Query 029861
Match_columns 186
No_of_seqs 97 out of 99
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 04:49:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029861.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029861hhsearch_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 1.8E-57 3.8E-62 382.7 3.1 144 1-148 1-147 (227)
2 PF10217 DUF2039: Uncharacteri 100.0 2.6E-46 5.7E-51 283.2 5.3 92 10-105 1-92 (92)
3 PF10235 Cript: Microtubule-as 94.6 0.014 3.1E-07 44.7 1.1 41 63-104 38-79 (90)
4 PRK04023 DNA polymerase II lar 83.2 0.57 1.2E-05 48.9 1.4 59 69-134 639-699 (1121)
5 KOG3476 Microtubule-associated 79.8 0.5 1.1E-05 36.8 -0.3 46 56-104 44-89 (100)
6 PRK14714 DNA polymerase II lar 78.7 0.73 1.6E-05 49.0 0.4 71 44-134 668-745 (1337)
7 COG4566 TtrR Response regulato 76.2 3.6 7.8E-05 35.9 3.8 58 118-175 132-198 (202)
8 PF14634 zf-RING_5: zinc-RING 74.4 1.2 2.5E-05 28.6 0.3 24 79-102 17-44 (44)
9 PRK11595 DNA utilization prote 67.1 2.8 6.2E-05 35.3 1.2 21 150-170 118-139 (227)
10 PF04161 Arv1: Arv1-like famil 64.9 3 6.5E-05 35.1 0.9 60 70-131 2-66 (208)
11 PF07191 zinc-ribbons_6: zinc- 63.7 0.32 6.9E-06 35.9 -4.5 47 44-102 2-48 (70)
12 PRK04023 DNA polymerase II lar 62.9 4 8.8E-05 42.9 1.5 44 58-105 615-662 (1121)
13 PF03833 PolC_DP2: DNA polymer 60.8 2.8 6.1E-05 43.2 0.0 60 68-134 667-728 (900)
14 PRK00420 hypothetical protein; 57.5 18 0.0004 28.7 4.1 16 167-182 93-108 (112)
15 COG1645 Uncharacterized Zn-fin 54.7 15 0.00033 30.0 3.3 27 80-108 26-58 (131)
16 KOG4739 Uncharacterized protei 53.4 4.3 9.4E-05 35.9 -0.0 37 70-106 5-49 (233)
17 PF13900 GVQW: Putative bindin 52.9 4.3 9.3E-05 28.1 -0.1 40 53-94 6-45 (48)
18 KOG0978 E3 ubiquitin ligase in 52.4 7.1 0.00015 39.4 1.3 35 69-103 644-687 (698)
19 PF13920 zf-C3HC4_3: Zinc fing 47.4 7.3 0.00016 25.3 0.3 23 84-106 22-49 (50)
20 PF09538 FYDLN_acid: Protein o 47.3 8 0.00017 30.2 0.6 21 86-106 11-38 (108)
21 PRK06759 RNA polymerase factor 46.6 20 0.00044 26.9 2.7 29 116-144 94-123 (154)
22 PF10083 DUF2321: Uncharacteri 46.2 6.2 0.00013 33.3 -0.2 43 95-142 69-111 (158)
23 PF13248 zf-ribbon_3: zinc-rib 43.8 7 0.00015 23.0 -0.2 10 94-103 16-25 (26)
24 PTZ00096 40S ribosomal protein 42.4 11 0.00023 31.3 0.7 48 121-178 29-83 (143)
25 PF06906 DUF1272: Protein of u 42.3 13 0.00028 26.7 1.0 18 85-102 30-49 (57)
26 COG5220 TFB3 Cdk activating ki 41.8 21 0.00046 32.7 2.5 72 81-164 33-115 (314)
27 TIGR00570 cdk7 CDK-activating 41.1 47 0.001 30.6 4.6 24 82-105 26-54 (309)
28 PF14149 YhfH: YhfH-like prote 38.1 13 0.00029 24.5 0.5 24 67-90 12-37 (37)
29 PF01486 K-box: K-box region; 33.7 20 0.00043 26.6 0.9 55 107-161 43-97 (100)
30 cd08168 Cytochrom_C3 Heme-bind 33.2 25 0.00054 25.0 1.2 44 44-95 17-69 (85)
31 PF12773 DZR: Double zinc ribb 31.4 21 0.00045 23.1 0.5 18 86-103 14-38 (50)
32 cd02249 ZZ Zinc finger, ZZ typ 30.8 9.8 0.00021 24.8 -1.1 30 70-102 2-31 (46)
33 PF08006 DUF1700: Protein of u 30.7 24 0.00051 28.6 0.9 40 120-159 8-60 (181)
34 PRK12515 RNA polymerase sigma 30.6 45 0.00098 26.3 2.5 30 120-149 123-153 (189)
35 TIGR00354 polC DNA polymerase, 30.5 23 0.00049 37.5 0.9 50 68-133 625-674 (1095)
36 PRK13919 putative RNA polymera 30.5 55 0.0012 25.5 2.9 30 119-148 126-156 (186)
37 TIGR00375 conserved hypothetic 30.4 19 0.00041 33.6 0.3 33 59-103 235-267 (374)
38 PF01907 Ribosomal_L37e: Ribos 29.9 15 0.00032 26.1 -0.3 22 84-105 15-41 (55)
39 COG5141 PHD zinc finger-contai 29.7 21 0.00046 35.5 0.6 28 67-97 312-339 (669)
40 PHA02683 ORF078 thioredoxin-li 29.4 18 0.0004 27.2 0.1 18 59-76 4-22 (75)
41 PRK13130 H/ACA RNA-protein com 27.9 45 0.00097 23.6 1.8 29 68-110 5-33 (56)
42 TIGR02300 FYDLN_acid conserved 27.4 25 0.00053 28.9 0.5 20 85-104 10-36 (129)
43 PF03660 PHF5: PHF5-like prote 27.4 19 0.00041 28.7 -0.2 26 66-93 53-79 (106)
44 PF08281 Sigma70_r4_2: Sigma-7 26.7 40 0.00087 21.6 1.3 22 120-141 2-23 (54)
45 PF02085 Cytochrom_CIII: Class 26.3 37 0.0008 24.9 1.2 41 45-94 33-86 (102)
46 KOG1100 Predicted E3 ubiquitin 26.1 18 0.0004 30.9 -0.5 37 68-104 158-199 (207)
47 PRK12496 hypothetical protein; 26.1 20 0.00043 29.5 -0.3 21 85-105 128-154 (164)
48 cd02341 ZZ_ZZZ3 Zinc finger, Z 26.0 16 0.00034 24.8 -0.8 32 70-102 2-34 (48)
49 PRK10236 hypothetical protein; 25.8 1.8E+02 0.0039 26.0 5.6 47 120-166 120-167 (237)
50 PRK09646 RNA polymerase sigma 25.6 61 0.0013 25.8 2.4 30 118-147 132-162 (194)
51 PRK07037 extracytoplasmic-func 25.2 70 0.0015 24.3 2.6 26 120-145 101-127 (163)
52 KOG3800 Predicted E3 ubiquitin 25.2 50 0.0011 30.5 2.0 23 81-103 22-49 (300)
53 cd02338 ZZ_PCMF_like Zinc fing 25.0 13 0.00029 24.8 -1.2 31 70-102 2-32 (49)
54 TIGR02983 SigE-fam_strep RNA p 24.6 78 0.0017 24.0 2.8 28 117-144 99-127 (162)
55 PF15135 UPF0515: Uncharacteri 24.4 31 0.00068 31.4 0.6 69 36-110 105-192 (278)
56 PRK14890 putative Zn-ribbon RN 24.1 15 0.00033 26.4 -1.2 36 68-103 7-45 (59)
57 COG0068 HypF Hydrogenase matur 23.8 73 0.0016 32.8 3.1 60 41-105 99-184 (750)
58 TIGR02939 RpoE_Sigma70 RNA pol 23.7 68 0.0015 24.9 2.3 25 120-144 130-155 (190)
59 cd02335 ZZ_ADA2 Zinc finger, Z 23.5 16 0.00035 24.2 -1.1 31 70-102 2-32 (49)
60 cd02345 ZZ_dah Zinc finger, ZZ 23.2 16 0.00035 24.5 -1.1 31 70-102 2-32 (49)
61 PF11331 DUF3133: Protein of u 22.9 32 0.00069 23.5 0.3 32 45-76 8-39 (46)
62 PRK06266 transcription initiat 22.9 64 0.0014 26.9 2.1 31 67-105 116-147 (178)
63 PF11793 FANCL_C: FANCL C-term 22.5 12 0.00025 26.7 -2.0 19 39-57 51-69 (70)
64 PRK12527 RNA polymerase sigma 22.4 85 0.0018 23.9 2.6 24 121-144 98-122 (159)
65 PRK12516 RNA polymerase sigma 22.1 99 0.0021 24.8 3.0 31 119-149 107-138 (187)
66 PRK04179 rpl37e 50S ribosomal 22.0 28 0.00061 25.3 -0.1 25 68-103 17-41 (62)
67 smart00834 CxxC_CXXC_SSSS Puta 21.9 22 0.00049 21.7 -0.6 13 93-105 25-37 (41)
68 PRK09641 RNA polymerase sigma 21.6 94 0.002 24.0 2.7 28 120-147 128-156 (187)
69 PRK09637 RNA polymerase sigma 21.5 94 0.002 24.8 2.8 32 118-149 96-128 (181)
70 PRK12380 hydrogenase nickel in 21.0 26 0.00056 27.1 -0.5 28 67-104 69-96 (113)
71 PRK14714 DNA polymerase II lar 21.0 39 0.00084 36.7 0.6 32 68-103 667-701 (1337)
72 TIGR02947 SigH_actino RNA poly 20.9 80 0.0017 25.0 2.2 43 120-162 123-171 (193)
