Query 042429
Match_columns 304
No_of_seqs 113 out of 142
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 06:05:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042429.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042429hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07887 Calmodulin_bind: Calm 100.0 3E-117 7E-122 835.0 26.9 267 33-302 1-269 (299)
2 TIGR02239 recomb_RAD51 DNA rep 89.9 0.37 8.1E-06 46.5 4.1 48 211-263 13-60 (316)
3 TIGR02238 recomb_DMC1 meiotic 87.7 0.6 1.3E-05 45.2 3.8 49 210-263 12-60 (313)
4 PLN03186 DNA repair protein RA 87.1 0.75 1.6E-05 45.2 4.2 60 199-263 28-87 (342)
5 PRK04301 radA DNA repair and r 84.9 0.67 1.4E-05 44.2 2.5 57 198-261 7-63 (317)
6 PLN03187 meiotic recombination 82.8 1.1 2.3E-05 44.2 3.1 60 198-262 30-89 (344)
7 PF14520 HHH_5: Helix-hairpin- 82.4 1.1 2.4E-05 32.8 2.3 51 202-259 10-60 (60)
8 PRK03609 umuC DNA polymerase V 79.6 1.5 3.3E-05 43.5 3.0 51 198-258 180-230 (422)
9 PTZ00035 Rad51 protein; Provis 76.5 3.3 7.1E-05 40.5 4.1 60 198-262 22-81 (337)
10 PRK02406 DNA polymerase IV; Va 74.6 2.9 6.2E-05 40.1 3.2 52 198-259 169-220 (343)
11 PRK03352 DNA polymerase IV; Va 73.8 2.5 5.4E-05 40.6 2.6 41 198-243 178-218 (346)
12 TIGR02236 recomb_radA DNA repa 73.2 2.7 5.9E-05 39.7 2.6 50 202-258 4-53 (310)
13 PRK03858 DNA polymerase IV; Va 69.5 2.4 5.1E-05 41.5 1.3 48 198-250 174-221 (396)
14 PRK03348 DNA polymerase IV; Pr 66.5 3.4 7.4E-05 41.8 1.8 48 198-250 181-228 (454)
15 PF14229 DUF4332: Domain of un 65.7 9.8 0.00021 32.0 4.2 48 211-260 7-56 (122)
16 PRK14133 DNA polymerase IV; Pr 64.2 7.1 0.00015 37.6 3.4 51 198-258 174-224 (347)
17 PRK01216 DNA polymerase IV; Va 64.0 7 0.00015 38.4 3.4 51 198-257 179-229 (351)
18 PRK02794 DNA polymerase IV; Pr 63.0 6 0.00013 39.3 2.8 55 198-262 210-264 (419)
19 cd01701 PolY_Rev1 DNA polymera 61.8 6.8 0.00015 38.9 2.9 54 198-258 223-276 (404)
20 cd01700 PolY_Pol_V_umuC umuC s 61.4 6.4 0.00014 37.8 2.6 51 198-258 177-227 (344)
21 PF03118 RNA_pol_A_CTD: Bacter 60.0 6 0.00013 30.0 1.7 37 212-253 24-60 (66)
22 PRK01172 ski2-like helicase; P 59.5 9.5 0.00021 40.1 3.7 44 211-259 624-667 (674)
23 cd01703 PolY_Pol_iota DNA Poly 59.4 10 0.00022 37.6 3.7 58 198-261 173-242 (379)
24 cd03586 PolY_Pol_IV_kappa DNA 58.2 9.8 0.00021 36.0 3.2 52 198-259 172-223 (334)
25 PRK01810 DNA polymerase IV; Va 56.6 9.5 0.00021 37.5 2.9 51 198-258 180-230 (407)
26 cd01702 PolY_Pol_eta DNA Polym 56.4 9.7 0.00021 37.5 2.9 55 198-259 183-238 (359)
27 PRK03103 DNA polymerase IV; Re 55.1 9.9 0.00022 37.4 2.8 52 198-259 182-233 (409)
28 cd00424 PolY Y-family of DNA p 49.1 15 0.00032 35.4 2.8 55 198-262 174-229 (343)
29 PF04994 TfoX_C: TfoX C-termin 48.2 5.7 0.00012 31.4 -0.1 30 200-231 6-35 (81)
30 COG3743 Uncharacterized conser 48.0 20 0.00044 31.3 3.2 56 197-259 67-126 (133)
31 PF02889 Sec63: Sec63 Brl doma 45.8 18 0.00039 33.8 2.8 54 198-258 149-202 (314)
32 PF11754 Velvet: Velvet factor 45.4 2.4E+02 0.0052 25.7 10.3 59 118-182 97-172 (203)
33 KOG4233 DNA-bridging protein B 44.0 28 0.0006 28.3 3.2 60 193-260 15-78 (90)
34 PRK07758 hypothetical protein; 36.2 55 0.0012 27.2 3.9 37 213-254 48-84 (95)
35 PF06594 HCBP_related: Haemoly 31.7 29 0.00063 23.8 1.4 18 133-150 24-41 (43)
36 cd07978 TAF13 The TATA Binding 30.5 83 0.0018 25.5 4.0 35 217-259 52-89 (92)
37 PRK05256 condesin subunit E; P 30.2 66 0.0014 30.7 3.8 50 213-262 107-160 (238)
38 PRK10917 ATP-dependent DNA hel 29.8 21 0.00046 38.0 0.6 39 193-233 5-43 (681)
39 KOG1520 Predicted alkaloid syn 29.7 1.9E+02 0.0041 29.5 7.1 118 109-241 150-303 (376)
40 cd03468 PolY_like DNA Polymera 28.2 35 0.00076 32.2 1.7 35 204-243 177-211 (335)
41 PF11033 ComJ: Competence prot 28.2 2.6E+02 0.0057 24.2 6.9 26 85-111 9-34 (125)
42 PF09816 EAF: RNA polymerase I 28.0 1.7E+02 0.0037 24.0 5.5 67 16-85 31-103 (109)
43 TIGR01954 nusA_Cterm_rpt trans 27.7 81 0.0018 21.5 3.1 41 213-258 7-47 (50)
44 COG5340 Predicted transcriptio 26.9 40 0.00087 32.4 1.8 41 215-256 25-65 (269)
45 PF00853 Runt: Runt domain; I 25.1 1.8E+02 0.0038 25.6 5.3 34 126-161 74-107 (135)
46 PRK14973 DNA topoisomerase I; 24.3 63 0.0014 36.3 3.0 54 199-259 879-932 (936)
47 PRK02362 ski2-like helicase; P 24.0 75 0.0016 34.0 3.4 51 201-260 656-706 (737)
48 PTZ00205 DNA polymerase kappa; 23.6 66 0.0014 34.3 2.9 53 198-252 310-367 (571)
49 PF04717 Phage_base_V: Phage-r 23.5 1.4E+02 0.0031 22.5 4.1 33 171-203 22-54 (79)
50 PF10657 RC-P840_PscD: Photosy 22.8 81 0.0018 27.7 2.8 28 272-299 115-142 (144)
51 PF13854 Kelch_5: Kelch motif 21.9 55 0.0012 22.0 1.3 27 258-284 9-37 (42)
52 PF14229 DUF4332: Domain of un 21.9 79 0.0017 26.5 2.5 37 200-241 56-92 (122)
53 PF05643 DUF799: Putative bact 20.6 82 0.0018 29.6 2.5 28 213-243 79-106 (215)
54 smart00611 SEC63 Domain of unk 20.4 1.3E+02 0.0028 28.2 3.9 53 198-257 152-204 (312)
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=3.3e-117 Score=835.03 Aligned_cols=267 Identities=54% Similarity=0.928 Sum_probs=262.9
Q ss_pred ceEEEEccCCCCCcccCCceeecCCCCeEEEEEEcCCCCeeecCCCCCccEEEEEEEcCCCCCCCCCCCCHHHHhhcccc
Q 042429 33 SLKLTFSEELSLPIFTGRKITDIENNPLQIVVVETRSSGRITPANLSQPIKILMVVLDWDFPSGDHDDWSQEEFESNIVK 112 (304)
Q Consensus 33 ~~~L~F~n~l~~pifT~~~I~a~~g~~I~V~l~D~~t~~~iv~~g~~ss~kveIvVLdGdF~~~~~e~WT~eeF~~~Iv~ 112 (304)
+|||+|+|+|++|||||++|+|+||+||+|+|+|++|+ |++||+||+|||||||||||+.+++++||+|||+++||+
T Consensus 1 ~~~L~F~n~l~~pifT~~~i~a~~g~~i~V~l~d~~~~---v~~g~lss~kieIvvLdGdF~~~~~~~wT~eeF~~~iv~ 77 (299)
