Query 029239
Match_columns 196
No_of_seqs 96 out of 98
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 09:44:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029239.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029239hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3241 Uncharacterized conser 100.0 1.3E-61 2.9E-66 410.4 5.8 167 1-171 1-175 (227)
2 PF10217 DUF2039: Uncharacteri 100.0 5.9E-46 1.3E-50 283.3 5.2 92 10-105 1-92 (92)
3 PF10235 Cript: Microtubule-as 94.6 0.015 3.2E-07 45.0 1.1 41 63-104 38-79 (90)
4 PRK04023 DNA polymerase II lar 81.8 0.66 1.4E-05 48.8 1.2 59 69-134 639-699 (1121)
5 KOG3476 Microtubule-associated 81.1 0.49 1.1E-05 37.2 0.0 46 56-104 44-89 (100)
6 PRK14714 DNA polymerase II lar 76.6 0.85 1.9E-05 48.9 0.2 71 44-134 668-745 (1337)
7 PF14634 zf-RING_5: zinc-RING 74.2 1.2 2.6E-05 28.8 0.3 24 79-102 17-44 (44)
8 PRK11595 DNA utilization prote 65.5 3.2 6.9E-05 35.3 1.2 22 122-143 74-95 (227)
9 PF04161 Arv1: Arv1-like famil 63.3 3.2 6.9E-05 35.2 0.8 60 70-131 2-66 (208)
10 PF07191 zinc-ribbons_6: zinc- 61.3 0.37 8.1E-06 35.8 -4.5 46 44-101 2-47 (70)
11 PRK04023 DNA polymerase II lar 60.7 4.5 9.8E-05 42.9 1.4 44 58-105 615-662 (1121)
12 PF03833 PolC_DP2: DNA polymer 59.4 3.1 6.6E-05 43.3 0.0 59 69-134 668-728 (900)
13 KOG4739 Uncharacterized protei 53.5 4.3 9.3E-05 36.2 -0.1 37 70-106 5-49 (233)
14 KOG0978 E3 ubiquitin ligase in 52.1 7.1 0.00015 39.7 1.2 36 69-104 644-688 (698)
15 PF13900 GVQW: Putative bindin 51.1 4.6 0.0001 28.2 -0.2 39 53-93 6-44 (48)
16 PRK00420 hypothetical protein; 49.4 47 0.001 26.6 5.2 16 177-192 93-108 (112)
17 PF10083 DUF2321: Uncharacteri 47.0 10 0.00022 32.2 1.2 40 95-139 69-108 (158)
18 PF09538 FYDLN_acid: Protein o 46.8 7.9 0.00017 30.5 0.5 22 85-106 10-38 (108)
19 PF13920 zf-C3HC4_3: Zinc fing 45.5 8.1 0.00018 25.3 0.3 23 84-106 22-49 (50)
20 COG1645 Uncharacterized Zn-fin 44.0 12 0.00025 30.9 1.1 27 80-108 26-58 (131)
21 PF06906 DUF1272: Protein of u 38.7 16 0.00034 26.5 0.9 17 85-101 30-48 (57)
22 PRK13919 putative RNA polymera 36.9 1.8E+02 0.0039 22.9 6.8 51 119-190 126-177 (186)
23 PF14149 YhfH: YhfH-like prote 35.9 15 0.00032 24.5 0.4 24 67-90 12-37 (37)
24 PF13376 OmdA: Bacteriocin-pro 33.4 28 0.00062 24.1 1.6 43 106-148 4-46 (63)
25 TIGR00570 cdk7 CDK-activating 33.4 53 0.0011 30.5 3.7 23 83-105 27-54 (309)
26 cd08168 Cytochrom_C3 Heme-bind 33.1 25 0.00055 25.1 1.3 44 44-95 17-69 (85)
27 TIGR00375 conserved hypothetic 32.1 17 0.00036 34.3 0.3 29 59-88 235-263 (374)
28 PRK06759 RNA polymerase factor 30.2 69 0.0015 24.3 3.3 55 116-191 94-149 (154)
29 cd02249 ZZ Zinc finger, ZZ typ 30.0 11 0.00023 24.8 -1.0 31 70-103 2-32 (46)
30 COG5141 PHD zinc finger-contai 29.8 21 0.00046 35.8 0.6 28 67-97 312-339 (669)
31 KOG0031 Myosin regulatory ligh 29.7 54 0.0012 28.3 2.9 63 116-190 28-95 (171)
32 PF01907 Ribosomal_L37e: Ribos 29.1 15 0.00033 26.3 -0.4 23 84-106 15-42 (55)
33 TIGR00595 priA primosomal prot 29.0 28 0.0006 33.4 1.2 32 69-103 223-262 (505)
34 PF15135 UPF0515: Uncharacteri 28.9 21 0.00046 32.8 0.3 68 37-110 106-192 (278)
35 PF04981 NMD3: NMD3 family ; 28.5 23 0.0005 30.5 0.5 31 71-102 1-43 (236)
36 TIGR00354 polC DNA polymerase, 28.4 25 0.00053 37.6 0.8 50 68-133 625-674 (1095)
37 KOG1100 Predicted E3 ubiquitin 28.4 15 0.00033 31.6 -0.6 38 68-105 158-200 (207)
38 PF12773 DZR: Double zinc ribb 28.0 25 0.00054 22.9 0.5 18 86-103 14-38 (50)
39 PHA02683 ORF078 thioredoxin-li 27.9 20 0.00044 27.2 0.1 18 59-76 4-22 (75)
40 PF02650 HTH_WhiA: WhiA C-term 27.7 83 0.0018 23.8 3.3 33 160-192 52-84 (85)
41 TIGR02300 FYDLN_acid conserved 27.6 23 0.0005 29.2 0.3 20 85-104 10-36 (129)
42 PF02085 Cytochrom_CIII: Class 26.6 36 0.00077 25.2 1.2 41 45-94 33-86 (102)
43 COG1040 ComFC Predicted amidop 25.8 46 0.001 28.7 1.9 73 65-144 21-100 (225)
44 PRK00133 metG methionyl-tRNA s 25.6 67 0.0014 31.8 3.1 73 69-144 140-223 (673)
45 PRK09646 RNA polymerase sigma 25.4 83 0.0018 25.3 3.2 25 118-142 132-157 (194)
46 PF13248 zf-ribbon_3: zinc-rib 25.0 24 0.00052 20.8 -0.0 9 94-102 16-24 (26)
47 PF08281 Sigma70_r4_2: Sigma-7 24.7 81 0.0018 20.3 2.5 26 120-145 2-27 (54)
48 PF03660 PHF5: PHF5-like prote 24.5 24 0.00052 28.4 -0.1 26 66-93 53-79 (106)
49 PRK12496 hypothetical protein; 24.3 21 0.00046 29.5 -0.4 21 85-105 128-154 (164)
50 cd02341 ZZ_ZZZ3 Zinc finger, Z 24.2 18 0.00038 24.7 -0.8 32 70-102 2-34 (48)
51 PRK13130 H/ACA RNA-protein com 24.0 55 0.0012 23.3 1.7 29 68-110 5-33 (56)
52 PRK14890 putative Zn-ribbon RN 24.0 15 0.00033 26.6 -1.2 36 68-103 7-45 (59)
53 PRK06266 transcription initiat 23.9 55 0.0012 27.5 1.9 37 67-114 116-153 (178)
54 cd02338 ZZ_PCMF_like Zinc fing 23.6 15 0.00032 24.8 -1.2 31 70-102 2-32 (49)
55 PF08006 DUF1700: Protein of u 23.4 56 0.0012 26.6 1.9 25 120-144 8-32 (181)
56 TIGR02989 Sig-70_gvs1 RNA poly 23.2 3.3E+02 0.0072 20.5 6.5 55 117-191 100-154 (159)
57 cd02335 ZZ_ADA2 Zinc finger, Z 22.9 17 0.00037 24.3 -1.0 32 70-103 2-33 (49)
58 PF11331 DUF3133: Protein of u 22.9 31 0.00068 23.7 0.2 32 45-76 8-39 (46)
59 cd02345 ZZ_dah Zinc finger, ZZ 22.6 17 0.00037 24.5 -1.1 31 70-102 2-32 (49)
60 PF11793 FANCL_C: FANCL C-term 22.6 12 0.00025 26.9 -2.0 19 39-57 51-69 (70)
61 PRK04179 rpl37e 50S ribosomal 21.6 28 0.00061 25.5 -0.2 25 68-103 17-41 (62)
62 COG0068 HypF Hydrogenase matur 21.6 86 0.0019 32.5 3.1 59 41-104 99-183 (750)
63 TIGR00373 conserved hypothetic 21.4 67 0.0014 26.3 1.9 47 67-127 108-155 (158)
64 PRK12543 RNA polymerase sigma 21.2 3.3E+02 0.0072 21.4 5.8 53 118-190 107-159 (179)
65 KOG0090 Signal recognition par 21.1 79 0.0017 28.6 2.4 70 115-187 163-236 (238)
66 PF13945 NST1: Salt tolerance 20.7 89 0.0019 27.1 2.6 24 116-139 101-124 (190)
67 PF01486 K-box: K-box region; 20.5 1.2E+02 0.0026 22.7 3.0 41 107-147 43-83 (100)
68 PRK12380 hydrogenase nickel in 20.1 27 0.0006 27.2 -0.6 28 67-104 69-96 (113)
69 cd02334 ZZ_dystrophin Zinc fin 20.1 23 0.0005 24.2 -0.9 31 70-102 2-32 (49)
70 PRK05580 primosome assembly pr 20.1 46 0.001 33.1 0.9 73 69-147 391-482 (679)
No 1
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.3e-61 Score=410.40 Aligned_cols=167 Identities=55% Similarity=0.950 Sum_probs=155.6
Q ss_pred CCC---CCCCCCCCCCccccccCCCCCCcchhhhhcCCCCCCCCccCchhhhHHHHHHHHHhCCCCCCCCcccccccccc
Q 029239 1 MSS---NSSRRGAPKHQNRYAWKPKAGQKINEREVGGKLRPYPEITGVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKR 77 (196)
Q Consensus 1 ms~---N~~RsrpQKHQN~~aFKnn~~~K~~e~~~~~k~~~~~~~~gVCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~qk 77 (196)
||| |++|+|||||||+|+|+|++++|. .++++| |++.|+||||||+++|+||++|+||||||++++|.+|.++
T Consensus 1 MsSq~GNVaRsRpqKHqN~f~fkndk~dkt---~q~~r~-na~~itgVCqRCkEqieWk~KY~KYKpLt~akkC~kC~~r 76 (227)
T KOG3241|consen 1 MSSQQGNVARSRPQKHQNKFAFKNDKIDKT---EQGGRF-NASEITGVCQRCKEQIEWKRKYGKYKPLTEAKKCQKCTKR 76 (227)
T ss_pred CCcccCccccccchhhccceeecccccccc---hhhcee-hhhHhhhHHHHHHHHHHHHHHhccccccchhHHHHHHHHH
Confidence 787 999999999999999999987664 455666 6899999999999999999999999999999999999999
Q ss_pred hhhHHhHhcChhHHhhccccccccCccccccCCCchhHHHHHHHHHHHHhhchhhhhhhHHHHHhhhcccccCccc----
Q 029239 78 AVRQAYHNLCPGCAKEQNVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERDRRILLRAVNLKIQQKIQPTK---- 153 (196)
Q Consensus 78 tVk~AYH~iC~~CA~~~~vCaKC~k~~~~i~~~~~~~~e~eq~ele~~lk~l~ER~RRt~lR~~~k~~~~~~~~~~---- 153 (196)
+|++|||++|++||.++.+||||+++.+.|..+++.+++.|++.|++.+++++||+||||||+|+|+++...+|+.