73 TIGR02989 Sig-70_gvs1 RNA poly 20.6 1E+02 0.0022 23.2 2.7 28 117-144 100-128 (159)
74 PRK12546 RNA polymerase sigma 20.5 1.1E+02 0.0025 24.6 3.1 30 120-149 105-135 (188)
75 PLN03109 ETHYLENE-INSENSITIVE3 20.5 2.5E+02 0.0053 28.3 5.8 49 126-183 53-101 (599)
76 PRK11924 RNA polymerase sigma 20.2 67 0.0015 24.3 1.6 24 119-142 116-140 (179)
77 COG1499 NMD3 NMD protein affec 20.1 57 0.0012 30.4 1.4 32 69-101 7-50 (355)
78 cd02334 ZZ_dystrophin Zinc fin 20.1 23 0.00049 24.1 -0.9 30 70-101 2-31 (49)
No 1
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.8e-57 Score=382.73 Aligned_cols=144 Identities=61% Similarity=1.042 Sum_probs=136.3
Q ss_pred CCC---CCCCCCCCCCccccccCCCCCCcchhhhhcCCCCCCCCccCchhhhHHHHHHHHHhCCCCCCCCcccccccccc
Q 029861 1 MSS---NSSRRGAPKHQNRYAWKPKAGQKINEREVGGKLRPYPEITGVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKR 77 (186)
Q Consensus 1 MSS---N~~R~rpQKHQN~~aFKnn~~~K~~e~~~~~k~~~~~~~~gVCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~qk 77 (186)
||| |++|+|||||||+|+|+|++++|. .++++| |++.++||||||+++|+||++|+||||||++++|.+|.++
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 999 999999999999999999987664 455566 6899999999999999999999999999999999999999
Q ss_pred hhhHHHHhcChhhHhhccccccccCCcccccCCCchhHHHHHHHHHHHHhhchhhccchhhhcccccccCC
Q 029861 78 AVRQAYHNLCPGCAKEQNVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERDRRILLRAPTKIKLGN 148 (186)
Q Consensus 78 tVk~AYH~iC~~CA~~~~vCaKC~k~~e~i~~~~~~~~e~eq~ele~~lk~l~ER~RRt~lR~~~k~~~~~ 148 (186)
+|++|||.+|++||.++.+||||+++.++|..+++.++++|++.|++.+++++||+||||||+|+|++.-+
T Consensus 77 ~Vk~aYH~~Cr~CA~e~~vCAKC~ks~~~i~i~d~~p~~~E~~~l~~t~~n~ser~RRt~lR~m~k~~k~~ 147 (227)
T KOG3241|consen 77 NVKQAYHKLCRGCAKEQKVCAKCCKSVDQILIRDIYPVEAEQKLLDETIKNASERDRRTLLRAMNKDNKPN 147 (227)
T ss_pred HHHHHHHHhcccHHHHHHHHHHHhccHHHhhhcCCCCCcHHHHHHHHHHhhhhHHHHHHHHHHHhcccCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999987765
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=2.6e-46 Score=283.24 Aligned_cols=92 Identities=50% Similarity=0.994 Sum_probs=84.8
Q ss_pred CCCCccccccCCCCCCcchhhhhcCCCCCCCCccCchhhhHHHHHHHHHhCCCCCCCCcccccccccchhhHHHHhcChh
Q 029861 10 APKHQNRYAWKPKAGQKINEREVGGKLRPYPEITGVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPG 89 (186)
Q Consensus 10 pQKHQN~~aFKnn~~~K~~e~~~~~k~~~~~~~~gVCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~qktVk~AYH~iC~~ 89 (186)
+|||||+|||+||++++.. +. +.+++.+++|||+||+|+||||++|||||||++|++|++|+++||++|||+||++
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 5999999999999999943 22 3456689999999999999999999999999999999999999999999999999
Q ss_pred hHhhccccccccCCcc
Q 029861 90 CAKEQNVCAKCCSRVD 105 (186)
Q Consensus 90 CA~~~~vCaKC~k~~e 105 (186)
||.++++|||||+++|
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=94.63 E-value=0.014 Score=44.66 Aligned_cols=41 Identities=29% Similarity=0.770 Sum_probs=32.0
Q ss_pred CCCCC-cccccccccchhhHHHHhcChhhHhhccccccccCCc
Q 029861 63 KPLSE-PAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRV 104 (186)
Q Consensus 63 KPLt~-p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~~ 104 (186)
-|..+ ..+|-.|.+ .|.++=|..|+.||-..++||.||++.
T Consensus 38 nPy~~~~~~C~~CK~-~v~q~g~~YCq~CAYkkGiCamCGKki 79 (90)
T PF10235_consen 38 NPYAPYSSKCKICKT-KVHQPGAKYCQTCAYKKGICAMCGKKI 79 (90)
T ss_pred CcccccCcccccccc-ccccCCCccChhhhcccCcccccCCee
Confidence 34443 678999944 566656668999999999999999975
No 4
>PRK04023 DNA polymerase II large subunit; Validated
Probab=83.15 E-value=0.57 Score=48.91 Aligned_cols=59 Identities=25% Similarity=0.536 Sum_probs=31.2
Q ss_pred ccccccccchhhHHHHhcChhhHhhc--cccccccCCcccccCCCchhHHHHHHHHHHHHhhchhhcc
Q 029861 69 AKCQRCTKRAVRQAYHNLCPGCAKEQ--NVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERDR 134 (186)
Q Consensus 69 ~KC~kC~qktVk~AYH~iC~~CA~~~--~vCaKC~k~~e~i~~~~~~~~e~eq~ele~~lk~l~ER~R 134 (186)
++|..|+..| ..+| -|+.|.... ..|++||.......- ..-.....+.++++++.+|+.
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 4555555553 2223 355555443 256666653331111 111234478899999999886
No 5
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=79.82 E-value=0.5 Score=36.84 Aligned_cols=46 Identities=33% Similarity=0.723 Sum_probs=33.5
Q ss_pred HHHhCCCCCCCCcccccccccchhhHHHHhcChhhHhhccccccccCCc
Q 029861 56 KRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRV 104 (186)
Q Consensus 56 KvkY~KYKPLt~p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~~ 104 (186)
+.+|.-|- +.-.+|-.|.+. |.+.=.+.|+.||-..+|||-||+..
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=78.68 E-value=0.73 Score=49.00 Aligned_cols=71 Identities=25% Similarity=0.601 Sum_probs=47.3
Q ss_pred CchhhhHHHHHHHHHhCCCCCCCCcccccccccchhhHHHHhcChhhHhhc-------cccccccCCcccccCCCchhHH
Q 029861 44 GVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPGCAKEQ-------NVCAKCCSRVDRVIGRDLAEVE 116 (186)
Q Consensus 44 gVCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~qktVk~AYH~iC~~CA~~~-------~vCaKC~k~~e~i~~~~~~~~e 116 (186)
..|+.|-..+- ...|..|+..+.. .| .|+.|..+. ..|+.||.+.-...... -
T Consensus 668 rkCPkCG~~t~-------------~~fCP~CGs~te~-vy--~CPsCGaev~~des~a~~CP~CGtplv~~~~~~----i 727 (1337)
T PRK14714 668 RRCPSCGTETY-------------ENRCPDCGTHTEP-VY--VCPDCGAEVPPDESGRVECPRCDVELTPYQRRT----I 727 (1337)
T ss_pred EECCCCCCccc-------------cccCcccCCcCCC-ce--eCccCCCccCCCccccccCCCCCCcccccceEE----e
Confidence 46999986532 1289999998754 34 799998863 27999997543221111 1
Q ss_pred HHHHHHHHHHhhchhhcc
Q 029861 117 AEQKMLEAALKNARERDR 134 (186)
Q Consensus 117 ~eq~ele~~lk~l~ER~R 134 (186)
.....+..+++++.+|+.
T Consensus 728 ~~~~~~~~A~~~~g~~~~ 745 (1337)
T PRK14714 728 NVKEEYRSALENVGEREN 745 (1337)
T ss_pred cHHHHHHHHHHHhCcccc
Confidence 233468888999888875
No 7
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=76.23 E-value=3.6 Score=35.85 Aligned_cols=58 Identities=19% Similarity=0.166 Sum_probs=41.6
Q ss_pred HHHHHHHHHhhchhhccchhhhc----ccccccC-----CCCchhHHHHHHHHHHhHhHHHHHHHHH
Q 029861 118 EQKMLEAALKNARERDRRILLRA----PTKIKLG-----NYFLPHHLRNMLQKAEVTKTITMVITWI 175 (186)
Q Consensus 118 eq~ele~~lk~l~ER~RRt~lR~----~~k~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 175 (186)
.+.++...+.+|++|+|.-|-+- +||+=-. +.+++-|++|+|+|....-+--+|--|.
