Query 012373
Match_columns 465
No_of_seqs 134 out of 157
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 01:57:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012373.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012373hhsearch_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 4E-125 9E-130 933.0 29.9 299 97-398 1-299 (299)
2 TIGR02239 recomb_RAD51 DNA rep 88.4 0.57 1.2E-05 47.9 4.4 48 274-326 13-60 (316)
3 TIGR02238 recomb_DMC1 meiotic 86.9 0.69 1.5E-05 47.3 4.0 49 273-326 12-60 (313)
4 PLN03186 DNA repair protein RA 86.9 0.73 1.6E-05 47.9 4.1 61 262-327 28-88 (342)
5 PLN03187 meiotic recombination 82.1 1.2 2.6E-05 46.4 3.3 60 261-325 30-89 (344)
6 PRK04301 radA DNA repair and r 81.7 1 2.2E-05 45.4 2.5 56 262-324 8-63 (317)
7 PTZ00035 Rad51 protein; Provis 75.4 3.3 7.2E-05 42.8 4.1 60 261-325 22-81 (337)
8 PF14520 HHH_5: Helix-hairpin- 73.2 2.3 5E-05 33.0 1.8 50 265-321 10-59 (60)
9 TIGR02236 recomb_radA DNA repa 70.4 3.2 6.9E-05 41.5 2.5 50 265-321 4-53 (310)
10 PRK03609 umuC DNA polymerase V 70.0 3.5 7.5E-05 43.4 2.8 51 261-321 180-230 (422)
11 PRK02406 DNA polymerase IV; Va 67.2 4.8 0.0001 40.9 3.0 52 261-322 169-220 (343)
12 PF14229 DUF4332: Domain of un 64.8 9.1 0.0002 34.2 4.0 52 274-327 7-60 (122)
13 PRK01172 ski2-like helicase; P 57.8 9.1 0.0002 42.6 3.3 45 273-322 623-667 (674)
14 PRK03352 DNA polymerase IV; Va 57.8 4.3 9.4E-05 41.2 0.8 41 261-306 178-218 (346)
15 PRK03858 DNA polymerase IV; Va 56.3 5.4 0.00012 41.3 1.2 48 261-313 174-221 (396)
16 PRK03348 DNA polymerase IV; Pr 54.9 6.6 0.00014 42.1 1.6 49 261-314 181-229 (454)
17 PRK14133 DNA polymerase IV; Pr 54.1 12 0.00026 38.2 3.2 51 261-321 174-224 (347)
18 PF10691 DUF2497: Protein of u 54.1 28 0.00061 29.2 4.8 41 34-74 33-73 (73)
19 PRK02794 DNA polymerase IV; Pr 52.6 11 0.00023 39.7 2.7 55 261-325 210-264 (419)
20 cd01700 PolY_Pol_V_umuC umuC s 50.8 11 0.00024 38.3 2.4 51 261-321 177-227 (344)
21 cd03586 PolY_Pol_IV_kappa DNA 49.2 15 0.00032 36.8 3.0 52 261-322 172-223 (334)
22 PRK01810 DNA polymerase IV; Va 45.6 16 0.00034 38.1 2.6 51 261-321 180-230 (407)
23 PRK03103 DNA polymerase IV; Re 45.5 16 0.00035 38.1 2.7 52 261-322 182-233 (409)
24 TIGR01954 nusA_Cterm_rpt trans 44.0 28 0.0006 25.4 3.0 42 275-321 6-47 (50)
25 COG3743 Uncharacterized conser 41.6 30 0.00064 32.3 3.4 59 260-322 67-126 (133)
26 COG4766 EutQ Ethanolamine util 41.4 38 0.00082 32.6 4.1 93 38-132 12-108 (176)
27 cd00424 PolY Y-family of DNA p 40.9 21 0.00045 36.4 2.6 55 261-325 174-229 (343)
28 PF04994 TfoX_C: TfoX C-termin 40.4 10 0.00022 31.9 0.2 74 262-375 5-79 (81)
29 PF02889 Sec63: Sec63 Brl doma 40.2 22 0.00048 35.2 2.6 54 261-321 149-202 (314)
30 cd01701 PolY_Rev1 DNA polymera 39.0 14 0.0003 38.9 1.0 54 261-321 223-276 (404)
31 PRK01216 DNA polymerase IV; Va 38.4 14 0.00031 38.4 0.9 51 261-320 179-229 (351)
32 PF03118 RNA_pol_A_CTD: Bacter 37.9 17 0.00038 29.3 1.2 37 275-316 24-60 (66)
33 cd01702 PolY_Pol_eta DNA Polym 35.3 18 0.00039 37.8 1.1 55 261-322 183-238 (359)
34 cd07978 TAF13 The TATA Binding 34.0 68 0.0015 27.8 4.2 35 280-322 52-89 (92)
35 cd01703 PolY_Pol_iota DNA Poly 32.1 23 0.00049 37.4 1.3 57 262-324 174-242 (379)
36 KOG4233 DNA-bridging protein B 30.9 54 0.0012 28.5 3.1 60 256-323 15-78 (90)
37 KOG1520 Predicted alkaloid syn 30.5 1.6E+02 0.0034 31.9 7.1 46 173-224 151-196 (376)
38 PRK07758 hypothetical protein; 29.7 63 0.0014 28.6 3.4 37 276-317 48-84 (95)
39 PF06594 HCBP_related: Haemoly 27.8 36 0.00079 25.0 1.4 18 196-213 24-41 (43)
40 PRK05256 condesin subunit E; P 25.6 96 0.0021 31.4 4.2 74 276-349 107-186 (238)
41 PF14229 DUF4332: Domain of un 25.2 36 0.00077 30.4 1.1 39 262-305 55-93 (122)
42 TIGR02979 phageshock_pspD phag 25.1 82 0.0018 25.7 3.0 25 37-65 29-53 (59)
43 cd03468 PolY_like DNA Polymera 22.3 48 0.001 33.2 1.5 35 267-306 177-211 (335)
44 PRK10917 ATP-dependent DNA hel 22.3 34 0.00073 38.6 0.5 38 256-295 5-42 (681)
45 PF09584 Phageshock_PspD: Phag 22.3 95 0.0021 25.9 2.9 15 52-66 45-59 (66)
46 COG3355 Predicted transcriptio 22.0 2.2E+02 0.0048 26.3 5.6 40 272-311 31-74 (126)
47 PRK15457 ethanolamine utilizat 21.9 1.4E+02 0.0031 30.2 4.7 72 56-129 90-162 (233)
48 COG3827 Uncharacterized protei 21.9 1.6E+02 0.0034 29.8 4.9 40 34-74 188-228 (231)
49 PF10148 SCHIP-1: Schwannomin- 20.9 1.4E+02 0.003 30.4 4.4 47 62-108 6-60 (238)
50 PF08806 Sep15_SelM: Sep15/Sel 20.7 57 0.0012 27.4 1.4 36 102-138 21-56 (78)
51 PF11754 Velvet: Velvet factor 20.2 2.1E+02 0.0046 27.7 5.4 62 181-245 97-172 (203)
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=4e-125 Score=932.98 Aligned_cols=299 Identities=70% Similarity=1.170 Sum_probs=294.8
Q ss_pred ceEEEEccCCCCCcccCCceeccCCCceEEEEEeCCCCceeccCCCccceEEEEEeeCCCCCCCCCCCCHHHHhhccccc
Q 012373 97 NLQLYFRSRLSLPLFTGGKVEGEQGAAIHVVLVDANTGHVVTSGPEASVKLDIVVLEGDFNNEDDDGWTQEEFESHVVKE 176 (465)
Q Consensus 97 ~~qL~F~n~L~~pifTg~kI~ae~g~~I~V~LvD~~t~~iVt~GplSs~kvEIvVLdGDF~~~~~e~WT~eEF~~~IVk~ 176 (465)
+|||+|.|+|++|||||++|+|+||+||+|+|+|++|+ |++||+|++|||||||||||+++++++||+|||++|||++
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 CCCCccccccceEEEecCceeeccCceeecCCccccccccEEEEEeecCCCCcceeeeeeccceEEeecCCcccccCCCC
Q 012373 177 REGKRPLLTGDLQVTLKEGVGTLGDLTFTDNSSWIRSRKFRLGLKVASGYCEGIRIREAKTEAFTVKDHRGELYKKHYPP 256 (465)
