Query 006693
Match_columns 635
No_of_seqs 146 out of 172
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 13:07:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006693.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006693hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07887 Calmodulin_bind: Calm 100.0 1E-119 3E-124 922.4 28.4 293 97-392 1-299 (299)
2 TIGR02239 recomb_RAD51 DNA rep 86.1 0.83 1.8E-05 48.5 4.2 49 273-326 12-60 (316)
3 PLN03186 DNA repair protein RA 84.3 0.86 1.9E-05 49.2 3.4 62 261-327 27-88 (342)
4 TIGR02238 recomb_DMC1 meiotic 83.5 1.2 2.6E-05 47.5 3.9 50 273-327 12-61 (313)
5 PRK04301 radA DNA repair and r 79.1 1.4 3E-05 46.3 2.6 58 261-325 7-64 (317)
6 PLN03187 meiotic recombination 77.9 2 4.4E-05 46.6 3.4 61 261-326 30-90 (344)
7 PF14520 HHH_5: Helix-hairpin- 73.4 0.88 1.9E-05 36.8 -0.6 53 263-322 8-60 (60)
8 PTZ00035 Rad51 protein; Provis 69.9 4.3 9.3E-05 43.7 3.5 61 261-326 22-82 (337)
9 PRK03609 umuC DNA polymerase V 66.3 4.4 9.6E-05 44.3 2.8 52 261-322 180-231 (422)
10 TIGR02236 recomb_radA DNA repa 63.9 4.9 0.00011 41.8 2.5 54 264-324 3-56 (310)
11 PRK02406 DNA polymerase IV; Va 63.1 6.1 0.00013 41.8 3.0 52 261-322 169-220 (343)
12 PF14229 DUF4332: Domain of un 62.9 9.2 0.0002 35.6 3.8 53 273-327 6-60 (122)
13 PF10691 DUF2497: Protein of u 55.7 25 0.00055 30.7 5.0 40 34-74 33-73 (73)
14 PRK03352 DNA polymerase IV; Va 53.3 5.8 0.00013 42.0 0.9 41 261-306 178-218 (346)
15 PRK03858 DNA polymerase IV; Va 51.2 7.2 0.00016 42.0 1.2 48 261-313 174-221 (396)
16 PRK03348 DNA polymerase IV; Pr 50.6 8.3 0.00018 43.0 1.6 48 261-313 181-228 (454)
17 PRK14133 DNA polymerase IV; Pr 49.9 14 0.00031 39.2 3.2 51 261-321 174-224 (347)
18 PRK01172 ski2-like helicase; P 49.7 16 0.00035 42.3 3.7 51 265-322 617-667 (674)
19 PRK02794 DNA polymerase IV; Pr 48.4 13 0.00029 40.6 2.7 55 261-325 210-264 (419)
20 cd01700 PolY_Pol_V_umuC umuC s 46.4 14 0.0003 39.2 2.4 51 261-321 177-227 (344)
21 COG3743 Uncharacterized conser 46.3 22 0.00047 34.5 3.4 60 259-322 66-126 (133)
22 cd03586 PolY_Pol_IV_kappa DNA 44.8 18 0.0004 37.7 3.0 52 261-322 172-223 (334)
23 PRK01810 DNA polymerase IV; Va 41.5 19 0.00042 39.1 2.6 51 261-321 180-230 (407)
24 PRK03103 DNA polymerase IV; Re 40.7 21 0.00045 38.8 2.7 52 261-322 182-233 (409)
25 PF04994 TfoX_C: TfoX C-termin 38.5 13 0.00029 32.5 0.7 70 261-370 4-74 (81)
26 PF11754 Velvet: Velvet factor 38.2 1.9E+02 0.0042 29.2 8.9 61 181-244 97-171 (203)
27 cd00424 PolY Y-family of DNA p 37.3 25 0.00054 37.3 2.6 56 261-326 174-230 (343)
28 cd01701 PolY_Rev1 DNA polymera 34.5 19 0.00041 39.5 1.2 54 261-321 223-276 (404)
29 PRK01216 DNA polymerase IV; Va 34.1 19 0.00041 39.0 1.1 51 261-320 179-229 (351)
30 PF02889 Sec63: Sec63 Brl doma 33.5 33 0.00071 35.4 2.7 55 260-321 148-202 (314)
31 cd01702 PolY_Pol_eta DNA Polym 32.4 22 0.00049 38.6 1.3 55 261-322 183-238 (359)
32 cd07978 TAF13 The TATA Binding 32.1 72 0.0016 28.8 4.2 35 280-322 52-89 (92)
33 PRK15457 ethanolamine utilizat 31.3 1.1E+02 0.0023 32.3 5.9 72 56-129 90-162 (233)
34 PF14229 DUF4332: Domain of un 29.9 33 0.00071 32.0 1.8 38 262-304 55-92 (122)
35 KOG4233 DNA-bridging protein B 28.6 57 0.0012 29.5 2.9 60 256-323 15-78 (90)
36 KOG2856 Adaptor protein PACSIN 27.8 93 0.002 35.0 5.0 25 374-398 286-310 (472)
37 cd01703 PolY_Pol_iota DNA Poly 27.1 30 0.00065 38.0 1.2 58 262-325 174-243 (379)
38 PF03118 RNA_pol_A_CTD: Bacter 26.8 32 0.00069 29.0 1.0 37 274-315 23-59 (66)
39 TIGR02979 phageshock_pspD phag 25.0 77 0.0017 27.0 2.9 25 37-65 29-53 (59)
40 COG4766 EutQ Ethanolamine util 23.2 2.6E+02 0.0056 28.2 6.6 94 38-132 12-108 (176)
41 COG3827 Uncharacterized protei 22.3 1.5E+02 0.0033 31.1 5.1 41 33-74 187-228 (231)
42 PRK10917 ATP-dependent DNA hel 22.2 35 0.00076 40.1 0.6 38 256-295 5-42 (681)
43 PF09584 Phageshock_PspD: Phag 22.1 90 0.002 27.1 2.8 15 52-66 45-59 (66)
44 PF11033 ComJ: Competence prot 22.0 2.7E+02 0.0058 26.9 6.3 26 148-174 9-34 (125)
45 PF06594 HCBP_related: Haemoly 20.6 63 0.0014 24.8 1.5 18 196-213 24-41 (43)
46 PRK10497 peripheral inner memb 20.1 1.1E+02 0.0024 27.1 3.0 14 52-65 52-65 (73)
No 1
>PF07887 Calmodulin_bind: Calmodulin binding protein-like; InterPro: IPR012416 The members of this family are putative or actual calmodulin binding proteins expressed by various plant species. Some members (for example, Q8H6T7 from SWISSPROT), are known to be involved in the induction of plant defence responses []. However, their precise function in this regard is as yet unknown.
