Query 006596
Match_columns 639
No_of_seqs 147 out of 172
Neff 3.9
Searched_HMMs 46136
Date Thu Mar 28 11:42:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006596.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006596hhsearch_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 3E-121 6E-126 936.2 29.1 299 97-398 1-299 (299)
2 TIGR02239 recomb_RAD51 DNA rep 85.7 0.88 1.9E-05 48.4 4.1 50 273-327 12-61 (316)
3 TIGR02238 recomb_DMC1 meiotic 83.8 1.1 2.4E-05 47.7 3.9 50 273-327 12-61 (313)
4 PLN03186 DNA repair protein RA 83.5 1.2 2.6E-05 48.3 4.0 62 261-327 27-88 (342)
5 PRK04301 radA DNA repair and r 77.2 1.6 3.4E-05 46.0 2.3 57 261-324 7-63 (317)
6 PLN03187 meiotic recombination 76.3 2.1 4.6E-05 46.4 3.1 61 261-326 30-90 (344)
7 PTZ00035 Rad51 protein; Provis 68.8 5.3 0.00012 43.1 3.9 61 261-326 22-82 (337)
8 PRK03609 umuC DNA polymerase V 64.8 4.7 0.0001 44.2 2.6 52 261-322 180-231 (422)
9 PF14229 DUF4332: Domain of un 63.9 9 0.00019 35.7 3.9 53 273-327 6-60 (122)
10 PF14520 HHH_5: Helix-hairpin- 63.4 4.3 9.3E-05 32.9 1.5 51 265-322 10-60 (60)
11 TIGR02236 recomb_radA DNA repa 61.4 5.5 0.00012 41.5 2.3 52 265-323 4-55 (310)
12 PRK02406 DNA polymerase IV; Va 61.2 6.6 0.00014 41.6 2.8 52 261-322 169-220 (343)
13 PF10691 DUF2497: Protein of u 53.9 29 0.00062 30.4 5.0 40 34-74 33-73 (73)
14 PRK03352 DNA polymerase IV; Va 50.1 6.5 0.00014 41.7 0.6 41 261-306 178-218 (346)
15 PRK03858 DNA polymerase IV; Va 48.2 8.1 0.00018 41.7 1.0 41 261-306 174-214 (396)
16 PRK03348 DNA polymerase IV; Pr 48.1 9.3 0.0002 42.7 1.5 48 261-313 181-228 (454)
17 PRK01172 ski2-like helicase; P 47.2 18 0.00038 42.1 3.6 51 265-322 617-667 (674)
18 PRK14133 DNA polymerase IV; Pr 47.2 16 0.00035 38.8 3.1 51 261-321 174-224 (347)
19 PRK02794 DNA polymerase IV; Pr 45.5 15 0.00032 40.3 2.5 55 261-325 210-264 (419)
20 cd01700 PolY_Pol_V_umuC umuC s 44.4 15 0.00032 39.0 2.2 51 261-321 177-227 (344)
21 cd03586 PolY_Pol_IV_kappa DNA 42.1 20 0.00044 37.5 2.8 52 261-322 172-223 (334)
22 PRK03103 DNA polymerase IV; Re 38.4 22 0.00048 38.7 2.5 52 261-322 182-233 (409)
23 PRK01810 DNA polymerase IV; Va 38.4 22 0.00048 38.7 2.5 51 261-321 180-230 (407)
24 COG3743 Uncharacterized conser 36.0 38 0.00083 32.9 3.3 59 260-322 67-126 (133)
25 PRK15457 ethanolamine utilizat 35.1 92 0.002 32.8 6.1 72 56-129 90-162 (233)
26 PF04994 TfoX_C: TfoX C-termin 34.9 14 0.0003 32.4 0.2 73 262-374 5-78 (81)
27 cd00424 PolY Y-family of DNA p 34.9 27 0.00059 37.1 2.4 56 261-326 174-230 (343)
28 KOG2856 Adaptor protein PACSIN 32.5 76 0.0017 35.7 5.3 25 379-403 285-309 (472)
29 cd01701 PolY_Rev1 DNA polymera 31.6 21 0.00045 39.2 0.9 54 261-321 223-276 (404)
30 PRK01216 DNA polymerase IV; Va 31.4 20 0.00044 38.9 0.8 51 261-320 179-229 (351)
31 PF02889 Sec63: Sec63 Brl doma 30.2 36 0.00078 35.2 2.4 55 261-322 149-203 (314)
32 cd07978 TAF13 The TATA Binding 28.6 89 0.0019 28.2 4.3 35 280-322 52-89 (92)
33 cd01702 PolY_Pol_eta DNA Polym 28.5 27 0.00058 38.1 1.1 55 261-322 183-238 (359)
34 KOG4233 DNA-bridging protein B 27.2 67 0.0014 29.1 3.1 60 256-323 15-78 (90)
35 PF14229 DUF4332: Domain of un 26.9 37 0.00079 31.7 1.6 39 262-305 55-93 (122)
36 PF03118 RNA_pol_A_CTD: Bacter 26.0 33 0.00072 28.9 1.0 36 275-315 24-59 (66)
37 cd01703 PolY_Pol_iota DNA Poly 25.6 33 0.00072 37.7 1.2 57 262-324 174-242 (379)
38 COG4766 EutQ Ethanolamine util 24.2 2.5E+02 0.0053 28.4 6.6 94 38-132 12-108 (176)
39 TIGR02979 phageshock_pspD phag 22.2 94 0.002 26.5 2.9 24 38-65 30-53 (59)
40 COG3827 Uncharacterized protei 21.6 1.6E+02 0.0035 30.9 5.1 41 33-74 187-228 (231)
41 PRK10917 ATP-dependent DNA hel 20.5 38 0.00082 39.9 0.4 37 256-294 5-41 (681)
