Query 016693
Match_columns 384
No_of_seqs 127 out of 148
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 09:08:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016693.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016693hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07887 Calmodulin_bind: Calm 100.0 2E-119 5E-124 873.9 27.1 290 87-380 1-296 (299)
2 TIGR02239 recomb_RAD51 DNA rep 87.5 0.49 1.1E-05 47.2 3.2 48 262-314 13-60 (316)
3 TIGR02238 recomb_DMC1 meiotic 85.9 0.66 1.4E-05 46.4 3.1 48 262-314 13-60 (313)
4 PLN03186 DNA repair protein RA 85.6 0.7 1.5E-05 46.9 3.2 61 250-315 28-88 (342)
5 PRK04301 radA DNA repair and r 82.7 0.68 1.5E-05 45.6 1.7 57 249-312 7-63 (317)
6 PLN03187 meiotic recombination 78.9 1.4 3.1E-05 44.8 2.5 60 249-313 30-89 (344)
7 PF14520 HHH_5: Helix-hairpin- 78.6 0.53 1.1E-05 35.7 -0.5 50 253-309 10-59 (60)
8 PTZ00035 Rad51 protein; Provis 72.2 3.8 8.2E-05 41.4 3.5 60 249-313 22-81 (337)
9 PRK03609 umuC DNA polymerase V 70.8 2.7 5.9E-05 43.1 2.2 51 249-309 180-230 (422)
10 PF14229 DUF4332: Domain of un 69.8 3.5 7.6E-05 35.9 2.3 50 262-313 7-58 (122)
11 TIGR02236 recomb_radA DNA repa 69.3 2.6 5.7E-05 41.1 1.6 50 253-309 4-53 (310)
12 PRK02406 DNA polymerase IV; Va 67.5 3.9 8.4E-05 40.6 2.4 52 249-310 169-220 (343)
13 PRK03352 DNA polymerase IV; Va 58.1 3.3 7.2E-05 41.1 0.0 41 249-294 178-218 (346)
14 PRK01172 ski2-like helicase; P 56.9 8.3 0.00018 41.9 2.8 51 253-310 617-667 (674)
15 PRK03858 DNA polymerase IV; Va 56.5 4.1 9E-05 41.1 0.4 48 249-301 174-221 (396)
16 PRK14133 DNA polymerase IV; Pr 54.7 9.5 0.00021 38.0 2.6 51 249-309 174-224 (347)
17 PRK03348 DNA polymerase IV; Pr 54.5 5.3 0.00012 41.8 0.8 48 249-301 181-228 (454)
18 PRK02794 DNA polymerase IV; Pr 53.6 8.5 0.00018 39.5 2.1 55 249-313 210-264 (419)
19 cd01700 PolY_Pol_V_umuC umuC s 52.6 8.5 0.00018 38.2 1.9 51 249-309 177-227 (344)
20 cd03586 PolY_Pol_IV_kappa DNA 49.3 12 0.00026 36.6 2.3 52 249-310 172-223 (334)
21 PF10691 DUF2497: Protein of u 46.8 45 0.00098 27.2 4.9 40 26-66 33-72 (73)
22 PRK03103 DNA polymerase IV; Re 45.5 14 0.00029 37.7 2.1 52 249-310 182-233 (409)
23 PRK01810 DNA polymerase IV; Va 45.1 14 0.0003 37.6 2.1 51 249-309 180-230 (407)
24 PF04994 TfoX_C: TfoX C-termin 43.7 6.5 0.00014 32.2 -0.4 29 250-280 5-33 (81)
25 cd00424 PolY Y-family of DNA p 41.2 17 0.00037 36.1 1.9 55 249-313 174-229 (343)
26 PF02889 Sec63: Sec63 Brl doma 41.0 16 0.00035 35.3 1.7 54 249-309 149-202 (314)
27 COG3743 Uncharacterized conser 39.6 25 0.00054 31.9 2.5 60 247-310 66-126 (133)
28 PF03118 RNA_pol_A_CTD: Bacter 39.5 14 0.00031 29.0 0.9 35 264-303 25-59 (66)
29 cd01701 PolY_Rev1 DNA polymera 39.3 11 0.00023 38.8 0.2 54 249-309 223-276 (404)
30 PRK01216 DNA polymerase IV; Va 38.8 11 0.00023 38.3 0.2 51 249-308 179-229 (351)
31 cd01702 PolY_Pol_eta DNA Polym 36.7 13 0.00028 37.8 0.4 55 249-310 183-238 (359)
32 PF06594 HCBP_related: Haemoly 35.2 28 0.0006 24.9 1.8 18 185-202 24-41 (43)
33 cd01703 PolY_Pol_iota DNA Poly 35.1 15 0.00033 37.7 0.6 58 249-312 173-242 (379)
34 COG4766 EutQ Ethanolamine util 32.9 1.4E+02 0.0031 28.1 6.4 91 31-121 13-108 (176)
35 TIGR01954 nusA_Cterm_rpt trans 29.5 51 0.0011 23.3 2.4 41 264-309 7-47 (50)
36 PF04270 Strep_his_triad: Stre 27.1 44 0.00096 25.8 1.8 22 347-368 31-52 (53)
37 PF14229 DUF4332: Domain of un 26.9 30 0.00064 30.1 0.9 39 250-293 55-93 (122)
38 PRK10917 ATP-dependent DNA hel 26.7 22 0.00047 39.2 0.1 38 244-283 5-42 (681)
39 PRK07758 hypothetical protein; 26.7 70 0.0015 27.5 3.1 37 264-305 48-84 (95)
40 PRK05256 condesin subunit E; P 25.4 78 0.0017 31.2 3.5 74 264-338 107-186 (238)
41 smart00100 cNMP Cyclic nucleot 25.2 1.6E+02 0.0034 22.4 4.6 41 295-335 4-44 (120)
42 PF09039 HTH_Tnp_Mu_2: Mu DNA 25.0 1.1E+02 0.0024 26.4 4.1 40 21-61 44-83 (108)
43 cd03468 PolY_like DNA Polymera 24.4 33 0.00071 33.5 0.8 35 255-294 177-211 (335)
44 KOG4233 DNA-bridging protein B 23.7 62 0.0013 27.4 2.1 60 244-311 15-78 (90)
45 COG4472 Uncharacterized protei 23.3 29 0.00062 29.3 0.1 40 333-372 36-83 (88)
46 cd07978 TAF13 The TATA Binding 23.2 1.3E+02 0.0028 25.3 4.1 35 268-310 52-89 (92)
47 PF00853 Runt: Runt domain; I 20.0 1.6E+02 0.0035 26.8 4.1 35 178-214 74-108 (135)
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=2.3e-119 Score=873.91 Aligned_cols=290 Identities=60% Similarity=1.008 Sum_probs=282.4
Q ss_pred ceEEEEecCCCCCcccCCcccccC-CccEEEEEeCCCCceeccCCCCcceEEEEEeeCCCCCCCCCCCCHHHHhhccccc
Q 016693 87 SLQLQFLNNLSLPVFTGARIEGDD-STIKVALVDTLTGQIVTSGPESSAKVEIVVLEGDFDGDESDNWTIEEFKNNIVRE 165 (384)
Q Consensus 87 ~~~L~F~n~l~~pifT~~kI~a~~-~~I~V~L~D~~t~~~V~~Gplss~kieIvVLdGDF~~~~~e~WT~eEF~~~IV~~ 165 (384)
++||+|.|+|++|+|||++|+|+| +||+|+|+|++|+ |++||+||+|||||||||||+++++++||+|||++|||++
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 589999999999999999999999 9999999999888 9999999999999999999999999999999999999999
Q ss_pred CCCCCccccccEEEEeccceeeccceeeecCCccccccceEEEEEeecCC-CccceeeecccceEEeecCCcccccCCCC
Q 016693 166 REGKKPLLTGDAFLTLKEGIGSVGEISFTDNSSWTRSRRFRLGARVVDNT-DETRVREAKTDSFIVRDHRGELYKKHHPP 244 (384)