Q Consensus 177 ReGk~pLL~Gdl~v~L~~Gva~l~di~FTDnSsw~rSrKFRLgaRv~~~~~~g~RI~EAvsE~FvVkDhRge~ykKh~pP 256 (465)
|+||+|||+|+++|+|+||+|+|+||+|||||||+|||||||||||+++++.|+|||||+||||+|||||||+|||||||
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 CCCccceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhcccccCCceEEEeeCC
Q 012373 257 ALNDDVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLSGKLYVYYPED 336 (465)
Q Consensus 257 ~L~DeVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~k~y~y~~~~ 336 (465)
+|+|||||||||||||+|||+|+++||+||+|||+|+++||++||+|||+|||++||++||+|||||++++++|+|| .+
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 55
Q ss_pred CCcEEEEEccccceeeeeeCCeeecCCCCChhhHHHHHHHHHHHHHhcccccccCCcccccc
Q 012373 337 SRNVGVVFNNIYELNGLISGEQYFPADALPESQKVYVDSQVKKAYDNWNQVVEYDGKSLLSL 398 (465)
Q Consensus 337 ~~~v~l~FN~i~~lvGa~~~g~y~s~d~L~~~qk~~V~~Lk~~AY~n~~~~~~~d~~~~~~~ 398 (465)
++|++|+|||||+||||.|+|+|++.|+||+.||++|++||++||+||++|++||++|++|+
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 78999999999999999999999999999999999999999999999999999999999875
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=88.37 E-value=0.57 Score=47.86 Aligned_cols=48 Identities=27% Similarity=0.302 Sum_probs=42.9
Q ss_pred hhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhcccccC
Q 012373 274 FHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLS 326 (465)
Q Consensus 274 ~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 326 (465)
--++|+++||.||+||+.. +|..|.+++ |+|...++.+..||.+|...
T Consensus 13 ~~~~l~~~g~~t~~~~~~~---~~~~L~~i~--~ls~~~~~~~~~~~~~~~~~ 60 (316)
T TIGR02239 13 DIKKLQEAGLHTVESVAYA---PKKQLLEIK--GISEAKADKILAEAAKLVPM 60 (316)
T ss_pred HHHHHHHcCCCcHHHHHhC---CHHHHHHHh--CCCHHHHHHHHHHHHHhccc
Confidence 3489999999999999876 899999998 89999999999999988653
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=86.95 E-value=0.69 Score=47.31 Aligned_cols=49 Identities=22% Similarity=0.294 Sum_probs=43.2
Q ss_pred hhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhcccccC
Q 012373 273 SFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLS 326 (465)
Q Consensus 273 ~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 326 (465)
..-++|+++||.||+||+.. ++..|.++. |+|...++.+++.|+.+...
T Consensus 12 ~~~~~L~~~g~~t~~~~~~~---~~~~L~~~~--gls~~~~~~i~~~~~~~~~~ 60 (313)
T TIGR02238 12 ADIKKLKSAGICTVNGVIMT---TRRALCKIK--GLSEAKVDKIKEAASKIINP 60 (313)
T ss_pred HHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHhhhcc
Confidence 34589999999999999876 899999997 89999999999999988654
No 4
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=86.85 E-value=0.73 Score=47.91 Aligned_cols=61 Identities=30% Similarity=0.347 Sum_probs=47.7
Q ss_pred ceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhcccccCC
Q 012373 262 VWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLSG 327 (465)
Q Consensus 262 VwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl~~ 327 (465)
+-+|+.-|-.-.--++|.++||.||+||+.. ++..|.++. |+|....+.+++||.+|....
T Consensus 28 ~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~---~~~~L~~i~--~is~~~~~~~~~~~~~~~~~~ 88 (342)
T PLN03186 28 IEQLQASGIAALDIKKLKDAGIHTVESLAYA---PKKDLLQIK--GISEAKVEKILEAASKLVPLG 88 (342)
T ss_pred HHHHHhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHHhcccc
Confidence 4444443333334599999999999999876 789999998 899999999999998886543
No 5
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=82.08 E-value=1.2 Score=46.41 Aligned_cols=60 Identities=20% Similarity=0.328 Sum_probs=47.4
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhccccc
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVL 325 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 325 (465)
++..|+.-|-.-.--++|.++||+||+|++.. ++..|-++. |+|...++.+++.|+..+.
T Consensus 30 ~~~~l~~~g~~~~~~~kL~~~g~~tv~~~~~~---~~~~L~~~~--g~s~~~~~ki~~~a~~~~~ 89 (344)
T PLN03187 30 SIDKLISQGINAGDVKKLQDAGIYTCNGLMMH---TKKNLTGIK--GLSEAKVDKICEAAEKLLN 89 (344)
T ss_pred CHHHHhhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHHhhc
Confidence 35566553433445699999999999999876 788899986 8999999999999987653
No 6
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=81.70 E-value=1 Score=45.44 Aligned_cols=56 Identities=20% Similarity=0.337 Sum_probs=44.7
Q ss_pred ceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhcccc
Q 012373 262 VWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCV 324 (465)
Q Consensus 262 VwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCv 324 (465)
+-.|.+||+ ...++|.++||.|++|++.+ |+..|.+++ |++.+.++.+++-|+.++
T Consensus 8 l~~l~gIg~--~~a~~L~~~Gi~t~~dl~~~---~~~~L~~~~--g~~~~~a~~l~~~a~~~~ 63 (317)
T PRK04301 8 LEDLPGVGP--ATAEKLREAGYDTVEAIAVA---SPKELSEAA--GIGESTAAKIIEAAREAA 63 (317)
T ss_pred HhhcCCCCH--HHHHHHHHcCCCCHHHHHcC---CHHHHHHhc--CCCHHHHHHHHHHHHHhh
Confidence 445555664 45689999999999999665 999999998 778889999988887644
No 7
>PTZ00035 Rad51 protein; Provisional
Probab=75.42 E-value=3.3 Score=42.79 Aligned_cols=60 Identities=27% Similarity=0.342 Sum_probs=46.5
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhccccc
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVL 325 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 325 (465)
++-.|+.-|-.-.--++|.++||+||+||+.. ++..|.++. |+|...=+.+++.|+.++.