T PF07887_consen 1 NLQLRFLNKLSLPIFTGSKIEAEDGAPIKVALVDANTG---VTSGPLSSAKIEIVVLDGDFNDEDCEDWTEEEFNSHIVK 77 (299)
T ss_pred CeEEEecCCCCCCcccCCceEecCCCcEEEEEEECCCC---ccCCCCCCcEEEEEEEccccCCCccCCCCHHHHhhcEee
Confidence 58999999999999999999999999999999998776 999999999999999999999999999999999999999
Q ss_pred cCCCCCccccccEEEEecCceeecCCeEEecCCccccCCceEEEEEeecCCCCceeeeeeeecceEEeecCCcccccCCC
Q 042429 113 ERIGKQPLLTGDVNVTIRNGVAPVEDIEFTDNSSWIRSRKFKISAKVAQGNYHGVRICEAITEAFVVKDHRGELYKKHHP 192 (304)
Q Consensus 113 ~R~Gk~pLL~Gd~~v~L~~G~a~l~di~FtdnSs~~rsrkFRLgarv~~~~~~g~rI~Eavse~FvVkd~Rge~~kKh~p 192 (304)
+|+||+|||+|+++|+|+||+|+|+||+|||||||+|||||||||||+++++.|+|||||+||||+|||||||+||||||
T Consensus 78 ~r~gk~pLL~G~~~v~L~~G~a~l~di~FtdnSs~~rsrKFRLgarv~~~~~~~~rI~Eavse~FvVkd~Rge~~kKh~p 157 (299)
T PF07887_consen 78 EREGKRPLLTGDLQVTLKNGVATLGDISFTDNSSWIRSRKFRLGARVVSGSCDGVRIREAVSEPFVVKDHRGELYKKHYP 157 (299)
T ss_pred cCCCCCCCCCccEEEEecCCEEEccccEEecCcccccCCcEEEEEEEccCCCCCceeEEeeecCEEEEecccccccCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhccccCCCceEEEe--
Q 042429 193 QMLEDEVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHARTCIMGNKLYIFR-- 270 (304)
Q Consensus 193 P~L~DeVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAktCvl~~k~y~y~-- 270 (304)
|+|+|||||||+|||+|+|||+|+++||+||+|||+++++||++||+|||+|||++||++|++|||||++++++|+|+
T Consensus 158 P~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 158 PSLDDEVWRLEKIGKDGAFHKRLKKNGINTVEDFLKLLNKDPQKLREILGSGMSNKMWETTVEHAKTCVLGDKLYVYYDE 237 (299)
T ss_pred CCCCCchhhhhhccccCHHHHHHHHcCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHHHHHHHHhcCCCCcEEEEEec
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcEEEEEccceeEeEeEECCEEeeCCCCCCC
Q 042429 271 GPNSIIFLNPICQVVRATINGQTFLTRDLPNL 302 (304)
Q Consensus 271 ~~~~~l~FN~i~~lvga~~~g~~~~~~~l~~~ 302 (304)
++|++|+||||||||||+|+|||++.++|+++
T Consensus 238 ~~nv~l~FN~i~~lvga~~~g~y~s~d~L~~~ 269 (299)
T PF07887_consen 238 EQNVGLFFNCIYELVGAIFGGQYVSLDNLSSA 269 (299)
T ss_pred CCceEEEEcchhhEEeEEECCEEEehHHcCHH
Confidence 67999999999999999999999999999986
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=89.92 E-value=0.37 Score=46.53 Aligned_cols=48 Identities=25% Similarity=0.266 Sum_probs=42.4
Q ss_pred hhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhccccCC
Q 042429 211 FYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHARTCIMG 263 (304)
Q Consensus 211 ~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAktCvl~ 263 (304)
.-++|+++||.||+||+.. +|..|.+++ ++|...++.+..||.+|...
T Consensus 13 ~~~~l~~~g~~t~~~~~~~---~~~~L~~i~--~ls~~~~~~~~~~~~~~~~~ 60 (316)
T TIGR02239 13 DIKKLQEAGLHTVESVAYA---PKKQLLEIK--GISEAKADKILAEAAKLVPM 60 (316)
T ss_pred HHHHHHHcCCCcHHHHHhC---CHHHHHHHh--CCCHHHHHHHHHHHHHhccc
Confidence 3488999999999999865 899999997 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=87.68 E-value=0.6 Score=45.16 Aligned_cols=49 Identities=29% Similarity=0.289 Sum_probs=42.7
Q ss_pred hhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhccccCC
Q 042429 210 TFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHARTCIMG 263 (304)
Q Consensus 210 ~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAktCvl~ 263 (304)
..-++|+++||.||+||+.. ++..|.++. |+|...++.+++.|+.+...
T Consensus 12 ~~~~~L~~~g~~t~~~~~~~---~~~~L~~~~--gls~~~~~~i~~~~~~~~~~ 60 (313)
T TIGR02238 12 ADIKKLKSAGICTVNGVIMT---TRRALCKIK--GLSEAKVDKIKEAASKIINP 60 (313)
T ss_pred HHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHhhhcc
Confidence 34589999999999998765 789999996 78999999999999988654
No 4
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=87.10 E-value=0.75 Score=45.21 Aligned_cols=60 Identities=27% Similarity=0.286 Sum_probs=46.7
Q ss_pred eeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhccccCC
Q 042429 199 VWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHARTCIMG 263 (304)
Q Consensus 199 VwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAktCvl~ 263 (304)
+.+|+.-|-.-..-++|+++||.||+||+.+ ++..|.+++ ++|....+.+++||.+|...
T Consensus 28 ~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~---~~~~L~~i~--~is~~~~~~~~~~~~~~~~~ 87 (342)
T PLN03186 28 IEQLQASGIAALDIKKLKDAGIHTVESLAYA---PKKDLLQIK--GISEAKVEKILEAASKLVPL 87 (342)
T ss_pred HHHHHhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHHhccc
Confidence 4444443333334488999999999999865 788999997 78999999999999888654
No 5
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=84.87 E-value=0.67 Score=44.19 Aligned_cols=57 Identities=25% Similarity=0.354 Sum_probs=44.8
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhcccc
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHARTCI 261 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAktCv 261 (304)
++..|.+||+ ...++|.++||.|++|++. .+++.|.+++ |++.+.++.+.+-|+.+.
T Consensus 7 ~l~~l~gIg~--~~a~~L~~~Gi~t~~dl~~---~~~~~L~~~~--g~~~~~a~~l~~~a~~~~ 63 (317)
T PRK04301 7 DLEDLPGVGP--ATAEKLREAGYDTVEAIAV---ASPKELSEAA--GIGESTAAKIIEAAREAA 63 (317)
T ss_pred cHhhcCCCCH--HHHHHHHHcCCCCHHHHHc---CCHHHHHHhc--CCCHHHHHHHHHHHHHhh
Confidence 3445556665 3458999999999999965 4899999998 678888998888887643
No 6
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=82.78 E-value=1.1 Score=44.21 Aligned_cols=60 Identities=23% Similarity=0.248 Sum_probs=47.1
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhccccC
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHARTCIM 262 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAktCvl 262 (304)
++..|+.-|-.-..-++|.++||.||+|++.. ++..|-++. |+|....+.+++.|+..+.