Probab=100.00 E-value=1.5e-119 Score=922.38 Aligned_cols=293 Identities=70% Similarity=1.178 Sum_probs=288.6
Q ss_pred ceEEEeccCCCCCcccCCcccccCCCceEEEEEeCCCCceeccCCCccceEEEEEeeCCCCCCCCCCCCHHHHhhccccc
Q 006693 97 NLQLYFRSRLSLPLFTGGKVEGEQGAAIHVVLVDANTGHVVTSGPEASVKLDIVVLEGDFNNEDDDGWTQEEFESHVVKE 176 (635)
Q Consensus 97 ~~~L~F~n~l~~pifTg~kI~ae~g~~I~V~LvD~~tg~iVt~GplSs~kvEIvVLdGDF~~~~~e~WT~eEF~~~IVk~ 176 (635)
+|||+|+|+|++|||||++|+|+||+||+|+|+|++|+ |++||+|++|||||||||||+++++++||+|||++|||++
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 CCCCCCccccceEEEEecceeccCCeeeecCCccccccccEEEEEeecCCCCcceeeeecccceEeeecCccccccCCCC
Q 006693 177 REGKRPLLTGDLQVTLKEGVGTLGDLTFTDNSSWIRSRKFRLGLKVASGYCEGIRIREAKTEAFTVKDHRGELYKKHYPP 256 (635)
Q Consensus 177 ReGKrpLL~Gdl~v~Lk~Gva~L~di~FTDnSSw~RSrKFRLgaRvv~~~~~g~RI~EAvsE~FvVkDhRgE~ykKh~pP 256 (635)
|+||+|||+|+|+|+|+||+|+|+||+|||||||+|||||||||||+++++.|+|||||+||||+|||||||+|||||||
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 CCCCccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhcccccCCceEEEecCC
Q 006693 257 ALNDDVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLSGKLYVYYPED 336 (635)
Q Consensus 257 ~L~DeVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAktCvl~~kly~y~~~~ 336 (635)
+|+|||||||||||||+|||+|+++||+||+|||+++++||++||+|||+|||++||++||+|||||++++++|+|| ++
T Consensus 159 ~L~DeVwRLe~Igk~G~~hk~L~~~~I~tV~dFl~l~~~d~~~Lr~ilg~~ms~k~We~~v~HA~tCvl~~~~y~y~-~~ 237 (299)
T PF07887_consen 159 SLDDEVWRLEKIGKDGAFHKRLKKNGINTVEDFLKLLNKDPQKLREILGSGMSNKMWETTVEHAKTCVLGDKLYVYY-DE 237 (299)
T ss_pred CCCCchhhhhhccccCHHHHHHHHcCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHHHHHHHHhcCCCCcEEEEE-ec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999 56
Q ss_pred CcceEEEEccccceeeeeeCCeeecCCCCChHhh------HHHHHHhcccccccCccccccc
Q 006693 337 SRNVGVVFNNIYELNGLISGEQYFPADALPESQK------VKKAYDNWNQVVEYDGKSLLSL 392 (635)
Q Consensus 337 ~~nvgl~FN~i~~lvG~~~~g~y~s~d~L~~~Qk------vk~AY~n~~~~~e~d~~~l~n~ 392 (635)
++|++|+|||||+||||+|+|+|+++|+|++.|| +++||+||++|++||++|++|+
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 7899999999999999999999999999999999 8899999999999999999985
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=86.11 E-value=0.83 Score=48.54 Aligned_cols=49 Identities=27% Similarity=0.308 Sum_probs=43.3
Q ss_pred hhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhcccccC
Q 006693 273 SFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLS 326 (635)
Q Consensus 273 ~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 326 (635)
.--++|+++||.||+||+. .++..|.+++ |+|...++.+..||.+|...
T Consensus 12 ~~~~~l~~~g~~t~~~~~~---~~~~~L~~i~--~ls~~~~~~~~~~~~~~~~~ 60 (316)
T TIGR02239 12 ADIKKLQEAGLHTVESVAY---APKKQLLEIK--GISEAKADKILAEAAKLVPM 60 (316)
T ss_pred HHHHHHHHcCCCcHHHHHh---CCHHHHHHHh--CCCHHHHHHHHHHHHHhccc
Confidence 4568999999999999986 4899999998 79999999999999999653
No 3
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=84.30 E-value=0.86 Score=49.22 Aligned_cols=62 Identities=29% Similarity=0.338 Sum_probs=49.4
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhcccccCC
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLSG 327 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAktCvl~~ 327 (635)
++-+|..-|..-.--++|+++||.||+||+.+ ++..|.+|+ |+|....+.+++||.+|....
T Consensus 27 ~~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~---~~~~L~~i~--~is~~~~~~~~~~~~~~~~~~ 88 (342)
T PLN03186 27 PIEQLQASGIAALDIKKLKDAGIHTVESLAYA---PKKDLLQIK--GISEAKVEKILEAASKLVPLG 88 (342)
T ss_pred cHHHHHhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHHhcccc
Confidence 35555553444456789999999999998764 788999998 799999999999999886543
No 4
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=83.47 E-value=1.2 Score=47.47 Aligned_cols=50 Identities=24% Similarity=0.339 Sum_probs=43.4
Q ss_pred hhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhcccccCC
Q 006693 273 SFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLSG 327 (635)
Q Consensus 273 ~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAktCvl~~ 327 (635)
.--++|+++||.||+||+. .++..|.++. |+|...++.+++.|+.+...+
T Consensus 12 ~~~~~L~~~g~~t~~~~~~---~~~~~L~~~~--gls~~~~~~i~~~~~~~~~~~ 61 (313)
T TIGR02238 12 ADIKKLKSAGICTVNGVIM---TTRRALCKIK--GLSEAKVDKIKEAASKIINPG 61 (313)
T ss_pred HHHHHHHHcCCCcHHHHHh---CCHHHHHHhc--CCCHHHHHHHHHHHHhhhccc
Confidence 4568999999999999876 4788999997 899999999999999986553
No 5
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=79.13 E-value=1.4 Score=46.27 Aligned_cols=58 Identities=21% Similarity=0.333 Sum_probs=47.0
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhccccc
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVL 325 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAktCvl 325 (635)
++-.|.+||+ ...++|.++||.|++|++. .|+..|.+++ |++.+.++.+++-|+.|+.