T Consensus 22 ~~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~~---~~~~L~~~~--gis~~~~~~i~~~~~~~~~ 81 (337)
T PTZ00035 22 EIEKLQSAGINAADIKKLKEAGICTVESVAYA---TKKDLCNIK--GISEAKVEKIKEAASKLVP 81 (337)
T ss_pred cHHHHhcCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhh--CCCHHHHHHHHHHHHHhcc
Confidence 35555443333344599999999999998866 888999997 8899999999998887664
No 8
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=73.15 E-value=2.3 Score=32.99 Aligned_cols=50 Identities=32% Similarity=0.547 Sum_probs=40.0
Q ss_pred eeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhc
Q 012373 265 LEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (465)
Q Consensus 265 LekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 321 (465)
+.+||+. ..++|.++||.|++|+..+ +++.|.++= |++.+.=+.+++.|+
T Consensus 10 I~Gig~~--~a~~L~~~G~~t~~~l~~a---~~~~L~~i~--Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 10 IPGIGPK--RAEKLYEAGIKTLEDLANA---DPEELAEIP--GIGEKTAEKIIEAAR 59 (60)
T ss_dssp STTCHHH--HHHHHHHTTCSSHHHHHTS---HHHHHHTST--TSSHHHHHHHHHHHH
T ss_pred CCCCCHH--HHHHHHhcCCCcHHHHHcC---CHHHHhcCC--CCCHHHHHHHHHHHh
Confidence 4455554 3488999999999998765 788899885 789999999998886
No 9
>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=70.36 E-value=3.2 Score=41.48 Aligned_cols=50 Identities=24% Similarity=0.394 Sum_probs=38.4
Q ss_pred eeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhc
Q 012373 265 LEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (465)
Q Consensus 265 LekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 321 (465)
|.+||+ ..-++|.++||.|++|++.+ |++.|.+++ |++.+..+.+.+-|+
T Consensus 4 i~gig~--~~~~~L~~~Gi~ti~dl~~~---~~~~L~~~~--g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 4 LPGVGP--ATAEKLREAGYDTFEAIAVA---SPKELSEIA--GISEGTAAKIIQAAR 53 (310)
T ss_pred cCCCCH--HHHHHHHHcCCCCHHHHHcC---CHHHHHhcc--CCCHHHHHHHHHHHH
Confidence 344554 34489999999999999886 899999998 567777777766665
No 10
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=69.99 E-value=3.5 Score=43.36 Aligned_cols=51 Identities=20% Similarity=0.272 Sum_probs=40.6
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhc
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 321 (465)
+|..|-+||+. ..++|.+.||+|++|+.++ ++..|++.||. .+..+..||.
T Consensus 180 Pv~~l~GiG~~--~~~~L~~lGi~TigdL~~~---~~~~L~~~fG~-----~~~~l~~~a~ 230 (422)
T PRK03609 180 PVEEVWGVGRR--ISKKLNAMGIKTALDLADT---NIRFIRKHFNV-----VLERTVRELR 230 (422)
T ss_pred ChhhcCCccHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHCH-----HHHHHHHHhC
Confidence 45555567774 4599999999999999987 88999999963 5777778875
No 11
>PRK02406 DNA polymerase IV; Validated
Probab=67.17 E-value=4.8 Score=40.90 Aligned_cols=52 Identities=23% Similarity=0.398 Sum_probs=39.9
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhcc
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 322 (465)
+|..|-+||+. .-++|...||+|++|+.++ +...|++.||. .+..+.++|.-
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 56666667753 4478999999999999886 78899999973 46666667753
No 12
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=64.81 E-value=9.1 Score=34.19 Aligned_cols=52 Identities=23% Similarity=0.270 Sum_probs=37.8
Q ss_pred hhhhhhhcCCccHHHHHHHhhcChHH--HHHHHcCCCChhhHHHHHHHhcccccCC
Q 012373 274 FHKRLNNAGIFSVEDFLRLVVRDPQK--LRSILGSGMSNKMWEALLDHAKTCVLSG 327 (465)
Q Consensus 274 ~hkrL~~~~I~tV~dFLrl~~~d~~k--LR~iLg~gmS~k~We~~v~HAktCvl~~ 327 (465)
...+|+..||+|++|||..-.....+ |-+-+ |++.+-=...+.+|.=|...+
T Consensus 7 ~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~--~i~~~~l~~w~~~AdL~ri~g 60 (122)
T PF14229_consen 7 EAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKL--GISERNLLKWVNQADLMRIPG 60 (122)
T ss_pred HHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhc--CCCHHHHHHHHhHHHhhhcCC
Confidence 45899999999999999986554444 55544 788887777777776554433
No 13
>PRK01172 ski2-like helicase; Provisional
Probab=57.78 E-value=9.1 Score=42.56 Aligned_cols=45 Identities=29% Similarity=0.566 Sum_probs=39.4
Q ss_pred hhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhcc
Q 012373 273 SFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (465)
Q Consensus 273 ~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 322 (465)
...++|.++||.||.|+.. .|+++|-+|+ |++++.=+.++++|+.
T Consensus 623 ~~a~~l~~~g~~~~~di~~---~~~~~~~~i~--~~~~~~~~~i~~~~~~ 667 (674)
T PRK01172 623 VRARRLYDAGFKTVDDIAR---SSPERIKKIY--GFSDTLANAIVNRAMK 667 (674)
T ss_pred HHHHHHHHcCCCCHHHHHh---CCHHHHHHHh--ccCHHHHHHHHHHHHH
Confidence 4669999999999999987 4888898898 6899999999999875
No 14
>PRK03352 DNA polymerase IV; Validated
Probab=57.76 E-value=4.3 Score=41.25 Aligned_cols=41 Identities=32% Similarity=0.424 Sum_probs=33.2
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcC
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGS 306 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~ 306 (465)
+|..|-+||+. ..++|...||+|++|++++ ++..|++.||.
