Query 030308
Match_columns 179
No_of_seqs 97 out of 99
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 11:45:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030308.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030308hhsearch_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 4.5E-57 9.7E-62 378.4 4.0 141 1-145 1-144 (227)
2 PF10217 DUF2039: Uncharacteri 100.0 6.2E-46 1.4E-50 279.7 5.4 92 10-105 1-92 (92)
3 PF10235 Cript: Microtubule-as 94.2 0.021 4.5E-07 43.6 1.1 42 63-105 38-80 (90)
4 KOG3476 Microtubule-associated 84.0 0.26 5.7E-06 38.2 -0.5 46 56-104 44-89 (100)
5 PRK04023 DNA polymerase II lar 81.8 0.72 1.6E-05 48.0 1.5 59 69-134 639-699 (1121)
6 PRK14714 DNA polymerase II lar 75.8 0.98 2.1E-05 47.8 0.4 71 44-134 668-745 (1337)
7 PF14634 zf-RING_5: zinc-RING 72.1 1.5 3.1E-05 28.0 0.3 24 79-102 17-44 (44)
8 PRK11595 DNA utilization prote 61.4 4.2 9.2E-05 34.0 1.2 35 68-103 5-43 (227)
9 PF07191 zinc-ribbons_6: zinc- 61.1 0.48 1E-05 34.8 -3.9 47 44-102 2-48 (70)
10 PF04161 Arv1: Arv1-like famil 56.9 5.1 0.00011 33.5 0.9 41 70-112 2-42 (208)
11 PF03833 PolC_DP2: DNA polymer 56.6 3.6 7.8E-05 42.2 0.0 59 69-134 668-728 (900)
12 PRK04023 DNA polymerase II lar 53.6 7.1 0.00015 41.0 1.5 44 58-105 615-662 (1121)
13 PF13900 GVQW: Putative bindin 53.3 4.1 8.8E-05 28.1 -0.2 38 53-92 6-43 (48)
14 PF13920 zf-C3HC4_3: Zinc fing 50.3 7.1 0.00015 25.2 0.6 24 84-107 22-50 (50)
15 TIGR00570 cdk7 CDK-activating 45.4 21 0.00045 32.7 3.0 24 82-105 26-54 (309)
16 KOG4739 Uncharacterized protei 44.8 7.5 0.00016 34.2 0.1 38 70-107 5-50 (233)
17 COG1645 Uncharacterized Zn-fin 44.0 13 0.00028 30.2 1.3 27 80-108 26-58 (131)
18 PF10083 DUF2321: Uncharacteri 42.5 11 0.00024 31.6 0.7 11 95-105 69-79 (158)
19 PF13248 zf-ribbon_3: zinc-rib 41.4 7.9 0.00017 22.6 -0.2 10 94-103 16-25 (26)
20 KOG0978 E3 ubiquitin ligase in 40.9 14 0.0003 37.2 1.3 36 69-104 644-688 (698)
21 PRK00133 metG methionyl-tRNA s 38.3 35 0.00076 33.2 3.5 79 69-150 140-229 (673)
22 TIGR00398 metG methionyl-tRNA 38.3 38 0.00083 31.5 3.7 76 69-147 137-226 (530)
23 PF06906 DUF1272: Protein of u 37.3 17 0.00038 25.9 1.0 18 85-102 30-49 (57)
24 PF09538 FYDLN_acid: Protein o 34.6 16 0.00036 28.3 0.6 21 86-106 11-38 (108)
25 PF10061 DUF2299: Uncharacteri 33.8 39 0.00084 27.1 2.6 34 124-159 62-95 (138)
26 COG5220 TFB3 Cdk activating ki 33.7 12 0.00026 34.0 -0.4 61 81-149 33-100 (314)
27 PF14149 YhfH: YhfH-like prote 33.2 18 0.00038 23.8 0.4 24 67-90 12-37 (37)
28 PRK06759 RNA polymerase factor 33.1 54 0.0012 24.5 3.1 27 116-142 94-121 (154)
29 PF15135 UPF0515: Uncharacteri 31.4 25 0.00055 31.8 1.3 68 37-110 106-192 (278)
30 TIGR00354 polC DNA polymerase, 31.1 23 0.0005 37.3 1.1 50 68-133 625-674 (1095)
31 COG5141 PHD zinc finger-contai 28.7 23 0.0005 35.1 0.6 28 67-97 312-339 (669)
32 cd08168 Cytochrom_C3 Heme-bind 28.7 33 0.00071 24.2 1.2 44 44-95 17-69 (85)
33 PF12773 DZR: Double zinc ribb 28.5 24 0.00053 22.6 0.5 18 86-103 14-38 (50)
34 TIGR00375 conserved hypothetic 27.2 23 0.0005 32.9 0.3 34 58-93 234-267 (374)
35 PRK00420 hypothetical protein; 27.1 79 0.0017 24.9 3.2 19 86-104 25-50 (112)
36 PRK13130 H/ACA RNA-protein com 26.7 56 0.0012 22.9 2.1 29 68-110 5-33 (56)
