Query 011961
Match_columns 474
No_of_seqs 128 out of 151
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 07:07:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011961.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011961hhsearch_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-120 5E-125 901.0 30.7 294 86-382 1-296 (299)
2 TIGR02239 recomb_RAD51 DNA rep 89.6 0.45 9.9E-06 48.7 4.7 48 264-316 13-60 (316)
3 TIGR02238 recomb_DMC1 meiotic 87.5 0.7 1.5E-05 47.4 4.4 49 263-316 12-60 (313)
4 PLN03186 DNA repair protein RA 87.0 0.6 1.3E-05 48.6 3.6 60 252-316 28-87 (342)
5 PLN03187 meiotic recombination 83.0 1.3 2.7E-05 46.4 3.8 60 251-315 30-89 (344)
6 PRK04301 radA DNA repair and r 82.8 1.1 2.4E-05 45.2 3.3 56 252-314 8-63 (317)
7 PTZ00035 Rad51 protein; Provis 76.4 2.8 6.1E-05 43.4 3.9 60 251-315 22-81 (337)
8 PF14520 HHH_5: Helix-hairpin- 72.8 2.8 6.1E-05 32.6 2.2 52 254-312 9-60 (60)
9 PRK03609 umuC DNA polymerase V 70.1 4.7 0.0001 42.5 3.8 51 251-311 180-230 (422)
10 TIGR02236 recomb_radA DNA repa 68.9 4.3 9.4E-05 40.6 3.1 50 255-311 4-53 (310)
11 PRK02406 DNA polymerase IV; Va 65.1 6.3 0.00014 40.1 3.4 52 251-312 169-220 (343)
12 PF14229 DUF4332: Domain of un 64.9 11 0.00023 33.8 4.4 50 264-315 7-58 (122)
13 PRK03352 DNA polymerase IV; Va 64.1 6.8 0.00015 40.0 3.4 52 251-311 178-229 (346)
14 PF10691 DUF2497: Protein of u 61.6 20 0.00043 30.1 5.2 41 24-64 33-73 (73)
15 PRK01172 ski2-like helicase; P 56.4 14 0.0003 41.3 4.4 51 255-312 617-667 (674)
16 PRK03858 DNA polymerase IV; Va 55.0 6.6 0.00014 40.7 1.6 41 251-296 174-214 (396)
17 PRK03348 DNA polymerase IV; Pr 54.3 7.7 0.00017 41.7 2.0 53 251-312 181-233 (454)
18 PRK01216 DNA polymerase IV; Va 52.9 14 0.0003 38.5 3.6 52 251-311 179-230 (351)
19 PRK14133 DNA polymerase IV; Pr 52.0 15 0.00033 37.5 3.7 51 251-311 174-224 (347)
20 cd01701 PolY_Rev1 DNA polymera 48.7 16 0.00035 38.5 3.2 54 251-311 223-276 (404)
21 PF11754 Velvet: Velvet factor 48.6 1.8E+02 0.0038 28.3 10.1 62 171-235 97-172 (203)
22 cd01700 PolY_Pol_V_umuC umuC s 47.5 18 0.00038 36.9 3.3 51 251-311 177-227 (344)
23 COG3743 Uncharacterized conser 46.4 25 0.00055 32.8 3.7 60 249-312 66-126 (133)
24 cd03586 PolY_Pol_IV_kappa DNA 46.2 20 0.00044 35.9 3.4 52 251-312 172-223 (334)
25 PRK03103 DNA polymerase IV; Re 44.8 23 0.00049 37.1 3.6 52 251-312 182-233 (409)
26 cd01702 PolY_Pol_eta DNA Polym 44.7 20 0.00043 37.5 3.1 57 251-314 183-240 (359)
27 PRK02794 DNA polymerase IV; Pr 43.9 25 0.00054 37.1 3.8 55 251-315 210-264 (419)
28 cd01703 PolY_Pol_iota DNA Poly 43.4 26 0.00056 37.0 3.8 59 251-315 173-243 (379)
29 PF14229 DUF4332: Domain of un 39.7 19 0.0004 32.3 1.8 38 252-294 55-92 (122)
30 PF03118 RNA_pol_A_CTD: Bacter 39.3 16 0.00036 29.5 1.3 37 265-306 24-60 (66)
31 PRK01810 DNA polymerase IV; Va 38.6 29 0.00063 36.3 3.3 51 251-311 180-230 (407)
32 PF04994 TfoX_C: TfoX C-termin 38.4 23 0.00049 29.9 2.0 75 252-362 5-79 (81)
33 PF02889 Sec63: Sec63 Brl doma 37.9 29 0.00063 34.4 3.1 54 251-311 149-202 (314)
34 KOG4233 DNA-bridging protein B 37.9 36 0.00078 29.6 3.1 57 246-314 15-79 (90)
35 cd00424 PolY Y-family of DNA p 36.2 32 0.00069 35.2 3.1 55 251-315 174-229 (343)
36 KOG1520 Predicted alkaloid syn 35.3 1.3E+02 0.0029 32.5 7.5 90 103-215 108-197 (376)
37 PF09584 Phageshock_PspD: Phag 32.0 34 0.00074 28.5 2.0 15 42-56 45-59 (66)
38 TIGR02979 phageshock_pspD phag 27.9 45 0.00098 27.3 2.0 14 42-55 40-53 (59)
39 COG4766 EutQ Ethanolamine util 27.3 1.2E+02 0.0026 29.4 5.0 92 29-120 13-107 (176)
40 PRK10497 peripheral inner memb 27.1 46 0.00099 28.3 2.0 15 42-56 52-66 (73)
41 TIGR01954 nusA_Cterm_rpt trans 26.9 89 0.0019 22.8 3.3 42 265-311 6-47 (50)
42 PF02961 BAF: Barrier to autoi 25.8 77 0.0017 27.9 3.2 57 246-314 15-79 (89)
43 cd07978 TAF13 The TATA Binding 25.6 1.1E+02 0.0024 26.5 4.2 36 270-313 52-90 (92)
44 PRK10917 ATP-dependent DNA hel 25.1 32 0.00069 38.9 1.0 38 246-285 5-42 (681)
45 PRK14973 DNA topoisomerase I; 22.4 72 0.0016 38.0 3.1 54 252-312 879-932 (936)
46 PRK15457 ethanolamine utilizat 22.3 1.4E+02 0.0031 30.3 4.7 17 45-61 89-105 (233)
47 KOG1104 Nuclear cap-binding co 22.0 93 0.002 36.3 3.8 22 1-24 1-22 (759)
48 PF06594 HCBP_related: Haemoly 21.9 58 0.0013 23.9 1.5 18 186-203 24-41 (43)
49 PF07182 DUF1402: Protein of u 21.4 1.6E+02 0.0035 30.7 5.0 31 332-363 72-102 (303)
50 COG3827 Uncharacterized protei 21.1 1.6E+02 0.0034 29.9 4.7 40 25-64 189-228 (231)
51 COG5340 Predicted transcriptio 21.0 59 0.0013 33.2 1.8 41 268-309 25-65 (269)
52 PRK02362 ski2-like helicase; P 20.8 1.1E+02 0.0024 34.9 4.1 51 254-313 656-706 (737)
53 PRK05256 condesin subunit E; P 20.0 1.7E+02 0.0036 29.9 4.7 50 266-315 107-160 (238)
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=2.1e-120 Score=900.97 Aligned_cols=294 Identities=56% Similarity=0.963 Sum_probs=288.5
Q ss_pred ceEEEEccCCCCCcccCCceeecCCCCeEEEEEEcCCCCeeecCCCCCcceEEEEEecCCCCCCCCCCCCHHHHhccccc
Q 011961 86 SLKLIFSQKLSLPIFTGSKITDVENNPLQIVVVDTRSNGLIAPASLPQPIKIELVVLDGDFPPGDRDHWTPEEFESNIVK 165 (474)
Q Consensus 86 ~~~L~F~n~l~~pifTg~kI~a~~g~~I~V~L~D~~t~n~iv~~g~~ss~kvEIvVLdGDF~~~~~e~WT~eEF~~~IV~ 165 (474)
+|||+|+|+|++|||||++|+|+||+||+|+|+|++|+ |++||+|++|||||||||||+.+++++||+|||++|||+
T Consensus 1 ~~~L~F~n~l~~pifT~~~i~a~~g~~i~V~l~d~~~~---v~~g~lss~kieIvvLdGdF~~~~~~~wT~eeF~~~iv~ 77 (299)
T PF07887_consen 1 NLQLRFLNKLSLPIFTGSKIEAEDGAPIKVALVDANTG---VTSGPLSSAKIEIVVLDGDFNDEDCEDWTEEEFNSHIVK 77 (299)
