVLDGDFNDEDCEDWTEEEFNSHIVK 77 (299)
T ss_pred CeEEEecCCCCCCcccCCceEecCCCcEEEEEEECC-CC--ccCCCCCCcEEEEEEEccccCCCccCCCCHHHHhhcEee
Confidence 589999999999999999999999999999999998 44 99999999999999 999999999
Q ss_pred cCCCccccccceEEEEEeCcEEeecCeEEecCCCcccCcceEEEEEEeecCCCceeeeeeeecceEEeecCCcccccCCC
Q 043314 77 ERTGKRLLLTGDVNVTIKNGVARVEDIEFTDNSNWIRSRKFRIGAKVAQWTYHGVRIREAITEAFVVKDHRGELYKKHHP 156 (273)
Q Consensus 77 ~R~Gk~pLL~Gdl~v~L~~Gva~l~di~FtDnSs~~rsrKFRLgarv~~~~~~~~rI~Eavse~FvVkd~Rge~~kKh~p 156 (273)
+|+||+|||+|+++|+|+||+|+|+||+|||||||+|||||||||||+++++.|+|||||+||||+|||||||+||||||
T Consensus 78 ~r~gk~pLL~G~~~v~L~~G~a~l~di~FtdnSs~~rsrKFRLgarv~~~~~~~~rI~Eavse~FvVkd~Rge~~kKh~p 157 (299)
T PF07887_consen 78 EREGKRPLLTGDLQVTLKNGVATLGDISFTDNSSWIRSRKFRLGARVVSGSCDGVRIREAVSEPFVVKDHRGELYKKHYP 157 (299)
T ss_pred cCCCCCCCCCccEEEEecCCEEEccccEEecCcccccCCcEEEEEEEccCCCCCceeEEeeecCEEEEecccccccCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhhcccCCCceEEEe--
Q 043314 157 PMLEDEVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHARTCSMGSKLYIFR-- 233 (273)
Q Consensus 157 P~L~DeVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAktC~l~~k~y~y~-- 233 (273)
|+|+|||||||+|||||+|||+|+++||+||+|||+++++||++||+|||+|||++||+ ||+|||||++++++|+|+
T Consensus 158 P~L~DeVwRLe~Igk~G~~hk~L~~~~I~tV~dFl~l~~~d~~~Lr~ilg~~ms~k~We~~v~HA~tCvl~~~~y~y~~~ 237 (299)
T PF07887_consen 158 PSLDDEVWRLEKIGKDGAFHKRLKKNGINTVEDFLKLLNKDPQKLREILGSGMSNKMWETTVEHAKTCVLGDKLYVYYDE 237 (299)
T ss_pred CCCCCchhhhhhccccCHHHHHHHHcCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHHHHHHHHhcCCCCcEEEEEec
Confidence 99999999999999999999999999999999999999999999999999999999999 999999999999999999
Q ss_pred cCcEEEEEcccceeeeeEECCEEeeCCCCCch------hhhhhhcC
Q 043314 234 GQNCIIILNPICQVVRATINGQTFLTRDLPNL------NGLKRAYS 273 (273)
Q Consensus 234 ~~~v~l~FN~i~~lvga~~~g~~~~~~~l~~~------~~~k~~~~ 273 (273)
++|++|+||||||||||+|+|||++.++|++. +.+++||.
T Consensus 238 ~~nv~l~FN~i~~lvga~~~g~y~s~d~L~~~qK~~v~~Lv~~AY~ 283 (299)
T PF07887_consen 238 EQNVGLFFNCIYELVGAIFGGQYVSLDNLSSAQKAYVDKLVKQAYE 283 (299)
T ss_pred CCceEEEEcchhhEEeEEECCEEEehHHcCHHHHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999 46788883
No 2
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=87.55 E-value=0.42 Score=45.43 Aligned_cols=47 Identities=26% Similarity=0.231 Sum_probs=41.1
Q ss_pred ccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhhcccCC
Q 043314 175 FCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHARTCSMG 226 (273)
Q Consensus 175 ~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAktC~l~ 226 (273)
--++|+++||.||+||+.. +|..|.+++ ++|...++ +..||.+|...
T Consensus 13 ~~~~l~~~g~~t~~~~~~~---~~~~L~~i~--~ls~~~~~~~~~~~~~~~~~ 60 (316)
T TIGR02239 13 DIKKLQEAGLHTVESVAYA---PKKQLLEIK--GISEAKADKILAEAAKLVPM 60 (316)
T ss_pred HHHHHHHcCCCcHHHHHhC---CHHHHHHHh--CCCHHHHHHHHHHHHHhccc
Confidence 3489999999999998865 899999997 69999999 99999988653
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=85.11 E-value=0.62 Score=44.31 Aligned_cols=48 Identities=27% Similarity=0.238 Sum_probs=41.1
Q ss_pred cccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhhcccCC
Q 043314 174 NFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHARTCSMG 226 (273)
Q Consensus 174 ~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAktC~l~ 226 (273)
.--++|+++||.||+||+.. ++..|.++. |+|...++ +++.|+.+...
T Consensus 12 ~~~~~L~~~g~~t~~~~~~~---~~~~L~~~~--gls~~~~~~i~~~~~~~~~~ 60 (313)
T TIGR02238 12 ADIKKLKSAGICTVNGVIMT---TRRALCKIK--GLSEAKVDKIKEAASKIINP 60 (313)
T ss_pred HHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHhhhcc
Confidence 34589999999999998765 789999996 69999999 99999887654
No 4
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=84.94 E-value=0.7 Score=44.67 Aligned_cols=59 Identities=24% Similarity=0.212 Sum_probs=45.1
Q ss_pred eeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhhcccCC
Q 043314 163 VWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHARTCSMG 226 (273)
Q Consensus 163 VwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAktC~l~ 226 (273)
+-.|..-|-.-.--++|+++||.||+|++.+ ++..|.++. ++|....+ ++.||.+|...
T Consensus 28 ~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~---~~~~L~~i~--~is~~~~~~~~~~~~~~~~~ 87 (342)
T PLN03186 28 IEQLQASGIAALDIKKLKDAGIHTVESLAYA---PKKDLLQIK--GISEAKVEKILEAASKLVPL 87 (342)
T ss_pred HHHHHhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHHhccc
Confidence 4444332332234599999999999998765 788999997 69999999 99999887653
No 5
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=77.64 E-value=0.87 Score=42.65 Aligned_cols=55 Identities=24% Similarity=0.343 Sum_probs=41.6
Q ss_pred eeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhhccc
Q 043314 163 VWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHARTCS 224 (273)
Q Consensus 163 VwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAktC~ 224 (273)
+-.|.+||+ ...++|.++||.|++|++. .+++.|.+++ |++.+.++ +++-|+.+.