T Consensus 77 ~Vk~aYH~~Cr~CA~e~~vCAKC~ks~~~i~i~d~~p~~~E~~~l~~t~~n~ser~RRt~lR~m~k~~k~~kd~~~~~~d 156 (227)
T KOG3241|consen 77 NVKQAYHKLCRGCAKEQKVCAKCCKSVDQILIRDIYPVEAEQKLLDETIKNASERDRRTLLRAMNKDNKPNKDEEASRSD 156 (227)
T ss_pred HHHHHHHHhcccHHHHHHHHHHHhccHHHhhhcCCCCCcHHHHHHHHHHhhhhHHHHHHHHHHHhcccCcccChhhhhcc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999887765544
Q ss_pred -cccCCccCccchHHHhhh
Q 029239 154 -IKLGNYFLPHHLRNMLQK 171 (196)
Q Consensus 154 -~~~g~~~~~~~~~~~~~~ 171 (196)
+++|++||+.++++|+.+
T Consensus 157 ~~~~~~~~~s~~~~~~~~~ 175 (227)
T KOG3241|consen 157 SSKVGDVFPSTSLEEYANK 175 (227)
T ss_pred hhhhcccccchhHHHHHhh
Confidence 788999999999999865
No 2
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=100.00 E-value=5.9e-46 Score=283.31 Aligned_cols=92 Identities=50% Similarity=0.994 Sum_probs=84.6
Q ss_pred CCCCccccccCCCCCCcchhhhhcCCCCCCCCccCchhhhHHHHHHHHHhCCCCCCCCcccccccccchhhHHhHhcChh
Q 029239 10 APKHQNRYAWKPKAGQKINEREVGGKLRPYPEITGVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPG 89 (196)
Q Consensus 10 pQKHQN~~aFKnn~~~K~~e~~~~~k~~~~~~~~gVCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~qktVk~AYH~iC~~ 89 (196)
+|||||+|||+||++++.. +. +.+++.+++|||+||+|+||||++|||||||++|++|++|+++||++|||+||++
T Consensus 1 ~qkhqN~~aFk~n~~~~~~-~~---~~i~~~~~~gvC~rC~~~IeWK~kY~KYKpLt~p~kC~~C~qktVk~AYh~iC~~ 76 (92)
T PF10217_consen 1 AQKHQNRFAFKNNKHDKSE-KT---KKINSLPIDGVCQRCKDIIEWKVKYGKYKPLTQPKKCNKCQQKTVKHAYHVICDP 76 (92)
T ss_pred CccccccccccCCCCCccH-HH---HHHHhCccccccHhHHHHHHHHHHhcCcccCCCCccccccccchHHHHHHHHHHH
Confidence 5999999999999999833 22 3456679999999999999999999999999999999999999999999999999
Q ss_pred HHhhccccccccCccc
Q 029239 90 CAKEQNVCAKCCSRVD 105 (196)
Q Consensus 90 CA~~~~vCaKC~k~~~ 105 (196)
||.++++|||||+++|
T Consensus 77 Ca~~~~vCaKC~k~~e 92 (92)
T PF10217_consen 77 CAKELKVCAKCGKPPE 92 (92)
T ss_pred HHHhhccCcccCCCCC
Confidence 9999999999999875
No 3
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=94.62 E-value=0.015 Score=44.96 Aligned_cols=41 Identities=29% Similarity=0.767 Sum_probs=32.1
Q ss_pred CCCCC-cccccccccchhhHHhHhcChhHHhhccccccccCcc
Q 029239 63 KPLSE-PAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRV 104 (196)
Q Consensus 63 KPLt~-p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~~ 104 (196)
-|..+ ..+|-.|. -.|.++=|..|+.||-..++||.||++.
T Consensus 38 nPy~~~~~~C~~CK-~~v~q~g~~YCq~CAYkkGiCamCGKki 79 (90)
T PF10235_consen 38 NPYAPYSSKCKICK-TKVHQPGAKYCQTCAYKKGICAMCGKKI 79 (90)
T ss_pred CcccccCccccccc-cccccCCCccChhhhcccCcccccCCee
Confidence 34443 67899994 4566666668999999999999999975
No 4
>PRK04023 DNA polymerase II large subunit; Validated
Probab=81.76 E-value=0.66 Score=48.80 Aligned_cols=59 Identities=25% Similarity=0.536 Sum_probs=30.4
Q ss_pred ccccccccchhhHHhHhcChhHHhhc--cccccccCccccccCCCchhHHHHHHHHHHHHhhchhhhh
Q 029239 69 AKCQRCTKRAVRQAYHNLCPGCAKEQ--NVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERDR 134 (196)
Q Consensus 69 ~KC~kC~qktVk~AYH~iC~~CA~~~--~vCaKC~k~~~~i~~~~~~~~e~eq~ele~~lk~l~ER~R 134 (196)
++|..|+..| ..+| -|+.|.... ..|++||.......- ..-.....+.+++++|.+|+.
T Consensus 639 frCP~CG~~T-e~i~--fCP~CG~~~~~y~CPKCG~El~~~s~----~~i~l~~~~~~A~~~lg~~~~ 699 (1121)
T PRK04023 639 RRCPFCGTHT-EPVY--RCPRCGIEVEEDECEKCGREPTPYSK----RKIDLKELYDRALENLGERKN 699 (1121)
T ss_pred ccCCCCCCCC-Ccce--eCccccCcCCCCcCCCCCCCCCccce----EEecHHHHHHHHHHHhCCcCC
Confidence 4555555543 2222 355554443 246666643321111 111234478889999999886
No 5
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=81.05 E-value=0.49 Score=37.16 Aligned_cols=46 Identities=33% Similarity=0.723 Sum_probs=33.6
Q ss_pred HHHhCCCCCCCCcccccccccchhhHHhHhcChhHHhhccccccccCcc
Q 029239 56 KRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRV 104 (196)
Q Consensus 56 KvkY~KYKPLt~p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~~ 104 (196)
+.+|.-|- +.-.+|-.|.+. |.+.=.+.|+.||-..+|||-||+..
T Consensus 44 k~r~~p~g--t~~~kC~iCk~~-vHQ~GshYC~tCAY~KgiCAMCGKki 89 (100)
T KOG3476|consen 44 KKRATPYG--TALAKCRICKQL-VHQPGSHYCQTCAYKKGICAMCGKKI 89 (100)
T ss_pred hhhcCccc--cccchhHHHHHH-hcCCcchhHhHhhhhhhHHHHhhhHh
Confidence 44444443 456788888554 55555559999999999999999863
No 6
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=76.57 E-value=0.85 Score=48.88 Aligned_cols=71 Identities=25% Similarity=0.583 Sum_probs=47.2
Q ss_pred CchhhhHHHHHHHHHhCCCCCCCCcccccccccchhhHHhHhcChhHHhhc-------cccccccCccccccCCCchhHH
Q 029239 44 GVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPGCAKEQ-------NVCAKCCSRVDRVIGRDLAEVE 116 (196)
Q Consensus 44 gVCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~qktVk~AYH~iC~~CA~~~-------~vCaKC~k~~~~i~~~~~~~~e 116 (196)
..|+.|-..+-+ ..|..|+..+.. .| .|+.|..+. ..|+.|+.+.-...... -
T Consensus 668 rkCPkCG~~t~~-------------~fCP~CGs~te~-vy--~CPsCGaev~~des~a~~CP~CGtplv~~~~~~----i 727 (1337)
T PRK14714 668 RRCPSCGTETYE-------------NRCPDCGTHTEP-VY--VCPDCGAEVPPDESGRVECPRCDVELTPYQRRT----I 727 (1337)
T ss_pred EECCCCCCcccc-------------ccCcccCCcCCC-ce--eCccCCCccCCCccccccCCCCCCcccccceEE----e
Confidence 469999865321 289999998754 34 799998863 27999997543221111 1
Q ss_pred HHHHHHHHHHhhchhhhh
Q 029239 117 AEQKMLEAALKNARERDR 134 (196)
Q Consensus 117 ~eq~ele~~lk~l~ER~R 134 (196)
.....+..+++++.+|+.
