Query 008593
Match_columns 560
No_of_seqs 138 out of 160
Neff 4.2
Searched_HMMs 46136
Date Thu Mar 28 14:07:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008593.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008593hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07887 Calmodulin_bind: Calm 100.0 1E-118 3E-123 906.5 30.2 294 88-385 1-298 (299)
2 TIGR02239 recomb_RAD51 DNA rep 89.1 0.38 8.2E-06 50.5 3.8 46 265-313 13-58 (316)
3 PLN03186 DNA repair protein RA 88.3 0.51 1.1E-05 50.3 4.1 59 252-313 27-85 (342)
4 TIGR02238 recomb_DMC1 meiotic 87.6 0.53 1.1E-05 49.4 3.7 49 264-315 12-60 (313)
5 PF14520 HHH_5: Helix-hairpin- 86.0 0.35 7.6E-06 38.6 1.0 54 252-310 6-59 (60)
6 PLN03187 meiotic recombination 85.5 0.87 1.9E-05 48.7 4.0 61 252-315 30-90 (344)
7 PRK04301 radA DNA repair and r 84.6 0.7 1.5E-05 47.9 2.8 57 252-313 7-63 (317)
8 PTZ00035 Rad51 protein; Provis 79.9 1.9 4.2E-05 45.7 4.0 60 252-314 22-81 (337)
9 PF14229 DUF4332: Domain of un 77.5 2.1 4.5E-05 39.2 3.0 52 265-316 7-60 (122)
10 PF04994 TfoX_C: TfoX C-termin 74.7 0.87 1.9E-05 39.2 -0.3 75 252-362 4-78 (81)
11 TIGR02236 recomb_radA DNA repa 72.3 2.4 5.3E-05 43.5 2.3 53 255-312 3-55 (310)
12 PRK03609 umuC DNA polymerase V 66.7 4.7 0.0001 43.6 3.0 52 252-311 180-231 (422)
13 PRK02406 DNA polymerase IV; Va 61.4 7.2 0.00016 40.8 3.2 52 252-311 169-220 (343)
14 PRK01172 ski2-like helicase; P 60.6 7.7 0.00017 44.4 3.4 47 264-313 623-669 (674)
15 PRK14133 DNA polymerase IV; Pr 50.6 14 0.00029 38.9 3.1 51 252-310 174-224 (347)
16 PF10691 DUF2497: Protein of u 50.4 44 0.00096 28.7 5.5 40 29-68 34-73 (73)
17 cd03586 PolY_Pol_IV_kappa DNA 48.5 15 0.00034 37.8 3.1 52 252-311 172-223 (334)
18 PRK02794 DNA polymerase IV; Pr 48.1 15 0.00032 39.8 3.0 54 252-313 210-263 (419)
19 PF02889 Sec63: Sec63 Brl doma 47.5 16 0.00035 37.2 3.0 56 251-311 148-203 (314)
20 cd01700 PolY_Pol_V_umuC umuC s 47.2 16 0.00034 38.3 2.9 51 252-310 177-227 (344)
21 PRK03352 DNA polymerase IV; Va 46.3 12 0.00026 39.2 1.9 52 252-310 178-229 (346)
22 PRK01810 DNA polymerase IV; Va 44.7 20 0.00042 38.6 3.2 52 252-311 180-231 (407)
23 PRK03103 DNA polymerase IV; Re 44.6 19 0.00042 38.7 3.1 52 252-311 182-233 (409)
24 PF03118 RNA_pol_A_CTD: Bacter 43.6 13 0.00027 30.9 1.2 37 266-305 24-60 (66)
25 COG3743 Uncharacterized conser 41.6 31 0.00066 32.9 3.6 59 251-311 67-126 (133)
26 TIGR01954 nusA_Cterm_rpt trans 40.8 29 0.00063 26.0 2.8 42 266-310 6-47 (50)
27 PRK03348 DNA polymerase IV; Pr 39.6 17 0.00037 40.1 1.8 54 252-312 181-234 (454)
28 cd00424 PolY Y-family of DNA p 39.6 23 0.00051 37.1 2.8 54 252-313 174-228 (343)
29 PRK03858 DNA polymerase IV; Va 37.7 20 0.00043 38.2 2.0 51 252-309 174-224 (396)
30 COG4766 EutQ Ethanolamine util 37.6 1E+02 0.0022 30.5 6.4 91 32-123 12-108 (176)
31 cd01701 PolY_Rev1 DNA polymera 36.2 32 0.00069 37.3 3.2 54 252-310 223-276 (404)
32 PRK01216 DNA polymerase IV; Va 33.7 24 0.00052 37.7 1.8 52 252-310 179-230 (351)
33 PF14229 DUF4332: Domain of un 33.1 34 0.00074 31.4 2.5 38 254-296 56-93 (122)
34 cd01702 PolY_Pol_eta DNA Polym 30.9 46 0.001 35.7 3.4 57 252-313 183-240 (359)
35 KOG1520 Predicted alkaloid syn 30.8 1.7E+02 0.0037 32.3 7.6 48 164-217 151-198 (376)
36 COG5340 Predicted transcriptio 28.6 39 0.00085 35.1 2.2 39 269-307 25-64 (269)
37 PRK15457 ethanolamine utilizat 28.4 91 0.002 32.3 4.8 16 50-65 90-105 (233)
38 PRK10917 ATP-dependent DNA hel 26.0 33 0.00072 39.8 1.3 38 246-285 4-41 (681)
39 PRK14973 DNA topoisomerase I; 23.1 56 0.0012 39.8 2.5 54 253-311 879-932 (936)
40 PF10148 SCHIP-1: Schwannomin- 22.6 1.2E+02 0.0025 31.7 4.3 44 56-99 6-60 (238)
41 PF11754 Velvet: Velvet factor 22.2 1.9E+02 0.004 28.8 5.6 62 172-236 97-172 (203)
42 PRK07758 hypothetical protein; 22.0 98 0.0021 28.1 3.2 37 267-306 48-84 (95)
43 KOG1104 Nuclear cap-binding co 21.6 90 0.0019 37.2 3.7 23 6-28 1-23 (759)
44 KOG4233 DNA-bridging protein B 21.0 67 0.0015 28.5 1.9 61 247-313 15-79 (90)
45 cd03468 PolY_like DNA Polymera 20.4 56 0.0012 33.7 1.6 45 258-310 177-221 (335)
46 PF02961 BAF: Barrier to autoi 20.1 1.5E+02 0.0032 26.7 3.9 57 247-313 15-79 (89)
47 cd01703 PolY_Pol_iota DNA Poly 20.0 60 0.0013 35.2 1.8 58 252-313 173-242 (379)
No 1
>PF07887 Calmodulin_bind: Calmodulin binding protein-like; InterPro: IPR012416 The members of this family are putative or actual calmodulin binding proteins expressed by various plant species. Some members (for example, Q8H6T7 from SWISSPROT), are known to be involved in the induction of plant defence responses []. However, their precise function in this regard is as yet unknown.