42 PF06594 HCBP_related: Haemoly 20.4 58 0.0013 25.0 1.3 18 196-213 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=2.7e-121 Score=936.25 Aligned_cols=299 Identities=70% Similarity=1.170 Sum_probs=295.2
Q ss_pred ceEEEeccCCCCccccCCcccccCCCceEEEEEeCCCCceeccCCCccceEEEEEeeCCCCCCCCCCCCHHHHhhccccc
Q 006596 97 NLQLYFRSRLSLPLFTGGKVEGEQGAAIHVVLVDANTGHVVTSGPEASVKLDIVVLEGDFNNEDDDGWTQEEFESHVVKE 176 (639)
Q Consensus 97 ~~~L~F~n~l~~pifTg~kI~ae~g~~I~V~LvD~~tg~iVtsGplSs~KvEIvVLdGDF~~~~~e~WT~eEF~~~IVk~ 176 (639)
+|||+|+|+|++|||||++|+|+||+||+|+|+|++|+ |++||+|++|||||||||||+++++++||+|||++|||++
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 CCCCcccccceEEEEecCceeeccCceeecCCCcccccccEEEEEeecCCCCccceeeecccceEeeecCccccccCCCC
Q 006596 177 REGKRPLLTGDLQVTLKEGVGTLGDLTFTDNSSWIRSRKFRLGLKVASGYCEGIRIREAKTEAFTVKDHRGELYKKHYPP 256 (639)
Q Consensus 177 ReGk~pLL~Gdl~v~L~~Gva~l~di~FTDnSsw~rSrKFRLgaRvv~~~~~g~RI~EAvsE~FvVkDhRge~ykKh~pP 256 (639)
|+||+|||+|+|+|+|+||+|+|+||+|||||||+|||||||||||+++++.|+|||||+||||+|||||||+|||||||
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 CCCCcceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcccccCCceEEEecCC
Q 006596 257 ALNDDVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLSGKLYVYYPED 336 (639)
Q Consensus 257 ~L~DeVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~k~y~y~~~~ 336 (639)
+|+|||||||||||||+|||+|+.+||+||+|||+++++||++||+|||+|||++||++||+|||||++++++|+|| .+
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 006596 337 SRNVGVVFNNIYELNGLISGEQYFPADALPESQKVYVDSQVKKAYDNWNQVVEYDGKSLLSL 398 (639)
Q Consensus 337 ~~nvgl~FN~i~~lVG~~~~g~y~s~d~L~~~qk~~V~~Lk~~AY~nw~~~~e~D~~~l~n~ 398 (639)
++|++|+|||||+||||+|+|+|++.|+||+.||++|++||++||+||++|++||++|++||
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=85.67 E-value=0.88 Score=48.44 Aligned_cols=50 Identities=28% Similarity=0.345 Sum_probs=43.6
Q ss_pred hhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcccccCC
Q 006596 273 SFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLSG 327 (639)
Q Consensus 273 ~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~ 327 (639)
.--++|+++||.||+||+. .++..|.+++ |+|...++.+..||.+|....
T Consensus 12 ~~~~~l~~~g~~t~~~~~~---~~~~~L~~i~--~ls~~~~~~~~~~~~~~~~~~ 61 (316)
T TIGR02239 12 ADIKKLQEAGLHTVESVAY---APKKQLLEIK--GISEAKADKILAEAAKLVPMG 61 (316)
T ss_pred HHHHHHHHcCCCcHHHHHh---CCHHHHHHHh--CCCHHHHHHHHHHHHHhcccc
Confidence 3568999999999999876 4899999998 799999999999999996543
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=83.78 E-value=1.1 Score=47.69 Aligned_cols=50 Identities=24% Similarity=0.339 Sum_probs=43.3
Q ss_pred hhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcccccCC
Q 006596 273 SFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLSG 327 (639)
Q Consensus 273 ~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~ 327 (639)
.--++|+++||+||+||+. .++..|.++. |+|...++.+++.|+.+...+
T Consensus 12 ~~~~~L~~~g~~t~~~~~~---~~~~~L~~~~--gls~~~~~~i~~~~~~~~~~~ 61 (313)
T TIGR02238 12 ADIKKLKSAGICTVNGVIM---TTRRALCKIK--GLSEAKVDKIKEAASKIINPG 61 (313)
T ss_pred HHHHHHHHcCCCcHHHHHh---CCHHHHHHhc--CCCHHHHHHHHHHHHhhhccc
Confidence 4568999999999999876 4889999997 799999999999999886553
No 4
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=83.49 E-value=1.2 Score=48.25 Aligned_cols=62 Identities=29% Similarity=0.338 Sum_probs=48.8
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcccccCC
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLSG 327 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~ 327 (639)
++-+|+.-|-.-.--++|+++||.||+||+.+ ++..|.+++ |+|....+.+++||.+|....