T Consensus 728 ~~~~~~~~A~~~~g~~~~ 745 (1337)
T PRK14714 728 NVKEEYRSALENVGEREN 745 (1337)
T ss_pred cHHHHHHHHHHHhCcccc
Confidence 233467888899888875
No 7
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=74.22 E-value=1.2 Score=28.84 Aligned_cols=24 Identities=25% Similarity=0.621 Sum_probs=19.4
Q ss_pred hhHHhHhcChhHHhhcc----ccccccC
Q 029239 79 VRQAYHNLCPGCAKEQN----VCAKCCS 102 (196)
Q Consensus 79 Vk~AYH~iC~~CA~~~~----vCaKC~k 102 (196)
++.=.|++|..|+..+. .|+-|++
T Consensus 17 l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 17 LTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred EcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 45557999999999988 8888864
No 8
>PRK11595 DNA utilization protein GntX; Provisional
Probab=65.51 E-value=3.2 Score=35.29 Aligned_cols=22 Identities=14% Similarity=0.131 Sum_probs=11.9
Q ss_pred HHHHHhhchhhhhhhHHHHHhh
Q 029239 122 LEAALKNARERDRRILLRAVNL 143 (196)
Q Consensus 122 le~~lk~l~ER~RRt~lR~~~k 143 (196)
+.++|..+.-+.++.+.+.+.+
T Consensus 74 ~r~lI~~~Ky~~~~~l~~~l~~ 95 (227)
T PRK11595 74 LSGLIHQLKFSRRSELASVLAR 95 (227)
T ss_pred HHHHHHHHHHCccHHHHHHHHH
Confidence 4455666666666555444443
No 9
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=63.32 E-value=3.2 Score=35.23 Aligned_cols=60 Identities=23% Similarity=0.402 Sum_probs=42.6
Q ss_pred cccccccchhhHHhHhcChhHHhhccccccccCccccccCCCchhH-----HHHHHHHHHHHhhchh
Q 029239 70 KCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRVDRVIGRDLAEV-----EAEQKMLEAALKNARE 131 (196)
Q Consensus 70 KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~~~~i~~~~~~~~-----e~eq~ele~~lk~l~E 131 (196)
.|+.|+.. |+.-|+...+. ...+..|++|++..|.-+..|..-. --+-+.-...|-|..|
T Consensus 2 iCIeCg~~-v~~Ly~~Ys~~-~irLt~C~~C~~vaDkYiE~d~vil~IDLlLlK~~AYRHllfN~~~ 66 (208)
T PF04161_consen 2 ICIECGHP-VKSLYRQYSPG-NIRLTKCPNCGKVADKYIEYDNVILFIDLLLLKPQAYRHLLFNRLE 66 (208)
T ss_pred EeccCCCc-chhhhhccCCC-cEEEeeccccCCcccceeccccHHHHHHHHHcchhhHHHhhccCCc
Confidence 69999888 99999988654 7788999999999998666654221 1123345667777544
No 10
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=61.26 E-value=0.37 Score=35.81 Aligned_cols=46 Identities=28% Similarity=0.931 Sum_probs=30.3
Q ss_pred CchhhhHHHHHHHHHhCCCCCCCCcccccccccchhhHHhHhcChhHHhhcccccccc
Q 029239 44 GVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCC 101 (196)
Q Consensus 44 gVCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~ 101 (196)
..|+.|..-|+|.- ....|..|++.-...| .|++|...+.+.-.||
T Consensus 2 ~~CP~C~~~L~~~~---------~~~~C~~C~~~~~~~a---~CPdC~~~Le~LkACG 47 (70)
T PF07191_consen 2 NTCPKCQQELEWQG---------GHYHCEACQKDYKKEA---FCPDCGQPLEVLKACG 47 (70)
T ss_dssp -B-SSS-SBEEEET---------TEEEETTT--EEEEEE---E-TTT-SB-EEEEETT
T ss_pred CcCCCCCCccEEeC---------CEEECccccccceecc---cCCCcccHHHHHHHhc
Confidence 46999999999983 4567999988644444 6999999999999998
No 11
>PRK04023 DNA polymerase II large subunit; Validated
Probab=60.66 E-value=4.5 Score=42.93 Aligned_cols=44 Identities=25% Similarity=0.627 Sum_probs=32.8
Q ss_pred HhCCCCCCC-CcccccccccchhhHHhHhcChhHHh---hccccccccCccc
Q 029239 58 RYGKYKPLS-EPAKCQRCTKRAVRQAYHNLCPGCAK---EQNVCAKCCSRVD 105 (196)
Q Consensus 58 kY~KYKPLt-~p~KC~kC~qktVk~AYH~iC~~CA~---~~~vCaKC~k~~~ 105 (196)
+|++.-.+. ..++|..|+..+ +...|+.|.. ....|++||....
T Consensus 615 ~~~g~~eVEVg~RfCpsCG~~t----~~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 615 KYKGTIEVEIGRRKCPSCGKET----FYRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred hcCCceeecccCccCCCCCCcC----CcccCCCCCCCCCcceeCccccCcCC
Confidence 443333333 588999999986 5579999987 4789999998755
No 12
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=59.38 E-value=3.1 Score=43.29 Aligned_cols=59 Identities=24% Similarity=0.517 Sum_probs=0.0
Q ss_pred ccccccccchhhHHhHhcChhHHhhc--cccccccCccccccCCCchhHHHHHHHHHHHHhhchhhhh
Q 029239 69 AKCQRCTKRAVRQAYHNLCPGCAKEQ--NVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERDR 134 (196)
Q Consensus 69 ~KC~kC~qktVk~AYH~iC~~CA~~~--~vCaKC~k~~~~i~~~~~~~~e~eq~ele~~lk~l~ER~R 134 (196)
.+|..|+..|... -.|+.|..+. ..|++|+........ ..-.....++.++++|-+|+.
T Consensus 668 ~~Cp~CG~~T~~~---~~Cp~C~~~~~~~~C~~C~~~~~~~~~----~~i~l~~~~~~A~e~lg~r~~ 728 (900)
T PF03833_consen 668 NRCPECGSHTEPV---YVCPDCGIEVEEDECPKCGRETTSYSK----QKIDLKEEYDRALENLGEREN 728 (900)
T ss_dssp --------------------------------------------------------------------
T ss_pred hcCcccCCccccc---eeccccccccCccccccccccCcccce----eecCHHHHHHHHHHhhccccc
Confidence 4677777665432 2477777664 578888764332111 111234478889999999885
No 13
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=53.50 E-value=4.3 Score=36.20 Aligned_cols=37 Identities=24% Similarity=0.677 Sum_probs=28.3
Q ss_pred cccccccchh------hHHhHhcChhHHhh-c-cccccccCcccc
Q 029239 70 KCQRCTKRAV------RQAYHNLCPGCAKE-Q-NVCAKCCSRVDR 106 (196)
Q Consensus 70 KC~kC~qktV------k~AYH~iC~~CA~~-~-~vCaKC~k~~~~ 106 (196)
-|++|..++- +.--|++|.+|... . .+|.-|.++..+
T Consensus 5 hCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 5 HCNKCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIRI 49 (233)
T ss_pred EeccccccCCCCceeeeechhhhhhhhcccCCccccccccceeee
Confidence 4788877764 34569999999887 3 389999998654
No 14
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=52.08 E-value=7.1 Score=39.70 Aligned_cols=36 Identities=31% Similarity=0.788 Sum_probs=27.4
Q ss_pred ccccccccc----hhhHHhHhcChhHHhh-----ccccccccCcc
Q 029239 69 AKCQRCTKR----AVRQAYHNLCPGCAKE-----QNVCAKCCSRV 104 (196)
Q Consensus 69 ~KC~kC~qk----tVk~AYH~iC~~CA~~-----~~vCaKC~k~~ 104 (196)
-+|..|..+ -|+.-||.-|.+|-.. .+-||+|+.+-
T Consensus 644 LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 644 LKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAF 688 (698)
T ss_pred eeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCC
Confidence 356666643 4777899999999875 58999999753
No 15
>PF13900 GVQW: Putative binding domain
Probab=51.09 E-value=4.6 Score=28.20 Aligned_cols=39 Identities=15% Similarity=0.313 Sum_probs=33.4
Q ss_pred HHHHHHhCCCCCCCCcccccccccchhhHHhHhcChhHHhh
Q 029239 53 IDWKRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPGCAKE 93 (196)
Q Consensus 53 IeWKvkY~KYKPLt~p~KC~kC~qktVk~AYH~iC~~CA~~ 93 (196)
+||. +.+..+|+++..|-..|+.....+.|+ .-+||-..
T Consensus 6 vqw~-~l~SLQp~ppg~k~~scLSlpssWDyr-~~pp~~an 44 (48)
T PF13900_consen 6 VQWH-DLSSLQPPPPGFKQFSCLSLPSSWDYR-HAPPHPAN 44 (48)
T ss_pred cccc-ccCcCCccccccccccccccccccccc-cCCCCcce
Confidence 5898 999999999999999999999999998 44555443
No 16
>PRK00420 hypothetical protein; Validated
Probab=49.38 E-value=47 Score=26.58 Aligned_cols=16 Identities=19% Similarity=0.472 Sum_probs=10.4
Q ss_pred hhhhHHHHHHHHHHHh
Q 029239 177 TITMVITWIKSMMKMM 192 (196)
Q Consensus 177 ~~~~~~~~~~~~~~~~ 192 (196)
.|.=++-||+.+++..
T Consensus 93 ri~Ei~~~l~~l~ki~ 108 (112)
T PRK00420 93 RITEIIRYLEVLERIR 108 (112)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3445667777777764
No 17
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=47.02 E-value=10 Score=32.20 Aligned_cols=40 Identities=10% Similarity=0.160 Sum_probs=21.0
Q ss_pred cccccccCccccccCCCchhHHHHHHHHHHHHhhchhhhhhhHHH
Q 029239 95 NVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERDRRILLR 139 (196)
Q Consensus 95 ~vCaKC~k~~~~i~~~~~~~~e~eq~ele~~lk~l~ER~RRt~lR 139 (196)
.-|-+||++-. ......+ --+||-+.+.+|+..++..|--
T Consensus 69 sYC~~CGkpyP----Wt~~~L~-aa~el~ee~eeLs~deke~~~~ 108 (158)
T PF10083_consen 69 SYCHNCGKPYP----WTENALE-AANELIEEDEELSPDEKEQFKE 108 (158)
T ss_pred hhHHhCCCCCc----hHHHHHH-HHHHHHHHhhcCCHHHHHHHHh
Confidence 36999998632 2111111 1224445666777766665543
No 18
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=46.79 E-value=7.9 Score=30.50 Aligned_cols=22 Identities=32% Similarity=0.821 Sum_probs=15.7
Q ss_pred hcChhHHhhc-------cccccccCcccc
Q 029239 85 NLCPGCAKEQ-------NVCAKCCSRVDR 106 (196)
Q Consensus 85 ~iC~~CA~~~-------~vCaKC~k~~~~ 106 (196)
.+|+.|++.| -||++||.....