Probab=100.00 E-value=1.2e-118 Score=906.46 Aligned_cols=294 Identities=56% Similarity=0.940 Sum_probs=289.6
Q ss_pred ceEEEEcCCCCCCcccCCceeeccCCceEEEEEeCCCCceeccCCCCcceEEEEEecCCCCCCCCCCCCHHHHhhccccc
Q 008593 88 GLQLLFVNKLPCPIYTGSRIEAEDGGPVKIVLVDPISKTRVTSGPYSSMKVEILVLNGDFGSDDHENWTEREFLEKIVRE 167 (560)
Q Consensus 88 ~~~L~F~n~l~~pifT~~kI~a~~g~~I~V~L~D~~t~~~Vt~Gplss~kvEIvVLdGDF~~~~~e~WT~eEF~~~IV~~ 167 (560)
++||+|+|+|++|||||++|+|+||+||+|+|+|++|+ |++||+|++|||||||||||+.+++++||+|||++|||++
T Consensus 1 ~~~L~F~n~l~~pifT~~~i~a~~g~~i~V~l~d~~~~--v~~g~lss~kieIvvLdGdF~~~~~~~wT~eeF~~~iv~~ 78 (299)
T PF07887_consen 1 NLQLRFLNKLSLPIFTGSKIEAEDGAPIKVALVDANTG--VTSGPLSSAKIEIVVLDGDFNDEDCEDWTEEEFNSHIVKE 78 (299)
T ss_pred CeEEEecCCCCCCcccCCceEecCCCcEEEEEEECCCC--ccCCCCCCcEEEEEEEccccCCCccCCCCHHHHhhcEeec
Confidence 58999999999999999999999999999999999887 9999999999999999999999999999999999999999
Q ss_pred CCCCcccccccEEEEecCceeeccceEeecCCcccccCccEEEEEEeeCCCCcceeeeeeecceEeecCCCcccccCCCC
Q 008593 168 REGKRPLVTGELHITLKDGVGILSDIVFTDNSSWIRCRKFRLGARVLQKGCREARIKEAKSEAFVVKDHRGELNKKHYPP 247 (560)
Q Consensus 168 R~Gk~pLL~Gdl~v~L~~Gva~l~di~FTDnSs~~rSrKFRLgvRv~~~~~~g~RI~EAvsE~FvVkd~Rge~~kKh~pP 247 (560)
|+||+|||+|+++|+|+||+|+|+||+|||||||+|||||||||||+++++.|+|||||+||||+|||||||+|||||||
T Consensus 79 r~gk~pLL~G~~~v~L~~G~a~l~di~FtdnSs~~rsrKFRLgarv~~~~~~~~rI~Eavse~FvVkd~Rge~~kKh~pP 158 (299)
T PF07887_consen 79 REGKRPLLTGDLQVTLKNGVATLGDISFTDNSSWIRSRKFRLGARVVSGSCDGVRIREAVSEPFVVKDHRGELYKKHYPP 158 (299)
T ss_pred CCCCCCCCCccEEEEecCCEEEccccEEecCcccccCCcEEEEEEEccCCCCCceeEEeeecCEEEEecccccccCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcchhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhc--CCcccHHHHHHhhcccccCCCceEEEe--
Q 008593 248 SLDDDIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIIS--ASNKTWETIVEHAATCVVNDGKLFAFT-- 323 (560)
Q Consensus 248 ~L~DeVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLg--ms~k~We~~v~HAktCv~~~~kly~y~-- 323 (560)
+|+|||||||||||+|+|||+|+.+||+||+|||+|+++||++||++|| ||+|||++||+|||||+ +++++|+|.
T Consensus 159 ~L~DeVwRLe~Igk~G~~hk~L~~~~I~tV~dFl~l~~~d~~~Lr~ilg~~ms~k~We~~v~HA~tCv-l~~~~y~y~~~ 237 (299)
T PF07887_consen 159 SLDDEVWRLEKIGKDGAFHKRLKKNGINTVEDFLKLLNKDPQKLREILGSGMSNKMWETTVEHAKTCV-LGDKLYVYYDE 237 (299)
T ss_pred CCCCchhhhhhccccCHHHHHHHHcCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHHHHHHHHhcC-CCCcEEEEEec
Confidence 9999999999999999999999999999999999999999999999999 99999999999999999 888999994
Q ss_pred cCceEEEEccceeEEeeeeCCeeeecCCCCChhhHHHHHHHHHHHHHhcccceeccccccCC
Q 008593 324 GDGIILLLNSIYKLVAVTFDGENCVHPNDLAFPQKISVENLKRVAYKNVNQFVLIDARANFG 385 (560)
Q Consensus 324 ~~~v~l~FN~i~~lVGa~~~g~~y~~~d~L~~~qk~~V~~lk~~AY~n~~~l~~~d~~~~~~ 385 (560)
++|++|+|||||+||||+|+|| |++.|+||+.||++|++||++||+||++|++||++++++
T Consensus 238 ~~nv~l~FN~i~~lvga~~~g~-y~s~d~L~~~qK~~v~~Lv~~AY~n~~~l~e~d~~~~~n 298 (299)
T PF07887_consen 238 EQNVGLFFNCIYELVGAIFGGQ-YVSLDNLSSAQKAYVDKLVKQAYENWDNLEEYDGKMLNN 298 (299)
T ss_pred CCceEEEEcchhhEEeEEECCE-EEehHHcCHHHHHHHHHHHHHHHHhhhhheecccchhcc
Confidence 8999999999999999999999 999999999999999999999999999999999999876
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=89.13 E-value=0.38 Score=50.48 Aligned_cols=46 Identities=22% Similarity=0.217 Sum_probs=42.4
Q ss_pred hhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcccc
Q 008593 265 YHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAATCV 313 (560)
Q Consensus 265 ~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAktCv 313 (560)
.-++|+++||.||+||+.. ++..|.+++|+|....+.+.+||.+|.
T Consensus 13 ~~~~l~~~g~~t~~~~~~~---~~~~L~~i~~ls~~~~~~~~~~~~~~~ 58 (316)
T TIGR02239 13 DIKKLQEAGLHTVESVAYA---PKKQLLEIKGISEAKADKILAEAAKLV 58 (316)
T ss_pred HHHHHHHcCCCcHHHHHhC---CHHHHHHHhCCCHHHHHHHHHHHHHhc
Confidence 4578999999999999865 899999999999999999999999987
No 3
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=88.31 E-value=0.51 Score=50.34 Aligned_cols=59 Identities=22% Similarity=0.206 Sum_probs=48.6
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcccc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAATCV 313 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAktCv 313 (560)
++-+|+.-|-.-..-++|.++||.||+||+.+ ++..|.++.|+|....+.+++||.+|.
T Consensus 27 ~~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~---~~~~L~~i~~is~~~~~~~~~~~~~~~ 85 (342)
T PLN03186 27 PIEQLQASGIAALDIKKLKDAGIHTVESLAYA---PKKDLLQIKGISEAKVEKILEAASKLV 85 (342)
T ss_pred cHHHHHhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhcCCCHHHHHHHHHHHHHhc
Confidence 45666553333345688999999999998865 789999999999999999999998887
No 4
>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=87.60 E-value=0.53 Score=49.44 Aligned_cols=49 Identities=22% Similarity=0.314 Sum_probs=43.4
Q ss_pred hhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcccccC
Q 008593 264 KYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAATCVVN 315 (560)
Q Consensus 264 ~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAktCv~~ 315 (560)
..-++|+++||.||+||+.. ++..|.++.|+|....+.+++.|+.+...