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 45666677774 4478999999999999986 78899999975
No 15
>PRK03858 DNA polymerase IV; Validated
Probab=56.31 E-value=5.4 Score=41.28 Aligned_cols=48 Identities=29% Similarity=0.372 Sum_probs=35.4
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhH
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMW 313 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~W 313 (465)
+|..|-+||+. .-++|.+.||+|++|+.++ ++..|++.||..+-...|
T Consensus 174 pl~~l~Gig~~--~~~~L~~~Gi~t~~dl~~l---~~~~L~~~fG~~~~~~l~ 221 (396)
T PRK03858 174 PVRRLWGVGPV--TAAKLRAHGITTVGDVAEL---PESALVSLLGPAAGRHLH 221 (396)
T ss_pred ChhhcCCCCHH--HHHHHHHhCCCcHHHHhcC---CHHHHHHHhCcHHHHHHH
Confidence 45555567774 4488999999999999864 888999999763333333
No 16
>PRK03348 DNA polymerase IV; Provisional
Probab=54.93 E-value=6.6 Score=42.13 Aligned_cols=49 Identities=24% Similarity=0.388 Sum_probs=37.8
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHH
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWE 314 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We 314 (465)
+|.+|-+||+. .-++|...||+|++||.++ +...|++.||..+-..-|+
T Consensus 181 Pv~~L~GIG~~--t~~~L~~lGI~TigDLa~l---~~~~L~~~fG~~~g~~L~~ 229 (454)
T PRK03348 181 PVRRLWGIGPV--TEEKLHRLGIETIGDLAAL---SEAEVANLLGATVGPALHR 229 (454)
T ss_pred CccccCCCCHH--HHHHHHHcCCccHHHHhcC---CHHHHHHHHCHHHHHHHHH
Confidence 67788888875 4478999999999999886 7889999997534344443
No 17
>PRK14133 DNA polymerase IV; Provisional
Probab=54.12 E-value=12 Score=38.18 Aligned_cols=51 Identities=29% Similarity=0.564 Sum_probs=39.1
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhc
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 321 (465)
+|..|-+||+.- -++|..-||+|++|++++ +...|+..|| +.|..+.++|.
T Consensus 174 pv~~l~gig~~~--~~~L~~~Gi~ti~dl~~l---~~~~L~~rfG-----~~g~~l~~~a~ 224 (347)
T PRK14133 174 PISKVHGIGKKS--VEKLNNIGIYTIEDLLKL---SREFLIEYFG-----KFGVEIYERIR 224 (347)
T ss_pred CccccCCCCHHH--HHHHHHcCCccHHHHhhC---CHHHHHHHHh-----HHHHHHHHHhC
Confidence 455566666543 478999999999999886 7788999996 35777777775
No 18
>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=54.11 E-value=28 Score=29.18 Aligned_cols=41 Identities=27% Similarity=0.352 Sum_probs=28.3
Q ss_pred cchhHHHHHHHhhhhHHHHHHhhhHHHHHHhHHHHHHHHHh
Q 012373 34 PALASVIVEALKVDSLQKLCSSLEPILRRVVSEEVERALAK 74 (465)
Q Consensus 34 p~l~svi~ea~~~~s~q~l~~~lEp~lrrvV~EEve~~l~~ 74 (465)
.++-.+++|+|+---=+=|=..|=.|+.|+|++||+|..++
T Consensus 33 ~TlE~lvremLRPmLkeWLD~nLP~lVErlVr~EIeRi~rr 73 (73)
T PF10691_consen 33 RTLEDLVREMLRPMLKEWLDENLPGLVERLVREEIERIARR 73 (73)
T ss_pred ccHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhcC
Confidence 46777777777653222234457778999999999997653
No 19
>PRK02794 DNA polymerase IV; Provisional
Probab=52.55 E-value=11 Score=39.71 Aligned_cols=55 Identities=27% Similarity=0.230 Sum_probs=42.1
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhccccc
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVL 325 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktCvl 325 (465)
+|..|-+||+ ..-++|...||+|++|+.++ +...|++.||. +|..+..+|.--+.
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 3445556664 45589999999999998875 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=50.82 E-value=11 Score=38.29 Aligned_cols=51 Identities=31% Similarity=0.433 Sum_probs=39.0
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhc
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 321 (465)
+|..|-+||+. .-++|...||+|++|+.++ +.+.|.+.||. .|....++|+
T Consensus 177 pl~~l~gig~~--~~~~L~~~Gi~ti~dL~~~---~~~~L~~rfG~-----~~~~l~~~a~ 227 (344)
T cd01700 177 PVGDVWGIGRR--TAKKLNAMGIHTAGDLAQA---DPDLLRKKFGV-----VGERLVRELN 227 (344)
T ss_pred ChhhcCccCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHHH-----HHHHHHHHhC
Confidence 35555566664 4478999999999999986 78899999974 4666777775
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=49.24 E-value=15 Score=36.83 Aligned_cols=52 Identities=27% Similarity=0.467 Sum_probs=40.3
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhcc
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 322 (465)
+|..|-+||+ ..-.+|...||+|++|+.++ ++..|++.+| +.|..+.+||+-
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 4555556665 44588999999999999876 7888999885 578888888874
No 22
>PRK01810 DNA polymerase IV; Validated
Probab=45.62 E-value=16 Score=38.14 Aligned_cols=51 Identities=27% Similarity=0.370 Sum_probs=38.4
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhc
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 321 (465)
+|..|-+||+. .-++|...||+|++|+.++ +...|++.||. .+..+.++|.
T Consensus 180 pv~~l~giG~~--~~~~L~~~Gi~tigdL~~~---~~~~L~~rfG~-----~g~~l~~~a~ 230 (407)
T PRK01810 180 PVGEMHGIGEK--TAEKLKDIGIQTIGDLAKA---DEHILRAKLGI-----NGVRLQRRAN 230 (407)
T ss_pred CHhhcCCcCHH--HHHHHHHcCCCcHHHHHhC---CHHHHHHHHhH-----HHHHHHHHhc
Confidence 45555566664 3488999999999999775 77889999964 4666777776
No 23
>PRK03103 DNA polymerase IV; Reviewed
Probab=45.51 E-value=16 Score=38.10 Aligned_cols=52 Identities=23% Similarity=0.297 Sum_probs=39.7
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhcc
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 322 (465)
+|..|-+||+. .-++|...||+|++|+.++ ++..|++.||. .|..+.++|.-
T Consensus 182 pi~~l~gig~~--~~~~L~~~Gi~tigdl~~~---~~~~L~~~fG~-----~~~~l~~~a~G 233 (409)
T PRK03103 182 PVRKLFGVGSR--MEKHLRRMGIRTIGQLANT---PLERLKKRWGI-----NGEVLWRTANG 233 (409)
T ss_pred CHhhcCCccHH--HHHHHHHcCCCCHHHHhcC---CHHHHHHHHCH-----HHHHHHHHhcC
Confidence 45556677764 5578999999999998875 78889999963 46677777753
No 24
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=44.04 E-value=28 Score=25.44 Aligned_cols=42 Identities=26% Similarity=0.375 Sum_probs=32.7
Q ss_pred hhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhc
Q 012373 275 HKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (465)
Q Consensus 275 hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 321 (465)
-.+|..+||.||+++..+ +++.|..+- |++...=+.++.=|+
T Consensus 6 ~~~L~~~G~~s~e~la~~---~~~eL~~i~--g~~~e~a~~ii~~a~ 47 (50)
T TIGR01954 6 AQLLVEEGFTTVEDLAYV---PIDELLSIE--GFDEETAKELINRAR 47 (50)
T ss_pred HHHHHHcCCCCHHHHHcc---CHHHHhcCC--CCCHHHHHHHHHHHH
Confidence 367999999999998766 778888875 678777777766655
No 25
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=41.61 E-value=30 Score=32.28 Aligned_cols=59 Identities=25% Similarity=0.393 Sum_probs=42.5
Q ss_pred ccceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHH-HHHHhcc
Q 012373 260 DDVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEA-LLDHAKT 322 (465)
Q Consensus 260 DeVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~-~v~HAkt 322 (465)
|+.-+|.+||. ++-+.|+..||+|-.+.-.+-..|-..+-..| +..-+.|.. -|+.|+.
