Query 006871
Match_columns 628
No_of_seqs 149 out of 174
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 15:41:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006871.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006871hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07887 Calmodulin_bind: Calm 100.0 1E-121 2E-126 938.1 29.4 299 92-393 1-299 (299)
2 TIGR02239 recomb_RAD51 DNA rep 85.5 0.87 1.9E-05 48.4 4.0 48 269-321 13-60 (316)
3 TIGR02238 recomb_DMC1 meiotic 83.4 1.1 2.4E-05 47.7 3.6 49 268-321 12-60 (313)
4 PLN03186 DNA repair protein RA 83.3 1.2 2.5E-05 48.2 3.8 61 257-322 28-88 (342)
5 PRK04301 radA DNA repair and r 78.2 1.3 2.9E-05 46.4 2.2 57 256-319 7-63 (317)
6 PLN03187 meiotic recombination 76.5 2 4.3E-05 46.6 2.9 61 256-321 30-90 (344)
7 PF14520 HHH_5: Helix-hairpin- 70.2 0.8 1.7E-05 37.0 -1.5 50 260-316 10-59 (60)
8 PTZ00035 Rad51 protein; Provis 68.6 5.2 0.00011 43.1 3.8 61 256-321 22-82 (337)
9 PRK03609 umuC DNA polymerase V 66.8 4.2 9E-05 44.6 2.7 52 256-317 180-231 (422)
10 PF14229 DUF4332: Domain of un 66.6 5 0.00011 37.3 2.8 52 269-322 7-60 (122)
11 PRK02406 DNA polymerase IV; Va 63.7 5.7 0.00012 42.0 2.9 52 256-317 169-220 (343)
12 TIGR02236 recomb_radA DNA repa 62.8 4.8 0.0001 41.9 2.1 52 260-318 4-55 (310)
13 PF10691 DUF2497: Protein of u 58.5 21 0.00046 31.1 5.0 40 30-70 33-73 (73)
14 PRK03352 DNA polymerase IV; Va 51.8 5.7 0.00012 42.1 0.5 41 256-301 178-218 (346)
15 PRK14133 DNA polymerase IV; Pr 50.1 14 0.00031 39.2 3.2 51 256-316 174-224 (347)
16 PRK03348 DNA polymerase IV; Pr 49.8 8.2 0.00018 43.1 1.4 53 256-317 181-233 (454)
17 PRK03858 DNA polymerase IV; Va 49.8 7.2 0.00016 42.0 0.9 41 256-301 174-214 (396)
18 PRK02794 DNA polymerase IV; Pr 48.0 13 0.00029 40.7 2.6 55 256-320 210-264 (419)
19 PRK01172 ski2-like helicase; P 47.9 16 0.00035 42.3 3.4 51 260-317 617-667 (674)
20 cd01700 PolY_Pol_V_umuC umuC s 47.0 13 0.00029 39.3 2.4 51 256-316 177-227 (344)
21 cd03586 PolY_Pol_IV_kappa DNA 44.8 18 0.00039 37.8 2.9 52 256-317 172-223 (334)
22 PRK01810 DNA polymerase IV; Va 41.2 20 0.00043 39.0 2.6 51 256-316 180-230 (407)
23 PRK03103 DNA polymerase IV; Re 40.9 20 0.00043 39.0 2.6 52 256-317 182-233 (409)
24 COG3743 Uncharacterized conser 39.8 34 0.00073 33.1 3.6 59 255-317 67-126 (133)
25 PRK15457 ethanolamine utilizat 39.7 70 0.0015 33.6 6.1 72 52-124 90-162 (233)
26 cd00424 PolY Y-family of DNA p 37.4 24 0.00052 37.5 2.5 56 256-321 174-230 (343)
27 PF04994 TfoX_C: TfoX C-termin 37.4 12 0.00026 32.7 0.2 73 257-369 5-78 (81)
28 PRK01216 DNA polymerase IV; Va 33.4 17 0.00038 39.3 0.7 51 256-315 179-229 (351)
29 cd01701 PolY_Rev1 DNA polymera 33.3 18 0.00039 39.6 0.8 54 256-316 223-276 (404)
30 PF11754 Velvet: Velvet factor 31.4 2.4E+02 0.0051 28.6 8.3 62 176-240 97-172 (203)
31 PF02889 Sec63: Sec63 Brl doma 31.2 33 0.00071 35.5 2.3 54 256-316 149-202 (314)
32 cd01702 PolY_Pol_eta DNA Polym 30.0 23 0.0005 38.5 0.9 55 256-317 183-238 (359)
33 cd07978 TAF13 The TATA Binding 28.3 89 0.0019 28.2 4.2 35 275-317 52-89 (92)
34 TIGR02979 phageshock_pspD phag 27.3 69 0.0015 27.2 3.0 25 33-61 29-53 (59)
35 PF03118 RNA_pol_A_CTD: Bacter 27.2 27 0.00059 29.4 0.7 27 270-299 24-50 (66)
36 KOG4233 DNA-bridging protein B 27.1 63 0.0014 29.1 2.9 60 251-318 15-78 (90)
37 cd01703 PolY_Pol_iota DNA Poly 26.7 29 0.00063 38.0 1.0 58 257-320 174-243 (379)
38 PF14229 DUF4332: Domain of un 24.8 42 0.00091 31.3 1.5 39 257-300 55-93 (122)
39 PF09584 Phageshock_PspD: Phag 23.8 83 0.0018 27.3 2.9 15 48-62 45-59 (66)
40 PRK10497 peripheral inner memb 22.0 98 0.0021 27.3 3.1 14 48-61 52-65 (73)
41 PF06594 HCBP_related: Haemoly 21.8 53 0.0011 25.2 1.3 18 191-208 24-41 (43)
42 PRK10917 ATP-dependent DNA hel 21.7 36 0.00077 40.0 0.5 38 251-290 5-42 (681)
43 COG3355 Predicted transcriptio 21.5 2.4E+02 0.0051 27.2 5.8 40 267-306 31-74 (126)
44 COG3827 Uncharacterized protei 21.3 1.6E+02 0.0035 30.8 5.0 39 31-70 189-228 (231)
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=1.1e-121 Score=938.09 Aligned_cols=299 Identities=69% Similarity=1.159 Sum_probs=295.2
Q ss_pred ceEEEEcCCCCCCcccCCcccccCCCceEEEEEeCCCCceeccCCCccceEEEEEeeCCCCCCCCCCCCHHHHhhccccc
Q 006871 92 NLQLHFRTRLSLPLFTGGKVEGEQGTAIHIVLIDANTGHVVTTGPESLVKLDVVVLEGDFNNEDDDNWTQEEFVSHVVKE 171 (628)