T Consensus 132 ~~~~~~~~l~tLT~RERqVl~~vV~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~a~ 198 (202)
T COG4566 132 RQAAIRARLATLTPRERQVLDLVVRGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRMAL 198 (202)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHHcCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHHHHH
Confidence 34466677999999998766553 3332111 2399999999999999887777777665
No 8
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=74.38 E-value=1.2 Score=28.65 Aligned_cols=24 Identities=25% Similarity=0.621 Sum_probs=19.4
Q ss_pred hhHHHHhcChhhHhhcc----ccccccC
Q 029861 79 VRQAYHNLCPGCAKEQN----VCAKCCS 102 (186)
Q Consensus 79 Vk~AYH~iC~~CA~~~~----vCaKC~k 102 (186)
++.=.|++|..|+..+. .|+-|++
T Consensus 17 l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 17 LTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred EcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 44557999999999988 8888864
No 9
>PRK11595 DNA utilization protein GntX; Provisional
Probab=67.07 E-value=2.8 Score=35.29 Aligned_cols=21 Identities=14% Similarity=0.175 Sum_probs=14.0
Q ss_pred CchhHHHHHHH-HHHhHhHHHH
Q 029861 150 FLPHHLRNMLQ-KAEVTKTITM 170 (186)
Q Consensus 150 ~~~~~~~~~~~-~~~~~~~~~~ 170 (186)
.+|-|...+.+ -|.|...|..
T Consensus 118 pVPl~~~r~~~RGfnq~~~la~ 139 (227)
T PRK11595 118 SVPLHQRRHWRRGFNQSDLLCR 139 (227)
T ss_pred ecCCCHHHHHHCCCCHHHHHHH
Confidence 77888777666 5666555544
No 10
>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=64.89 E-value=3 Score=35.14 Aligned_cols=60 Identities=23% Similarity=0.402 Sum_probs=41.5
Q ss_pred cccccccchhhHHHHhcChhhHhhccccccccCCcccccCCCchhH-----HHHHHHHHHHHhhchh
Q 029861 70 KCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRVDRVIGRDLAEV-----EAEQKMLEAALKNARE 131 (186)
Q Consensus 70 KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~~e~i~~~~~~~~-----e~eq~ele~~lk~l~E 131 (186)
.|+.|+.. |+.-|+...++ ...+..|++|++..|.-+..|..-. --+-+.-...|-|..|
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 99999988544 7788999999999887666554221 1122345555666444
No 11
>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=63.70 E-value=0.32 Score=35.91 Aligned_cols=47 Identities=28% Similarity=0.919 Sum_probs=30.6
Q ss_pred CchhhhHHHHHHHHHhCCCCCCCCcccccccccchhhHHHHhcChhhHhhccccccccC
Q 029861 44 GVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCS 102 (186)
Q Consensus 44 gVCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k 102 (186)
..|+.|..-|+|.- ....|..|++.-...| .|++|...+.+.-.||-
T Consensus 2 ~~CP~C~~~L~~~~---------~~~~C~~C~~~~~~~a---~CPdC~~~Le~LkACGA 48 (70)
T PF07191_consen 2 NTCPKCQQELEWQG---------GHYHCEACQKDYKKEA---FCPDCGQPLEVLKACGA 48 (70)
T ss_dssp -B-SSS-SBEEEET---------TEEEETTT--EEEEEE---E-TTT-SB-EEEEETTE
T ss_pred CcCCCCCCccEEeC---------CEEECccccccceecc---cCCCcccHHHHHHHhcc
Confidence 46999999999983 4567999988644444 69999999999999983
No 12
>PRK04023 DNA polymerase II large subunit; Validated
Probab=62.87 E-value=4 Score=42.94 Aligned_cols=44 Identities=25% Similarity=0.627 Sum_probs=32.8
Q ss_pred HhCCCCCCC-CcccccccccchhhHHHHhcChhhHh---hccccccccCCcc
Q 029861 58 RYGKYKPLS-EPAKCQRCTKRAVRQAYHNLCPGCAK---EQNVCAKCCSRVD 105 (186)
Q Consensus 58 kY~KYKPLt-~p~KC~kC~qktVk~AYH~iC~~CA~---~~~vCaKC~k~~e 105 (186)
+|++.-... ..++|..|+..+ +...|+.|.. ....|++||....
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 5569999987 4789999998755
No 13
>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=60.76 E-value=2.8 Score=43.24 Aligned_cols=60 Identities=23% Similarity=0.490 Sum_probs=0.0
Q ss_pred cccccccccchhhHHHHhcChhhHhhc--cccccccCCcccccCCCchhHHHHHHHHHHHHhhchhhcc
Q 029861 68 PAKCQRCTKRAVRQAYHNLCPGCAKEQ--NVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERDR 134 (186)
Q Consensus 68 p~KC~kC~qktVk~AYH~iC~~CA~~~--~vCaKC~k~~e~i~~~~~~~~e~eq~ele~~lk~l~ER~R 134 (186)
-.+|..|+..|... -.|+.|..+. ..|++|+......... .-.....++.++++|-+|+.
T Consensus 667 ~~~Cp~CG~~T~~~---~~Cp~C~~~~~~~~C~~C~~~~~~~~~~----~i~l~~~~~~A~e~lg~r~~ 728 (900)
T PF03833_consen 667 YNRCPECGSHTEPV---YVCPDCGIEVEEDECPKCGRETTSYSKQ----KIDLKEEYDRALENLGEREN 728 (900)
T ss_dssp ---------------------------------------------------------------------
T ss_pred hhcCcccCCccccc---eeccccccccCccccccccccCccccee----ecCHHHHHHHHHHhhccccc
Confidence 34677777665432 2477777664 5788887653321111 11233478888999888885
No 14
>PRK00420 hypothetical protein; Validated
Probab=57.47 E-value=18 Score=28.65 Aligned_cols=16 Identities=19% Similarity=0.472 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHHHh
Q 029861 167 TITMVITWIKSMMKMM 182 (186)
Q Consensus 167 ~~~~~~~~~~~~~~~~ 182 (186)
.|.-++.||+.+++..
T Consensus 93 ri~Ei~~~l~~l~ki~ 108 (112)
T PRK00420 93 RITEIIRYLEVLERIR 108 (112)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4555667777777654
No 15
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=54.74 E-value=15 Score=29.98 Aligned_cols=27 Identities=33% Similarity=0.559 Sum_probs=18.7
Q ss_pred hHHHHhcChhhHhhc------cccccccCCccccc
Q 029861 80 RQAYHNLCPGCAKEQ------NVCAKCCSRVDRVI 108 (186)
Q Consensus 80 k~AYH~iC~~CA~~~------~vCaKC~k~~e~i~ 108 (186)
--||| |+-|...+ -+|+-||.....+.
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 38999987555443
No 16
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=53.44 E-value=4.3 Score=35.89 Aligned_cols=37 Identities=24% Similarity=0.677 Sum_probs=28.1
Q ss_pred cccccccchh------hHHHHhcChhhHhh-c-cccccccCCccc
Q 029861 70 KCQRCTKRAV------RQAYHNLCPGCAKE-Q-NVCAKCCSRVDR 106 (186)
Q Consensus 70 KC~kC~qktV------k~AYH~iC~~CA~~-~-~vCaKC~k~~e~ 106 (186)
-|++|...+- +.--|+.|.+|+.. . .+|.-|+++..+
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 34469999999887 3 389999998554
No 17
>PF13900 GVQW: Putative binding domain
Probab=52.89 E-value=4.3 Score=28.14 Aligned_cols=40 Identities=15% Similarity=0.284 Sum_probs=33.8
Q ss_pred HHHHHHhCCCCCCCCcccccccccchhhHHHHhcChhhHhhc
Q 029861 53 IDWKRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPGCAKEQ 94 (186)
Q Consensus 53 IeWKvkY~KYKPLt~p~KC~kC~qktVk~AYH~iC~~CA~~~ 94 (186)
+||. +.+..+|+++..|-..|......+.|+ .-+||-..+
T Consensus 6 vqw~-~l~SLQp~ppg~k~~scLSlpssWDyr-~~pp~~anF 45 (48)
T PF13900_consen 6 VQWH-DLSSLQPPPPGFKQFSCLSLPSSWDYR-HAPPHPANF 45 (48)
T ss_pred cccc-ccCcCCccccccccccccccccccccc-cCCCCcceE
Confidence 5898 999999999999999999999999998 445554433
No 18
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=52.36 E-value=7.1 Score=39.40 Aligned_cols=35 Identities=31% Similarity=0.809 Sum_probs=27.1
Q ss_pred ccccccccc----hhhHHHHhcChhhHhh-----ccccccccCC
Q 029861 69 AKCQRCTKR----AVRQAYHNLCPGCAKE-----QNVCAKCCSR 103 (186)
Q Consensus 69 ~KC~kC~qk----tVk~AYH~iC~~CA~~-----~~vCaKC~k~ 103 (186)
-+|..|..+ -++.-||.-|.+|-.. .+-||+|+.+
T Consensus 644 LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~a 687 (698)
T KOG0978|consen 644 LKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAA 687 (698)
T ss_pred eeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCC
Confidence 356666643 4677899999999865 5899999975
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=47.43 E-value=7.3 Score=25.30 Aligned_cols=23 Identities=26% Similarity=0.755 Sum_probs=18.7
Q ss_pred Hh-cChhhHhhc----cccccccCCccc
Q 029861 84 HN-LCPGCAKEQ----NVCAKCCSRVDR 106 (186)
Q Consensus 84 H~-iC~~CA~~~----~vCaKC~k~~e~ 106 (186)
|. +|..|+... ..|+-|..+.+.