T Consensus 8 l~~l~gIg~--~~a~~L~~~Gi~t~~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~a~~~~ 63 (317)
T PRK04301 8 LEDLPGVGP--ATAEKLREAGYDTVEAIAV---ASPKELSEAA--GIGESTAAKIIEAAREAA 63 (317)
T ss_pred HhhcCCCCH--HHHHHHHHcCCCCHHHHHc---CCHHHHHHhc--CCCHHHHHHHHHHHHHhh
Confidence 344555664 4569999999999999865 4899999998 57777888 777776533
No 6
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=77.28 E-value=1.2 Score=43.32 Aligned_cols=59 Identities=24% Similarity=0.212 Sum_probs=45.1
Q ss_pred ceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhhcccC
Q 043314 162 EVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHARTCSM 225 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAktC~l 225 (273)
++..|+.-|-.-.--++|+++||.||+|++.. ++..|-++. |+|...++ +++.|+..+.
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 35556553333345699999999999998765 688899885 79999999 9998887653
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=77.07 E-value=0.99 Score=32.48 Aligned_cols=49 Identities=35% Similarity=0.548 Sum_probs=37.0
Q ss_pred eeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhh
Q 043314 166 LGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHAR 221 (273)
Q Consensus 166 Le~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAk 221 (273)
+.+||+. ..++|.++||.|++|+..+ +++.|.++= |++.+.=+ +++.|+
T Consensus 10 I~Gig~~--~a~~L~~~G~~t~~~l~~a---~~~~L~~i~--Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 10 IPGIGPK--RAEKLYEAGIKTLEDLANA---DPEELAEIP--GIGEKTAEKIIEAAR 59 (60)
T ss_dssp STTCHHH--HHHHHHHTTCSSHHHHHTS---HHHHHHTST--TSSHHHHHHHHHHHH
T ss_pred CCCCCHH--HHHHHHhcCCCcHHHHHcC---CHHHHhcCC--CCCHHHHHHHHHHHh
Confidence 3445543 3488999999999998764 788899884 67888877 877775
No 8
>PTZ00035 Rad51 protein; Provisional
Probab=71.07 E-value=3.2 Score=39.83 Aligned_cols=59 Identities=25% Similarity=0.231 Sum_probs=43.1
Q ss_pred ceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhhcccC
Q 043314 162 EVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHARTCSM 225 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAktC~l 225 (273)
++-.|..-|-.-.--++|+++||.||+||+.. ++..|.++. |+|...=+ +++.|+.++.
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 35555442222334599999999999998764 788899886 68888888 8888877654
No 9
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=66.39 E-value=2.6 Score=41.10 Aligned_cols=50 Identities=28% Similarity=0.395 Sum_probs=37.3
Q ss_pred ceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhh
Q 043314 162 EVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHAR 221 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAk 221 (273)
+|..|-+||+. ..++|...||+|++|+.++ ++..|++.||. .+. +..||.
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 34555567763 4599999999999999886 78899999972 345 666664
No 10
>PRK02406 DNA polymerase IV; Validated
Probab=63.62 E-value=3.7 Score=38.71 Aligned_cols=50 Identities=30% Similarity=0.353 Sum_probs=37.3
Q ss_pred ceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhh
Q 043314 162 EVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHAR 221 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAk 221 (273)
+|..|-+||+ ..-++|...||.|++|+.++ ++..|++.||. .+. ...||.
T Consensus 169 pi~~l~giG~--~~~~~L~~~Gi~ti~dl~~l---~~~~L~~~fG~-----~~~~l~~~a~ 219 (343)
T PRK02406 169 PVEKIPGVGK--VTAEKLHALGIYTCADLQKY---DLAELIRHFGK-----FGRRLYERAR 219 (343)
T ss_pred CcchhcCCCH--HHHHHHHHcCCCcHHHHHhC---CHHHHHHHHhH-----HHHHHHHHhC
Confidence 4666666775 34588999999999999885 78889999973 345 555654
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=58.52 E-value=3.9 Score=37.90 Aligned_cols=49 Identities=29% Similarity=0.410 Sum_probs=34.3
Q ss_pred eeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhh
Q 043314 166 LGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHAR 221 (273)
Q Consensus 166 Le~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAk 221 (273)
|.+||+ ...++|.++||.|++|++.+ +++.|.+++| ++.+..+ +.+-|+
T Consensus 4 i~gig~--~~~~~L~~~Gi~ti~dl~~~---~~~~L~~~~g--~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 4 LPGVGP--ATAEKLREAGYDTFEAIAVA---SPKELSEIAG--ISEGTAAKIIQAAR 53 (310)
T ss_pred cCCCCH--HHHHHHHHcCCCCHHHHHcC---CHHHHHhccC--CCHHHHHHHHHHHH
Confidence 334443 24589999999999998774 8888988874 5555555 444444
No 12
>PRK03352 DNA polymerase IV; Validated
Probab=57.80 E-value=2.5 Score=39.90 Aligned_cols=41 Identities=32% Similarity=0.413 Sum_probs=32.3
Q ss_pred ceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcC
Q 043314 162 EVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGT 207 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~ 207 (273)
+|..|-+||+. ..++|...||+|++|++++ ++..|++.||.
