Query 007352
Match_columns 607
No_of_seqs 139 out of 168
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 22:25:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007352.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007352hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07887 Calmodulin_bind: Calm 100.0 2E-121 3E-126 933.9 29.8 299 93-394 1-299 (299)
2 TIGR02239 recomb_RAD51 DNA rep 86.0 0.89 1.9E-05 48.2 4.3 49 269-322 12-60 (316)
3 PLN03186 DNA repair protein RA 83.4 0.92 2E-05 48.8 3.1 62 257-323 27-88 (342)
4 TIGR02238 recomb_DMC1 meiotic 83.3 1.2 2.6E-05 47.2 3.9 49 269-322 12-60 (313)
5 PRK04301 radA DNA repair and r 78.9 1.5 3.2E-05 45.9 2.7 57 257-320 7-63 (317)
6 PLN03187 meiotic recombination 77.0 2.1 4.6E-05 46.2 3.3 61 257-322 30-90 (344)
7 PF14520 HHH_5: Helix-hairpin- 74.3 1.3 2.7E-05 35.8 0.5 52 260-318 9-60 (60)
8 PTZ00035 Rad51 protein; Provis 68.9 5.3 0.00011 42.8 3.9 60 257-321 22-81 (337)
9 PRK03609 umuC DNA polymerase V 67.3 4.4 9.6E-05 44.1 3.0 52 257-318 180-231 (422)
10 TIGR02236 recomb_radA DNA repa 64.2 5.1 0.00011 41.5 2.6 52 260-318 3-54 (310)
11 PF14229 DUF4332: Domain of un 63.9 9.4 0.0002 35.4 4.0 52 269-322 6-59 (122)
12 PRK02406 DNA polymerase IV; Va 63.4 6.3 0.00014 41.5 3.2 52 257-318 169-220 (343)
13 PRK03352 DNA polymerase IV; Va 52.3 6 0.00013 41.7 0.8 41 257-302 178-218 (346)
14 PF10691 DUF2497: Protein of u 51.1 35 0.00076 29.6 5.1 39 32-71 34-73 (73)
15 PRK03858 DNA polymerase IV; Va 50.7 7.4 0.00016 41.8 1.2 41 257-302 174-214 (396)
16 PRK01172 ski2-like helicase; P 50.5 16 0.00035 42.2 3.9 51 261-318 617-667 (674)
17 PRK14133 DNA polymerase IV; Pr 50.1 15 0.00034 38.8 3.4 51 257-317 174-224 (347)
18 PRK03348 DNA polymerase IV; Pr 49.6 8.8 0.00019 42.7 1.6 53 257-318 181-233 (454)
19 PRK02794 DNA polymerase IV; Pr 48.1 14 0.00031 40.3 2.8 55 257-321 210-264 (419)
20 cd01700 PolY_Pol_V_umuC umuC s 47.7 14 0.00031 39.0 2.7 51 257-317 177-227 (344)
21 cd03586 PolY_Pol_IV_kappa DNA 44.7 19 0.00042 37.4 3.1 52 257-318 172-223 (334)
22 PF04994 TfoX_C: TfoX C-termin 42.3 12 0.00026 32.6 1.0 74 257-370 4-78 (81)
23 PRK01810 DNA polymerase IV; Va 41.8 21 0.00045 38.7 2.9 51 257-317 180-230 (407)
24 PRK03103 DNA polymerase IV; Re 41.5 21 0.00046 38.6 2.9 52 257-318 182-233 (409)
25 COG3743 Uncharacterized conser 41.0 34 0.00073 33.0 3.8 59 256-318 67-126 (133)
26 PRK15457 ethanolamine utilizat 40.0 74 0.0016 33.3 6.3 72 53-125 90-162 (233)
27 cd00424 PolY Y-family of DNA p 37.9 26 0.00056 37.1 2.8 55 257-321 174-229 (343)
28 PF02889 Sec63: Sec63 Brl doma 34.3 32 0.00069 35.4 2.8 54 257-317 149-202 (314)
29 COG1200 RecG RecG-like helicas 33.9 18 0.00039 42.7 0.9 41 257-299 11-51 (677)
30 cd01701 PolY_Rev1 DNA polymera 33.6 19 0.00041 39.3 1.1 54 257-317 223-276 (404)
31 PRK01216 DNA polymerase IV; Va 33.2 19 0.00041 38.9 0.9 51 257-316 179-229 (351)
32 PF14229 DUF4332: Domain of un 32.3 34 0.00074 31.7 2.3 39 258-301 55-93 (122)
33 cd01702 PolY_Pol_eta DNA Polym 30.8 25 0.00053 38.1 1.3 55 257-318 183-238 (359)
34 KOG4233 DNA-bridging protein B 30.7 54 0.0012 29.4 3.1 60 252-319 15-78 (90)
35 KOG4456 Inner centromere prote 29.4 1.2E+02 0.0025 29.4 5.3 47 26-72 62-117 (134)
36 PF03118 RNA_pol_A_CTD: Bacter 28.8 17 0.00036 30.5 -0.3 27 271-300 24-50 (66)
37 cd01703 PolY_Pol_iota DNA Poly 27.2 30 0.00066 37.8 1.2 57 258-320 174-242 (379)