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 899999877554
No 20
>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=47.30 E-value=8 Score=30.22 Aligned_cols=21 Identities=33% Similarity=0.855 Sum_probs=15.5
Q ss_pred cChhhHhhc-------cccccccCCccc
Q 029861 86 LCPGCAKEQ-------NVCAKCCSRVDR 106 (186)
Q Consensus 86 iC~~CA~~~-------~vCaKC~k~~e~ 106 (186)
+|+.|++.| -||++||.....
T Consensus 11 ~Cp~CG~kFYDLnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 11 TCPSCGAKFYDLNKDPIVCPKCGTEFPP 38 (108)
T ss_pred cCCCCcchhccCCCCCccCCCCCCccCc
Confidence 677777776 489999975543
No 21
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=46.58 E-value=20 Score=26.93 Aligned_cols=29 Identities=14% Similarity=0.108 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHhhchhhccchh-hhccccc
Q 029861 116 EAEQKMLEAALKNARERDRRIL-LRAPTKI 144 (186)
Q Consensus 116 e~eq~ele~~lk~l~ER~RRt~-lR~~~k~ 144 (186)
++....+.++|..|++++|+-| |++.+..
T Consensus 94 ~~~~~~l~~~l~~L~~~~r~ii~l~~~~~~ 123 (154)
T PRK06759 94 EDVEMKVKDFMSVLDEKEKYIIFERFFVGK 123 (154)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHhcCC
Confidence 3345678999999999999998 6777544
No 22
>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=46.19 E-value=6.2 Score=33.26 Aligned_cols=43 Identities=9% Similarity=0.140 Sum_probs=23.0
Q ss_pred cccccccCCcccccCCCchhHHHHHHHHHHHHhhchhhccchhhhccc
Q 029861 95 NVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERDRRILLRAPT 142 (186)
Q Consensus 95 ~vCaKC~k~~e~i~~~~~~~~e~eq~ele~~lk~l~ER~RRt~lR~~~ 142 (186)
.-|..||++-. ......+ --+||-+.+.+|+..++..|--.+.
T Consensus 69 sYC~~CGkpyP----Wt~~~L~-aa~el~ee~eeLs~deke~~~~sl~ 111 (158)
T PF10083_consen 69 SYCHNCGKPYP----WTENALE-AANELIEEDEELSPDEKEQFKESLP 111 (158)
T ss_pred hhHHhCCCCCc----hHHHHHH-HHHHHHHHhhcCCHHHHHHHHhhhH
Confidence 36999998632 2111111 1224445667777777666654443
No 23
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=43.84 E-value=7 Score=23.00 Aligned_cols=10 Identities=20% Similarity=0.886 Sum_probs=5.7
Q ss_pred ccccccccCC
Q 029861 94 QNVCAKCCSR 103 (186)
Q Consensus 94 ~~vCaKC~k~ 103 (186)
...|+.||.+
T Consensus 16 ~~fC~~CG~~ 25 (26)
T PF13248_consen 16 AKFCPNCGAK 25 (26)
T ss_pred cccChhhCCC
Confidence 3466666653
No 24
>PTZ00096 40S ribosomal protein S15; Provisional
Probab=42.42 E-value=11 Score=31.31 Aligned_cols=48 Identities=25% Similarity=0.263 Sum_probs=32.0
Q ss_pred HHHHHHhhchhhccchhhhcccccccCCCCchhHHHHHHHHHHhHhHH-------HHHHHHHHHH
Q 029861 121 MLEAALKNARERDRRILLRAPTKIKLGNYFLPHHLRNMLQKAEVTKTI-------TMVITWIKSM 178 (186)
Q Consensus 121 ele~~lk~l~ER~RRt~lR~~~k~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~ 178 (186)
.+|+.++-|+-|.||+|.|-+... ++| |++|.+..+.- ..|-||..+|
T Consensus 29 ~~~e~~~L~~aR~RR~~~RGl~~~-------~~~---LlkKirk~~~~~~~~~k~~~ikT~~R~~ 83 (143)
T PTZ00096 29 PEEELVELFRARQRRRINRGIKRK-------HPT---LLKKLRKAKKATKPGEKPKAVKTHLRDM 83 (143)
T ss_pred CHHHHHHHcCcccccccccCCCHH-------HHH---HHHHHHHHhhhcccccCCcceeEecccC
Confidence 568889999999999999966443 344 45555443332 3366777665
No 25
>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=42.27 E-value=13 Score=26.69 Aligned_cols=18 Identities=33% Similarity=1.012 Sum_probs=15.6
Q ss_pred hcChhhHhhc--cccccccC
Q 029861 85 NLCPGCAKEQ--NVCAKCCS 102 (186)
Q Consensus 85 ~iC~~CA~~~--~vCaKC~k 102 (186)
+-|.+||... ++|+.||-
T Consensus 30 TFC~~C~e~~l~~~CPNCgG 49 (57)
T PF06906_consen 30 TFCADCAETMLNGVCPNCGG 49 (57)
T ss_pred cccHHHHHHHhcCcCcCCCC
Confidence 5689999997 99999983
No 26
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=41.85 E-value=21 Score=32.66 Aligned_cols=72 Identities=22% Similarity=0.338 Sum_probs=39.7
Q ss_pred HHHHhcChhhHhh-----ccccc--cccCCcccc---c-CCCchhHHHHHHHHHHHHhhchhhccchhhhcccccccCCC
Q 029861 81 QAYHNLCPGCAKE-----QNVCA--KCCSRVDRV---I-GRDLAEVEAEQKMLEAALKNARERDRRILLRAPTKIKLGNY 149 (186)
Q Consensus 81 ~AYH~iC~~CA~~-----~~vCa--KC~k~~e~i---~-~~~~~~~e~eq~ele~~lk~l~ER~RRt~lR~~~k~~~~~~ 149 (186)
.-||.+|..|... ..-|+ .|++=.--+ . .++-.++ ++|.+ -|+.++|..||+..+-.
T Consensus 33 ECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK~kf~~qtFeD~~v---EkEvd---------vRkr~~r~Fnk~~~eF~ 100 (314)
T COG5220 33 ECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKIKFIKQTFEDITV---EKEVD---------VRKRLLRAFNKEEEEFG 100 (314)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHHhcccccccchhhh---hhhhh---------HHHHHHHHhccchhhhC
Confidence 4799999999754 45788 887521110 0 1111111 12221 26678999988765534
Q ss_pred CchhHHHHHHHHHHh
Q 029861 150 FLPHHLRNMLQKAEV 164 (186)
Q Consensus 150 ~~~~~~~~~~~~~~~ 164 (186)
+.-..--..++++|.
T Consensus 101 gdl~~YNdYLEevE~ 115 (314)
T COG5220 101 GDLAKYNDYLEEVEE 115 (314)
T ss_pred ccHHHHHHHHHHHHH
Confidence 444444555555553
No 27
>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=41.13 E-value=47 Score=30.59 Aligned_cols=24 Identities=25% Similarity=0.679 Sum_probs=19.1
Q ss_pred HHHhcChhhHhhc-----cccccccCCcc
Q 029861 82 AYHNLCPGCAKEQ-----NVCAKCCSRVD 105 (186)
Q Consensus 82 AYH~iC~~CA~~~-----~vCaKC~k~~e 105 (186)
=||.+|..|...+ ..|+.|+++..
T Consensus 26 CGH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 26 CGHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 3899999998873 47999987544
No 28
>PF14149 YhfH: YhfH-like protein
Probab=38.11 E-value=13 Score=24.47 Aligned_cols=24 Identities=38% Similarity=0.880 Sum_probs=17.4
Q ss_pred Ccccccccccchh--hHHHHhcChhh
Q 029861 67 EPAKCQRCTKRAV--RQAYHNLCPGC 90 (186)
Q Consensus 67 ~p~KC~kC~qktV--k~AYH~iC~~C 90 (186)
+++.|..|++.-. ..+|.+.|+.|
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 35688888876
No 29
>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=33.70 E-value=20 Score=26.63 Aligned_cols=55 Identities=25% Similarity=0.321 Sum_probs=38.2
Q ss_pred ccCCCchhHHHHHHHHHHHHhhchhhccchhhhcccccccCCCCchhHHHHHHHH
Q 029861 107 VIGRDLAEVEAEQKMLEAALKNARERDRRILLRAPTKIKLGNYFLPHHLRNMLQK 161 (186)
Q Consensus 107 i~~~~~~~~e~eq~ele~~lk~l~ER~RRt~lR~~~k~~~~~~~~~~~~~~~~~~ 161 (186)
+.+-...+...-++.|+.+|+..|.|+..-++..++.-+.+....-..+..|-++
T Consensus 43 L~~Ls~~eL~~LE~~Le~aL~~VR~rK~~~l~~~i~~l~~ke~~l~~en~~L~~~ 97 (100)
T PF01486_consen 43 LESLSLKELQQLEQQLESALKRVRSRKDQLLMEQIEELKKKERELEEENNQLRQK 97 (100)
T ss_pred ccccchHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444556666777889999999999999999888876665554444444444443
No 30
>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=33.15 E-value=25 Score=24.97 Aligned_cols=44 Identities=34% Similarity=0.779 Sum_probs=32.6
Q ss_pred CchhhhHHHHHHHHHhCCCCCCCCcccccccccc---------hhhHHHHhcChhhHhhcc
Q 029861 44 GVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKR---------AVRQAYHNLCPGCAKEQN 95 (186)
Q Consensus 44 gVCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~qk---------tVk~AYH~iC~~CA~~~~ 95 (186)
.-|..|+...+= ....+.+|..|+.. ....|||..|..|=.+..