T Consensus 7 ~l~~l~gIg~--~~a~~L~~~Gi~t~~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~a~~~~~ 64 (317)
T PRK04301 7 DLEDLPGVGP--ATAEKLREAGYDTVEAIAV---ASPKELSEAA--GIGESTAAKIIEAAREAAD 64 (317)
T ss_pred cHhhcCCCCH--HHHHHHHHcCCCCHHHHHc---CCHHHHHHhc--CCCHHHHHHHHHHHHHhhc
Confidence 3555666775 4569999999999999965 5999999998 7889999999999886553
No 6
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=77.93 E-value=2 Score=46.58 Aligned_cols=61 Identities=20% Similarity=0.323 Sum_probs=48.6
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhcccccC
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLS 326 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 326 (635)
++..|+.-|-.=.--++|.++||+||+|++.. ++..|-++. |+|....+.+++.|+..+..
T Consensus 30 ~~~~l~~~g~~~~~~~kL~~~g~~tv~~~~~~---~~~~L~~~~--g~s~~~~~ki~~~a~~~~~~ 90 (344)
T PLN03187 30 SIDKLISQGINAGDVKKLQDAGIYTCNGLMMH---TKKNLTGIK--GLSEAKVDKICEAAEKLLNQ 90 (344)
T ss_pred CHHHHhhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHHhhcc
Confidence 46667654444456799999999999998764 788899986 89999999999999887643
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=73.39 E-value=0.88 Score=36.84 Aligned_cols=53 Identities=30% Similarity=0.528 Sum_probs=42.0
Q ss_pred ceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006693 263 WRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (635)
Q Consensus 263 wRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAkt 322 (635)
-.+.+||+.- .++|.++||.|++|+.. .+++.|.++= |++.+.=+.+++.|+.
T Consensus 8 ~~I~Gig~~~--a~~L~~~G~~t~~~l~~---a~~~~L~~i~--Gig~~~a~~i~~~~~~ 60 (60)
T PF14520_consen 8 LSIPGIGPKR--AEKLYEAGIKTLEDLAN---ADPEELAEIP--GIGEKTAEKIIEAARE 60 (60)
T ss_dssp HTSTTCHHHH--HHHHHHTTCSSHHHHHT---SHHHHHHTST--TSSHHHHHHHHHHHHH
T ss_pred ccCCCCCHHH--HHHHHhcCCCcHHHHHc---CCHHHHhcCC--CCCHHHHHHHHHHHhC
Confidence 3456677654 48999999999999866 4778899874 7899999999988863
No 8
>PTZ00035 Rad51 protein; Provisional
Probab=69.86 E-value=4.3 Score=43.68 Aligned_cols=61 Identities=26% Similarity=0.332 Sum_probs=48.2
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhcccccC
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVLS 326 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 326 (635)
++..|..-|-.=.--++|+++||+||+||+. .++..|-++. |+|...=+.+++.|+.++..
T Consensus 22 ~~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~---~~~~~L~~~~--gis~~~~~~i~~~~~~~~~~ 82 (337)
T PTZ00035 22 EIEKLQSAGINAADIKKLKEAGICTVESVAY---ATKKDLCNIK--GISEAKVEKIKEAASKLVPM 82 (337)
T ss_pred cHHHHhcCCCCHHHHHHHHHcCCCcHHHHHh---CCHHHHHHhh--CCCHHHHHHHHHHHHHhccc
Confidence 4666655333334669999999999999876 4788999997 79999999999999887643
No 9
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=66.34 E-value=4.4 Score=44.32 Aligned_cols=52 Identities=19% Similarity=0.261 Sum_probs=41.7
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAkt 322 (635)
+|..|-+||+ ...++|.+.||+|++|+.++ ++..|++.||. .+..+..||.-
T Consensus 180 Pv~~l~GiG~--~~~~~L~~lGi~TigdL~~~---~~~~L~~~fG~-----~~~~l~~~a~G 231 (422)
T PRK03609 180 PVEEVWGVGR--RISKKLNAMGIKTALDLADT---NIRFIRKHFNV-----VLERTVRELRG 231 (422)
T ss_pred ChhhcCCccH--HHHHHHHHcCCCcHHHHhcC---CHHHHHHHHCH-----HHHHHHHHhCC
Confidence 4566667887 45599999999999999985 88899999973 57778888753
No 10
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=63.90 E-value=4.9 Score=41.80 Aligned_cols=54 Identities=22% Similarity=0.362 Sum_probs=41.7
Q ss_pred eeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhcccc
Q 006693 264 RLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCV 324 (635)
Q Consensus 264 RLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAktCv 324 (635)
.|.+||+. .-++|.++||.|++|++. .|++.|.+++ |++.+..+.+.+-|+.|.
T Consensus 3 ~i~gig~~--~~~~L~~~Gi~ti~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~~~~~~ 56 (310)
T TIGR02236 3 DLPGVGPA--TAEKLREAGYDTFEAIAV---ASPKELSEIA--GISEGTAAKIIQAARKAA 56 (310)
T ss_pred ccCCCCHH--HHHHHHHcCCCCHHHHHc---CCHHHHHhcc--CCCHHHHHHHHHHHHHHh
Confidence 34556653 458999999999999877 4889999998 577778777777776443
No 11
>PRK02406 DNA polymerase IV; Validated
Probab=63.09 E-value=6.1 Score=41.82 Aligned_cols=52 Identities=23% Similarity=0.398 Sum_probs=40.3
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAkt 322 (635)
+|..|-+||+. .-++|...||+|++|+.++ +...|++.||. .+..+.+||.-
T Consensus 169 pi~~l~giG~~--~~~~L~~~Gi~ti~dl~~l---~~~~L~~~fG~-----~~~~l~~~a~G 220 (343)
T PRK02406 169 PVEKIPGVGKV--TAEKLHALGIYTCADLQKY---DLAELIRHFGK-----FGRRLYERARG 220 (343)
T ss_pred CcchhcCCCHH--HHHHHHHcCCCcHHHHHhC---CHHHHHHHHhH-----HHHHHHHHhCC
Confidence 56677777764 4588999999999999885 78899999973 46666667653
No 12
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=62.87 E-value=9.2 Score=35.59 Aligned_cols=53 Identities=23% Similarity=0.266 Sum_probs=39.7
Q ss_pred hhhhhhhccCCccHHHHHHHHhcChHH--HHHHHccCCChhhHHHHHHhhcccccCC
Q 006693 273 SFHKRLNNAGIFSVEDFLRLVVRDPQK--LRSILGSGMSNKMWEALLDHAKTCVLSG 327 (635)
Q Consensus 273 ~~hkrL~~~~I~TV~dFLrl~~~D~~k--LR~iLg~gmS~k~We~~v~HAktCvl~~ 327 (635)
...++|+..||+|++|||..-.....+ |-+-+ |++.+-=...+.+|.-|...+
T Consensus 6 ~~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~--~i~~~~l~~w~~~AdL~ri~g 60 (122)
T PF14229_consen 6 KEAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKL--GISERNLLKWVNQADLMRIPG 60 (122)
T ss_pred HHHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhc--CCCHHHHHHHHhHHHhhhcCC
Confidence 355899999999999999986655544 55555 688887777788887665544
No 13
>PF10691 DUF2497: Protein of unknown function (DUF2497) ; InterPro: IPR019632 Members of this family belong to the Alphaproteobacteria. The function of the family is not known.