Q Consensus 92 ~~~L~F~n~l~~pifTg~kI~ae~g~~I~V~L~D~~tg~iVt~GplSs~kvEIvVLdGDF~~~~~e~WT~eEF~~~IVk~ 171 (628)
+|||+|+|+|++|||||++|+|+||+||+|+|+|++|+ |++||+|++|||||||||||+++++++||+|||++|||++
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 68999999999999999999999999999999999988 9999999999999999999999999999999999999999
Q ss_pred CCCCCCccccceEEEecCceeeccCceeecCCCcccccccEEEEEeecCCCCccceeeecccceEEeeCCccccccCCCC
Q 006871 172 REGKRPLLSGDLQVTLKEGVGTLGDLTFTDNSSWIRSRKFRLGLKVASGYCEGIRIREAKTDAFTVKDHRGELYKKHYPP 251 (628)
Q Consensus 172 ReGk~pLL~Gdl~v~L~~Gva~l~di~FTDnSsw~rSrKFRLgaRv~~~~~~g~RI~EAvsE~FvVkDhRge~ykKh~pP 251 (628)
|+||+|||+|+|+|+|+||+|+|+||+|||||||+|||||||||||+++++.|+|||||+||||+|||||||+|||||||
T Consensus 79 r~gk~pLL~G~~~v~L~~G~a~l~di~FtdnSs~~rsrKFRLgarv~~~~~~~~rI~Eavse~FvVkd~Rge~~kKh~pP 158 (299)
T PF07887_consen 79 REGKRPLLTGDLQVTLKNGVATLGDISFTDNSSWIRSRKFRLGARVVSGSCDGVRIREAVSEPFVVKDHRGELYKKHYPP 158 (299)
T ss_pred CCCCCCCCCccEEEEecCCEEEccccEEecCcccccCCcEEEEEEEccCCCCCceeEEeeecCEEEEecccccccCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhcccccCCceEEEecCC
Q 006871 252 ALNDEVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCVLSGKLYVYYPDD 331 (628)
Q Consensus 252 ~L~DeVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~k~y~y~~~~ 331 (628)
+|+|||||||||||||+|||+|+.+||+||+|||+++++||++||+|||+|||++||++||+|||||++++++|+|| ++
T Consensus 159 ~L~DeVwRLe~Igk~G~~hk~L~~~~I~tV~dFl~l~~~d~~~Lr~ilg~~ms~k~We~~v~HA~tCvl~~~~y~y~-~~ 237 (299)
T PF07887_consen 159 SLDDEVWRLEKIGKDGAFHKRLKKNGINTVEDFLKLLNKDPQKLREILGSGMSNKMWETTVEHAKTCVLGDKLYVYY-DE 237 (299)
T ss_pred CCCCchhhhhhccccCHHHHHHHHcCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHHHHHHHHhcCCCCcEEEEE-ec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999 56
Q ss_pred CCceEEEEccccceeeeecCCeeecCCCCChHhHHHHHHHHHHHHhcccccccccCccccCc
Q 006871 332 PRNVGVVFNNIYEFCGLIADGQYHSADSLSESQKVHVDTLVKKAYDNWMHVIEYDGKSLLGF 393 (628)
Q Consensus 332 ~~nvgl~FN~i~~lvG~~~~g~y~s~d~L~~~qk~~V~~Lk~~AY~nw~~~~e~D~~~l~n~ 393 (628)
++|++|+|||||+||||+|+|+|++.|+||+.||++|++||++||+||++|++||++|++||
T Consensus 238 ~~nv~l~FN~i~~lvga~~~g~y~s~d~L~~~qK~~v~~Lv~~AY~n~~~l~e~d~~~~~n~ 299 (299)
T PF07887_consen 238 EQNVGLFFNCIYELVGAIFGGQYVSLDNLSSAQKAYVDKLVKQAYENWDNLEEYDGKMLNNY 299 (299)
T ss_pred CCceEEEEcchhhEEeEEECCEEEehHHcCHHHHHHHHHHHHHHHHhhhhheecccchhccC
Confidence 79999999999999999999999999999999999999999999999999999999999986
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=85.55 E-value=0.87 Score=48.41 Aligned_cols=48 Identities=29% Similarity=0.315 Sum_probs=42.7
Q ss_pred hhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhcccccC
Q 006871 269 FHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCVLS 321 (628)
Q Consensus 269 ~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 321 (628)
--++|+++||.||+||+. .++..|.+++ |+|...++.+..||.+|...
T Consensus 13 ~~~~l~~~g~~t~~~~~~---~~~~~L~~i~--~ls~~~~~~~~~~~~~~~~~ 60 (316)
T TIGR02239 13 DIKKLQEAGLHTVESVAY---APKKQLLEIK--GISEAKADKILAEAAKLVPM 60 (316)
T ss_pred HHHHHHHcCCCcHHHHHh---CCHHHHHHHh--CCCHHHHHHHHHHHHHhccc
Confidence 348999999999999986 4899999998 79999999999999999654
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=83.44 E-value=1.1 Score=47.73 Aligned_cols=49 Identities=27% Similarity=0.318 Sum_probs=42.9
Q ss_pred hhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhcccccC
Q 006871 268 SFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCVLS 321 (628)
Q Consensus 268 ~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 321 (628)
.--++|+++||.||+||+. .++..|.++. |+|...++.+++.|+.+...
T Consensus 12 ~~~~~L~~~g~~t~~~~~~---~~~~~L~~~~--gls~~~~~~i~~~~~~~~~~ 60 (313)
T TIGR02238 12 ADIKKLKSAGICTVNGVIM---TTRRALCKIK--GLSEAKVDKIKEAASKIINP 60 (313)
T ss_pred HHHHHHHHcCCCcHHHHHh---CCHHHHHHhc--CCCHHHHHHHHHHHHhhhcc
Confidence 3458999999999999876 4889999997 79999999999999988655
No 4
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=83.29 E-value=1.2 Score=48.23 Aligned_cols=61 Identities=28% Similarity=0.322 Sum_probs=47.4
Q ss_pred ceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhcccccCC
Q 006871 257 VWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCVLSG 322 (628)
Q Consensus 257 VwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~ 322 (628)
+-+|+.-|-.-.--++|.++||.||+||+.+ ++..|.+|+ |+|....+.+++||.+|....