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTEFPP 38 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCccCc
Confidence 3677777766 479999975543
No 19
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=45.47 E-value=8.1 Score=25.27 Aligned_cols=23 Identities=26% Similarity=0.755 Sum_probs=18.7
Q ss_pred Hh-cChhHHhhc----cccccccCcccc
Q 029239 84 HN-LCPGCAKEQ----NVCAKCCSRVDR 106 (196)
Q Consensus 84 H~-iC~~CA~~~----~vCaKC~k~~~~ 106 (196)
|. +|..|+... ..|+-|..+.+.
T Consensus 22 H~~~C~~C~~~~~~~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 22 HLCFCEECAERLLKRKKKCPICRQPIES 49 (50)
T ss_dssp EEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred ChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence 77 899999998 899999876554
No 20
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=44.05 E-value=12 Score=30.94 Aligned_cols=27 Identities=33% Similarity=0.559 Sum_probs=18.7
Q ss_pred hHHhHhcChhHHhhc------cccccccCcccccc
Q 029239 80 RQAYHNLCPGCAKEQ------NVCAKCCSRVDRVI 108 (196)
Q Consensus 80 k~AYH~iC~~CA~~~------~vCaKC~k~~~~i~ 108 (196)
--||| |+-|...+ -+|+-|+.....+.
T Consensus 26 ML~~h--Cp~Cg~PLF~KdG~v~CPvC~~~~~~v~ 58 (131)
T COG1645 26 MLAKH--CPKCGTPLFRKDGEVFCPVCGYREVVVE 58 (131)
T ss_pred HHHhh--CcccCCcceeeCCeEECCCCCceEEEee
Confidence 34666 88888775 38999997555443
No 21
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=38.71 E-value=16 Score=26.49 Aligned_cols=17 Identities=35% Similarity=1.064 Sum_probs=15.2
Q ss_pred hcChhHHhhc--ccccccc
Q 029239 85 NLCPGCAKEQ--NVCAKCC 101 (196)
Q Consensus 85 ~iC~~CA~~~--~vCaKC~ 101 (196)
+.|.+||... ++|+.||
T Consensus 30 TFC~~C~e~~l~~~CPNCg 48 (57)
T PF06906_consen 30 TFCADCAETMLNGVCPNCG 48 (57)
T ss_pred cccHHHHHHHhcCcCcCCC
Confidence 5689999997 9999998
No 22
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=36.92 E-value=1.8e+02 Score=22.85 Aligned_cols=51 Identities=18% Similarity=0.162 Sum_probs=36.2
Q ss_pred HHHHHHHHhhchhhhhhhHH-HHHhhhcccccCccccccCCccCccchHHHhhhccccchhhhHHHHHHHHHH
Q 029239 119 QKMLEAALKNARERDRRILL-RAVNLKIQQKIQPTKIKLGNYFLPHHLRNMLQKAEVTKTITMVITWIKSMMK 190 (196)
Q Consensus 119 q~ele~~lk~l~ER~RRt~l-R~~~k~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 190 (196)
...|.++|..|++++|+.|+ ++++ ..|.+|.++..+++ +..|-+++...++
T Consensus 126 ~~~l~~~l~~L~~~~r~vl~l~~~~-------------------~~s~~eIA~~lgis--~~~V~~~l~ra~~ 177 (186)
T PRK13919 126 RTRLGRALKALSPEERRVIEVLYYQ-------------------GYTHREAAQLLGLP--LGTLKTRARRALS 177 (186)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHc-------------------CCCHHHHHHHHCcC--HHHHHHHHHHHHH
Confidence 34688999999999999996 5544 45667777777666 4566666655544
No 23
>PF14149 YhfH: YhfH-like protein
Probab=35.94 E-value=15 Score=24.47 Aligned_cols=24 Identities=38% Similarity=0.880 Sum_probs=17.3
Q ss_pred Ccccccccccchh--hHHhHhcChhH
Q 029239 67 EPAKCQRCTKRAV--RQAYHNLCPGC 90 (196)
Q Consensus 67 ~p~KC~kC~qktV--k~AYH~iC~~C 90 (196)
+++.|..|++.-. ..+|.+.|+.|
T Consensus 12 p~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 12 PPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred CCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 5678888887643 34688888776
No 24
>PF13376 OmdA: Bacteriocin-protection, YdeI or OmpD-Associated
Probab=33.40 E-value=28 Score=24.12 Aligned_cols=43 Identities=14% Similarity=0.117 Sum_probs=29.6
Q ss_pred cccCCCchhHHHHHHHHHHHHhhchhhhhhhHHHHHhhhcccc
Q 029239 106 RVIGRDLAEVEAEQKMLEAALKNARERDRRILLRAVNLKIQQK 148 (196)
Q Consensus 106 ~i~~~~~~~~e~eq~ele~~lk~l~ER~RRt~lR~~~k~~~~~ 148 (196)
..+|.|....-++..+..+....|+.-.||.+++.+...+..+
T Consensus 4 ~~vP~dl~~aL~~~p~a~~~f~~l~~~~rr~~i~wi~~AK~~e 46 (63)
T PF13376_consen 4 VEVPEDLEAALEANPEAKEFFESLTPSYRREYIRWINSAKTEE 46 (63)
T ss_pred CCCCHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHcCCHH
Confidence 3445444333334446667889999999999999999666544
No 25
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.37 E-value=53 Score=30.53 Aligned_cols=23 Identities=26% Similarity=0.702 Sum_probs=18.8
Q ss_pred hHhcChhHHhhc-----cccccccCccc
Q 029239 83 YHNLCPGCAKEQ-----NVCAKCCSRVD 105 (196)
Q Consensus 83 YH~iC~~CA~~~-----~vCaKC~k~~~ 105 (196)
||.+|..|...+ ..|+.|+++..
T Consensus 27 GH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 27 GHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 899999999874 47999987544
No 26
>cd08168 Cytochrom_C3 Heme-binding domain of the class III cytochrome C family and related proteins. This alignment models heme binding core motifs as encountered in the cytochrome C3 family and related proteins. Cytochrome C3 is a tetraheme protein found in sulfate-reducing bacteria which use either thiosulfate or sulfate as the ultimate electron acceptors. C3 is an integral part of a complex electron transfer chain. The model also contains triheme cytochromes C7 which function in electron transfer during Fe(III) respiration by Geobacter sulfurreducens (PpcA, PpcB, PpcC, PpcD, and PpcE) and four repeated core motifs as found in the 16-heme cytochrome C HmcA of Desulfovibrio vulgaris Hildenborough which plays a role in electron transfer through the membrane following periplasmic oxidation of hydrogen (resulting in sulfate reduction in the cytoplasm).
Probab=33.09 E-value=25 Score=25.11 Aligned_cols=44 Identities=34% Similarity=0.779 Sum_probs=32.7
Q ss_pred CchhhhHHHHHHHHHhCCCCCCCCcccccccccc---------hhhHHhHhcChhHHhhcc
Q 029239 44 GVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKR---------AVRQAYHNLCPGCAKEQN 95 (196)
Q Consensus 44 gVCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~qk---------tVk~AYH~iC~~CA~~~~ 95 (196)
.-|..|+...+= ....+.+|..|+.. ....|||..|..|=.+..
T Consensus 17 ~~C~~CH~~~~~--------~~~~~~~C~~CH~~~~~~~~~~~~~~~a~H~~C~~CH~~~~ 69 (85)
T cd08168 17 IDCRTCHHKYEG--------GKGEPQKCAECHSHDGTDDPDFVSLKDAFHNSCIGCHKEMA 69 (85)
T ss_pred cChhhcCCCCcC--------CCCCCCchhhcCCCCcccCCccchhhHHHHHhHHHHHHHHH
Confidence 359999875321 46788899999863 569999999988866543
No 27
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=32.06 E-value=17 Score=34.25 Aligned_cols=29 Identities=21% Similarity=0.371 Sum_probs=18.3
Q ss_pred hCCCCCCCCcccccccccchhhHHhHhcCh
Q 029239 59 YGKYKPLSEPAKCQRCTKRAVRQAYHNLCP 88 (196)
Q Consensus 59 Y~KYKPLt~p~KC~kC~qktVk~AYH~iC~ 88 (196)
-|||. +|...+|..|....-..+|+..|+
T Consensus 235 ~GKYh-~~~c~~C~~~~~~~~~~~~~~~Cp 263 (374)
T TIGR00375 235 LGKYH-QTACEACGEPAVSEDAETACANCP 263 (374)
T ss_pred CCccc-hhhhcccCCcCCchhhhhcCCCCC
Confidence 46776 666677777666666666664444
No 28
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=30.25 E-value=69 Score=24.26 Aligned_cols=55 Identities=13% Similarity=0.129 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHhhchhhhhhhH-HHHHhhhcccccCccccccCCccCccchHHHhhhccccchhhhHHHHHHHHHHH
Q 029239 116 EAEQKMLEAALKNARERDRRIL-LRAVNLKIQQKIQPTKIKLGNYFLPHHLRNMLQKAEVTKTITMVITWIKSMMKM 191 (196)
Q Consensus 116 e~eq~ele~~lk~l~ER~RRt~-lR~~~k~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 (196)
++....+.++|..|++++|+-| |++++ ..|.+|.++..+++ ++-|-+++...++.
T Consensus 94 ~~~~~~l~~~l~~L~~~~r~ii~l~~~~-------------------~~s~~EIA~~l~is--~~tV~~~~~ra~~~ 149 (154)
T PRK06759 94 EDVEMKVKDFMSVLDEKEKYIIFERFFV-------------------GKTMGEIALETEMT--YYQVRWIYRQALEK 149 (154)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHhc-------------------CCCHHHHHHHHCCC--HHHHHHHHHHHHHH
Confidence 3345678999999999999998 56654 34566666666554 34455555554443
No 29
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=29.99 E-value=11 Score=24.80 Aligned_cols=31 Identities=23% Similarity=0.758 Sum_probs=22.8
Q ss_pred cccccccchhhHHhHhcChhHHhhccccccccCc
Q 029239 70 KCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSR 103 (196)
Q Consensus 70 KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~ 103 (196)
.|..|++ .+.- ++.-|..|. +..+|..|-..