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 47799999999996665554333444444445 677777765 6666653
No 26
>COG4766 EutQ Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=41.39 E-value=38 Score=32.64 Aligned_cols=93 Identities=15% Similarity=0.245 Sum_probs=61.3
Q ss_pred HHHHHHHhhhh-HHHHHHh-hhHHHHHHhHHHHHHHHHhcCCCccC-C-CCCCCCCccCCCCCceEEEEccCCCCCcccC
Q 012373 38 SVIVEALKVDS-LQKLCSS-LEPILRRVVSEEVERALAKLGPARLN-N-GRASPKRIEGPDGRNLQLYFRSRLSLPLFTG 113 (465)
Q Consensus 38 svi~ea~~~~s-~q~l~~~-lEp~lrrvV~EEve~~l~~~~~~~~~-~-~rs~~~~i~~~~~~~~qL~F~n~L~~pifTg 113 (465)
+-|+|.+..+- .-.+|+. +|-++++|++|+.-.......+. +. + +||--+ ....+.-...|+|...=+.-+||+
T Consensus 12 ~~i~~si~a~l~~~~~~~~l~~Qlm~kVmkek~s~~~~~~~~~-~k~v~~ksgik-vvk~s~vk~~~r~d~gqp~~V~~t 89 (176)
T COG4766 12 QRIRESIIAQLPEGQFTKELVEQLMEKVMKEKQSLECGWMQPS-FKSVDGKSGIK-VVKLSSVKFGLRFDTGQPDCVYTT 89 (176)
T ss_pred HHHHHHHHHhCChhhhhHHHHHHHHHHHHhchhhhhhhhcccc-eeecccCCcee-EEecccceeEeeecCCCCCeEEee
Confidence 44566554432 3356665 56699999999976655443332 22 1 233222 223334578889998877889999
Q ss_pred CceeccCCCceEEEEEeCC
Q 012373 114 GKVEGEQGAAIHVVLVDAN 132 (465)
Q Consensus 114 ~kI~ae~g~~I~V~LvD~~ 132 (465)
+-+.-.+|.++-+.+..-.
T Consensus 90 dLvt~~~g~~l~aG~m~~~ 108 (176)
T COG4766 90 DLVTEQEGSRLGAGLMEMK 108 (176)
T ss_pred ceeecccCCccccceeeec
Confidence 9999999999999988754
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=40.93 E-value=21 Score=36.40 Aligned_cols=55 Identities=25% Similarity=0.141 Sum_probs=40.6
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcC-hHHHHHHHcCCCChhhHHHHHHHhccccc
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRD-PQKLRSILGSGMSNKMWEALLDHAKTCVL 325 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d-~~kLR~iLg~gmS~k~We~~v~HAktCvl 325 (465)
+|..|-+||+. .-++|.+.||+|++|+.++ + ...|+..+| +.+..+.++|+--+.
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 46666667774 4488999999999998876 6 566777775 467788888875543
No 28
>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=40.42 E-value=10 Score=31.88 Aligned_cols=74 Identities=30% Similarity=0.449 Sum_probs=42.2
Q ss_pred ceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcCh-HHHHHHHcCCCChhhHHHHHHHhcccccCCceEEEeeCCCCcE
Q 012373 262 VWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDP-QKLRSILGSGMSNKMWEALLDHAKTCVLSGKLYVYYPEDSRNV 340 (465)
Q Consensus 262 VwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~-~kLR~iLg~gmS~k~We~~v~HAktCvl~~k~y~y~~~~~~~v 340 (465)
+..|-+||.. .-+.|.+.||+||+||..+=.+.. -+|++. | .
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 3344555553 338899999999999998843332 244443 1 2
Q ss_pred EEEEccccceeeeeeCCeeecCCCCChhhHHHHHH
Q 012373 341 GVVFNNIYELNGLISGEQYFPADALPESQKVYVDS 375 (465)
Q Consensus 341 ~l~FN~i~~lvGa~~~g~y~s~d~L~~~qk~~V~~ 375 (465)
.+-+|-.|.|.||+-|=+ ...|++.+|.....
T Consensus 48 ~~~~~~L~aL~gAi~g~~---~~~L~~~~K~~L~~ 79 (81)
T PF04994_consen 48 SVCLNLLYALEGAIQGIH---WADLPDEEKQELLE 79 (81)
T ss_dssp T--HHHHHHHHHHHCTS----GGGS-HHHHHHHHH
T ss_pred CCCHHHHHHHHHHHcCCC---HHHCCHHHHHHHHh
Confidence 355778899999988743 35677777765543
No 29
>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=40.17 E-value=22 Score=35.16 Aligned_cols=54 Identities=26% Similarity=0.492 Sum_probs=37.5
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhc
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 321 (465)
...-|.+|+.+.+ ++|..+||.|+++|+++ ++++|..+| +......+.+.+.|.
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 4455667777654 88999999999999966 899999999 456688888888876
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=38.97 E-value=14 Score=38.90 Aligned_cols=54 Identities=22% Similarity=0.233 Sum_probs=39.5
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhc
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAk 321 (465)
+|..|-+||+. .-++|...||.|++|+..+- .++..|++.||. +.+..+.++|.