T ss_pred CeEEEecCCCCCCcccCCceEecCCCcEEEEEEECCCC---ccCCCCCCcEEEEEEEccccCCCccCCCCHHHHhhcEee
Confidence 58999999999999999999999999999999998876 999999999999999999999999999999999999999
Q ss_pred cCCCCCcccccceEEEecCceeecCCeeeecCCccccccceEEEEEEecCCCCccceeeeeecceEEeecCCcccccCCC
Q 011961 166 ERTGKRPLLTGDVNVTARDGVAPIGDIEFTDNSSWIRSRKFRIGAKVARGSYQGVRICEAITDAFVVKDHRGELYKKHHP 245 (474)
Q Consensus 166 ~ReGk~pLL~Gdl~v~L~~Gva~L~di~FTDnSsw~rSrKFRLgaRvv~~~~~g~RI~EAvsE~FvVkDhRge~~kKh~p 245 (474)
+|+||+|||+|+++|+|+||+|+|+||+|||||||+|||||||||||+++++.|+|||||+||||+|||||||+||||||
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 CCCCcceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhhccCCCcEEEEe--
Q 011961 246 PMLEDEVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVMGNKLYIFR-- 323 (474)
Q Consensus 246 P~L~DeVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~kly~y~-- 323 (474)
|+|+|||||||+|||+|+|||+|+++||+||+|||+++++||++||+|||+|||++||++||+|||||++++++|+|+
T Consensus 158 P~L~DeVwRLe~Igk~G~~hk~L~~~~I~tV~dFl~l~~~d~~~Lr~ilg~~ms~k~We~~v~HA~tCvl~~~~y~y~~~ 237 (299)
T PF07887_consen 158 PSLDDEVWRLEKIGKDGAFHKRLKKNGINTVEDFLKLLNKDPQKLREILGSGMSNKMWETTVEHAKTCVLGDKLYVYYDE 237 (299)
T ss_pred CCCCCchhhhhhccccCHHHHHHHHcCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHHHHHHHHhcCCCCcEEEEEec
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCceEEEEccceeeeeEEECCeEeeCCCCCHHhHHHHHHHHHHHHHhccccchhccccc
Q 011961 324 GHNCIILLNPICQVVRAVINNQTYLTRDLTKLNRTYIENTVRQAYLNWRELEVAEGVLN 382 (474)
Q Consensus 324 ~~nv~L~FN~i~~lVGa~f~G~~~~~~~L~~~qk~~V~~Lk~~AYenw~~l~e~~~~~n 382 (474)
++|++|+|||||+||||+|+|||++.++|++.||++|++|+++||+||++|+++|+.+.
T Consensus 238 ~~nv~l~FN~i~~lvga~~~g~y~s~d~L~~~qK~~v~~Lv~~AY~n~~~l~e~d~~~~ 296 (299)
T PF07887_consen 238 EQNVGLFFNCIYELVGAIFGGQYVSLDNLSSAQKAYVDKLVKQAYENWDNLEEYDGKML 296 (299)
T ss_pred CCceEEEEcchhhEEeEEECCEEEehHHcCHHHHHHHHHHHHHHHHhhhhheecccchh
Confidence 68999999999999999999999999999999999999999999999999999987653
No 2
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=89.62 E-value=0.45 Score=48.68 Aligned_cols=48 Identities=31% Similarity=0.284 Sum_probs=42.8
Q ss_pred hhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhhccCC
Q 011961 264 FHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVMG 316 (474)
Q Consensus 264 ~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 316 (474)
.-++|+++||.||+||+.. +|..|.+++ ++|...++.+..||.+|...
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 4488999999999999875 899999998 78999999999999998653
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=87.45 E-value=0.7 Score=47.39 Aligned_cols=49 Identities=35% Similarity=0.311 Sum_probs=43.1
Q ss_pred hhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhhccCC
Q 011961 263 AFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVMG 316 (474)
Q Consensus 263 ~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 316 (474)
..-++|+++||.||+||+.. ++..|.++. |+|...++.+++.|+++...
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 45589999999999998765 789999997 79999999999999998754
No 4
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=87.04 E-value=0.6 Score=48.64 Aligned_cols=60 Identities=32% Similarity=0.287 Sum_probs=47.4
Q ss_pred eeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhhccCC
Q 011961 252 VWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVMG 316 (474)
Q Consensus 252 VwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 316 (474)
+-+|+.-|-.-..-++|+++||.||+||+.. ++..|.+++ ++|....+.+++||.+|...
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 4445443333334589999999999998875 788999998 78999999999999888654
No 5
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=82.97 E-value=1.3 Score=46.42 Aligned_cols=60 Identities=27% Similarity=0.271 Sum_probs=47.9
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhhccC
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVM 315 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 315 (474)
++..|+.-|-.-..-++|.++||+||+|++.. ++..|-++. |+|....+.+++.|++.+.
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 35666554444446699999999999998765 688899987 7999999999999988764
No 6
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=82.83 E-value=1.1 Score=45.24 Aligned_cols=56 Identities=25% Similarity=0.356 Sum_probs=45.0
Q ss_pred eeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhhcc
Q 011961 252 VWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCV 314 (474)
Q Consensus 252 VwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCv 314 (474)
+..|.+||+. .-++|.++||.|++|++. .+++.|.+++ |++.+.++.+++-|+.++
T Consensus 8 l~~l~gIg~~--~a~~L~~~Gi~t~~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~a~~~~ 63 (317)
T PRK04301 8 LEDLPGVGPA--TAEKLREAGYDTVEAIAV---ASPKELSEAA--GIGESTAAKIIEAAREAA 63 (317)
T ss_pred HhhcCCCCHH--HHHHHHHcCCCCHHHHHc---CCHHHHHHhc--CCCHHHHHHHHHHHHHhh
Confidence 4455666644 568999999999999966 4899999999 678889999998887644
No 7
>PTZ00035 Rad51 protein; Provisional
Probab=76.45 E-value=2.8 Score=43.44 Aligned_cols=60 Identities=35% Similarity=0.327 Sum_probs=46.9
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhhccC
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVM 315 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 315 (474)
++..|+.-|-.-..-++|+++||+||+||+.. ++..|.++. |+|...=+.+++.|++++.