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 45555567764 4588999999999999986 67789999874
No 13
>PRK03858 DNA polymerase IV; Validated
Probab=57.51 E-value=2.9 Score=40.13 Aligned_cols=48 Identities=31% Similarity=0.401 Sum_probs=34.4
Q ss_pred ceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccch
Q 043314 162 EVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMW 214 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W 214 (273)
+|..|-+||+. .-++|.+.||+|++|+.+ .++..|++.||..+-...|
T Consensus 174 pl~~l~Gig~~--~~~~L~~~Gi~t~~dl~~---l~~~~L~~~fG~~~~~~l~ 221 (396)
T PRK03858 174 PVRRLWGVGPV--TAAKLRAHGITTVGDVAE---LPESALVSLLGPAAGRHLH 221 (396)
T ss_pred ChhhcCCCCHH--HHHHHHHhCCCcHHHHhc---CCHHHHHHHhCcHHHHHHH
Confidence 34555567764 458999999999999986 4788899988753333333
No 14
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=57.01 E-value=9.5 Score=31.57 Aligned_cols=47 Identities=32% Similarity=0.348 Sum_probs=32.4
Q ss_pred ccchhhhCCCccHHHHHHHhccChHH--HHHHHcCCCCccchh-hhhhhhcc
Q 043314 175 FCGKLAASGIKTVQDFLKVSIVEPQK--LRRILGTGMSEKMWD-TMKHARTC 223 (273)
Q Consensus 175 ~hk~L~~~~I~tV~dFLkl~~~d~~k--Lr~iLg~~ms~k~W~-~v~HAktC 223 (273)
...+|+..||+|++|||..-.....+ |-+-+ |++.+.=. .+.+|.=|
T Consensus 7 ~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~--~i~~~~l~~w~~~AdL~ 56 (122)
T PF14229_consen 7 EAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKL--GISERNLLKWVNQADLM 56 (122)
T ss_pred HHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhc--CCCHHHHHHHHhHHHhh
Confidence 45899999999999999987665544 55554 46665544 55555443
No 15
>PRK03348 DNA polymerase IV; Provisional
Probab=53.24 E-value=4.1 Score=40.58 Aligned_cols=48 Identities=27% Similarity=0.352 Sum_probs=36.5
Q ss_pred ceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccch
Q 043314 162 EVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMW 214 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W 214 (273)
+|..|-+||+. .-++|...||+|++||.++ +...|++.||..+-..-|
T Consensus 181 Pv~~L~GIG~~--t~~~L~~lGI~TigDLa~l---~~~~L~~~fG~~~g~~L~ 228 (454)
T PRK03348 181 PVRRLWGIGPV--TEEKLHRLGIETIGDLAAL---SEAEVANLLGATVGPALH 228 (454)
T ss_pred CccccCCCCHH--HHHHHHHcCCccHHHHhcC---CHHHHHHHHCHHHHHHHH
Confidence 57778788875 4588999999999999875 788899999743333333
No 16
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=51.40 E-value=11 Score=32.41 Aligned_cols=58 Identities=17% Similarity=0.215 Sum_probs=41.9
Q ss_pred CceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh--hhhhhhc
Q 043314 161 DEVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD--TMKHART 222 (273)
Q Consensus 161 DeVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~--~v~HAkt 222 (273)
|+.-||.+||. ++-+.|+..||+|-.+.-.+-..|-..+-..| +..-+.|. -|+.|+.
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 47799999999997665544444444444445 67777776 6666653
No 17
>PRK01172 ski2-like helicase; Provisional
Probab=50.12 E-value=9.6 Score=39.36 Aligned_cols=50 Identities=28% Similarity=0.555 Sum_probs=36.2
Q ss_pred eeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhhc
Q 043314 166 LGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHART 222 (273)
Q Consensus 166 Le~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAkt 222 (273)
|.++++. ..++|.++||.||.|+.. .++++|-+|+ |++++.=+ ++++|+.
T Consensus 617 ip~~~~~--~a~~l~~~g~~~~~di~~---~~~~~~~~i~--~~~~~~~~~i~~~~~~ 667 (674)
T PRK01172 617 IPKVGRV--RARRLYDAGFKTVDDIAR---SSPERIKKIY--GFSDTLANAIVNRAMK 667 (674)
T ss_pred CCCCCHH--HHHHHHHcCCCCHHHHHh---CCHHHHHHHh--ccCHHHHHHHHHHHHH
Confidence 3444443 568888889999888766 5777787787 47777777 8888764
No 18
>PRK14133 DNA polymerase IV; Provisional
Probab=49.13 E-value=9.7 Score=36.02 Aligned_cols=50 Identities=26% Similarity=0.358 Sum_probs=36.1
Q ss_pred ceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhh
Q 043314 162 EVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHAR 221 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAk 221 (273)
+|..|-+||+. .-++|.+.||+|++|++++ +...|++.||. .|. ..++|.
T Consensus 174 pv~~l~gig~~--~~~~L~~~Gi~ti~dl~~l---~~~~L~~rfG~-----~g~~l~~~a~ 224 (347)
T PRK14133 174 PISKVHGIGKK--SVEKLNNIGIYTIEDLLKL---SREFLIEYFGK-----FGVEIYERIR 224 (347)
T ss_pred CccccCCCCHH--HHHHHHHcCCccHHHHhhC---CHHHHHHHHhH-----HHHHHHHHhC
Confidence 45555566654 3478999999999999875 67889999972 355 556653
No 19
>PRK02794 DNA polymerase IV; Provisional
Probab=48.89 E-value=7.7 Score=37.83 Aligned_cols=52 Identities=27% Similarity=0.349 Sum_probs=38.4
Q ss_pred eeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhhccc
Q 043314 163 VWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHARTCS 224 (273)
Q Consensus 163 VwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAktC~ 224 (273)
|..|-+||+ ..-++|...||+|++|+.++ +...|++.||. +|. ...+|.--+
T Consensus 211 l~~L~GiG~--~~~~~L~~~GI~tigdL~~l---~~~~L~~rfG~-----~g~~l~~~a~G~d 263 (419)
T PRK02794 211 VGIIWGVGP--ATAARLARDGIRTIGDLQRA---DEADLMRRFGS-----MGLRLWRLARGID 263 (419)
T ss_pred hhhhCCCCH--HHHHHHHHhccchHHHHhhC---CHHHHHHHHhH-----HHHHHHHHhCCCC
Confidence 444445664 45689999999999998875 78889999973 466 777776544
No 20
>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=46.75 E-value=6.4 Score=29.42 Aligned_cols=26 Identities=35% Similarity=0.471 Sum_probs=17.8
Q ss_pred chhhhCCCccHHHHHHHhccChHHHHHHH
Q 043314 177 GKLAASGIKTVQDFLKVSIVEPQKLRRIL 205 (273)
Q Consensus 177 k~L~~~~I~tV~dFLkl~~~d~~kLr~iL 205 (273)
..|..+||+||+|++++ +++.|.++=
T Consensus 25 n~L~~~~I~tv~dL~~~---s~~~L~~i~ 50 (66)
T PF03118_consen 25 NCLKRAGIHTVGDLVKY---SEEDLLKIK 50 (66)
T ss_dssp HHHHCTT--BHHHHHCS----HHHHHTST
T ss_pred HHHHHhCCcCHHHHHhC---CHHHHHhCC
Confidence 67889999999997765 566777663
No 21
>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=45.71 E-value=9.2 Score=36.05 Aligned_cols=49 Identities=31% Similarity=0.451 Sum_probs=35.6
Q ss_pred eeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhh
Q 043314 163 VWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHAR 221 (273)
Q Consensus 163 VwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAk 221 (273)
|..|-+||+ ..-++|+..||+|++|+.++ +.+.|.+.||. .|. ...+|+
T Consensus 178 l~~l~gig~--~~~~~L~~~Gi~ti~dL~~~---~~~~L~~rfG~-----~~~~l~~~a~ 227 (344)
T cd01700 178 VGDVWGIGR--RTAKKLNAMGIHTAGDLAQA---DPDLLRKKFGV-----VGERLVRELN 227 (344)
T ss_pred hhhcCccCH--HHHHHHHHcCCCcHHHHhcC---CHHHHHHHHHH-----HHHHHHHHhC
Confidence 444555665 34588999999999999886 77889999973 355 555554
No 22
>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=44.75 E-value=13 Score=28.93 Aligned_cols=29 Identities=34% Similarity=0.394 Sum_probs=17.8
Q ss_pred eeeeecCCCcccchhhhCCCccHHHHHHHhc
Q 043314 165 RLGKIGRGGNFCGKLAASGIKTVQDFLKVSI 195 (273)
Q Consensus 165 RLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~ 195 (273)
.|-+||.. .-+.|.+.||+||+||..+=.