38 cd07978 TAF13 The TATA Binding 25.0 1.1E+02 0.0025 27.4 4.2 35 276-318 52-89 (92)
39 PRK10917 ATP-dependent DNA hel 23.7 35 0.00076 39.9 1.0 38 252-291 5-42 (681)
40 TIGR02979 phageshock_pspD phag 23.2 94 0.002 26.3 3.1 24 35-62 30-53 (59)
41 PF11754 Velvet: Velvet factor 22.7 1.5E+02 0.0033 29.7 5.2 62 177-241 97-172 (203)
42 COG3355 Predicted transcriptio 22.3 2.6E+02 0.0056 26.8 6.2 40 268-307 31-74 (126)
43 PF09584 Phageshock_PspD: Phag 21.8 98 0.0021 26.7 3.0 15 49-63 45-59 (66)
44 PF06594 HCBP_related: Haemoly 21.6 55 0.0012 24.9 1.4 18 192-209 24-41 (43)
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=1.5e-121 Score=933.87 Aligned_cols=299 Identities=66% Similarity=1.116 Sum_probs=295.0
Q ss_pred ceEEEEcCCCCCCcccCCcccccCCCceEEEEEeCCCCCeeccCCCCcceEEEEEeeCCCCCCcCCCCCHHHHhcccccc
Q 007352 93 NLQLHYKTRMPPHLFTGGKVEGDQGAAIHVVLIDMNTGDVVQTGPESSAKLNVVVLEGDFNEEEDDNWTKEHFESHEVKE 172 (607)
Q Consensus 93 ~~~L~F~n~l~~pifTg~kI~ae~g~~I~V~L~D~~tg~iVt~GplSs~kiEIvVLdGDF~~~~~e~WT~eEF~~~IVk~ 172 (607)
+|||+|+|+|++|||||++|+|+||+||+|+|+|++|+ |++||+|++|||||||||||+++++++||+|||++|||++
T Consensus 1 ~~~L~F~n~l~~pifT~~~i~a~~g~~i~V~l~d~~~~--v~~g~lss~kieIvvLdGdF~~~~~~~wT~eeF~~~iv~~ 78 (299)
T PF07887_consen 1 NLQLRFLNKLSLPIFTGSKIEAEDGAPIKVALVDANTG--VTSGPLSSAKIEIVVLDGDFNDEDCEDWTEEEFNSHIVKE 78 (299)
T ss_pred CeEEEecCCCCCCcccCCceEecCCCcEEEEEEECCCC--ccCCCCCCcEEEEEEEccccCCCccCCCCHHHHhhcEeec
Confidence 58999999999999999999999999999999999988 9999999999999999999999999999999999999999
Q ss_pred CCCCCcceeeeEEEEeccceeeccCceeecCCcccccccceEEEEecCCCCCCcceeeeeecceEeeeCCccccccCCCC
Q 007352 173 REGKRPILTGDLLVTLKEGFGTLGDLTFTDNSSWIRSRKFRLGLKVSPGYCDGIRVREAKTEGFAVKDHRGELYKKHYPP 252 (607)
Q Consensus 173 ReGk~pLL~Gdl~v~L~~Gva~l~di~FTDnSsw~rSrKFRLgaRv~~~~~~g~RI~EAvsE~FvVkDhRge~ykKh~pP 252 (607)
|+||+|||+|+|+|+|+||+|+|+||+|||||||+|||||||||||+++++.|+|||||+||||+|||||||+|||||||
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 CCCCcceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhcccCCCeeEEEEecC
Q 007352 253 ALHDEVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVLGGKLYVYYADG 332 (607)
Q Consensus 253 ~L~DeVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~k~y~y~~~~ 332 (607)
+|+|||||||||||||+|||+|+.+||+||+|||+++++||++||+|||+|||++||++||+|||||++++++|+|| ++
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 CccEEEEEcccceeeeeecCCeeeeCCCCChHhHHHHHHHHHHHHhccccccccCcccccCc
Q 007352 333 TQNTGVVFNNIYELRGLIDDGQFVSLESLTHSQKISVDSLVKRAYDNWHQVLEYDGKFLSSL 394 (607)
Q Consensus 333 ~~nvgl~FN~i~~lVG~~~~g~y~s~d~L~~~qk~~V~~Lk~~AY~nw~~~~e~D~~~l~n~ 394 (607)
++|++|+|||||+||||+|+|+|++.|+||+.||++|++||++||+||++|++||++|++||
T Consensus 238 ~~nv~l~FN~i~~lvga~~~g~y~s~d~L~~~qK~~v~~Lv~~AY~n~~~l~e~d~~~~~n~ 299 (299)
T PF07887_consen 238 EQNVGLFFNCIYELVGAIFGGQYVSLDNLSSAQKAYVDKLVKQAYENWDNLEEYDGKMLNNY 299 (299)
T ss_pred CCceEEEEcchhhEEeEEECCEEEehHHcCHHHHHHHHHHHHHHHHhhhhheecccchhccC
Confidence 78999999999999999999999999999999999999999999999999999999999986
No 2
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=85.99 E-value=0.89 Score=48.15 Aligned_cols=49 Identities=29% Similarity=0.225 Sum_probs=43.4
Q ss_pred hhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhcccCC
Q 007352 269 ALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVLG 322 (607)
Q Consensus 269 ~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 322 (607)
.--++|+++||.||+||+. .+|..|.+++ |+|...++.+..||.+|...