T Consensus 28 ~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~---~~~~L~~i~--~is~~~~~~~~~~~~~~~~~~ 88 (342)
T PLN03186 28 IEQLQASGIAALDIKKLKDAGIHTVESLAYA---PKKDLLQIK--GISEAKVEKILEAASKLVPLG 88 (342)
T ss_pred HHHHHhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHHhcccc
Confidence 4444442333334599999999999998764 788999998 799999999999998886543
No 5
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=78.17 E-value=1.3 Score=46.40 Aligned_cols=57 Identities=19% Similarity=0.307 Sum_probs=45.6
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhcccc
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCV 319 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCv 319 (628)
++-.|.+||+ ...++|.++||+|++|++. .|+..|.+++ |++.+.++.+++-|+.|+
T Consensus 7 ~l~~l~gIg~--~~a~~L~~~Gi~t~~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~a~~~~ 63 (317)
T PRK04301 7 DLEDLPGVGP--ATAEKLREAGYDTVEAIAV---ASPKELSEAA--GIGESTAAKIIEAAREAA 63 (317)
T ss_pred cHhhcCCCCH--HHHHHHHHcCCCCHHHHHc---CCHHHHHHhc--CCCHHHHHHHHHHHHHhh
Confidence 3445556665 4559999999999999965 5999999998 688889999998888654
No 6
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=76.45 E-value=2 Score=46.62 Aligned_cols=61 Identities=23% Similarity=0.331 Sum_probs=47.5
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhcccccC
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCVLS 321 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 321 (628)
++..|+.-|-.-.--++|.++||+||+|++.. ++..|-++. |+|....+.+++.|+..+..
T Consensus 30 ~~~~l~~~g~~~~~~~kL~~~g~~tv~~~~~~---~~~~L~~~~--g~s~~~~~ki~~~a~~~~~~ 90 (344)
T PLN03187 30 SIDKLISQGINAGDVKKLQDAGIYTCNGLMMH---TKKNLTGIK--GLSEAKVDKICEAAEKLLNQ 90 (344)
T ss_pred CHHHHhhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHHhhcc
Confidence 35566553333445699999999999998764 788899986 79999999999999876543
No 7
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=70.17 E-value=0.8 Score=37.05 Aligned_cols=50 Identities=30% Similarity=0.513 Sum_probs=39.9
Q ss_pred eeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhc
Q 006871 260 LEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAK 316 (628)
Q Consensus 260 LekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 316 (628)
+.+||+.- .++|.+.||.|++|+.. .+++.|.++= |++.+.=+.+++.|+
T Consensus 10 I~Gig~~~--a~~L~~~G~~t~~~l~~---a~~~~L~~i~--Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 10 IPGIGPKR--AEKLYEAGIKTLEDLAN---ADPEELAEIP--GIGEKTAEKIIEAAR 59 (60)
T ss_dssp STTCHHHH--HHHHHHTTCSSHHHHHT---SHHHHHHTST--TSSHHHHHHHHHHHH
T ss_pred CCCCCHHH--HHHHHhcCCCcHHHHHc---CCHHHHhcCC--CCCHHHHHHHHHHHh
Confidence 45566553 38899999999999866 4788899975 789999999998886
No 8
>PTZ00035 Rad51 protein; Provisional
Probab=68.62 E-value=5.2 Score=43.10 Aligned_cols=61 Identities=30% Similarity=0.349 Sum_probs=46.8
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhcccccC
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCVLS 321 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 321 (628)
++-.|+.-|-.-.--++|.++||+||+||+. .++..|-++. |+|...=+.+++.|+.++..
T Consensus 22 ~~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~---~~~~~L~~~~--gis~~~~~~i~~~~~~~~~~ 82 (337)
T PTZ00035 22 EIEKLQSAGINAADIKKLKEAGICTVESVAY---ATKKDLCNIK--GISEAKVEKIKEAASKLVPM 82 (337)
T ss_pred cHHHHhcCCCCHHHHHHHHHcCCCcHHHHHh---CCHHHHHHhh--CCCHHHHHHHHHHHHHhccc
Confidence 3555544233333459999999999999876 4888999997 79999999999999887643
No 9
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=66.80 E-value=4.2 Score=44.55 Aligned_cols=52 Identities=21% Similarity=0.273 Sum_probs=41.4
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhcc
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKT 317 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 317 (628)
+|..|-+||+. ..++|...||+|++|+.++ ++..|++.||. .+..+..||.-
T Consensus 180 Pv~~l~GiG~~--~~~~L~~lGi~TigdL~~~---~~~~L~~~fG~-----~~~~l~~~a~G 231 (422)
T PRK03609 180 PVEEVWGVGRR--ISKKLNAMGIKTALDLADT---NIRFIRKHFNV-----VLERTVRELRG 231 (422)
T ss_pred ChhhcCCccHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHCH-----HHHHHHHHhCC
Confidence 45556677774 4499999999999999985 88999999973 67788888753
No 10
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=66.62 E-value=5 Score=37.28 Aligned_cols=52 Identities=29% Similarity=0.289 Sum_probs=37.8
Q ss_pred hhhhhhhcCCccHHHHHHHHhhChHH--HHHHHccCCCchhHHHHHHhhcccccCC
Q 006871 269 FHKRLNKAGIFTVEDFLRLVVRDSQR--LRNILGSGMSNKMWDVLVDHAKTCVLSG 322 (628)
Q Consensus 269 ~hkrL~~~gI~tV~dFLrl~~~d~~k--LR~iLg~gmS~k~We~~v~HAktCvl~~ 322 (628)
..++|+..||+|++|||..-.....+ |-+-+ |++.+-=...+.+|.=|...+
T Consensus 7 ~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~--~i~~~~l~~w~~~AdL~ri~g 60 (122)
T PF14229_consen 7 EAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKL--GISERNLLKWVNQADLMRIPG 60 (122)
T ss_pred HHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhc--CCCHHHHHHHHhHHHhhhcCC
Confidence 45899999999999999986655444 55555 678777667777776554443
No 11
>PRK02406 DNA polymerase IV; Validated
Probab=63.70 E-value=5.7 Score=42.02 Aligned_cols=52 Identities=25% Similarity=0.384 Sum_probs=40.2