T Consensus 12 ~~~~~L~~~g~~t~~~~~~~---~~~~L~~~~gls~~~~~~i~~~~~~~~~~ 60 (313)
T TIGR02238 12 ADIKKLKSAGICTVNGVIMT---TRRALCKIKGLSEAKVDKIKEAASKIINP 60 (313)
T ss_pred HHHHHHHHcCCCcHHHHHhC---CHHHHHHhcCCCHHHHHHHHHHHHhhhcc
Confidence 34589999999999998765 79999999999999999999999988733
No 5
>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=85.97 E-value=0.35 Score=38.56 Aligned_cols=54 Identities=30% Similarity=0.452 Sum_probs=44.1
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAA 310 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAk 310 (560)
+.-.+.+||+.-+ ++|.+.||.|++|+..+ +++.|.++=|++.+.=+.+++.|+
T Consensus 6 ~L~~I~Gig~~~a--~~L~~~G~~t~~~l~~a---~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 6 DLLSIPGIGPKRA--EKLYEAGIKTLEDLANA---DPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHHTSTTCHHHHH--HHHHHTTCSSHHHHHTS---HHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred hhccCCCCCHHHH--HHHHhcCCCcHHHHHcC---CHHHHhcCCCCCHHHHHHHHHHHh
Confidence 3445667777544 88999999999998664 888999999999999999998886
No 6
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=85.51 E-value=0.87 Score=48.71 Aligned_cols=61 Identities=18% Similarity=0.215 Sum_probs=49.4
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcccccC
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAATCVVN 315 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAktCv~~ 315 (560)
++..|+.-|-.=..-++|.++||+||+|++.. ++..|.++.|+|....+.+++.|+..+..
T Consensus 30 ~~~~l~~~g~~~~~~~kL~~~g~~tv~~~~~~---~~~~L~~~~g~s~~~~~ki~~~a~~~~~~ 90 (344)
T PLN03187 30 SIDKLISQGINAGDVKKLQDAGIYTCNGLMMH---TKKNLTGIKGLSEAKVDKICEAAEKLLNQ 90 (344)
T ss_pred CHHHHhhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhcCCCHHHHHHHHHHHHHhhcc
Confidence 46677663433345689999999999998765 78899999999999999999999887634
No 7
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=84.65 E-value=0.7 Score=47.93 Aligned_cols=57 Identities=21% Similarity=0.264 Sum_probs=47.3
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcccc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAATCV 313 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAktCv 313 (560)
++-.|..||+. .-++|.++||.|++|++. .++..|.+++|++.+.++.+++-|+.++
T Consensus 7 ~l~~l~gIg~~--~a~~L~~~Gi~t~~dl~~---~~~~~L~~~~g~~~~~a~~l~~~a~~~~ 63 (317)
T PRK04301 7 DLEDLPGVGPA--TAEKLREAGYDTVEAIAV---ASPKELSEAAGIGESTAAKIIEAAREAA 63 (317)
T ss_pred cHhhcCCCCHH--HHHHHHHcCCCCHHHHHc---CCHHHHHHhcCCCHHHHHHHHHHHHHhh
Confidence 45566677754 458999999999999965 4899999999999999999999888644
No 8
>PTZ00035 Rad51 protein; Provisional
Probab=79.92 E-value=1.9 Score=45.70 Aligned_cols=60 Identities=23% Similarity=0.305 Sum_probs=48.0
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhccccc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAATCVV 314 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAktCv~ 314 (560)
++..|+.-|-.=..-++|.++||+||+||+.. ++..|.++.|+|...=+.+++.|+.++.
T Consensus 22 ~~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~~---~~~~L~~~~gis~~~~~~i~~~~~~~~~ 81 (337)
T PTZ00035 22 EIEKLQSAGINAADIKKLKEAGICTVESVAYA---TKKDLCNIKGISEAKVEKIKEAASKLVP 81 (337)
T ss_pred cHHHHhcCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhhCCCHHHHHHHHHHHHHhcc
Confidence 46667553333345589999999999998765 8899999999999999999999988773
No 9
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=77.53 E-value=2.1 Score=39.23 Aligned_cols=52 Identities=21% Similarity=0.250 Sum_probs=39.7
Q ss_pred hhhhHhhCCCccHHHHHHHhcCChhH--HHHHhcCCcccHHHHHHhhcccccCC
Q 008593 265 YHERLAKKGVYNVKDFLRMHTTDPGS--LCKIISASNKTWETIVEHAATCVVND 316 (560)
Q Consensus 265 ~hk~L~~~gI~tV~dFLrl~~~d~~k--Lr~iLgms~k~We~~v~HAktCv~~~ 316 (560)
+-.+|...||+|++|||..-.....+ |-+.+|++.+-=...+.+|.=|.++|
T Consensus 7 ~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~~i~~~~l~~w~~~AdL~ri~g 60 (122)
T PF14229_consen 7 EAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKLGISERNLLKWVNQADLMRIPG 60 (122)
T ss_pred HHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhcCCCHHHHHHHHhHHHhhhcCC
Confidence 45789999999999999997765554 88888888876666677776554344
No 10
>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=74.68 E-value=0.87 Score=39.17 Aligned_cols=75 Identities=20% Similarity=0.227 Sum_probs=44.0
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcccccCCCceEEEecCceEEEE
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAATCVVNDGKLFAFTGDGIILLL 331 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAktCv~~~~kly~y~~~~v~l~F 331 (560)
.+..|.+||.. .-+.|.+.||+||+||..+=.+ +.|-.+..+-.+ +-+
T Consensus 4 ~l~~LpNig~~--~e~~L~~vGI~t~~~L~~~Ga~-------------~a~~~Lk~~~~~-----------------~~~ 51 (81)
T PF04994_consen 4 RLKDLPNIGPK--SERMLAKVGIHTVEDLRELGAV-------------EAYLRLKASGPS-----------------VCL 51 (81)
T ss_dssp -GCGSTT--HH--HHHHHHHTT--SHHHHHHHHHH-------------HHHHHHHHH-TT-------------------H
T ss_pred chhhCCCCCHH--HHHHHHHcCCCCHHHHHHhCHH-------------HHHHHHHHHCCC-----------------CCH
Confidence 45566777764 3378999999999999887333 344444444222 335
Q ss_pred ccceeEEeeeeCCeeeecCCCCChhhHHHHH
Q 008593 332 NSIYKLVAVTFDGENCVHPNDLAFPQKISVE 362 (560)
Q Consensus 332 N~i~~lVGa~~~g~~y~~~d~L~~~qk~~V~ 362 (560)
|-.|.|.||.-|=+ ...|++.+|....