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 45566553333345589999999999998764 788999998 6899999999999988764
No 8
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=72.77 E-value=2.8 Score=32.59 Aligned_cols=52 Identities=37% Similarity=0.546 Sum_probs=41.1
Q ss_pred eeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhh
Q 011961 254 RLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARK 312 (474)
Q Consensus 254 RLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 312 (474)
.+.+||+. ..++|.+.||.|++|+..+ +++.|.++= |++.+.=+.+++.|+.
T Consensus 9 ~I~Gig~~--~a~~L~~~G~~t~~~l~~a---~~~~L~~i~--Gig~~~a~~i~~~~~~ 60 (60)
T PF14520_consen 9 SIPGIGPK--RAEKLYEAGIKTLEDLANA---DPEELAEIP--GIGEKTAEKIIEAARE 60 (60)
T ss_dssp TSTTCHHH--HHHHHHHTTCSSHHHHHTS---HHHHHHTST--TSSHHHHHHHHHHHHH
T ss_pred cCCCCCHH--HHHHHHhcCCCcHHHHHcC---CHHHHhcCC--CCCHHHHHHHHHHHhC
Confidence 34556655 3488999999999998764 778899975 6899999999998863
No 9
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=70.06 E-value=4.7 Score=42.50 Aligned_cols=51 Identities=31% Similarity=0.384 Sum_probs=40.2
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhh
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 311 (474)
+|..|-+||+. .-++|.+.||+|++|+.++ ++..|++.|| ..+..+..||.
T Consensus 180 Pv~~l~GiG~~--~~~~L~~lGi~TigdL~~~---~~~~L~~~fG-----~~~~~l~~~a~ 230 (422)
T PRK03609 180 PVEEVWGVGRR--ISKKLNAMGIKTALDLADT---NIRFIRKHFN-----VVLERTVRELR 230 (422)
T ss_pred ChhhcCCccHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHC-----HHHHHHHHHhC
Confidence 45556667774 5589999999999999986 7889999997 35666777776
No 10
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=68.95 E-value=4.3 Score=40.63 Aligned_cols=50 Identities=32% Similarity=0.417 Sum_probs=38.5
Q ss_pred eeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhh
Q 011961 255 LEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (474)
Q Consensus 255 LekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 311 (474)
|.+||+. .-++|.++||.|++|++.+ +++.|.+++ |++.+..+.+.+-|+
T Consensus 4 i~gig~~--~~~~L~~~Gi~ti~dl~~~---~~~~L~~~~--g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 4 LPGVGPA--TAEKLREAGYDTFEAIAVA---SPKELSEIA--GISEGTAAKIIQAAR 53 (310)
T ss_pred cCCCCHH--HHHHHHHcCCCCHHHHHcC---CHHHHHhcc--CCCHHHHHHHHHHHH
Confidence 4455543 4588999999999998875 889999998 467777777766665
No 11
>PRK02406 DNA polymerase IV; Validated
Probab=65.08 E-value=6.3 Score=40.11 Aligned_cols=52 Identities=29% Similarity=0.332 Sum_probs=39.6
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhh
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARK 312 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 312 (474)
+|..|-+||+. .-++|...||.|++|+.++ +...|++.||. .+..+..||.-
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 46666677754 4578999999999999885 78899999972 45666666654
No 12
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=64.91 E-value=11 Score=33.85 Aligned_cols=50 Identities=36% Similarity=0.327 Sum_probs=37.4
Q ss_pred hhhhhhhcCCccHHHHHHHhhcChHH--HHHHhcCCCChhhHHHHHHHhhhccC
Q 011961 264 FHKKLSAAGIKTVQDFLKLSIVEPQR--LRKILGPGMSEKMWEVTMQHARKCVM 315 (474)
Q Consensus 264 ~hk~L~~~gI~TV~dFLkl~~~d~~k--LR~iLg~gmS~k~We~~v~HAktCvl 315 (474)
.-.+|...||+|++|||..-.....+ |-+-+ |++.+-=...+.+|.=|..
T Consensus 7 ~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~--~i~~~~l~~w~~~AdL~ri 58 (122)
T PF14229_consen 7 EAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKL--GISERNLLKWVNQADLMRI 58 (122)
T ss_pred HHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhc--CCCHHHHHHHHhHHHhhhc
Confidence 45789999999999999987765555 66655 6788776667777765533
No 13
>PRK03352 DNA polymerase IV; Validated
Probab=64.09 E-value=6.8 Score=39.95 Aligned_cols=52 Identities=31% Similarity=0.373 Sum_probs=37.9
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhh
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 311 (474)
+|..|-+||+. ..++|.+.||+|++|++++ ++..|++.||. +.+..+..+|.
T Consensus 178 pl~~l~gig~~--~~~~L~~~Gi~ti~dl~~l---~~~~L~~~fG~----~~~~~l~~~a~ 229 (346)
T PRK03352 178 PTDALWGVGPK--TAKRLAALGITTVADLAAA---DPAELAATFGP----TTGPWLLLLAR 229 (346)
T ss_pred CHHHcCCCCHH--HHHHHHHcCCccHHHHhcC---CHHHHHHHhCh----HHHHHHHHHhC
Confidence 46666677774 4578999999999999986 77889999973 23444444443
No 14
>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=61.64 E-value=20 Score=30.12 Aligned_cols=41 Identities=20% Similarity=0.239 Sum_probs=30.3
Q ss_pred CchHHHHHHHHHHhhHHHHHHhhhHHHHHHhHHHHHHhhhc
Q 011961 24 PSFASVIGEAVMVNSFQNFFSALEPLLRRVVNEEVQRGVSK 64 (474)
Q Consensus 24 p~~~~vi~e~~~~~~~q~~~~~lEp~lrrvV~EEve~~l~~ 64 (474)
.++-.++++.++-+--+=|=..|=.++.|+|++||+|..++
T Consensus 33 ~TlE~lvremLRPmLkeWLD~nLP~lVErlVr~EIeRi~rr 73 (73)
T PF10691_consen 33 RTLEDLVREMLRPMLKEWLDENLPGLVERLVREEIERIARR 73 (73)
T ss_pred ccHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhcC
Confidence 36666777777766544455577788899999999998764
No 15
>PRK01172 ski2-like helicase; Provisional
Probab=56.42 E-value=14 Score=41.29 Aligned_cols=51 Identities=33% Similarity=0.595 Sum_probs=41.7
Q ss_pred eeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhh
Q 011961 255 LEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARK 312 (474)
Q Consensus 255 LekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 312 (474)
|.++++. ..++|.++||.||.|+.. .++++|-+|+ |++++.=+.++++|+.
T Consensus 617 ip~~~~~--~a~~l~~~g~~~~~di~~---~~~~~~~~i~--~~~~~~~~~i~~~~~~ 667 (674)
T PRK01172 617 IPKVGRV--RARRLYDAGFKTVDDIAR---SSPERIKKIY--GFSDTLANAIVNRAMK 667 (674)
T ss_pred CCCCCHH--HHHHHHHcCCCCHHHHHh---CCHHHHHHHh--ccCHHHHHHHHHHHHH
Confidence 3444444 668999999999999877 6788898898 5899999999999875
No 16
>PRK03858 DNA polymerase IV; Validated
Probab=54.99 E-value=6.6 Score=40.72 Aligned_cols=41 Identities=39% Similarity=0.488 Sum_probs=32.8
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcC
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGP 296 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~ 296 (474)
+|..|-+||+. .-++|.+.||+|++|+++ .++..|++.||.