T Consensus 30 ~~~~l~~~g~~~~~~~kL~~~g~~tv~~~~~~---~~~~L~~~~--g~s~~~~~ki~~~a~~~~~ 89 (344)
T PLN03187 30 SIDKLISQGINAGDVKKLQDAGIYTCNGLMMH---TKKNLTGIK--GLSEAKVDKICEAAEKLLN 89 (344)
T ss_pred CHHHHhhCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhc--CCCHHHHHHHHHHHHHhhc
Confidence 35566553333345599999999999998764 788899985 7999999999999987764
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=82.42 E-value=1.1 Score=32.79 Aligned_cols=51 Identities=37% Similarity=0.561 Sum_probs=40.1
Q ss_pred eeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhcc
Q 042429 202 LEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHART 259 (304)
Q Consensus 202 Le~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAkt 259 (304)
+.+||+. ..++|.++||.|++|+..+ +++.|.++ .|++.+.=+.+++.|+.
T Consensus 10 I~Gig~~--~a~~L~~~G~~t~~~l~~a---~~~~L~~i--~Gig~~~a~~i~~~~~~ 60 (60)
T PF14520_consen 10 IPGIGPK--RAEKLYEAGIKTLEDLANA---DPEELAEI--PGIGEKTAEKIIEAARE 60 (60)
T ss_dssp STTCHHH--HHHHHHHTTCSSHHHHHTS---HHHHHHTS--TTSSHHHHHHHHHHHHH
T ss_pred CCCCCHH--HHHHHHhcCCCcHHHHHcC---CHHHHhcC--CCCCHHHHHHHHHHHhC
Confidence 4455554 3378999999999998764 88899997 47899999999988863
No 8
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=79.61 E-value=1.5 Score=43.46 Aligned_cols=51 Identities=31% Similarity=0.407 Sum_probs=40.7
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhc
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHAR 258 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAk 258 (304)
+|..|-+||+. .-++|.+.||+|++|+.++ ++..|++.|| ..+..+..||.
T Consensus 180 Pv~~l~GiG~~--~~~~L~~lGi~TigdL~~~---~~~~L~~~fG-----~~~~~l~~~a~ 230 (422)
T PRK03609 180 PVEEVWGVGRR--ISKKLNAMGIKTALDLADT---NIRFIRKHFN-----VVLERTVRELR 230 (422)
T ss_pred ChhhcCCccHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHC-----HHHHHHHHHhC
Confidence 56677778884 4489999999999999986 7889999997 34666777765
No 9
>PTZ00035 Rad51 protein; Provisional
Probab=76.47 E-value=3.3 Score=40.49 Aligned_cols=60 Identities=28% Similarity=0.295 Sum_probs=45.9
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhccccC
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHARTCIM 262 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAktCvl 262 (304)
++..|+.-|-.-..-++|+++||.||+||+.. ++..|.++. |+|...=+.+++.|+.++.
T Consensus 22 ~~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~~---~~~~L~~~~--gis~~~~~~i~~~~~~~~~ 81 (337)
T PTZ00035 22 EIEKLQSAGINAADIKKLKEAGICTVESVAYA---TKKDLCNIK--GISEAKVEKIKEAASKLVP 81 (337)
T ss_pred cHHHHhcCCCCHHHHHHHHHcCCCcHHHHHhC---CHHHHHHhh--CCCHHHHHHHHHHHHHhcc
Confidence 35556542333334589999999999998764 788999986 7899999999998888764
No 10
>PRK02406 DNA polymerase IV; Validated
Probab=74.60 E-value=2.9 Score=40.13 Aligned_cols=52 Identities=29% Similarity=0.349 Sum_probs=39.7
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhcc
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHART 259 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAkt 259 (304)
+|..|-+||+. .-++|...||.|++|+.++ +...|++.||. .+..+..+|.-
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 57777778764 3478999999999999885 78899999972 45556666653
No 11
>PRK03352 DNA polymerase IV; Validated
Probab=73.84 E-value=2.5 Score=40.59 Aligned_cols=41 Identities=32% Similarity=0.413 Sum_probs=33.8
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcC
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGT 243 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~ 243 (304)
+|..|-+||+. ..++|.+.||+|++|++++ ++..|++.||.
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 57777788874 4478999999999999986 78889999973
No 12
>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=73.19 E-value=2.7 Score=39.68 Aligned_cols=50 Identities=30% Similarity=0.420 Sum_probs=37.6
Q ss_pred eeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhc
Q 042429 202 LEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHAR 258 (304)
Q Consensus 202 Le~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAk 258 (304)
|.+||+. .-++|.++||.|++|++.+ +++.|.+++ |++.+..+.+.+-|+
T Consensus 4 i~gig~~--~~~~L~~~Gi~ti~dl~~~---~~~~L~~~~--g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 4 LPGVGPA--TAEKLREAGYDTFEAIAVA---SPKELSEIA--GISEGTAAKIIQAAR 53 (310)
T ss_pred cCCCCHH--HHHHHHHcCCCCHHHHHcC---CHHHHHhcc--CCCHHHHHHHHHHHH
Confidence 4455543 3488999999999998874 889999998 466777666666665
No 13
>PRK03858 DNA polymerase IV; Validated
Probab=69.50 E-value=2.4 Score=41.48 Aligned_cols=48 Identities=31% Similarity=0.400 Sum_probs=36.1
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhH
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMW 250 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W 250 (304)
+|..|-+||+.- -++|.+.||+|++|+.+ .++..|++.||..+-...|
T Consensus 174 pl~~l~Gig~~~--~~~L~~~Gi~t~~dl~~---l~~~~L~~~fG~~~~~~l~ 221 (396)
T PRK03858 174 PVRRLWGVGPVT--AAKLRAHGITTVGDVAE---LPESALVSLLGPAAGRHLH 221 (396)
T ss_pred ChhhcCCCCHHH--HHHHHHhCCCcHHHHhc---CCHHHHHHHhCcHHHHHHH
Confidence 466666788754 48899999999999986 4788999999843333333
No 14
>PRK03348 DNA polymerase IV; Provisional
Probab=66.54 E-value=3.4 Score=41.82 Aligned_cols=48 Identities=27% Similarity=0.400 Sum_probs=37.2
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhH
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMW 250 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W 250 (304)
+|.+|-+||+.. -++|.+.||+|++||.++ +...|++.||..+-..-|
T Consensus 181 Pv~~L~GIG~~t--~~~L~~lGI~TigDLa~l---~~~~L~~~fG~~~g~~L~ 228 (454)
T PRK03348 181 PVRRLWGIGPVT--EEKLHRLGIETIGDLAAL---SEAEVANLLGATVGPALH 228 (454)
T ss_pred CccccCCCCHHH--HHHHHHcCCccHHHHhcC---CHHHHHHHHCHHHHHHHH
Confidence 688888888754 478999999999999875 788899999733333333
No 15
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=65.68 E-value=9.8 Score=31.98 Aligned_cols=48 Identities=31% Similarity=0.330 Sum_probs=34.9
Q ss_pred hhchhhhcCCccHHHHHHhhcCChHH--HHHHHcCCCChhhHHHHHHhhccc
Q 042429 211 FYKKLTASGIKTVQDFLKMSIVEPQK--LRRILGTGMSEKMWEATIKHARTC 260 (304)
Q Consensus 211 ~hk~L~~~~I~tV~dFlkl~~~d~~k--Lr~iLg~~ms~k~W~~~v~HAktC 260 (304)
+-.+|...||+|++|||..-.....+ |-+-+ |++.+-=...+.+|.=|
T Consensus 7 ~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~--~i~~~~l~~w~~~AdL~ 56 (122)
T PF14229_consen 7 EAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKL--GISERNLLKWVNQADLM 56 (122)
T ss_pred HHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhc--CCCHHHHHHHHhHHHhh
Confidence 44789999999999999987765555 55554 56777666666666544
No 16
>PRK14133 DNA polymerase IV; Provisional
Probab=64.22 E-value=7.1 Score=37.60 Aligned_cols=51 Identities=27% Similarity=0.440 Sum_probs=39.2
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhc
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHAR 258 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAk 258 (304)
+|..|.+||+.-. ++|.+.||+|++|++++ +...|++.|| +.|..+.++|.