T Consensus 12 ~~~~~l~~~g~~t~~~~~~---~~~~~L~~i~--~ls~~~~~~~~~~~~~~~~~ 60 (316)
T TIGR02239 12 ADIKKLQEAGLHTVESVAY---APKKQLLEIK--GISEAKADKILAEAAKLVPM 60 (316)
T ss_pred HHHHHHHHcCCCcHHHHHh---CCHHHHHHHh--CCCHHHHHHHHHHHHHhccc
Confidence 4568999999999999986 4899999998 79999999999999998654
No 3
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=83.42 E-value=0.92 Score=48.79 Aligned_cols=62 Identities=29% Similarity=0.223 Sum_probs=49.0
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhcccCCC
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVLGG 323 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~ 323 (607)
++-+|+.-|-.-.--++|+++||.||+||+.+ ++..|.++. |+|....+.+++||.+|....
T Consensus 27 ~~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~---~~~~L~~i~--~is~~~~~~~~~~~~~~~~~~ 88 (342)
T PLN03186 27 PIEQLQASGIAALDIKKLKDAGIHTVESLAYA---PKKDLLQIK--GISEAKVEKILEAASKLVPLG 88 (342)
T ss_pred cHHHHHhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHHhcccc
Confidence 34555443333456799999999999998764 788999998 799999999999998886543
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=83.34 E-value=1.2 Score=47.17 Aligned_cols=49 Identities=29% Similarity=0.249 Sum_probs=43.0
Q ss_pred hhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhcccCC
Q 007352 269 ALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVLG 322 (607)
Q Consensus 269 ~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 322 (607)
.--++|+++||.||+||+. .++..|.++. |+|...++.+++.|+.+...
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 4568999999999999876 4889999997 79999999999999988655
No 5
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=78.92 E-value=1.5 Score=45.94 Aligned_cols=57 Identities=23% Similarity=0.293 Sum_probs=45.9
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhccc
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCV 320 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCv 320 (607)
++-.|.+||+ ...++|.++||+|++|++. .|+..|.+++ |++.+.++.+++-|+.++
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 3455666775 4569999999999999965 5999999998 678889999998887644
No 6
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=77.03 E-value=2.1 Score=46.17 Aligned_cols=61 Identities=21% Similarity=0.212 Sum_probs=47.9
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhcccCC
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVLG 322 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 322 (607)
++..|+.-|-.=.--++|.++||+||+|++. .++..|-++. |+|....+.+++.|+..+..
T Consensus 30 ~~~~l~~~g~~~~~~~kL~~~g~~tv~~~~~---~~~~~L~~~~--g~s~~~~~ki~~~a~~~~~~ 90 (344)
T PLN03187 30 SIDKLISQGINAGDVKKLQDAGIYTCNGLMM---HTKKNLTGIK--GLSEAKVDKICEAAEKLLNQ 90 (344)
T ss_pred CHHHHhhCCCCHHHHHHHHHcCCCcHHHHHh---CCHHHHHHhc--CCCHHHHHHHHHHHHHhhcc
Confidence 3666655333345669999999999999876 4788899986 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=74.25 E-value=1.3 Score=35.75 Aligned_cols=52 Identities=31% Similarity=0.486 Sum_probs=41.3
Q ss_pred eeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhc
Q 007352 260 RLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (607)
Q Consensus 260 RLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 318 (607)
.+.+||+.- .++|.+.||.|++|+.. .+++.|.++= |++.+.=+.+++.|+.
T Consensus 9 ~I~Gig~~~--a~~L~~~G~~t~~~l~~---a~~~~L~~i~--Gig~~~a~~i~~~~~~ 60 (60)
T PF14520_consen 9 SIPGIGPKR--AEKLYEAGIKTLEDLAN---ADPEELAEIP--GIGEKTAEKIIEAARE 60 (60)
T ss_dssp TSTTCHHHH--HHHHHHTTCSSHHHHHT---SHHHHHHTST--TSSHHHHHHHHHHHHH
T ss_pred cCCCCCHHH--HHHHHhcCCCcHHHHHc---CCHHHHhcCC--CCCHHHHHHHHHHHhC
Confidence 355666654 48999999999999866 4788899974 7899999999988863
No 8
>PTZ00035 Rad51 protein; Provisional
Probab=68.89 E-value=5.3 Score=42.84 Aligned_cols=60 Identities=33% Similarity=0.297 Sum_probs=46.9
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhcccC
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVL 321 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 321 (607)
++-.|+.-|-.=.--++|.++||+||+||+. .++..|-++. |+|...=+.+++.|+.++.
T Consensus 22 ~~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~---~~~~~L~~~~--gis~~~~~~i~~~~~~~~~ 81 (337)
T PTZ00035 22 EIEKLQSAGINAADIKKLKEAGICTVESVAY---ATKKDLCNIK--GISEAKVEKIKEAASKLVP 81 (337)
T ss_pred cHHHHhcCCCCHHHHHHHHHcCCCcHHHHHh---CCHHHHHHhh--CCCHHHHHHHHHHHHHhcc
Confidence 4556654333334569999999999999876 4888999997 7899999999999988764
No 9
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=67.33 E-value=4.4 Score=44.15 Aligned_cols=52 Identities=21% Similarity=0.222 Sum_probs=41.8
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhc
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 318 (607)
+|..|-+||+. ..++|.+.||+|++|+.++ ++..|++.||. .+..+..||.-
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 45566678884 4599999999999999985 88999999973 67778888753
No 10
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=64.16 E-value=5.1 Score=41.54 Aligned_cols=52 Identities=25% Similarity=0.321 Sum_probs=39.9
Q ss_pred eeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhc
Q 007352 260 RLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (607)
Q Consensus 260 RLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 318 (607)
.|.+||+ ...++|.++||.|++|++. .|++.|.+++ |++.+..+.+.+-|+.