T Consensus 7 ~LpNig~~--~e~~L~~vGI~t~~~L~~~Ga 35 (81)
T PF04994_consen 7 DLPNIGPK--SERMLAKVGIHTVEDLRELGA 35 (81)
T ss_dssp GSTT--HH--HHHHHHHTT--SHHHHHHHHH
T ss_pred hCCCCCHH--HHHHHHHcCCCCHHHHHHhCH
Confidence 34445543 348899999999999987643
No 23
>PRK01216 DNA polymerase IV; Validated
Probab=43.19 E-value=12 Score=36.10 Aligned_cols=40 Identities=28% Similarity=0.449 Sum_probs=31.9
Q ss_pred ceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHc
Q 043314 162 EVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILG 206 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg 206 (273)
+|..|.+||+. -..+|...||.|++|+.++ +...|++.||
T Consensus 179 Pi~~l~giG~~--~~~~L~~~Gi~TigdL~~~---~~~~L~~rfG 218 (351)
T PRK01216 179 DIADIPGIGDI--TAEKLKKLGVNKLVDTLRI---EFDELKGIIG 218 (351)
T ss_pred CcccccCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHC
Confidence 46777777754 4599999999999998865 6677888887
No 24
>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=42.50 E-value=13 Score=34.54 Aligned_cols=50 Identities=30% Similarity=0.462 Sum_probs=35.7
Q ss_pred ceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhh
Q 043314 162 EVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHAR 221 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAk 221 (273)
+|..|-+||+ ....+|...||+|++|+.++ ++..|++.+| ..|. ...||+
T Consensus 172 pl~~l~gig~--~~~~~L~~~Gi~ti~dl~~~---~~~~L~~~~g-----~~~~~l~~~~~ 222 (334)
T cd03586 172 PVRKIPGVGK--VTAEKLKELGIKTIGDLAKL---DVELLKKLFG-----KSGRRLYELAR 222 (334)
T ss_pred CchhhCCcCH--HHHHHHHHcCCcCHHHHHcC---CHHHHHHHHh-----HHHHHHHHHhC
Confidence 4555556665 34589999999999999875 6777888775 3456 666664
No 25
>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=42.07 E-value=72 Score=27.58 Aligned_cols=35 Identities=31% Similarity=0.528 Sum_probs=26.5
Q ss_pred EEEEEeCcEEeecCeEEecCCCcccCcceEEEEEEee
Q 043314 89 VNVTIKNGVARVEDIEFTDNSNWIRSRKFRIGAKVAQ 125 (273)
Q Consensus 89 l~v~L~~Gva~l~di~FtDnSs~~rsrKFRLgarv~~ 125 (273)
..-.|+|++|...|+.|---|. |.+.|-|-.-+..
T Consensus 73 ~tavmknqvA~FnDLRFvGRSG--RGKsFtltItv~t 107 (135)
T PF00853_consen 73 ATAVMKNQVARFNDLRFVGRSG--RGKSFTLTITVFT 107 (135)
T ss_dssp -EEEEETTEEEESS-EECST-T--TTSEEEEEEEE-S
T ss_pred hhhhhhcccccccccccccccC--CccceEEEEEEeC
Confidence 3678999999999999999777 4666999888774
No 26
>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=41.60 E-value=12 Score=36.57 Aligned_cols=43 Identities=26% Similarity=0.251 Sum_probs=32.7
Q ss_pred ceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcC
Q 043314 162 EVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGT 207 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~ 207 (273)
+|..|-+||+. ..++|...||.|+.|+..+- .++..|++.||.
T Consensus 223 Pv~~l~GIG~~--~~~~L~~~Gi~t~~dl~~~~-~~~~~L~~~fG~ 265 (404)
T cd01701 223 KVGDLPGVGSS--LAEKLVKLFGDTCGGLELRS-KTKEKLQKVLGP 265 (404)
T ss_pred CHhHhCCCCHH--HHHHHHHcCCcchHHHHhCc-ccHHHHHHHHCH
Confidence 56666677754 56999999999999998762 127788888873
No 27
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=40.59 E-value=12 Score=30.89 Aligned_cols=39 Identities=31% Similarity=0.593 Sum_probs=29.3
Q ss_pred eeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHc
Q 043314 163 VWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILG 206 (273)
Q Consensus 163 VwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg 206 (273)
..|..+|+. .|..-|...||.||+++ ...+|++|.+-++
T Consensus 55 L~ri~gi~~--~~a~LL~~AGv~Tv~~L---A~~~p~~L~~~l~ 93 (122)
T PF14229_consen 55 LMRIPGIGP--QYAELLEHAGVDTVEEL---AQRNPQNLHQKLG 93 (122)
T ss_pred hhhcCCCCH--HHHHHHHHhCcCcHHHH---HhCCHHHHHHHHH
Confidence 346666665 46789999999999997 4478988886543
No 28
>PRK03103 DNA polymerase IV; Reviewed
Probab=40.51 E-value=16 Score=35.44 Aligned_cols=40 Identities=23% Similarity=0.373 Sum_probs=31.1
Q ss_pred ceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHc
Q 043314 162 EVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILG 206 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg 206 (273)
+|..|-+||+. .-++|...||.|++|+.++ ++..|++.||
T Consensus 182 pi~~l~gig~~--~~~~L~~~Gi~tigdl~~~---~~~~L~~~fG 221 (409)
T PRK03103 182 PVRKLFGVGSR--MEKHLRRMGIRTIGQLANT---PLERLKKRWG 221 (409)
T ss_pred CHhhcCCccHH--HHHHHHHcCCCCHHHHhcC---CHHHHHHHHC
Confidence 45555567764 5688999999999998864 6778888887
No 29
>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=39.98 E-value=17 Score=24.58 Aligned_cols=18 Identities=44% Similarity=0.890 Sum_probs=15.1
Q ss_pred EEeecCeEEecCCCcccC
Q 043314 97 VARVEDIEFTDNSNWIRS 114 (273)
Q Consensus 97 va~l~di~FtDnSs~~rs 114 (273)
-..+..+.|-|++.|++.