T Consensus 174 pv~~l~gig~~~~--~~L~~~Gi~ti~dl~~l---~~~~L~~rfG-----~~g~~l~~~a~ 224 (347)
T PRK14133 174 PISKVHGIGKKSV--EKLNNIGIYTIEDLLKL---SREFLIEYFG-----KFGVEIYERIR 224 (347)
T ss_pred CccccCCCCHHHH--HHHHHcCCccHHHHhhC---CHHHHHHHHh-----HHHHHHHHHhC
Confidence 5667777776444 77999999999999885 7788999997 34666767774
No 17
>PRK01216 DNA polymerase IV; Validated
Probab=63.96 E-value=7 Score=38.36 Aligned_cols=51 Identities=25% Similarity=0.356 Sum_probs=38.2
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhh
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHA 257 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HA 257 (304)
+|..|.+||+. ...+|...||.|++|+.++ +...|++.|| ...+..+-.+|
T Consensus 179 Pi~~l~giG~~--~~~~L~~~Gi~TigdL~~~---~~~~L~~rfG----~~~~~~L~~~a 229 (351)
T PRK01216 179 DIADIPGIGDI--TAEKLKKLGVNKLVDTLRI---EFDELKGIIG----EAKAKYLFSLA 229 (351)
T ss_pred CcccccCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHC----HHHHHHHHHHh
Confidence 57778888864 4489999999999998865 6788999997 23344444555
No 18
>PRK02794 DNA polymerase IV; Provisional
Probab=62.99 E-value=6 Score=39.26 Aligned_cols=55 Identities=24% Similarity=0.248 Sum_probs=42.5
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhccccC
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHARTCIM 262 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAktCvl 262 (304)
+|..|.+||+ ..-++|...||+|++|+.++ +...|++.||. +|..+..+|.--+.
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 4566666775 44588999999999998875 78899999972 57888888875543
No 19
>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=61.77 E-value=6.8 Score=38.89 Aligned_cols=54 Identities=28% Similarity=0.236 Sum_probs=39.5
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhc
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHAR 258 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAk 258 (304)
+|..|-+||+. .-++|.+.||.|++|+..+- .++..|++.||. +++..+..+|+
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 45899999999999998762 137889999973 34455555554
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=61.37 E-value=6.4 Score=37.79 Aligned_cols=51 Identities=33% Similarity=0.447 Sum_probs=38.9
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhc
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHAR 258 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAk 258 (304)
+|..|-+||+. .-++|...||+|++|+.++ +.+.|.+.||. .|.....+|+
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 46666677774 4478999999999999986 78889999973 4566666665
No 21
>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=60.01 E-value=6 Score=30.02 Aligned_cols=37 Identities=32% Similarity=0.487 Sum_probs=23.5
Q ss_pred hchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHH
Q 042429 212 YKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEAT 253 (304)
Q Consensus 212 hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~ 253 (304)
...|..+||+||+|++++ +++.|.++= |+..+.-+.+
T Consensus 24 ~n~L~~~~I~tv~dL~~~---s~~~L~~i~--n~G~ksl~EI 60 (66)
T PF03118_consen 24 YNCLKRAGIHTVGDLVKY---SEEDLLKIK--NFGKKSLEEI 60 (66)
T ss_dssp HHHHHCTT--BHHHHHCS----HHHHHTST--TSHHHHHHHH
T ss_pred HHHHHHhCCcCHHHHHhC---CHHHHHhCC--CCCHhHHHHH
Confidence 356999999999997765 667788773 4445554443
No 22
>PRK01172 ski2-like helicase; Provisional
Probab=59.53 E-value=9.5 Score=40.08 Aligned_cols=44 Identities=27% Similarity=0.542 Sum_probs=37.7
Q ss_pred hhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhcc
Q 042429 211 FYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHART 259 (304)
Q Consensus 211 ~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAkt 259 (304)
..++|.++||.||.|+.. .++++|-+|+ ||+++.=+.++++|+.
T Consensus 624 ~a~~l~~~g~~~~~di~~---~~~~~~~~i~--~~~~~~~~~i~~~~~~ 667 (674)
T PRK01172 624 RARRLYDAGFKTVDDIAR---SSPERIKKIY--GFSDTLANAIVNRAMK 667 (674)
T ss_pred HHHHHHHcCCCCHHHHHh---CCHHHHHHHh--ccCHHHHHHHHHHHHH
Confidence 558899999999999877 6788888887 5888999999999875
No 23
>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=59.44 E-value=10 Score=37.65 Aligned_cols=58 Identities=24% Similarity=0.271 Sum_probs=40.9
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhc------------CChHHHHHHHcCCCChhhHHHHHHhhcccc
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSI------------VEPQKLRRILGTGMSEKMWEATIKHARTCI 261 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~------------~d~~kLr~iLg~~ms~k~W~~~v~HAktCv 261 (304)
+|..|-+||+.-. ++|.+.||.|++|+..+-+ .+.+.|++.|| ++.+..+..+|+--+
T Consensus 173 pv~~l~GiG~~~~--~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG----~~~g~~l~~~a~G~d 242 (379)
T cd01703 173 DLRKIPGIGYKTA--AKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFG----EGIGQRIWKLLFGRD 242 (379)
T ss_pred CccccCCcCHHHH--HHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHC----HHHHHHHHHHHCCCC
Confidence 4666667887654 8999999999999987641 12778999997 334555556666444
No 24
>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=58.19 E-value=9.8 Score=35.95 Aligned_cols=52 Identities=29% Similarity=0.454 Sum_probs=40.4
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhcc
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHART 259 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAkt 259 (304)
+|..|-+||+. .-.+|...||+|++|+.++ ++..|++.+| +.|.....||+-
T Consensus 172 pl~~l~gig~~--~~~~L~~~Gi~ti~dl~~~---~~~~L~~~~g-----~~~~~l~~~~~G 223 (334)
T cd03586 172 PVRKIPGVGKV--TAEKLKELGIKTIGDLAKL---DVELLKKLFG-----KSGRRLYELARG 223 (334)
T ss_pred CchhhCCcCHH--HHHHHHHcCCcCHHHHHcC---CHHHHHHHHh-----HHHHHHHHHhCC
Confidence 46666677754 4488999999999999875 7788999885 567778888763
No 25
>PRK01810 DNA polymerase IV; Validated
Probab=56.65 E-value=9.5 Score=37.54 Aligned_cols=51 Identities=29% Similarity=0.339 Sum_probs=38.4
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhc
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHAR 258 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAk 258 (304)
+|..|-+||+.- -++|...||+|++|+.++ +...|++.||. .+..+.++|+
T Consensus 180 pv~~l~giG~~~--~~~L~~~Gi~tigdL~~~---~~~~L~~rfG~-----~g~~l~~~a~ 230 (407)
T PRK01810 180 PVGEMHGIGEKT--AEKLKDIGIQTIGDLAKA---DEHILRAKLGI-----NGVRLQRRAN 230 (407)
T ss_pred CHhhcCCcCHHH--HHHHHHcCCCcHHHHHhC---CHHHHHHHHhH-----HHHHHHHHhc
Confidence 466666777643 488999999999999774 77889999972 3555666666
No 26
>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=56.37 E-value=9.7 Score=37.47 Aligned_cols=55 Identities=16% Similarity=0.212 Sum_probs=38.7
Q ss_pred ceeeeeeecccchhhch-hhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhcc
Q 042429 198 EVWRLEKIGRSGTFYKK-LTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHART 259 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~-L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAkt 259 (304)
+|..|-+||+. .-++ |...||.|++|+.++. .++..|++.||. +.++.+..+|+-
T Consensus 183 pv~~l~GiG~~--~~~~ll~~~Gi~ti~dl~~~~-~~~~~L~~~fG~----~~g~~l~~~a~G 238 (359)
T cd01702 183 PITSIRGLGGK--LGEEIIDLLGLPTEGDVAGFR-SSESDLQEHFGE----KLGEWLYNLLRG 238 (359)
T ss_pred cHHHhCCcCHH--HHHHHHHHcCCcCHHHHHhcc-CCHHHHHHHHHH----HHHHHHHHHhCC
Confidence 57777788842 2244 5889999999998765 578889999873 344555555553
No 27
>PRK03103 DNA polymerase IV; Reviewed
Probab=55.11 E-value=9.9 Score=37.44 Aligned_cols=52 Identities=23% Similarity=0.315 Sum_probs=38.9
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhcc
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHART 259 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAkt 259 (304)
+|..|-+||+. .-++|.+.||.|++|+.++ ++..|++.||. +|..+.++|.-
T Consensus 182 pi~~l~gig~~--~~~~L~~~Gi~tigdl~~~---~~~~L~~~fG~-----~~~~l~~~a~G 233 (409)
T PRK03103 182 PVRKLFGVGSR--MEKHLRRMGIRTIGQLANT---PLERLKKRWGI-----NGEVLWRTANG 233 (409)
T ss_pred CHhhcCCccHH--HHHHHHHcCCCCHHHHhcC---CHHHHHHHHCH-----HHHHHHHHhcC
Confidence 56667778874 4578999999999998864 67889999972 35556666553
No 28
>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=49.12 E-value=15 Score=35.36 Aligned_cols=55 Identities=25% Similarity=0.136 Sum_probs=40.1
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCC-hHHHHHHHcCCCChhhHHHHHHhhccccC
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVE-PQKLRRILGTGMSEKMWEATIKHARTCIM 262 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d-~~kLr~iLg~~ms~k~W~~~v~HAktCvl 262 (304)
+|..|-+||+. .-++|.+.||+|++|++++ + ...|+..+| +.+..+.++|+--+.