Probab=55.69 E-value=25 Score=30.68 Aligned_cols=40 Identities=30% Similarity=0.466 Sum_probs=30.5
Q ss_pred cchhHHHHHHHHHhhHHH-HHHhhhhHHHHHhHHHHHHHHHh
Q 006693 34 PALASVIVEALKVDSLQK-LCSSLEPILRRVVSEEVERALAK 74 (635)
Q Consensus 34 p~~~svi~ea~~~~s~q~-l~~~lEp~lrrvV~EEve~~l~~ 74 (635)
.++-.+++|+|+-- |+. |=..|=.|+.|+|++||+|..+|
T Consensus 33 ~TlE~lvremLRPm-LkeWLD~nLP~lVErlVr~EIeRi~rr 73 (73)
T PF10691_consen 33 RTLEDLVREMLRPM-LKEWLDENLPGLVERLVREEIERIARR 73 (73)
T ss_pred ccHHHHHHHHHHHH-HHHHHHhccHHHHHHHHHHHHHHHhcC
Confidence 46778888888764 333 55578889999999999998654
No 14
>PRK03352 DNA polymerase IV; Validated
Probab=53.31 E-value=5.8 Score=42.01 Aligned_cols=41 Identities=32% Similarity=0.424 Sum_probs=33.8
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHcc
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGS 306 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~ 306 (635)
+|..|-+||+. ..++|...||+|++|++++ ++..|++.||.
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 56667678774 4588999999999999985 78889999975
No 15
>PRK03858 DNA polymerase IV; Validated
Probab=51.21 E-value=7.2 Score=42.01 Aligned_cols=48 Identities=27% Similarity=0.329 Sum_probs=36.1
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhH
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMW 313 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~W 313 (635)
+|..|-+||+. .-++|.+.||+|++|+.+ .++..|++.||..+-...|
T Consensus 174 pl~~l~Gig~~--~~~~L~~~Gi~t~~dl~~---l~~~~L~~~fG~~~~~~l~ 221 (396)
T PRK03858 174 PVRRLWGVGPV--TAAKLRAHGITTVGDVAE---LPESALVSLLGPAAGRHLH 221 (396)
T ss_pred ChhhcCCCCHH--HHHHHHHhCCCcHHHHhc---CCHHHHHHHhCcHHHHHHH
Confidence 46666678875 458999999999999986 5888999999763333333
No 16
>PRK03348 DNA polymerase IV; Provisional
Probab=50.63 E-value=8.3 Score=43.05 Aligned_cols=48 Identities=25% Similarity=0.394 Sum_probs=37.4
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhH
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMW 313 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~W 313 (635)
+|.+|-+||+. .-++|...||+|++||.++ +...|++.||..+-..-|
T Consensus 181 Pv~~L~GIG~~--t~~~L~~lGI~TigDLa~l---~~~~L~~~fG~~~g~~L~ 228 (454)
T PRK03348 181 PVRRLWGIGPV--TEEKLHRLGIETIGDLAAL---SEAEVANLLGATVGPALH 228 (454)
T ss_pred CccccCCCCHH--HHHHHHHcCCccHHHHhcC---CHHHHHHHHCHHHHHHHH
Confidence 68888888875 4488999999999999874 788899999753333333
No 17
>PRK14133 DNA polymerase IV; Provisional
Probab=49.93 E-value=14 Score=39.17 Aligned_cols=51 Identities=29% Similarity=0.564 Sum_probs=39.5
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhc
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAk 321 (635)
+|..|-+||+.- -++|.+.||+|++|++++ +...|++.|| +.|..+.++|.
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 466666777644 478999999999999874 7788999996 35777777774
No 18
>PRK01172 ski2-like helicase; Provisional
Probab=49.72 E-value=16 Score=42.33 Aligned_cols=51 Identities=29% Similarity=0.604 Sum_probs=42.2
Q ss_pred eeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006693 265 LEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (635)
Q Consensus 265 LekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAkt 322 (635)
|.+|++. ..++|.++||.||.|+.. .|+++|-+|+ |++++.=+.++++|+.
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 4444443 669999999999999877 7888898888 6899999999999875
No 19
>PRK02794 DNA polymerase IV; Provisional
Probab=48.38 E-value=13 Score=40.61 Aligned_cols=55 Identities=27% Similarity=0.230 Sum_probs=42.7
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhccccc
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTCVL 325 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAktCvl 325 (635)
+|..|-+||+ ..-++|...||+|++|+.++ +...|++.||. .|..+..+|.--+.
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 3555556765 55699999999999998874 78889999974 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=46.43 E-value=14 Score=39.19 Aligned_cols=51 Identities=31% Similarity=0.433 Sum_probs=39.4
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhc
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAk 321 (635)
+|..|-+||+. .-++|...||+|++|++++ +...|.+.||. .|.....+|+
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 45666667774 4478999999999999985 77889999974 4666777765
No 21
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=46.27 E-value=22 Score=34.46 Aligned_cols=60 Identities=25% Similarity=0.391 Sum_probs=44.3
Q ss_pred CCccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHH-HHHhhcc
Q 006693 259 NDDVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEA-LLDHAKT 322 (635)
Q Consensus 259 ~DeVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~-~v~HAkt 322 (635)
.|+.-||.+||. ++-+.|+..||+|-.+.-.+-..|-..+-..| +..-+.|.. -|+.|+.
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 57899999999997766555444444555555 677777765 6777664
No 22
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=44.81 E-value=18 Score=37.69 Aligned_cols=52 Identities=27% Similarity=0.467 Sum_probs=40.7
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAkt 322 (635)
+|..|-+||+ ...++|...||+|++|+.++ ++..|++.+| +.|..+.+||+-
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 4566666775 44589999999999999874 7788999885 578888888864
No 23
>PRK01810 DNA polymerase IV; Validated
Probab=41.51 E-value=19 Score=39.05 Aligned_cols=51 Identities=27% Similarity=0.374 Sum_probs=39.0
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhc
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAk 321 (635)
+|..|-+||+. .-++|...||+|++|+.+ .+...|++.||. .+..+.+||.