37 PRK09646 RNA polymerase sigma 26.5 72 0.0016 25.3 3.0 25 118-142 132-157 (194)
38 PHA02683 ORF078 thioredoxin-li 25.7 24 0.00051 26.5 0.1 18 59-76 4-22 (75)
39 PF01907 Ribosomal_L37e: Ribos 25.7 19 0.00041 25.4 -0.4 23 84-106 15-42 (55)
40 PF03660 PHF5: PHF5-like prote 25.2 22 0.00047 28.2 -0.2 26 66-93 53-79 (106)
41 PF09334 tRNA-synt_1g: tRNA sy 24.2 22 0.00048 32.5 -0.4 32 118-149 191-226 (391)
42 cd02249 ZZ Zinc finger, ZZ typ 24.1 15 0.00032 23.8 -1.2 30 70-102 2-31 (46)
43 cd00817 ValRS_core catalytic c 23.9 78 0.0017 28.6 3.0 57 87-143 143-208 (382)
44 PF11793 FANCL_C: FANCL C-term 23.7 12 0.00027 26.4 -1.7 19 39-57 51-69 (70)
45 PF08281 Sigma70_r4_2: Sigma-7 23.7 78 0.0017 20.1 2.3 25 120-144 2-26 (54)
46 TIGR00100 hypA hydrogenase nic 23.6 39 0.00086 26.0 1.0 32 67-108 69-100 (115)
47 PF02085 Cytochrom_CIII: Class 23.2 46 0.001 24.2 1.2 41 45-94 33-86 (102)
48 PF11331 DUF3133: Protein of u 22.8 33 0.00071 23.3 0.3 32 45-76 8-39 (46)
49 COG1040 ComFC Predicted amidop 22.5 56 0.0012 27.8 1.7 38 65-104 21-62 (225)
50 PF08006 DUF1700: Protein of u 22.1 66 0.0014 25.8 2.0 24 120-143 8-31 (181)
51 PRK13919 putative RNA polymera 21.6 1.2E+02 0.0025 23.5 3.3 25 119-143 126-151 (186)
52 TIGR00595 priA primosomal prot 21.3 44 0.00096 31.6 1.0 33 69-104 223-263 (505)
53 PRK12515 RNA polymerase sigma 21.0 1.1E+02 0.0025 23.9 3.1 24 120-143 123-147 (189)
54 PF00816 Histone_HNS: H-NS his 20.9 1E+02 0.0022 22.3 2.7 29 115-143 3-31 (93)
55 PRK14890 putative Zn-ribbon RN 20.7 19 0.0004 25.8 -1.3 36 68-103 7-45 (59)
56 cd02341 ZZ_ZZZ3 Zinc finger, Z 20.6 23 0.00049 23.8 -0.8 32 70-102 2-34 (48)
57 PF13945 NST1: Salt tolerance 20.4 86 0.0019 26.8 2.4 24 116-139 101-124 (190)
58 PRK12496 hypothetical protein; 20.3 30 0.00065 28.3 -0.3 20 86-105 129-154 (164)
59 PF13376 OmdA: Bacteriocin-pro 20.2 76 0.0016 21.6 1.7 39 106-144 4-42 (63)
No 1
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=4.5e-57 Score=378.40 Aligned_cols=141 Identities=61% Similarity=1.069 Sum_probs=134.0
Q ss_pred CCC---CCCCCCCCCCccccccCCCCCCccchhhccCccCCCCCccCcchhhHHHHHHHHHhCCCCCCCCcccccccccc
Q 030308 1 MSS---NSSRRGAPKHQNRYAWKPKAGQKINEREVGGKLRPYPEITGVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKR 77 (179)
Q Consensus 1 MSS---N~~R~r~QKHQN~~aFKnn~~~K~~e~~~~~k~~~~~~~~gvCqRC~eiIeWK~kY~KYKpLt~p~KC~kC~qk 77 (179)
||| |++|+|||||||+|+|+|++++| +.++++| |++.++||||||+++||||++|+||||||++++|.+|.++
T Consensus 1 MsSq~GNVaRsRpqKHqN~f~fkndk~dk---t~q~~r~-na~~itgVCqRCkEqieWk~KY~KYKpLt~akkC~kC~~r 76 (227)
T KOG3241|consen 1 MSSQQGNVARSRPQKHQNKFAFKNDKIDK---TEQGGRF-NASEITGVCQRCKEQIEWKRKYGKYKPLTEAKKCQKCTKR 76 (227)
T ss_pred CCcccCccccccchhhccceeeccccccc---chhhcee-hhhHhhhHHHHHHHHHHHHHHhccccccchhHHHHHHHHH
Confidence 999 99999999999999999998765 4455665 6899999999999999999999999999999999999999
Q ss_pred hhhHHHHhcChhHHhhccccccccCccceecCCCchhHHHHHHHHHHHHhhchhhchhhHHHhhhhcc
Q 030308 78 AVRQAYHNLCPGCAKEQNVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERDRRILLRAVSSYT 145 (179)
Q Consensus 78 tV~~AYh~iC~~CA~~~~vCaKC~k~~~~i~~~~~~e~e~eq~ele~~lk~l~ER~RRt~lR~~~k~~ 145 (179)
+|++|||.+|++||.+..+||||+++.++|..+++.+++.|++.|++++++++||+||||||+|+|+.