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 56667777764 55999999999999999871 127899999974 34555555654
No 31
>PRK01216 DNA polymerase IV; Validated
Probab=38.41 E-value=14 Score=38.44 Aligned_cols=51 Identities=25% Similarity=0.397 Sum_probs=38.3
Q ss_pred cceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHh
Q 012373 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHA 320 (465)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HA 320 (465)
+|..|..||+. -.++|...||+|++|+.++ +...|++.||. ..+..+-.+|
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 56777777764 4489999999999998876 67889999973 3344455556
No 32
>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=37.94 E-value=17 Score=29.32 Aligned_cols=37 Identities=27% Similarity=0.419 Sum_probs=23.3
Q ss_pred hhhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHH
Q 012373 275 HKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEAL 316 (465)
Q Consensus 275 hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~ 316 (465)
...|..+||+||+|++++ +++.|.++= |+..+.-+.+
T Consensus 24 ~n~L~~~~I~tv~dL~~~---s~~~L~~i~--n~G~ksl~EI 60 (66)
T PF03118_consen 24 YNCLKRAGIHTVGDLVKY---SEEDLLKIK--NFGKKSLEEI 60 (66)
T ss_dssp HHHHHCTT--BHHHHHCS----HHHHHTST--TSHHHHHHHH
T ss_pred HHHHHHhCCcCHHHHHhC---CHHHHHhCC--CCCHhHHHHH
Confidence 367889999999997766 667777774 4444444443
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=35.27 E-value=18 Score=37.76 Aligned_cols=55 Identities=15% Similarity=0.236 Sum_probs=37.9
Q ss_pred cceeeeeeccCchhhhh-hhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhcc
Q 012373 261 DVWRLEKIGKDGSFHKR-LNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (465)
Q Consensus 261 eVwRLekIgKdG~~hkr-L~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAkt 322 (465)
+|..|-+||+ ..-++ |...||.|++|+.++. .++..|++.||. +.+..+.++|+-
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 4666767774 22244 5889999999998764 578889999874 344555556653
No 34
>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=33.97 E-value=68 Score=27.77 Aligned_cols=35 Identities=34% Similarity=0.585 Sum_probs=28.1
Q ss_pred hcCCccHHHHHHHhhcChHHH---HHHHcCCCChhhHHHHHHHhcc
Q 012373 280 NAGIFSVEDFLRLVVRDPQKL---RSILGSGMSNKMWEALLDHAKT 322 (465)
Q Consensus 280 ~~~I~tV~dFLrl~~~d~~kL---R~iLg~gmS~k~We~~v~HAkt 322 (465)
...| +++||+=++-.||.|| +++| .|+..++-||.
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 3567 9999999999999655 5556 68888888875
No 35
>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=32.08 E-value=23 Score=37.36 Aligned_cols=57 Identities=16% Similarity=0.151 Sum_probs=38.8
Q ss_pred ceeeeeeccCchhhhhhhhcCCccHHHHHHHhh------------cChHHHHHHHcCCCChhhHHHHHHHhcccc
Q 012373 262 VWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVV------------RDPQKLRSILGSGMSNKMWEALLDHAKTCV 324 (465)
Q Consensus 262 VwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~------------~d~~kLR~iLg~gmS~k~We~~v~HAktCv 324 (465)
|-.|-+||+.. -++|.+.||.|++|+..+-+ .+...|++.||. +.+..+.++|+--+
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 34444677654 48999999999999987641 117789999864 34555666676444
No 36
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=30.88 E-value=54 Score=28.48 Aligned_cols=60 Identities=28% Similarity=0.432 Sum_probs=40.3
Q ss_pred CCCCccceeeeeeccCchhhhhhhhcCCcc----HHHHHHHhhcChHHHHHHHcCCCChhhHHHHHHHhccc
Q 012373 256 PALNDDVWRLEKIGKDGSFHKRLNNAGIFS----VEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTC 323 (465)
Q Consensus 256 P~L~DeVwRLekIgKdG~~hkrL~~~~I~t----V~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v~HAktC 323 (465)
|+=+-+|--|.+||.. +-.+|..+|+.. .++|| ++.+|++-.+.-| ...--++-+||++|
T Consensus 15 PmGeK~V~~laGIg~~--lg~~L~~~GfdkAYvllGQfL-llkKdE~lF~~Wl-----k~~~gat~~~a~~~ 78 (90)
T KOG4233|consen 15 PMGEKDVTWLAGIGET--LGIKLVDAGFDKAYVLLGQFL-LLKKDEDLFQEWL-----KETCGATAKQAQDC 78 (90)
T ss_pred ccCCCcceeeccccHH--hhhhHHhccccHHHHHHHHHH-HhcccHHHHHHHH-----HHHcCccHHHHHHH
Confidence 5666788899999874 568999999976 46776 4477876555533 11122356677766
No 37
>KOG1520 consensus Predicted alkaloid synthase/Surface mucin Hemomucin [General function prediction only]
Probab=30.51 E-value=1.6e+02 Score=31.87 Aligned_cols=46 Identities=33% Similarity=0.393 Sum_probs=31.0
Q ss_pred ccccCCCCccccccceEEEecCceeeccCceeecCCccccccccEEEEEeec
Q 012373 173 VVKEREGKRPLLTGDLQVTLKEGVGTLGDLTFTDNSSWIRSRKFRLGLKVAS 224 (465)
Q Consensus 173 IVk~ReGk~pLL~Gdl~v~L~~Gva~l~di~FTDnSsw~rSrKFRLgaRv~~ 224 (465)
++-+=+|+...++.++.|.= +| .|-|||+||.--.|.|-+++--.+
T Consensus 151 l~~~~~G~~~kf~N~ldI~~-~g-----~vyFTDSSsk~~~rd~~~a~l~g~ 196 (376)
T KOG1520|consen 151 LADEAEGKPFKFLNDLDIDP-EG-----VVYFTDSSSKYDRRDFVFAALEGD 196 (376)
T ss_pred ccccccCeeeeecCceeEcC-CC-----eEEEeccccccchhheEEeeecCC
Confidence 33445777766666666544 44 578999999766688888775543
No 38
>PRK07758 hypothetical protein; Provisional
Probab=29.70 E-value=63 Score=28.62 Aligned_cols=37 Identities=22% Similarity=0.405 Sum_probs=25.6
Q ss_pred hhhhhcCCccHHHHHHHhhcChHHHHHHHcCCCChhhHHHHH
Q 012373 276 KRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALL 317 (465)
Q Consensus 276 krL~~~~I~tV~dFLrl~~~d~~kLR~iLg~gmS~k~We~~v 317 (465)
..|..+||+||+|+.++ +++.|-+|= |+..|.-+.+.
T Consensus 48 N~Lk~AGI~TL~dLv~~---te~ELl~ik--nlGkKSL~EIk 84 (95)
T PRK07758 48 RALEHHGIHTVEELSKY---SEKEILKLH--GMGPASLPKLR 84 (95)
T ss_pred HHHHHcCCCcHHHHHcC---CHHHHHHcc--CCCHHHHHHHH
Confidence 66889999999998765 556666663 45555555544
No 39
>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=27.77 E-value=36 Score=24.96 Aligned_cols=18 Identities=22% Similarity=0.612 Sum_probs=15.2
Q ss_pred eeeccCceeecCCccccc
Q 012373 196 VGTLGDLTFTDNSSWIRS 213 (465)
Q Consensus 196 va~l~di~FTDnSsw~rS 213 (465)
-..|..+.|-|++.|++.