T Consensus 24 ~~~Ie~i~FaDGt~w~~~ 41 (43)
T PF06594_consen 24 SYRIEQIEFADGTVWTRA 41 (43)
T ss_pred CCcEeEEEEcCCCEecHH
Confidence 556899999999999763
No 30
>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=34.01 E-value=18 Score=34.22 Aligned_cols=51 Identities=24% Similarity=0.175 Sum_probs=33.8
Q ss_pred ceeeeeeecCCCcccchhhhCCCccHHHHHHHhccC-hHHHHHHHcCCCCccchh-hhhhhhc
Q 043314 162 EVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVE-PQKLRRILGTGMSEKMWD-TMKHART 222 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d-~~kLr~iLg~~ms~k~W~-~v~HAkt 222 (273)
+|..|-+||+. .-++|.+.||+|++|++++ + ...|+..+| +.+. ...+|+-
T Consensus 174 pi~~l~giG~~--~~~~L~~~Gi~ti~dl~~~---~~~~~l~~~fg-----~~~~~l~~~a~G 226 (343)
T cd00424 174 PLTDLPGIGAV--TAKRLEAVGINPIGDLLAA---SPDALLALWGG-----VSGERLWYALRG 226 (343)
T ss_pred ChhhcCCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHhh-----HHHHHHHHHhCC
Confidence 45556667764 4589999999999998765 5 455666665 2344 5555543
No 31
>PRK01810 DNA polymerase IV; Validated
Probab=33.59 E-value=18 Score=34.93 Aligned_cols=50 Identities=30% Similarity=0.329 Sum_probs=35.0
Q ss_pred ceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhh
Q 043314 162 EVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHAR 221 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAk 221 (273)
+|..|-+||+. .-++|...||+|++|+.++ +...|++.||. .+. ...+|+
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 34445556653 4488999999999998774 67789998873 244 555554
No 32
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=32.08 E-value=47 Score=26.73 Aligned_cols=59 Identities=29% Similarity=0.417 Sum_probs=40.5
Q ss_pred CCCCCceeeeeeecCCCcccchhhhCCCcc----HHHHHHHhccChHHHHHHHcCCCCccchh-hhhhhhcc
Q 043314 157 PMLEDEVWRLGKIGRGGNFCGKLAASGIKT----VQDFLKVSIVEPQKLRRILGTGMSEKMWD-TMKHARTC 223 (273)
Q Consensus 157 P~L~DeVwRLe~IgKdG~~hk~L~~~~I~t----V~dFLkl~~~d~~kLr~iLg~~ms~k~W~-~v~HAktC 223 (273)
|+=+-+|--|.+||.. +-.+|..+|+.. .++|| ++.+|++-.++-|. ..-- +-.||++|
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 6667789999999974 568999999976 46776 45678766554331 1112 56677776
No 33
>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=30.30 E-value=12 Score=36.14 Aligned_cols=42 Identities=14% Similarity=0.247 Sum_probs=30.7
Q ss_pred ceeeeeeecCCCcccch-hhhCCCccHHHHHHHhccChHHHHHHHc
Q 043314 162 EVWRLGKIGRGGNFCGK-LAASGIKTVQDFLKVSIVEPQKLRRILG 206 (273)
Q Consensus 162 eVwRLe~IgKdG~~hk~-L~~~~I~tV~dFLkl~~~d~~kLr~iLg 206 (273)
+|..|-+||+ ..-++ |+..||.|++|+.++. .++..|++.||
T Consensus 183 pv~~l~GiG~--~~~~~ll~~~Gi~ti~dl~~~~-~~~~~L~~~fG 225 (359)
T cd01702 183 PITSIRGLGG--KLGEEIIDLLGLPTEGDVAGFR-SSESDLQEHFG 225 (359)
T ss_pred cHHHhCCcCH--HHHHHHHHHcCCcCHHHHHhcc-CCHHHHHHHHH
Confidence 4666667774 22245 5889999999998764 47788988887
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=29.76 E-value=15 Score=35.95 Aligned_cols=42 Identities=29% Similarity=0.412 Sum_probs=30.5
Q ss_pred eeeeeeecCCCcccchhhhCCCccHHHHHHHhc------------cChHHHHHHHc
Q 043314 163 VWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSI------------VEPQKLRRILG 206 (273)
Q Consensus 163 VwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~------------~d~~kLr~iLg 206 (273)
|-.|-+||+.. -++|.+.||.|++|+..+-+ .++..|++.||
T Consensus 174 v~~l~GiG~~~--~~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG 227 (379)
T cd01703 174 LRKIPGIGYKT--AAKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFG 227 (379)
T ss_pred ccccCCcCHHH--HHHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHC
Confidence 44444677654 48999999999999986641 12677888887
No 35
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=29.60 E-value=17 Score=37.98 Aligned_cols=38 Identities=34% Similarity=0.347 Sum_probs=31.5
Q ss_pred CCCCCceeeeeeecCCCcccchhhhCCCccHHHHHHHhcc
Q 043314 157 PMLEDEVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIV 196 (273)
Q Consensus 157 P~L~DeVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~ 196 (273)
+.|+++|-.|++||+.- .+.|++.||+||.|.|..+=.
T Consensus 5 ~~~~~~~~~l~gvg~~~--~~~l~~lgi~t~~dll~~~P~ 42 (681)
T PRK10917 5 LLLDAPLTSLKGVGPKT--AEKLAKLGIHTVQDLLLHLPR 42 (681)
T ss_pred ccccCChhhcCCCCHHH--HHHHHHcCCCCHHHHhhcCCC
Confidence 45778999999998643 488999999999999988743
No 36
>PF04717 Phage_base_V: Phage-related baseplate assembly protein; InterPro: IPR006531 This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells []. Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].; PDB: 3AQJ_C 3QR8_A 2P5Z_X.