T Consensus 77 ~Vk~aYH~~Cr~CA~e~~vCAKC~ks~~~i~i~d~~p~~~E~~~l~~t~~n~ser~RRt~lR~m~k~~ 144 (227)
T KOG3241|consen 77 NVKQAYHKLCRGCAKEQKVCAKCCKSVDQILIRDIYPVEAEQKLLDETIKNASERDRRTLLRAMNKDN 144 (227)
T ss_pred HHHHHHHHhcccHHHHHHHHHHHhccHHHhhhcCCCCCcHHHHHHHHHHhhhhHHHHHHHHHHHhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999965
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=6.2e-46 Score=279.74 Aligned_cols=92 Identities=51% Similarity=1.003 Sum_probs=84.9
Q ss_pred CCCCccccccCCCCCCccchhhccCccCCCCCccCcchhhHHHHHHHHHhCCCCCCCCcccccccccchhhHHHHhcChh
Q 030308 10 APKHQNRYAWKPKAGQKINEREVGGKLRPYPEITGVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPG 89 (179)
Q Consensus 10 ~QKHQN~~aFKnn~~~K~~e~~~~~k~~~~~~~~gvCqRC~eiIeWK~kY~KYKpLt~p~KC~kC~qktV~~AYh~iC~~ 89 (179)
+|||||++||+||++++. ++. +.+++++++|||+||+|+||||++|||||||++|++|++|+++||++|||+||++
T Consensus 1 ~qkhqN~~aFk~n~~~~~-~~~---~~i~~~~~~gvC~rC~~~IeWK~kY~KYKpLt~p~kC~~C~qktVk~AYh~iC~~ 76 (92)
T PF10217_consen 1 AQKHQNRFAFKNNKHDKS-EKT---KKINSLPIDGVCQRCKDIIEWKVKYGKYKPLTQPKKCNKCQQKTVKHAYHVICDP 76 (92)
T ss_pred CccccccccccCCCCCcc-HHH---HHHHhCccccccHhHHHHHHHHHHhcCcccCCCCccccccccchHHHHHHHHHHH
Confidence 599999999999999983 322 3456689999999999999999999999999999999999999999999999999
Q ss_pred HHhhccccccccCccc
Q 030308 90 CAKEQNVCAKCCSRVD 105 (179)
Q Consensus 90 CA~~~~vCaKC~k~~~ 105 (179)
||.++++|||||+++|
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=94.21 E-value=0.021 Score=43.57 Aligned_cols=42 Identities=29% Similarity=0.720 Sum_probs=32.4
Q ss_pred CCCCC-cccccccccchhhHHHHhcChhHHhhccccccccCccc
Q 030308 63 KPLSE-PAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRVD 105 (179)
Q Consensus 63 KpLt~-p~KC~kC~qktV~~AYh~iC~~CA~~~~vCaKC~k~~~ 105 (179)
-|..+ ..+|-.|.+ .|.++=|..|+.||-..++||.||++.-
T Consensus 38 nPy~~~~~~C~~CK~-~v~q~g~~YCq~CAYkkGiCamCGKki~ 80 (90)
T PF10235_consen 38 NPYAPYSSKCKICKT-KVHQPGAKYCQTCAYKKGICAMCGKKIL 80 (90)
T ss_pred CcccccCcccccccc-ccccCCCccChhhhcccCcccccCCeec
Confidence 34443 678999954 5666566689999999999999999753
No 4
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=83.95 E-value=0.26 Score=38.17 Aligned_cols=46 Identities=33% Similarity=0.723 Sum_probs=33.7
Q ss_pred HHHhCCCCCCCCcccccccccchhhHHHHhcChhHHhhccccccccCcc
Q 030308 56 KRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRV 104 (179)
Q Consensus 56 K~kY~KYKpLt~p~KC~kC~qktV~~AYh~iC~~CA~~~~vCaKC~k~~ 104 (179)
+.+|.-|- +.-.+|-.|.+. |.+.=.+.|..||-..+|||.||+..
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 44444444 456788888654 55555459999999999999999864
No 5
>PRK04023 DNA polymerase II large subunit; Validated
Probab=81.83 E-value=0.72 Score=47.96 Aligned_cols=59 Identities=25% Similarity=0.540 Sum_probs=29.2
Q ss_pred ccccccccchhhHHHHhcChhHHhhc--cccccccCccceecCCCchhHHHHHHHHHHHHhhchhhch
Q 030308 69 AKCQRCTKRAVRQAYHNLCPGCAKEQ--NVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERDR 134 (179)
Q Consensus 69 ~KC~kC~qktV~~AYh~iC~~CA~~~--~vCaKC~k~~~~i~~~~~~e~e~eq~ele~~lk~l~ER~R 134 (179)
.+|..|+..| ..+| -|+.|.... ..|++||....... ...-.....+.+++++|.+|+.