T Consensus 24 ~~~Ie~i~FaDGt~w~~~ 41 (43)
T PF06594_consen 24 SYRIEQIEFADGTVWTRA 41 (43)
T ss_pred CCcEeEEEEcCCCEecHH
Confidence 567889999999999863
No 40
>PRK05256 condesin subunit E; Provisional
Probab=25.55 E-value=96 Score=31.44 Aligned_cols=74 Identities=19% Similarity=0.298 Sum_probs=51.5
Q ss_pred hhhhhcCCccHHHHHHHhh--cChHHHHHHHc--CCCChhhHHHHHHHhcccc--cCCceEEEeeCCCCcEEEEEccccc
Q 012373 276 KRLNNAGIFSVEDFLRLVV--RDPQKLRSILG--SGMSNKMWEALLDHAKTCV--LSGKLYVYYPEDSRNVGVVFNNIYE 349 (465)
Q Consensus 276 krL~~~~I~tV~dFLrl~~--~d~~kLR~iLg--~gmS~k~We~~v~HAktCv--l~~k~y~y~~~~~~~v~l~FN~i~~ 349 (465)
++|++.||.|+++.+.-+. .|+.||.+.++ .+-|+-+-+++.+-.++|- |..-=.++...+..+...+=++||-
T Consensus 107 erLa~~gift~qeL~deL~~ladE~kllklvn~R~~GsDlD~~Kl~ekvr~sLrrLrRlgmI~~l~~d~~kF~iteAvfR 186 (238)
T PRK05256 107 ERLAHEGIFTQQELYDELLTLADEAKLLKLVNNRSTGSDLDKQKLQEKVRTSLNRLRRLGMVWFMGHDSSKFRITESVFR 186 (238)
T ss_pred HHHhcCCceeHHHHHHHHHHhhcHHHHHHHhcCCCCcchhhHHHHHHHHHHHHHHHHhccceeeecCCCceEEecHHHHh
Confidence 7999999999999886544 48999999984 3337778888999999986 3333355544433344444455554
No 41
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=25.16 E-value=36 Score=30.44 Aligned_cols=39 Identities=36% Similarity=0.673 Sum_probs=29.5
Q ss_pred ceeeeeeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHc
Q 012373 262 VWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILG 305 (465)
Q Consensus 262 VwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg 305 (465)
.+|..+||. .|..-|..+||.||+++-. .+|++|.+.++
T Consensus 55 L~ri~gi~~--~~a~LL~~AGv~Tv~~LA~---~~p~~L~~~l~ 93 (122)
T PF14229_consen 55 LMRIPGIGP--QYAELLEHAGVDTVEELAQ---RNPQNLHQKLG 93 (122)
T ss_pred hhhcCCCCH--HHHHHHHHhCcCcHHHHHh---CCHHHHHHHHH
Confidence 346666655 4668899999999999854 68998888653
No 42
>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=25.06 E-value=82 Score=25.73 Aligned_cols=25 Identities=44% Similarity=0.666 Sum_probs=16.1
Q ss_pred hHHHHHHHhhhhHHHHHHhhhHHHHHHhH
Q 012373 37 ASVIVEALKVDSLQKLCSSLEPILRRVVS 65 (465)
Q Consensus 37 ~svi~ea~~~~s~q~l~~~lEp~lrrvV~ 65 (465)
+||-+.=+++ + |.-.|||+|||...
T Consensus 29 KsVsrkPLr~--l--La~aLEPllkr~~~ 53 (59)
T TIGR02979 29 KSVARRPLKM--L--LAIALEPMLKRAAN 53 (59)
T ss_pred HHHhhccHHH--H--HHHHHHHHHHHHHH
Confidence 4444444444 2 45589999999854
No 43
>cd03468 PolY_like DNA Polymerase Y-family. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.
Probab=22.31 E-value=48 Score=33.17 Aligned_cols=35 Identities=17% Similarity=0.278 Sum_probs=28.8
Q ss_pred eeccCchhhhhhhhcCCccHHHHHHHhhcChHHHHHHHcC
Q 012373 267 KIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGS 306 (465)
Q Consensus 267 kIgKdG~~hkrL~~~~I~tV~dFLrl~~~d~~kLR~iLg~ 306 (465)
.||+.. -.+|.+.||+|++||..+ +...|++.||.
T Consensus 177 gig~~~--~~~L~~~Gi~t~~dl~~~---~~~~l~~rfG~ 211 (335)
T cd03468 177 RLPPET--VELLARLGLRTLGDLAAL---PRAELARRFGL 211 (335)
T ss_pred CCCHHH--HHHHHHhCcccHHHHHhC---ChHHHHhhcCH
Confidence 566654 488999999999998886 78889999975
No 44
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=22.30 E-value=34 Score=38.64 Aligned_cols=38 Identities=26% Similarity=0.415 Sum_probs=31.3
Q ss_pred CCCCccceeeeeeccCchhhhhhhhcCCccHHHHHHHhhc
Q 012373 256 PALNDDVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVR 295 (465)
Q Consensus 256 P~L~DeVwRLekIgKdG~~hkrL~~~~I~tV~dFLrl~~~ 295 (465)
..|+++|-.|++||+.- .+.|++-||+||.|.|..+=+
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 45778999999998654 478889999999999988654
No 45
>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=22.25 E-value=95 Score=25.91 Aligned_cols=15 Identities=47% Similarity=0.789 Sum_probs=11.8
Q ss_pred HHHhhhHHHHHHhHH
Q 012373 52 LCSSLEPILRRVVSE 66 (465)
Q Consensus 52 l~~~lEp~lrrvV~E 66 (465)
|.-.|||+|||.++.
T Consensus 45 La~~LEPllrr~~~~ 59 (66)
T PF09584_consen 45 LALALEPLLRRGLNK 59 (66)
T ss_pred HHHHHHHHHHHHHHH
Confidence 445899999999653
No 46
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=22.04 E-value=2.2e+02 Score=26.28 Aligned_cols=40 Identities=18% Similarity=0.485 Sum_probs=30.7
Q ss_pred chhhhhhhhcCCccHHHHHHHhhcCh----HHHHHHHcCCCChh
Q 012373 272 GSFHKRLNNAGIFSVEDFLRLVVRDP----QKLRSILGSGMSNK 311 (465)
Q Consensus 272 G~~hkrL~~~~I~tV~dFLrl~~~d~----~kLR~iLg~gmS~k 311 (465)
.+|+.-|+.+|=.||+|.-.-++++. ..|++++-.|+=.+
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 46778787899999999999999995 46777765555433
No 47
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=21.94 E-value=1.4e+02 Score=30.24 Aligned_cols=72 Identities=14% Similarity=0.260 Sum_probs=35.0
Q ss_pred hhHHHHHHhHHHHHHHHHhcCCCccCCCCCCCCCccCCCCCceEE-EEccCCCCCcccCCceeccCCCceEEEEE
Q 012373 56 LEPILRRVVSEEVERALAKLGPARLNNGRASPKRIEGPDGRNLQL-YFRSRLSLPLFTGGKVEGEQGAAIHVVLV 129 (465)
Q Consensus 56 lEp~lrrvV~EEve~~l~~~~~~~~~~~rs~~~~i~~~~~~~~qL-~F~n~L~~pifTg~kI~ae~g~~I~V~Lv 129 (465)
||-++|+|+.|++-..+.-..++ +. .-..|.+|--..++.+++ +|....+..+|+.+-+..++|..+-..++
T Consensus 90 i~~lv~~v~~e~~~~~~~~~~~~-~~-~~~~~~Gi~vVrg~svk~~~fdg~~~~~v~~~d~~~~~d~s~m~aGf~ 162 (233)
T PRK15457 90 VAQLMEKVMKEKQSLEQGAMQPS-FK-SVTGKGGIKVIDGSSVKFGRFDGAEPHCVGLTDLVTGDDGSSMAAGFM 162 (233)
T ss_pred HHHHHHHHHHHHhcccccccCCC-cc-ceeCCCceEEEECCeEEEeecCCCCcccEEeeeeeccCCCCceeeEEE
Confidence 67799999988854332110000 00 001122333233445555 55444455556665555555555554444
No 48
>COG3827 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.91 E-value=1.6e+02 Score=29.83 Aligned_cols=40 Identities=30% Similarity=0.461 Sum_probs=26.2
Q ss_pred cchhHHHHHHHhhhhHHHHHH-hhhHHHHHHhHHHHHHHHHh
Q 012373 34 PALASVIVEALKVDSLQKLCS-SLEPILRRVVSEEVERALAK 74 (465)
Q Consensus 34 p~l~svi~ea~~~~s~q~l~~-~lEp~lrrvV~EEve~~l~~ 74 (465)
-+|-.+..|+|+- -||.-+. .|=-++.|.|+|||||..+.