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 359999874321 46788899999863 569999998888866543
No 31
>PF12773 DZR: Double zinc ribbon
Probab=31.44 E-value=21 Score=23.07 Aligned_cols=18 Identities=28% Similarity=1.027 Sum_probs=11.4
Q ss_pred cChhhHhhcc-------ccccccCC
Q 029861 86 LCPGCAKEQN-------VCAKCCSR 103 (186)
Q Consensus 86 iC~~CA~~~~-------vCaKC~k~ 103 (186)
.|+.|...+. +|+.||..
T Consensus 14 fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 14 FCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred CChhhcCChhhccCCCCCCcCCcCC
Confidence 5666665555 57777764
No 32
>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=30.84 E-value=9.8 Score=24.77 Aligned_cols=30 Identities=23% Similarity=0.753 Sum_probs=22.4
Q ss_pred cccccccchhhHHHHhcChhhHhhccccccccC
Q 029861 70 KCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCS 102 (186)
Q Consensus 70 KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k 102 (186)
.|..|++ .+.- ++.-|..|. +..+|..|-.
T Consensus 2 ~C~~C~~-~i~g-~r~~C~~C~-d~dLC~~Cf~ 31 (46)
T cd02249 2 SCDGCLK-PIVG-VRYHCLVCE-DFDLCSSCYA 31 (46)
T ss_pred CCcCCCC-CCcC-CEEECCCCC-CCcCHHHHHC
Confidence 5888877 5554 677888885 6888888854
No 33
>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=30.65 E-value=24 Score=28.56 Aligned_cols=40 Identities=23% Similarity=0.194 Sum_probs=29.1
Q ss_pred HHHHHHHhhchhhccchhhhcccc--------cccCC-----CCchhHHHHHH
Q 029861 120 KMLEAALKNARERDRRILLRAPTK--------IKLGN-----YFLPHHLRNML 159 (186)
Q Consensus 120 ~ele~~lk~l~ER~RRt~lR~~~k--------~~~~~-----~~~~~~~~~~~ 159 (186)
++|+..|+.|++.+|+..+.+-+. +++++ .+.|+++++=+
T Consensus 8 ~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i 60 (181)
T PF08006_consen 8 NELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREI 60 (181)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHH
Confidence 478999999999999999887652 22222 38888877543
No 34
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=30.62 E-value=45 Score=26.32 Aligned_cols=30 Identities=20% Similarity=0.189 Sum_probs=22.8
Q ss_pred HHHHHHHhhchhhccchh-hhcccccccCCC
Q 029861 120 KMLEAALKNARERDRRIL-LRAPTKIKLGNY 149 (186)
Q Consensus 120 ~ele~~lk~l~ER~RRt~-lR~~~k~~~~~~ 149 (186)
..+.++|..|+++.|..| |++++...-++|
T Consensus 123 ~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eI 153 (189)
T PRK12515 123 AALRACLAKLSPAHREIIDLVYYHEKSVEEV 153 (189)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHH
Confidence 357889999999999999 667765544443
No 35
>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=30.54 E-value=23 Score=37.53 Aligned_cols=50 Identities=20% Similarity=0.332 Sum_probs=29.7
Q ss_pred cccccccccchhhHHHHhcChhhHhhccccccccCCcccccCCCchhHHHHHHHHHHHHhhchhhc
Q 029861 68 PAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERD 133 (186)
Q Consensus 68 p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~~e~i~~~~~~~~e~eq~ele~~lk~l~ER~ 133 (186)
-++|.+|+..|. ...|++||.+.+.+-+- ...-.....+.++++++.+|+
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 566666666543 35677777765443322 111123347888899998887
No 36
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=30.46 E-value=55 Score=25.53 Aligned_cols=30 Identities=20% Similarity=0.161 Sum_probs=22.9
Q ss_pred HHHHHHHHhhchhhccchhh-hcccccccCC
Q 029861 119 QKMLEAALKNARERDRRILL-RAPTKIKLGN 148 (186)
Q Consensus 119 q~ele~~lk~l~ER~RRt~l-R~~~k~~~~~ 148 (186)
...+.++|..|++++|+.|+ ++++...-++
T Consensus 126 ~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~e 156 (186)
T PRK13919 126 RTRLGRALKALSPEERRVIEVLYYQGYTHRE 156 (186)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCCCHHH
Confidence 34688999999999999996 6776544433
No 37
>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=30.43 E-value=19 Score=33.62 Aligned_cols=33 Identities=21% Similarity=0.408 Sum_probs=20.1
Q ss_pred hCCCCCCCCcccccccccchhhHHHHhcChhhHhhccccccccCC
Q 029861 59 YGKYKPLSEPAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSR 103 (186)
Q Consensus 59 Y~KYKPLt~p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~ 103 (186)
-|||. +|.-.+|..|....-..+|+ ..|+ ||++
T Consensus 235 ~GKYh-~~~c~~C~~~~~~~~~~~~~----------~~Cp-CG~~ 267 (374)
T TIGR00375 235 LGKYH-QTACEACGEPAVSEDAETAC----------ANCP-CGGR 267 (374)
T ss_pred CCccc-hhhhcccCCcCCchhhhhcC----------CCCC-CCCc
Confidence 46776 56666666666655555555 4566 6665
No 38
>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=29.92 E-value=15 Score=26.15 Aligned_cols=22 Identities=32% Similarity=0.898 Sum_probs=14.2
Q ss_pred HhcChhhHh-----hccccccccCCcc
Q 029861 84 HNLCPGCAK-----EQNVCAKCCSRVD 105 (186)
Q Consensus 84 H~iC~~CA~-----~~~vCaKC~k~~e 105 (186)
|++|.-|.. ....||.||-|..
T Consensus 15 H~~CrRCG~~syH~qK~~CasCGyp~~ 41 (55)
T PF01907_consen 15 HTLCRRCGRRSYHIQKKTCASCGYPAA 41 (55)
T ss_dssp EEE-TTTSSEEEETTTTEETTTBTTTS
T ss_pred EeeecccCCeeeecCCCcccccCCCcc
Confidence 455555543 5689999997654
No 39
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=29.75 E-value=21 Score=35.49 Aligned_cols=28 Identities=25% Similarity=0.511 Sum_probs=22.1
Q ss_pred CcccccccccchhhHHHHhcChhhHhhcccc
Q 029861 67 EPAKCQRCTKRAVRQAYHNLCPGCAKEQNVC 97 (186)
Q Consensus 67 ~p~KC~kC~qktVk~AYH~iC~~CA~~~~vC 97 (186)
..+.|+.|.+++-+.|||+- ||...+..
T Consensus 312 ~~GtcIqCs~~nC~~aYHVt---CArrag~f 339 (669)
T COG5141 312 FGGTCIQCSYFNCTRAYHVT---CARRAGYF 339 (669)
T ss_pred cCcceeeecccchhhhhhhh---hhhhcchh
Confidence 46899999999999999975 45554433
No 40
>PHA02683 ORF078 thioredoxin-like protein; Provisional
Probab=29.42 E-value=18 Score=27.19 Aligned_cols=18 Identities=39% Similarity=1.084 Sum_probs=11.4
Q ss_pred hCCCC-CCCCccccccccc
Q 029861 59 YGKYK-PLSEPAKCQRCTK 76 (186)
Q Consensus 59 Y~KYK-PLt~p~KC~kC~q 76 (186)
|.+|+ -|.+|.+|.+|..
T Consensus 4 y~~Y~~~LdpP~rCs~C~~ 22 (75)
T PHA02683 4 YAKYNVVLDPPRRCSKCAS 22 (75)
T ss_pred hhheeeecCCCCcchHHHH
Confidence 44554 4667788877753
No 41
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=27.91 E-value=45 Score=23.55 Aligned_cols=29 Identities=17% Similarity=0.527 Sum_probs=20.2
Q ss_pred cccccccccchhhHHHHhcChhhHhhccccccccCCcccccCC
Q 029861 68 PAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRVDRVIGR 110 (186)
Q Consensus 68 p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~~e~i~~~ 110 (186)
-.+|..|+..|. ..+|+.||.+.....|.
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 457777877665 35788899877765553
No 42
>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=27.42 E-value=25 Score=28.87 Aligned_cols=20 Identities=15% Similarity=0.368 Sum_probs=14.6
Q ss_pred hcChhhHhhc-------cccccccCCc
Q 029861 85 NLCPGCAKEQ-------NVCAKCCSRV 104 (186)
Q Consensus 85 ~iC~~CA~~~-------~vCaKC~k~~ 104 (186)
.+|+.|++.| -+|++||...