T Consensus 174 pi~~l~giG~~--~~~~L~~~Gi~ti~dl~~~---~~~~~l~~~fg-----~~~~~l~~~a~G~d~ 229 (343)
T cd00424 174 PLTDLPGIGAV--TAKRLEAVGINPIGDLLAA---SPDALLALWGG-----VSGERLWYALRGIDD 229 (343)
T ss_pred ChhhcCCCCHH--HHHHHHHcCCCcHHHHhcC---CHHHHHHHHhh-----HHHHHHHHHhCCcCC
Confidence 57777778874 4488999999999998865 5 556777775 456777777775443
No 29
>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=48.19 E-value=5.7 Score=31.37 Aligned_cols=30 Identities=30% Similarity=0.403 Sum_probs=18.0
Q ss_pred eeeeeecccchhhchhhhcCCccHHHHHHhhc
Q 042429 200 WRLEKIGRSGTFYKKLTASGIKTVQDFLKMSI 231 (304)
Q Consensus 200 wRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~ 231 (304)
..|-+||.. .-+.|.+.||+||+||.++=.
T Consensus 6 ~~LpNig~~--~e~~L~~vGI~t~~~L~~~Ga 35 (81)
T PF04994_consen 6 KDLPNIGPK--SERMLAKVGIHTVEDLRELGA 35 (81)
T ss_dssp CGSTT--HH--HHHHHHHTT--SHHHHHHHHH
T ss_pred hhCCCCCHH--HHHHHHHcCCCCHHHHHHhCH
Confidence 334455543 237799999999999987643
No 30
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=48.01 E-value=20 Score=31.34 Aligned_cols=56 Identities=21% Similarity=0.284 Sum_probs=41.0
Q ss_pred CceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHH---HHcCCCChhhHHH-HHHhhcc
Q 042429 197 DEVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRR---ILGTGMSEKMWEA-TIKHART 259 (304)
Q Consensus 197 DeVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~---iLg~~ms~k~W~~-~v~HAkt 259 (304)
|+.-+|.+||. ++-+.|+..||+|-.|. ..+++..+-. .| +..-+.|.. -|+.|+.
T Consensus 67 DDLt~I~GIGP--k~e~~Ln~~GI~tfaQI---AAwt~~di~~id~~l--~f~GRi~RDdWi~QAk~ 126 (133)
T COG3743 67 DDLTRISGIGP--KLEKVLNELGIFTFAQI---AAWTRADIAWIDDYL--NFDGRIERDDWIAQAKA 126 (133)
T ss_pred ccchhhcccCH--HHHHHHHHcCCccHHHH---HhcCHHHHHHHHhhc--CCcchhHHHHHHHHHHH
Confidence 99999999998 46799999999996655 4455555444 44 677777765 6666653
No 31
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. ; PDB: 3IM2_A 3IM1_A 3HIB_A 2Q0Z_X.
Probab=45.85 E-value=18 Score=33.75 Aligned_cols=54 Identities=30% Similarity=0.482 Sum_probs=37.0
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhc
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHAR 258 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAk 258 (304)
...-|.+|+.+.+ ++|..+||.|.++|+++ +++++..+| ++.....+.+.+.|.
T Consensus 149 ~L~Qlp~i~~~~~--~~l~~~~i~~l~~l~~~---~~~e~~~ll--~~~~~~~~~i~~~~~ 202 (314)
T PF02889_consen 149 PLLQLPHIGEESL--KKLEKRGIKTLQDLRDL---SPEELEELL--NRNPPFGKEILEVAS 202 (314)
T ss_dssp GGGGSTT--HHHH--HHHHHTT--SHHHHHHS----HHHHHHHH---S-HHHHHHHHHHHC
T ss_pred hhhcCCCCCHHHH--HHHhccCCCcHHHHhhC---CHHHHHHHH--hhhhhhHHHHHHHHH
Confidence 4455667777654 78999999999999965 889999998 456678888888776
No 32
>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=45.40 E-value=2.4e+02 Score=25.67 Aligned_cols=59 Identities=14% Similarity=0.251 Sum_probs=38.0
Q ss_pred CccccccEEEEe---c--Cce--e---ecCCeEEecCCccccCCceEEEEEeecCCC-------CceeeeeeeecceEEe
Q 042429 118 QPLLTGDVNVTI---R--NGV--A---PVEDIEFTDNSSWIRSRKFKISAKVAQGNY-------HGVRICEAITEAFVVK 180 (304)
Q Consensus 118 ~pLL~Gd~~v~L---~--~G~--a---~l~di~FtdnSs~~rsrkFRLgarv~~~~~-------~g~rI~Eavse~FvVk 180 (304)
.+.|.|.+...+ + +|. | .++||++. .-+.|||-.++..=.. ...-+-|+.|+||.|-
T Consensus 97 ~r~L~Gs~vss~~~l~d~~~~~~g~fFvF~DLsVR------~eG~frLrf~l~~i~~~~~~~~~~~~~la~~~S~~F~V~ 170 (203)
T PF11754_consen 97 TRNLVGSLVSSAFRLKDPDGKEPGGFFVFPDLSVR------TEGRFRLRFSLFDIGPSPGQGGGSSPVLAEVFSDPFTVY 170 (203)
T ss_pred cccCcccEeeeeEEecCCCCCeEEEEEEeCCceEC------cCCEEEEEEEEEEecCCccccCCCCcEEEEEECcCEEEE
Confidence 478889876432 2 343 2 23555332 2578999999886322 2356889999999996
Q ss_pred ec
Q 042429 181 DH 182 (304)
Q Consensus 181 d~ 182 (304)
..