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 34455443333456789999999999998764 788999998 799999999999998886544
No 5
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=77.24 E-value=1.6 Score=45.99 Aligned_cols=57 Identities=21% Similarity=0.362 Sum_probs=45.8
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcccc
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCV 324 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCv 324 (639)
++-.|.+||+ ...++|.++||+|++|++. .|+..|.+++ |++.+.++.+++-|+.|+
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 3445556664 4569999999999999865 5999999998 678899999999888654
No 6
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=76.29 E-value=2.1 Score=46.44 Aligned_cols=61 Identities=20% Similarity=0.337 Sum_probs=47.9
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcccccC
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLS 326 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 326 (639)
++..|+.-|-.=.--++|.++||+||+|++. .++..|-++. |+|....+.+++.|+..+..
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 3566655344445679999999999999876 4788899986 79999999999999877643
No 7
>PTZ00035 Rad51 protein; Provisional
Probab=68.80 E-value=5.3 Score=43.06 Aligned_cols=61 Identities=26% Similarity=0.332 Sum_probs=47.5
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcccccC
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLS 326 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 326 (639)
++-.|+.-|-.=.--++|.++||+||+||+. .++..|-++. |+|...=+.+++.|+.++..
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 4556654333334668999999999999876 5888999997 78999999999999887643
No 8
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=64.84 E-value=4.7 Score=44.21 Aligned_cols=52 Identities=19% Similarity=0.260 Sum_probs=41.5
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 322 (639)
+|..|-+||+. ..++|.+.||+|++|+.++ ++..|++.||. .+..+..||.-
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 5599999999999999885 88999999973 57778888753
No 9
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=63.94 E-value=9 Score=35.70 Aligned_cols=53 Identities=23% Similarity=0.266 Sum_probs=38.9
Q ss_pred hhhhhhhhcCCccHHHHHHHhhcChHH--HHHHHccCCChhhHHHHHHhhcccccCC
Q 006596 273 SFHKRLNNAGIFSVEDFLRLVVRDPQK--LRSILGSGMSNKMWEALLDHAKTCVLSG 327 (639)
Q Consensus 273 ~~hkrL~~~gI~tV~dFLrl~~~d~~k--LR~iLg~gmS~k~We~~v~HAktCvl~~ 327 (639)
...++|+..||+|++|||..-.....+ |-+-+ |++.+-=...+.+|.=|...+
T Consensus 6 ~~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~--~i~~~~l~~w~~~AdL~ri~g 60 (122)
T PF14229_consen 6 KEAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKL--GISERNLLKWVNQADLMRIPG 60 (122)
T ss_pred HHHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhc--CCCHHHHHHHHhHHHhhhcCC
Confidence 355899999999999999987665544 55555 678877777777777665444
No 10
>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=63.43 E-value=4.3 Score=32.87 Aligned_cols=51 Identities=31% Similarity=0.540 Sum_probs=40.3
Q ss_pred eeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006596 265 LEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (639)
Q Consensus 265 LekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 322 (639)
+.+||+. ..++|.+.||.|++|+.. .+++.|.++= |++.+.=+.+++.|+.