T Consensus 180 pv~~l~giG~~--~~~~L~~~Gi~tigdL~~---~~~~~L~~rfG~-----~g~~l~~~a~ 230 (407)
T PRK01810 180 PVGEMHGIGEK--TAEKLKDIGIQTIGDLAK---ADEHILRAKLGI-----NGVRLQRRAN 230 (407)
T ss_pred CHhhcCCcCHH--HHHHHHHcCCCcHHHHHh---CCHHHHHHHHhH-----HHHHHHHHhc
Confidence 45566677764 448899999999999877 477889999964 4666777776
No 24
>PRK03103 DNA polymerase IV; Reviewed
Probab=40.71 E-value=21 Score=38.83 Aligned_cols=52 Identities=23% Similarity=0.304 Sum_probs=40.3
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAkt 322 (635)
+|..|-+||+. .-++|...||+|++||.+ .++..|++.||. .|..+.++|.-
T Consensus 182 pi~~l~gig~~--~~~~L~~~Gi~tigdl~~---~~~~~L~~~fG~-----~~~~l~~~a~G 233 (409)
T PRK03103 182 PVRKLFGVGSR--MEKHLRRMGIRTIGQLAN---TPLERLKKRWGI-----NGEVLWRTANG 233 (409)
T ss_pred CHhhcCCccHH--HHHHHHHcCCCCHHHHhc---CCHHHHHHHHCH-----HHHHHHHHhcC
Confidence 56666678874 558899999999999886 478889999963 46777777754
No 25
>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=38.48 E-value=13 Score=32.50 Aligned_cols=70 Identities=31% Similarity=0.539 Sum_probs=39.1
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcCh-HHHHHHHccCCChhhHHHHHHhhcccccCCceEEEecCCCcc
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDP-QKLRSILGSGMSNKMWEALLDHAKTCVLSGKLYVYYPEDSRN 339 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~-~kLR~iLg~gmS~k~We~~v~HAktCvl~~kly~y~~~~~~n 339 (635)
.+..|.+||.. .-+.|.+.||+||+||..+=.+.. -+|++. |
T Consensus 4 ~l~~LpNig~~--~e~~L~~vGI~t~~~L~~~Ga~~a~~~Lk~~-~---------------------------------- 46 (81)
T PF04994_consen 4 RLKDLPNIGPK--SERMLAKVGIHTVEDLRELGAVEAYLRLKAS-G---------------------------------- 46 (81)
T ss_dssp -GCGSTT--HH--HHHHHHHTT--SHHHHHHHHHHHHHHHHHHH------------------------------------
T ss_pred chhhCCCCCHH--HHHHHHHcCCCCHHHHHHhCHHHHHHHHHHH-C----------------------------------
Confidence 44556667764 458999999999999988644432 344443 2
Q ss_pred eEEEEccccceeeeeeCCeeecCCCCChHhh
Q 006693 340 VGVVFNNIYELNGLISGEQYFPADALPESQK 370 (635)
Q Consensus 340 vgl~FN~i~~lvG~~~~g~y~s~d~L~~~Qk 370 (635)
..+-+|-+|.|.||+-|-++ ..|++..|
T Consensus 47 ~~~~~~~L~aL~gAi~g~~~---~~L~~~~K 74 (81)
T PF04994_consen 47 PSVCLNLLYALEGAIQGIHW---ADLPDEEK 74 (81)
T ss_dssp TT--HHHHHHHHHHHCTS-G---GGS-HHHH
T ss_pred CCCCHHHHHHHHHHHcCCCH---HHCCHHHH
Confidence 12456778888888877543 34455544
No 26
>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=38.24 E-value=1.9e+02 Score=29.19 Aligned_cols=61 Identities=28% Similarity=0.316 Sum_probs=37.2
Q ss_pred CCccccceEEE---Ee--cce--eccCCeeeecCCccccccccEEEEEeecCCC-------CcceeeeecccceEeee
Q 006693 181 RPLLTGDLQVT---LK--EGV--GTLGDLTFTDNSSWIRSRKFRLGLKVASGYC-------EGIRIREAKTEAFTVKD 244 (635)
Q Consensus 181 rpLL~Gdl~v~---Lk--~Gv--a~L~di~FTDnSSw~RSrKFRLgaRvv~~~~-------~g~RI~EAvsE~FvVkD 244 (635)
...|.|.+... |+ +|. |. =..|.|=|-. .-+.|||-.++..=.. ...-+-|+.|+||.|-.
T Consensus 97 ~r~L~Gs~vss~~~l~d~~~~~~g~--fFvF~DLsVR-~eG~frLrf~l~~i~~~~~~~~~~~~~la~~~S~~F~V~s 171 (203)
T PF11754_consen 97 TRNLVGSLVSSAFRLKDPDGKEPGG--FFVFPDLSVR-TEGRFRLRFSLFDIGPSPGQGGGSSPVLAEVFSDPFTVYS 171 (203)
T ss_pred cccCcccEeeeeEEecCCCCCeEEE--EEEeCCceEC-cCCEEEEEEEEEEecCCccccCCCCcEEEEEECcCEEEEC
Confidence 56788886554 33 333 21 1234444433 2468999998864322 23568999999999964
No 27
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=37.30 E-value=25 Score=37.32 Aligned_cols=56 Identities=25% Similarity=0.140 Sum_probs=41.6
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcC-hHHHHHHHccCCChhhHHHHHHhhcccccC
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRD-PQKLRSILGSGMSNKMWEALLDHAKTCVLS 326 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D-~~kLR~iLg~gmS~k~We~~v~HAktCvl~ 326 (635)
+|..|-+||+. .-++|.+.||+|++|++++ + ...|+..+| +.+..+.++|+--+..
T Consensus 174 pi~~l~giG~~--~~~~L~~~Gi~ti~dl~~~---~~~~~l~~~fg-----~~~~~l~~~a~G~d~~ 230 (343)
T cd00424 174 PLTDLPGIGAV--TAKRLEAVGINPIGDLLAA---SPDALLALWGG-----VSGERLWYALRGIDDE 230 (343)
T ss_pred ChhhcCCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHhh-----HHHHHHHHHhCCcCCC
Confidence 46667778874 4589999999999998764 6 566777775 4677888888755443
No 28
>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=34.48 E-value=19 Score=39.48 Aligned_cols=54 Identities=22% Similarity=0.233 Sum_probs=39.9
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhc
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAk 321 (635)
+|..|-+||+. .-++|...||.|+.|+..+- .++..|++.||. +.+..+..+|.