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCcc
Confidence 3677777665 5999999754
No 43
>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=27.40 E-value=19 Score=28.68 Aligned_cols=26 Identities=31% Similarity=0.613 Sum_probs=16.2
Q ss_pred CCcccccccc-cchhhHHHHhcChhhHhh
Q 029861 66 SEPAKCQRCT-KRAVRQAYHNLCPGCAKE 93 (186)
Q Consensus 66 t~p~KC~kC~-qktVk~AYH~iC~~CA~~ 93 (186)
+...+|+.|+ ...+..||. |..|..-
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 3467899999 889999997 8888544
No 44
>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=26.67 E-value=40 Score=21.62 Aligned_cols=22 Identities=36% Similarity=0.440 Sum_probs=17.5
Q ss_pred HHHHHHHhhchhhccchhhhcc
Q 029861 120 KMLEAALKNARERDRRILLRAP 141 (186)
Q Consensus 120 ~ele~~lk~l~ER~RRt~lR~~ 141 (186)
+.++++|..|++++|.-|+-.-
T Consensus 2 ~~l~~~l~~L~~~~r~i~~l~~ 23 (54)
T PF08281_consen 2 EALQQALAQLPERQREIFLLRY 23 (54)
T ss_dssp HHHHHHHHCS-HHHHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHHHH
Confidence 4688899999999999987744
No 45
>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=26.29 E-value=37 Score=24.89 Aligned_cols=41 Identities=27% Similarity=0.689 Sum_probs=32.1
Q ss_pred chhhhHHHHHHHHHhCCCCCCCCcccccccccc--------hhhHHHHh-----cChhhHhhc
Q 029861 45 VCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKR--------AVRQAYHN-----LCPGCAKEQ 94 (186)
Q Consensus 45 VCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~qk--------tVk~AYH~-----iC~~CA~~~ 94 (186)
-|..|+.- ........+|..|+.. ....|||. .|-.|=.+.
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 5566677899999854 45899999 888886654
No 46
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.12 E-value=18 Score=30.94 Aligned_cols=37 Identities=24% Similarity=0.566 Sum_probs=30.1
Q ss_pred cccccccccchhhHH-----HHhcChhhHhhccccccccCCc
Q 029861 68 PAKCQRCTKRAVRQA-----YHNLCPGCAKEQNVCAKCCSRV 104 (186)
Q Consensus 68 p~KC~kC~qktVk~A-----YH~iC~~CA~~~~vCaKC~k~~ 104 (186)
++.|..|.+++++=. .|.+|.+|+....+|+-|..+.
T Consensus 158 ~~~Cr~C~~~~~~VlllPCrHl~lC~~C~~~~~~CPiC~~~~ 199 (207)
T KOG1100|consen 158 MRSCRKCGEREATVLLLPCRHLCLCGICDESLRICPICRSPK 199 (207)
T ss_pred cccceecCcCCceEEeecccceEecccccccCccCCCCcChh
Confidence 445999999988743 5689999999899999997654
No 47
>PRK12496 hypothetical protein; Provisional
Probab=26.11 E-value=20 Score=29.50 Aligned_cols=21 Identities=43% Similarity=1.009 Sum_probs=14.4
Q ss_pred hcChhhHhhc------cccccccCCcc
Q 029861 85 NLCPGCAKEQ------NVCAKCCSRVD 105 (186)
Q Consensus 85 ~iC~~CA~~~------~vCaKC~k~~e 105 (186)
..|..|...+ ..|+.||.+..
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSPVK 154 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCChhh
Confidence 3577777665 46999997643
No 48
>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=25.99 E-value=16 Score=24.78 Aligned_cols=32 Identities=22% Similarity=0.747 Sum_probs=23.8
Q ss_pred cccccccchhhHHHHhcChhhHh-hccccccccC
Q 029861 70 KCQRCTKRAVRQAYHNLCPGCAK-EQNVCAKCCS 102 (186)
Q Consensus 70 KC~kC~qktVk~AYH~iC~~CA~-~~~vCaKC~k 102 (186)
+|..|++.+|. -.+--|..|.. ...+|..|-.
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 58888887776 55667888875 7888888844
No 49
>PRK10236 hypothetical protein; Provisional
Probab=25.85 E-value=1.8e+02 Score=26.03 Aligned_cols=47 Identities=19% Similarity=0.229 Sum_probs=34.0
Q ss_pred HHHHHHHhhchhhccchhhhcccccc-cCCCCchhHHHHHHHHHHhHh
Q 029861 120 KMLEAALKNARERDRRILLRAPTKIK-LGNYFLPHHLRNMLQKAEVTK 166 (186)
Q Consensus 120 ~ele~~lk~l~ER~RRt~lR~~~k~~-~~~~~~~~~~~~~~~~~~~~~ 166 (186)
+-++.+++.|+|.+|++|.+.|+... ..+...|..+..+.-.+.+.-
T Consensus 120 kll~~a~~kms~eE~~~L~~~l~~~l~~~~~~~~~ll~~~~~~~~~~g 167 (237)
T PRK10236 120 QFLRNTWKKMDEEHKQEFLHAVDARVNELEELLPLLMKDKLLAKGVSH 167 (237)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHhhhccCcccchHHHHHHHHHHHhhcc
Confidence 36788999999999999999998762 123477777666555444443
No 50
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=25.61 E-value=61 Score=25.83 Aligned_cols=30 Identities=13% Similarity=0.181 Sum_probs=22.6
Q ss_pred HHHHHHHHHhhchhhccchh-hhcccccccC
Q 029861 118 EQKMLEAALKNARERDRRIL-LRAPTKIKLG 147 (186)
Q Consensus 118 eq~ele~~lk~l~ER~RRt~-lR~~~k~~~~ 147 (186)
+...+.++|..|++++|.-| |++++...-.
T Consensus 132 ~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~ 162 (194)
T PRK09646 132 ERERVRDCLDALTDTQRESVTLAYYGGLTYR 162 (194)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHcCCCHH
Confidence 44568899999999999999 6666554333
No 51
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=25.19 E-value=70 Score=24.32 Aligned_cols=26 Identities=15% Similarity=0.144 Sum_probs=20.2
Q ss_pred HHHHHHHhhchhhccchh-hhcccccc
Q 029861 120 KMLEAALKNARERDRRIL-LRAPTKIK 145 (186)
Q Consensus 120 ~ele~~lk~l~ER~RRt~-lR~~~k~~ 145 (186)
..+..+|..|++++|..| |++++...
T Consensus 101 ~~l~~~l~~L~~~~r~v~~l~~~~~~s 127 (163)
T PRK07037 101 RHVADALSELPARTRYAFEMYRLHGET 127 (163)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCC
Confidence 457888999999999999 56665443
No 52
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=25.17 E-value=50 Score=30.50 Aligned_cols=23 Identities=26% Similarity=0.733 Sum_probs=18.5
Q ss_pred HHHHhcChhhHhh-----ccccccccCC
Q 029861 81 QAYHNLCPGCAKE-----QNVCAKCCSR 103 (186)
Q Consensus 81 ~AYH~iC~~CA~~-----~~vCaKC~k~ 103 (186)
--||.+|..|-.- ...|+.|++.
T Consensus 22 ~C~H~lCEsCvd~iF~~g~~~CpeC~~i 49 (300)
T KOG3800|consen 22 ECGHRLCESCVDRIFSLGPAQCPECMVI 49 (300)
T ss_pred cccchHHHHHHHHHHhcCCCCCCcccch
Confidence 4589999999754 4789999874
No 53
>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=24.97 E-value=13 Score=24.78 Aligned_cols=31 Identities=26% Similarity=0.701 Sum_probs=22.9
Q ss_pred cccccccchhhHHHHhcChhhHhhccccccccC
Q 029861 70 KCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCS 102 (186)
Q Consensus 70 KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k 102 (186)
.|..|....+. -.+..|..|. +..+|..|=.
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 57888877777 4666788886 6888888854
No 54
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=24.60 E-value=78 Score=24.04 Aligned_cols=28 Identities=29% Similarity=0.381 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhhchhhccchh-hhccccc
Q 029861 117 AEQKMLEAALKNARERDRRIL-LRAPTKI 144 (186)
Q Consensus 117 ~eq~ele~~lk~l~ER~RRt~-lR~~~k~ 144 (186)
.....++++|..|+++.|.-| |++++..