T Consensus 2 ~C~~C~~-~i~g-~r~~C~~C~-d~dLC~~Cf~~ 32 (46)
T cd02249 2 SCDGCLK-PIVG-VRYHCLVCE-DFDLCSSCYAK 32 (46)
T ss_pred CCcCCCC-CCcC-CEEECCCCC-CCcCHHHHHCc
Confidence 5888877 5554 677788885 68888888643
No 30
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=29.79 E-value=21 Score=35.77 Aligned_cols=28 Identities=25% Similarity=0.511 Sum_probs=22.1
Q ss_pred CcccccccccchhhHHhHhcChhHHhhcccc
Q 029239 67 EPAKCQRCTKRAVRQAYHNLCPGCAKEQNVC 97 (196)
Q Consensus 67 ~p~KC~kC~qktVk~AYH~iC~~CA~~~~vC 97 (196)
..+.|+.|.+++-+.|||+- ||...+..
T Consensus 312 ~~GtcIqCs~~nC~~aYHVt---CArrag~f 339 (669)
T COG5141 312 FGGTCIQCSYFNCTRAYHVT---CARRAGYF 339 (669)
T ss_pred cCcceeeecccchhhhhhhh---hhhhcchh
Confidence 46899999999999999975 55554443
No 31
>KOG0031 consensus Myosin regulatory light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=29.73 E-value=54 Score=28.30 Aligned_cols=63 Identities=14% Similarity=0.206 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHhhchhhhhhhHHHHHhhhcccccCccc-----cccCCccCccchHHHhhhccccchhhhHHHHHHHHHH
Q 029239 116 EAEQKMLEAALKNARERDRRILLRAVNLKIQQKIQPTK-----IKLGNYFLPHHLRNMLQKAEVTKTITMVITWIKSMMK 190 (196)
Q Consensus 116 e~eq~ele~~lk~l~ER~RRt~lR~~~k~~~~~~~~~~-----~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 190 (196)
+.+.+||.|+. -.|+++.+...+..+ ...|.+.+.-+|+++|..+.-.-..||.||.+-+++.
T Consensus 28 q~QIqEfKEAF------------~~mDqnrDG~IdkeDL~d~~aSlGk~~~d~elDaM~~Ea~gPINft~FLTmfGekL~ 95 (171)
T KOG0031|consen 28 QSQIQEFKEAF------------NLMDQNRDGFIDKEDLRDMLASLGKIASDEELDAMMKEAPGPINFTVFLTMFGEKLN 95 (171)
T ss_pred HHHHHHHHHHH------------HHHhccCCCcccHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCeeHHHHHHHHHHHhc
Confidence 34455666654 346666666665555 6779999999999999999999999999999887764
No 32
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=29.13 E-value=15 Score=26.33 Aligned_cols=23 Identities=30% Similarity=0.898 Sum_probs=14.6
Q ss_pred HhcChhHHh-----hccccccccCcccc
Q 029239 84 HNLCPGCAK-----EQNVCAKCCSRVDR 106 (196)
Q Consensus 84 H~iC~~CA~-----~~~vCaKC~k~~~~ 106 (196)
|++|.-|.. ....||.||-|...
T Consensus 15 H~~CrRCG~~syH~qK~~CasCGyp~~k 42 (55)
T PF01907_consen 15 HTLCRRCGRRSYHIQKKTCASCGYPAAK 42 (55)
T ss_dssp EEE-TTTSSEEEETTTTEETTTBTTTSS
T ss_pred EeeecccCCeeeecCCCcccccCCCccc
Confidence 455555543 56899999976543
No 33
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.04 E-value=28 Score=33.42 Aligned_cols=32 Identities=31% Similarity=0.789 Sum_probs=22.3
Q ss_pred ccccccccchhhHHhH-----hcChhHHhhc---cccccccCc
Q 029239 69 AKCQRCTKRAVRQAYH-----NLCPGCAKEQ---NVCAKCCSR 103 (196)
Q Consensus 69 ~KC~kC~qktVk~AYH-----~iC~~CA~~~---~vCaKC~k~ 103 (196)
.+|..|. +--.|| -.|.-|.... ..|+.||-.
T Consensus 223 ~~C~~C~---~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCD---VSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCC---CceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 4688884 344454 3688888775 489999864
No 34
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=28.91 E-value=21 Score=32.75 Aligned_cols=68 Identities=28% Similarity=0.633 Sum_probs=42.3
Q ss_pred CCCCCccCchhhhHHHHHHHHHhCCCCCCCCcccccccccc--------hhhHHhHhcChhHHhhcc---------cccc
Q 029239 37 RPYPEITGVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKR--------AVRQAYHNLCPGCAKEQN---------VCAK 99 (196)
Q Consensus 37 ~~~~~~~gVCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~qk--------tVk~AYH~iC~~CA~~~~---------vCaK 99 (196)
|+.......|.-| |.+=|| +-..+|+. .+|-+|..+ -.-.|+- -|+.|...+. -|-.
T Consensus 106 ip~~drqFaC~~C-d~~WwR-rvp~rKeV---SRCr~C~~rYDPVP~dkmwG~aef-~C~~C~h~F~G~~qm~v~sPCy~ 179 (278)
T PF15135_consen 106 IPSVDRQFACSSC-DHMWWR-RVPQRKEV---SRCRKCRKRYDPVPCDKMWGIAEF-HCPKCRHNFRGFAQMGVPSPCYG 179 (278)
T ss_pred ccccceeeecccc-chHHHh-ccCccccc---ccccccccccCCCccccccceeee-ecccccccchhhhhcCCCCCccC
Confidence 3444566789999 888888 55555555 456666544 2223333 3999988875 4667
Q ss_pred ccCccc--cccCC
Q 029239 100 CCSRVD--RVIGR 110 (196)
Q Consensus 100 C~k~~~--~i~~~ 110 (196)
|+.+.. .|.|+
T Consensus 180 C~~~v~P~~IlPP 192 (278)
T PF15135_consen 180 CGNPVYPSRILPP 192 (278)
T ss_pred CCCccCcccccCC
Confidence 876544 35554
No 35
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=28.49 E-value=23 Score=30.47 Aligned_cols=31 Identities=32% Similarity=0.964 Sum_probs=20.7
Q ss_pred ccccccchhhHHhHhcChhHHhh------------ccccccccC
Q 029239 71 CQRCTKRAVRQAYHNLCPGCAKE------------QNVCAKCCS 102 (196)
Q Consensus 71 C~kC~qktVk~AYH~iC~~CA~~------------~~vCaKC~k 102 (196)
|..|+.. +..-+..+|..|-.+ ..+|+.||.
T Consensus 1 C~~CG~~-~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~ 43 (236)
T PF04981_consen 1 CPRCGRE-IEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGR 43 (236)
T ss_pred CCCCCCC-CCCcccccChHHhcccCCeeecCCccCceECCCCCC
Confidence 6677763 333455688888543 468999995
No 36
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=28.44 E-value=25 Score=37.58 Aligned_cols=50 Identities=20% Similarity=0.332 Sum_probs=29.7
Q ss_pred cccccccccchhhHHhHhcChhHHhhccccccccCccccccCCCchhHHHHHHHHHHHHhhchhhh
Q 029239 68 PAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERD 133 (196)
Q Consensus 68 p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~~~~i~~~~~~~~e~eq~ele~~lk~l~ER~ 133 (196)
-++|.+|+..|. ...|++||.+.+.+-+- ...-.....+.++++++.+|+
T Consensus 625 ~RKCPkCG~yTl--------------k~rCP~CG~~Te~~~pc--~~~i~l~~~~~~A~~~lg~~~ 674 (1095)
T TIGR00354 625 IRKCPQCGKESF--------------WLKCPVCGELTEQLYYG--KRKVDLRELYEEAIANLGEYK 674 (1095)
T ss_pred EEECCCCCcccc--------------cccCCCCCCccccccce--eEEecHHHHHHHHHHHhCCCC
Confidence 566777766543 35677777765443322 111123446788889988887
No 37
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.39 E-value=15 Score=31.64 Aligned_cols=38 Identities=24% Similarity=0.551 Sum_probs=30.7
Q ss_pred cccccccccchhhHH-----hHhcChhHHhhccccccccCccc
Q 029239 68 PAKCQRCTKRAVRQA-----YHNLCPGCAKEQNVCAKCCSRVD 105 (196)
Q Consensus 68 p~KC~kC~qktVk~A-----YH~iC~~CA~~~~vCaKC~k~~~ 105 (196)
++.|..|.+++++=. .|.+|.+|+....+|+-|..+..
T Consensus 158 ~~~Cr~C~~~~~~VlllPCrHl~lC~~C~~~~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 158 MRSCRKCGEREATVLLLPCRHLCLCGICDESLRICPICRSPKT 200 (207)
T ss_pred cccceecCcCCceEEeecccceEecccccccCccCCCCcChhh
Confidence 445999999988743 57899999998999999986543
No 38
>PF12773 DZR: Double zinc ribbon
Probab=28.03 E-value=25 Score=22.85 Aligned_cols=18 Identities=28% Similarity=1.027 Sum_probs=11.4
Q ss_pred cChhHHhhcc-------ccccccCc
Q 029239 86 LCPGCAKEQN-------VCAKCCSR 103 (196)
Q Consensus 86 iC~~CA~~~~-------vCaKC~k~ 103 (196)
.|+.|...+. +|++||..
T Consensus 14 fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 14 FCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred CChhhcCChhhccCCCCCCcCCcCC
Confidence 5666666555 57777754
No 39
>PHA02683 ORF078 thioredoxin-like protein; Provisional
Probab=27.95 E-value=20 Score=27.17 Aligned_cols=18 Identities=39% Similarity=1.084 Sum_probs=11.6
Q ss_pred hCCCC-CCCCccccccccc
Q 029239 59 YGKYK-PLSEPAKCQRCTK 76 (196)
Q Consensus 59 Y~KYK-PLt~p~KC~kC~q 76 (196)
|.+|+ -|.+|.+|.+|..
T Consensus 4 y~~Y~~~LdpP~rCs~C~~ 22 (75)
T PHA02683 4 YAKYNVVLDPPRRCSKCAS 22 (75)
T ss_pred hhheeeecCCCCcchHHHH
Confidence 44554 4667888888753
No 40
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=27.69 E-value=83 Score=23.78 Aligned_cols=33 Identities=12% Similarity=0.055 Sum_probs=23.1
Q ss_pred cCccchHHHhhhccccchhhhHHHHHHHHHHHh
Q 029239 160 FLPHHLRNMLQKAEVTKTITMVITWIKSMMKMM 192 (196)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 192 (196)
+|.+||.|+.+..+-.-+=|.|--|++-+++|.