T Consensus 174 pl~~l~Gig~~--~~~~L~~~Gi~t~~dl~~---l~~~~L~~~fG~ 214 (396)
T PRK03858 174 PVRRLWGVGPV--TAAKLRAHGITTVGDVAE---LPESALVSLLGP 214 (396)
T ss_pred ChhhcCCCCHH--HHHHHHHhCCCcHHHHhc---CCHHHHHHHhCc
Confidence 35556677775 458899999999999986 478899999984
No 17
>PRK03348 DNA polymerase IV; Provisional
Probab=54.27 E-value=7.7 Score=41.70 Aligned_cols=53 Identities=30% Similarity=0.357 Sum_probs=39.5
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhh
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARK 312 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 312 (474)
.|.+|-+||+. .-++|.+.||+|++||.++ +...|++.||..+ ...+..+|+-
T Consensus 181 Pv~~L~GIG~~--t~~~L~~lGI~TigDLa~l---~~~~L~~~fG~~~----g~~L~~~a~G 233 (454)
T PRK03348 181 PVRRLWGIGPV--TEEKLHRLGIETIGDLAAL---SEAEVANLLGATV----GPALHRLARG 233 (454)
T ss_pred CccccCCCCHH--HHHHHHHcCCccHHHHhcC---CHHHHHHHHCHHH----HHHHHHHHcC
Confidence 57888888875 4578999999999999885 7889999997323 3344445543
No 18
>PRK01216 DNA polymerase IV; Validated
Probab=52.86 E-value=14 Score=38.53 Aligned_cols=52 Identities=27% Similarity=0.394 Sum_probs=39.3
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhh
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 311 (474)
+|..|-+||+. ..++|.+.||.|++|+.++ +...|++.|| ...+..+-.+|.
T Consensus 179 Pi~~l~giG~~--~~~~L~~~Gi~TigdL~~~---~~~~L~~rfG----~~~~~~L~~~a~ 230 (351)
T PRK01216 179 DIADIPGIGDI--TAEKLKKLGVNKLVDTLRI---EFDELKGIIG----EAKAKYLFSLAR 230 (351)
T ss_pred CcccccCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHC----HHHHHHHHHHhC
Confidence 47777788864 4589999999999998865 6688999997 334555556663
No 19
>PRK14133 DNA polymerase IV; Provisional
Probab=51.99 E-value=15 Score=37.47 Aligned_cols=51 Identities=31% Similarity=0.428 Sum_probs=39.0
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhh
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 311 (474)
+|..|-+||+. .-++|.+.||+|++|++++ +...|++.|| +.|..+.++|.
T Consensus 174 pv~~l~gig~~--~~~~L~~~Gi~ti~dl~~l---~~~~L~~rfG-----~~g~~l~~~a~ 224 (347)
T PRK14133 174 PISKVHGIGKK--SVEKLNNIGIYTIEDLLKL---SREFLIEYFG-----KFGVEIYERIR 224 (347)
T ss_pred CccccCCCCHH--HHHHHHHcCCccHHHHhhC---CHHHHHHHHh-----HHHHHHHHHhC
Confidence 46666667654 3477999999999999885 6788999996 35777777775
No 20
>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=48.72 E-value=16 Score=38.52 Aligned_cols=54 Identities=26% Similarity=0.226 Sum_probs=40.1
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhh
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 311 (474)
+|..|-+||+. .-++|.+.||.|++|+..+- .++..|++.|| .+.+..+..+|+
T Consensus 223 Pv~~l~GIG~~--~~~~L~~~Gi~t~~dl~~~~-~~~~~L~~~fG----~~~g~~L~~~a~ 276 (404)
T cd01701 223 KVGDLPGVGSS--LAEKLVKLFGDTCGGLELRS-KTKEKLQKVLG----PKTGEKLYDYCR 276 (404)
T ss_pred CHhHhCCCCHH--HHHHHHHcCCcchHHHHhCc-ccHHHHHHHHC----HHHHHHHHHHhC
Confidence 56677777754 56899999999999998772 12788999997 345555666664
No 21
>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=48.60 E-value=1.8e+02 Score=28.32 Aligned_cols=62 Identities=23% Similarity=0.287 Sum_probs=37.9
Q ss_pred CcccccceEEEe---c--Cce--eecCCeeeecCCccccccceEEEEEEecCCC-------CccceeeeeecceEEeec
Q 011961 171 RPLLTGDVNVTA---R--DGV--APIGDIEFTDNSSWIRSRKFRIGAKVARGSY-------QGVRICEAITDAFVVKDH 235 (474)
Q Consensus 171 ~pLL~Gdl~v~L---~--~Gv--a~L~di~FTDnSsw~rSrKFRLgaRvv~~~~-------~g~RI~EAvsE~FvVkDh 235 (474)
.+.|.|.+...+ + +|. |.. ..|.|=|-.+ -+.|||-.++..=.. ...-+-|+.|+||.|-..
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 467888876443 2 343 221 2334434322 478999998885322 235678999999999653
No 22
>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=47.53 E-value=18 Score=36.94 Aligned_cols=51 Identities=33% Similarity=0.411 Sum_probs=38.8
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhh
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 311 (474)
+|..|-+||+. .-++|...||+|++|++++ +.+.|.+.||. .|.....+|+
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 35555566664 4578999999999999986 77889999973 4666777765
No 23
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=46.38 E-value=25 Score=32.82 Aligned_cols=60 Identities=18% Similarity=0.277 Sum_probs=43.2
Q ss_pred CcceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHH-HHHHhhh
Q 011961 249 EDEVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEV-TMQHARK 312 (474)
Q Consensus 249 ~DeVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~-~v~HAkt 312 (474)
.|+.-||.+||.. +-+.|+..||+|-.+.-.+-..|-..+-..| +..-+.|.. -|+.|+.
T Consensus 66 ~DDLt~I~GIGPk--~e~~Ln~~GI~tfaQIAAwt~~di~~id~~l--~f~GRi~RDdWi~QAk~ 126 (133)
T COG3743 66 KDDLTRISGIGPK--LEKVLNELGIFTFAQIAAWTRADIAWIDDYL--NFDGRIERDDWIAQAKA 126 (133)
T ss_pred cccchhhcccCHH--HHHHHHHcCCccHHHHHhcCHHHHHHHHhhc--CCcchhHHHHHHHHHHH
Confidence 3999999999986 7799999999996665544443434444455 677777765 6777764
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=46.16 E-value=20 Score=35.90 Aligned_cols=52 Identities=35% Similarity=0.468 Sum_probs=40.4
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhh
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARK 312 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 312 (474)
+|..|-+||+. .-++|...||+|++|+.++ ++..|++.+| +.|.....||+-
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 4588999999999999875 6788999885 578888888874
No 25
>PRK03103 DNA polymerase IV; Reviewed
Probab=44.80 E-value=23 Score=37.09 Aligned_cols=52 Identities=29% Similarity=0.358 Sum_probs=39.3
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhh
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARK 312 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 312 (474)
.|..|-+||+. .-++|.+.||+|++|+.++ ++..|++.||. .|..+.++|.-
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 45666677764 5578999999999998875 67889999962 46666666654
No 26
>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=44.72 E-value=20 Score=37.54 Aligned_cols=57 Identities=18% Similarity=0.238 Sum_probs=40.0
Q ss_pred ceeeeeeecccchhhhh-hhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhhcc
Q 011961 251 EVWRLEKIGKDGAFHKK-LSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCV 314 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~-L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCv 314 (474)
+|..|-+||+. .-++ |...||.|++|+.++. .++..|++.|| .+.+..+..+|+--+
T Consensus 183 pv~~l~GiG~~--~~~~ll~~~Gi~ti~dl~~~~-~~~~~L~~~fG----~~~g~~l~~~a~G~d 240 (359)
T cd01702 183 PITSIRGLGGK--LGEEIIDLLGLPTEGDVAGFR-SSESDLQEHFG----EKLGEWLYNLLRGID 240 (359)
T ss_pred cHHHhCCcCHH--HHHHHHHHcCCcCHHHHHhcc-CCHHHHHHHHH----HHHHHHHHHHhCCCC
Confidence 46777777742 2244 6889999999998765 57889999997 344555656666443
No 27
>PRK02794 DNA polymerase IV; Provisional
Probab=43.93 E-value=25 Score=37.09 Aligned_cols=55 Identities=24% Similarity=0.235 Sum_probs=42.1
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhhccC
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVM 315 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 315 (474)
+|..|-+||+ ..-++|.+.||+|++|+.++ +...|++.||. .|..+..+|.--+.