T Consensus 52 ~~L~aL~gAi~g~~----~~~L~~~~K~~L~ 78 (81)
T PF04994_consen 52 NLLYALEGAIQGIH----WADLPDEEKQELL 78 (81)
T ss_dssp HHHHHHHHHHCTS-----GGGS-HHHHHHHH
T ss_pred HHHHHHHHHHcCCC----HHHCCHHHHHHHH
Confidence 77888888887755 5667777776544
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=72.33 E-value=2.4 Score=43.53 Aligned_cols=53 Identities=21% Similarity=0.257 Sum_probs=41.8
Q ss_pred hhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhccc
Q 008593 255 RLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAATC 312 (560)
Q Consensus 255 RLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAktC 312 (560)
.|.+||+. .-++|.++||.|++|++.+ +++.|.+++|++.+..+.+.+-|+.|
T Consensus 3 ~i~gig~~--~~~~L~~~Gi~ti~dl~~~---~~~~L~~~~g~~~~~a~~l~~~~~~~ 55 (310)
T TIGR02236 3 DLPGVGPA--TAEKLREAGYDTFEAIAVA---SPKELSEIAGISEGTAAKIIQAARKA 55 (310)
T ss_pred ccCCCCHH--HHHHHHHcCCCCHHHHHcC---CHHHHHhccCCCHHHHHHHHHHHHHH
Confidence 34556653 4489999999999998875 89999999999888877777777633
No 12
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=66.74 E-value=4.7 Score=43.62 Aligned_cols=52 Identities=12% Similarity=0.114 Sum_probs=41.7
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAAT 311 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAkt 311 (560)
.|..|-+||+. .-++|.+.||+|++|+.++ ++..|++.+| ..+..+..||.-
T Consensus 180 Pv~~l~GiG~~--~~~~L~~lGi~TigdL~~~---~~~~L~~~fG---~~~~~l~~~a~G 231 (422)
T PRK03609 180 PVEEVWGVGRR--ISKKLNAMGIKTALDLADT---NIRFIRKHFN---VVLERTVRELRG 231 (422)
T ss_pred ChhhcCCccHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHC---HHHHHHHHHhCC
Confidence 46666677774 4589999999999999986 7899999999 457777777753
No 13
>PRK02406 DNA polymerase IV; Validated
Probab=61.44 E-value=7.2 Score=40.78 Aligned_cols=52 Identities=21% Similarity=0.303 Sum_probs=40.3
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAAT 311 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAkt 311 (560)
+|..|-.||+. .-++|...||.|++|+.++ +...|++.|| +.+..+.+||.-
T Consensus 169 pi~~l~giG~~--~~~~L~~~Gi~ti~dl~~l---~~~~L~~~fG---~~~~~l~~~a~G 220 (343)
T PRK02406 169 PVEKIPGVGKV--TAEKLHALGIYTCADLQKY---DLAELIRHFG---KFGRRLYERARG 220 (343)
T ss_pred CcchhcCCCHH--HHHHHHHcCCCcHHHHHhC---CHHHHHHHHh---HHHHHHHHHhCC
Confidence 56777777764 4478999999999999885 7889999999 346666667654
No 14
>PRK01172 ski2-like helicase; Provisional
Probab=60.59 E-value=7.7 Score=44.39 Aligned_cols=47 Identities=28% Similarity=0.312 Sum_probs=41.0
Q ss_pred hhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcccc
Q 008593 264 KYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAATCV 313 (560)
Q Consensus 264 ~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAktCv 313 (560)
...++|.++||.||.|+.. .++++|-+++|++++.=+.++++|+.=+
T Consensus 623 ~~a~~l~~~g~~~~~di~~---~~~~~~~~i~~~~~~~~~~i~~~~~~~~ 669 (674)
T PRK01172 623 VRARRLYDAGFKTVDDIAR---SSPERIKKIYGFSDTLANAIVNRAMKIS 669 (674)
T ss_pred HHHHHHHHcCCCCHHHHHh---CCHHHHHHHhccCHHHHHHHHHHHHHHH
Confidence 3668899999999999877 6889999999999999999999998643
No 15
>PRK14133 DNA polymerase IV; Provisional
Probab=50.63 E-value=14 Score=38.90 Aligned_cols=51 Identities=25% Similarity=0.389 Sum_probs=40.1
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAA 310 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAk 310 (560)
+|..|-.||+.-. ++|.+-||+|++|++++ +...|++.+| +.|..+.++|.
T Consensus 174 pv~~l~gig~~~~--~~L~~~Gi~ti~dl~~l---~~~~L~~rfG---~~g~~l~~~a~ 224 (347)
T PRK14133 174 PISKVHGIGKKSV--EKLNNIGIYTIEDLLKL---SREFLIEYFG---KFGVEIYERIR 224 (347)
T ss_pred CccccCCCCHHHH--HHHHHcCCccHHHHhhC---CHHHHHHHHh---HHHHHHHHHhC
Confidence 4666666766444 78999999999999885 7788999999 45777777775
No 16
>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=50.37 E-value=44 Score=28.68 Aligned_cols=40 Identities=25% Similarity=0.408 Sum_probs=24.4
Q ss_pred chhHHHHHHHhhhHHHHHHHhhHHHHHHHHHHHHHHHHcC
Q 008593 29 TLKKVVDDVMKGNWQNKMVASLEPCIRSVVREELERVLLP 68 (560)
Q Consensus 29 ~~~svi~e~~~~~~~q~l~~~lEp~lRrvV~EEve~~l~~ 68 (560)
++-.+++|+++---=+=|=..|=.|+.|+|++||++..++
T Consensus 34 TlE~lvremLRPmLkeWLD~nLP~lVErlVr~EIeRi~rr 73 (73)
T PF10691_consen 34 TLEDLVREMLRPMLKEWLDENLPGLVERLVREEIERIARR 73 (73)
T ss_pred cHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhcC
Confidence 4555556655533211222345567889999999998654
No 17
>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=48.55 E-value=15 Score=37.78 Aligned_cols=52 Identities=21% Similarity=0.319 Sum_probs=40.8
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAAT 311 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAkt 311 (560)
+|..|-.||+. .-++|...||+|++|+.++ ++..|++.+| +.|....+||+-
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 45666667654 4588999999999999875 7788999888 568888888864
No 18
>PRK02794 DNA polymerase IV; Provisional
Probab=48.14 E-value=15 Score=39.80 Aligned_cols=54 Identities=17% Similarity=0.162 Sum_probs=42.5
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcccc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAATCV 313 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAktCv 313 (560)
.|..|-.||+ ..-++|...||+|++|+.++ +...|++.+|. .+..+.++|.--+
T Consensus 210 Pl~~L~GiG~--~~~~~L~~~GI~tigdL~~l---~~~~L~~rfG~---~g~~l~~~a~G~d 263 (419)
T PRK02794 210 PVGIIWGVGP--ATAARLARDGIRTIGDLQRA---DEADLMRRFGS---MGLRLWRLARGID 263 (419)
T ss_pred ChhhhCCCCH--HHHHHHHHhccchHHHHhhC---CHHHHHHHHhH---HHHHHHHHhCCCC
Confidence 4556666665 45589999999999998875 78899999993 5888888887554
No 19
>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=47.47 E-value=16 Score=37.19 Aligned_cols=56 Identities=20% Similarity=0.400 Sum_probs=39.5
Q ss_pred cchhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcc
Q 008593 251 DDIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAAT 311 (560)
Q Consensus 251 DeVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAkt 311 (560)
....-|.+|+.+.+ ++|..+||.|+++|+++ ++++|..+|+......+.+.+.|..