Q Consensus 166 R~Gk~pLL~Gdl~v~L~~Gva~l~di~FtDnSs~~rsrKFRLgaRvv~~~-~g~RI~EAvse~FvVkd~Rge~~kKh~pP 244 (384)
|+||+|||+|+++|+|+||+|+|+||+|||||||+|||||||||||++++ .|+|||||+||||+|||||||+|||||||
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 99999999999999999999999999999999999999999999999998 99999999999999999999999999999
Q ss_pred CCCCcceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhccccCCCcEEEEcCCC
Q 016693 245 VLFDEVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHARTCVLDKRVYLYCPPG 324 (384)
Q Consensus 245 ~L~DeVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAktCvl~~~~y~y~~~~ 324 (384)
+|+|||||||||||||+|||+|+++||+||+|||+++++||++||+|||+|||++||++||+|||||++++++|+|+.+
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 SLDDEVWRLEKIGKDGAFHKRLKKNGINTVEDFLKLLNKDPQKLREILGSGMSNKMWETTVEHAKTCVLGDKLYVYYDE- 237 (299)
T ss_pred CCCCchhhhhhccccCHHHHHHHHcCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHHHHHHHHhcCCCCcEEEEEec-
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999954
Q ss_pred CCcceEEEEeccceeeeeeeCCEEeeCCCCChhhhhhhhhhHHHH---Hhhh-hhHHhhh
Q 016693 325 TQQKSGVVFNVVGQVMGLLSECQYVPIDKLSETQKAYFPYHIRSF---VSCL-LFSYIIF 380 (384)
Q Consensus 325 ~~~~v~l~FN~i~~lvG~~~~g~y~s~~~L~~~qk~~v~~~~~~~---~~~~-~f~y~~~ 380 (384)
++|++|+|||||+||||+|+|||+|.|+||+.||++|+.|+++| ++++ .||..|.
T Consensus 238 -~~nv~l~FN~i~~lvga~~~g~y~s~d~L~~~qK~~v~~Lv~~AY~n~~~l~e~d~~~~ 296 (299)
T PF07887_consen 238 -EQNVGLFFNCIYELVGAIFGGQYVSLDNLSSAQKAYVDKLVKQAYENWDNLEEYDGKML 296 (299)
T ss_pred -CCceEEEEcchhhEEeEEECCEEEehHHcCHHHHHHHHHHHHHHHHhhhhheecccchh
Confidence 88999999999999999999999999999999999999999999 5556 7777664
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=87.52 E-value=0.49 Score=47.21 Aligned_cols=48 Identities=21% Similarity=0.161 Sum_probs=42.5
Q ss_pred hcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhccccCC
Q 016693 262 FHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHARTCVLD 314 (384)
Q Consensus 262 ~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAktCvl~ 314 (384)
--++|+++||.||+||+. .+|..|.+++ |+|...++.+..||.+|...
T Consensus 13 ~~~~l~~~g~~t~~~~~~---~~~~~L~~i~--~ls~~~~~~~~~~~~~~~~~ 60 (316)
T TIGR02239 13 DIKKLQEAGLHTVESVAY---APKKQLLEIK--GISEAKADKILAEAAKLVPM 60 (316)
T ss_pred HHHHHHHcCCCcHHHHHh---CCHHHHHHHh--CCCHHHHHHHHHHHHHhccc
Confidence 348999999999999977 5899999998 78999999999999988653
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=85.91 E-value=0.66 Score=46.36 Aligned_cols=48 Identities=23% Similarity=0.178 Sum_probs=42.3
Q ss_pred hcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhccccCC
Q 016693 262 FHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHARTCVLD 314 (384)
Q Consensus 262 ~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAktCvl~ 314 (384)
--++|+++||.||+||+. .++..|.++. |+|...++.+++.|+.+...
T Consensus 13 ~~~~L~~~g~~t~~~~~~---~~~~~L~~~~--gls~~~~~~i~~~~~~~~~~ 60 (313)
T TIGR02238 13 DIKKLKSAGICTVNGVIM---TTRRALCKIK--GLSEAKVDKIKEAASKIINP 60 (313)
T ss_pred HHHHHHHcCCCcHHHHHh---CCHHHHHHhc--CCCHHHHHHHHHHHHhhhcc
Confidence 448999999999999876 5889999997 89999999999999988654
No 4
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=85.61 E-value=0.7 Score=46.89 Aligned_cols=61 Identities=25% Similarity=0.188 Sum_probs=47.3
Q ss_pred ceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhccccCCC
Q 016693 250 VWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHARTCVLDK 315 (384)
Q Consensus 250 VwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAktCvl~~ 315 (384)
+-+|+.-|-.-.--++|+++||.||+|++. .++..|.++. |+|....+.+.+||.+|....
T Consensus 28 ~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~---~~~~~L~~i~--~is~~~~~~~~~~~~~~~~~~ 88 (342)
T PLN03186 28 IEQLQASGIAALDIKKLKDAGIHTVESLAY---APKKDLLQIK--GISEAKVEKILEAASKLVPLG 88 (342)
T ss_pred HHHHHhCCCCHHHHHHHHHcCCCcHHHHHh---CCHHHHHHhc--CCCHHHHHHHHHHHHHhcccc
Confidence 444444233333449999999999999876 4788999998 789999999999998876543
No 5
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=82.69 E-value=0.68 Score=45.57 Aligned_cols=57 Identities=19% Similarity=0.299 Sum_probs=45.4
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhcccc
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHARTCV 312 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAktCv 312 (384)
++-.|..||+. .-++|.++||+|++|++. .+++.|.+++ |++.+.++.+.+-|+.+.
T Consensus 7 ~l~~l~gIg~~--~a~~L~~~Gi~t~~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~a~~~~ 63 (317)
T PRK04301 7 DLEDLPGVGPA--TAEKLREAGYDTVEAIAV---ASPKELSEAA--GIGESTAAKIIEAAREAA 63 (317)
T ss_pred cHhhcCCCCHH--HHHHHHHcCCCCHHHHHc---CCHHHHHHhc--CCCHHHHHHHHHHHHHhh
Confidence 45556667754 459999999999999865 5999999998 678889998888887644
No 6
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=78.86 E-value=1.4 Score=44.81 Aligned_cols=60 Identities=20% Similarity=0.194 Sum_probs=47.0
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhccccC
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHARTCVL 313 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAktCvl 313 (384)
++..|+.-|-.-.--++|.++||+||+|++. .++..|-++. |+|...++.+++.|+..+.