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhcc
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKT 317 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 317 (628)
+|..|-+||+. .-++|...||+|++|+.++ +...|++.||. .+..+.+||.-
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 56667677754 3488999999999999885 78899999973 46667677653
No 12
>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=62.84 E-value=4.8 Score=41.94 Aligned_cols=52 Identities=23% Similarity=0.331 Sum_probs=39.7
Q ss_pred eeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhccc
Q 006871 260 LEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTC 318 (628)
Q Consensus 260 LekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktC 318 (628)
|.+||+. .-++|.++||.|++|++. .|++.|.+++ |++.+..+.+.+-|+.|
T Consensus 4 i~gig~~--~~~~L~~~Gi~ti~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~~~~~ 55 (310)
T TIGR02236 4 LPGVGPA--TAEKLREAGYDTFEAIAV---ASPKELSEIA--GISEGTAAKIIQAARKA 55 (310)
T ss_pred cCCCCHH--HHHHHHHcCCCCHHHHHc---CCHHHHHhcc--CCCHHHHHHHHHHHHHH
Confidence 4455543 448999999999999877 4899999998 57777777777777643
No 13
>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=58.47 E-value=21 Score=31.08 Aligned_cols=40 Identities=30% Similarity=0.466 Sum_probs=30.2
Q ss_pred chhhHHHHHHHHHhhHHH-HHHhhhhHHHHHHHHHHHHHHHh
Q 006871 30 PALASVIVEALKVDSLQK-LCSSLEPILRRVVSEEVERALAK 70 (628)
Q Consensus 30 p~~~svi~ea~~~~s~q~-l~~~lEp~lrrvV~EEve~~l~~ 70 (628)
.++-.+++|+|+-- |+. |=..|=.|+.|+|++||+|..+|
T Consensus 33 ~TlE~lvremLRPm-LkeWLD~nLP~lVErlVr~EIeRi~rr 73 (73)
T PF10691_consen 33 RTLEDLVREMLRPM-LKEWLDENLPGLVERLVREEIERIARR 73 (73)
T ss_pred ccHHHHHHHHHHHH-HHHHHHhccHHHHHHHHHHHHHHHhcC
Confidence 46778888888764 333 55578888999999999998754
No 14
>PRK03352 DNA polymerase IV; Validated
Probab=51.76 E-value=5.7 Score=42.10 Aligned_cols=41 Identities=32% Similarity=0.357 Sum_probs=33.4
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcc
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGS 301 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~ 301 (628)
+|..|-+||+. ..++|...||+|++|++++ ++..|++.||.
T Consensus 178 pl~~l~gig~~--~~~~L~~~Gi~ti~dl~~l---~~~~L~~~fG~ 218 (346)
T PRK03352 178 PTDALWGVGPK--TAKRLAALGITTVADLAAA---DPAELAATFGP 218 (346)
T ss_pred CHHHcCCCCHH--HHHHHHHcCCccHHHHhcC---CHHHHHHHhCh
Confidence 46666677774 4488999999999999985 78899999975
No 15
>PRK14133 DNA polymerase IV; Provisional
Probab=50.07 E-value=14 Score=39.23 Aligned_cols=51 Identities=29% Similarity=0.542 Sum_probs=39.5
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhc
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAK 316 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 316 (628)
+|..|-+||+... ++|...||+|++|++++ +...|++.|| +.|..+.++|.
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 78999999999999874 7888999996 35777777775
No 16
>PRK03348 DNA polymerase IV; Provisional
Probab=49.82 E-value=8.2 Score=43.08 Aligned_cols=53 Identities=30% Similarity=0.391 Sum_probs=39.6
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhcc
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKT 317 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 317 (628)
+|.+|-+||+... ++|...||+|++||.++ +...|++.||..+ ...+..+|.-
T Consensus 181 Pv~~L~GIG~~t~--~~L~~lGI~TigDLa~l---~~~~L~~~fG~~~----g~~L~~~a~G 233 (454)
T PRK03348 181 PVRRLWGIGPVTE--EKLHRLGIETIGDLAAL---SEAEVANLLGATV----GPALHRLARG 233 (454)
T ss_pred CccccCCCCHHHH--HHHHHcCCccHHHHhcC---CHHHHHHHHCHHH----HHHHHHHHcC
Confidence 6788888887544 88999999999999874 7889999997433 3334445543
No 17
>PRK03858 DNA polymerase IV; Validated
Probab=49.81 E-value=7.2 Score=42.05 Aligned_cols=41 Identities=32% Similarity=0.370 Sum_probs=33.2
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHcc
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGS 301 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~ 301 (628)
+|..|-+||+.- -++|.+.||+|++|+.+ .++..|++.||.
T Consensus 174 pl~~l~Gig~~~--~~~L~~~Gi~t~~dl~~---l~~~~L~~~fG~ 214 (396)
T PRK03858 174 PVRRLWGVGPVT--AAKLRAHGITTVGDVAE---LPESALVSLLGP 214 (396)
T ss_pred ChhhcCCCCHHH--HHHHHHhCCCcHHHHhc---CCHHHHHHHhCc
Confidence 455565777754 48999999999999986 588899999975
No 18
>PRK02794 DNA polymerase IV; Provisional
Probab=47.97 E-value=13 Score=40.67 Aligned_cols=55 Identities=29% Similarity=0.227 Sum_probs=42.3
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhccccc
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTCVL 320 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 320 (628)
+|..|-+||+ ..-++|...||+|++|+.++ +...|++.||. .|..+..+|.--+.
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 3555556665 44589999999999998874 88899999974 58888888875543
No 19
>PRK01172 ski2-like helicase; Provisional
Probab=47.89 E-value=16 Score=42.34 Aligned_cols=51 Identities=31% Similarity=0.586 Sum_probs=41.8
Q ss_pred eeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhcc
Q 006871 260 LEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKT 317 (628)
Q Consensus 260 LekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 317 (628)
|.+|++ ...++|.++||.||.|+.. .|+++|-+|+ |++++.=+.++++|+.