T Consensus 223 Pv~~l~GIG~~--~~~~L~~~Gi~t~~dl~~~~-~~~~~L~~~fG~----~~g~~L~~~a~ 276 (404)
T cd01701 223 KVGDLPGVGSS--LAEKLVKLFGDTCGGLELRS-KTKEKLQKVLGP----KTGEKLYDYCR 276 (404)
T ss_pred CHhHhCCCCHH--HHHHHHHcCCcchHHHHhCc-ccHHHHHHHHCH----HHHHHHHHHhC
Confidence 67777788864 56999999999999998761 127889999974 34555555554
No 29
>PRK01216 DNA polymerase IV; Validated
Probab=34.11 E-value=19 Score=39.01 Aligned_cols=51 Identities=25% Similarity=0.397 Sum_probs=38.5
Q ss_pred ccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhh
Q 006693 261 DVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHA 320 (635)
Q Consensus 261 eVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HA 320 (635)
+|..|-+||+. -.++|...||+|++|+.++ +...|++.||. ..+..+-.+|
T Consensus 179 Pi~~l~giG~~--~~~~L~~~Gi~TigdL~~~---~~~~L~~rfG~----~~~~~L~~~a 229 (351)
T PRK01216 179 DIADIPGIGDI--TAEKLKKLGVNKLVDTLRI---EFDELKGIIGE----AKAKYLFSLA 229 (351)
T ss_pred CcccccCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHCH----HHHHHHHHHh
Confidence 57777788864 4599999999999998764 67889999973 3344455556
No 30
>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=33.53 E-value=33 Score=35.43 Aligned_cols=55 Identities=25% Similarity=0.486 Sum_probs=38.0
Q ss_pred CccceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhc
Q 006693 260 DDVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAK 321 (635)
Q Consensus 260 DeVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAk 321 (635)
....-|.+|+.+.+ ++|..+||.|+++|+++ ++.+|..+| +......+.+.+.|.
T Consensus 148 ~~L~Qlp~i~~~~~--~~l~~~~i~~l~~l~~~---~~~e~~~ll--~~~~~~~~~i~~~~~ 202 (314)
T PF02889_consen 148 SPLLQLPHIGEESL--KKLEKRGIKTLQDLRDL---SPEELEELL--NRNPPFGKEILEVAS 202 (314)
T ss_dssp -GGGGSTT--HHHH--HHHHHTT--SHHHHHHS----HHHHHHHH---S-HHHHHHHHHHHC
T ss_pred ChhhcCCCCCHHHH--HHHhccCCCcHHHHhhC---CHHHHHHHH--hhhhhhHHHHHHHHH
Confidence 34566778888665 89999999999999854 889999998 456678888888776
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=32.38 E-value=22 Score=38.55 Aligned_cols=55 Identities=15% Similarity=0.236 Sum_probs=38.2
Q ss_pred ccceeeccccCchhhhh-hhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhcc
Q 006693 261 DVWRLEKIGKDGSFHKR-LNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKT 322 (635)
Q Consensus 261 eVwRLekIgKdG~~hkr-L~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAkt 322 (635)
+|..|-+||+ ..-++ |...||.|++|+.++. .++..|++.||. +.++.+..+|+-
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 4777778884 22245 5889999999998754 478889999874 344455555553
No 32
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=32.11 E-value=72 Score=28.79 Aligned_cols=35 Identities=34% Similarity=0.585 Sum_probs=28.6
Q ss_pred ccCCccHHHHHHHHhcChHH---HHHHHccCCChhhHHHHHHhhcc
Q 006693 280 NAGIFSVEDFLRLVVRDPQK---LRSILGSGMSNKMWEALLDHAKT 322 (635)
Q Consensus 280 ~~~I~TV~dFLrl~~~D~~k---LR~iLg~gmS~k~We~~v~HAkt 322 (635)
...| +++||+=++..||.| |+++| .|+..++-||.
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 999999999999976 55566 68889988875
No 33
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=31.30 E-value=1.1e+02 Score=32.33 Aligned_cols=72 Identities=14% Similarity=0.236 Sum_probs=33.8
Q ss_pred hhhHHHHHhHHHHHHHHHhhCCCcccCCCCCCCCccCCCCCceEE-EeccCCCCCcccCCcccccCCCceEEEEE
Q 006693 56 LEPILRRVVSEEVERALAKLGPARLNNGRASPKRIEGPDGRNLQL-YFRSRLSLPLFTGGKVEGEQGAAIHVVLV 129 (635)
Q Consensus 56 lEp~lrrvV~EEve~~l~~~~~~~~~~~rs~~~~i~~~~~~~~~L-~F~n~l~~pifTg~kI~ae~g~~I~V~Lv 129 (635)
||-++|+|+.|++-..+.-..+.. . .-..|.+|--..++.+++ +|....+..+|+.+-+..++|..+-..++
T Consensus 90 i~~lv~~v~~e~~~~~~~~~~~~~-~-~~~~~~Gi~vVrg~svk~~~fdg~~~~~v~~~d~~~~~d~s~m~aGf~ 162 (233)
T PRK15457 90 VAQLMEKVMKEKQSLEQGAMQPSF-K-SVTGKGGIKVIDGSSVKFGRFDGAEPHCVGLTDLVTGDDGSSMAAGFM 162 (233)
T ss_pred HHHHHHHHHHHHhcccccccCCCc-c-ceeCCCceEEEECCeEEEeecCCCCcccEEeeeeeccCCCCceeeEEE
Confidence 677999999988643322100100 0 000122333333345555 45444444555555555555555544443
No 34
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=29.93 E-value=33 Score=32.00 Aligned_cols=38 Identities=34% Similarity=0.607 Sum_probs=29.5
Q ss_pred cceeeccccCchhhhhhhccCCccHHHHHHHHhcChHHHHHHH
Q 006693 262 VWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVRDPQKLRSIL 304 (635)
Q Consensus 262 VwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iL 304 (635)
..|+.+|+. .|..-|.++||.||+++- ..+|++|.+.+
T Consensus 55 L~ri~gi~~--~~a~LL~~AGv~Tv~~LA---~~~p~~L~~~l 92 (122)
T PF14229_consen 55 LMRIPGIGP--QYAELLEHAGVDTVEELA---QRNPQNLHQKL 92 (122)
T ss_pred hhhcCCCCH--HHHHHHHHhCcCcHHHHH---hCCHHHHHHHH
Confidence 446666765 477899999999999974 47888887755
No 35