T Consensus 52 ~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl~~ia 84 (85)
T PF02650_consen 52 NPDASLKELGELLEPPISKSGVNHRLRKLKKIA 84 (85)
T ss_dssp -TTS-HHHHHHTT--T--HHHHHHHHHHHHHHH
T ss_pred CccccHHHHHHHHcCcCcHHHHHHHHHHHHHHh
Confidence 789999999999966555578999999888763
No 41
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=27.55 E-value=23 Score=29.25 Aligned_cols=20 Identities=15% Similarity=0.368 Sum_probs=14.1
Q ss_pred hcChhHHhhc-------cccccccCcc
Q 029239 85 NLCPGCAKEQ-------NVCAKCCSRV 104 (196)
Q Consensus 85 ~iC~~CA~~~-------~vCaKC~k~~ 104 (196)
.+|+.|++.| -+|++||...
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCcc
Confidence 3677777665 5899999754
No 42
>PF02085 Cytochrom_CIII: Class III cytochrome C family; InterPro: IPR020942 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes []. Ambler [] recognised four classes of cytC. Class III comprises the low redox potential multiple haem cytochromes: cyt C7 (trihaem), C3 (tetrahaem), and high-molecular-weight cytC, HMC (hexadecahaem), with only 30-40 residues per haem group. The haem c groups, all bis-histidinyl coordinated, are structurally and functionally nonequivalent and present different redox potentials in the range 0 to -400 mV []. The 3D structures of a number of cyt C3 proteins have been determined. The proteins consist of 4-5 alpha-helices and 2 beta-strands wrapped around a compact core of four non-parallel haems, which present a relatively high degree of exposure to the solvent. The overall protein architecture, haem plane orientations and iron-iron distances are highly conserved [].; GO: 0009055 electron carrier activity, 0020037 heme binding; PDB: 1AQE_A 1CZJ_A 1H29_B 1GWS_A 2CVC_A 2KMY_A 1DUW_A 1UPD_A 1I77_A 1GMB_A ....
Probab=26.63 E-value=36 Score=25.17 Aligned_cols=41 Identities=27% Similarity=0.677 Sum_probs=32.2
Q ss_pred chhhhHHHHHHHHHhCCCCCCCCcccccccccch--------hhHHhHh-----cChhHHhhc
Q 029239 45 VCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKRA--------VRQAYHN-----LCPGCAKEQ 94 (196)
Q Consensus 45 VCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~qkt--------Vk~AYH~-----iC~~CA~~~ 94 (196)
-|..|+.- ........+|..|+... ...|||. .|-.|=.+.
T Consensus 33 ~C~~CHh~---------~~~~~~~~~C~~CH~~~~~~~~~~~~~~a~H~~~~~~~C~~CH~~~ 86 (102)
T PF02085_consen 33 DCSTCHHK---------SAGGGSIESCMSCHDENGKKKDKPSFKKAFHQKKQMKSCMGCHKEM 86 (102)
T ss_dssp GGGGTSTT---------CTTTSSSSSCTCSSSSSSTSTSTTBHHHHHHHSSSSTHHHHHHHHH
T ss_pred ChhhCCCC---------CcCCCCcchHHHhcCcccccccchhHHHHhcCccccchHHHHHHHH
Confidence 69999987 55666778999998544 5899999 888886654
No 43
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=25.81 E-value=46 Score=28.70 Aligned_cols=73 Identities=16% Similarity=0.270 Sum_probs=38.8
Q ss_pred CCCcccccccccchhhHHhHhcChhHHhhccc----cccccCcccc---ccCCCchhHHHHHHHHHHHHhhchhhhhhhH
Q 029239 65 LSEPAKCQRCTKRAVRQAYHNLCPGCAKEQNV----CAKCCSRVDR---VIGRDLAEVEAEQKMLEAALKNARERDRRIL 137 (196)
Q Consensus 65 Lt~p~KC~kC~qktVk~AYH~iC~~CA~~~~v----CaKC~k~~~~---i~~~~~~~~e~eq~ele~~lk~l~ER~RRt~ 137 (196)
|..+.-|..|...--.... +|+.|+.++.. |+.|...+.. ........ -.+.++|..+.-+.+..+
T Consensus 21 l~~~~~C~~C~~~~~~~~~--~C~~C~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Y~-----~~l~~~i~~~Kf~~~~~l 93 (225)
T COG1040 21 LFFPGLCSGCQADLPLIGN--LCPLCGLPLSSHACRCGECLAKPPPFERLRSLGSYN-----GPLRELISQLKFQGDLDL 93 (225)
T ss_pred ccCCCcChhhhhchhHHHh--hhHhhhChhccccccCHHHhcCCCcceeEEEEEEcc-----HHHHHHHHHhhhCCchhH
Confidence 3333778888554433333 78888888655 4555544433 11111111 135556666666666665
Q ss_pred HHHHhhh
Q 029239 138 LRAVNLK 144 (196)
Q Consensus 138 lR~~~k~ 144 (196)
-+-+.+.
T Consensus 94 ~~~la~~ 100 (225)
T COG1040 94 AKLLARL 100 (225)
T ss_pred HHHHHHH
Confidence 5555443
No 44
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=25.56 E-value=67 Score=31.79 Aligned_cols=73 Identities=10% Similarity=0.155 Sum_probs=44.3
Q ss_pred ccccccccchhhHHhHhcChhHHhhc-------cccccccCccccccCCCc-hhHHHHHHHHHHHHhh---chhhhhhhH
Q 029239 69 AKCQRCTKRAVRQAYHNLCPGCAKEQ-------NVCAKCCSRVDRVIGRDL-AEVEAEQKMLEAALKN---ARERDRRIL 137 (196)
Q Consensus 69 ~KC~kC~qktVk~AYH~iC~~CA~~~-------~vCaKC~k~~~~i~~~~~-~~~e~eq~ele~~lk~---l~ER~RRt~ 137 (196)
+.|..|+.. .||-..|+.|+..+ .+|..||.+++.+....- -...+-+..|.+.+.. ++++-+..+
T Consensus 140 g~cp~C~~~---d~~g~~ce~cg~~~~~~~l~~~~~~~~g~~~e~~~~~~~f~~l~~~~~~l~~~~~~~~~~~~~~~~~~ 216 (673)
T PRK00133 140 GTCPKCGAE---DQYGDNCEVCGATYSPTELINPKSAISGATPVLKESEHFFFKLPRFEEFLKEWITRSGELQPNVANKM 216 (673)
T ss_pred cccCCCCCc---ccCCchhhhccccCChHhhcCCccccCCCcceEEecceEEEEHHHHHHHHHHHHhcCCCCCHHHHHHH
Confidence 567777654 46777788887733 479999987765432210 1123344455555532 667777777
Q ss_pred HHHHhhh
Q 029239 138 LRAVNLK 144 (196)
Q Consensus 138 lR~~~k~ 144 (196)
++.++.+
T Consensus 217 ~~~l~~~ 223 (673)
T PRK00133 217 KEWLEEG 223 (673)
T ss_pred HHHHhCC
Confidence 7878754
No 45
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=25.38 E-value=83 Score=25.27 Aligned_cols=25 Identities=16% Similarity=0.252 Sum_probs=19.7
Q ss_pred HHHHHHHHHhhchhhhhhhH-HHHHh
Q 029239 118 EQKMLEAALKNARERDRRIL-LRAVN 142 (196)
Q Consensus 118 eq~ele~~lk~l~ER~RRt~-lR~~~ 142 (196)
+...+.++|..|++++|.-| |++++
T Consensus 132 ~~~~l~~~l~~L~~~~r~vl~l~~~~ 157 (194)
T PRK09646 132 ERERVRDCLDALTDTQRESVTLAYYG 157 (194)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHc
Confidence 44568899999999999999 55543
No 46
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=24.97 E-value=24 Score=20.84 Aligned_cols=9 Identities=22% Similarity=0.885 Sum_probs=5.1
Q ss_pred ccccccccC
Q 029239 94 QNVCAKCCS 102 (196)
Q Consensus 94 ~~vCaKC~k 102 (196)
...|+.||.
T Consensus 16 ~~fC~~CG~ 24 (26)
T PF13248_consen 16 AKFCPNCGA 24 (26)
T ss_pred cccChhhCC
Confidence 345666664
No 47
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=24.69 E-value=81 Score=20.34 Aligned_cols=26 Identities=31% Similarity=0.356 Sum_probs=19.1
Q ss_pred HHHHHHHhhchhhhhhhHHHHHhhhc
Q 029239 120 KMLEAALKNARERDRRILLRAVNLKI 145 (196)
Q Consensus 120 ~ele~~lk~l~ER~RRt~lR~~~k~~ 145 (196)
+.+.++|..|++++|.-|+-.--.|.
T Consensus 2 ~~l~~~l~~L~~~~r~i~~l~~~~g~ 27 (54)
T PF08281_consen 2 EALQQALAQLPERQREIFLLRYFQGM 27 (54)
T ss_dssp HHHHHHHHCS-HHHHHHHHHHHTS--
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCc
Confidence 46788999999999999988655443
No 48
>PF03660 PHF5: PHF5-like protein; InterPro: IPR005345 Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins. At least one example, from Mus musculus (Mouse), may act as a chromatin-associated protein []. The Schizosaccharomyces pombe (Fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.; PDB: 2K0A_A.
Probab=24.50 E-value=24 Score=28.36 Aligned_cols=26 Identities=31% Similarity=0.613 Sum_probs=16.4
Q ss_pred CCcccccccc-cchhhHHhHhcChhHHhh
Q 029239 66 SEPAKCQRCT-KRAVRQAYHNLCPGCAKE 93 (196)
Q Consensus 66 t~p~KC~kC~-qktVk~AYH~iC~~CA~~ 93 (196)
+...+|+.|+ ...+..||. |..|..-
T Consensus 53 ~~~~rCIiCg~~~g~sdAYY--C~eC~~l 79 (106)
T PF03660_consen 53 SLQGRCIICGSGPGVSDAYY--CWECVRL 79 (106)
T ss_dssp STTSB-TTTSSSB--EE-EE---HHHHHH
T ss_pred CcCceEEEecCCCCccccee--hhhhHhh
Confidence 3468999999 899999997 8888544
No 49
>PRK12496 hypothetical protein; Provisional
Probab=24.33 E-value=21 Score=29.52 Aligned_cols=21 Identities=43% Similarity=1.009 Sum_probs=14.2
Q ss_pred hcChhHHhhc------cccccccCccc
Q 029239 85 NLCPGCAKEQ------NVCAKCCSRVD 105 (196)
Q Consensus 85 ~iC~~CA~~~------~vCaKC~k~~~ 105 (196)
..|..|...+ ..|+.||.+..