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 3555556664 45688999999999998875 78899999973 58888888875554
No 28
>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=43.41 E-value=26 Score=37.03 Aligned_cols=59 Identities=24% Similarity=0.250 Sum_probs=41.7
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhh------------cChHHHHHHhcCCCChhhHHHHHHHhhhccC
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSI------------VEPQRLRKILGPGMSEKMWEVTMQHARKCVM 315 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~------------~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 315 (474)
+|..|-+||+.- -++|.+.||.|++|+..+-+ .+...|++.|| .+.+..+.++|+--+.
T Consensus 173 pv~~l~GiG~~~--~~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG----~~~g~~l~~~a~G~d~ 243 (379)
T cd01703 173 DLRKIPGIGYKT--AAKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFG----EGIGQRIWKLLFGRDT 243 (379)
T ss_pred CccccCCcCHHH--HHHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHC----HHHHHHHHHHHCCCCC
Confidence 345555677664 48999999999999987641 12778999997 3456666677775554
No 29
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=39.71 E-value=19 Score=32.32 Aligned_cols=38 Identities=32% Similarity=0.589 Sum_probs=28.7
Q ss_pred eeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHh
Q 011961 252 VWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKIL 294 (474)
Q Consensus 252 VwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iL 294 (474)
..|..+||.. |...|..+||.||+++-. .+|++|.+.+
T Consensus 55 L~ri~gi~~~--~a~LL~~AGv~Tv~~LA~---~~p~~L~~~l 92 (122)
T PF14229_consen 55 LMRIPGIGPQ--YAELLEHAGVDTVEELAQ---RNPQNLHQKL 92 (122)
T ss_pred hhhcCCCCHH--HHHHHHHhCcCcHHHHHh---CCHHHHHHHH
Confidence 3466666655 678899999999999854 6788887654
No 30
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=39.30 E-value=16 Score=29.52 Aligned_cols=37 Identities=35% Similarity=0.391 Sum_probs=23.5
Q ss_pred hhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHH
Q 011961 265 HKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVT 306 (474)
Q Consensus 265 hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~ 306 (474)
...|..+||+||+|++++ +++.|.++= |+..+.-+.+
T Consensus 24 ~n~L~~~~I~tv~dL~~~---s~~~L~~i~--n~G~ksl~EI 60 (66)
T PF03118_consen 24 YNCLKRAGIHTVGDLVKY---SEEDLLKIK--NFGKKSLEEI 60 (66)
T ss_dssp HHHHHCTT--BHHHHHCS----HHHHHTST--TSHHHHHHHH
T ss_pred HHHHHHhCCcCHHHHHhC---CHHHHHhCC--CCCHhHHHHH
Confidence 467999999999997765 667777774 3445544443
No 31
>PRK01810 DNA polymerase IV; Validated
Probab=38.62 E-value=29 Score=36.32 Aligned_cols=51 Identities=29% Similarity=0.328 Sum_probs=38.3
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhh
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 311 (474)
+|..|-+||+. .-++|.+.||+|++|+.++ +...|++.||. .+..+.+||+
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 35555567664 4488999999999999775 77889999972 3566777776
No 32
>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=38.37 E-value=23 Score=29.88 Aligned_cols=75 Identities=20% Similarity=0.236 Sum_probs=39.3
Q ss_pred eeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhhccCCCcEEEEecCceEEEE
Q 011961 252 VWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKCVMGNKLYIFRGHNCIILL 331 (474)
Q Consensus 252 VwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~kly~y~~~nv~L~F 331 (474)
+..|-.||.. .-+.|.+.||+||+||.++=. .+.|-.+..+-.+ +-+
T Consensus 5 l~~LpNig~~--~e~~L~~vGI~t~~~L~~~Ga---------------~~a~~~Lk~~~~~----------------~~~ 51 (81)
T PF04994_consen 5 LKDLPNIGPK--SERMLAKVGIHTVEDLRELGA---------------VEAYLRLKASGPS----------------VCL 51 (81)
T ss_dssp GCGSTT--HH--HHHHHHHTT--SHHHHHHHHH---------------HHHHHHHHHH-TT------------------H
T ss_pred hhhCCCCCHH--HHHHHHHcCCCCHHHHHHhCH---------------HHHHHHHHHHCCC----------------CCH
Confidence 3344555544 337799999999999987533 3333333333222 223
Q ss_pred ccceeeeeEEECCeEeeCCCCCHHhHHHHHH
Q 011961 332 NPICQVVRAVINNQTYLTRDLTKLNRTYIEN 362 (474)
Q Consensus 332 N~i~~lVGa~f~G~~~~~~~L~~~qk~~V~~ 362 (474)
|-.|.|.||.-+ +...+|++.+|..+..
T Consensus 52 ~~L~aL~gAi~g---~~~~~L~~~~K~~L~~ 79 (81)
T PF04994_consen 52 NLLYALEGAIQG---IHWADLPDEEKQELLE 79 (81)
T ss_dssp HHHHHHHHHHCT---S-GGGS-HHHHHHHHH
T ss_pred HHHHHHHHHHcC---CCHHHCCHHHHHHHHh
Confidence 667777777555 3345566776665543
No 33
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. ; PDB: 3IM2_A 3IM1_A 3HIB_A 2Q0Z_X.
Probab=37.94 E-value=29 Score=34.41 Aligned_cols=54 Identities=31% Similarity=0.497 Sum_probs=36.7
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhh
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 311 (474)
...-|.+|+.+. -++|.++||.|+++|+++ ++++|..+| +......+.+.+.|.