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=28.57 E-value=57 Score=29.48 Aligned_cols=60 Identities=28% Similarity=0.432 Sum_probs=40.6
Q ss_pred CCCCCccceeeccccCchhhhhhhccCCcc----HHHHHHHHhcChHHHHHHHccCCChhhHHHHHHhhccc
Q 006693 256 PALNDDVWRLEKIGKDGSFHKRLNNAGIFS----VEDFLRLVVRDPQKLRSILGSGMSNKMWEALLDHAKTC 323 (635)
Q Consensus 256 P~L~DeVwRLekIgKdG~~hkrL~~~~I~T----V~dFLrl~~~D~~kLR~iLg~gmS~k~We~~v~HAktC 323 (635)
|+=+-+|--|.+||.. +-.+|..+|+.. .++|| ++.+|++-.+.-| ...--++-+||++|
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 668999999976 46676 4567876555433 11112356677776
No 36
>KOG2856 consensus Adaptor protein PACSIN [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=27.78 E-value=93 Score=35.04 Aligned_cols=25 Identities=20% Similarity=0.336 Sum_probs=17.3
Q ss_pred HHHhcccccccCccccccccccccc
Q 006693 374 AYDNWNQVVEYDGKSLLSLKQNKRS 398 (635)
Q Consensus 374 AY~n~~~~~e~d~~~l~n~~~~kk~ 398 (635)
+.-||-+++||--....++....|+
T Consensus 286 mamnWPqF~E~s~d~~rtia~r~ks 310 (472)
T KOG2856|consen 286 MAMNWPQFEEWSPDLQRTIAKREKS 310 (472)
T ss_pred cccCCchHhhcChhhhhHHHhccCC
Confidence 6678888888887776666644443
No 37
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=27.09 E-value=30 Score=37.96 Aligned_cols=58 Identities=16% Similarity=0.151 Sum_probs=40.0
Q ss_pred cceeeccccCchhhhhhhccCCccHHHHHHHHh------------cChHHHHHHHccCCChhhHHHHHHhhccccc
Q 006693 262 VWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVV------------RDPQKLRSILGSGMSNKMWEALLDHAKTCVL 325 (635)
Q Consensus 262 VwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~------------~D~~kLR~iLg~gmS~k~We~~v~HAktCvl 325 (635)
|-.|-+||+... ++|.+.||.|++|+..+-+ .+...|++.||. +.+..+.++|+--+.
T Consensus 174 v~~l~GiG~~~~--~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~----~~g~~l~~~a~G~d~ 243 (379)
T cd01703 174 LRKIPGIGYKTA--AKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGE----GIGQRIWKLLFGRDT 243 (379)
T ss_pred ccccCCcCHHHH--HHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHCH----HHHHHHHHHHCCCCC
Confidence 444557777654 8999999999999986541 117789999864 345556667765443
No 38
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=26.79 E-value=32 Score=29.01 Aligned_cols=37 Identities=27% Similarity=0.373 Sum_probs=22.8
Q ss_pred hhhhhhccCCccHHHHHHHHhcChHHHHHHHccCCChhhHHH
Q 006693 274 FHKRLNNAGIFSVEDFLRLVVRDPQKLRSILGSGMSNKMWEA 315 (635)
Q Consensus 274 ~hkrL~~~~I~TV~dFLrl~~~D~~kLR~iLg~gmS~k~We~ 315 (635)
-...|..+||+||+|++++ +++.|.++= |+..+.-+.
T Consensus 23 a~n~L~~~~I~tv~dL~~~---s~~~L~~i~--n~G~ksl~E 59 (66)
T PF03118_consen 23 AYNCLKRAGIHTVGDLVKY---SEEDLLKIK--NFGKKSLEE 59 (66)
T ss_dssp HHHHHHCTT--BHHHHHCS----HHHHHTST--TSHHHHHHH
T ss_pred HHHHHHHhCCcCHHHHHhC---CHHHHHhCC--CCCHhHHHH
Confidence 3467889999999997664 666777774 344444443
No 39
>TIGR02979 phageshock_pspD phage shock protein PspD. Members of this family are phage shock protein PspD, found in a minority of bacteria that carry the defining genes of the phage shock regulon (pspA, pspB, pspC, and pspF). It is found in Escherichia coli, Yersinia pestis, and closely related species, where it is part of the phage shock operon. It is known to be expressed but its function is unknown.
Probab=25.02 E-value=77 Score=26.97 Aligned_cols=25 Identities=40% Similarity=0.559 Sum_probs=16.2
Q ss_pred hHHHHHHHHHhhHHHHHHhhhhHHHHHhH
Q 006693 37 ASVIVEALKVDSLQKLCSSLEPILRRVVS 65 (635)
Q Consensus 37 ~svi~ea~~~~s~q~l~~~lEp~lrrvV~ 65 (635)
.||-+.=+++- |...|||+|||...
T Consensus 29 KsVsrkPLr~l----La~aLEPllkr~~~ 53 (59)
T TIGR02979 29 KSVARRPLKML----LAIALEPMLKRAAN 53 (59)
T ss_pred HHHhhccHHHH----HHHHHHHHHHHHHH
Confidence 34444444441 56689999999753
No 40
>COG4766 EutQ Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=23.22 E-value=2.6e+02 Score=28.24 Aligned_cols=94 Identities=15% Similarity=0.233 Sum_probs=60.9
Q ss_pred HHHHHHHHHh-hHHHHHHh-hhhHHHHHhHHHHHHHHHhhCCCcccC-CCCCCCCccCCCCCceEEEeccCCCCCcccCC
Q 006693 38 SVIVEALKVD-SLQKLCSS-LEPILRRVVSEEVERALAKLGPARLNN-GRASPKRIEGPDGRNLQLYFRSRLSLPLFTGG 114 (635)
Q Consensus 38 svi~ea~~~~-s~q~l~~~-lEp~lrrvV~EEve~~l~~~~~~~~~~-~rs~~~~i~~~~~~~~~L~F~n~l~~pifTg~ 114 (635)
+-|+|++..+ +.-++|+. +|-++++|++|+.-....-..|..-.+ +||--+-+. ...-...|+|...=+.-+||++
T Consensus 12 ~~i~~si~a~l~~~~~~~~l~~Qlm~kVmkek~s~~~~~~~~~~k~v~~ksgikvvk-~s~vk~~~r~d~gqp~~V~~td 90 (176)
T COG4766 12 QRIRESIIAQLPEGQFTKELVEQLMEKVMKEKQSLECGWMQPSFKSVDGKSGIKVVK-LSSVKFGLRFDTGQPDCVYTTD 90 (176)
T ss_pred HHHHHHHHHhCChhhhhHHHHHHHHHHHHhchhhhhhhhcccceeecccCCceeEEe-cccceeEeeecCCCCCeEEeec
Confidence 4466655543 34456765 567899999999766654433321111 344222221 2223678889888778999999
Q ss_pred cccccCCCceEEEEEeCC
Q 006693 115 KVEGEQGAAIHVVLVDAN 132 (635)
Q Consensus 115 kI~ae~g~~I~V~LvD~~ 132 (635)
-+.-.+|.++-+.+..-.