T Consensus 10 I~Gig~~--~a~~L~~~G~~t~~~l~~---a~~~~L~~i~--Gig~~~a~~i~~~~~~ 60 (60)
T PF14520_consen 10 IPGIGPK--RAEKLYEAGIKTLEDLAN---ADPEELAEIP--GIGEKTAEKIIEAARE 60 (60)
T ss_dssp STTCHHH--HHHHHHHTTCSSHHHHHT---SHHHHHHTST--TSSHHHHHHHHHHHHH
T ss_pred CCCCCHH--HHHHHHhcCCCcHHHHHc---CCHHHHhcCC--CCCHHHHHHHHHHHhC
Confidence 4556654 448899999999998866 4788899974 7899999999988863
No 11
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=61.45 E-value=5.5 Score=41.54 Aligned_cols=52 Identities=23% Similarity=0.386 Sum_probs=39.8
Q ss_pred eeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhccc
Q 006596 265 LEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTC 323 (639)
Q Consensus 265 LekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktC 323 (639)
|.+||+ ...++|.++||.|++|++. .|++.|.+++ |++.+..+.+.+-|+.|
T Consensus 4 i~gig~--~~~~~L~~~Gi~ti~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~~~~~ 55 (310)
T TIGR02236 4 LPGVGP--ATAEKLREAGYDTFEAIAV---ASPKELSEIA--GISEGTAAKIIQAARKA 55 (310)
T ss_pred cCCCCH--HHHHHHHHcCCCCHHHHHc---CCHHHHHhcc--CCCHHHHHHHHHHHHHH
Confidence 445554 3558999999999999877 4899999998 56777777777777643
No 12
>PRK02406 DNA polymerase IV; Validated
Probab=61.20 E-value=6.6 Score=41.63 Aligned_cols=52 Identities=23% Similarity=0.410 Sum_probs=40.1
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 322 (639)
+|..|-+||+ ..-++|...||+|++|+.++ +...|++.||. .+..+..||.-
T Consensus 169 pi~~l~giG~--~~~~~L~~~Gi~ti~dl~~l---~~~~L~~~fG~-----~~~~l~~~a~G 220 (343)
T PRK02406 169 PVEKIPGVGK--VTAEKLHALGIYTCADLQKY---DLAELIRHFGK-----FGRRLYERARG 220 (343)
T ss_pred CcchhcCCCH--HHHHHHHHcCCCcHHHHHhC---CHHHHHHHHhH-----HHHHHHHHhCC
Confidence 5666767775 44588999999999999885 78899999973 46666667653
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=53.87 E-value=29 Score=30.38 Aligned_cols=40 Identities=30% Similarity=0.466 Sum_probs=30.5
Q ss_pred cchHHHHHHHHHHhhHHH-HHHhhhhHHHHHhHHHHHHHHHh
Q 006596 34 PALASVIVEALKVDSLQK-LCSSLEPILRRVVSEEVERALAK 74 (639)
Q Consensus 34 p~~~svi~ea~~~~s~q~-~~~~lEp~lrrvV~EEve~~l~~ 74 (639)
.++-.+++|+|+-- |+. |=..|=.++.|+|++||+|..+|
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 46777888888764 433 55578889999999999998754
No 14
>PRK03352 DNA polymerase IV; Validated
Probab=50.14 E-value=6.5 Score=41.74 Aligned_cols=41 Identities=32% Similarity=0.424 Sum_probs=33.4
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcc
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGS 306 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~ 306 (639)
+|..|-+||+. ..++|...||+|++||+++ ++..|++.||.
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 56666677774 4578999999999999885 78899999975
No 15
>PRK03858 DNA polymerase IV; Validated
Probab=48.17 E-value=8.1 Score=41.70 Aligned_cols=41 Identities=32% Similarity=0.359 Sum_probs=33.2
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcc
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGS 306 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~ 306 (639)
+|..|-+||+. .-++|.+.||+|++|+.+ .++..|++.||.
T Consensus 174 pl~~l~Gig~~--~~~~L~~~Gi~t~~dl~~---l~~~~L~~~fG~ 214 (396)
T PRK03858 174 PVRRLWGVGPV--TAAKLRAHGITTVGDVAE---LPESALVSLLGP 214 (396)
T ss_pred ChhhcCCCCHH--HHHHHHHhCCCcHHHHhc---CCHHHHHHHhCc
Confidence 45556677774 458999999999999986 588899999975
No 16
>PRK03348 DNA polymerase IV; Provisional
Probab=48.07 E-value=9.3 Score=42.72 Aligned_cols=48 Identities=25% Similarity=0.394 Sum_probs=37.1
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhH
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMW 313 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~W 313 (639)
+|.+|-+||+. .-++|...||+|++||.++ +...|++.||..+-..-|
T Consensus 181 Pv~~L~GIG~~--t~~~L~~lGI~TigDLa~l---~~~~L~~~fG~~~g~~L~ 228 (454)
T PRK03348 181 PVRRLWGIGPV--TEEKLHRLGIETIGDLAAL---SEAEVANLLGATVGPALH 228 (454)
T ss_pred CccccCCCCHH--HHHHHHHcCCccHHHHhcC---CHHHHHHHHCHHHHHHHH
Confidence 67888888875 4488999999999999874 788999999743333333
No 17
>PRK01172 ski2-like helicase; Provisional
Probab=47.19 E-value=18 Score=42.09 Aligned_cols=51 Identities=29% Similarity=0.616 Sum_probs=41.9
Q ss_pred eeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006596 265 LEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (639)
Q Consensus 265 LekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 322 (639)
|.+|++ ...++|.++||.||.|+.. .|+++|-+|+ |++++.=+.++++|+.
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 4679999999999999877 7888898898 6899999999999875
No 18
>PRK14133 DNA polymerase IV; Provisional
Probab=47.16 E-value=16 Score=38.83 Aligned_cols=51 Identities=29% Similarity=0.543 Sum_probs=39.3
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhc
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 321 (639)
+|..|-+||+. .-++|...||+|++|++++ +...|++.|| +.|..+.++|.