T Consensus 149 ~L~Qlp~i~~~~--~~~l~~~~i~~l~~l~~~---~~~e~~~ll--~~~~~~~~~i~~~~~ 202 (314)
T PF02889_consen 149 PLLQLPHIGEES--LKKLEKRGIKTLQDLRDL---SPEELEELL--NRNPPFGKEILEVAS 202 (314)
T ss_dssp GGGGSTT--HHH--HHHHHHTT--SHHHHHHS----HHHHHHHH---S-HHHHHHHHHHHC
T ss_pred hhhcCCCCCHHH--HHHHhccCCCcHHHHhhC---CHHHHHHHH--hhhhhhHHHHHHHHH
Confidence 445566777765 478999999999999965 889999999 456677777777776
No 34
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=37.91 E-value=36 Score=29.61 Aligned_cols=57 Identities=32% Similarity=0.492 Sum_probs=41.0
Q ss_pred CCCCcceeeeeeecccchhhhhhhhcCCcc----HHHHHHHhhcChHHHH----HHhcCCCChhhHHHHHHHhhhcc
Q 011961 246 PMLEDEVWRLEKIGKDGAFHKKLSAAGIKT----VQDFLKLSIVEPQRLR----KILGPGMSEKMWEVTMQHARKCV 314 (474)
Q Consensus 246 P~L~DeVwRLekIgKdG~~hk~L~~~gI~T----V~dFLkl~~~d~~kLR----~iLg~gmS~k~We~~v~HAktCv 314 (474)
|+=+-+|--|.+||.. +-.+|..+|+.. .++|| ++.+|++-.+ ..+|. +-+||++|-
T Consensus 15 PmGeK~V~~laGIg~~--lg~~L~~~GfdkAYvllGQfL-llkKdE~lF~~Wlk~~~ga---------t~~~a~~~~ 79 (90)
T KOG4233|consen 15 PMGEKDVTWLAGIGET--LGIKLVDAGFDKAYVLLGQFL-LLKKDEDLFQEWLKETCGA---------TAKQAQDCF 79 (90)
T ss_pred ccCCCcceeeccccHH--hhhhHHhccccHHHHHHHHHH-HhcccHHHHHHHHHHHcCc---------cHHHHHHHH
Confidence 6667789999999976 568999999976 46776 4557775544 44543 677888873
No 35
>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=36.20 E-value=32 Score=35.16 Aligned_cols=55 Identities=25% Similarity=0.144 Sum_probs=40.8
Q ss_pred ceeeeeeecccchhhhhhhhcCCccHHHHHHHhhcC-hHHHHHHhcCCCChhhHHHHHHHhhhccC
Q 011961 251 EVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVE-PQRLRKILGPGMSEKMWEVTMQHARKCVM 315 (474)
Q Consensus 251 eVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d-~~kLR~iLg~gmS~k~We~~v~HAktCvl 315 (474)
+|..|-+||+. .-++|.+.||+|++|++++ + ...|+..+| +.+..+..+|+--+.
T Consensus 174 pi~~l~giG~~--~~~~L~~~Gi~ti~dl~~~---~~~~~l~~~fg-----~~~~~l~~~a~G~d~ 229 (343)
T cd00424 174 PLTDLPGIGAV--TAKRLEAVGINPIGDLLAA---SPDALLALWGG-----VSGERLWYALRGIDD 229 (343)
T ss_pred ChhhcCCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHhh-----HHHHHHHHHhCCcCC
Confidence 46667777775 4588999999999998865 5 556777775 457778888876554
No 36
>KOG1520 consensus Predicted alkaloid synthase/Surface mucin Hemomucin [General function prediction only]
Probab=35.33 E-value=1.3e+02 Score=32.50 Aligned_cols=90 Identities=21% Similarity=0.248 Sum_probs=51.5
Q ss_pred CceeecCCCCeEEEEEEcCCCCeeecCCCCCcceEEEEEecCCCCCCCCCCCCHHHHhccccccCCCCCcccccceEEEe
Q 011961 103 SKITDVENNPLQIVVVDTRSNGLIAPASLPQPIKIELVVLDGDFPPGDRDHWTPEEFESNIVKERTGKRPLLTGDVNVTA 182 (474)
Q Consensus 103 ~kI~a~~g~~I~V~L~D~~t~n~iv~~g~~ss~kvEIvVLdGDF~~~~~e~WT~eEF~~~IV~~ReGk~pLL~Gdl~v~L 182 (474)
-+-+..||-|+=|+. |..||+-+|.+... =+.+++.+=. . ...++-+=+|+...++.++.|.=
T Consensus 108 ~~~e~~CGRPLGl~f-~~~ggdL~VaDAYl-----GL~~V~p~g~----------~-a~~l~~~~~G~~~kf~N~ldI~~ 170 (376)
T KOG1520|consen 108 FETEPLCGRPLGIRF-DKKGGDLYVADAYL-----GLLKVGPEGG----------L-AELLADEAEGKPFKFLNDLDIDP 170 (376)
T ss_pred eecccccCCcceEEe-ccCCCeEEEEecce-----eeEEECCCCC----------c-ceeccccccCeeeeecCceeEcC
Confidence 344555677776665 44454345543332 2222222111 1 23344455777777777766654
Q ss_pred cCceeecCCeeeecCCccccccceEEEEEEecC
Q 011961 183 RDGVAPIGDIEFTDNSSWIRSRKFRIGAKVARG 215 (474)
Q Consensus 183 ~~Gva~L~di~FTDnSsw~rSrKFRLgaRvv~~ 215 (474)
+| .|-|||+||.--.|.|.+++--...
T Consensus 171 -~g-----~vyFTDSSsk~~~rd~~~a~l~g~~ 197 (376)
T KOG1520|consen 171 -EG-----VVYFTDSSSKYDRRDFVFAALEGDP 197 (376)
T ss_pred -CC-----eEEEeccccccchhheEEeeecCCC
Confidence 44 5789999997666889888765543
No 37
>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=31.95 E-value=34 Score=28.54 Aligned_cols=15 Identities=60% Similarity=0.802 Sum_probs=11.9
Q ss_pred HHHhhhHHHHHHhHH
Q 011961 42 FFSALEPLLRRVVNE 56 (474)
Q Consensus 42 ~~~~lEp~lrrvV~E 56 (474)
+.-.|||+|||.++-
T Consensus 45 La~~LEPllrr~~~~ 59 (66)
T PF09584_consen 45 LALALEPLLRRGLNK 59 (66)
T ss_pred HHHHHHHHHHHHHHH
Confidence 345899999999764
No 38
>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=27.86 E-value=45 Score=27.28 Aligned_cols=14 Identities=50% Similarity=0.802 Sum_probs=11.2
Q ss_pred HHHhhhHHHHHHhH
Q 011961 42 FFSALEPLLRRVVN 55 (474)
Q Consensus 42 ~~~~lEp~lrrvV~ 55 (474)
+.-+|||+|+|..+
T Consensus 40 La~aLEPllkr~~~ 53 (59)
T TIGR02979 40 LAIALEPMLKRAAN 53 (59)
T ss_pred HHHHHHHHHHHHHH
Confidence 34589999999854
No 39
>COG4766 EutQ Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=27.28 E-value=1.2e+02 Score=29.40 Aligned_cols=92 Identities=18% Similarity=0.300 Sum_probs=58.6
Q ss_pred HHHHHHHHh-hHHHHHHh-hhHHHHHHhHHHHHHhhhccCCC-cccccCCccccccCCCCceEEEEccCCCCCcccCCce
Q 011961 29 VIGEAVMVN-SFQNFFSA-LEPLLRRVVNEEVQRGVSKYNPC-RSLTRSSSLRIQALEPSSLKLIFSQKLSLPIFTGSKI 105 (474)
Q Consensus 29 vi~e~~~~~-~~q~~~~~-lEp~lrrvV~EEve~~l~~~~~~-~~~~rs~~~~i~~~~~~~~~L~F~n~l~~pifTg~kI 105 (474)
-|+|.+..+ +.-.+|+. +|-++++|++|+.-....-..|. ....|.+...........+.|+|...=+.-+||++-+
T Consensus 13 ~i~~si~a~l~~~~~~~~l~~Qlm~kVmkek~s~~~~~~~~~~k~v~~ksgikvvk~s~vk~~~r~d~gqp~~V~~tdLv 92 (176)
T COG4766 13 RIRESIIAQLPEGQFTKELVEQLMEKVMKEKQSLECGWMQPSFKSVDGKSGIKVVKLSSVKFGLRFDTGQPDCVYTTDLV 92 (176)