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--RCPRCGIEVEEDECEKCGREPTPYS----KRKIDLKELYDRALENLGERKN 699 (1121)
T ss_pred ccCCCCCCCC-Ccce--eCccccCcCCCCcCCCCCCCCCccc----eEEecHHHHHHHHHHHhCCcCC
Confidence 4455555442 2222 355554443 24666654332211 1111234467888888888876
No 6
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=75.82 E-value=0.98 Score=47.82 Aligned_cols=71 Identities=25% Similarity=0.582 Sum_probs=46.6
Q ss_pred CcchhhHHHHHHHHHhCCCCCCCCcccccccccchhhHHHHhcChhHHhhc-------cccccccCccceecCCCchhHH
Q 030308 44 GVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPGCAKEQ-------NVCAKCCSRVDRVIGRDLAEVE 116 (179)
Q Consensus 44 gvCqRC~eiIeWK~kY~KYKpLt~p~KC~kC~qktV~~AYh~iC~~CA~~~-------~vCaKC~k~~~~i~~~~~~e~e 116 (179)
-.|+.|-..+-| ..|..|+..+.. .| .|+.|..+. ..|+.||.+.-..... + -
T Consensus 668 rkCPkCG~~t~~-------------~fCP~CGs~te~-vy--~CPsCGaev~~des~a~~CP~CGtplv~~~~~---~-i 727 (1337)
T PRK14714 668 RRCPSCGTETYE-------------NRCPDCGTHTEP-VY--VCPDCGAEVPPDESGRVECPRCDVELTPYQRR---T-I 727 (1337)
T ss_pred EECCCCCCcccc-------------ccCcccCCcCCC-ce--eCccCCCccCCCccccccCCCCCCcccccceE---E-e
Confidence 469999865321 289999998754 33 799998863 2799999765432111 1 1
Q ss_pred HHHHHHHHHHhhchhhch
Q 030308 117 AEQKMLEAALKNARERDR 134 (179)
Q Consensus 117 ~eq~ele~~lk~l~ER~R 134 (179)
.....+..+++++.+|+.
T Consensus 728 ~~~~~~~~A~~~~g~~~~ 745 (1337)
T PRK14714 728 NVKEEYRSALENVGEREN 745 (1337)
T ss_pred cHHHHHHHHHHHhCcccc
Confidence 233467788888888764
No 7
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=72.09 E-value=1.5 Score=28.05 Aligned_cols=24 Identities=25% Similarity=0.621 Sum_probs=19.4
Q ss_pred hhHHHHhcChhHHhhcc----ccccccC
Q 030308 79 VRQAYHNLCPGCAKEQN----VCAKCCS 102 (179)
Q Consensus 79 V~~AYh~iC~~CA~~~~----vCaKC~k 102 (179)
++.=.|++|..|+.... .|+-|++
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=61.42 E-value=4.2 Score=34.05 Aligned_cols=35 Identities=20% Similarity=0.620 Sum_probs=18.7
Q ss_pred cccccccccchhhHHHHhcChhHHhhc----cccccccCc
Q 030308 68 PAKCQRCTKRAVRQAYHNLCPGCAKEQ----NVCAKCCSR 103 (179)
Q Consensus 68 p~KC~kC~qktV~~AYh~iC~~CA~~~----~vCaKC~k~ 103 (179)
|..|..|++. +......+|+.|...+ ..|+.||.+
T Consensus 5 P~~C~~C~~~-~~~~~~~lC~~C~~~l~~~~~~C~~Cg~~ 43 (227)
T PRK11595 5 PGLCWLCRMP-LALSHWGICSVCSRALRTLKTCCPQCGLP 43 (227)
T ss_pred CCcCccCCCc-cCCCCCcccHHHHhhCCcccCcCccCCCc
Confidence 4566667643 2222224677776554 347777654
No 9
>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=61.11 E-value=0.48 Score=34.76 Aligned_cols=47 Identities=28% Similarity=0.919 Sum_probs=30.2
Q ss_pred CcchhhHHHHHHHHHhCCCCCCCCcccccccccchhhHHHHhcChhHHhhccccccccC
Q 030308 44 GVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCS 102 (179)
Q Consensus 44 gvCqRC~eiIeWK~kY~KYKpLt~p~KC~kC~qktV~~AYh~iC~~CA~~~~vCaKC~k 102 (179)
..|+.|...|+|.- ....|..|++.-...| .|+.|..++.+.-.||-
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 4567999987644444 68999999998888874
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=56.87 E-value=5.1 Score=33.53 Aligned_cols=41 Identities=27% Similarity=0.581 Sum_probs=33.1
Q ss_pred cccccccchhhHHHHhcChhHHhhccccccccCccceecCCCc
Q 030308 70 KCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRVDRVIGRDL 112 (179)
Q Consensus 70 KC~kC~qktV~~AYh~iC~~CA~~~~vCaKC~k~~~~i~~~~~ 112 (179)
.|+.|+.. |+.-|+...+. ...+..|++|++..|.-+..|.