T Consensus 174 pv~~l~gig~~--~~~~L~~~Gi~ti~dl~~l---~~~~L~~rfG-----~~g~~l~~~a~ 224 (347)
T PRK14133 174 PISKVHGIGKK--SVEKLNNIGIYTIEDLLKL---SREFLIEYFG-----KFGVEIYERIR 224 (347)
T ss_pred CccccCCCCHH--HHHHHHHcCCccHHHHhhC---CHHHHHHHHh-----HHHHHHHHHhC
Confidence 46666667664 4478999999999999874 7888999996 35777777775
No 19
>PRK02794 DNA polymerase IV; Provisional
Probab=45.50 E-value=15 Score=40.34 Aligned_cols=55 Identities=27% Similarity=0.230 Sum_probs=42.5
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhccccc
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVL 325 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 325 (639)
+|..|-+||+ ..-++|...||+|++|+.++ +...|++.||. .|..+..+|.--+.
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 55689999999999998874 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=44.42 E-value=15 Score=39.02 Aligned_cols=51 Identities=31% Similarity=0.433 Sum_probs=39.1
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhc
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 321 (639)
+|..|-+||+. .-++|...||+|++|++++ +...|.+.||. .|.....+|+
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 45556667764 4578999999999999885 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=42.10 E-value=20 Score=37.45 Aligned_cols=52 Identities=27% Similarity=0.467 Sum_probs=40.4
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 322 (639)
+|..|-+||+ ...++|...||+|++|+.++ ++..|++.+| +.|..+..||+-
T Consensus 172 pl~~l~gig~--~~~~~L~~~Gi~ti~dl~~~---~~~~L~~~~g-----~~~~~l~~~~~G 223 (334)
T cd03586 172 PVRKIPGVGK--VTAEKLKELGIKTIGDLAKL---DVELLKKLFG-----KSGRRLYELARG 223 (334)
T ss_pred CchhhCCcCH--HHHHHHHHcCCcCHHHHHcC---CHHHHHHHHh-----HHHHHHHHHhCC
Confidence 4555666665 45589999999999999874 7888999885 578888888864
No 22
>PRK03103 DNA polymerase IV; Reviewed
Probab=38.45 E-value=22 Score=38.70 Aligned_cols=52 Identities=23% Similarity=0.304 Sum_probs=40.0
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 322 (639)
+|..|-+||+. .-++|...||+|++||.+ .++..|++.||. .|..+.++|.-
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 46666677764 558899999999999876 478899999963 46777777754
No 23
>PRK01810 DNA polymerase IV; Validated
Probab=38.41 E-value=22 Score=38.70 Aligned_cols=51 Identities=27% Similarity=0.374 Sum_probs=38.7
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhc
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 321 (639)
+|..|-+||+. .-++|...||+|++|+.+ .+...|++.||. .+..+.+||.
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 45555567764 448899999999999877 478899999964 4666777776
No 24
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=36.00 E-value=38 Score=32.85 Aligned_cols=59 Identities=25% Similarity=0.393 Sum_probs=43.1
Q ss_pred CcceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHH-HHHhhcc
Q 006596 260 DDVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEA-LLDHAKT 322 (639)
Q Consensus 260 DeVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~-~v~HAkt 322 (639)
|+.-+|.+||. ++-+.|+..||+|-.+.-.+-..|-..+-..| +..-+.|.. -|+.|+.
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 57799999999997765554444444555555 567777765 6776664
No 25
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=35.14 E-value=92 Score=32.85 Aligned_cols=72 Identities=14% Similarity=0.236 Sum_probs=34.6
Q ss_pred hhhHHHHHhHHHHHHHHHhhCCCcccCCCCCCCCccCCCCCceEE-EeccCCCCccccCCcccccCCCceEEEEE
Q 006596 56 LEPILRRVVSEEVERALAKLGPARLNNGRASPKRIEGPDGRNLQL-YFRSRLSLPLFTGGKVEGEQGAAIHVVLV 129 (639)
Q Consensus 56 lEp~lrrvV~EEve~~l~~~~~~~~~~~rs~~~~i~~~~~~~~~L-~F~n~l~~pifTg~kI~ae~g~~I~V~Lv 129 (639)
||-++|+|+.|++-....-..+.. . .-..|.+|--..++.+++ +|....+..+|+.+-+..++|..+-..++
T Consensus 90 i~~lv~~v~~e~~~~~~~~~~~~~-~-~~~~~~Gi~vVrg~svk~~~fdg~~~~~v~~~d~~~~~d~s~m~aGf~ 162 (233)
T PRK15457 90 VAQLMEKVMKEKQSLEQGAMQPSF-K-SVTGKGGIKVIDGSSVKFGRFDGAEPHCVGLTDLVTGDDGSSMAAGFM 162 (233)
T ss_pred HHHHHHHHHHHHhcccccccCCCc-c-ceeCCCceEEEECCeEEEeecCCCCcccEEeeeeeccCCCCceeeEEE
Confidence 677999999998643322100110 0 001122333333445555 55444445555555555555555554443
No 26
>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=34.93 E-value=14 Score=32.43 Aligned_cols=73 Identities=30% Similarity=0.489 Sum_probs=42.2
Q ss_pred ceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcCh-HHHHHHHccCCChhhHHHHHHhhcccccCCceEEEecCCCcce
Q 006596 262 VWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDP-QKLRSILGSGMSNKMWEALLDHAKTCVLSGKLYVYYPEDSRNV 340 (639)
Q Consensus 262 VwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~-~kLR~iLg~gmS~k~We~~v~HAktCvl~~k~y~y~~~~~~nv 340 (639)
+..|..||.. .-+.|.+.||+||+||..+=.+.. -+|++. | .