Probab=29.54 E-value=1e+02 Score=22.96 Aligned_cols=38 Identities=24% Similarity=0.350 Sum_probs=22.4
Q ss_pred ceeee-----eeeecceEEeecCCcccccCCCCCCCCceeeee
Q 043314 130 GVRIR-----EAITEAFVVKDHRGELYKKHHPPMLEDEVWRLG 167 (273)
Q Consensus 130 ~~rI~-----Eavse~FvVkd~Rge~~kKh~pP~L~DeVwRLe 167 (273)
.+||+ +..|....|...+.-..+-+.||...|+|+-+=
T Consensus 12 rvrV~~~~~~~~~s~Wl~~~~~~ag~~g~~~~P~iGeqV~v~~ 54 (79)
T PF04717_consen 12 RVRVRFPDDGDIVSDWLPVLQPRAGGWGFWFPPEIGEQVLVLF 54 (79)
T ss_dssp EEEEE-B-CTTEEEEEEEE--S-BSSSB------TT-EEEEEE
T ss_pred EEEEEEecCCCccceEEEeeehhccCCeeEccCCCCcEEEEEc
Confidence 45555 567899999998888889999999999999876
No 37
>KOG1520 consensus Predicted alkaloid synthase/Surface mucin Hemomucin [General function prediction only]
Probab=28.74 E-value=1.5e+02 Score=29.80 Aligned_cols=160 Identities=18% Similarity=0.186 Sum_probs=80.8
Q ss_pred CceeecCCCceEEEEEEcCCCCceecCCCCCceEEeehHhhhhcccccCCCccccccceEEEEEeCcEEeecCeEEecCC
Q 043314 30 SKITNIESDHLQIVVVKTRSGSRIAPANLSQPIKILMVEEFESNIVKERTGKRLLLTGDVNVTIKNGVARVEDIEFTDNS 109 (273)
Q Consensus 30 ~~I~a~~g~~i~V~L~D~~~~~~iv~~g~~ss~kieIveeF~~~Iv~~R~Gk~pLL~Gdl~v~L~~Gva~l~di~FtDnS 109 (273)
-+-+..||-|+=|+.-... ++=+|.....--++|.-=.+-...++-+=+|+...++.++.|.= + +.|-|||+|
T Consensus 108 ~~~e~~CGRPLGl~f~~~g-gdL~VaDAYlGL~~V~p~g~~a~~l~~~~~G~~~kf~N~ldI~~-~-----g~vyFTDSS 180 (376)
T KOG1520|consen 108 FETEPLCGRPLGIRFDKKG-GDLYVADAYLGLLKVGPEGGLAELLADEAEGKPFKFLNDLDIDP-E-----GVVYFTDSS 180 (376)
T ss_pred eecccccCCcceEEeccCC-CeEEEEecceeeEEECCCCCcceeccccccCeeeeecCceeEcC-C-----CeEEEeccc
Confidence 3445567777777763331 23333333321111111012222223333444444444444432 3 367899999
Q ss_pred CcccCcceEEEEEEeecCCC----------------ceee----eeeeecceEEeecCCc-------ccccCC-------
Q 043314 110 NWIRSRKFRIGAKVAQWTYH----------------GVRI----REAITEAFVVKDHRGE-------LYKKHH------- 155 (273)
Q Consensus 110 s~~rsrKFRLgarv~~~~~~----------------~~rI----~Eavse~FvVkd~Rge-------~~kKh~------- 155 (273)
|.--.|.|-+++--.++++- +.+. +=-..+.|++--.=+- ....+.
T Consensus 181 sk~~~rd~~~a~l~g~~~GRl~~YD~~tK~~~VLld~L~F~NGlaLS~d~sfvl~~Et~~~ri~rywi~g~k~gt~EvFa 260 (376)
T KOG1520|consen 181 SKYDRRDFVFAALEGDPTGRLFRYDPSTKVTKVLLDGLYFPNGLALSPDGSFVLVAETTTARIKRYWIKGPKAGTSEVFA 260 (376)
T ss_pred cccchhheEEeeecCCCccceEEecCcccchhhhhhcccccccccCCCCCCEEEEEeeccceeeeeEecCCccCchhhHh
Confidence 97666888888765533220 0111 1112356665433222 222222
Q ss_pred --CCCCCCceeeeeeecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHH
Q 043314 156 --PPMLEDEVWRLGKIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRIL 205 (273)
Q Consensus 156 --pP~L~DeVwRLe~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iL 205 (273)
-|-.-|.+-|= .+|.|.=.|....=. |.+++...| -+|+++
T Consensus 261 ~~LPG~PDNIR~~----~~G~fWVal~~~~~~----~~~~~~~~p-~vr~~~ 303 (376)
T KOG1520|consen 261 EGLPGYPDNIRRD----STGHFWVALHSKRST----LWRLLMKYP-WVRKFI 303 (376)
T ss_pred hcCCCCCcceeEC----CCCCEEEEEecccch----HHHhhhcCh-HHHHHH
Confidence 56677776543 677777666544332 888888777 788765
No 38
>PF05224 NDT80_PhoG: NDT80 / PhoG like DNA-binding family; InterPro: IPR024061 The NDT80 DNA-binding domain is found in the following proteins, which might all be involved in sensing nutritional status []: Yeast meiosis-specific transcription factor NDT80, the key transcription factor that ultimately allows the continuation of meiosis after the successful completion of recombination. Emericella nidulans phoG (xprG), a transcriptional activator involved in the response to nutrient limitation. Emericella nidulans putative uncharacterised protein AN6015.2. Neurospora crassa transcription factor vib-1, involved in the control of heterokaryon incompatibility. Neurospora crassa related to acid phosphatase NCU04729. Neurospora crassa related to meiosis-specific protein NDT80 NCU09915. The proteolytically resistant core NDT80 DNA-binding domain reveals a central beta-sandwich characteristic of an s-type Ig fold. The beta-sandwich contains a three-stranded sheet composed of strands a, b and e, packed against a four-stranded sheet composed of strands c', c, f and g. Each sheet of the beta-sandwich contains an additional beta-strand, as well as a variety of peripheral secondary structure elements. The NDT80 DNA-binding domain contains an N-terminal extension, which consists of a beta-hairpin and a loop []. ; GO: 0003677 DNA binding; PDB: 2EVJ_A 2EUW_A 1M6U_A 2EVF_A 1M7U_B 1MN4_A 2EVG_A 2EUV_A 2EVI_A 2EVH_A ....
Probab=27.89 E-value=1.3e+02 Score=26.60 Aligned_cols=51 Identities=20% Similarity=0.246 Sum_probs=33.5
Q ss_pred cEEeecCeEEecCCCcccCc----ceEEEEEEee------cCCCceeeeeeeecceEEeec
Q 043314 96 GVARVEDIEFTDNSNWIRSR----KFRIGAKVAQ------WTYHGVRIREAITEAFVVKDH 146 (273)
Q Consensus 96 Gva~l~di~FtDnSs~~rsr----KFRLgarv~~------~~~~~~rI~Eavse~FvVkd~ 146 (273)
-++++.-|.|...-.=-..| -|.|-|.+.. +++..+-|.|..|+|.+|+-+
T Consensus 118 ~~~~~eRLQF~~ATaNNgrr~~Qqyf~L~V~L~A~v~~~~~~~~~v~ia~~~S~piIVRGR 178 (186)
T PF05224_consen 118 TVATFERLQFKSATANNGRRRAQQYFHLVVELLAVVANTLSDGQWVKIAERQSPPIIVRGR 178 (186)
T ss_dssp SSEEEEEEEEETTTTSBSTTSTBEEEEEEEEEEEEE-SSSSEEEEEEEEEEE-S-EEEE-S
T ss_pred eEEEEEEeEEeehhccCCCccCCceEEEEEEEEEEeCccCCCCcEEEEEEccCCCEEEECC
Confidence 46788899997643332222 2888888776 223458999999999999854
No 39
>smart00198 SCP SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. Human glioma pathogenesis-related protein GliPR and the plant pathogenesis-related protein represent functional links between plant defense systems and human immune system. This family has no known function.