T Consensus 617 ip~~~~--~~a~~l~~~g~~~~~di~~---~~~~~~~~i~--~~~~~~~~~i~~~~~~ 667 (674)
T PRK01172 617 IPKVGR--VRARRLYDAGFKTVDDIAR---SSPERIKKIY--GFSDTLANAIVNRAMK 667 (674)
T ss_pred CCCCCH--HHHHHHHHcCCCCHHHHHh---CCHHHHHHHh--ccCHHHHHHHHHHHHH
Confidence 344444 4669999999999999877 7888898888 6899999999999875
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=46.95 E-value=13 Score=39.30 Aligned_cols=51 Identities=31% Similarity=0.400 Sum_probs=39.2
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhc
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAK 316 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 316 (628)
+|..|-+||+.. -++|...||+|++|+.++ +...|.+.||. .|.....+|+
T Consensus 177 pl~~l~gig~~~--~~~L~~~Gi~ti~dL~~~---~~~~L~~rfG~-----~~~~l~~~a~ 227 (344)
T cd01700 177 PVGDVWGIGRRT--AKKLNAMGIHTAGDLAQA---DPDLLRKKFGV-----VGERLVRELN 227 (344)
T ss_pred ChhhcCccCHHH--HHHHHHcCCCcHHHHhcC---CHHHHHHHHHH-----HHHHHHHHhC
Confidence 355566677644 478999999999999985 78899999974 4667777765
No 21
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=44.77 E-value=18 Score=37.81 Aligned_cols=52 Identities=29% Similarity=0.453 Sum_probs=40.4
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhcc
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKT 317 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 317 (628)
+|..|-+||+. .-++|...||+|++|+.++ ++..|++.+| +.|..+.+||+-
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 45556666654 4589999999999999874 7888999885 578888888864
No 22
>PRK01810 DNA polymerase IV; Validated
Probab=41.16 E-value=20 Score=39.02 Aligned_cols=51 Identities=29% Similarity=0.356 Sum_probs=38.8
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhc
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAK 316 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 316 (628)
+|..|-+||+.- -++|...||+|++|+.+ .+...|++.||. .+..+.+||.
T Consensus 180 pv~~l~giG~~~--~~~L~~~Gi~tigdL~~---~~~~~L~~rfG~-----~g~~l~~~a~ 230 (407)
T PRK01810 180 PVGEMHGIGEKT--AEKLKDIGIQTIGDLAK---ADEHILRAKLGI-----NGVRLQRRAN 230 (407)
T ss_pred CHhhcCCcCHHH--HHHHHHcCCCcHHHHHh---CCHHHHHHHHhH-----HHHHHHHHhc
Confidence 455555677643 48899999999999877 478889999964 4666777776
No 23
>PRK03103 DNA polymerase IV; Reviewed
Probab=40.87 E-value=20 Score=39.01 Aligned_cols=52 Identities=27% Similarity=0.349 Sum_probs=40.0
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhcc
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKT 317 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 317 (628)
.|..|-+||+. .-++|...||+|++||.+ .++..|++.||. .|..+.++|.-
T Consensus 182 pi~~l~gig~~--~~~~L~~~Gi~tigdl~~---~~~~~L~~~fG~-----~~~~l~~~a~G 233 (409)
T PRK03103 182 PVRKLFGVGSR--MEKHLRRMGIRTIGQLAN---TPLERLKKRWGI-----NGEVLWRTANG 233 (409)
T ss_pred CHhhcCCccHH--HHHHHHHcCCCCHHHHhc---CCHHHHHHHHCH-----HHHHHHHHhcC
Confidence 45666677774 458899999999999886 478899999963 46777777764
No 24
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=39.77 E-value=34 Score=33.14 Aligned_cols=59 Identities=25% Similarity=0.397 Sum_probs=43.3
Q ss_pred ccceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHH-HHHhhcc
Q 006871 255 DEVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDV-LVDHAKT 317 (628)
Q Consensus 255 DeVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~-~v~HAkt 317 (628)
|+.-+|.+||. ++-+.|+..||+|-.+.-.+-..|-..+-..| +..-+.|.. -|+.|+.
T Consensus 67 DDLt~I~GIGP--k~e~~Ln~~GI~tfaQIAAwt~~di~~id~~l--~f~GRi~RDdWi~QAk~ 126 (133)
T COG3743 67 DDLTRISGIGP--KLEKVLNELGIFTFAQIAAWTRADIAWIDDYL--NFDGRIERDDWIAQAKA 126 (133)
T ss_pred ccchhhcccCH--HHHHHHHHcCCccHHHHHhcCHHHHHHHHhhc--CCcchhHHHHHHHHHHH
Confidence 99999999998 47799999999997766554444444555555 677777765 6776664
No 25
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=39.73 E-value=70 Score=33.60 Aligned_cols=72 Identities=14% Similarity=0.266 Sum_probs=34.9
Q ss_pred hhhHHHHHHHHHHHHHHHhcCCCCcCCCCCCCcccCCCCCceEE-EEcCCCCCCcccCCcccccCCCceEEEEE
Q 006871 52 LEPILRRVVSEEVERALAKLGPAKLTGRSSPKRIEGPDGRNLQL-HFRTRLSLPLFTGGKVEGEQGTAIHIVLI 124 (628)
Q Consensus 52 lEp~lrrvV~EEve~~l~~~~~~~~~~rs~~~~i~~~~~~~~~L-~F~n~l~~pifTg~kI~ae~g~~I~V~L~ 124 (628)
||-++|+|+.|++-..+.-..+. +..-..|..|-.-.++.+++ +|....+..+|+.+-+..++|..+-..++
T Consensus 90 i~~lv~~v~~e~~~~~~~~~~~~-~~~~~~~~Gi~vVrg~svk~~~fdg~~~~~v~~~d~~~~~d~s~m~aGf~ 162 (233)
T PRK15457 90 VAQLMEKVMKEKQSLEQGAMQPS-FKSVTGKGGIKVIDGSSVKFGRFDGAEPHCVGLTDLVTGDDGSSMAAGFM 162 (233)
T ss_pred HHHHHHHHHHHHhcccccccCCC-ccceeCCCceEEEECCeEEEeecCCCCcccEEeeeeeccCCCCceeeEEE
Confidence 67799999998864332110010 00001122333333445655 55444445555555555555555554443
No 26
>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=37.44 E-value=24 Score=37.50 Aligned_cols=56 Identities=23% Similarity=0.121 Sum_probs=41.4
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhC-hHHHHHHHccCCCchhHHHHHHhhcccccC
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRD-SQRLRNILGSGMSNKMWDVLVDHAKTCVLS 321 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d-~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 321 (628)
+|..|-+||+.- -++|...||+|++|++++ + ...|+..+| +.+..+.++|+--+..