T Consensus 3 ~i~gig~--~~~~~L~~~Gi~ti~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~~~~ 54 (310)
T TIGR02236 3 DLPGVGP--ATAEKLREAGYDTFEAIAV---ASPKELSEIA--GISEGTAAKIIQAARK 54 (310)
T ss_pred ccCCCCH--HHHHHHHHcCCCCHHHHHc---CCHHHHHhcc--CCCHHHHHHHHHHHHH
Confidence 3455665 3558999999999999877 4899999998 5677777777776663
No 11
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=63.88 E-value=9.4 Score=35.35 Aligned_cols=52 Identities=27% Similarity=0.188 Sum_probs=37.6
Q ss_pred hhhhhhhhCCcccHHHHHHHHhcChHH--HHHHHcCCCCchhHHHHHHhhhcccCC
Q 007352 269 ALHKKLMKADIVTVEDFLRILVRDPQK--LRNILGSGMSNRMWENTVEHAKTCVLG 322 (607)
Q Consensus 269 ~~hkrL~~~gI~tV~dFLrl~~~d~~k--LR~iLg~gmS~k~We~~v~HAktCvl~ 322 (607)
...++|+..||+|++|||..-.....+ |-+-+ |++.+-=...+.+|.=|...
T Consensus 6 ~~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~--~i~~~~l~~w~~~AdL~ri~ 59 (122)
T PF14229_consen 6 KEAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKL--GISERNLLKWVNQADLMRIP 59 (122)
T ss_pred HHHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhc--CCCHHHHHHHHhHHHhhhcC
Confidence 356899999999999999986665444 55554 67877766677777655433
No 12
>PRK02406 DNA polymerase IV; Validated
Probab=63.37 E-value=6.3 Score=41.52 Aligned_cols=52 Identities=23% Similarity=0.247 Sum_probs=40.3
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhc
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 318 (607)
+|..|-+||+. .-++|...||+|++|+.++ +...|++.||. .+..+..||.-
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 56677777764 4588999999999999885 78899999973 46666667653
No 13
>PRK03352 DNA polymerase IV; Validated
Probab=52.34 E-value=6 Score=41.72 Aligned_cols=41 Identities=27% Similarity=0.322 Sum_probs=33.7
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcC
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGS 302 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~ 302 (607)
+|..|-+||+. ..++|...||+|++|++++ ++..|++.||.
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 56666678774 4588999999999999985 78899999974
No 14
>PF10691 DUF2497: Protein of unknown function (DUF2497) ; InterPro: IPR019632 Members of this family belong to the Alphaproteobacteria. The function of the family is not known.
Probab=51.14 E-value=35 Score=29.63 Aligned_cols=39 Identities=33% Similarity=0.496 Sum_probs=29.0
Q ss_pred hhHHHHHHHHHHhHHHH-HHHhhhhHHHHHHHHHHHHHHHh
Q 007352 32 ALASVIVEALKMDSLQR-LCSSLEPLLRRIVSEEVERALTK 71 (607)
Q Consensus 32 ~~~svi~ea~~~~s~q~-l~~~lEp~lrrvV~EEve~~l~~ 71 (607)
++-.+++|+|+-- |+. |=..|=.|+.|+|++||+|..+|
T Consensus 34 TlE~lvremLRPm-LkeWLD~nLP~lVErlVr~EIeRi~rr 73 (73)
T PF10691_consen 34 TLEDLVREMLRPM-LKEWLDENLPGLVERLVREEIERIARR 73 (73)
T ss_pred cHHHHHHHHHHHH-HHHHHHhccHHHHHHHHHHHHHHHhcC
Confidence 5667777777764 333 55578888999999999998754
No 15
>PRK03858 DNA polymerase IV; Validated
Probab=50.74 E-value=7.4 Score=41.75 Aligned_cols=41 Identities=29% Similarity=0.264 Sum_probs=33.5
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcC
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGS 302 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~ 302 (607)
+|..|-+||+.- -++|.+.||+|++|+.+ .++..|++.||.
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 455666788754 58999999999999986 588899999975
No 16
>PRK01172 ski2-like helicase; Provisional
Probab=50.55 E-value=16 Score=42.20 Aligned_cols=51 Identities=24% Similarity=0.509 Sum_probs=42.1
Q ss_pred eeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhc
Q 007352 261 LDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (607)
Q Consensus 261 LekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 318 (607)
|.+|++ ...++|.++||.||.|+.. .|+++|-+|+ |++++.=+.++++|+.
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 7888898898 6899999999999875
No 17
>PRK14133 DNA polymerase IV; Provisional
Probab=50.06 E-value=15 Score=38.78 Aligned_cols=51 Identities=24% Similarity=0.384 Sum_probs=39.7
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhh
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 317 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 317 (607)
+|..|-+||+... ++|...||+|++|++++ +...|+..|| +.|..+.++|.