Probab=27.79 E-value=84 Score=25.15 Aligned_cols=43 Identities=28% Similarity=0.426 Sum_probs=28.6
Q ss_pred HHHHHHHcCC---------CCccchh-hh-----hhhhcccCCCceEEEecCcEEEEE
Q 043314 199 QKLRRILGTG---------MSEKMWD-TM-----KHARTCSMGSKLYIFRGQNCIIIL 241 (273)
Q Consensus 199 ~kLr~iLg~~---------ms~k~W~-~v-----~HAktC~l~~k~y~y~~~~v~l~F 241 (273)
+.+|+.++.| |..-.|+ .+ .||++|.+...-..+.++|+....
T Consensus 11 N~~R~~~a~G~~~~p~a~~m~~l~Wd~~La~~A~~~a~~C~~~~~~~~~~GeNi~~~~ 68 (144)
T smart00198 11 NKLRSQVAKGLLANPAASNMLKLTWDCELASSAQNWANQCPFGHSTPRGYGENLAWWS 68 (144)
T ss_pred HHHHHHHhcCCCCCCcccccccccCCHHHHHHHHHHHHhCCCcCCCcCCcCcceEEec
Confidence 3788887655 8999998 55 478999876433224455655443
No 40
>KOG1690 consensus emp24/gp25L/p24 family of membrane trafficking proteins [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.46 E-value=1.7e+02 Score=27.19 Aligned_cols=95 Identities=19% Similarity=0.285 Sum_probs=66.1
Q ss_pred EEEccCCCCC-cccCCceeecCCCceEEEEEEcCCCCceecCCCCCceEEeehHhhhh-cccccCCCccccccceEEEE-
Q 043314 16 LNFSKKLSLP-IFTGSKITNIESDHLQIVVVKTRSGSRIAPANLSQPIKILMVEEFES-NIVKERTGKRLLLTGDVNVT- 92 (273)
Q Consensus 16 L~F~n~l~~p-ifT~~~I~a~~g~~i~V~L~D~~~~~~iv~~g~~ss~kieIveeF~~-~Iv~~R~Gk~pLL~Gdl~v~- 92 (273)
=||...||.. .+||. -+..|+|.+ .+. -.+.|..+|.|||=|-|++ |.|-.+++. -+|++.++
T Consensus 31 KCF~eelpk~tmv~G~---------yk~qlyd~~-~~~-y~~~p~~gm~VeV~e~fdnnh~Vl~q~~s---s~G~ftFta 96 (215)
T KOG1690|consen 31 KCFIEELPKGTMVTGN---------YKAQLYDDQ-LKG-YGSYPNIGMHVEVKETFDNNHVVLSQQYS---SEGDFTFTA 96 (215)
T ss_pred cchhhhCCCCcEEEee---------eeeeeecch-hcc-cccCCCceEEEEeecCCCCceEEEeecCC---CCCceEEEc
Confidence 4677777753 67765 578899987 332 3377888999999999987 455555553 36887754
Q ss_pred EeCcEEeecCeEEecCCC-cccCcceEEEEEEeecC
Q 043314 93 IKNGVARVEDIEFTDNSN-WIRSRKFRIGAKVAQWT 127 (273)
Q Consensus 93 L~~Gva~l~di~FtDnSs-~~rsrKFRLgarv~~~~ 127 (273)
+.-|+=. |.++-||. |.-+.|.|+=+=...++
T Consensus 97 ~~~GeH~---IC~~s~s~awf~~aklRvhld~qvG~ 129 (215)
T KOG1690|consen 97 LTPGEHR---ICIQSNSTAWFNGAKLRVHLDIQVGD 129 (215)
T ss_pred cCCCceE---EEEecccchhhccceEEEEEEEeeCc
Confidence 4568754 44555554 88899999887776654
No 41
>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=25.81 E-value=86 Score=25.06 Aligned_cols=34 Identities=26% Similarity=0.454 Sum_probs=26.2
Q ss_pred hCCCccHHHHHHHhccChHHHH---HHHcCCCCccchh-hhhhhhc
Q 043314 181 ASGIKTVQDFLKVSIVEPQKLR---RILGTGMSEKMWD-TMKHART 222 (273)
Q Consensus 181 ~~~I~tV~dFLkl~~~d~~kLr---~iLg~~ms~k~W~-~v~HAkt 222 (273)
...| +++||+=++..||.||- ++| .|+ .++-|+.
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 99999999999997754 556 367 7777765
No 42
>PRK05256 condesin subunit E; Provisional
Probab=24.30 E-value=83 Score=29.60 Aligned_cols=49 Identities=22% Similarity=0.228 Sum_probs=36.8
Q ss_pred chhhhCCCccHHHHHHHhc--cChHHHHHHHcCC--CCccchh-hhhhhhcccC
Q 043314 177 GKLAASGIKTVQDFLKVSI--VEPQKLRRILGTG--MSEKMWD-TMKHARTCSM 225 (273)
Q Consensus 177 k~L~~~~I~tV~dFLkl~~--~d~~kLr~iLg~~--ms~k~W~-~v~HAktC~l 225 (273)
++|++.||+|+++.+.-+. .|+++|.+.++.- -|+-+-+ .-+-.++|--
T Consensus 107 erLa~~gift~qeL~deL~~ladE~kllklvn~R~~GsDlD~~Kl~ekvr~sLr 160 (238)
T PRK05256 107 ERLAHEGIFTQQELYDELLTLADEAKLLKLVNNRSTGSDLDKQKLQEKVRTSLN 160 (238)
T ss_pred HHHhcCCceeHHHHHHHHHHhhcHHHHHHHhcCCCCcchhhHHHHHHHHHHHHH
Confidence 7999999999999887653 4899999998522 2554445 7778888853
No 43
>COG0540 PyrB Aspartate carbamoyltransferase, catalytic chain [Nucleotide transport and metabolism]
Probab=23.69 E-value=40 Score=32.96 Aligned_cols=69 Identities=30% Similarity=0.404 Sum_probs=49.4
Q ss_pred HhhhhcccccCCCccccccceEEEEEeCcEEeecCeEEecCCCcccCc----ceEEEEEEee------cCCCc------e
Q 043314 68 EEFESNIVKERTGKRLLLTGDVNVTIKNGVARVEDIEFTDNSNWIRSR----KFRIGAKVAQ------WTYHG------V 131 (273)
Q Consensus 68 eeF~~~Iv~~R~Gk~pLL~Gdl~v~L~~Gva~l~di~FtDnSs~~rsr----KFRLgarv~~------~~~~~------~ 131 (273)
++|... ...+++.++|.|....+| |=+||-.||+- -=|||+.|+. ++..| .