T Consensus 148 ~~L~Qlp~i~~~~~--~~l~~~~i~~l~~l~~~---~~~e~~~ll~~~~~~~~~i~~~~~~ 203 (314)
T PF02889_consen 148 SPLLQLPHIGEESL--KKLEKRGIKTLQDLRDL---SPEELEELLNRNPPFGKEILEVASR 203 (314)
T ss_dssp -GGGGSTT--HHHH--HHHHHTT--SHHHHHHS----HHHHHHHH-S-HHHHHHHHHHHCC
T ss_pred ChhhcCCCCCHHHH--HHHhccCCCcHHHHhhC---CHHHHHHHHhhhhhhHHHHHHHHHH
Confidence 35566778888765 89999999999999865 8899999999888888888888763
No 20
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=47.17 E-value=16 Score=38.34 Aligned_cols=51 Identities=20% Similarity=0.234 Sum_probs=39.7
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAA 310 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAk 310 (560)
.|..|-+||+. .-++|...||+|++|++++ +...|.+.+| ..+....++|+
T Consensus 177 pl~~l~gig~~--~~~~L~~~Gi~ti~dL~~~---~~~~L~~rfG---~~~~~l~~~a~ 227 (344)
T cd01700 177 PVGDVWGIGRR--TAKKLNAMGIHTAGDLAQA---DPDLLRKKFG---VVGERLVRELN 227 (344)
T ss_pred ChhhcCccCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHH---HHHHHHHHHhC
Confidence 46666667774 4478999999999999986 7789999999 25677777765
No 21
>PRK03352 DNA polymerase IV; Validated
Probab=46.25 E-value=12 Score=39.16 Aligned_cols=52 Identities=23% Similarity=0.217 Sum_probs=38.5
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAA 310 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAk 310 (560)
+|..|-+||+. ..++|...||+|++|++++ ++..|++.+|-. .+..+..+|.
T Consensus 178 pl~~l~gig~~--~~~~L~~~Gi~ti~dl~~l---~~~~L~~~fG~~--~~~~l~~~a~ 229 (346)
T PRK03352 178 PTDALWGVGPK--TAKRLAALGITTVADLAAA---DPAELAATFGPT--TGPWLLLLAR 229 (346)
T ss_pred CHHHcCCCCHH--HHHHHHHcCCccHHHHhcC---CHHHHHHHhChH--HHHHHHHHhC
Confidence 57777777774 4478999999999999986 778899999932 3444444443
No 22
>PRK01810 DNA polymerase IV; Validated
Probab=44.67 E-value=20 Score=38.55 Aligned_cols=52 Identities=15% Similarity=0.198 Sum_probs=40.3
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAAT 311 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAkt 311 (560)
.|..|-.||+.- -++|...||+|++|+.++ +...|++.+| ..+..+.++|.-
T Consensus 180 pv~~l~giG~~~--~~~L~~~Gi~tigdL~~~---~~~~L~~rfG---~~g~~l~~~a~G 231 (407)
T PRK01810 180 PVGEMHGIGEKT--AEKLKDIGIQTIGDLAKA---DEHILRAKLG---INGVRLQRRANG 231 (407)
T ss_pred CHhhcCCcCHHH--HHHHHHcCCCcHHHHHhC---CHHHHHHHHh---HHHHHHHHHhcC
Confidence 466666777643 488999999999998775 7789999999 346777788763
No 23
>PRK03103 DNA polymerase IV; Reviewed
Probab=44.56 E-value=19 Score=38.65 Aligned_cols=52 Identities=13% Similarity=0.132 Sum_probs=41.0
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAAT 311 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAkt 311 (560)
.|..|-.||+. .-++|...||+|++|+.++ ++..|++.+| ..+..+.++|.-
T Consensus 182 pi~~l~gig~~--~~~~L~~~Gi~tigdl~~~---~~~~L~~~fG---~~~~~l~~~a~G 233 (409)
T PRK03103 182 PVRKLFGVGSR--MEKHLRRMGIRTIGQLANT---PLERLKKRWG---INGEVLWRTANG 233 (409)
T ss_pred CHhhcCCccHH--HHHHHHHcCCCCHHHHhcC---CHHHHHHHHC---HHHHHHHHHhcC
Confidence 56666678774 4578999999999998864 7789999999 357777777764
No 24
>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=43.58 E-value=13 Score=30.87 Aligned_cols=37 Identities=27% Similarity=0.382 Sum_probs=24.1
Q ss_pred hhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHH
Q 008593 266 HERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETI 305 (560)
Q Consensus 266 hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~ 305 (560)
...|..+||+||+|++++ +++.|.++=|+..+.=+.+
T Consensus 24 ~n~L~~~~I~tv~dL~~~---s~~~L~~i~n~G~ksl~EI 60 (66)
T PF03118_consen 24 YNCLKRAGIHTVGDLVKY---SEEDLLKIKNFGKKSLEEI 60 (66)
T ss_dssp HHHHHCTT--BHHHHHCS----HHHHHTSTTSHHHHHHHH
T ss_pred HHHHHHhCCcCHHHHHhC---CHHHHHhCCCCCHhHHHHH
Confidence 467999999999997665 6677887766555544443
No 25
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=41.58 E-value=31 Score=32.91 Aligned_cols=59 Identities=15% Similarity=0.246 Sum_probs=42.3
Q ss_pred cchhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHH-HHHhhcc
Q 008593 251 DDIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWET-IVEHAAT 311 (560)
Q Consensus 251 DeVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~-~v~HAkt 311 (560)
|+.-+|.+||. ++-+.|+..||+|-.+.-.+-..|-..+-..|+..-+-|.. -|+.|+.
T Consensus 67 DDLt~I~GIGP--k~e~~Ln~~GI~tfaQIAAwt~~di~~id~~l~f~GRi~RDdWi~QAk~ 126 (133)
T COG3743 67 DDLTRISGIGP--KLEKVLNELGIFTFAQIAAWTRADIAWIDDYLNFDGRIERDDWIAQAKA 126 (133)
T ss_pred ccchhhcccCH--HHHHHHHHcCCccHHHHHhcCHHHHHHHHhhcCCcchhHHHHHHHHHHH
Confidence 99999999998 57799999999997665544444444555556666666655 5666653
No 26
>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=40.76 E-value=29 Score=26.02 Aligned_cols=42 Identities=19% Similarity=0.237 Sum_probs=32.6
Q ss_pred hhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhc
Q 008593 266 HERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAA 310 (560)