T Consensus 174 pi~~l~giG~~~--~~~L~~~Gi~ti~dl~~~---~~~~~l~~~fg-----~~~~~l~~~a~G~d~~ 230 (343)
T cd00424 174 PLTDLPGIGAVT--AKRLEAVGINPIGDLLAA---SPDALLALWGG-----VSGERLWYALRGIDDE 230 (343)
T ss_pred ChhhcCCCCHHH--HHHHHHcCCCcHHHHhcC---CHHHHHHHHhh-----HHHHHHHHHhCCcCCC
Confidence 466667777754 489999999999998764 6 566777775 4678888888755443
No 27
>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=37.38 E-value=12 Score=32.71 Aligned_cols=73 Identities=30% Similarity=0.429 Sum_probs=42.8
Q ss_pred ceeeeeecccchhhhhhhhcCCccHHHHHHHHhhCh-HHHHHHHccCCCchhHHHHHHhhcccccCCceEEEecCCCCce
Q 006871 257 VWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDS-QRLRNILGSGMSNKMWDVLVDHAKTCVLSGKLYVYYPDDPRNV 335 (628)
Q Consensus 257 VwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~-~kLR~iLg~gmS~k~We~~v~HAktCvl~~k~y~y~~~~~~nv 335 (628)
+..|.+||.. .-+.|.+.||+||+||..+=.+.. -+|++. | .
T Consensus 5 l~~LpNig~~--~e~~L~~vGI~t~~~L~~~Ga~~a~~~Lk~~-~----------------------------------~ 47 (81)
T PF04994_consen 5 LKDLPNIGPK--SERMLAKVGIHTVEDLRELGAVEAYLRLKAS-G----------------------------------P 47 (81)
T ss_dssp GCGSTT--HH--HHHHHHHTT--SHHHHHHHHHHHHHHHHHHH------------------------------------T
T ss_pred hhhCCCCCHH--HHHHHHHcCCCCHHHHHHhCHHHHHHHHHHH-C----------------------------------C
Confidence 3345555553 338899999999999998655443 345554 2 1
Q ss_pred EEEEccccceeeeecCCeeecCCCCChHhHHHHH
Q 006871 336 GVVFNNIYEFCGLIADGQYHSADSLSESQKVHVD 369 (628)
Q Consensus 336 gl~FN~i~~lvG~~~~g~y~s~d~L~~~qk~~V~ 369 (628)
.+-+|-+|.|.||+-|-++ ..|++.+|....
T Consensus 48 ~~~~~~L~aL~gAi~g~~~---~~L~~~~K~~L~ 78 (81)
T PF04994_consen 48 SVCLNLLYALEGAIQGIHW---ADLPDEEKQELL 78 (81)
T ss_dssp T--HHHHHHHHHHHCTS-G---GGS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHcCCCH---HHCCHHHHHHHH
Confidence 2557788999999887554 456777776544
No 28
>PRK01216 DNA polymerase IV; Validated
Probab=33.45 E-value=17 Score=39.30 Aligned_cols=51 Identities=25% Similarity=0.391 Sum_probs=38.4
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhh
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHA 315 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HA 315 (628)
+|..|.+||+. -.++|...||+|++|+.++ +...|++.||. ..+..+-.+|
T Consensus 179 Pi~~l~giG~~--~~~~L~~~Gi~TigdL~~~---~~~~L~~rfG~----~~~~~L~~~a 229 (351)
T PRK01216 179 DIADIPGIGDI--TAEKLKKLGVNKLVDTLRI---EFDELKGIIGE----AKAKYLFSLA 229 (351)
T ss_pred CcccccCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHCH----HHHHHHHHHh
Confidence 57777788864 4489999999999998764 77889999973 3345555566
No 29
>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=33.25 E-value=18 Score=39.62 Aligned_cols=54 Identities=22% Similarity=0.243 Sum_probs=39.7
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhc
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAK 316 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 316 (628)
+|..|-+||+. .-++|...||.|++|+..+- .++..|++.||. +.+..+..+|.
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 57777778764 45999999999999998761 127899999974 34555555654
No 30
>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=31.39 E-value=2.4e+02 Score=28.55 Aligned_cols=62 Identities=29% Similarity=0.347 Sum_probs=36.9
Q ss_pred CCccccceEEE---ec--Cce--eeccCceeecCCCcccccccEEEEEeecCCC-------CccceeeecccceEEeeC
Q 006871 176 RPLLSGDLQVT---LK--EGV--GTLGDLTFTDNSSWIRSRKFRLGLKVASGYC-------EGIRIREAKTDAFTVKDH 240 (628)
Q Consensus 176 ~pLL~Gdl~v~---L~--~Gv--a~l~di~FTDnSsw~rSrKFRLgaRv~~~~~-------~g~RI~EAvsE~FvVkDh 240 (628)
...|.|.+... |+ +|. |.. ..|.|=|-. .-+.|||-.++..=.. ...-+-|+.|+||.|-..
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--FVFPDLSVR-TEGRFRLRFSLFDIGPSPGQGGGSSPVLAEVFSDPFTVYSA 172 (203)
T ss_pred cccCcccEeeeeEEecCCCCCeEEEE--EEeCCceEC-cCCEEEEEEEEEEecCCccccCCCCcEEEEEECcCEEEECH
Confidence 46788876543 33 333 211 233343332 2468999988864322 235679999999999653
No 31
>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=31.22 E-value=33 Score=35.47 Aligned_cols=54 Identities=26% Similarity=0.440 Sum_probs=37.0
Q ss_pred cceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhc
Q 006871 256 EVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAK 316 (628)
Q Consensus 256 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 316 (628)
...-|.+|+.+.+ ++|...||.|+++|+++ ++.+|..+| +......+.+.+.|.