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSPVK 154 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCChhh
Confidence 3577777665 46999996543
No 50
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=24.23 E-value=18 Score=24.72 Aligned_cols=32 Identities=22% Similarity=0.747 Sum_probs=23.7
Q ss_pred cccccccchhhHHhHhcChhHHh-hccccccccC
Q 029239 70 KCQRCTKRAVRQAYHNLCPGCAK-EQNVCAKCCS 102 (196)
Q Consensus 70 KC~kC~qktVk~AYH~iC~~CA~-~~~vCaKC~k 102 (196)
+|..|++.+|. -.+--|..|.. ...+|..|-.
T Consensus 2 ~Cd~C~~~pI~-G~R~~C~~C~~~d~DlC~~C~~ 34 (48)
T cd02341 2 KCDSCGIEPIP-GTRYHCSECDDGDFDLCQDCVV 34 (48)
T ss_pred CCCCCCCCccc-cceEECCCCCCCCCccCHHHHh
Confidence 58888887766 55667888875 6888888854
No 51
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=24.04 E-value=55 Score=23.28 Aligned_cols=29 Identities=17% Similarity=0.527 Sum_probs=20.3
Q ss_pred cccccccccchhhHHhHhcChhHHhhccccccccCccccccCC
Q 029239 68 PAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRVDRVIGR 110 (196)
Q Consensus 68 p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~~~~i~~~ 110 (196)
-.+|..|+..|. ..+|+.||.+.....|.
T Consensus 5 mr~C~~CgvYTL--------------k~~CP~CG~~t~~~~P~ 33 (56)
T PRK13130 5 IRKCPKCGVYTL--------------KEICPVCGGKTKNPHPP 33 (56)
T ss_pred ceECCCCCCEEc--------------cccCcCCCCCCCCCCCC
Confidence 457888877765 35788899877665553
No 52
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=24.01 E-value=15 Score=26.64 Aligned_cols=36 Identities=33% Similarity=0.798 Sum_probs=22.8
Q ss_pred cccccccccchh--hHHhHhcChhHHhh-ccccccccCc
Q 029239 68 PAKCQRCTKRAV--RQAYHNLCPGCAKE-QNVCAKCCSR 103 (196)
Q Consensus 68 p~KC~kC~qktV--k~AYH~iC~~CA~~-~~vCaKC~k~ 103 (196)
+-+|.+|+..-. -.+=+-.|+.|.+. -..|++|.+-
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~ 45 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQ 45 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhc
Confidence 446777764433 22555578888777 6777777653
No 53
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=23.89 E-value=55 Score=27.52 Aligned_cols=37 Identities=22% Similarity=0.357 Sum_probs=20.7
Q ss_pred Ccccccccccc-hhhHHhHhcChhHHhhccccccccCccccccCCCchh
Q 029239 67 EPAKCQRCTKR-AVRQAYHNLCPGCAKEQNVCAKCCSRVDRVIGRDLAE 114 (196)
Q Consensus 67 ~p~KC~kC~qk-tVk~AYH~iC~~CA~~~~vCaKC~k~~~~i~~~~~~~ 114 (196)
+-..|..|+.+ |.-.|.- ..-.|+.||..-. ..|+++
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~---~~dn~~ 153 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME--------YGFRCPQCGEMLE---EYDNSE 153 (178)
T ss_pred CEEECCCCCcEEeHHHHhh--------cCCcCCCCCCCCe---ecccHH
Confidence 45567777533 3334432 3568999996543 345444
No 54
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=23.63 E-value=15 Score=24.79 Aligned_cols=31 Identities=26% Similarity=0.701 Sum_probs=22.8
Q ss_pred cccccccchhhHHhHhcChhHHhhccccccccC
Q 029239 70 KCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCS 102 (196)
Q Consensus 70 KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k 102 (196)
.|..|....+. -.+..|..|. +..+|..|-.
T Consensus 2 ~C~~C~~~~i~-g~R~~C~~C~-d~dlC~~Cf~ 32 (49)
T cd02338 2 SCDGCGKSNFT-GRRYKCLICY-DYDLCADCYD 32 (49)
T ss_pred CCCCCcCCCcE-EeeEEeCCCC-CCccchhHHh
Confidence 57788777777 4666788886 6888888854
No 55
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=23.38 E-value=56 Score=26.60 Aligned_cols=25 Identities=28% Similarity=0.251 Sum_probs=21.9
Q ss_pred HHHHHHHhhchhhhhhhHHHHHhhh
Q 029239 120 KMLEAALKNARERDRRILLRAVNLK 144 (196)
Q Consensus 120 ~ele~~lk~l~ER~RRt~lR~~~k~ 144 (196)
++|+..|+.|++.+|+..+.+-+..
T Consensus 8 ~~L~~~L~~lp~~e~~e~l~~Y~e~ 32 (181)
T PF08006_consen 8 NELEKYLKKLPEEEREEILEYYEEY 32 (181)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 4789999999999999999887764
No 56
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=23.23 E-value=3.3e+02 Score=20.52 Aligned_cols=55 Identities=20% Similarity=0.163 Sum_probs=35.0
Q ss_pred HHHHHHHHHHhhchhhhhhhHHHHHhhhcccccCccccccCCccCccchHHHhhhccccchhhhHHHHHHHHHHH
Q 029239 117 AEQKMLEAALKNARERDRRILLRAVNLKIQQKIQPTKIKLGNYFLPHHLRNMLQKAEVTKTITMVITWIKSMMKM 191 (196)
Q Consensus 117 ~eq~ele~~lk~l~ER~RRt~lR~~~k~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 (196)
++...+.++|..|++++|.-|.-.. |...+.+|.++..+++- +.|-.+|...++.
T Consensus 100 ~~~~~l~~~i~~L~~~~r~v~~l~~------------------~~g~~~~eIA~~l~is~--~tv~~~l~Rar~~ 154 (159)
T TIGR02989 100 DELQALEGCLEKLPERQRELLQLRY------------------QRGVSLTALAEQLGRTV--NAVYKALSRLRVR 154 (159)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHH------------------hcCCCHHHHHHHhCCCH--HHHHHHHHHHHHH
Confidence 3445688999999999999987732 22345566666666553 4444555444443
No 57
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=22.92 E-value=17 Score=24.29 Aligned_cols=32 Identities=25% Similarity=0.784 Sum_probs=24.1
Q ss_pred cccccccchhhHHhHhcChhHHhhccccccccCc
Q 029239 70 KCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSR 103 (196)
Q Consensus 70 KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~ 103 (196)
.|..|.+ .+...+|..|..|. ++.+|..|=..
T Consensus 2 ~Cd~C~~-~~~~g~r~~C~~C~-d~dLC~~Cf~~ 33 (49)
T cd02335 2 HCDYCSK-DITGTIRIKCAECP-DFDLCLECFSA 33 (49)
T ss_pred CCCCcCC-CCCCCcEEECCCCC-CcchhHHhhhC
Confidence 5888865 44455888899997 69999998653
No 58
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=22.85 E-value=31 Score=23.71 Aligned_cols=32 Identities=19% Similarity=0.593 Sum_probs=21.7
Q ss_pred chhhhHHHHHHHHHhCCCCCCCCccccccccc
Q 029239 45 VCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTK 76 (196)
Q Consensus 45 VCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~q 76 (196)
+|..|-++|||=.++.=-+.-.+--+|-.|.+
T Consensus 8 ~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~ 39 (46)
T PF11331_consen 8 VCSSCFELLQLPAKFSLSKKNQQKLRCGACSE 39 (46)
T ss_pred ECccHHHHHcCCCccCCCccceeEEeCCCCce
Confidence 69999999999766544333334556777754
No 59
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=22.61 E-value=17 Score=24.55 Aligned_cols=31 Identities=23% Similarity=0.743 Sum_probs=24.0
Q ss_pred cccccccchhhHHhHhcChhHHhhccccccccC
Q 029239 70 KCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCS 102 (196)
Q Consensus 70 KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k 102 (196)
.|..|.+.+|. -.|.-|..|. +..+|..|-.
T Consensus 2 ~C~~C~~~~i~-g~R~~C~~C~-dydLC~~Cf~ 32 (49)
T cd02345 2 SCSACRKQDIS-GIRFPCQVCR-DYSLCLGCYT 32 (49)
T ss_pred cCCCCCCCCce-EeeEECCCCC-CcCchHHHHh
Confidence 58888887888 4677888884 6888888853
No 60
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=22.59 E-value=12 Score=26.90 Aligned_cols=19 Identities=37% Similarity=0.934 Sum_probs=12.8
Q ss_pred CCCccCchhhhHHHHHHHH
Q 029239 39 YPEITGVCPRCKDQIDWKR 57 (196)
Q Consensus 39 ~~~~~gVCqRC~eiIeWKv 57 (196)
..++.|-|+.|...|.|+.
T Consensus 51 ~~~~~G~CP~C~~~i~~~~ 69 (70)
T PF11793_consen 51 FIPIFGECPYCSSPISWSF 69 (70)
T ss_dssp TT--EEE-TTT-SEEEGGG
T ss_pred ecccccCCcCCCCeeeEec
Confidence 3578899999999999985
No 61
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=21.62 E-value=28 Score=25.53 Aligned_cols=25 Identities=28% Similarity=0.818 Sum_probs=16.6
Q ss_pred cccccccccchhhHHhHhcChhHHhhccccccccCc
Q 029239 68 PAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSR 103 (196)
Q Consensus 68 p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~ 103 (196)
.-.|..|+.+ ||| .....||.||-.