T Consensus 171 s~ 172 (203)
T PF11754_consen 171 SA 172 (203)
T ss_pred CH
Confidence 54
No 33
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=44.01 E-value=28 Score=28.34 Aligned_cols=60 Identities=28% Similarity=0.406 Sum_probs=40.6
Q ss_pred CCCCCceeeeeeecccchhhchhhhcCCcc----HHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhccc
Q 042429 193 QMLEDEVWRLEKIGRSGTFYKKLTASGIKT----VQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHARTC 260 (304)
Q Consensus 193 P~L~DeVwRLe~Igk~G~~hk~L~~~~I~t----V~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAktC 260 (304)
|+=+-+|--|.+||.. +-.+|..+|+.. .++|| ++.+|++-.+.-| ...--++-+||++|
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 6677789999999974 557899999975 46776 4457876544432 11112367788877
No 34
>PRK07758 hypothetical protein; Provisional
Probab=36.23 E-value=55 Score=27.15 Aligned_cols=37 Identities=22% Similarity=0.353 Sum_probs=24.4
Q ss_pred chhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHH
Q 042429 213 KKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATI 254 (304)
Q Consensus 213 k~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v 254 (304)
..|..+||+||+|+.+ ++++.|-++= |+..|.-+.+.
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 5588999999999865 4555565552 44455555543
No 35
>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=31.70 E-value=29 Score=23.85 Aligned_cols=18 Identities=39% Similarity=0.809 Sum_probs=15.1
Q ss_pred eeecCCeEEecCCccccC
Q 042429 133 VAPVEDIEFTDNSSWIRS 150 (304)
Q Consensus 133 ~a~l~di~FtdnSs~~rs 150 (304)
-..+..+.|-|++.|.+.
T Consensus 24 ~~~Ie~i~FaDGt~w~~~ 41 (43)
T PF06594_consen 24 SYRIEQIEFADGTVWTRA 41 (43)
T ss_pred CCcEeEEEEcCCCEecHH
Confidence 567889999999999753
No 36
>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=30.54 E-value=83 Score=25.51 Aligned_cols=35 Identities=26% Similarity=0.454 Sum_probs=28.0
Q ss_pred hcCCccHHHHHHhhcCChHHHH---HHHcCCCChhhHHHHHHhhcc
Q 042429 217 ASGIKTVQDFLKMSIVEPQKLR---RILGTGMSEKMWEATIKHART 259 (304)
Q Consensus 217 ~~~I~tV~dFlkl~~~d~~kLr---~iLg~~ms~k~W~~~v~HAkt 259 (304)
...| +++||+=++..||.||- ++| .|+..++-|+.
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 99999999999997755 555 48888888875
No 37
>PRK05256 condesin subunit E; Provisional
Probab=30.19 E-value=66 Score=30.66 Aligned_cols=50 Identities=20% Similarity=0.260 Sum_probs=39.8
Q ss_pred chhhhcCCccHHHHHHhhc--CChHHHHHHHc--CCCChhhHHHHHHhhccccC
Q 042429 213 KKLTASGIKTVQDFLKMSI--VEPQKLRRILG--TGMSEKMWEATIKHARTCIM 262 (304)
Q Consensus 213 k~L~~~~I~tV~dFlkl~~--~d~~kLr~iLg--~~ms~k~W~~~v~HAktCvl 262 (304)
++|++.||+|+++.+.-+. .|+++|.+.++ ..-|+-+=+++.+-.++|--
T Consensus 107 erLa~~gift~qeL~deL~~ladE~kllklvn~R~~GsDlD~~Kl~ekvr~sLr 160 (238)
T PRK05256 107 ERLAHEGIFTQQELYDELLTLADEAKLLKLVNNRSTGSDLDKQKLQEKVRTSLN 160 (238)
T ss_pred HHHhcCCceeHHHHHHHHHHhhcHHHHHHHhcCCCCcchhhHHHHHHHHHHHHH
Confidence 6899999999999887654 58999999984 22367777788888888853
No 38
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=29.83 E-value=21 Score=37.97 Aligned_cols=39 Identities=31% Similarity=0.362 Sum_probs=32.4
Q ss_pred CCCCCceeeeeeecccchhhchhhhcCCccHHHHHHhhcCC
Q 042429 193 QMLEDEVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVE 233 (304)
Q Consensus 193 P~L~DeVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d 233 (304)
+.|+++|..|++||+.- .+.|++.||.||.|.|..+-+.
T Consensus 5 ~~~~~~~~~l~gvg~~~--~~~l~~lgi~t~~dll~~~P~~ 43 (681)
T PRK10917 5 LLLDAPLTSLKGVGPKT--AEKLAKLGIHTVQDLLLHLPRR 43 (681)
T ss_pred ccccCChhhcCCCCHHH--HHHHHHcCCCCHHHHhhcCCCc
Confidence 45778999999998754 3789999999999999988654
No 39
>KOG1520 consensus Predicted alkaloid synthase/Surface mucin Hemomucin [General function prediction only]
Probab=29.70 E-value=1.9e+02 Score=29.47 Aligned_cols=118 Identities=19% Similarity=0.269 Sum_probs=64.9
Q ss_pred cccccCCCCCccccccEEEEecCceeecCCeEEecCCccccCCceEEEEEeecCCCC----------------ceee---
Q 042429 109 NIVKERIGKQPLLTGDVNVTIRNGVAPVEDIEFTDNSSWIRSRKFKISAKVAQGNYH----------------GVRI--- 169 (304)
Q Consensus 109 ~Iv~~R~Gk~pLL~Gd~~v~L~~G~a~l~di~FtdnSs~~rsrkFRLgarv~~~~~~----------------g~rI--- 169 (304)
.++-+=+|+...++.++.|.= +| .|-|||+||.--.|.|.+++---++++. +.+.
T Consensus 150 ~l~~~~~G~~~kf~N~ldI~~-~g-----~vyFTDSSsk~~~rd~~~a~l~g~~~GRl~~YD~~tK~~~VLld~L~F~NG 223 (376)
T KOG1520|consen 150 LLADEAEGKPFKFLNDLDIDP-EG-----VVYFTDSSSKYDRRDFVFAALEGDPTGRLFRYDPSTKVTKVLLDGLYFPNG 223 (376)
T ss_pred eccccccCeeeeecCceeEcC-CC-----eEEEeccccccchhheEEeeecCCCccceEEecCcccchhhhhhccccccc
Confidence 344445677666666665543 44 5789999997666888888765543220 1111
Q ss_pred -eeeeecceEEeecCCc-------ccccCC---------CCCCCCceeeeeeecccchhhchhhhcCCccHHHHHHhhcC
Q 042429 170 -CEAITEAFVVKDHRGE-------LYKKHH---------PQMLEDEVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIV 232 (304)
Q Consensus 170 -~Eavse~FvVkd~Rge-------~~kKh~---------pP~L~DeVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~ 232 (304)
+=-..+.|++--.=.- ....+. -|-.-|.+-|= .+|.|.-.|....=. |.++++.
T Consensus 224 laLS~d~sfvl~~Et~~~ri~rywi~g~k~gt~EvFa~~LPG~PDNIR~~----~~G~fWVal~~~~~~----~~~~~~~ 295 (376)
T KOG1520|consen 224 LALSPDGSFVLVAETTTARIKRYWIKGPKAGTSEVFAEGLPGYPDNIRRD----STGHFWVALHSKRST----LWRLLMK 295 (376)
T ss_pred ccCCCCCCEEEEEeeccceeeeeEecCCccCchhhHhhcCCCCCcceeEC----CCCCEEEEEecccch----HHHhhhc
Confidence 1112356665433222 122222 56666666543 566666555443222 7777777
Q ss_pred ChHHHHHHH
Q 042429 233 EPQKLRRIL 241 (304)
Q Consensus 233 d~~kLr~iL 241 (304)
.| -+|+++
T Consensus 296 ~p-~vr~~~ 303 (376)
T KOG1520|consen 296 YP-WVRKFI 303 (376)
T ss_pred Ch-HHHHHH
Confidence 76 677764
No 40
>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=28.19 E-value=35 Score=32.16 Aligned_cols=35 Identities=20% Similarity=0.373 Sum_probs=28.2
Q ss_pred eecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcC
Q 042429 204 KIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGT 243 (304)
Q Consensus 204 ~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~ 243 (304)
+||+... .+|.+.||+|++||..+ +...|++.||.