T Consensus 30 ~~~~l~~~g~~~~~~~kL~~~g~~tv~~~~~---~~~~~L~~~~--g~s~~~~~ki~~~a~~~~~ 89 (344)
T PLN03187 30 SIDKLISQGINAGDVKKLQDAGIYTCNGLMM---HTKKNLTGIK--GLSEAKVDKICEAAEKLLN 89 (344)
T ss_pred CHHHHhhCCCCHHHHHHHHHcCCCcHHHHHh---CCHHHHHHhc--CCCHHHHHHHHHHHHHhhc
Confidence 3556655333334559999999999999876 5788899986 8899999999999887654
No 7
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=78.56 E-value=0.53 Score=35.66 Aligned_cols=50 Identities=34% Similarity=0.508 Sum_probs=40.1
Q ss_pred eeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhc
Q 016693 253 LEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHAR 309 (384)
Q Consensus 253 LekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAk 309 (384)
+.+||+.-+ ++|.++||.|++|+.. -+++.|.++= |++.+.=+.+++.|+
T Consensus 10 I~Gig~~~a--~~L~~~G~~t~~~l~~---a~~~~L~~i~--Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 10 IPGIGPKRA--EKLYEAGIKTLEDLAN---ADPEELAEIP--GIGEKTAEKIIEAAR 59 (60)
T ss_dssp STTCHHHHH--HHHHHTTCSSHHHHHT---SHHHHHHTST--TSSHHHHHHHHHHHH
T ss_pred CCCCCHHHH--HHHHhcCCCcHHHHHc---CCHHHHhcCC--CCCHHHHHHHHHHHh
Confidence 455666544 8899999999999866 4888899985 789999999998886
No 8
>PTZ00035 Rad51 protein; Provisional
Probab=72.16 E-value=3.8 Score=41.39 Aligned_cols=60 Identities=28% Similarity=0.250 Sum_probs=46.0
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhccccC
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHARTCVL 313 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAktCvl 313 (384)
++..|+.-|-.-.--++|.++||+||+||+. .++..|.++. |+|...=+.+++.|+.++.
T Consensus 22 ~~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~---~~~~~L~~~~--gis~~~~~~i~~~~~~~~~ 81 (337)
T PTZ00035 22 EIEKLQSAGINAADIKKLKEAGICTVESVAY---ATKKDLCNIK--GISEAKVEKIKEAASKLVP 81 (337)
T ss_pred cHHHHhcCCCCHHHHHHHHHcCCCcHHHHHh---CCHHHHHHhh--CCCHHHHHHHHHHHHHhcc
Confidence 4555654222233449999999999999876 5888999997 7899988999998887764
No 9
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=70.78 E-value=2.7 Score=43.07 Aligned_cols=51 Identities=24% Similarity=0.259 Sum_probs=40.7
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhc
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHAR 309 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAk 309 (384)
+|..|-+||+.-. ++|.+.||+|++|+.++ ++..|++.||. .+..+..||.
T Consensus 180 Pv~~l~GiG~~~~--~~L~~lGi~TigdL~~~---~~~~L~~~fG~-----~~~~l~~~a~ 230 (422)
T PRK03609 180 PVEEVWGVGRRIS--KKLNAMGIKTALDLADT---NIRFIRKHFNV-----VLERTVRELR 230 (422)
T ss_pred ChhhcCCccHHHH--HHHHHcCCCcHHHHhcC---CHHHHHHHHCH-----HHHHHHHHhC
Confidence 4666667887544 99999999999999885 88999999963 5777777775
No 10
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=69.81 E-value=3.5 Score=35.88 Aligned_cols=50 Identities=24% Similarity=0.173 Sum_probs=36.2
Q ss_pred hcccccccCCccHHHHHHHhccChHH--HHHHHccCCCchhHHHHHHhhccccC
Q 016693 262 FHKRLSRESINTVKDFLTLLVLDPSR--LRHILGTGMSTKMWEVTVEHARTCVL 313 (384)
Q Consensus 262 ~hk~L~~~~I~tV~dFL~l~~~d~~k--Lr~iLg~gms~k~W~~~v~HAktCvl 313 (384)
.-.+|+..||+|++|||..-.....+ |-+-+ |++.+-=...+.+|.=|..
T Consensus 7 ~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~--~i~~~~l~~w~~~AdL~ri 58 (122)
T PF14229_consen 7 EAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKL--GISERNLLKWVNQADLMRI 58 (122)
T ss_pred HHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhc--CCCHHHHHHHHhHHHhhhc
Confidence 44899999999999999986655444 55554 6777776666777765533
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=69.31 E-value=2.6 Score=41.08 Aligned_cols=50 Identities=22% Similarity=0.339 Sum_probs=38.0
Q ss_pred eeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhc
Q 016693 253 LEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHAR 309 (384)
Q Consensus 253 LekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAk 309 (384)
+.+||+. .-++|.++||.|++|++. .+++.|.+++ |++.+..+.+.+-|+
T Consensus 4 i~gig~~--~~~~L~~~Gi~ti~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 4 LPGVGPA--TAEKLREAGYDTFEAIAV---ASPKELSEIA--GISEGTAAKIIQAAR 53 (310)
T ss_pred cCCCCHH--HHHHHHHcCCCCHHHHHc---CCHHHHHhcc--CCCHHHHHHHHHHHH
Confidence 4455553 348999999999999877 5889999998 567777666666665
No 12
>PRK02406 DNA polymerase IV; Validated
Probab=67.45 E-value=3.9 Score=40.56 Aligned_cols=52 Identities=27% Similarity=0.289 Sum_probs=40.1
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhcc
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHART 310 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAkt 310 (384)
+|..|-+||+.-. ++|...||+|++|+.++ ++..|++.||. .+..+.+||.-
T Consensus 169 pi~~l~giG~~~~--~~L~~~Gi~ti~dl~~l---~~~~L~~~fG~-----~~~~l~~~a~G 220 (343)
T PRK02406 169 PVEKIPGVGKVTA--EKLHALGIYTCADLQKY---DLAELIRHFGK-----FGRRLYERARG 220 (343)
T ss_pred CcchhcCCCHHHH--HHHHHcCCCcHHHHHhC---CHHHHHHHHhH-----HHHHHHHHhCC
Confidence 5777777886544 88999999999999884 78899999974 45666666653
No 13
>PRK03352 DNA polymerase IV; Validated
Probab=58.09 E-value=3.3 Score=41.07 Aligned_cols=41 Identities=34% Similarity=0.429 Sum_probs=33.9
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHcc
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGT 294 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~ 294 (384)
+|..|-+||+... ++|...||+|++|++++ ++..|.+.||.
T Consensus 178 pl~~l~gig~~~~--~~L~~~Gi~ti~dl~~l---~~~~L~~~fG~ 218 (346)
T PRK03352 178 PTDALWGVGPKTA--KRLAALGITTVADLAAA---DPAELAATFGP 218 (346)
T ss_pred CHHHcCCCCHHHH--HHHHHcCCccHHHHhcC---CHHHHHHHhCh
Confidence 5677777888544 88999999999999885 78889999975
No 14
>PRK01172 ski2-like helicase; Provisional
Probab=56.89 E-value=8.3 Score=41.88 Aligned_cols=51 Identities=27% Similarity=0.458 Sum_probs=41.7
Q ss_pred eeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhcc
Q 016693 253 LEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHART 310 (384)
Q Consensus 253 LekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAkt 310 (384)
|.++++. ..++|.++||.||.|+.. .++++|-+|+ |++++.=+.++++|+.