T ss_pred HHHHHHHHhCChhhhhHHHHHHHHHHHHhchhhhhhhhcccceeecccCCceeEEecccceeEeeecCCCCCeEEeecee
Confidence 344444433 23334553 57789999999976655322210 2223222333332233468889998877889999999
Q ss_pred eecCCCCeEEEEEEc
Q 011961 106 TDVENNPLQIVVVDT 120 (474)
Q Consensus 106 ~a~~g~~I~V~L~D~ 120 (474)
.-.+|.++-+.+..-
T Consensus 93 t~~~g~~l~aG~m~~ 107 (176)
T COG4766 93 TEQEGSRLGAGLMEM 107 (176)
T ss_pred ecccCCccccceeee
Confidence 999999999998774
No 40
>PRK10497 peripheral inner membrane phage-shock protein; Provisional
Probab=27.12 E-value=46 Score=28.29 Aligned_cols=15 Identities=53% Similarity=0.820 Sum_probs=11.7
Q ss_pred HHHhhhHHHHHHhHH
Q 011961 42 FFSALEPLLRRVVNE 56 (474)
Q Consensus 42 ~~~~lEp~lrrvV~E 56 (474)
|.-.|||+|||.++-
T Consensus 52 L~~~LEPlLkr~~~~ 66 (73)
T PRK10497 52 LAVALEPLLKRAANK 66 (73)
T ss_pred HHHHHHHHHHHHHHH
Confidence 345899999999654
No 41
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=26.87 E-value=89 Score=22.80 Aligned_cols=42 Identities=29% Similarity=0.344 Sum_probs=31.9
Q ss_pred hhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhh
Q 011961 265 HKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHAR 311 (474)
Q Consensus 265 hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 311 (474)
-.+|..+||.||+++.. .+++.|..+- |++...=+.++.=|+
T Consensus 6 ~~~L~~~G~~s~e~la~---~~~~eL~~i~--g~~~e~a~~ii~~a~ 47 (50)
T TIGR01954 6 AQLLVEEGFTTVEDLAY---VPIDELLSIE--GFDEETAKELINRAR 47 (50)
T ss_pred HHHHHHcCCCCHHHHHc---cCHHHHhcCC--CCCHHHHHHHHHHHH
Confidence 46799999999999865 4667788875 578777777766665
No 42
>PF02961 BAF: Barrier to autointegration factor; InterPro: IPR004122 Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein []. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organisation, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans []. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA []. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA.; GO: 0003677 DNA binding; PDB: 2ODG_A 2BZF_A 2EZX_B 2EZY_B 1QCK_B 1CI4_B 2EZZ_B.
Probab=25.76 E-value=77 Score=27.88 Aligned_cols=57 Identities=30% Similarity=0.465 Sum_probs=32.8
Q ss_pred CCCCcceeeeeeecccchhhhhhhhcCCccH----HHHHHHhhcChHH----HHHHhcCCCChhhHHHHHHHhhhcc
Q 011961 246 PMLEDEVWRLEKIGKDGAFHKKLSAAGIKTV----QDFLKLSIVEPQR----LRKILGPGMSEKMWEVTMQHARKCV 314 (474)
Q Consensus 246 P~L~DeVwRLekIgKdG~~hk~L~~~gI~TV----~dFLkl~~~d~~k----LR~iLg~gmS~k~We~~v~HAktCv 314 (474)
|+=+-+|-.|-+||.. +-++|+.+|+... ++|| ++.+|++. |+.+.|. ..+||..|-
T Consensus 15 PMGeK~V~~laGIG~~--lg~~L~~~GfdKAy~vLGqfL-ll~kde~~F~~WLk~~~gA---------n~kqa~dcy 79 (89)
T PF02961_consen 15 PMGEKPVTELAGIGPV--LGKRLEEKGFDKAYVVLGQFL-LLKKDEELFQDWLKDTCGA---------NSKQAQDCY 79 (89)
T ss_dssp --TT-BGGGSTT--HH--HHHHHHHTT--BHHHHHHHHH-HTTT-HHHHHHHHHHHH------------HHHHHHHH
T ss_pred ccCCCCccccCCcCHH--HHHHHHHCCCcHHHHHhhhhh-hccCcHHHHHHHHHHHhCC---------CHHHHHHHH
Confidence 7778889999999986 5589999999885 5555 34567654 5555543 567787773
No 43
>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=25.56 E-value=1.1e+02 Score=26.49 Aligned_cols=36 Identities=25% Similarity=0.450 Sum_probs=28.5
Q ss_pred hcCCccHHHHHHHhhcChHHHH---HHhcCCCChhhHHHHHHHhhhc
Q 011961 270 AAGIKTVQDFLKLSIVEPQRLR---KILGPGMSEKMWEVTMQHARKC 313 (474)
Q Consensus 270 ~~gI~TV~dFLkl~~~d~~kLR---~iLg~gmS~k~We~~v~HAktC 313 (474)
...| +++||+=++..||.||- ++| .|+..++-|+..
T Consensus 52 ~~k~-~~eD~~FliR~D~~Kl~Rl~~lL-------~~k~~~k~ark~ 90 (92)
T cd07978 52 RGKV-KVEDLIFLLRKDPKKLARLRELL-------SMKDELKKARKA 90 (92)
T ss_pred CCCC-CHHHHHHHHhcCHHHHHHHHHHH-------HHHHHHHHHHhc
Confidence 4567 99999999999997755 556 588888888753
No 44
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=25.13 E-value=32 Score=38.94 Aligned_cols=38 Identities=32% Similarity=0.387 Sum_probs=31.5
Q ss_pred CCCCcceeeeeeecccchhhhhhhhcCCccHHHHHHHhhc
Q 011961 246 PMLEDEVWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIV 285 (474)
Q Consensus 246 P~L~DeVwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~ 285 (474)
..|++.|..|++||+.- .++|++.||+||.|.|..+=+
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 45778999999998653 478999999999999988743
No 45
>PRK14973 DNA topoisomerase I; Provisional
Probab=22.39 E-value=72 Score=38.04 Aligned_cols=54 Identities=24% Similarity=0.372 Sum_probs=44.2
Q ss_pred eeeeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhh
Q 011961 252 VWRLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARK 312 (474)
Q Consensus 252 VwRLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 312 (474)
.=.++++|.+.. .+|..+||.+|+|+++. |+.+|-..- |++.|.-..+..+|+.
T Consensus 879 l~~vkg~ge~t~--~~l~~ag~~~~e~l~~~---d~~~la~~~--~i~~k~~~~~~~~~~~ 932 (936)
T PRK14973 879 LLSVPGLGETTL--EKLYLAGVYDGDLLVSA---DPKKLAKVT--GIDEKKLRNLQAYAKK 932 (936)
T ss_pred hhhccCCCHHHH--HHHHHcCCCCHHHhccC---CHHHHhhhc--CCCHHHHHHHHHHHhh
Confidence 345567777766 88999999999999987 888998876 6788888888888764
No 46
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=22.29 E-value=1.4e+02 Score=30.33 Aligned_cols=17 Identities=18% Similarity=0.327 Sum_probs=12.9
Q ss_pred hhhHHHHHHhHHHHHHh
Q 011961 45 ALEPLLRRVVNEEVQRG 61 (474)
Q Consensus 45 ~lEp~lrrvV~EEve~~ 61 (474)
-||-++|+|+.|++-..