T Consensus 149 ~L~Qlp~i~~~~~--~~l~~~~i~~l~~l~~~---~~~e~~~ll--~~~~~~~~~i~~~~~ 202 (314)
T PF02889_consen 149 PLLQLPHIGEESL--KKLEKRGIKTLQDLRDL---SPEELEELL--NRNPPFGKEILEVAS 202 (314)
T ss_dssp GGGGSTT--HHHH--HHHHHTT--SHHHHHHS----HHHHHHHH---S-HHHHHHHHHHHC
T ss_pred hhhcCCCCCHHHH--HHHhccCCCcHHHHhhC---CHHHHHHHH--hhhhhhHHHHHHHHH
Confidence 3455667877665 88999999999999854 899999998 455677888887776
No 32
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=30.04 E-value=23 Score=38.49 Aligned_cols=55 Identities=15% Similarity=0.249 Sum_probs=38.2
Q ss_pred cceeeeeecccchhhhh-hhhcCCccHHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhcc
Q 006871 256 EVWRLEKIGKDGSFHKR-LNKAGIFTVEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKT 317 (628)
Q Consensus 256 eVwRLekIgKdG~~hkr-L~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 317 (628)
+|..|-+||+. .-++ |...||.|++|+.++. .++..|++.||. +.++.+..+|+-
T Consensus 183 pv~~l~GiG~~--~~~~ll~~~Gi~ti~dl~~~~-~~~~~L~~~fG~----~~g~~l~~~a~G 238 (359)
T cd01702 183 PITSIRGLGGK--LGEEIIDLLGLPTEGDVAGFR-SSESDLQEHFGE----KLGEWLYNLLRG 238 (359)
T ss_pred cHHHhCCcCHH--HHHHHHHHcCCcCHHHHHhcc-CCHHHHHHHHHH----HHHHHHHHHhCC
Confidence 46777777742 2244 5889999999998754 478889999874 344555556554
No 33
>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=28.28 E-value=89 Score=28.16 Aligned_cols=35 Identities=26% Similarity=0.489 Sum_probs=28.1
Q ss_pred hcCCccHHHHHHHHhhChHHH---HHHHccCCCchhHHHHHHhhcc
Q 006871 275 KAGIFTVEDFLRLVVRDSQRL---RNILGSGMSNKMWDVLVDHAKT 317 (628)
Q Consensus 275 ~~gI~tV~dFLrl~~~d~~kL---R~iLg~gmS~k~We~~v~HAkt 317 (628)
...| +++||+=++-.||.|| +++| .|+..++-||.
T Consensus 52 ~~k~-~~eD~~FliR~D~~Kl~Rl~~lL-------~~k~~~k~ark 89 (92)
T cd07978 52 RGKV-KVEDLIFLLRKDPKKLARLRELL-------SMKDELKKARK 89 (92)
T ss_pred CCCC-CHHHHHHHHhcCHHHHHHHHHHH-------HHHHHHHHHHh
Confidence 3457 9999999999999755 4556 68889988875
No 34
>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=27.26 E-value=69 Score=27.17 Aligned_cols=25 Identities=40% Similarity=0.559 Sum_probs=16.2
Q ss_pred hHHHHHHHHHhhHHHHHHhhhhHHHHHHH
Q 006871 33 ASVIVEALKVDSLQKLCSSLEPILRRVVS 61 (628)
Q Consensus 33 ~svi~ea~~~~s~q~l~~~lEp~lrrvV~ 61 (628)
+||-+.=+++- |...|||+|||...
T Consensus 29 KsVsrkPLr~l----La~aLEPllkr~~~ 53 (59)
T TIGR02979 29 KSVARRPLKML----LAIALEPMLKRAAN 53 (59)
T ss_pred HHHhhccHHHH----HHHHHHHHHHHHHH
Confidence 34444444441 56689999999753
No 35
>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=27.17 E-value=27 Score=29.39 Aligned_cols=27 Identities=33% Similarity=0.491 Sum_probs=18.5
Q ss_pred hhhhhhcCCccHHHHHHHHhhChHHHHHHH
Q 006871 270 HKRLNKAGIFTVEDFLRLVVRDSQRLRNIL 299 (628)
Q Consensus 270 hkrL~~~gI~tV~dFLrl~~~d~~kLR~iL 299 (628)
...|..+||+||+|++++ +++.|.++=
T Consensus 24 ~n~L~~~~I~tv~dL~~~---s~~~L~~i~ 50 (66)
T PF03118_consen 24 YNCLKRAGIHTVGDLVKY---SEEDLLKIK 50 (66)
T ss_dssp HHHHHCTT--BHHHHHCS----HHHHHTST
T ss_pred HHHHHHhCCcCHHHHHhC---CHHHHHhCC
Confidence 367899999999997664 666777774
No 36
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=27.14 E-value=63 Score=29.11 Aligned_cols=60 Identities=25% Similarity=0.408 Sum_probs=40.1
Q ss_pred CCCCccceeeeeecccchhhhhhhhcCCcc----HHHHHHHHhhChHHHHHHHccCCCchhHHHHHHhhccc
Q 006871 251 PALNDEVWRLEKIGKDGSFHKRLNKAGIFT----VEDFLRLVVRDSQRLRNILGSGMSNKMWDVLVDHAKTC 318 (628)
Q Consensus 251 P~L~DeVwRLekIgKdG~~hkrL~~~gI~t----V~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktC 318 (628)
|+=+-+|--|.+||.. +-.+|..+|+.. .++|| ++.+|++-.+.-|. ..--++-+||++|
T Consensus 15 PmGeK~V~~laGIg~~--lg~~L~~~GfdkAYvllGQfL-llkKdE~lF~~Wlk-----~~~gat~~~a~~~ 78 (90)
T KOG4233|consen 15 PMGEKDVTWLAGIGET--LGIKLVDAGFDKAYVLLGQFL-LLKKDEDLFQEWLK-----ETCGATAKQAQDC 78 (90)
T ss_pred ccCCCcceeeccccHH--hhhhHHhccccHHHHHHHHHH-HhcccHHHHHHHHH-----HHcCccHHHHHHH
Confidence 5667789999999874 568999999876 36666 45678765555431 1112355677766
No 37
>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=26.75 E-value=29 Score=38.04 Aligned_cols=58 Identities=14% Similarity=0.128 Sum_probs=40.0
Q ss_pred ceeeeeecccchhhhhhhhcCCccHHHHHHHHh------------hChHHHHHHHccCCCchhHHHHHHhhccccc
Q 006871 257 VWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVV------------RDSQRLRNILGSGMSNKMWDVLVDHAKTCVL 320 (628)
Q Consensus 257 VwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~------------~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 320 (628)
|-.|-+||+... ++|.+.||.|++|+..+-+ .+...|++.||. +.+..+.++|.--+.