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 5676543 88999999999998875 67789999873
No 41
>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=28.17 E-value=2.6e+02 Score=24.24 Aligned_cols=26 Identities=23% Similarity=0.397 Sum_probs=18.8
Q ss_pred EEEEEcCCCCCCCCCCCCHHHHhhccc
Q 042429 85 LMVVLDWDFPSGDHDDWSQEEFESNIV 111 (304)
Q Consensus 85 eIvVLdGdF~~~~~e~WT~eeF~~~Iv 111 (304)
+|.|..+||... -.+||.|+|..--+
T Consensus 9 Qi~v~~~~~~~p-~~dWtde~i~qG~a 34 (125)
T PF11033_consen 9 QITVFNRDGEPP-YIDWTDEDIEQGYA 34 (125)
T ss_pred eEEEEccCCCCc-ccccCHhHHhCcce
Confidence 577888888752 26899999986433
No 42
>PF09816 EAF: RNA polymerase II transcription elongation factor; InterPro: IPR019194 This entry represents the N-terminal domain of ELL-associated factor (Eaf) proteins, which act as transcriptional transactivators of ELL and ELL2 RNA Polymerase II (Pol II) transcriptional elongation factors [, , , ]. Eaf proteins form a stable heterodimer complex with ELL proteins to facilitate the binding of RNA polymerase II to activate transcription elongation. ELL and EAF1 are components of Cajal bodies, which have a role in leukemogenesis []. EAF1 also has the capacity to interact with ELL1 and ELL2. The N terminus of approx 120 of EAF1 has a region of high serine, aspartic acid, and glutamic acid residues [, ].
Probab=27.95 E-value=1.7e+02 Score=23.98 Aligned_cols=67 Identities=16% Similarity=0.222 Sum_probs=42.1
Q ss_pred ccccCCCccccccC-CCCceEEEEcc-CCC----CCcccCCceeecCCCCeEEEEEEcCCCCeeecCCCCCccEEE
Q 042429 16 QSLTRSLPLCFQAL-ESSSLKLTFSE-ELS----LPIFTGRKITDIENNPLQIVVVETRSSGRITPANLSQPIKIL 85 (304)
Q Consensus 16 ~~~~rs~~~~~~~~-~~~~~~L~F~n-~l~----~pifT~~~I~a~~g~~I~V~l~D~~t~~~iv~~g~~ss~kve 85 (304)
.++..+.+-.+... ....++|.|-+ .-. .-+|.|..=.+ ..-=.|-|||..++ ..+=..+.+.+++-
T Consensus 31 ~S~d~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~f~G~~~~~--~~~ecVLifD~~~~-~f~LErl~s~~~~n 103 (109)
T PF09816_consen 31 ASVDTSKPGTLYVGSSNDEYTLTLPNPNGSGNNETYVFKGSQRPS--KEKECVLIFDPETG-EFVLERLSSTINLN 103 (109)
T ss_pred CCCCCCCCeEEEecCCCCeEEEEEeCCCCCCCcccEEEEeccCCC--CCcEEEEEEECCCC-EEEEEEcceEEEEE
Confidence 45666655556544 56689999933 221 25899983322 33445888999887 77766666666553
No 43
>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=27.66 E-value=81 Score=21.46 Aligned_cols=41 Identities=32% Similarity=0.401 Sum_probs=31.1
Q ss_pred chhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhc
Q 042429 213 KKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHAR 258 (304)
Q Consensus 213 k~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAk 258 (304)
.+|..+|+.||+++.. .+++.|..+- |++...=+.++.=|+
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 5799999999999865 4677788874 577777666666554
No 44
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=26.89 E-value=40 Score=32.37 Aligned_cols=41 Identities=24% Similarity=0.374 Sum_probs=34.9
Q ss_pred hhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHh
Q 042429 215 LTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKH 256 (304)
Q Consensus 215 L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~H 256 (304)
-+.++|.|+.|-..+...+|+.||++++ -+.+|.|=.=|+-
T Consensus 25 ae~hkiiTirdvae~~ev~~n~lr~las-rLekkG~LeRi~r 65 (269)
T COG5340 25 AEGHKIITIRDVAETLEVAPNTLRELAS-RLEKKGWLERILR 65 (269)
T ss_pred HHhCceEEeHHhhhhccCCHHHHHHHHh-hhhhcchhhhhcC
Confidence 3457999999999999999999999996 6889999765543
No 45
>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=25.14 E-value=1.8e+02 Score=25.59 Aligned_cols=34 Identities=26% Similarity=0.512 Sum_probs=25.7
Q ss_pred EEEecCceeecCCeEEecCCccccCCceEEEEEeec
Q 042429 126 NVTIRNGVAPVEDIEFTDNSSWIRSRKFKISAKVAQ 161 (304)
Q Consensus 126 ~v~L~~G~a~l~di~FtdnSs~~rsrkFRLgarv~~ 161 (304)
.-.|+|++|-..|+.|-.-|. |.+.|-|-.-+..
T Consensus 74 tavmknqvA~FnDLRFvGRSG--RGKsFtltItv~t 107 (135)
T PF00853_consen 74 TAVMKNQVARFNDLRFVGRSG--RGKSFTLTITVFT 107 (135)
T ss_dssp EEEEETTEEEESS-EECST-T--TTSEEEEEEEE-S
T ss_pred hhhhhcccccccccccccccC--CccceEEEEEEeC
Confidence 578999999999999999877 3555999887764
No 46
>PRK14973 DNA topoisomerase I; Provisional
Probab=24.30 E-value=63 Score=36.29 Aligned_cols=54 Identities=22% Similarity=0.380 Sum_probs=43.6
Q ss_pred eeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhcc
Q 042429 199 VWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHART 259 (304)
Q Consensus 199 VwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAkt 259 (304)
.=.++++|.+.. .+|..+||.+|+|+++. |+.+|-.. .|++.|.-..+..+|+.
T Consensus 879 l~~vkg~ge~t~--~~l~~ag~~~~e~l~~~---d~~~la~~--~~i~~k~~~~~~~~~~~ 932 (936)
T PRK14973 879 LLSVPGLGETTL--EKLYLAGVYDGDLLVSA---DPKKLAKV--TGIDEKKLRNLQAYAKK 932 (936)
T ss_pred hhhccCCCHHHH--HHHHHcCCCCHHHhccC---CHHHHhhh--cCCCHHHHHHHHHHHhh
Confidence 335567777777 88999999999999987 88888887 37788888888887763
No 47
>PRK02362 ski2-like helicase; Provisional
Probab=23.97 E-value=75 Score=34.03 Aligned_cols=51 Identities=27% Similarity=0.395 Sum_probs=39.4
Q ss_pred eeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhhccc
Q 042429 201 RLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHARTC 260 (304)
Q Consensus 201 RLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HAktC 260 (304)
+|.+|++. ..++|.++||.|+.|+. ..++++|.++|| .|.=+.+++.|+.-
T Consensus 656 ~ip~i~~~--~a~~l~~~gi~s~~dl~---~~~~~~l~~~~g----~~~~~~i~~~~~~~ 706 (737)
T PRK02362 656 GLRGVGRV--RARRLYNAGIESRADLR---AADKSVVLAILG----EKIAENILEQAGRR 706 (737)
T ss_pred CCCCCCHH--HHHHHHHcCCCCHHHHH---hCCHHHHHHHHC----HHHHHHHHHHhCcc
Confidence 45555554 45888899999999998 468899999976 67777788888743
No 48
>PTZ00205 DNA polymerase kappa; Provisional
Probab=23.60 E-value=66 Score=34.28 Aligned_cols=53 Identities=19% Similarity=0.388 Sum_probs=36.7
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhc-----CChHHHHHHHcCCCChhhHHH
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSI-----VEPQKLRRILGTGMSEKMWEA 252 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~-----~d~~kLr~iLg~~ms~k~W~~ 252 (304)
+|-+|-+||+... ++|...||.|++|+.+.-. ..+..|+.+||..+--..|..