T Consensus 2 iCIeCg~~-v~~Ly~~Ys~~-~irLt~C~~C~~vaDkYiE~d~ 42 (208)
T PF04161_consen 2 ICIECGHP-VKSLYRQYSPG-NIRLTKCPNCGKVADKYIEYDN 42 (208)
T ss_pred EeccCCCc-chhhhhccCCC-cEEEeeccccCCcccceecccc
Confidence 69999888 99999988543 7778999999999887665543
No 11
>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=56.65 E-value=3.6 Score=42.22 Aligned_cols=59 Identities=24% Similarity=0.517 Sum_probs=0.0
Q ss_pred ccccccccchhhHHHHhcChhHHhhc--cccccccCccceecCCCchhHHHHHHHHHHHHhhchhhch
Q 030308 69 AKCQRCTKRAVRQAYHNLCPGCAKEQ--NVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERDR 134 (179)
Q Consensus 69 ~KC~kC~qktV~~AYh~iC~~CA~~~--~vCaKC~k~~~~i~~~~~~e~e~eq~ele~~lk~l~ER~R 134 (179)
.+|..|+..|... -.|+.|..+. ..|++|+........ ..-.....++.++++|.+|+.
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 2477777663 578888765432111 111233467788888888874
No 12
>PRK04023 DNA polymerase II large subunit; Validated
Probab=53.61 E-value=7.1 Score=41.00 Aligned_cols=44 Identities=25% Similarity=0.627 Sum_probs=32.7
Q ss_pred HhCCCCCCC-CcccccccccchhhHHHHhcChhHHh---hccccccccCccc
Q 030308 58 RYGKYKPLS-EPAKCQRCTKRAVRQAYHNLCPGCAK---EQNVCAKCCSRVD 105 (179)
Q Consensus 58 kY~KYKpLt-~p~KC~kC~qktV~~AYh~iC~~CA~---~~~vCaKC~k~~~ 105 (179)
+|++.-... ..++|..|+..+ +...|+.|.. ....|++||....
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 4789999998765
No 13
>PF13900 GVQW: Putative binding domain
Probab=53.30 E-value=4.1 Score=28.09 Aligned_cols=38 Identities=16% Similarity=0.314 Sum_probs=32.8
Q ss_pred HHHHHHhCCCCCCCCcccccccccchhhHHHHhcChhHHh
Q 030308 53 IDWKRRYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPGCAK 92 (179)
Q Consensus 53 IeWK~kY~KYKpLt~p~KC~kC~qktV~~AYh~iC~~CA~ 92 (179)
+||+ +.+..+|+++..|-..|+.....+.|+ .-+||-.
T Consensus 6 vqw~-~l~SLQp~ppg~k~~scLSlpssWDyr-~~pp~~a 43 (48)
T PF13900_consen 6 VQWH-DLSSLQPPPPGFKQFSCLSLPSSWDYR-HAPPHPA 43 (48)
T ss_pred cccc-ccCcCCccccccccccccccccccccc-cCCCCcc
Confidence 5898 999999999999999999999999998 4445543
No 14
>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=50.26 E-value=7.1 Score=25.19 Aligned_cols=24 Identities=29% Similarity=0.771 Sum_probs=19.3
Q ss_pred Hh-cChhHHhhc----cccccccCcccee
Q 030308 84 HN-LCPGCAKEQ----NVCAKCCSRVDRV 107 (179)
Q Consensus 84 h~-iC~~CA~~~----~vCaKC~k~~~~i 107 (179)
|. +|..|+... ..|+-|..+.+.|
T Consensus 22 H~~~C~~C~~~~~~~~~~CP~Cr~~i~~V 50 (50)
T PF13920_consen 22 HLCFCEECAERLLKRKKKCPICRQPIESV 50 (50)
T ss_dssp EEEEEHHHHHHHHHTTSBBTTTTBB-SEE
T ss_pred ChHHHHHHhHHhcccCCCCCcCChhhcCC
Confidence 77 899999988 8999998876543
No 15
>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=45.40 E-value=21 Score=32.65 Aligned_cols=24 Identities=25% Similarity=0.679 Sum_probs=19.1
Q ss_pred HHHhcChhHHhhc-----cccccccCccc
Q 030308 82 AYHNLCPGCAKEQ-----NVCAKCCSRVD 105 (179)
Q Consensus 82 AYh~iC~~CA~~~-----~vCaKC~k~~~ 105 (179)
=||.+|..|...+ ..|+.|+++.-
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 16
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=44.84 E-value=7.5 Score=34.22 Aligned_cols=38 Identities=24% Similarity=0.686 Sum_probs=28.7
Q ss_pred cccccccchh------hHHHHhcChhHHhh-c-cccccccCcccee
Q 030308 70 KCQRCTKRAV------RQAYHNLCPGCAKE-Q-NVCAKCCSRVDRV 107 (179)
Q Consensus 70 KC~kC~qktV------~~AYh~iC~~CA~~-~-~vCaKC~k~~~~i 107 (179)
-|++|...+- +.--|+.|.+|+.. . .+|.-|+++..+|
T Consensus 5 hCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir~i 50 (233)
T KOG4739|consen 5 HCNKCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIRII 50 (233)
T ss_pred EeccccccCCCCceeeeechhhhhhhhcccCCccccccccceeeee
Confidence 4778877764 44569999999887 3 3899999986543
No 17
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=44.02 E-value=13 Score=30.22 Aligned_cols=27 Identities=33% Similarity=0.559 Sum_probs=19.1
Q ss_pred hHHHHhcChhHHhhc------cccccccCccceec
Q 030308 80 RQAYHNLCPGCAKEQ------NVCAKCCSRVDRVI 108 (179)
Q Consensus 80 ~~AYh~iC~~CA~~~------~vCaKC~k~~~~i~ 108 (179)
--|+| |+-|...+ -+|+-||.....+.