T Consensus 99 ~~~~~l~~~l~~L~~~~r~i~~l~~~~g~ 127 (162)
T TIGR02983 99 ALRAALARALRRLPARQRAVVVLRYYEDL 127 (162)
T ss_pred HHHHHHHHHHHhCCHHHHHHhhhHHHhcC
Confidence 345578999999999999999 5565543
No 55
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=24.41 E-value=31 Score=31.41 Aligned_cols=69 Identities=30% Similarity=0.649 Sum_probs=42.3
Q ss_pred CCCCCCccCchhhhHHHHHHHHHhCCCCCCCCcccccccccc--------hhhHHHHhcChhhHhhcc---------ccc
Q 029861 36 LRPYPEITGVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKR--------AVRQAYHNLCPGCAKEQN---------VCA 98 (186)
Q Consensus 36 ~~~~~~~~gVCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~qk--------tVk~AYH~iC~~CA~~~~---------vCa 98 (186)
+|++......|.-| |.+=|| +-..+|+.+ +|-+|..+ -.-.|+- -|+.|...+. -|-
T Consensus 105 ~ip~~drqFaC~~C-d~~WwR-rvp~rKeVS---RCr~C~~rYDPVP~dkmwG~aef-~C~~C~h~F~G~~qm~v~sPCy 178 (278)
T PF15135_consen 105 LIPSVDRQFACSSC-DHMWWR-RVPQRKEVS---RCRKCRKRYDPVPCDKMWGIAEF-HCPKCRHNFRGFAQMGVPSPCY 178 (278)
T ss_pred cccccceeeecccc-chHHHh-ccCcccccc---cccccccccCCCccccccceeee-ecccccccchhhhhcCCCCCcc
Confidence 34444566789999 888888 555555554 55556544 2223333 3888888775 466
Q ss_pred cccCCcc--cccCC
Q 029861 99 KCCSRVD--RVIGR 110 (186)
Q Consensus 99 KC~k~~e--~i~~~ 110 (186)
.|+.+.. .|+|+
T Consensus 179 ~C~~~v~P~~IlPP 192 (278)
T PF15135_consen 179 GCGNPVYPSRILPP 192 (278)
T ss_pred CCCCccCcccccCC
Confidence 7776543 45554
No 56
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=24.09 E-value=15 Score=26.43 Aligned_cols=36 Identities=33% Similarity=0.798 Sum_probs=22.8
Q ss_pred cccccccccchh--hHHHHhcChhhHhh-ccccccccCC
Q 029861 68 PAKCQRCTKRAV--RQAYHNLCPGCAKE-QNVCAKCCSR 103 (186)
Q Consensus 68 p~KC~kC~qktV--k~AYH~iC~~CA~~-~~vCaKC~k~ 103 (186)
+-+|.+|+..-. -.|=+-.|+.|.++ -..|++|.+.
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~ 45 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQ 45 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhc
Confidence 446777764433 22455578888777 6777777653
No 57
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=23.82 E-value=73 Score=32.77 Aligned_cols=60 Identities=28% Similarity=0.595 Sum_probs=41.5
Q ss_pred CccCchhhhHHHH-HHHHHhCCCCCCCCccccccccc-------------chhhHHHHhcChhhHhhcc-----------
Q 029861 41 EITGVCPRCKDQI-DWKRRYGKYKPLSEPAKCQRCTK-------------RAVRQAYHNLCPGCAKEQN----------- 95 (186)
Q Consensus 41 ~~~gVCqRC~eiI-eWKvkY~KYKPLt~p~KC~kC~q-------------ktVk~AYH~iC~~CA~~~~----------- 95 (186)
+-.++|.-|.+-| +=.-+|=.| +=-.|+.|+= .|...++- +|+.|..+.+
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 -ccccccCCcc
Q 029861 96 -VCAKCCSRVD 105 (186)
Q Consensus 96 -vCaKC~k~~e 105 (186)
.|++||=...
T Consensus 174 ~aCp~CGP~~~ 184 (750)
T COG0068 174 IACPKCGPHLF 184 (750)
T ss_pred ccCcccCCCeE
Confidence 8999995433
No 58
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=23.70 E-value=68 Score=24.87 Aligned_cols=25 Identities=20% Similarity=0.227 Sum_probs=19.6
Q ss_pred HHHHHHHhhchhhccchh-hhccccc
Q 029861 120 KMLEAALKNARERDRRIL-LRAPTKI 144 (186)
Q Consensus 120 ~ele~~lk~l~ER~RRt~-lR~~~k~ 144 (186)
..+..+|..|+++.|.-| |++++..
T Consensus 130 ~~l~~~l~~L~~~~r~v~~l~~~~~~ 155 (190)
T TIGR02939 130 QTVMRAVEALPEDLRTAITLRELEGL 155 (190)
T ss_pred HHHHHHHHcCCHHHhhhhhhhhhcCC
Confidence 468889999999999998 4555443
No 59
>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=23.50 E-value=16 Score=24.22 Aligned_cols=31 Identities=26% Similarity=0.816 Sum_probs=23.6
Q ss_pred cccccccchhhHHHHhcChhhHhhccccccccC
Q 029861 70 KCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCS 102 (186)
Q Consensus 70 KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k 102 (186)
.|..|.+ .+...+|..|..|. ++.+|..|=.
T Consensus 2 ~Cd~C~~-~~~~g~r~~C~~C~-d~dLC~~Cf~ 32 (49)
T cd02335 2 HCDYCSK-DITGTIRIKCAECP-DFDLCLECFS 32 (49)
T ss_pred CCCCcCC-CCCCCcEEECCCCC-CcchhHHhhh
Confidence 5888865 44455888899997 6999999954
No 60
>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=23.23 E-value=16 Score=24.47 Aligned_cols=31 Identities=23% Similarity=0.743 Sum_probs=24.0
Q ss_pred cccccccchhhHHHHhcChhhHhhccccccccC
Q 029861 70 KCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCS 102 (186)
Q Consensus 70 KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k 102 (186)
.|..|.+.+|. -.|.-|..|. +..+|..|-.
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 6889988843
No 61
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=22.87 E-value=32 Score=23.50 Aligned_cols=32 Identities=19% Similarity=0.593 Sum_probs=21.6
Q ss_pred chhhhHHHHHHHHHhCCCCCCCCccccccccc
Q 029861 45 VCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTK 76 (186)
Q Consensus 45 VCqRC~eiIeWKvkY~KYKPLt~p~KC~kC~q 76 (186)
+|..|-++|||=.++.=-+.-.+--+|-.|++
T Consensus 8 ~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~ 39 (46)
T PF11331_consen 8 VCSSCFELLQLPAKFSLSKKNQQKLRCGACSE 39 (46)
T ss_pred ECccHHHHHcCCCccCCCccceeEEeCCCCce
Confidence 69999999999766544333334556777754
No 62
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=22.86 E-value=64 Score=26.89 Aligned_cols=31 Identities=19% Similarity=0.385 Sum_probs=18.4
Q ss_pred Ccccccccccc-hhhHHHHhcChhhHhhccccccccCCcc
Q 029861 67 EPAKCQRCTKR-AVRQAYHNLCPGCAKEQNVCAKCCSRVD 105 (186)
Q Consensus 67 ~p~KC~kC~qk-tVk~AYH~iC~~CA~~~~vCaKC~k~~e 105 (186)
+-..|..|+.+ |.-.|.- ..-.|+.||....
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME--------YGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHhh--------cCCcCCCCCCCCe
Confidence 45667777533 3344432 3568999997544
No 63
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=22.49 E-value=12 Score=26.68 Aligned_cols=19 Identities=37% Similarity=0.934 Sum_probs=12.8
Q ss_pred CCCccCchhhhHHHHHHHH
Q 029861 39 YPEITGVCPRCKDQIDWKR 57 (186)
Q Consensus 39 ~~~~~gVCqRC~eiIeWKv 57 (186)
..++.|-|+.|...|.|+.
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 4578899999999999985
No 64
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=22.40 E-value=85 Score=23.89 Aligned_cols=24 Identities=25% Similarity=0.288 Sum_probs=19.0
Q ss_pred HHHHHHhhchhhccchhh-hccccc
Q 029861 121 MLEAALKNARERDRRILL-RAPTKI 144 (186)
Q Consensus 121 ele~~lk~l~ER~RRt~l-R~~~k~ 144 (186)
.++++|..|++++|.-|. ++.+..
T Consensus 98 ~l~~~l~~L~~~~r~v~~l~~~~~~ 122 (159)
T PRK12527 98 LLQRALAELPPACRDSFLLRKLEGL 122 (159)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCC
Confidence 688999999999999984 455443
No 65
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=22.10 E-value=99 Score=24.83 Aligned_cols=31 Identities=13% Similarity=0.197 Sum_probs=22.8
Q ss_pred HHHHHHHHhhchhhccchhh-hcccccccCCC
Q 029861 119 QKMLEAALKNARERDRRILL-RAPTKIKLGNY 149 (186)
Q Consensus 119 q~ele~~lk~l~ER~RRt~l-R~~~k~~~~~~ 149 (186)
...+..+|..|+++.|..|+ ++++...-.+|
T Consensus 107 ~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EI 138 (187)
T PRK12516 107 LQDFRAALDQLPDDQREAIILVGASGFAYEEA 138 (187)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHH
Confidence 45688999999999999985 46655444443
No 66
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=22.04 E-value=28 Score=25.35 Aligned_cols=25 Identities=28% Similarity=0.818 Sum_probs=16.6
Q ss_pred cccccccccchhhHHHHhcChhhHhhccccccccCC
Q 029861 68 PAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSR 103 (186)
Q Consensus 68 p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~ 103 (186)
.-.|..|+.+ ||| .....||.||-.
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 67
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.93 E-value=22 Score=21.74 Aligned_cols=13 Identities=23% Similarity=0.598 Sum_probs=8.1
Q ss_pred hccccccccCCcc
Q 029861 93 EQNVCAKCCSRVD 105 (186)
Q Consensus 93 ~~~vCaKC~k~~e 105 (186)
+.-.|+.||....