T Consensus 188 rsleE~a~eMLRP-mLqdWLDkNLPtLVErLVrEEIeRv~RG 228 (231)
T COG3827 188 RSLEEMAAEMLRP-MLQDWLDKNLPTLVERLVREEIERVVRG 228 (231)
T ss_pred ccHHHHHHHHHHH-HHHHHHHccchHHHHHHHHHHHHHHHcc
Confidence 3666666666653 2443333 46667889999999997653
No 49
>PF10148 SCHIP-1: Schwannomin-interacting protein 1; InterPro: IPR015649 SCHIP-1 is a coiled-coil protein that specifically associates with schwannomin in vitro and in vivo. The product of the neurofibromatosis type 2 (NF2) tumour suppressor gene, known as schwannomin or merlin, is involved in NF2-associated and sporadic schwannomas and meningiomas. It is closely related to the ezrin-radixin-moesin family members, which link membrane proteins to the cytoskeleton. Association with SCHIP-1 can be observed only with some naturally occurring mutants of schwannomin, or a schwannomin spliced isoform lacking exons 2 and 3, but not with the schwannomin isoform exhibiting growth-suppressive activity []. This entry consists of mammalian SCHIP-1 proteins from Mus musculus (Mouse) and Homo sapiens (Human).
Probab=20.91 E-value=1.4e+02 Score=30.39 Aligned_cols=47 Identities=26% Similarity=0.240 Sum_probs=26.2
Q ss_pred HHhHHHHHHHHHhcC--CC---ccCC---CCCCCCCccCCCCCceEEEEccCCCC
Q 012373 62 RVVSEEVERALAKLG--PA---RLNN---GRASPKRIEGPDGRNLQLYFRSRLSL 108 (465)
Q Consensus 62 rvV~EEve~~l~~~~--~~---~~~~---~rs~~~~i~~~~~~~~qL~F~n~L~~ 108 (465)
|-=+|||++.|+=-. .. .|+. .+.+....--+.+.++|.||.|.++.
T Consensus 6 r~eREeIrrrlA~g~~~ed~~~~yt~~~~~~k~sl~~RLqsgmNLQVCFmNE~~s 60 (238)
T PF10148_consen 6 RNEREEIRRRLAMGSFAEDNWEKYTSSSKSGKPSLSSRLQSGMNLQVCFMNETSS 60 (238)
T ss_pred cccHHHHHHHHhcCCcccccceeccccccCCCcccccccCCCceeeEEeecCCCC
Confidence 444789998887311 00 1221 11122222235578999999999854
No 50
>PF08806 Sep15_SelM: Sep15/SelM redox domain; InterPro: IPR014912 Sep15 and SelM are eukaryotic selenoproteins that have a thioredoxin-like domain and a surface accessible active site redox motif []. This suggests that they function as thiol-disulphide isomerases involved in disulphide bond formation in the endoplasmic reticulum []. ; PDB: 2A4H_A 2A2P_A.
Probab=20.67 E-value=57 Score=27.38 Aligned_cols=36 Identities=31% Similarity=0.403 Sum_probs=23.1
Q ss_pred EccCCCCCcccCCceeccCCCceEEEEEeCCCCceec
Q 012373 102 FRSRLSLPLFTGGKVEGEQGAAIHVVLVDANTGHVVT 138 (465)
Q Consensus 102 F~n~L~~pifTg~kI~ae~g~~I~V~LvD~~t~~iVt 138 (465)
|.+.=..+.|.+-.|+-..|++=.+.|+|.+ |+.+.
T Consensus 21 Fi~~~~~~~y~~v~vk~i~G~~P~L~l~d~~-g~~~E 56 (78)
T PF08806_consen 21 FIKSDVPPLYPNVEVKYIPGAPPELVLLDED-GEEVE 56 (78)
T ss_dssp HCCCCCGHHBTTEEEEEESS---EEEEE-SS-S--SE
T ss_pred HHhccchhccCceEEEEeCCCCCEEEEEcCC-CCEEE
Confidence 5554446889999999999999999999974 66554
No 51
>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=20.17 E-value=2.1e+02 Score=27.69 Aligned_cols=62 Identities=27% Similarity=0.339 Sum_probs=37.3
Q ss_pred ccccccceEEE---ec--Cce--eeccCceeecCCccccccccEEEEEeecCCC-------CcceeeeeeccceEEeec
Q 012373 181 RPLLTGDLQVT---LK--EGV--GTLGDLTFTDNSSWIRSRKFRLGLKVASGYC-------EGIRIREAKTEAFTVKDH 245 (465)
Q Consensus 181 ~pLL~Gdl~v~---L~--~Gv--a~l~di~FTDnSsw~rSrKFRLgaRv~~~~~-------~g~RI~EAvsE~FvVkDh 245 (465)
.+.|.|.+... |+ +|. |.. ..|.|=|-.+ -+.|||-.++..=.. ...-+-|+.|+||.|-..
T Consensus 97 ~r~L~Gs~vss~~~l~d~~~~~~g~f--FvF~DLsVR~-eG~frLrf~l~~i~~~~~~~~~~~~~la~~~S~~F~V~s~ 172 (203)
T PF11754_consen 97 TRNLVGSLVSSAFRLKDPDGKEPGGF--FVFPDLSVRT-EGRFRLRFSLFDIGPSPGQGGGSSPVLAEVFSDPFTVYSA 172 (203)
T ss_pred cccCcccEeeeeEEecCCCCCeEEEE--EEeCCceECc-CCEEEEEEEEEEecCCccccCCCCcEEEEEECcCEEEECH
Confidence 46788876543 33 343 211 2333433322 568999999876322 234589999999999653
Done!