T Consensus 89 ~i~~lv~~v~~e~~~~~ 105 (233)
T PRK15457 89 LVAQLMEKVMKEKQSLE 105 (233)
T ss_pred HHHHHHHHHHHHHhccc
Confidence 47779999998886543
No 47
>KOG1104 consensus Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]
Probab=22.04 E-value=93 Score=36.31 Aligned_cols=22 Identities=27% Similarity=0.329 Sum_probs=12.4
Q ss_pred CCcccCCCCCCCCCCCccccCCCC
Q 011961 1 MAAKRFLNGSDPEEPPEKRTRTRP 24 (474)
Q Consensus 1 m~~kr~~~~~~~~~~~~~r~r~~p 24 (474)
|..+|..|++| +..++|||+.|
T Consensus 1 msrRrr~d~ed--E~y~~rr~r~~ 22 (759)
T KOG1104|consen 1 MSRRRRGDDED--ENYDDRRRRIS 22 (759)
T ss_pred CCCCccCCccc--cccccccccCC
Confidence 77888888433 33444444444
No 48
>PF06594 HCBP_related: Haemolysin-type calcium binding protein related domain; InterPro: IPR010566 This family consists of a number of bacteria specific domains, which are found in haemolysin-type calcium binding proteins. This family is found in conjunction with IPR001343 from INTERPRO and is often found in multiple copies.
Probab=21.86 E-value=58 Score=23.94 Aligned_cols=18 Identities=39% Similarity=0.745 Sum_probs=15.0
Q ss_pred eeecCCeeeecCCccccc
Q 011961 186 VAPIGDIEFTDNSSWIRS 203 (474)
Q Consensus 186 va~L~di~FTDnSsw~rS 203 (474)
-..+..+.|-|++.|.+.
T Consensus 24 ~~~Ie~i~FaDGt~w~~~ 41 (43)
T PF06594_consen 24 SYRIEQIEFADGTVWTRA 41 (43)
T ss_pred CCcEeEEEEcCCCEecHH
Confidence 566889999999999753
No 49
>PF07182 DUF1402: Protein of unknown function (DUF1402); InterPro: IPR009842 This family consists of several hypothetical bacterial proteins of around 310 residues in length. Members of this family seem to be found exclusively in Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Probab=21.38 E-value=1.6e+02 Score=30.67 Aligned_cols=31 Identities=26% Similarity=0.555 Sum_probs=27.7
Q ss_pred ccceeeeeEEECCeEeeCCCCCHHhHHHHHHH
Q 011961 332 NPICQVVRAVINNQTYLTRDLTKLNRTYIENT 363 (474)
Q Consensus 332 N~i~~lVGa~f~G~~~~~~~L~~~qk~~V~~L 363 (474)
++|| +|||+.+.|.|-.+-++..|-=||+.+
T Consensus 72 dPIH-ivGAiVGEHTYNvda~DrlQsYYVKA~ 102 (303)
T PF07182_consen 72 DPIH-IVGAIVGEHTYNVDAYDRLQSYYVKAL 102 (303)
T ss_pred Cchh-eeeeeecccccccchhHHHHHHHHHHH
Confidence 7899 799999999999999999998888665
No 50
>COG3827 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.07 E-value=1.6e+02 Score=29.87 Aligned_cols=40 Identities=25% Similarity=0.253 Sum_probs=25.6
Q ss_pred chHHHHHHHHHHhhHHHHHHhhhHHHHHHhHHHHHHhhhc
Q 011961 25 SFASVIGEAVMVNSFQNFFSALEPLLRRVVNEEVQRGVSK 64 (474)
Q Consensus 25 ~~~~vi~e~~~~~~~q~~~~~lEp~lrrvV~EEve~~l~~ 64 (474)
+|-.+..|.++-+--.=|=..|=-++.|.|+|||||..+.
T Consensus 189 sleE~a~eMLRPmLqdWLDkNLPtLVErLVrEEIeRv~RG 228 (231)
T COG3827 189 SLEEMAAEMLRPMLQDWLDKNLPTLVERLVREEIERVVRG 228 (231)
T ss_pred cHHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHHcc
Confidence 5666666665554222223355566789999999998764
No 51
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=21.02 E-value=59 Score=33.25 Aligned_cols=41 Identities=22% Similarity=0.346 Sum_probs=35.0
Q ss_pred hhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHH
Q 011961 268 LSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQH 309 (474)
Q Consensus 268 L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~H 309 (474)
-+.++|.|+.|-..+...+|+.||++++ -+.+|.|-.=|+-
T Consensus 25 ae~hkiiTirdvae~~ev~~n~lr~las-rLekkG~LeRi~r 65 (269)
T COG5340 25 AEGHKIITIRDVAETLEVAPNTLRELAS-RLEKKGWLERILR 65 (269)
T ss_pred HHhCceEEeHHhhhhccCCHHHHHHHHh-hhhhcchhhhhcC
Confidence 4457999999999999999999999997 6889999765543
No 52
>PRK02362 ski2-like helicase; Provisional
Probab=20.82 E-value=1.1e+02 Score=34.89 Aligned_cols=51 Identities=27% Similarity=0.397 Sum_probs=39.3
Q ss_pred eeeeecccchhhhhhhhcCCccHHHHHHHhhcChHHHHHHhcCCCChhhHHHHHHHhhhc
Q 011961 254 RLEKIGKDGAFHKKLSAAGIKTVQDFLKLSIVEPQRLRKILGPGMSEKMWEVTMQHARKC 313 (474)
Q Consensus 254 RLekIgKdG~~hk~L~~~gI~TV~dFLkl~~~d~~kLR~iLg~gmS~k~We~~v~HAktC 313 (474)
+|.+|++. ..++|.++||.|+.|+. ..++++|.++|| .|.=+.+++.|+.-
T Consensus 656 ~ip~i~~~--~a~~l~~~gi~s~~dl~---~~~~~~l~~~~g----~~~~~~i~~~~~~~ 706 (737)
T PRK02362 656 GLRGVGRV--RARRLYNAGIESRADLR---AADKSVVLAILG----EKIAENILEQAGRR 706 (737)
T ss_pred CCCCCCHH--HHHHHHHcCCCCHHHHH---hCCHHHHHHHHC----HHHHHHHHHHhCcc
Confidence 45555554 55788899999999998 468899999987 57777788887743
No 53
>PRK05256 condesin subunit E; Provisional
Probab=20.04 E-value=1.7e+02 Score=29.89 Aligned_cols=50 Identities=18% Similarity=0.227 Sum_probs=40.5
Q ss_pred hhhhhcCCccHHHHHHHhh--cChHHHHHHhc--CCCChhhHHHHHHHhhhccC
Q 011961 266 KKLSAAGIKTVQDFLKLSI--VEPQRLRKILG--PGMSEKMWEVTMQHARKCVM 315 (474)
Q Consensus 266 k~L~~~gI~TV~dFLkl~~--~d~~kLR~iLg--~gmS~k~We~~v~HAktCvl 315 (474)
++|++.||+|+++.+.-+. .|++||.+.++ ..-|+-+=+++.+-.++|--
T Consensus 107 erLa~~gift~qeL~deL~~ladE~kllklvn~R~~GsDlD~~Kl~ekvr~sLr 160 (238)
T PRK05256 107 ERLAHEGIFTQQELYDELLTLADEAKLLKLVNNRSTGSDLDKQKLQEKVRTSLN 160 (238)
T ss_pred HHHhcCCceeHHHHHHHHHHhhcHHHHHHHhcCCCCcchhhHHHHHHHHHHHHH
Confidence 7899999999999887654 58999999984 22377777888889999864
Done!