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 45666 88888775 38999997655544
No 18
>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=42.53 E-value=11 Score=31.62 Aligned_cols=11 Identities=18% Similarity=0.552 Sum_probs=8.3
Q ss_pred cccccccCccc
Q 030308 95 NVCAKCCSRVD 105 (179)
Q Consensus 95 ~vCaKC~k~~~ 105 (179)
.-|.+||+|-.
T Consensus 69 sYC~~CGkpyP 79 (158)
T PF10083_consen 69 SYCHNCGKPYP 79 (158)
T ss_pred hhHHhCCCCCc
Confidence 36999998753
No 19
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=41.41 E-value=7.9 Score=22.63 Aligned_cols=10 Identities=20% Similarity=0.886 Sum_probs=5.6
Q ss_pred ccccccccCc
Q 030308 94 QNVCAKCCSR 103 (179)
Q Consensus 94 ~~vCaKC~k~ 103 (179)
...|+.||.+
T Consensus 16 ~~fC~~CG~~ 25 (26)
T PF13248_consen 16 AKFCPNCGAK 25 (26)
T ss_pred cccChhhCCC
Confidence 3456666653
No 20
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=40.91 E-value=14 Score=37.20 Aligned_cols=36 Identities=31% Similarity=0.788 Sum_probs=27.5
Q ss_pred ccccccccc----hhhHHHHhcChhHHhh-----ccccccccCcc
Q 030308 69 AKCQRCTKR----AVRQAYHNLCPGCAKE-----QNVCAKCCSRV 104 (179)
Q Consensus 69 ~KC~kC~qk----tV~~AYh~iC~~CA~~-----~~vCaKC~k~~ 104 (179)
-+|..|..+ -++.-||.-|.+|-.. .+-||+|+.+-
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 4677899999999865 58999999764
No 21
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=38.31 E-value=35 Score=33.22 Aligned_cols=79 Identities=10% Similarity=0.148 Sum_probs=47.2
Q ss_pred ccccccccchhhHHHHhcChhHHhhc-------cccccccCccceecCCCc-hhHHHHHHHHHHHHhh---chhhchhhH
Q 030308 69 AKCQRCTKRAVRQAYHNLCPGCAKEQ-------NVCAKCCSRVDRVIGRDL-AEVEAEQKMLEAALKN---ARERDRRIL 137 (179)
Q Consensus 69 ~KC~kC~qktV~~AYh~iC~~CA~~~-------~vCaKC~k~~~~i~~~~~-~e~e~eq~ele~~lk~---l~ER~RRt~ 137 (179)
+.|..|+.. .||-..|+.|+..+ .+|..||.+++.+....- -...+-+..|.+.+.. ++++-+..+
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 556677653 46667788887633 479999988875443211 1123334455555532 677777777
Q ss_pred HHhhhhccccccc
Q 030308 138 LRAVSSYTAILDL 150 (179)
Q Consensus 138 lR~~~k~~~~~d~ 150 (179)
++-++.+..+|.+
T Consensus 217 ~~~l~~~l~d~~I 229 (673)
T PRK00133 217 KEWLEEGLQDWDI 229 (673)
T ss_pred HHHHhCCCcccce
Confidence 8878766555443
No 22
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=38.31 E-value=38 Score=31.49 Aligned_cols=76 Identities=14% Similarity=0.253 Sum_probs=42.7
Q ss_pred ccccccccchhhHHHHhcChhHHhhc-------cccccccCccceecCCCc-hhHHHHHHHHHHHHh------hchhhch
Q 030308 69 AKCQRCTKRAVRQAYHNLCPGCAKEQ-------NVCAKCCSRVDRVIGRDL-AEVEAEQKMLEAALK------NARERDR 134 (179)
Q Consensus 69 ~KC~kC~qktV~~AYh~iC~~CA~~~-------~vCaKC~k~~~~i~~~~~-~e~e~eq~ele~~lk------~l~ER~R 134 (179)
+.|..|+.. .||-.+|..|+... ..|..||.+++....+.- -...+-+..|.+.++ .++++-+
T Consensus 137 g~cp~c~~~---~~~g~~ce~cg~~~~~~~l~~p~~~~~~~~~e~~~~~~~f~~l~~~~~~l~~~~~~~~~~~~~~~~~~ 213 (530)
T TIGR00398 137 GTCPKCGSE---DARGDHCEVCGRHLEPTELINPRCKICGAKPELRDSEHYFFRLSAFEKELEEWIRKNPESGSPASNVK 213 (530)
T ss_pred CCCCCCCCc---ccccchhhhccccCCHHHhcCCccccCCCcceEEecceEEEEhHHHHHHHHHHHHhCCccCCCcHHHH
Confidence 466677553 46777888887644 358888887765332210 112233334444444 3566666
Q ss_pred hhHHHhhhhcccc
Q 030308 135 RILLRAVSSYTAI 147 (179)
Q Consensus 135 Rt~lR~~~k~~~~ 147 (179)
.-+.+.|+.+..+
T Consensus 214 ~~~~~~l~~~l~d 226 (530)
T TIGR00398 214 NKAQNWLKGGLKD 226 (530)
T ss_pred HHHHHHHhCCCCC
Confidence 5566777764433
No 23
>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=37.34 E-value=17 Score=25.87 Aligned_cols=18 Identities=33% Similarity=1.012 Sum_probs=15.6
Q ss_pred hcChhHHhhc--cccccccC
Q 030308 85 NLCPGCAKEQ--NVCAKCCS 102 (179)
Q Consensus 85 ~iC~~CA~~~--~vCaKC~k 102 (179)
+-|.+||... ++|+.||-
T Consensus 30 TFC~~C~e~~l~~~CPNCgG 49 (57)
T PF06906_consen 30 TFCADCAETMLNGVCPNCGG 49 (57)
T ss_pred cccHHHHHHHhcCcCcCCCC
Confidence 5689999997 99999984
No 24
>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=34.60 E-value=16 Score=28.31 Aligned_cols=21 Identities=33% Similarity=0.855 Sum_probs=15.3
Q ss_pred cChhHHhhc-------cccccccCccce
Q 030308 86 LCPGCAKEQ-------NVCAKCCSRVDR 106 (179)
Q Consensus 86 iC~~CA~~~-------~vCaKC~k~~~~ 106 (179)
+|+.|++.+ -||++||.....