T Consensus 25 ~~~~CP~Cg~~~~ 37 (41)
T smart00834 25 PLATCPECGGDVR 37 (41)
T ss_pred CCCCCCCCCCcce
Confidence 4556888876433
No 68
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=21.61 E-value=94 Score=24.02 Aligned_cols=28 Identities=18% Similarity=0.344 Sum_probs=21.0
Q ss_pred HHHHHHHhhchhhccchh-hhcccccccC
Q 029861 120 KMLEAALKNARERDRRIL-LRAPTKIKLG 147 (186)
Q Consensus 120 ~ele~~lk~l~ER~RRt~-lR~~~k~~~~ 147 (186)
..+...|..|++++|..| |++++.....
T Consensus 128 ~~l~~~l~~L~~~~r~il~l~~~~~~s~~ 156 (187)
T PRK09641 128 ETIQEAILQLPEKYRTVIVLKYIEDLSLK 156 (187)
T ss_pred HHHHHHHHhCCHHHHHHhhhHHhhCCCHH
Confidence 468889999999999999 5566544333
No 69
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=21.51 E-value=94 Score=24.76 Aligned_cols=32 Identities=13% Similarity=0.065 Sum_probs=23.5
Q ss_pred HHHHHHHHHhhchhhccchh-hhcccccccCCC
Q 029861 118 EQKMLEAALKNARERDRRIL-LRAPTKIKLGNY 149 (186)
Q Consensus 118 eq~ele~~lk~l~ER~RRt~-lR~~~k~~~~~~ 149 (186)
....++.+|..|++++|.-| |++++....++|
T Consensus 96 ~~~~l~~~l~~L~~~~r~i~~l~~~~g~~~~EI 128 (181)
T PRK09637 96 LAPCLRPFIDALPEKYAEALRLTELEGLSQKEI 128 (181)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHH
Confidence 34468888999999999999 666765544443
No 70
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=21.01 E-value=26 Score=27.12 Aligned_cols=28 Identities=18% Similarity=0.410 Sum_probs=16.0
Q ss_pred CcccccccccchhhHHHHhcChhhHhhccccccccCCc
Q 029861 67 EPAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRV 104 (186)
Q Consensus 67 ~p~KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~k~~ 104 (186)
...+|..|+...-...++ -.|+.||.+.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~----------~~CP~Cgs~~ 96 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQHD----------AQCPHCHGER 96 (113)
T ss_pred cEEEcccCCCEEecCCcC----------ccCcCCCCCC
Confidence 356788887544333332 2488888543
No 71
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=20.95 E-value=39 Score=36.70 Aligned_cols=32 Identities=28% Similarity=0.851 Sum_probs=25.4
Q ss_pred cccccccccchhhHHHHhcChhhHhhc---cccccccCC
Q 029861 68 PAKCQRCTKRAVRQAYHNLCPGCAKEQ---NVCAKCCSR 103 (186)
Q Consensus 68 p~KC~kC~qktVk~AYH~iC~~CA~~~---~vCaKC~k~ 103 (186)
..+|.+|+.-+.. ..|+.|.... -.|+.||..
T Consensus 667 ~rkCPkCG~~t~~----~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 667 RRRCPSCGTETYE----NRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred EEECCCCCCcccc----ccCcccCCcCCCceeCccCCCc
Confidence 5899999986543 3999999874 479999974
No 72
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=20.85 E-value=80 Score=25.01 Aligned_cols=43 Identities=14% Similarity=0.109 Sum_probs=28.2
Q ss_pred HHHHHHHhhchhhccchh-hhcccccccCCC-----CchhHHHHHHHHH
Q 029861 120 KMLEAALKNARERDRRIL-LRAPTKIKLGNY-----FLPHHLRNMLQKA 162 (186)
Q Consensus 120 ~ele~~lk~l~ER~RRt~-lR~~~k~~~~~~-----~~~~~~~~~~~~~ 162 (186)
..+..+|..|+++.|..| |++++...-.+| -.+.+.++.+..+
T Consensus 123 ~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Ra 171 (193)
T TIGR02947 123 QDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSRLHRG 171 (193)
T ss_pred HHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 568899999999999998 556655444443 3444444444433
No 73
>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=20.59 E-value=1e+02 Score=23.16 Aligned_cols=28 Identities=29% Similarity=0.379 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhhchhhccchhhh-ccccc
Q 029861 117 AEQKMLEAALKNARERDRRILLR-APTKI 144 (186)
Q Consensus 117 ~eq~ele~~lk~l~ER~RRt~lR-~~~k~ 144 (186)
++...+.++|..|++++|..|.- +++..
T Consensus 100 ~~~~~l~~~i~~L~~~~r~v~~l~~~~g~ 128 (159)
T TIGR02989 100 DELQALEGCLEKLPERQRELLQLRYQRGV 128 (159)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHhcCC
Confidence 34457889999999999999977 55433
No 74
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=20.52 E-value=1.1e+02 Score=24.60 Aligned_cols=30 Identities=17% Similarity=0.213 Sum_probs=23.1
Q ss_pred HHHHHHHhhchhhccchh-hhcccccccCCC
Q 029861 120 KMLEAALKNARERDRRIL-LRAPTKIKLGNY 149 (186)
Q Consensus 120 ~ele~~lk~l~ER~RRt~-lR~~~k~~~~~~ 149 (186)
..++++|..|+++.|.-| |++++.....+|
T Consensus 105 ~~l~~~L~~Lp~~~r~v~~L~~~~g~s~~EI 135 (188)
T PRK12546 105 SDFRAAFAQLPDEQREALILVGASGFSYEEA 135 (188)
T ss_pred HHHHHHHHhCCHHHhHHhhhHHhcCCCHHHH
Confidence 478899999999999999 556765554444
No 75
>PLN03109 ETHYLENE-INSENSITIVE3-like3 protein; Provisional
Probab=20.50 E-value=2.5e+02 Score=28.34 Aligned_cols=49 Identities=27% Similarity=0.324 Sum_probs=25.0
Q ss_pred HhhchhhccchhhhcccccccCCCCchhHHHHHHHHHHhHhHHHHHHHHHHHHHHHhh
Q 029861 126 LKNARERDRRILLRAPTKIKLGNYFLPHHLRNMLQKAEVTKTITMVITWIKSMMKMMV 183 (186)
Q Consensus 126 lk~l~ER~RRt~lR~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 183 (186)
|+.|.||.+-.--..+++.+.+.. .++-+++-|-.|.- .-+|-|+|||-
T Consensus 53 l~rlke~~~~~~~~~~e~~~~~~~-~~~arrkkm~raqd--------gilkymlk~me 101 (599)
T PLN03109 53 LKRIKERQKKLQQAALEKSKPKKI-SDQARRKKMSRAQD--------GILKYMLKLME 101 (599)
T ss_pred HHHHHHHhhhhhhhhhhhcCcccc-HHHHHHHHHHHHHH--------HHHHHHHHHHH
Confidence 677777765433333334333333 33444444433332 34688999984
No 76
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=20.25 E-value=67 Score=24.27 Aligned_cols=24 Identities=13% Similarity=0.188 Sum_probs=18.6
Q ss_pred HHHHHHHHhhchhhccchhhh-ccc
Q 029861 119 QKMLEAALKNARERDRRILLR-APT 142 (186)
Q Consensus 119 q~ele~~lk~l~ER~RRt~lR-~~~ 142 (186)
...+..+|..|+++.|.-|.. +++
T Consensus 116 ~~~l~~~l~~L~~~~r~i~~l~~~~ 140 (179)
T PRK11924 116 LARIDRCLDALPVKQREVFLLRYVE 140 (179)
T ss_pred HHHHHHHHHhCCHHHHHHhhHHHHc
Confidence 346778899999999999844 454
No 77
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=20.11 E-value=57 Score=30.42 Aligned_cols=32 Identities=31% Similarity=0.725 Sum_probs=0.0
Q ss_pred ccccccccchhhHHHHhcChhhHhh------------cccccccc
Q 029861 69 AKCQRCTKRAVRQAYHNLCPGCAKE------------QNVCAKCC 101 (186)
Q Consensus 69 ~KC~kC~qktVk~AYH~iC~~CA~~------------~~vCaKC~ 101 (186)
..|..|+.-.. .-++.+|+.|-.+ ..+|+.||
T Consensus 7 ~~C~~CGr~~~-~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cg 50 (355)
T COG1499 7 ILCVRCGRSVD-PLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCG 50 (355)
T ss_pred cEeccCCCcCc-hhhccccHHHHhccCccccCCCceEEEECCcCC
No 78
>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=20.06 E-value=23 Score=24.06 Aligned_cols=30 Identities=23% Similarity=0.772 Sum_probs=21.6
Q ss_pred cccccccchhhHHHHhcChhhHhhcccccccc
Q 029861 70 KCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCC 101 (186)
Q Consensus 70 KC~kC~qktVk~AYH~iC~~CA~~~~vCaKC~ 101 (186)
.|..|+..+|.- .+.-|..|. ++.+|..|=
T Consensus 2 ~Cd~C~~~pi~g-~RykC~~C~-d~DLC~~Cf 31 (49)
T cd02334 2 KCNICKEFPITG-FRYRCLKCF-NYDLCQSCF 31 (49)
T ss_pred CCCCCCCCCcee-eeEECCCCC-CcCchHHHH
Confidence 577777766664 566788886 688888884
Done!