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 4666667776544 78999999999999874 7888999996 35777777775
No 18
>PRK03348 DNA polymerase IV; Provisional
Probab=49.61 E-value=8.8 Score=42.67 Aligned_cols=53 Identities=25% Similarity=0.271 Sum_probs=39.7
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhc
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 318 (607)
+|.+|-+||+.. -++|...||+|++||.++ +...|++.||..+ ...+..+|.-
T Consensus 181 Pv~~L~GIG~~t--~~~L~~lGI~TigDLa~l---~~~~L~~~fG~~~----g~~L~~~a~G 233 (454)
T PRK03348 181 PVRRLWGIGPVT--EEKLHRLGIETIGDLAAL---SEAEVANLLGATV----GPALHRLARG 233 (454)
T ss_pred CccccCCCCHHH--HHHHHHcCCccHHHHhcC---CHHHHHHHHCHHH----HHHHHHHHcC
Confidence 688888888754 488999999999999874 7889999997433 3334445543
No 19
>PRK02794 DNA polymerase IV; Provisional
Probab=48.15 E-value=14 Score=40.27 Aligned_cols=55 Identities=24% Similarity=0.149 Sum_probs=42.7
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhcccC
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTCVL 321 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 321 (607)
+|..|-+||+ ..-++|...||+|++|+.++ +...|++.||. .|..+..+|.--+.
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 3555556775 45589999999999998874 78899999974 58888888875543
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=47.68 E-value=14 Score=38.96 Aligned_cols=51 Identities=29% Similarity=0.304 Sum_probs=39.5
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhh
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 317 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 317 (607)
+|..|-+||+. .-++|...||+|++|+.++ +...|.+.||. .|.....+|+
T Consensus 177 pl~~l~gig~~--~~~~L~~~Gi~ti~dL~~~---~~~~L~~rfG~-----~~~~l~~~a~ 227 (344)
T cd01700 177 PVGDVWGIGRR--TAKKLNAMGIHTAGDLAQA---DPDLLRKKFGV-----VGERLVRELN 227 (344)
T ss_pred ChhhcCccCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHHH-----HHHHHHHHhC
Confidence 45566677774 4478999999999999985 78899999974 4666777765
No 21
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=44.71 E-value=19 Score=37.36 Aligned_cols=52 Identities=23% Similarity=0.353 Sum_probs=40.6
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhc
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 318 (607)
+|..|-+||+. ..++|...||+|++|+.++ ++..|++.+| +.|..+..||+-
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 45566667654 4589999999999999874 7888999885 578888888864
No 22
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=42.28 E-value=12 Score=32.55 Aligned_cols=74 Identities=26% Similarity=0.340 Sum_probs=43.0
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcCh-HHHHHHHcCCCCchhHHHHHHhhhcccCCCeeEEEEecCCcc
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDP-QKLRNILGSGMSNRMWENTVEHAKTCVLGGKLYVYYADGTQN 335 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~-~kLR~iLg~gmS~k~We~~v~HAktCvl~~k~y~y~~~~~~n 335 (607)
.+..|-+||.. .-+.|.+.||+||+||..+=.+.. -+|++. |
T Consensus 4 ~l~~LpNig~~--~e~~L~~vGI~t~~~L~~~Ga~~a~~~Lk~~-~---------------------------------- 46 (81)
T PF04994_consen 4 RLKDLPNIGPK--SERMLAKVGIHTVEDLRELGAVEAYLRLKAS-G---------------------------------- 46 (81)
T ss_dssp -GCGSTT--HH--HHHHHHHTT--SHHHHHHHHHHHHHHHHHHH------------------------------------
T ss_pred chhhCCCCCHH--HHHHHHHcCCCCHHHHHHhCHHHHHHHHHHH-C----------------------------------
Confidence 34456667664 458999999999999998644432 344443 2
Q ss_pred EEEEEcccceeeeeecCCeeeeCCCCChHhHHHHH
Q 007352 336 TGVVFNNIYELRGLIDDGQFVSLESLTHSQKISVD 370 (607)
Q Consensus 336 vgl~FN~i~~lVG~~~~g~y~s~d~L~~~qk~~V~ 370 (607)
..+-+|-.|.|.||+-|-+ ...|++.+|....
T Consensus 47 ~~~~~~~L~aL~gAi~g~~---~~~L~~~~K~~L~ 78 (81)
T PF04994_consen 47 PSVCLNLLYALEGAIQGIH---WADLPDEEKQELL 78 (81)
T ss_dssp TT--HHHHHHHHHHHCTS----GGGS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHcCCC---HHHCCHHHHHHHH
Confidence 2255778899999988744 3456777766543
No 23
>PRK01810 DNA polymerase IV; Validated
Probab=41.83 E-value=21 Score=38.68 Aligned_cols=51 Identities=25% Similarity=0.259 Sum_probs=39.2
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhh
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 317 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 317 (607)
+|..|-+||+. .-++|...||+|++|+.+ .+...|++.||. .+..+.+||.