Q Consensus 266 hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAk 310 (560)
-.+|..+||.||+++.. .+++.|..+-|++...=+.++.=|+
T Consensus 6 ~~~L~~~G~~s~e~la~---~~~~eL~~i~g~~~e~a~~ii~~a~ 47 (50)
T TIGR01954 6 AQLLVEEGFTTVEDLAY---VPIDELLSIEGFDEETAKELINRAR 47 (50)
T ss_pred HHHHHHcCCCCHHHHHc---cCHHHHhcCCCCCHHHHHHHHHHHH
Confidence 36899999999999765 4778888888888776666665554
No 27
>PRK03348 DNA polymerase IV; Provisional
Probab=39.62 E-value=17 Score=40.14 Aligned_cols=54 Identities=17% Similarity=0.247 Sum_probs=40.1
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhccc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAATC 312 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAktC 312 (560)
.|.+|-.||+... ++|.+.||+|++||.++ +...|++.||- +....+..+|.--
T Consensus 181 Pv~~L~GIG~~t~--~~L~~lGI~TigDLa~l---~~~~L~~~fG~--~~g~~L~~~a~G~ 234 (454)
T PRK03348 181 PVRRLWGIGPVTE--EKLHRLGIETIGDLAAL---SEAEVANLLGA--TVGPALHRLARGI 234 (454)
T ss_pred CccccCCCCHHHH--HHHHHcCCccHHHHhcC---CHHHHHHHHCH--HHHHHHHHHHcCC
Confidence 6788888887544 78999999999999875 78899999982 1234444555443
No 28
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=39.61 E-value=23 Score=37.08 Aligned_cols=54 Identities=17% Similarity=0.066 Sum_probs=41.3
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCC-hhHHHHHhcCCcccHHHHHHhhcccc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTD-PGSLCKIISASNKTWETIVEHAATCV 313 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d-~~kLr~iLgms~k~We~~v~HAktCv 313 (560)
.|..|-.||+.- -++|.+.||+|++|++++ + ...|+..+| +.+..+.++|+--+
T Consensus 174 pi~~l~giG~~~--~~~L~~~Gi~ti~dl~~~---~~~~~l~~~fg---~~~~~l~~~a~G~d 228 (343)
T cd00424 174 PLTDLPGIGAVT--AKRLEAVGINPIGDLLAA---SPDALLALWGG---VSGERLWYALRGID 228 (343)
T ss_pred ChhhcCCCCHHH--HHHHHHcCCCcHHHHhcC---CHHHHHHHHhh---HHHHHHHHHhCCcC
Confidence 567777788744 488999999999998765 5 567778887 55777888887554
No 29
>PRK03858 DNA polymerase IV; Validated
Probab=37.71 E-value=20 Score=38.24 Aligned_cols=51 Identities=16% Similarity=0.199 Sum_probs=37.9
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhh
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHA 309 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HA 309 (560)
.|..|-+||+.- -++|.+.||+|++|+++ .++..|++.||. +..+.+.++|
T Consensus 174 pl~~l~Gig~~~--~~~L~~~Gi~t~~dl~~---l~~~~L~~~fG~--~~~~~l~~~a 224 (396)
T PRK03858 174 PVRRLWGVGPVT--AAKLRAHGITTVGDVAE---LPESALVSLLGP--AAGRHLHALA 224 (396)
T ss_pred ChhhcCCCCHHH--HHHHHHhCCCcHHHHhc---CCHHHHHHHhCc--HHHHHHHHHh
Confidence 466666787754 48899999999999986 478899999993 2344444455
No 30
>COG4766 EutQ Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=37.55 E-value=1e+02 Score=30.50 Aligned_cols=91 Identities=12% Similarity=0.116 Sum_probs=60.1
Q ss_pred HHHHHHHhhh-HHHHHHHh-hHHHHHHHHHHHHHHHHcCCCC---CCC-CCCCCcccCCCCCceEEEEcCCCCCCcccCC
Q 008593 32 KVVDDVMKGN-WQNKMVAS-LEPCIRSVVREELERVLLPRFH---PGA-RSSFNQAETSEGRGLQLLFVNKLPCPIYTGS 105 (560)
Q Consensus 32 svi~e~~~~~-~~q~l~~~-lEp~lRrvV~EEve~~l~~~~~---~~~-rs~~~~i~~~~~~~~~L~F~n~l~~pifT~~ 105 (560)
+-|+|.+-.+ ..-.+|+. +|-++++|+.|+.-....-..+ ... ||-.+ ....+.-.+.|+|...=+.-+||++
T Consensus 12 ~~i~~si~a~l~~~~~~~~l~~Qlm~kVmkek~s~~~~~~~~~~k~v~~ksgik-vvk~s~vk~~~r~d~gqp~~V~~td 90 (176)
T COG4766 12 QRIRESIIAQLPEGQFTKELVEQLMEKVMKEKQSLECGWMQPSFKSVDGKSGIK-VVKLSSVKFGLRFDTGQPDCVYTTD 90 (176)
T ss_pred HHHHHHHHHhCChhhhhHHHHHHHHHHHHhchhhhhhhhcccceeecccCCcee-EEecccceeEeeecCCCCCeEEeec
Confidence 3455555443 45666765 5668999999997666543332 111 22222 2223334688889888888899999
Q ss_pred ceeeccCCceEEEEEeCC
Q 008593 106 RIEAEDGGPVKIVLVDPI 123 (560)
Q Consensus 106 kI~a~~g~~I~V~L~D~~ 123 (560)
-+.-.+|.++-+.+..-.
T Consensus 91 Lvt~~~g~~l~aG~m~~~ 108 (176)
T COG4766 91 LVTEQEGSRLGAGLMEMK 108 (176)
T ss_pred eeecccCCccccceeeec
Confidence 999999999999888753
No 31
>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=36.24 E-value=32 Score=37.25 Aligned_cols=54 Identities=17% Similarity=0.111 Sum_probs=40.3
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAA 310 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAk 310 (560)
.|..|-.||+. .-++|...||.|++|+..+- .++..|++.+|- +.+..+.++|.
T Consensus 223 Pv~~l~GIG~~--~~~~L~~~Gi~t~~dl~~~~-~~~~~L~~~fG~--~~g~~L~~~a~ 276 (404)
T cd01701 223 KVGDLPGVGSS--LAEKLVKLFGDTCGGLELRS-KTKEKLQKVLGP--KTGEKLYDYCR 276 (404)
T ss_pred CHhHhCCCCHH--HHHHHHHcCCcchHHHHhCc-ccHHHHHHHHCH--HHHHHHHHHhC
Confidence 67777788864 45899999999999998771 127899999982 24555556654
No 32
>PRK01216 DNA polymerase IV; Validated
Probab=33.74 E-value=24 Score=37.73 Aligned_cols=52 Identities=29% Similarity=0.289 Sum_probs=38.6
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAA 310 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAk 310 (560)
.|..|-.||+. ..++|...||.|++|+.++ +...|++.+|. ..+..+-.+|.