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 4445566653 448899999999999988654432 344443 1 2
Q ss_pred EEEEccccceeeeecCCeeecCCCCChhhHHHHH
Q 006596 341 GVVFNNIYELNGLISGEQYFPADALPESQKVYVD 374 (639)
Q Consensus 341 gl~FN~i~~lVG~~~~g~y~s~d~L~~~qk~~V~ 374 (639)
.+-+|-+|.|.||+-|-++ ..|++.+|....
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 2567788999999887543 456666665543
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=34.88 E-value=27 Score=37.13 Aligned_cols=56 Identities=25% Similarity=0.140 Sum_probs=41.2
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcC-hHHHHHHHccCCChhhHHHHHHhhcccccC
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRD-PQKLRSILGSGMSNKMWEALLDHAKTCVLS 326 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d-~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 326 (639)
+|..|-+||+. .-++|...||+|++|++++ + ...|+..+| +.+..+.++|+--+..
T Consensus 174 pi~~l~giG~~--~~~~L~~~Gi~ti~dl~~~---~~~~~l~~~fg-----~~~~~l~~~a~G~d~~ 230 (343)
T cd00424 174 PLTDLPGIGAV--TAKRLEAVGINPIGDLLAA---SPDALLALWGG-----VSGERLWYALRGIDDE 230 (343)
T ss_pred ChhhcCCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHhh-----HHHHHHHHHhCCcCCC
Confidence 46666677774 4588999999999998764 6 566777775 4677888888755433
No 28
>KOG2856 consensus Adaptor protein PACSIN [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=32.49 E-value=76 Score=35.71 Aligned_cols=25 Identities=16% Similarity=0.292 Sum_probs=17.2
Q ss_pred HHHhccccccccCCccccccccccc
Q 006596 379 KAYDNWNQVVEYDGKSLLSLKQNKR 403 (639)
Q Consensus 379 ~AY~nw~~~~e~D~~~l~n~~~~kk 403 (639)
.+.-||-+++||.-..-.++....|
T Consensus 285 ~mamnWPqF~E~s~d~~rtia~r~k 309 (472)
T KOG2856|consen 285 GMAMNWPQFEEWSPDLQRTIAKREK 309 (472)
T ss_pred ccccCCchHhhcChhhhhHHHhccC
Confidence 3567888888888777666654333
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=31.63 E-value=21 Score=39.23 Aligned_cols=54 Identities=22% Similarity=0.233 Sum_probs=39.6
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhc
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 321 (639)
+|..|-+||+. .-++|...||.|++|+..+- .++..|++.||. +.+..+..+|.
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 56999999999999998761 127899999974 34555555554
No 30
>PRK01216 DNA polymerase IV; Validated
Probab=31.45 E-value=20 Score=38.88 Aligned_cols=51 Identities=25% Similarity=0.397 Sum_probs=38.4
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhh
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHA 320 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HA 320 (639)
+|..|-+||+. -.++|...||+|++|+.++ +...|++.||. ..+..+-.+|
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 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=30.17 E-value=36 Score=35.20 Aligned_cols=55 Identities=24% Similarity=0.445 Sum_probs=37.4
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006596 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (639)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 322 (639)
...-|.+|+.+.+ ++|...||.|+++|++ .++.+|..+| +......+.+.+.|..
T Consensus 149 ~L~Qlp~i~~~~~--~~l~~~~i~~l~~l~~---~~~~e~~~ll--~~~~~~~~~i~~~~~~ 203 (314)
T PF02889_consen 149 PLLQLPHIGEESL--KKLEKRGIKTLQDLRD---LSPEELEELL--NRNPPFGKEILEVASR 203 (314)
T ss_dssp GGGGSTT--HHHH--HHHHHTT--SHHHHHH---S-HHHHHHHH---S-HHHHHHHHHHHCC
T ss_pred hhhcCCCCCHHHH--HHHhccCCCcHHHHhh---CCHHHHHHHH--hhhhhhHHHHHHHHHH
Confidence 4455668887654 8899999999999885 4899999999 4566778888887763
No 32
>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=28.61 E-value=89 Score=28.22 Aligned_cols=35 Identities=34% Similarity=0.585 Sum_probs=28.1
Q ss_pred hcCCccHHHHHHHhhcChHHH---HHHHccCCChhhHHHHHHhhcc
Q 006596 280 NAGIFSVEDFLRLVVRDPQKL---RSILGSGMSNKMWEALLDHAKT 322 (639)
Q Consensus 280 ~~gI~tV~dFLrl~~~d~~kL---R~iLg~gmS~k~We~~v~HAkt 322 (639)
...| +++||+=++-.||.|| +++| .|+..++-||.