T Consensus 11 ~Cp~CG~kFYDLnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 11 TCPSCGAKFYDLNKDPIVCPKCGTEFPP 38 (108)
T ss_pred cCCCCcchhccCCCCCccCCCCCCccCc
Confidence 677777765 479999976544
No 25
>PF10061 DUF2299: Uncharacterized conserved protein (DUF2299); InterPro: IPR018747 Members of this family of hypothetical bacterial proteins have no known function. ; PDB: 3CXJ_D.
Probab=33.77 E-value=39 Score=27.14 Aligned_cols=34 Identities=18% Similarity=0.280 Sum_probs=25.0
Q ss_pred HHHhhchhhchhhHHHhhhhccccccccceeeeecc
Q 030308 124 AALKNARERDRRILLRAVSSYTAILDLNICVSFCQV 159 (179)
Q Consensus 124 ~~lk~l~ER~RRt~lR~~~k~~~~~d~~~~~~~~~~ 159 (179)
++|.+|++.+|+.|+..+-..- +-+++|..|.|.
T Consensus 62 ~~l~~l~~~eR~~fl~~i~~~l--l~~~vd~~~~pp 95 (138)
T PF10061_consen 62 RALRSLKPEEREEFLWEIKREL--LRMPVDFVFTPP 95 (138)
T ss_dssp HHHHHS-HHHHHHHHHHHHHHH--TTTT-EEEEE-T
T ss_pred HHHHhCCHHHHHHHHHHHHHHH--HhCCCcEEEcCC
Confidence 4599999999999999887544 555888888776
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=33.67 E-value=12 Score=33.98 Aligned_cols=61 Identities=21% Similarity=0.441 Sum_probs=32.7
Q ss_pred HHHHhcChhHHhh-----ccccc--cccCccceecCCCchhHHHHHHHHHHHHhhchhhchhhHHHhhhhcccccc
Q 030308 81 QAYHNLCPGCAKE-----QNVCA--KCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERDRRILLRAVSSYTAILD 149 (179)
Q Consensus 81 ~AYh~iC~~CA~~-----~~vCa--KC~k~~~~i~~~~~~e~e~eq~ele~~lk~l~ER~RRt~lR~~~k~~~~~d 149 (179)
.-||.+|..|... ..-|+ .|++=.--+- . .++.=|..+.|... .-|+.++|.+||+....|
T Consensus 33 ECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK~k-f--~~qtFeD~~vEkEv-----dvRkr~~r~Fnk~~~eF~ 100 (314)
T COG5220 33 ECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKIK-F--IKQTFEDITVEKEV-----DVRKRLLRAFNKEEEEFG 100 (314)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHHhc-c--cccccchhhhhhhh-----hHHHHHHHHhccchhhhC
Confidence 4799999999754 45787 8875211110 0 00000111121111 126778999999875544
No 27
>PF14149 YhfH: YhfH-like protein
Probab=33.20 E-value=18 Score=23.77 Aligned_cols=24 Identities=38% Similarity=0.880 Sum_probs=16.9
Q ss_pred Ccccccccccchh--hHHHHhcChhH
Q 030308 67 EPAKCQRCTKRAV--RQAYHNLCPGC 90 (179)
Q Consensus 67 ~p~KC~kC~qktV--~~AYh~iC~~C 90 (179)
++++|..|++.-. ..+|.+.|+.|
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 28
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=33.10 E-value=54 Score=24.47 Aligned_cols=27 Identities=15% Similarity=0.191 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHhhchhhchhhH-HHhhh
Q 030308 116 EAEQKMLEAALKNARERDRRIL-LRAVS 142 (179)
Q Consensus 116 e~eq~ele~~lk~l~ER~RRt~-lR~~~ 142 (179)
++....+.++|..|++++|+-| +++++
T Consensus 94 ~~~~~~l~~~l~~L~~~~r~ii~l~~~~ 121 (154)
T PRK06759 94 EDVEMKVKDFMSVLDEKEKYIIFERFFV 121 (154)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHhc
Confidence 3345678999999999999997 56655
No 29
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=31.41 E-value=25 Score=31.83 Aligned_cols=68 Identities=28% Similarity=0.633 Sum_probs=42.0
Q ss_pred CCCCCccCcchhhHHHHHHHHHhCCCCCCCCcccccccccc--------hhhHHHHhcChhHHhhcc---------cccc
Q 030308 37 RPYPEITGVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKR--------AVRQAYHNLCPGCAKEQN---------VCAK 99 (179)
Q Consensus 37 ~~~~~~~gvCqRC~eiIeWK~kY~KYKpLt~p~KC~kC~qk--------tV~~AYh~iC~~CA~~~~---------vCaK 99 (179)
|++......|.-| +.+=|| +-..+|+. ++|-+|..+ -.-.|+- -|+.|...+. -|-.