T Consensus 310 pV~ki~GIG~~t~--~~L~~~GI~TigDLa~~~~~l~~~f~~k~l~~llG~~~G~~l~~~ 367 (571)
T PTZ00205 310 GLRSVPGVGKVTE--ALLKGLGITTLSDIYNRRVELCYILHNNLFRFLLGASIGIMQWPD 367 (571)
T ss_pred CcceeCCcCHHHH--HHHHHcCCCcHHHHhcCCHHHHHHhHHHHHHHHhCchhhHHHHHH
Confidence 5788889998655 8999999999999976421 223457777774333344544
No 49
>PF04717 Phage_base_V: Phage-related baseplate assembly protein; InterPro: IPR006531 This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells []. Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].; PDB: 3AQJ_C 3QR8_A 2P5Z_X.
Probab=23.47 E-value=1.4e+02 Score=22.52 Aligned_cols=33 Identities=15% Similarity=0.187 Sum_probs=19.8
Q ss_pred eeeecceEEeecCCcccccCCCCCCCCceeeee
Q 042429 171 EAITEAFVVKDHRGELYKKHHPQMLEDEVWRLE 203 (304)
Q Consensus 171 Eavse~FvVkd~Rge~~kKh~pP~L~DeVwRLe 203 (304)
+..|...-|...+.-..+-+.||.+.|+|+-+-
T Consensus 22 ~~~s~Wl~~~~~~ag~~g~~~~P~iGeqV~v~~ 54 (79)
T PF04717_consen 22 DIVSDWLPVLQPRAGGWGFWFPPEIGEQVLVLF 54 (79)
T ss_dssp TEEEEEEEE--S-BSSSB------TT-EEEEEE
T ss_pred CccceEEEeeehhccCCeeEccCCCCcEEEEEc
Confidence 567899999998888889999999999999876
No 50
>PF10657 RC-P840_PscD: Photosystem P840 reaction centre protein PscD; InterPro: IPR019608 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. The photosynthetic reaction centres (RCs) of aerotolerant organisms contain a heterodimeric core, built up of two strongly homologous polypeptides each of which contributes five transmembrane peptide helices to hold a pseudo-symmetric double set of redox components. Two molecules of PscD are housed within a subunit. PscD may be involved in stabilising the PscB component since it is found to co-precipitate with FMO (Fenna-Mathews-Olson BChl a-protein) and PscB. It may also be involved in the interaction with ferredoxin [].
Probab=22.75 E-value=81 Score=27.66 Aligned_cols=28 Identities=14% Similarity=0.349 Sum_probs=25.4
Q ss_pred CcEEEEEccceeEeEeEECCEEeeCCCC
Q 042429 272 PNSIIFLNPICQVVRATINGQTFLTRDL 299 (304)
Q Consensus 272 ~~~~l~FN~i~~lvga~~~g~~~~~~~l 299 (304)
..+-+|||+...=+.+.+||+.|++++|
T Consensus 115 RdipVfy~~~~~~l~Veid~r~YtL~eF 142 (144)
T PF10657_consen 115 RDIPVFYNSLTRQLCVEIDRRTYTLDEF 142 (144)
T ss_pred ecCceEEccCCcEEEEEECCeEEehHhh
Confidence 4678999999999999999999999886
No 51
>PF13854 Kelch_5: Kelch motif
Probab=21.92 E-value=55 Score=21.99 Aligned_cols=27 Identities=26% Similarity=0.572 Sum_probs=19.7
Q ss_pred ccccCCCceEEEecCc--EEEEEccceeE
Q 042429 258 RTCIMGNKLYIFRGPN--SIIFLNPICQV 284 (304)
Q Consensus 258 ktCvl~~k~y~y~~~~--~~l~FN~i~~l 284 (304)
-.|+.++++|+|=+.+ -...+|.+|.+
T Consensus 9 s~~~~~~~iyi~GG~~~~~~~~~~d~~~l 37 (42)
T PF13854_consen 9 SAVVVGNNIYIFGGYSGNNNSYSNDLYVL 37 (42)
T ss_pred EEEEECCEEEEEcCccCCCCCEECcEEEE
Confidence 3456689999998754 46778888764
No 52
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=21.88 E-value=79 Score=26.54 Aligned_cols=37 Identities=30% Similarity=0.556 Sum_probs=27.8
Q ss_pred eeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHH
Q 042429 200 WRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRIL 241 (304)
Q Consensus 200 wRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iL 241 (304)
.|..+||. .|...|...||.||+++-. .+|++|.+-+
T Consensus 56 ~ri~gi~~--~~a~LL~~AGv~Tv~~LA~---~~p~~L~~~l 92 (122)
T PF14229_consen 56 MRIPGIGP--QYAELLEHAGVDTVEELAQ---RNPQNLHQKL 92 (122)
T ss_pred hhcCCCCH--HHHHHHHHhCcCcHHHHHh---CCHHHHHHHH
Confidence 35666655 4668899999999999854 6888887654
No 53
>PF05643 DUF799: Putative bacterial lipoprotein (DUF799); InterPro: IPR008517 This family consists of several bacterial proteins of unknown function. Some of the family members are described as putative lipoproteins.
Probab=20.55 E-value=82 Score=29.63 Aligned_cols=28 Identities=32% Similarity=0.666 Sum_probs=23.5
Q ss_pred chhhhcCCccHHHHHHhhcCChHHHHHHHcC
Q 042429 213 KKLTASGIKTVQDFLKMSIVEPQKLRRILGT 243 (304)
Q Consensus 213 k~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~ 243 (304)
.-|+++||.+-+|+ ...+++||++|||.
T Consensus 79 e~fkqnGlt~~~~i---~~v~~~kL~eiFGA 106 (215)
T PF05643_consen 79 ETFKQNGLTDAEDI---HAVPPAKLREIFGA 106 (215)
T ss_pred HHHHHcCCCCHHHh---ccCCHHHHHHHhCC
Confidence 34789999999998 45789999999983
No 54
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=20.40 E-value=1.3e+02 Score=28.21 Aligned_cols=53 Identities=19% Similarity=0.305 Sum_probs=37.6
Q ss_pred ceeeeeeecccchhhchhhhcCCccHHHHHHhhcCChHHHHHHHcCCCChhhHHHHHHhh
Q 042429 198 EVWRLEKIGRSGTFYKKLTASGIKTVQDFLKMSIVEPQKLRRILGTGMSEKMWEATIKHA 257 (304)
Q Consensus 198 eVwRLe~Igk~G~~hk~L~~~~I~tV~dFlkl~~~d~~kLr~iLg~~ms~k~W~~~v~HA 257 (304)
+..-|.+|+++- .++|.++||.|.+|+..+ +++++..++| +..+.=+.+.+.+
T Consensus 152 ~L~Qlp~i~~~~--~~~l~~~~i~s~~~l~~~---~~~~~~~ll~--~~~~~~~~i~~~~ 204 (312)
T smart00611 152 PLLQLPHLPEEI--LKRLEKKKVLSLEDLLEL---EDEERGELLG--LLDAEGERVYKVL 204 (312)
T ss_pred ccccCCCCCHHH--HHHHHhCCCCCHHHHHhc---CHHHHHHHHc--CCHHHHHHHHHHH
Confidence 455677787754 478899999999998765 7788888884 5555555555544
Done!