T Consensus 180 pv~~l~giG~~--~~~~L~~~Gi~tigdL~~---~~~~~L~~rfG~-----~g~~l~~~a~ 230 (407)
T PRK01810 180 PVGEMHGIGEK--TAEKLKDIGIQTIGDLAK---ADEHILRAKLGI-----NGVRLQRRAN 230 (407)
T ss_pred CHhhcCCcCHH--HHHHHHHcCCCcHHHHHh---CCHHHHHHHHhH-----HHHHHHHHhc
Confidence 45556677764 448899999999999877 478889999964 4666777776
No 24
>PRK03103 DNA polymerase IV; Reviewed
Probab=41.50 E-value=21 Score=38.63 Aligned_cols=52 Identities=19% Similarity=0.194 Sum_probs=40.3
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhc
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 318 (607)
+|..|-+||+. .-++|...||+|++|+.+ .++..|++.||. .|..+.++|.-
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 56666678874 558899999999999886 478899999963 46777777764
No 25
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=41.04 E-value=34 Score=33.01 Aligned_cols=59 Identities=22% Similarity=0.267 Sum_probs=43.6
Q ss_pred CcceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHH-HHHhhhc
Q 007352 256 DEVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWEN-TVEHAKT 318 (607)
Q Consensus 256 DeVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~-~v~HAkt 318 (607)
|+.-+|.+||. ++-+.|+..||+|-.+.-.+-..|-..+-..| +..-+.|.. -|+.|+.
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 57899999999997766554444444555555 677777765 6777664
No 26
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=40.03 E-value=74 Score=33.31 Aligned_cols=72 Identities=11% Similarity=0.201 Sum_probs=35.4
Q ss_pred hhhHHHHHHHHHHHHHHHhcccccCCCCCCCCCccCCCCCceEE-EEcCCCCCCcccCCcccccCCCceEEEEE
Q 007352 53 LEPLLRRIVSEEVERALTKFGHAKLAARSPPPRIHGPGEKNLQL-HYKTRMPPHLFTGGKVEGDQGAAIHVVLI 125 (607)
Q Consensus 53 lEp~lrrvV~EEve~~l~~~~~~~~~~rs~~~~i~~~~~~~~~L-~F~n~l~~pifTg~kI~ae~g~~I~V~L~ 125 (607)
||-++|+|+.|++-....-..+ .+..-..|.++--..++++++ +|....+..+|+.+-+..++|..+-..++
T Consensus 90 i~~lv~~v~~e~~~~~~~~~~~-~~~~~~~~~Gi~vVrg~svk~~~fdg~~~~~v~~~d~~~~~d~s~m~aGf~ 162 (233)
T PRK15457 90 VAQLMEKVMKEKQSLEQGAMQP-SFKSVTGKGGIKVIDGSSVKFGRFDGAEPHCVGLTDLVTGDDGSSMAAGFM 162 (233)
T ss_pred HHHHHHHHHHHHhcccccccCC-CccceeCCCceEEEECCeEEEeecCCCCcccEEeeeeeccCCCCceeeEEE
Confidence 6679999999986433211000 000001223333333455665 55444455555555555555555555444
No 27
>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=37.93 E-value=26 Score=37.07 Aligned_cols=55 Identities=18% Similarity=0.002 Sum_probs=41.1
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcC-hHHHHHHHcCCCCchhHHHHHHhhhcccC
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRD-PQKLRNILGSGMSNRMWENTVEHAKTCVL 321 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d-~~kLR~iLg~gmS~k~We~~v~HAktCvl 321 (607)
+|..|-+||+. .-++|...||+|++|++++ + ...|+..+| +.+..+..+|+--+.
T Consensus 174 pi~~l~giG~~--~~~~L~~~Gi~ti~dl~~~---~~~~~l~~~fg-----~~~~~l~~~a~G~d~ 229 (343)
T cd00424 174 PLTDLPGIGAV--TAKRLEAVGINPIGDLLAA---SPDALLALWGG-----VSGERLWYALRGIDD 229 (343)
T ss_pred ChhhcCCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHhh-----HHHHHHHHHhCCcCC
Confidence 46667778874 4489999999999998764 6 566777775 467788888875543
No 28
>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=34.33 E-value=32 Score=35.37 Aligned_cols=54 Identities=26% Similarity=0.408 Sum_probs=37.2
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhh
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 317 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 317 (607)
...-|.+|+.+.+ ++|.+.||.|+++|+++ ++++|..+| +......+.+.+.|.
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 4456668888765 89999999999999854 899999999 455677777777776
No 29
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=33.93 E-value=18 Score=42.71 Aligned_cols=41 Identities=32% Similarity=0.299 Sum_probs=33.8
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHH
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNI 299 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~i 299 (607)
++..|.+||...+ ++|++-||+||+|.|-++=.+=+..+.+
T Consensus 11 ~l~~l~gig~~~a--~~l~~Lgi~tv~DLL~~~P~~YeD~~~~ 51 (677)
T COG1200 11 PLSTLKGIGPKTA--EKLKKLGIHTVQDLLLYLPRRYEDRTLL 51 (677)
T ss_pred chhhhcCcCHHHH--HHHHHcCCCcHHHHHHhCccchhhcccc
Confidence 5899999999888 8999999999999998887664444443
No 30
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=33.62 E-value=19 Score=39.27 Aligned_cols=54 Identities=22% Similarity=0.221 Sum_probs=39.9
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhh
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAK 317 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 317 (607)
+|..|-+||+. .-++|...||.|++|+..+- .++..|++.||. +.+..+..+|.