T Consensus 179 Pi~~l~giG~~--~~~~L~~~Gi~TigdL~~~---~~~~L~~rfG~--~~~~~L~~~a~ 230 (351)
T PRK01216 179 DIADIPGIGDI--TAEKLKKLGVNKLVDTLRI---EFDELKGIIGE--AKAKYLFSLAR 230 (351)
T ss_pred CcccccCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHCH--HHHHHHHHHhC
Confidence 57777788864 4489999999999998865 67889999992 23444555563
No 33
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=33.07 E-value=34 Score=31.37 Aligned_cols=38 Identities=26% Similarity=0.470 Sum_probs=28.9
Q ss_pred hhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhc
Q 008593 254 WRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIIS 296 (560)
Q Consensus 254 wRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLg 296 (560)
.|..+||. .|...|...||.||+++- ..+|++|.+.++
T Consensus 56 ~ri~gi~~--~~a~LL~~AGv~Tv~~LA---~~~p~~L~~~l~ 93 (122)
T PF14229_consen 56 MRIPGIGP--QYAELLEHAGVDTVEELA---QRNPQNLHQKLG 93 (122)
T ss_pred hhcCCCCH--HHHHHHHHhCcCcHHHHH---hCCHHHHHHHHH
Confidence 35555554 466889999999999974 478888888765
No 34
>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=30.87 E-value=46 Score=35.70 Aligned_cols=57 Identities=12% Similarity=0.056 Sum_probs=39.7
Q ss_pred chhhhhhhhccchhhhh-HhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcccc
Q 008593 252 DIWRLEKIAKDGKYHER-LAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAATCV 313 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~-L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAktCv 313 (560)
.|..|-.||+. .-++ |...||.|++|+.++. .++..|++.+|- +.++.+.++|+--+
T Consensus 183 pv~~l~GiG~~--~~~~ll~~~Gi~ti~dl~~~~-~~~~~L~~~fG~--~~g~~l~~~a~G~d 240 (359)
T cd01702 183 PITSIRGLGGK--LGEEIIDLLGLPTEGDVAGFR-SSESDLQEHFGE--KLGEWLYNLLRGID 240 (359)
T ss_pred cHHHhCCcCHH--HHHHHHHHcCCcCHHHHHhcc-CCHHHHHHHHHH--HHHHHHHHHhCCCC
Confidence 57777788742 2244 6889999999998764 578899999982 34555556665433
No 35
>KOG1520 consensus Predicted alkaloid synthase/Surface mucin Hemomucin [General function prediction only]
Probab=30.80 E-value=1.7e+02 Score=32.34 Aligned_cols=48 Identities=31% Similarity=0.329 Sum_probs=32.4
Q ss_pred ccccCCCCcccccccEEEEecCceeeccceEeecCCcccccCccEEEEEEeeCC
Q 008593 164 IVREREGKRPLVTGELHITLKDGVGILSDIVFTDNSSWIRCRKFRLGARVLQKG 217 (560)
Q Consensus 164 IV~~R~Gk~pLL~Gdl~v~L~~Gva~l~di~FTDnSs~~rSrKFRLgvRv~~~~ 217 (560)
++-+=+|+...++.++.|.= +| .|-|||+|+.--.|.|.+++--.+.+
T Consensus 151 l~~~~~G~~~kf~N~ldI~~-~g-----~vyFTDSSsk~~~rd~~~a~l~g~~~ 198 (376)
T KOG1520|consen 151 LADEAEGKPFKFLNDLDIDP-EG-----VVYFTDSSSKYDRRDFVFAALEGDPT 198 (376)
T ss_pred ccccccCeeeeecCceeEcC-CC-----eEEEeccccccchhheEEeeecCCCc
Confidence 44455777766776666544 44 57899999976568888877655443
No 36
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=28.61 E-value=39 Score=35.14 Aligned_cols=39 Identities=15% Similarity=0.299 Sum_probs=34.3
Q ss_pred HhhCCCccHHHHHHHhcCChhHHHHHhc-CCcccHHHHHH
Q 008593 269 LAKKGVYNVKDFLRMHTTDPGSLCKIIS-ASNKTWETIVE 307 (560)
Q Consensus 269 L~~~gI~tV~dFLrl~~~d~~kLr~iLg-ms~k~We~~v~ 307 (560)
-+.++|.|+.|-..+...+|+.||++++ +.+|.|-.=|+
T Consensus 25 ae~hkiiTirdvae~~ev~~n~lr~lasrLekkG~LeRi~ 64 (269)
T COG5340 25 AEGHKIITIRDVAETLEVAPNTLRELASRLEKKGWLERIL 64 (269)
T ss_pred HHhCceEEeHHhhhhccCCHHHHHHHHhhhhhcchhhhhc
Confidence 3457999999999999999999999999 99999976554
No 37
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=28.39 E-value=91 Score=32.31 Aligned_cols=16 Identities=13% Similarity=0.212 Sum_probs=12.2
Q ss_pred hHHHHHHHHHHHHHHH
Q 008593 50 LEPCIRSVVREELERV 65 (560)
Q Consensus 50 lEp~lRrvV~EEve~~ 65 (560)
||-++|+|+.|++-..
T Consensus 90 i~~lv~~v~~e~~~~~ 105 (233)
T PRK15457 90 VAQLMEKVMKEKQSLE 105 (233)
T ss_pred HHHHHHHHHHHHhccc
Confidence 6778999988886543
No 38
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=26.03 E-value=33 Score=39.80 Aligned_cols=38 Identities=29% Similarity=0.337 Sum_probs=31.7
Q ss_pred CCCCCcchhhhhhhhccchhhhhHhhCCCccHHHHHHHhc
Q 008593 246 PPSLDDDIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHT 285 (560)
Q Consensus 246 pP~L~DeVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~ 285 (560)
...|++.|..|++||+.-+ ++|++.||+||+|.|..+=
T Consensus 4 ~~~~~~~~~~l~gvg~~~~--~~l~~lgi~t~~dll~~~P 41 (681)
T PRK10917 4 LLLLDAPLTSLKGVGPKTA--EKLAKLGIHTVQDLLLHLP 41 (681)
T ss_pred cccccCChhhcCCCCHHHH--HHHHHcCCCCHHHHhhcCC
Confidence 3457789999999987544 8899999999999998874
No 39
>PRK14973 DNA topoisomerase I; Provisional
Probab=23.10 E-value=56 Score=39.80 Aligned_cols=54 Identities=20% Similarity=0.324 Sum_probs=45.6
Q ss_pred hhhhhhhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcc
Q 008593 253 IWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAAT 311 (560)
Q Consensus 253 VwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAkt 311 (560)
.=.++++|.+.. .+|..+||.+|+|+++. |+.+|-..-|++.|.-..+..+|+.
T Consensus 879 l~~vkg~ge~t~--~~l~~ag~~~~e~l~~~---d~~~la~~~~i~~k~~~~~~~~~~~ 932 (936)
T PRK14973 879 LLSVPGLGETTL--EKLYLAGVYDGDLLVSA---DPKKLAKVTGIDEKKLRNLQAYAKK 932 (936)
T ss_pred hhhccCCCHHHH--HHHHHcCCCCHHHhccC---CHHHHhhhcCCCHHHHHHHHHHHhh
Confidence 335567777777 88999999999999987 9999999999999988888888864
No 40
>PF10148 SCHIP-1: Schwannomin-interacting protein 1; InterPro: IPR015649 SCHIP-1 is a coiled-coil protein that specifically associates with schwannomin in vitro and in vivo. The product of the neurofibromatosis type 2 (NF2) tumour suppressor gene, known as schwannomin or merlin, is involved in NF2-associated and sporadic schwannomas and meningiomas. It is closely related to the ezrin-radixin-moesin family members, which link membrane proteins to the cytoskeleton. Association with SCHIP-1 can be observed only with some naturally occurring mutants of schwannomin, or a schwannomin spliced isoform lacking exons 2 and 3, but not with the schwannomin isoform exhibiting growth-suppressive activity []. This entry consists of mammalian SCHIP-1 proteins from Mus musculus (Mouse) and Homo sapiens (Human).
Probab=22.62 E-value=1.2e+02 Score=31.70 Aligned_cols=44 Identities=23% Similarity=0.227 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHcC----------CCC-CCCCCCCCcccCCCCCceEEEEcCCCCC
Q 008593 56 SVVREELERVLLP----------RFH-PGARSSFNQAETSEGRGLQLLFVNKLPC 99 (560)
Q Consensus 56 rvV~EEve~~l~~----------~~~-~~~rs~~~~i~~~~~~~~~L~F~n~l~~ 99 (560)
|-=||||++.|+= +.. ...+.+....--+++.++|.||+|.+..