T Consensus 617 ip~~~~~--~a~~l~~~g~~~~~di~~---~~~~~~~~i~--~~~~~~~~~i~~~~~~ 667 (674)
T PRK01172 617 IPKVGRV--RARRLYDAGFKTVDDIAR---SSPERIKKIY--GFSDTLANAIVNRAMK 667 (674)
T ss_pred CCCCCHH--HHHHHHHcCCCCHHHHHh---CCHHHHHHHh--ccCHHHHHHHHHHHHH
Confidence 3444443 559999999999999877 7888898898 6889999999999874
No 15
>PRK03858 DNA polymerase IV; Validated
Probab=56.54 E-value=4.1 Score=41.08 Aligned_cols=48 Identities=31% Similarity=0.373 Sum_probs=36.2
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhH
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMW 301 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W 301 (384)
+|..|-+||+.-. ++|.+.||+|++|+.+ .++..|++.||..+-...|
T Consensus 174 pl~~l~Gig~~~~--~~L~~~Gi~t~~dl~~---l~~~~L~~~fG~~~~~~l~ 221 (396)
T PRK03858 174 PVRRLWGVGPVTA--AKLRAHGITTVGDVAE---LPESALVSLLGPAAGRHLH 221 (396)
T ss_pred ChhhcCCCCHHHH--HHHHHhCCCcHHHHhc---CCHHHHHHHhCcHHHHHHH
Confidence 4666667888554 8999999999999986 5888999999753333333
No 16
>PRK14133 DNA polymerase IV; Provisional
Probab=54.73 E-value=9.5 Score=37.96 Aligned_cols=51 Identities=25% Similarity=0.365 Sum_probs=39.6
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhc
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHAR 309 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAk 309 (384)
+|..|-+||+... ++|.+-||+|++|++++ +...|+..||. .|..+.++|.
T Consensus 174 pv~~l~gig~~~~--~~L~~~Gi~ti~dl~~l---~~~~L~~rfG~-----~g~~l~~~a~ 224 (347)
T PRK14133 174 PISKVHGIGKKSV--EKLNNIGIYTIEDLLKL---SREFLIEYFGK-----FGVEIYERIR 224 (347)
T ss_pred CccccCCCCHHHH--HHHHHcCCccHHHHhhC---CHHHHHHHHhH-----HHHHHHHHhC
Confidence 5666667776544 78999999999999874 78889999963 4677777774
No 17
>PRK03348 DNA polymerase IV; Provisional
Probab=54.51 E-value=5.3 Score=41.77 Aligned_cols=48 Identities=27% Similarity=0.422 Sum_probs=37.7
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhH
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMW 301 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W 301 (384)
+|.+|-+||+... ++|...||+|++||.++ +...|++.||..+-..-|
T Consensus 181 Pv~~L~GIG~~t~--~~L~~lGI~TigDLa~l---~~~~L~~~fG~~~g~~L~ 228 (454)
T PRK03348 181 PVRRLWGIGPVTE--EKLHRLGIETIGDLAAL---SEAEVANLLGATVGPALH 228 (454)
T ss_pred CccccCCCCHHHH--HHHHHcCCccHHHHhcC---CHHHHHHHHCHHHHHHHH
Confidence 6888888887655 88999999999999874 788999999743333333
No 18
>PRK02794 DNA polymerase IV; Provisional
Probab=53.55 E-value=8.5 Score=39.51 Aligned_cols=55 Identities=25% Similarity=0.203 Sum_probs=42.3
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhccccC
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHARTCVL 313 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAktCvl 313 (384)
+|..|-+||+. .-++|...||+|++|+.++ +...|++.||. +|..+..+|.--+.
T Consensus 210 Pl~~L~GiG~~--~~~~L~~~GI~tigdL~~l---~~~~L~~rfG~-----~g~~l~~~a~G~d~ 264 (419)
T PRK02794 210 PVGIIWGVGPA--TAARLARDGIRTIGDLQRA---DEADLMRRFGS-----MGLRLWRLARGIDD 264 (419)
T ss_pred ChhhhCCCCHH--HHHHHHHhccchHHHHhhC---CHHHHHHHHhH-----HHHHHHHHhCCCCC
Confidence 45556667764 4489999999999998874 78899999974 57888888875543
No 19
>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=52.57 E-value=8.5 Score=38.17 Aligned_cols=51 Identities=31% Similarity=0.371 Sum_probs=39.5
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhc
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHAR 309 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAk 309 (384)
+|..|-+||+... ++|...||+|++|+.++ +.+.|.+.||. .|....++|+
T Consensus 177 pl~~l~gig~~~~--~~L~~~Gi~ti~dL~~~---~~~~L~~rfG~-----~~~~l~~~a~ 227 (344)
T cd01700 177 PVGDVWGIGRRTA--KKLNAMGIHTAGDLAQA---DPDLLRKKFGV-----VGERLVRELN 227 (344)
T ss_pred ChhhcCccCHHHH--HHHHHcCCCcHHHHhcC---CHHHHHHHHHH-----HHHHHHHHhC
Confidence 5666667777544 78999999999999885 78899999974 4666666765
No 20
>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=49.32 E-value=12 Score=36.57 Aligned_cols=52 Identities=29% Similarity=0.381 Sum_probs=40.2
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhcc
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHART 310 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAkt 310 (384)
+|..|-.||+.. -.+|...||+|++|+.++ ++..|.+.+| ..|....+||+-
T Consensus 172 pl~~l~gig~~~--~~~L~~~Gi~ti~dl~~~---~~~~L~~~~g-----~~~~~l~~~~~G 223 (334)
T cd03586 172 PVRKIPGVGKVT--AEKLKELGIKTIGDLAKL---DVELLKKLFG-----KSGRRLYELARG 223 (334)
T ss_pred CchhhCCcCHHH--HHHHHHcCCcCHHHHHcC---CHHHHHHHHh-----HHHHHHHHHhCC
Confidence 456666677544 488999999999999874 7888999885 468888888864
No 21
>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=46.82 E-value=45 Score=27.19 Aligned_cols=40 Identities=28% Similarity=0.535 Sum_probs=27.0
Q ss_pred CChhHHHHHHHHHHhHHHHhhhhhhHHHHHHhHHHHHHHHH
Q 016693 26 HTFKNVVQEVMKIQSVQHFLEPVLEPLIRRVVKEEVELALK 66 (384)
Q Consensus 26 ~~~~~vi~e~~~~~~~q~~~~~~lEp~lrrvV~EEve~~l~ 66 (384)
.++-.+++|+|+--- +.-+...|=.++.|+|++||++..+
T Consensus 33 ~TlE~lvremLRPmL-keWLD~nLP~lVErlVr~EIeRi~r 72 (73)
T PF10691_consen 33 RTLEDLVREMLRPML-KEWLDENLPGLVERLVREEIERIAR 72 (73)
T ss_pred ccHHHHHHHHHHHHH-HHHHHhccHHHHHHHHHHHHHHHhc
Confidence 347777777776432 2223335667899999999999764
No 22
>PRK03103 DNA polymerase IV; Reviewed
Probab=45.46 E-value=14 Score=37.72 Aligned_cols=52 Identities=27% Similarity=0.294 Sum_probs=39.3
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhcc
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHART 310 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAkt 310 (384)
+|..|-+||+. .-++|...||+|++|+.+ .++..|++.||. .|..+.++|.-
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 56666678875 448899999999999876 478889999963 35666666653
No 23
>PRK01810 DNA polymerase IV; Validated
Probab=45.13 E-value=14 Score=37.62 Aligned_cols=51 Identities=27% Similarity=0.277 Sum_probs=38.7
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhc
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHAR 309 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAk 309 (384)
+|..|-+||+.-. ++|...||+|++|+.+ .+...|++.||. .+..+.+||.