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 55999999999999998761 127889999974 34555555554
No 31
>PRK01216 DNA polymerase IV; Validated
Probab=33.17 E-value=19 Score=38.88 Aligned_cols=51 Identities=24% Similarity=0.281 Sum_probs=38.7
Q ss_pred cceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhh
Q 007352 257 EVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHA 316 (607)
Q Consensus 257 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HA 316 (607)
+|..|-+||+. -.++|...||+|++|+.++ +...|++.||. ..+..+-.+|
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 4589999999999998764 77889999973 3344555566
No 32
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=32.30 E-value=34 Score=31.70 Aligned_cols=39 Identities=33% Similarity=0.490 Sum_probs=30.4
Q ss_pred ceeeeeecccchhhhhhhhCCcccHHHHHHHHhcChHHHHHHHc
Q 007352 258 VWRLDRIAKDGALHKKLMKADIVTVEDFLRILVRDPQKLRNILG 301 (607)
Q Consensus 258 VwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg 301 (607)
..|+.+|+. .|..-|..+||.||+++- ..+|++|.+.++
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 477899999999999974 478998888653
No 33
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=30.75 E-value=25 Score=38.09 Aligned_cols=55 Identities=11% Similarity=0.117 Sum_probs=38.4
Q ss_pred cceeeeeecccchhhhh-hhhCCcccHHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhc
Q 007352 257 EVWRLDRIAKDGALHKK-LMKADIVTVEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKT 318 (607)
Q Consensus 257 eVwRLekIgKdG~~hkr-L~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 318 (607)
+|..|-+||+. .-++ |...||+|++|+.++. .++..|++.||. +.+..+..+|+-
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 57777788742 2244 5889999999998754 478889999874 344555556554
No 34
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=30.73 E-value=54 Score=29.39 Aligned_cols=60 Identities=27% Similarity=0.393 Sum_probs=40.8
Q ss_pred CCCCCcceeeeeecccchhhhhhhhCCccc----HHHHHHHHhcChHHHHHHHcCCCCchhHHHHHHhhhcc
Q 007352 252 PALHDEVWRLDRIAKDGALHKKLMKADIVT----VEDFLRILVRDPQKLRNILGSGMSNRMWENTVEHAKTC 319 (607)
Q Consensus 252 P~L~DeVwRLekIgKdG~~hkrL~~~gI~t----V~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktC 319 (607)
|+=+-+|--|.+||.. +-.+|..+|+.. .++|| ++.+|++-.+.-|. ..--++-+||++|
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 6667789999999984 668999999975 46776 45678765555431 1112356677776
No 35
>KOG4456 consensus Inner centromere protein (INCENP), C-terminal domain [Cell cycle control, cell division, chromosome partitioning]
Probab=29.39 E-value=1.2e+02 Score=29.39 Aligned_cols=47 Identities=28% Similarity=0.406 Sum_probs=35.2
Q ss_pred cccCCChhHH--HHHHHHHHhH------HHHHHHhhh-hHHHHHHHHHHHHHHHhc
Q 007352 26 KKSKLPALAS--VIVEALKMDS------LQRLCSSLE-PLLRRIVSEEVERALTKF 72 (607)
Q Consensus 26 kr~r~p~~~s--vi~ea~~~~s------~q~l~~~lE-p~lrrvV~EEve~~l~~~ 72 (607)
+|+-.|..|+ ||+||+.+++ |..|+.+|+ |=|.-|-.+=|-+.+.|-
T Consensus 62 pRkp~PtWar~~v~~eai~~qa~~pp~~v~~Ff~~~pkpdLkeIF~~~~p~~~KR~ 117 (134)
T KOG4456|consen 62 PRKPFPTWARDMVIVEAIEEQAKNPPFNVNTFFGSMPKPDLKEIFGEMVPSKKKRG 117 (134)
T ss_pred CCCCCchhhhhchHHHHHHHHhhCCchHHHHHhcccCCcCHHHHHHhhhhhhhhcc
Confidence 5666888884 9999999876 456788888 777777777666666653
No 36
>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=28.76 E-value=17 Score=30.50 Aligned_cols=27 Identities=30% Similarity=0.346 Sum_probs=18.6
Q ss_pred hhhhhhCCcccHHHHHHHHhcChHHHHHHH
Q 007352 271 HKKLMKADIVTVEDFLRILVRDPQKLRNIL 300 (607)
Q Consensus 271 hkrL~~~gI~tV~dFLrl~~~d~~kLR~iL 300 (607)
...|..+||+||+|++++ +++.|.++=
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 467899999999997664 667777774
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=27.16 E-value=30 Score=37.77 Aligned_cols=57 Identities=14% Similarity=0.058 Sum_probs=39.7
Q ss_pred ceeeeeecccchhhhhhhhCCcccHHHHHHHHh------------cChHHHHHHHcCCCCchhHHHHHHhhhccc
Q 007352 258 VWRLDRIAKDGALHKKLMKADIVTVEDFLRILV------------RDPQKLRNILGSGMSNRMWENTVEHAKTCV 320 (607)
Q Consensus 258 VwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~------------~d~~kLR~iLg~gmS~k~We~~v~HAktCv 320 (607)
|-.|-+||+... ++|.+.||.|++|+..+-+ .+...|++.||. +.+..+..+|+--+
T Consensus 174 v~~l~GiG~~~~--~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~----~~g~~l~~~a~G~d 242 (379)
T cd01703 174 LRKIPGIGYKTA--AKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGE----GIGQRIWKLLFGRD 242 (379)
T ss_pred ccccCCcCHHHH--HHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHCH----HHHHHHHHHHCCCC
Confidence 444447777654 8999999999999986541 117789999864 34556666776544
No 38
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=25.00 E-value=1.1e+02 Score=27.37 Aligned_cols=35 Identities=29% Similarity=0.624 Sum_probs=28.1
Q ss_pred hCCcccHHHHHHHHhcChHHHH---HHHcCCCCchhHHHHHHhhhc
Q 007352 276 KADIVTVEDFLRILVRDPQKLR---NILGSGMSNRMWENTVEHAKT 318 (607)
Q Consensus 276 ~~gI~tV~dFLrl~~~d~~kLR---~iLg~gmS~k~We~~v~HAkt 318 (607)
...| +++||+=++-.||.||- ++| .|+..++-||.