T Consensus 6 r~eREeIrrrlA~g~~~ed~~~~yt~~~~~~k~sl~~RLqsgmNLQVCFmNE~~s 60 (238)
T PF10148_consen 6 RNEREEIRRRLAMGSFAEDNWEKYTSSSKSGKPSLSSRLQSGMNLQVCFMNETSS 60 (238)
T ss_pred cccHHHHHHHHhcCCcccccceeccccccCCCcccccccCCCceeeEEeecCCCC
Confidence 3347899998871 111 0112122222234577999999999864
No 41
>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=22.18 E-value=1.9e+02 Score=28.84 Aligned_cols=62 Identities=31% Similarity=0.381 Sum_probs=38.5
Q ss_pred cccccccEEEE---ec--Cce--eeccceEeecCCcccccCccEEEEEEeeCCC-------CcceeeeeeecceEeecC
Q 008593 172 RPLVTGELHIT---LK--DGV--GILSDIVFTDNSSWIRCRKFRLGARVLQKGC-------REARIKEAKSEAFVVKDH 236 (560)
Q Consensus 172 ~pLL~Gdl~v~---L~--~Gv--a~l~di~FTDnSs~~rSrKFRLgvRv~~~~~-------~g~RI~EAvsE~FvVkd~ 236 (560)
.+.|.|.+... |+ +|. |.. ..|.|=|-.+ -+.|||-.++..-.. ...-+-|+.|+||.|-..
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 46888986543 33 343 221 2344443322 578999999886332 235689999999999654
No 42
>PRK07758 hypothetical protein; Provisional
Probab=22.02 E-value=98 Score=28.05 Aligned_cols=37 Identities=11% Similarity=0.244 Sum_probs=24.7
Q ss_pred hhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHH
Q 008593 267 ERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIV 306 (560)
Q Consensus 267 k~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v 306 (560)
..|..+||+||+|+.++ +++.|-++=|+-.|.-+.+.
T Consensus 48 N~Lk~AGI~TL~dLv~~---te~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 48 RALEHHGIHTVEELSKY---SEKEILKLHGMGPASLPKLR 84 (95)
T ss_pred HHHHHcCCCcHHHHHcC---CHHHHHHccCCCHHHHHHHH
Confidence 55899999999997654 55556665555555544443
No 43
>KOG1104 consensus Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]
Probab=21.65 E-value=90 Score=37.16 Aligned_cols=23 Identities=26% Similarity=0.190 Sum_probs=11.6
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCC
Q 008593 6 MVPKRPFDDDGFGVLVPEPRKRP 28 (560)
Q Consensus 6 ~~~kr~~~~~~~~~~~~~~~~~p 28 (560)
|..+|-.|++|++++..+||.+|
T Consensus 1 msrRrr~d~edE~y~~rr~r~~~ 23 (759)
T KOG1104|consen 1 MSRRRRGDDEDENYDDRRRRISP 23 (759)
T ss_pred CCCCccCCccccccccccccCCc
Confidence 45667677555554433333333
No 44
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=21.03 E-value=67 Score=28.48 Aligned_cols=61 Identities=20% Similarity=0.328 Sum_probs=39.4
Q ss_pred CCCCcchhhhhhhhccchhhhhHhhCCCcc----HHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhcccc
Q 008593 247 PSLDDDIWRLEKIAKDGKYHERLAKKGVYN----VKDFLRMHTTDPGSLCKIISASNKTWETIVEHAATCV 313 (560)
Q Consensus 247 P~L~DeVwRLekIgKdG~~hk~L~~~gI~t----V~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAktCv 313 (560)
|+=+-+|--|.+||.. +-.+|..+|+.. .++|| ++.+|++-.++=|+ ..--++-+||++|-
T Consensus 15 PmGeK~V~~laGIg~~--lg~~L~~~GfdkAYvllGQfL-llkKdE~lF~~Wlk---~~~gat~~~a~~~~ 79 (90)
T KOG4233|consen 15 PMGEKDVTWLAGIGET--LGIKLVDAGFDKAYVLLGQFL-LLKKDEDLFQEWLK---ETCGATAKQAQDCF 79 (90)
T ss_pred ccCCCcceeeccccHH--hhhhHHhccccHHHHHHHHHH-HhcccHHHHHHHHH---HHcCccHHHHHHHH
Confidence 5566688889999874 567999999975 46776 44677755444332 11113456777774
No 45
>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=20.43 E-value=56 Score=33.69 Aligned_cols=45 Identities=16% Similarity=0.242 Sum_probs=33.3
Q ss_pred hhhccchhhhhHhhCCCccHHHHHHHhcCChhHHHHHhcCCcccHHHHHHhhc
Q 008593 258 KIAKDGKYHERLAKKGVYNVKDFLRMHTTDPGSLCKIISASNKTWETIVEHAA 310 (560)
Q Consensus 258 kIgKdG~~hk~L~~~gI~tV~dFLrl~~~d~~kLr~iLgms~k~We~~v~HAk 310 (560)
.||+... .+|.+.||+|++||..+ +...|++.+|. .+..+..+|.
T Consensus 177 gig~~~~--~~L~~~Gi~t~~dl~~~---~~~~l~~rfG~---~~~~l~~~~~ 221 (335)
T cd03468 177 RLPPETV--ELLARLGLRTLGDLAAL---PRAELARRFGL---ALLLRLDQAY 221 (335)
T ss_pred CCCHHHH--HHHHHhCcccHHHHHhC---ChHHHHhhcCH---HHHHHHHHHC
Confidence 6776544 88999999999998875 67889999992 2444444444
No 46
>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=20.06 E-value=1.5e+02 Score=26.68 Aligned_cols=57 Identities=25% Similarity=0.305 Sum_probs=31.9
Q ss_pred CCCCcchhhhhhhhccchhhhhHhhCCCccH----HHHHHHhcCChh----HHHHHhcCCcccHHHHHHhhcccc
Q 008593 247 PSLDDDIWRLEKIAKDGKYHERLAKKGVYNV----KDFLRMHTTDPG----SLCKIISASNKTWETIVEHAATCV 313 (560)
Q Consensus 247 P~L~DeVwRLekIgKdG~~hk~L~~~gI~tV----~dFLrl~~~d~~----kLr~iLgms~k~We~~v~HAktCv 313 (560)
|+=+-+|-.|-+||.. +-++|+.+|+.+. ++|| ++.+|++ -|+.++|. ..+||..|-
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 6777789999999984 5589999999875 5555 2356754 45555553 345777664
No 47
>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=20.02 E-value=60 Score=35.22 Aligned_cols=58 Identities=14% Similarity=0.142 Sum_probs=40.8
Q ss_pred chhhhhhhhccchhhhhHhhCCCccHHHHHHHhc------------CChhHHHHHhcCCcccHHHHHHhhcccc
Q 008593 252 DIWRLEKIAKDGKYHERLAKKGVYNVKDFLRMHT------------TDPGSLCKIISASNKTWETIVEHAATCV 313 (560)
Q Consensus 252 eVwRLekIgKdG~~hk~L~~~gI~tV~dFLrl~~------------~d~~kLr~iLgms~k~We~~v~HAktCv 313 (560)
+|..|-+||+... ++|.+.||.|++|+..+-+ .+...|++.||- +....+.++|.--+
T Consensus 173 pv~~l~GiG~~~~--~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~--~~g~~l~~~a~G~d 242 (379)
T cd01703 173 DLRKIPGIGYKTA--AKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGE--GIGQRIWKLLFGRD 242 (379)
T ss_pred CccccCCcCHHHH--HHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHCH--HHHHHHHHHHCCCC
Confidence 3555557877654 8999999999999987641 127789998982 24566667776555
Done!