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 9999999999999655 4556 68889988875
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=28.49 E-value=27 Score=38.05 Aligned_cols=55 Identities=15% Similarity=0.236 Sum_probs=38.1
Q ss_pred cceeeeeeccCchhhhh-hhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006596 261 DVWRLEKIGKDGSFHKR-LNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (639)
Q Consensus 261 eVwRLekIgKdG~~hkr-L~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 322 (639)
+|..|-+||+ ..-++ |...||+|++|+.++. .++..|++.||. +.++.+..+|+-
T Consensus 183 pv~~l~GiG~--~~~~~ll~~~Gi~ti~dl~~~~-~~~~~L~~~fG~----~~g~~l~~~a~G 238 (359)
T cd01702 183 PITSIRGLGG--KLGEEIIDLLGLPTEGDVAGFR-SSESDLQEHFGE----KLGEWLYNLLRG 238 (359)
T ss_pred cHHHhCCcCH--HHHHHHHHHcCCcCHHHHHhcc-CCHHHHHHHHHH----HHHHHHHHHhCC
Confidence 4677777774 22245 5889999999998754 478889999874 344555555554
No 34
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=27.21 E-value=67 Score=29.07 Aligned_cols=60 Identities=28% Similarity=0.422 Sum_probs=40.3
Q ss_pred CCCCCcceeeeeeccCchhhhhhhhcCCcc----HHHHHHHhhcChHHHHHHHccCCChhhHHHHHHhhccc
Q 006596 256 PALNDDVWRLEKIGKDGSFHKRLNNAGIFS----VEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTC 323 (639)
Q Consensus 256 P~L~DeVwRLekIgKdG~~hkrL~~~gI~t----V~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktC 323 (639)
|+=+-+|--|.+||.. +-.+|..+|+.. .++|| ++.+|++-.+.-|. ..--++-+||++|
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 6667789999999874 668999999975 36676 45678765555431 1122355677766
No 35
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=26.87 E-value=37 Score=31.70 Aligned_cols=39 Identities=36% Similarity=0.658 Sum_probs=30.1
Q ss_pred ceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHc
Q 006596 262 VWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILG 305 (639)
Q Consensus 262 VwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg 305 (639)
..|+.+|+. .|..-|..+||.||+++ ...+|++|.+.++
T Consensus 55 L~ri~gi~~--~~a~LL~~AGv~Tv~~L---A~~~p~~L~~~l~ 93 (122)
T PF14229_consen 55 LMRIPGIGP--QYAELLEHAGVDTVEEL---AQRNPQNLHQKLG 93 (122)
T ss_pred hhhcCCCCH--HHHHHHHHhCcCcHHHH---HhCCHHHHHHHHH
Confidence 446666664 57788999999999987 4578988888763
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=26.01 E-value=33 Score=28.94 Aligned_cols=36 Identities=28% Similarity=0.405 Sum_probs=22.2
Q ss_pred hhhhhhcCCccHHHHHHHhhcChHHHHHHHccCCChhhHHH
Q 006596 275 HKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEA 315 (639)
Q Consensus 275 hkrL~~~gI~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~ 315 (639)
...|..+||+||+|++++ +++.|.++= |+..+.-+.
T Consensus 24 ~n~L~~~~I~tv~dL~~~---s~~~L~~i~--n~G~ksl~E 59 (66)
T PF03118_consen 24 YNCLKRAGIHTVGDLVKY---SEEDLLKIK--NFGKKSLEE 59 (66)
T ss_dssp HHHHHCTT--BHHHHHCS----HHHHHTST--TSHHHHHHH
T ss_pred HHHHHHhCCcCHHHHHhC---CHHHHHhCC--CCCHhHHHH
Confidence 357889999999997664 667777774 344444443
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=25.62 E-value=33 Score=37.69 Aligned_cols=57 Identities=16% Similarity=0.151 Sum_probs=39.4
Q ss_pred ceeeeeeccCchhhhhhhhcCCccHHHHHHHhh------------cChHHHHHHHccCCChhhHHHHHHhhcccc
Q 006596 262 VWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVV------------RDPQKLRSILGSGMSNKMWEALLDHAKTCV 324 (639)
Q Consensus 262 VwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~------------~d~~kLR~iLg~gmS~k~We~~v~HAktCv 324 (639)
|-.|-+||+.. -++|.+.||.|++|+..+-+ .+...|++.||. +.+..+.++|+--+
T Consensus 174 v~~l~GiG~~~--~~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~----~~g~~l~~~a~G~d 242 (379)