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 3467 99999999999997654 456 68888888875
No 39
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=23.69 E-value=35 Score=39.94 Aligned_cols=38 Identities=32% Similarity=0.316 Sum_probs=31.7
Q ss_pred CCCCCcceeeeeecccchhhhhhhhCCcccHHHHHHHHhc
Q 007352 252 PALHDEVWRLDRIAKDGALHKKLMKADIVTVEDFLRILVR 291 (607)
Q Consensus 252 P~L~DeVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~ 291 (607)
..|++.|-.|++||+.- .++|++.||+||.|.|..+=+
T Consensus 5 ~~~~~~~~~l~gvg~~~--~~~l~~lgi~t~~dll~~~P~ 42 (681)
T PRK10917 5 LLLDAPLTSLKGVGPKT--AEKLAKLGIHTVQDLLLHLPR 42 (681)
T ss_pred ccccCChhhcCCCCHHH--HHHHHHcCCCCHHHHhhcCCC
Confidence 45778999999998754 488999999999999988654
No 40
>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=23.18 E-value=94 Score=26.30 Aligned_cols=24 Identities=46% Similarity=0.617 Sum_probs=15.6
Q ss_pred HHHHHHHHHhHHHHHHHhhhhHHHHHHH
Q 007352 35 SVIVEALKMDSLQRLCSSLEPLLRRIVS 62 (607)
Q Consensus 35 svi~ea~~~~s~q~l~~~lEp~lrrvV~ 62 (607)
||-+.=+++- |.-.|||+|||...
T Consensus 30 sVsrkPLr~l----La~aLEPllkr~~~ 53 (59)
T TIGR02979 30 SVARRPLKML----LAIALEPMLKRAAN 53 (59)
T ss_pred HHhhccHHHH----HHHHHHHHHHHHHH
Confidence 4444444441 56689999999753
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=22.70 E-value=1.5e+02 Score=29.72 Aligned_cols=62 Identities=26% Similarity=0.324 Sum_probs=36.6
Q ss_pred CcceeeeEEEE---ec--cce--eeccCceeecCCcccccccceEEEEecCCC-------CCCcceeeeeecceEeeeC
Q 007352 177 RPILTGDLLVT---LK--EGF--GTLGDLTFTDNSSWIRSRKFRLGLKVSPGY-------CDGIRVREAKTEGFAVKDH 241 (607)
Q Consensus 177 ~pLL~Gdl~v~---L~--~Gv--a~l~di~FTDnSsw~rSrKFRLgaRv~~~~-------~~g~RI~EAvsE~FvVkDh 241 (607)
...|.|.+... |+ +|. |.. ..|.|=|-. .-+.|||-.++..=. ....-+-|+.|+||.|-..
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 246899988876422 1235689999999999653
No 42
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=22.30 E-value=2.6e+02 Score=26.81 Aligned_cols=40 Identities=28% Similarity=0.453 Sum_probs=31.5
Q ss_pred chhhhhhhhCCcccHHHHHHHHhcCh----HHHHHHHcCCCCch
Q 007352 268 GALHKKLMKADIVTVEDFLRILVRDP----QKLRNILGSGMSNR 307 (607)
Q Consensus 268 G~~hkrL~~~gI~tV~dFLrl~~~d~----~kLR~iLg~gmS~k 307 (607)
.+|+.-|+.+|=.||+|.-..++++. ..|++++-.||=.+
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 57888888999999999999999995 46777765555443
No 43
>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=21.84 E-value=98 Score=26.75 Aligned_cols=15 Identities=53% Similarity=0.789 Sum_probs=11.8
Q ss_pred HHHhhhhHHHHHHHH
Q 007352 49 LCSSLEPLLRRIVSE 63 (607)
Q Consensus 49 l~~~lEp~lrrvV~E 63 (607)
|.-.|||+|||.++-
T Consensus 45 La~~LEPllrr~~~~ 59 (66)
T PF09584_consen 45 LALALEPLLRRGLNK 59 (66)
T ss_pred HHHHHHHHHHHHHHH
Confidence 555899999998653
No 44
>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=21.59 E-value=55 Score=24.93 Aligned_cols=18 Identities=22% Similarity=0.578 Sum_probs=15.1
Q ss_pred eeeccCceeecCCccccc
Q 007352 192 FGTLGDLTFTDNSSWIRS 209 (607)
Q Consensus 192 va~l~di~FTDnSsw~rS 209 (607)
-..|..+.|-|++.|++.
T Consensus 24 ~~~Ie~i~FaDGt~w~~~ 41 (43)
T PF06594_consen 24 SYRIEQIEFADGTVWTRA 41 (43)
T ss_pred CCcEeEEEEcCCCEecHH
Confidence 567889999999999753
Done!