T Consensus 29 ~~~~~~--~~~~~~~~~l~gk~v~~l-----------FFEpSTRTr~SFE~A~krLG~~Vv~~~~~~sSs~KGEtL~DT~ 95 (316)
T COG0540 29 DEFKAV--ARAEKKLDLLKGKVVANL-----------FFEPSTRTRLSFETAMKRLGADVVNFSDSESSSKKGETLADTI 95 (316)
T ss_pred HHHHHh--hhccCCcchhcCcEEEEE-----------EecCCCchhhhHHHHHHHcCCcEEeecCCcccccccccHHHHH
Confidence 667766 445778899999977765 99999887755 3789999984 11233 4
Q ss_pred eeeeee-ecceEEeecCCcc
Q 043314 132 RIREAI-TEAFVVKDHRGEL 150 (273)
Q Consensus 132 rI~Eav-se~FvVkd~Rge~ 150 (273)
|.-+|+ .+.||++ |+-+.
T Consensus 96 ~tl~ayg~D~iViR-H~~eg 114 (316)
T COG0540 96 RTLSAYGVDAIVIR-HPEEG 114 (316)
T ss_pred HHHHhhCCCEEEEe-Ccccc
Confidence 788999 7888776 44443
No 44
>PF05643 DUF799: Putative bacterial lipoprotein (DUF799); InterPro: IPR008517 This family consists of several bacterial proteins of unknown function. Some of the family members are described as putative lipoproteins.
Probab=23.37 E-value=65 Score=29.86 Aligned_cols=74 Identities=26% Similarity=0.336 Sum_probs=45.2
Q ss_pred cCCCcccCcceEEEEEEeecCCCce----eeeeeeecceEEeecCCcccccC---CCCCCCCceeeeeeecCCCcccchh
Q 043314 107 DNSNWIRSRKFRIGAKVAQWTYHGV----RIREAITEAFVVKDHRGELYKKH---HPPMLEDEVWRLGKIGRGGNFCGKL 179 (273)
Q Consensus 107 DnSs~~rsrKFRLgarv~~~~~~~~----rI~Eavse~FvVkd~Rge~~kKh---~pP~L~DeVwRLe~IgKdG~~hk~L 179 (273)
|-|.+-.++.=.+.|-..-+....+ .++.-++.|+ +++. .|+.+-|| -|
T Consensus 26 dy~a~~~~kPrSILVlPp~N~S~dV~A~~~~ls~~~~PL---------Ae~GYYV~Pv~~vde---------------~f 81 (215)
T PF05643_consen 26 DYTAFKESKPRSILVLPPVNESPDVKAAYYVLSTVTYPL---------AEKGYYVFPVALVDE---------------TF 81 (215)
T ss_pred cHHHHhcCCCceEEEeCCCCCCcccchHHHHHHHHHHHH---------HhCCceecCHHHHHH---------------HH
Confidence 4455555565556665554444333 3333444443 2333 35555554 47
Q ss_pred hhCCCccHHHHHHHhccChHHHHHHHcC
Q 043314 180 AASGIKTVQDFLKVSIVEPQKLRRILGT 207 (273)
Q Consensus 180 ~~~~I~tV~dFLkl~~~d~~kLr~iLg~ 207 (273)
+++||.+-+|+ ...+++||++|||.
T Consensus 82 kqnGlt~~~~i---~~v~~~kL~eiFGA 106 (215)
T PF05643_consen 82 KQNGLTDAEDI---HAVPPAKLREIFGA 106 (215)
T ss_pred HHcCCCCHHHh---ccCCHHHHHHHhCC
Confidence 88999999988 56789999999983
No 45
>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=22.96 E-value=1.1e+02 Score=27.31 Aligned_cols=62 Identities=19% Similarity=0.238 Sum_probs=37.8
Q ss_pred cccccceEEEEE---e--CcE--EeecCeEEecCCCcccCcceEEEEEEeecCC-------CceeeeeeeecceEEeec
Q 043314 82 RLLLTGDVNVTI---K--NGV--ARVEDIEFTDNSNWIRSRKFRIGAKVAQWTY-------HGVRIREAITEAFVVKDH 146 (273)
Q Consensus 82 ~pLL~Gdl~v~L---~--~Gv--a~l~di~FtDnSs~~rsrKFRLgarv~~~~~-------~~~rI~Eavse~FvVkd~ 146 (273)
.+.|.|.+...+ + +|. |.. ..|.|=|-.+ -+.|||-.++..-.. ...-+.|+.|+||.|-..
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 367888865443 2 343 221 2234434322 477999998886332 236778999999999653
No 46
>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=22.78 E-value=54 Score=30.34 Aligned_cols=34 Identities=24% Similarity=0.364 Sum_probs=26.9
Q ss_pred eecCCCcccchhhhCCCccHHHHHHHhccChHHHHHHHc
Q 043314 168 KIGRGGNFCGKLAASGIKTVQDFLKVSIVEPQKLRRILG 206 (273)
Q Consensus 168 ~IgKdG~~hk~L~~~~I~tV~dFLkl~~~d~~kLr~iLg 206 (273)
+||+. .-.+|.+.||+|++||..+ +...|++.||
T Consensus 177 gig~~--~~~~L~~~Gi~t~~dl~~~---~~~~l~~rfG 210 (335)
T cd03468 177 RLPPE--TVELLARLGLRTLGDLAAL---PRAELARRFG 210 (335)
T ss_pred CCCHH--HHHHHHHhCcccHHHHHhC---ChHHHHhhcC
Confidence 56664 3489999999999998875 5667888876
No 47
>PF10657 RC-P840_PscD: Photosystem P840 reaction centre protein PscD; InterPro: IPR019608 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. The photosynthetic reaction centres (RCs) of aerotolerant organisms contain a heterodimeric core, built up of two strongly homologous polypeptides each of which contributes five transmembrane peptide helices to hold a pseudo-symmetric double set of redox components. Two molecules of PscD are housed within a subunit. PscD may be involved in stabilising the PscB component since it is found to co-precipitate with FMO (Fenna-Mathews-Olson BChl a-protein) and PscB. It may also be involved in the interaction with ferredoxin [].
Probab=20.00 E-value=1.2e+02 Score=26.37 Aligned_cols=28 Identities=11% Similarity=0.315 Sum_probs=25.2
Q ss_pred CcEEEEEcccceeeeeEECCEEeeCCCC
Q 043314 235 QNCIIILNPICQVVRATINGQTFLTRDL 262 (273)
Q Consensus 235 ~~v~l~FN~i~~lvga~~~g~~~~~~~l 262 (273)
..+-+|||+...=+-+.++|+.|++++|
T Consensus 115 RdipVfy~~~~~~l~Veid~r~YtL~eF 142 (144)
T PF10657_consen 115 RDIPVFYNSLTRQLCVEIDRRTYTLDEF 142 (144)
T ss_pred ecCceEEccCCcEEEEEECCeEEehHhh
Confidence 3677999999999999999999999886
Done!