T cd01703 174 LRKIPGIGYKT--AAKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGE----GIGQRIWKLLFGRD 242 (379)
T ss_pred ccccCCcCHHH--HHHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHCH----HHHHHHHHHHCCCC
Confidence 44444677654 48999999999999986541 117789999864 34556666776544
No 38
>COG4766 EutQ Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=24.15 E-value=2.5e+02 Score=28.41 Aligned_cols=94 Identities=15% Similarity=0.233 Sum_probs=60.9
Q ss_pred HHHHHHHHHh-hHHHHHHh-hhhHHHHHhHHHHHHHHHhhCCCcccC-CCCCCCCccCCCCCceEEEeccCCCCccccCC
Q 006596 38 SVIVEALKVD-SLQKLCSS-LEPILRRVVSEEVERALAKLGPARLNN-GRASPKRIEGPDGRNLQLYFRSRLSLPLFTGG 114 (639)
Q Consensus 38 svi~ea~~~~-s~q~~~~~-lEp~lrrvV~EEve~~l~~~~~~~~~~-~rs~~~~i~~~~~~~~~L~F~n~l~~pifTg~ 114 (639)
+-|+|++..+ +.-++|+. +|-++++|++|+.-....-..|..-.+ +||--+-+. ...-...|+|...=+.-+||++
T Consensus 12 ~~i~~si~a~l~~~~~~~~l~~Qlm~kVmkek~s~~~~~~~~~~k~v~~ksgikvvk-~s~vk~~~r~d~gqp~~V~~td 90 (176)
T COG4766 12 QRIRESIIAQLPEGQFTKELVEQLMEKVMKEKQSLECGWMQPSFKSVDGKSGIKVVK-LSSVKFGLRFDTGQPDCVYTTD 90 (176)
T ss_pred HHHHHHHHHhCChhhhhHHHHHHHHHHHHhchhhhhhhhcccceeecccCCceeEEe-cccceeEeeecCCCCCeEEeec
Confidence 4466665543 34456765 567899999999766654433321111 344222221 1223678889888778999999
Q ss_pred cccccCCCceEEEEEeCC
Q 006596 115 KVEGEQGAAIHVVLVDAN 132 (639)
Q Consensus 115 kI~ae~g~~I~V~LvD~~ 132 (639)
-++-.+|.++-+.+..-.
T Consensus 91 Lvt~~~g~~l~aG~m~~~ 108 (176)
T COG4766 91 LVTEQEGSRLGAGLMEMK 108 (176)
T ss_pred eeecccCCccccceeeec
Confidence 999999999999887643
No 39
>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=22.18 E-value=94 Score=26.48 Aligned_cols=24 Identities=42% Similarity=0.588 Sum_probs=15.7
Q ss_pred HHHHHHHHHhhHHHHHHhhhhHHHHHhH
Q 006596 38 SVIVEALKVDSLQKLCSSLEPILRRVVS 65 (639)
Q Consensus 38 svi~ea~~~~s~q~~~~~lEp~lrrvV~ 65 (639)
||-+.=+++- |.-.|||+|||...
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 40
>COG3827 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.62 E-value=1.6e+02 Score=30.90 Aligned_cols=41 Identities=32% Similarity=0.475 Sum_probs=30.6
Q ss_pred CcchHHHHHHHHHHhhHHHHHH-hhhhHHHHHhHHHHHHHHHh
Q 006596 33 RPALASVIVEALKVDSLQKLCS-SLEPILRRVVSEEVERALAK 74 (639)
Q Consensus 33 rp~~~svi~ea~~~~s~q~~~~-~lEp~lrrvV~EEve~~l~~ 74 (639)
|-+|-.+..|+|+-- ||.-+. .|=-++.|+|+|||||..+.
T Consensus 187 rrsleE~a~eMLRPm-LqdWLDkNLPtLVErLVrEEIeRv~RG 228 (231)
T COG3827 187 RRSLEEMAAEMLRPM-LQDWLDKNLPTLVERLVREEIERVVRG 228 (231)
T ss_pred cccHHHHHHHHHHHH-HHHHHHccchHHHHHHHHHHHHHHHcc
Confidence 347888887877764 666443 68888899999999997653
No 41
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=20.48 E-value=38 Score=39.85 Aligned_cols=37 Identities=24% Similarity=0.384 Sum_probs=31.1
Q ss_pred CCCCCcceeeeeeccCchhhhhhhhcCCccHHHHHHHhh
Q 006596 256 PALNDDVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVV 294 (639)
Q Consensus 256 P~L~DeVwRLekIgKdG~~hkrL~~~gI~tV~dFLrl~~ 294 (639)
..|++.|-.|++||+.- .++|++.||+||.|.|..+=
T Consensus 5 ~~~~~~~~~l~gvg~~~--~~~l~~lgi~t~~dll~~~P 41 (681)
T PRK10917 5 LLLDAPLTSLKGVGPKT--AEKLAKLGIHTVQDLLLHLP 41 (681)
T ss_pred ccccCChhhcCCCCHHH--HHHHHHcCCCCHHHHhhcCC
Confidence 45778999999998654 48899999999999998874
No 42
>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=20.38 E-value=58 Score=24.97 Aligned_cols=18 Identities=22% Similarity=0.612 Sum_probs=15.1
Q ss_pred eeeccCceeecCCCcccc
Q 006596 196 VGTLGDLTFTDNSSWIRS 213 (639)
Q Consensus 196 va~l~di~FTDnSsw~rS 213 (639)
-..|..+.|-|++.|++.
T Consensus 24 ~~~Ie~i~FaDGt~w~~~ 41 (43)
T PF06594_consen 24 SYRIEQIEFADGTVWTRA 41 (43)
T ss_pred CCcEeEEEEcCCCEecHH
Confidence 567889999999999753
Done!