T Consensus 180 pv~~l~giG~~~~--~~L~~~Gi~tigdL~~---~~~~~L~~rfG~-----~g~~l~~~a~ 230 (407)
T PRK01810 180 PVGEMHGIGEKTA--EKLKDIGIQTIGDLAK---ADEHILRAKLGI-----NGVRLQRRAN 230 (407)
T ss_pred CHhhcCCcCHHHH--HHHHHcCCCcHHHHHh---CCHHHHHHHHhH-----HHHHHHHHhc
Confidence 4666667777544 8899999999999877 477889999964 3555666775
No 24
>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=43.70 E-value=6.5 Score=32.16 Aligned_cols=29 Identities=31% Similarity=0.479 Sum_probs=18.1
Q ss_pred ceeeeeecccchhcccccccCCccHHHHHHH
Q 016693 250 VWRLEKIGKDGAFHKRLSRESINTVKDFLTL 280 (384)
Q Consensus 250 VwRLekIgKdG~~hk~L~~~~I~tV~dFL~l 280 (384)
+..|-+||..- -+.|.+.||+||+||..+
T Consensus 5 l~~LpNig~~~--e~~L~~vGI~t~~~L~~~ 33 (81)
T PF04994_consen 5 LKDLPNIGPKS--ERMLAKVGIHTVEDLREL 33 (81)
T ss_dssp GCGSTT--HHH--HHHHHHTT--SHHHHHHH
T ss_pred hhhCCCCCHHH--HHHHHHcCCCCHHHHHHh
Confidence 34455565543 388999999999999875
No 25
>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=41.17 E-value=17 Score=36.14 Aligned_cols=55 Identities=27% Similarity=0.127 Sum_probs=40.5
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccC-hHHHHHHHccCCCchhHHHHHHhhccccC
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLD-PSRLRHILGTGMSTKMWEVTVEHARTCVL 313 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d-~~kLr~iLg~gms~k~W~~~v~HAktCvl 313 (384)
+|..|-+||+.-. ++|.+.||+|++|+.++ + ...|+..+| +.+..+.++|+--+.
T Consensus 174 pi~~l~giG~~~~--~~L~~~Gi~ti~dl~~~---~~~~~l~~~fg-----~~~~~l~~~a~G~d~ 229 (343)
T cd00424 174 PLTDLPGIGAVTA--KRLEAVGINPIGDLLAA---SPDALLALWGG-----VSGERLWYALRGIDD 229 (343)
T ss_pred ChhhcCCCCHHHH--HHHHHcCCCcHHHHhcC---CHHHHHHHHhh-----HHHHHHHHHhCCcCC
Confidence 5667777888544 89999999999998764 6 566777775 357777777765443
No 26
>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=40.96 E-value=16 Score=35.29 Aligned_cols=54 Identities=26% Similarity=0.457 Sum_probs=37.8
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhc
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHAR 309 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAk 309 (384)
...-|.+|+.+.+ ++|..+||.|+++++++ +++++..+| +......+.+.+.|.
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 4455668888765 89999999999999864 899999999 456688888888876
No 27
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=39.63 E-value=25 Score=31.92 Aligned_cols=60 Identities=18% Similarity=0.215 Sum_probs=43.1
Q ss_pred CCcceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHH-HHHhhcc
Q 016693 247 FDEVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEV-TVEHART 310 (384)
Q Consensus 247 ~DeVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~-~v~HAkt 310 (384)
.|+.-+|.+||. ++-+.|+..||+|-.|.-.+-..|-..+-..| +..-+.|.. -|+.|+.
T Consensus 66 ~DDLt~I~GIGP--k~e~~Ln~~GI~tfaQIAAwt~~di~~id~~l--~f~GRi~RDdWi~QAk~ 126 (133)
T COG3743 66 KDDLTRISGIGP--KLEKVLNELGIFTFAQIAAWTRADIAWIDDYL--NFDGRIERDDWIAQAKA 126 (133)
T ss_pred cccchhhcccCH--HHHHHHHHcCCccHHHHHhcCHHHHHHHHhhc--CCcchhHHHHHHHHHHH
Confidence 399999999998 46799999999997776554444444444455 567777765 6666653
No 28
>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=39.49 E-value=14 Score=29.02 Aligned_cols=35 Identities=29% Similarity=0.343 Sum_probs=22.4
Q ss_pred ccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHH
Q 016693 264 KRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEV 303 (384)
Q Consensus 264 k~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~ 303 (384)
..|..+||+||+|+++ .+++.|.++= |+..+.-+.
T Consensus 25 n~L~~~~I~tv~dL~~---~s~~~L~~i~--n~G~ksl~E 59 (66)
T PF03118_consen 25 NCLKRAGIHTVGDLVK---YSEEDLLKIK--NFGKKSLEE 59 (66)
T ss_dssp HHHHCTT--BHHHHHC---S-HHHHHTST--TSHHHHHHH
T ss_pred HHHHHhCCcCHHHHHh---CCHHHHHhCC--CCCHhHHHH
Confidence 6788999999999766 4667788874 444444444
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=39.25 E-value=11 Score=38.76 Aligned_cols=54 Identities=20% Similarity=0.178 Sum_probs=39.4
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhc
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHAR 309 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAk 309 (384)
+|..|-+||+.. -++|...||.|++|+..+- .++..|++.||. +.+..+..+|.