T Consensus 17 Ht~CrRCG~~----syh-------~qK~~CasCGyg 41 (62)
T PRK04179 17 HIRCRRCGRH----SYN-------VRKKYCAACGFG 41 (62)
T ss_pred cchhcccCcc----ccc-------ccccchhhcCCC
Confidence 4456666543 566 357899999973
No 62
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=21.60 E-value=86 Score=32.54 Aligned_cols=59 Identities=29% Similarity=0.631 Sum_probs=41.0
Q ss_pred CccCchhhhHHHH-HHHHHhCCCCCCCCccccccccc-------------chhhHHhHhcChhHHhhcc-----------
Q 029239 41 EITGVCPRCKDQI-DWKRRYGKYKPLSEPAKCQRCTK-------------RAVRQAYHNLCPGCAKEQN----------- 95 (196)
Q Consensus 41 ~~~gVCqRC~eiI-eWKvkY~KYKPLt~p~KC~kC~q-------------ktVk~AYH~iC~~CA~~~~----------- 95 (196)
+=.++|.-|.+-| +=.-+|=.| +=-.|+.|+= .|...++- +|+.|.++.+
T Consensus 99 pD~a~C~~Cl~Ei~dp~~rrY~Y----PF~~CT~CGPRfTIi~alPYDR~nTsM~~F~-lC~~C~~EY~dP~nRRfHAQp 173 (750)
T COG0068 99 PDAATCEDCLEEIFDPNSRRYLY----PFINCTNCGPRFTIIEALPYDRENTSMADFP-LCPFCDKEYKDPLNRRFHAQP 173 (750)
T ss_pred CchhhhHHHHHHhcCCCCcceec----cccccCCCCcceeeeccCCCCcccCccccCc-CCHHHHHHhcCcccccccccc
Confidence 4467899999877 322223233 3457999984 46666776 9999998764
Q ss_pred -ccccccCcc
Q 029239 96 -VCAKCCSRV 104 (196)
Q Consensus 96 -vCaKC~k~~ 104 (196)
.|++||=..
T Consensus 174 ~aCp~CGP~~ 183 (750)
T COG0068 174 IACPKCGPHL 183 (750)
T ss_pred ccCcccCCCe
Confidence 899999433
No 63
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=21.36 E-value=67 Score=26.35 Aligned_cols=47 Identities=19% Similarity=0.201 Sum_probs=27.1
Q ss_pred Cccccccccc-chhhHHhHhcChhHHhhccccccccCccccccCCCchhHHHHHHHHHHHHh
Q 029239 67 EPAKCQRCTK-RAVRQAYHNLCPGCAKEQNVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALK 127 (196)
Q Consensus 67 ~p~KC~kC~q-ktVk~AYH~iC~~CA~~~~vCaKC~k~~~~i~~~~~~~~e~eq~ele~~lk 127 (196)
+--.|..|+. -|.-.|.. ..-.|+.||.. +...|+++ .-+.|++.|+
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~---L~~~dn~~---~i~~l~~~i~ 155 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME--------LNFTCPRCGAM---LDYLDNSE---AIEKLEEQIK 155 (158)
T ss_pred CeEECCCCCcEeeHHHHHH--------cCCcCCCCCCE---eeeccCHH---HHHHHHHHHH
Confidence 4566877763 34555553 25789999964 34455544 3344555444
No 64
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=21.19 E-value=3.3e+02 Score=21.43 Aligned_cols=53 Identities=13% Similarity=0.168 Sum_probs=34.8
Q ss_pred HHHHHHHHHhhchhhhhhhHHHHHhhhcccccCccccccCCccCccchHHHhhhccccchhhhHHHHHHHHHH
Q 029239 118 EQKMLEAALKNARERDRRILLRAVNLKIQQKIQPTKIKLGNYFLPHHLRNMLQKAEVTKTITMVITWIKSMMK 190 (196)
Q Consensus 118 eq~ele~~lk~l~ER~RRt~lR~~~k~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 190 (196)
....+.++|..|+++.|.-|+-.. |...|..|.++..+++ +..|-+.+...++
T Consensus 107 ~~~~l~~~l~~Lp~~~r~i~~l~~------------------~e~~s~~EIA~~lgis--~~tV~~~l~ra~~ 159 (179)
T PRK12543 107 SNQELIELIHKLPYKLRQVIILRY------------------LHDYSQEEIAQLLQIP--IGTVKSRIHAALK 159 (179)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHH------------------HccCCHHHHHHHHCCC--HHHHHHHHHHHHH
Confidence 345788999999999998887642 2344666777776665 3445555444443
No 65
>KOG0090 consensus Signal recognition particle receptor, beta subunit (small G protein superfamily) [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.13 E-value=79 Score=28.59 Aligned_cols=70 Identities=27% Similarity=0.312 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHhhchhhhhhhHHHHHhhhcccccCccccccCCccCccchHH----HhhhccccchhhhHHHHHHH
Q 029239 115 VEAEQKMLEAALKNARERDRRILLRAVNLKIQQKIQPTKIKLGNYFLPHHLRN----MLQKAEVTKTITMVITWIKS 187 (196)
Q Consensus 115 ~e~eq~ele~~lk~l~ER~RRt~lR~~~k~~~~~~~~~~~~~g~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~ 187 (196)
.+.+++.||..|..++|+ |+-+|.+.-++..+ ..+....|.-|.-..+++ .++.-..++-|.=+..||.+
T Consensus 163 ~~~Ir~~LEkEi~~lr~s--Rsa~~~~~~ed~~~-~~tlg~~g~dF~fs~l~~~~V~F~e~S~~~~~i~~~~~wi~~ 236 (238)
T KOG0090|consen 163 AEKIRQQLEKEIHKLRES--RSALRSISDEDIAK-DFTLGKEGEDFKFSHLEDQKVTFAEASAKTGEIDQWESWIRE 236 (238)
T ss_pred HHHHHHHHHHHHHHHHHH--Hhhhhccccccccc-cccccccccccchhhcccceeEEeecccCcCChHHHHHHHHH
Confidence 467899999999998765 55566665554433 444577777777777762 23333334456667777764
No 66
>PF13945 NST1: Salt tolerance down-regulator
Probab=20.73 E-value=89 Score=27.14 Aligned_cols=24 Identities=25% Similarity=0.450 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHhhchhhhhhhHHH
Q 029239 116 EAEQKMLEAALKNARERDRRILLR 139 (196)
Q Consensus 116 e~eq~ele~~lk~l~ER~RRt~lR 139 (196)
++|+..|.+.-.+|.|-+||.|||
T Consensus 101 ~eEre~LkeFW~SL~eeERr~LVk 124 (190)
T PF13945_consen 101 QEEREKLKEFWESLSEEERRSLVK 124 (190)
T ss_pred HHHHHHHHHHHHccCHHHHHHHHH
Confidence 456678888999999999999886
No 67
>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development. The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=20.49 E-value=1.2e+02 Score=22.65 Aligned_cols=41 Identities=24% Similarity=0.387 Sum_probs=32.4
Q ss_pred ccCCCchhHHHHHHHHHHHHhhchhhhhhhHHHHHhhhccc
Q 029239 107 VIGRDLAEVEAEQKMLEAALKNARERDRRILLRAVNLKIQQ 147 (196)
Q Consensus 107 i~~~~~~~~e~eq~ele~~lk~l~ER~RRt~lR~~~k~~~~ 147 (196)
+.+-...+...-++.|+.+|+..|.|+..-++..++.-..+
T Consensus 43 L~~Ls~~eL~~LE~~Le~aL~~VR~rK~~~l~~~i~~l~~k 83 (100)
T PF01486_consen 43 LESLSLKELQQLEQQLESALKRVRSRKDQLLMEQIEELKKK 83 (100)
T ss_pred ccccchHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 44445566677788999999999999999999888876544
No 68
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=20.09 E-value=27 Score=27.19 Aligned_cols=28 Identities=18% Similarity=0.410 Sum_probs=16.0
Q ss_pred CcccccccccchhhHHhHhcChhHHhhccccccccCcc
Q 029239 67 EPAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRV 104 (196)
Q Consensus 67 ~p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~~ 104 (196)
...+|..|+...-...++ -.|+.||.+.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~----------~~CP~Cgs~~ 96 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQHD----------AQCPHCHGER 96 (113)
T ss_pred cEEEcccCCCEEecCCcC----------ccCcCCCCCC
Confidence 356788887544333333 2478888543
No 69
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=20.09 E-value=23 Score=24.23 Aligned_cols=31 Identities=23% Similarity=0.717 Sum_probs=21.8
Q ss_pred cccccccchhhHHhHhcChhHHhhccccccccC
Q 029239 70 KCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCS 102 (196)
Q Consensus 70 KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k 102 (196)
.|..|+..+|.- .+.-|..|. ++.+|..|-.
T Consensus 2 ~Cd~C~~~pi~g-~RykC~~C~-d~DLC~~Cf~ 32 (49)
T cd02334 2 KCNICKEFPITG-FRYRCLKCF-NYDLCQSCFF 32 (49)
T ss_pred CCCCCCCCCcee-eeEECCCCC-CcCchHHHHh
Confidence 577777666664 566777776 6888888853
No 70
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.06 E-value=46 Score=33.06 Aligned_cols=73 Identities=21% Similarity=0.361 Sum_probs=40.7
Q ss_pred ccccccccchhhHHhH-----hcChhHHhhc---cccccccCccccccCCCchhHHHHHHHHHHHHhh-----c------
Q 029239 69 AKCQRCTKRAVRQAYH-----NLCPGCAKEQ---NVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKN-----A------ 129 (196)
Q Consensus 69 ~KC~kC~qktVk~AYH-----~iC~~CA~~~---~vCaKC~k~~~~i~~~~~~~~e~eq~ele~~lk~-----l------ 129 (196)
.+|..|.- --.|| -.|.-|.... ..|+.||...-...+... |..+.+|.+.+.+ |
T Consensus 391 ~~C~~C~~---~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~~~g~G~---e~~~e~l~~~fp~~~v~~~~~d~~~ 464 (679)
T PRK05580 391 AECPHCDA---SLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDLVPVGPGT---ERLEEELAELFPEARILRIDRDTTR 464 (679)
T ss_pred cCCCCCCC---ceeEECCCCeEECCCCcCCCCCCCCCCCCcCCeeEEeeccH---HHHHHHHHHhCCCCcEEEEeccccc
Confidence 46777764 33344 2699998874 489999865322222222 3333344443222 1
Q ss_pred hhhhhhhHHHHHhhhccc
Q 029239 130 RERDRRILLRAVNLKIQQ 147 (196)
Q Consensus 130 ~ER~RRt~lR~~~k~~~~ 147 (196)
+..+|...|..+..++..
T Consensus 465 ~~~~~~~~l~~f~~g~~~ 482 (679)
T PRK05580 465 RKGALEQLLAQFARGEAD 482 (679)
T ss_pred cchhHHHHHHHHhcCCCC
Confidence 134577788888876543
Done!