T Consensus 174 v~~l~GiG~~~~--~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~----~~g~~l~~~a~G~d~ 243 (379)
T cd01703 174 LRKIPGIGYKTA--AKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGE----GIGQRIWKLLFGRDT 243 (379)
T ss_pred ccccCCcCHHHH--HHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHCH----HHHHHHHHHHCCCCC
Confidence 444446777654 8999999999999986541 117789999864 345666667765443
No 38
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=24.78 E-value=42 Score=31.25 Aligned_cols=39 Identities=36% Similarity=0.589 Sum_probs=29.9
Q ss_pred ceeeeeecccchhhhhhhhcCCccHHHHHHHHhhChHHHHHHHc
Q 006871 257 VWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVRDSQRLRNILG 300 (628)
Q Consensus 257 VwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg 300 (628)
..|+.+||. .|..-|..+||.||+++- ..+|++|.+.++
T Consensus 55 L~ri~gi~~--~~a~LL~~AGv~Tv~~LA---~~~p~~L~~~l~ 93 (122)
T PF14229_consen 55 LMRIPGIGP--QYAELLEHAGVDTVEELA---QRNPQNLHQKLG 93 (122)
T ss_pred hhhcCCCCH--HHHHHHHHhCcCcHHHHH---hCCHHHHHHHHH
Confidence 446666665 466889999999999974 478988888653
No 39
>PF09584 Phageshock_PspD: Phage shock protein PspD (Phageshock_PspD); InterPro: IPR014321 Members of this entry are phage shock protein PspD, they are found in a minority of bacteria that carry the defining genes of the phage shock regulon (pspA, pspB, pspC, and pspF). It is found in Escherichia coli, Yersinia pestis, and closely related species, where it is part of the phage shock operon. It is known to be expressed but its function is unknown.
Probab=23.80 E-value=83 Score=27.28 Aligned_cols=15 Identities=47% Similarity=0.789 Sum_probs=11.9
Q ss_pred HHHhhhhHHHHHHHH
Q 006871 48 LCSSLEPILRRVVSE 62 (628)
Q Consensus 48 l~~~lEp~lrrvV~E 62 (628)
|.-.|||+|||+++-
T Consensus 45 La~~LEPllrr~~~~ 59 (66)
T PF09584_consen 45 LALALEPLLRRGLNK 59 (66)
T ss_pred HHHHHHHHHHHHHHH
Confidence 555899999998653
No 40
>PRK10497 peripheral inner membrane phage-shock protein; Provisional
Probab=21.96 E-value=98 Score=27.30 Aligned_cols=14 Identities=43% Similarity=0.835 Sum_probs=11.4
Q ss_pred HHHhhhhHHHHHHH
Q 006871 48 LCSSLEPILRRVVS 61 (628)
Q Consensus 48 l~~~lEp~lrrvV~ 61 (628)
|.-.|||+|||.++
T Consensus 52 L~~~LEPlLkr~~~ 65 (73)
T PRK10497 52 LAVALEPLLKRAAN 65 (73)
T ss_pred HHHHHHHHHHHHHH
Confidence 45589999999864
No 41
>PF06594 HCBP_related: Haemolysin-type calcium binding protein related domain; InterPro: IPR010566 This family consists of a number of bacteria specific domains, which are found in haemolysin-type calcium binding proteins. This family is found in conjunction with IPR001343 from INTERPRO and is often found in multiple copies.
Probab=21.76 E-value=53 Score=25.15 Aligned_cols=18 Identities=22% Similarity=0.612 Sum_probs=15.1
Q ss_pred eeeccCceeecCCCcccc
Q 006871 191 VGTLGDLTFTDNSSWIRS 208 (628)
Q Consensus 191 va~l~di~FTDnSsw~rS 208 (628)
-..|..+.|-|++.|++.
T Consensus 24 ~~~Ie~i~FaDGt~w~~~ 41 (43)
T PF06594_consen 24 SYRIEQIEFADGTVWTRA 41 (43)
T ss_pred CCcEeEEEEcCCCEecHH
Confidence 567889999999999753
No 42
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=21.66 E-value=36 Score=40.03 Aligned_cols=38 Identities=32% Similarity=0.463 Sum_probs=31.6
Q ss_pred CCCCccceeeeeecccchhhhhhhhcCCccHHHHHHHHhh
Q 006871 251 PALNDEVWRLEKIGKDGSFHKRLNKAGIFTVEDFLRLVVR 290 (628)
Q Consensus 251 P~L~DeVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~ 290 (628)
..|++.|-.|++||+.-+ ++|++.||+||.|.|..+=+
T Consensus 5 ~~~~~~~~~l~gvg~~~~--~~l~~lgi~t~~dll~~~P~ 42 (681)
T PRK10917 5 LLLDAPLTSLKGVGPKTA--EKLAKLGIHTVQDLLLHLPR 42 (681)
T ss_pred ccccCChhhcCCCCHHHH--HHHHHcCCCCHHHHhhcCCC
Confidence 457789999999987544 88999999999999988654
No 43
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=21.53 E-value=2.4e+02 Score=27.18 Aligned_cols=40 Identities=23% Similarity=0.523 Sum_probs=31.4
Q ss_pred chhhhhhhhcCCccHHHHHHHHhhCh----HHHHHHHccCCCch
Q 006871 267 GSFHKRLNKAGIFTVEDFLRLVVRDS----QRLRNILGSGMSNK 306 (628)
Q Consensus 267 G~~hkrL~~~gI~tV~dFLrl~~~d~----~kLR~iLg~gmS~k 306 (628)
.+|+.-|+.+|=.||+|.-.-++++. ..|++++-.|+=.+
T Consensus 31 ~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~R 74 (126)
T COG3355 31 EVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVER 74 (126)
T ss_pred HHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeee
Confidence 56888888999999999999999995 46777765555443
No 44
>COG3827 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.25 E-value=1.6e+02 Score=30.82 Aligned_cols=39 Identities=31% Similarity=0.463 Sum_probs=28.2
Q ss_pred hhhHHHHHHHHHhhHHHHH-HhhhhHHHHHHHHHHHHHHHh
Q 006871 31 ALASVIVEALKVDSLQKLC-SSLEPILRRVVSEEVERALAK 70 (628)
Q Consensus 31 ~~~svi~ea~~~~s~q~l~-~~lEp~lrrvV~EEve~~l~~ 70 (628)
+|-.+..|+|+-- ||.-+ ..|=-++.|+|+|||||..+.
T Consensus 189 sleE~a~eMLRPm-LqdWLDkNLPtLVErLVrEEIeRv~RG 228 (231)
T COG3827 189 SLEEMAAEMLRPM-LQDWLDKNLPTLVERLVREEIERVVRG 228 (231)
T ss_pred cHHHHHHHHHHHH-HHHHHHccchHHHHHHHHHHHHHHHcc
Confidence 4777777777653 55533 367778899999999997653
Done!