T Consensus 223 Pv~~l~GIG~~~--~~~L~~~Gi~t~~dl~~~~-~~~~~L~~~fG~----~~g~~L~~~a~ 276 (404)
T cd01701 223 KVGDLPGVGSSL--AEKLVKLFGDTCGGLELRS-KTKEKLQKVLGP----KTGEKLYDYCR 276 (404)
T ss_pred CHhHhCCCCHHH--HHHHHHcCCcchHHHHhCc-ccHHHHHHHHCH----HHHHHHHHHhC
Confidence 677777888654 4999999999999998751 127889999974 23444555553
No 30
>PRK01216 DNA polymerase IV; Validated
Probab=38.75 E-value=11 Score=38.31 Aligned_cols=51 Identities=22% Similarity=0.320 Sum_probs=38.0
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhh
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHA 308 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HA 308 (384)
+|..|-.||+... .+|...||+|++|+.+ .+...|++.||. ..+..+-.+|
T Consensus 179 Pi~~l~giG~~~~--~~L~~~Gi~TigdL~~---~~~~~L~~rfG~----~~~~~L~~~a 229 (351)
T PRK01216 179 DIADIPGIGDITA--EKLKKLGVNKLVDTLR---IEFDELKGIIGE----AKAKYLFSLA 229 (351)
T ss_pred CcccccCCCHHHH--HHHHHcCCCcHHHHhc---CCHHHHHHHHCH----HHHHHHHHHh
Confidence 5777778886544 9999999999999876 477889999974 2344444555
No 31
>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=36.70 E-value=13 Score=37.80 Aligned_cols=55 Identities=15% Similarity=0.148 Sum_probs=37.4
Q ss_pred cceeeeeecccchhccc-ccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhcc
Q 016693 249 EVWRLEKIGKDGAFHKR-LSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHART 310 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~-L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAkt 310 (384)
+|..|-.||+. .-++ |+..||.|++|+.++. .++..|++.||.. .+..+..+|+-
T Consensus 183 pv~~l~GiG~~--~~~~ll~~~Gi~ti~dl~~~~-~~~~~L~~~fG~~----~g~~l~~~a~G 238 (359)
T cd01702 183 PITSIRGLGGK--LGEEIIDLLGLPTEGDVAGFR-SSESDLQEHFGEK----LGEWLYNLLRG 238 (359)
T ss_pred cHHHhCCcCHH--HHHHHHHHcCCcCHHHHHhcc-CCHHHHHHHHHHH----HHHHHHHHhCC
Confidence 57777788742 2244 5889999999998754 4788899998742 34444455543
No 32
>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=35.21 E-value=28 Score=24.86 Aligned_cols=18 Identities=33% Similarity=0.702 Sum_probs=15.3
Q ss_pred eeeccceeeecCCccccc
Q 016693 185 IGSVGEISFTDNSSWTRS 202 (384)
Q Consensus 185 va~l~di~FtDnSs~~rs 202 (384)
-..+..+.|-|++.|++.
T Consensus 24 ~~~Ie~i~FaDGt~w~~~ 41 (43)
T PF06594_consen 24 SYRIEQIEFADGTVWTRA 41 (43)
T ss_pred CCcEeEEEEcCCCEecHH
Confidence 567899999999999863
No 33
>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=35.14 E-value=15 Score=37.66 Aligned_cols=58 Identities=16% Similarity=0.168 Sum_probs=39.1
Q ss_pred cceeeeeecccchhcccccccCCccHHHHHHHhc------------cChHHHHHHHccCCCchhHHHHHHhhcccc
Q 016693 249 EVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLV------------LDPSRLRHILGTGMSTKMWEVTVEHARTCV 312 (384)
Q Consensus 249 eVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~------------~d~~kLr~iLg~gms~k~W~~~v~HAktCv 312 (384)
+|..|-+||+... ++|.+.||.|++|+..+-+ .++..|++.||. +.+..+.++|+--+
T Consensus 173 pv~~l~GiG~~~~--~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~----~~g~~l~~~a~G~d 242 (379)
T cd01703 173 DLRKIPGIGYKTA--AKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGE----GIGQRIWKLLFGRD 242 (379)
T ss_pred CccccCCcCHHHH--HHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHCH----HHHHHHHHHHCCCC
Confidence 3445557877655 8999999999999986541 117789999864 23444555555433
No 34
>COG4766 EutQ Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=32.86 E-value=1.4e+02 Score=28.07 Aligned_cols=91 Identities=20% Similarity=0.225 Sum_probs=61.0
Q ss_pred HHHHHHHHH-hHHHHhhhhhhHHHHHHhHHHHHHHHHhcccc---ccCCCCCCcCCCCCCceEEEEecCCCCCcccCCcc
Q 016693 31 VVQEVMKIQ-SVQHFLEPVLEPLIRRVVKEEVELALKKHLAN---MKRNSEKEVHFPESRSLQLQFLNNLSLPVFTGARI 106 (384)
Q Consensus 31 vi~e~~~~~-~~q~~~~~~lEp~lrrvV~EEve~~l~~~~~~---~~rs~~~~~~~~~~~~~~L~F~n~l~~pifT~~kI 106 (384)
-|+|.+-.+ ++-++|+.-+|.++++|++|+.-....--.++ ..|-+.-..+-.+.-.+.|+|...=+.-+||++-+
T Consensus 13 ~i~~si~a~l~~~~~~~~l~~Qlm~kVmkek~s~~~~~~~~~~k~v~~ksgikvvk~s~vk~~~r~d~gqp~~V~~tdLv 92 (176)
T COG4766 13 RIRESIIAQLPEGQFTKELVEQLMEKVMKEKQSLECGWMQPSFKSVDGKSGIKVVKLSSVKFGLRFDTGQPDCVYTTDLV 92 (176)
T ss_pred HHHHHHHHhCChhhhhHHHHHHHHHHHHhchhhhhhhhcccceeecccCCceeEEecccceeEeeecCCCCCeEEeecee
Confidence 377766554 37778886677899999999976554433332 12222222233344568888988777889999988
Q ss_pred cccC-CccEEEEEeCC
Q 016693 107 EGDD-STIKVALVDTL 121 (384)
Q Consensus 107 ~a~~-~~I~V~L~D~~ 121 (384)
...+ .++-+.+..-.
T Consensus 93 t~~~g~~l~aG~m~~~ 108 (176)
T COG4766 93 TEQEGSRLGAGLMEMK 108 (176)
T ss_pred ecccCCccccceeeec
Confidence 8887 88888777643
No 35
>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=29.45 E-value=51 Score=23.35 Aligned_cols=41 Identities=24% Similarity=0.298 Sum_probs=31.4
Q ss_pred ccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhc
Q 016693 264 KRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHAR 309 (384)
Q Consensus 264 k~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAk 309 (384)
.+|..+||.||+++.. .+++.|..+- |++...=+.++.=|+
T Consensus 7 ~~L~~~G~~s~e~la~---~~~~eL~~i~--g~~~e~a~~ii~~a~ 47 (50)
T TIGR01954 7 QLLVEEGFTTVEDLAY---VPIDELLSIE--GFDEETAKELINRAR 47 (50)
T ss_pred HHHHHcCCCCHHHHHc---cCHHHHhcCC--CCCHHHHHHHHHHHH
Confidence 5789999999999754 6777888875 578777666666554
No 36
>PF04270 Strep_his_triad: Streptococcal histidine triad protein ; InterPro: IPR006270 This entry represents a repeated sequence region that includes a His-X-X-His-X-His (histidine triad) motif, which is found in family of Streptococcal proteins. Members of the family are suggested to cleave human complement component 3, and family member PhpA has been shown in vaccine studies to be a protective antigen in mice []. ; PDB: 2CS7_C.