T Consensus 91 Lvt~~~g~~l~aG~m~~~ 108 (176)
T COG4766 91 LVTEQEGSRLGAGLMEMK 108 (176)
T ss_pred eeecccCCccccceeeec
Confidence 999999999998887643
No 41
>COG3827 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.31 E-value=1.5e+02 Score=31.07 Aligned_cols=41 Identities=32% Similarity=0.472 Sum_probs=30.6
Q ss_pred CcchhHHHHHHHHHhhHHHHH-HhhhhHHHHHhHHHHHHHHHh
Q 006693 33 RPALASVIVEALKVDSLQKLC-SSLEPILRRVVSEEVERALAK 74 (635)
Q Consensus 33 rp~~~svi~ea~~~~s~q~l~-~~lEp~lrrvV~EEve~~l~~ 74 (635)
|-+|-.+..|+|+-- ||.-+ ..|=-++.|+|+|||||..+.
T Consensus 187 rrsleE~a~eMLRPm-LqdWLDkNLPtLVErLVrEEIeRv~RG 228 (231)
T COG3827 187 RRSLEEMAAEMLRPM-LQDWLDKNLPTLVERLVREEIERVVRG 228 (231)
T ss_pred cccHHHHHHHHHHHH-HHHHHHccchHHHHHHHHHHHHHHHcc
Confidence 347888888887764 66644 368888899999999997653
No 42
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=22.19 E-value=35 Score=40.08 Aligned_cols=38 Identities=26% Similarity=0.415 Sum_probs=31.8
Q ss_pred CCCCCccceeeccccCchhhhhhhccCCccHHHHHHHHhc
Q 006693 256 PALNDDVWRLEKIGKDGSFHKRLNNAGIFSVEDFLRLVVR 295 (635)
Q Consensus 256 P~L~DeVwRLekIgKdG~~hkrL~~~~I~TV~dFLrl~~~ 295 (635)
..|+++|-.|++||+.- .+.|++.||+||.|.|..+=+
T Consensus 5 ~~~~~~~~~l~gvg~~~--~~~l~~lgi~t~~dll~~~P~ 42 (681)
T PRK10917 5 LLLDAPLTSLKGVGPKT--AEKLAKLGIHTVQDLLLHLPR 42 (681)
T ss_pred ccccCChhhcCCCCHHH--HHHHHHcCCCCHHHHhhcCCC
Confidence 45778999999998754 488999999999999988654
No 43
>PF09584 Phageshock_PspD: Phage shock protein PspD (Phageshock_PspD); InterPro: IPR014321 Members of this entry are phage shock protein PspD, they are found in a minority of bacteria that carry the defining genes of the phage shock regulon (pspA, pspB, pspC, and pspF). It is found in Escherichia coli, Yersinia pestis, and closely related species, where it is part of the phage shock operon. It is known to be expressed but its function is unknown.
Probab=22.07 E-value=90 Score=27.13 Aligned_cols=15 Identities=47% Similarity=0.789 Sum_probs=11.9
Q ss_pred HHHhhhhHHHHHhHH
Q 006693 52 LCSSLEPILRRVVSE 66 (635)
Q Consensus 52 l~~~lEp~lrrvV~E 66 (635)
|.-.|||+|||+++-
T Consensus 45 La~~LEPllrr~~~~ 59 (66)
T PF09584_consen 45 LALALEPLLRRGLNK 59 (66)
T ss_pred HHHHHHHHHHHHHHH
Confidence 555899999998653
No 44
>PF11033 ComJ: Competence protein J (ComJ); InterPro: IPR020354 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. The proteins in this entry play a role in the competence of cells to be transformed. They inhibit the activity of the DNA-entry nuclease. DNA-entry nuclease inhibitor is a subunit of a 75 kDa protein complex, which governs binding and entry of donor DNA. The complex is a tetramer of two subunits of the DNA-entry nuclease and two subunits of a competence-specific protein ComJ. Only the complex is able to bind ds- and ss-DNA []. It is found in the plasma membrane.
Probab=21.98 E-value=2.7e+02 Score=26.91 Aligned_cols=26 Identities=27% Similarity=0.373 Sum_probs=19.4
Q ss_pred EEEEeeCCCCCCCCCCCCHHHHhhccc
Q 006693 148 DIVVLEGDFNNEDDDGWTQEEFESHVV 174 (635)
Q Consensus 148 EIvVLdGDF~~~~~e~WT~eEF~~~IV 174 (635)
+|.|-.+||.... .+||.|+|..--+
T Consensus 9 Qi~v~~~~~~~p~-~dWtde~i~qG~a 34 (125)
T PF11033_consen 9 QITVFNRDGEPPY-IDWTDEDIEQGYA 34 (125)
T ss_pred eEEEEccCCCCcc-cccCHhHHhCcce
Confidence 5677888887643 4799999986644
No 45
>PF06594 HCBP_related: Haemolysin-type calcium binding protein related domain; InterPro: IPR010566 This family consists of a number of bacteria specific domains, which are found in haemolysin-type calcium binding proteins. This family is found in conjunction with IPR001343 from INTERPRO and is often found in multiple copies.
Probab=20.57 E-value=63 Score=24.78 Aligned_cols=18 Identities=22% Similarity=0.612 Sum_probs=14.9
Q ss_pred eeccCCeeeecCCccccc
Q 006693 196 VGTLGDLTFTDNSSWIRS 213 (635)
Q Consensus 196 va~L~di~FTDnSSw~RS 213 (635)
-..|..+.|-|++.|.+.
T Consensus 24 ~~~Ie~i~FaDGt~w~~~ 41 (43)
T PF06594_consen 24 SYRIEQIEFADGTVWTRA 41 (43)
T ss_pred CCcEeEEEEcCCCEecHH
Confidence 456889999999999753
No 46
>PRK10497 peripheral inner membrane phage-shock protein; Provisional
Probab=20.14 E-value=1.1e+02 Score=27.12 Aligned_cols=14 Identities=43% Similarity=0.835 Sum_probs=11.4
Q ss_pred HHHhhhhHHHHHhH
Q 006693 52 LCSSLEPILRRVVS 65 (635)
Q Consensus 52 l~~~lEp~lrrvV~ 65 (635)
|.-.|||+|||.++
T Consensus 52 L~~~LEPlLkr~~~ 65 (73)
T PRK10497 52 LAVALEPLLKRAAN 65 (73)
T ss_pred HHHHHHHHHHHHHH
Confidence 45589999999864
Done!