Probab=27.09 E-value=44 Score=25.85 Aligned_cols=22 Identities=18% Similarity=0.289 Sum_probs=17.6
Q ss_pred EEeeCCCCChhhhhhhhhhHHH
Q 016693 347 QYVPIDKLSETQKAYFPYHIRS 368 (384)
Q Consensus 347 ~y~s~~~L~~~qk~~v~~~~~~ 368 (384)
+||+..+||+.|...++..+.+
T Consensus 31 HyI~k~dLs~~E~~aA~~~~~~ 52 (53)
T PF04270_consen 31 HYIPKSDLSASELKAAQAYLAG 52 (53)
T ss_dssp EEEEGGGS-HHHHHHHHHHHH-
T ss_pred cCCchhhCCHHHHHHHHHHHhc
Confidence 4999999999999999887654
No 37
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=26.95 E-value=30 Score=30.15 Aligned_cols=39 Identities=26% Similarity=0.529 Sum_probs=29.5
Q ss_pred ceeeeeecccchhcccccccCCccHHHHHHHhccChHHHHHHHc
Q 016693 250 VWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILG 293 (384)
Q Consensus 250 VwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg 293 (384)
.+|..+||. .|..-|..+||.||+++- ..+|++|.+-++
T Consensus 55 L~ri~gi~~--~~a~LL~~AGv~Tv~~LA---~~~p~~L~~~l~ 93 (122)
T PF14229_consen 55 LMRIPGIGP--QYAELLEHAGVDTVEELA---QRNPQNLHQKLG 93 (122)
T ss_pred hhhcCCCCH--HHHHHHHHhCcCcHHHHH---hCCHHHHHHHHH
Confidence 446666665 466899999999999974 488988887543
No 38
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=26.73 E-value=22 Score=39.15 Aligned_cols=38 Identities=29% Similarity=0.358 Sum_probs=31.7
Q ss_pred CCCCCcceeeeeecccchhcccccccCCccHHHHHHHhcc
Q 016693 244 PVLFDEVWRLEKIGKDGAFHKRLSRESINTVKDFLTLLVL 283 (384)
Q Consensus 244 P~L~DeVwRLekIgKdG~~hk~L~~~~I~tV~dFL~l~~~ 283 (384)
+.|+++|-.|++||+.-+ +.|++-||+||.|.|..+=+
T Consensus 5 ~~~~~~~~~l~gvg~~~~--~~l~~lgi~t~~dll~~~P~ 42 (681)
T PRK10917 5 LLLDAPLTSLKGVGPKTA--EKLAKLGIHTVQDLLLHLPR 42 (681)
T ss_pred ccccCChhhcCCCCHHHH--HHHHHcCCCCHHHHhhcCCC
Confidence 457789999999987554 88889999999999988643
No 39
>PRK07758 hypothetical protein; Provisional
Probab=26.66 E-value=70 Score=27.53 Aligned_cols=37 Identities=16% Similarity=0.260 Sum_probs=24.9
Q ss_pred ccccccCCccHHHHHHHhccChHHHHHHHccCCCchhHHHHH
Q 016693 264 KRLSRESINTVKDFLTLLVLDPSRLRHILGTGMSTKMWEVTV 305 (384)
Q Consensus 264 k~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v 305 (384)
..|..+||+||+|+.+ .+++.|-++= |+..+.-+.+.
T Consensus 48 N~Lk~AGI~TL~dLv~---~te~ELl~ik--nlGkKSL~EIk 84 (95)
T PRK07758 48 RALEHHGIHTVEELSK---YSEKEILKLH--GMGPASLPKLR 84 (95)
T ss_pred HHHHHcCCCcHHHHHc---CCHHHHHHcc--CCCHHHHHHHH
Confidence 6677899999999766 5555666663 44555555543
No 40
>PRK05256 condesin subunit E; Provisional
Probab=25.37 E-value=78 Score=31.24 Aligned_cols=74 Identities=18% Similarity=0.142 Sum_probs=50.1
Q ss_pred ccccccCCccHHHHHHHhc--cChHHHHHHHc--cCCCchhHHHHHHhhccccC--CCcEEEEcCCCCCcceEEEEeccc
Q 016693 264 KRLSRESINTVKDFLTLLV--LDPSRLRHILG--TGMSTKMWEVTVEHARTCVL--DKRVYLYCPPGTQQKSGVVFNVVG 337 (384)
Q Consensus 264 k~L~~~~I~tV~dFL~l~~--~d~~kLr~iLg--~gms~k~W~~~v~HAktCvl--~~~~y~y~~~~~~~~v~l~FN~i~ 337 (384)
++|++.||.|+++.+.-+. .|+++|.+.++ .+-|+-+-+++.+-.+||-- ..-=.+|... +..+..-+=++||
T Consensus 107 erLa~~gift~qeL~deL~~ladE~kllklvn~R~~GsDlD~~Kl~ekvr~sLrrLrRlgmI~~l~-~d~~kF~iteAvf 185 (238)
T PRK05256 107 ERLAHEGIFTQQELYDELLTLADEAKLLKLVNNRSTGSDLDKQKLQEKVRTSLNRLRRLGMVWFMG-HDSSKFRITESVF 185 (238)
T ss_pred HHHhcCCceeHHHHHHHHHHhhcHHHHHHHhcCCCCcchhhHHHHHHHHHHHHHHHHhccceeeec-CCCceEEecHHHH
Confidence 7999999999999886544 58999999985 22377777888888898863 3322344333 1334444445555
Q ss_pred e
Q 016693 338 Q 338 (384)
Q Consensus 338 ~ 338 (384)
.
T Consensus 186 R 186 (238)
T PRK05256 186 R 186 (238)
T ss_pred h
Confidence 4
No 41
>smart00100 cNMP Cyclic nucleotide-monophosphate binding domain. Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.
Probab=25.24 E-value=1.6e+02 Score=22.36 Aligned_cols=41 Identities=0% Similarity=-0.067 Sum_probs=26.4
Q ss_pred CCCchhHHHHHHhhccccCCCcEEEEcCCCCCcceEEEEec
Q 016693 295 GMSTKMWEVTVEHARTCVLDKRVYLYCPPGTQQKSGVVFNV 335 (384)
Q Consensus 295 gms~k~W~~~v~HAktCvl~~~~y~y~~~~~~~~v~l~FN~ 335 (384)
+++...|+.+.+|++...+...-++|+......++.++-+-
T Consensus 4 ~l~~~~~~~l~~~~~~~~~~~g~~l~~~g~~~~~~y~v~~G 44 (120)
T smart00100 4 NLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIILSG 44 (120)
T ss_pred CCCHHHHHHHHHhceEEEeCCCCEEEeCCCcCCcEEEEEee
Confidence 58999999999999887766655555543223334444333
No 42
>PF09039 HTH_Tnp_Mu_2: Mu DNA binding, I gamma subdomain; InterPro: IPR015126 This domain is responsible for binding the DNA attachment sites at each end of the Mu genome. They adopt a secondary structure comprising a four helix bundle tightly packed around a hydrophobic core consisting of aliphatic and aromatic amino acid residues. Helices 1 and 2 are oriented antiparallel to each other. Helix 3 crosses helices 1 and 2 at angles of 60 and 120 degrees, respectively. Excluding the C-terminal helix 4, the fold of the I-gamma subdomain is remarkably similar to that of the homeodomain family of helix-turn-helix DNA-binding proteins, although their amino acid sequences are completely unrelated []. ; PDB: 2EZL_A 2EZH_A 2EZI_A 2EZK_A.
Probab=24.98 E-value=1.1e+02 Score=26.43 Aligned_cols=40 Identities=20% Similarity=0.300 Sum_probs=21.7
Q ss_pred cccCCCChhHHHHHHHHHHhHHHHhhhhhhHHHHHHhHHHH
Q 016693 21 KRRKGHTFKNVVQEVMKIQSVQHFLEPVLEPLIRRVVKEEV 61 (384)
Q Consensus 21 kr~~~~~~~~vi~e~~~~~~~q~~~~~~lEp~lrrvV~EEv 61 (384)
-|+..|+|+...+++..+-.-+.+-.|++-.+-||+ .+||
T Consensus 44 Lr~e~Ps~~~cyrr~~~~a~~~Gw~iPS~~t~rRri-~~ev 83 (108)
T PF09039_consen 44 LRPEKPSFSACYRRLKRAAKENGWPIPSEKTLRRRI-EREV 83 (108)
T ss_dssp TSTT---HHHHHHHHHHHHHHHT-----HHHHHHHH--HHH
T ss_pred cCccCCCHHHHHHHHHHHHHHcCCCCCCHHHHHHHH-HHhC
Confidence 345678999988888777666666667777766666 5555
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=24.42 E-value=33 Score=33.49 Aligned_cols=35 Identities=20% Similarity=0.350 Sum_probs=29.1
Q ss_pred eecccchhcccccccCCccHHHHHHHhccChHHHHHHHcc
Q 016693 255 KIGKDGAFHKRLSRESINTVKDFLTLLVLDPSRLRHILGT 294 (384)
Q Consensus 255 kIgKdG~~hk~L~~~~I~tV~dFL~l~~~d~~kLr~iLg~ 294 (384)
.||+... .+|.+.||+|++||..+ +...|++.||.
T Consensus 177 gig~~~~--~~L~~~Gi~t~~dl~~~---~~~~l~~rfG~ 211 (335)
T cd03468 177 RLPPETV--ELLARLGLRTLGDLAAL---PRAELARRFGL 211 (335)
T ss_pred CCCHHHH--HHHHHhCcccHHHHHhC---ChHHHHhhcCH
Confidence 5777655 89999999999998874 77889999975
No 44
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=23.68 E-value=62 Score=27.36 Aligned_cols=60 Identities=25% Similarity=0.387 Sum_probs=40.9
Q ss_pred CCCCCcceeeeeecccchhcccccccCCcc----HHHHHHHhccChHHHHHHHccCCCchhHHHHHHhhccc
Q 016693 244 PVLFDEVWRLEKIGKDGAFHKRLSRESINT----VKDFLTLLVLDPSRLRHILGTGMSTKMWEVTVEHARTC 311 (384)
Q Consensus 244 P~L~DeVwRLekIgKdG~~hk~L~~~~I~t----V~dFL~l~~~d~~kLr~iLg~gms~k~W~~~v~HAktC 311 (384)
|+=+-+|--|.+||.. +-.+|..+|+.. .++|| ++.+|++-.+.-| ...--++-+||++|
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 6667789999999984 558999999976 47777 4678876555433 11112266777776
No 45
>COG4472 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.26 E-value=29 Score=29.29 Aligned_cols=40 Identities=18% Similarity=0.347 Sum_probs=28.9
Q ss_pred EeccceeeeeeeCCE--EeeCCCCChhhh------hhhhhhHHHHHhh
Q 016693 333 FNVVGQVMGLLSECQ--YVPIDKLSETQK------AYFPYHIRSFVSC 372 (384)
Q Consensus 333 FN~i~~lvG~~~~g~--y~s~~~L~~~qk------~~v~~~~~~~~~~ 372 (384)
+|+|.||||-..-|. |+|-.+=-.+|- ..++.||+.+|++
T Consensus 36 YNpiNQiVGYllSGDPaYIpr~ndARn~IRk~eRDeIvEElvk~YLk~ 83 (88)
T COG4472 36 YNPINQIVGYLLSGDPAYIPRYNDARNQIRKLERDEIVEELVKYYLKG 83 (88)
T ss_pred CChHHHHHhhhccCCccccCccccHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 699999999887774 999765444432 3456788888765
No 46
>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=23.24 E-value=1.3e+02 Score=25.29 Aligned_cols=35 Identities=31% Similarity=0.529 Sum_probs=27.8
Q ss_pred ccCCccHHHHHHHhccChHHHHH---HHccCCCchhHHHHHHhhcc
Q 016693 268 RESINTVKDFLTLLVLDPSRLRH---ILGTGMSTKMWEVTVEHART 310 (384)
Q Consensus 268 ~~~I~tV~dFL~l~~~d~~kLr~---iLg~gms~k~W~~~v~HAkt 310 (384)
...| +++||+=++-.||.||-. +| .|+..++-|+.
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 4567 999999999999976655 45 58888888875
No 47
>PF00853 Runt: Runt domain; InterPro: IPR013524 The AML1 gene is rearranged by the t(8;21) translocation in acute myeloid leukemia []. The gene is highly similar to the Drosophila melanogaster segmentation gene runt and to the mouse transcription factor PEBP2 alpha subunit gene []. The region of shared similarity, known as the Runt domain, is responsible for DNA-binding and protein-protein interaction. In addition to the highly-conserved Runt domain, the AML-1 gene product carries a putative ATP-binding site (GRSGRGKS), and has a C-terminal region rich in proline and serine residues. The protein (known as acute myeloid leukemia 1 protein, oncogene AML-1, core-binding factor (CBF), alpha-B subunit, etc.) binds to the core site, 5'-pygpyggt-3', of a number of enhancers and promoters. The protein is a heterodimer of alpha- and beta-subunits. The alpha-subunit binds DNA as a monomer, and appears to have a role in the development of normal hematopoiesis. CBF is a nuclear protein expressed in numerous tissue types, except brain and heart; highest levels have been found to occur in thymus, bone marrow and peripheral blood. This domain occurs towards the N terminus of the proteins in this entry.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1E50_E 1LJM_A 1CO1_A 1H9D_C 1CMO_A 1EAO_B 1HJC_D 1HJB_F 2J6W_B 1EAN_A ....
Probab=20.01 E-value=1.6e+02 Score=26.80 Aligned_cols=35 Identities=23% Similarity=0.432 Sum_probs=26.4
Q ss_pred EEEeccceeeccceeeecCCccccccceEEEEEeecC
Q 016693 178 FLTLKEGIGSVGEISFTDNSSWTRSRRFRLGARVVDN 214 (384)
Q Consensus 178 ~v~L~~Gva~l~di~FtDnSs~~rsrKFRLgaRvv~~ 214 (384)
.-.|+|++|-+.|+.|.--|. |.+.|-|-.-+...
T Consensus 74 tavmknqvA~FnDLRFvGRSG--RGKsFtltItv~t~ 108 (135)
T PF00853_consen 74 TAVMKNQVARFNDLRFVGRSG--RGKSFTLTITVFTN 108 (135)
T ss_dssp EEEEETTEEEESS-EECST-T--TTSEEEEEEEE-SS
T ss_pred hhhhhcccccccccccccccC--CccceEEEEEEeCC
Confidence 678999999999999998666 44569998887754
Done!