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 3444456789999 888888 55555554 556666544 2222333 3888888775 4667
Q ss_pred ccCccc--eecCC
Q 030308 100 CCSRVD--RVIGR 110 (179)
Q Consensus 100 C~k~~~--~i~~~ 110 (179)
|+.+.. .|+|+
T Consensus 180 C~~~v~P~~IlPP 192 (278)
T PF15135_consen 180 CGNPVYPSRILPP 192 (278)
T ss_pred CCCccCcccccCC
Confidence 876654 46655
No 30
>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=31.07 E-value=23 Score=37.26 Aligned_cols=50 Identities=20% Similarity=0.333 Sum_probs=28.6
Q ss_pred cccccccccchhhHHHHhcChhHHhhccccccccCccceecCCCchhHHHHHHHHHHHHhhchhhc
Q 030308 68 PAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRVDRVIGRDLAEVEAEQKMLEAALKNARERD 133 (179)
Q Consensus 68 p~KC~kC~qktV~~AYh~iC~~CA~~~~vCaKC~k~~~~i~~~~~~e~e~eq~ele~~lk~l~ER~ 133 (179)
-++|.+|+..|. ...|++||.+.+.+-+- ..+ -.....+.++++++.+|+
T Consensus 625 ~RKCPkCG~yTl--------------k~rCP~CG~~Te~~~pc-~~~-i~l~~~~~~A~~~lg~~~ 674 (1095)
T TIGR00354 625 IRKCPQCGKESF--------------WLKCPVCGELTEQLYYG-KRK-VDLRELYEEAIANLGEYK 674 (1095)
T ss_pred EEECCCCCcccc--------------cccCCCCCCccccccce-eEE-ecHHHHHHHHHHHhCCCC
Confidence 566666666543 35678888776543322 111 123346777788877775
No 31
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=28.69 E-value=23 Score=35.09 Aligned_cols=28 Identities=25% Similarity=0.511 Sum_probs=22.0
Q ss_pred CcccccccccchhhHHHHhcChhHHhhcccc
Q 030308 67 EPAKCQRCTKRAVRQAYHNLCPGCAKEQNVC 97 (179)
Q Consensus 67 ~p~KC~kC~qktV~~AYh~iC~~CA~~~~vC 97 (179)
..+.|+.|.+++-+.|||+-| |...+..
T Consensus 312 ~~GtcIqCs~~nC~~aYHVtC---Arrag~f 339 (669)
T COG5141 312 FGGTCIQCSYFNCTRAYHVTC---ARRAGYF 339 (669)
T ss_pred cCcceeeecccchhhhhhhhh---hhhcchh
Confidence 478999999999999999754 5544433
No 32
>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=28.69 E-value=33 Score=24.17 Aligned_cols=44 Identities=34% Similarity=0.779 Sum_probs=32.4
Q ss_pred CcchhhHHHHHHHHHhCCCCCCCCcccccccccc---------hhhHHHHhcChhHHhhcc
Q 030308 44 GVCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKR---------AVRQAYHNLCPGCAKEQN 95 (179)
Q Consensus 44 gvCqRC~eiIeWK~kY~KYKpLt~p~KC~kC~qk---------tV~~AYh~iC~~CA~~~~ 95 (179)
.-|..|+...+= ....+.+|..|+.. ....|||..|..|=.+..
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 358889874321 46788899999863 568999998888866543
No 33
>PF12773 DZR: Double zinc ribbon
Probab=28.48 E-value=24 Score=22.56 Aligned_cols=18 Identities=28% Similarity=1.027 Sum_probs=11.1
Q ss_pred cChhHHhhcc-------ccccccCc
Q 030308 86 LCPGCAKEQN-------VCAKCCSR 103 (179)
Q Consensus 86 iC~~CA~~~~-------vCaKC~k~ 103 (179)
.|+.|...+. +|++||..
T Consensus 14 fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 14 FCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred CChhhcCChhhccCCCCCCcCCcCC
Confidence 5666655554 57777764
No 34
>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=27.22 E-value=23 Score=32.90 Aligned_cols=34 Identities=21% Similarity=0.406 Sum_probs=24.2
Q ss_pred HhCCCCCCCCcccccccccchhhHHHHhcChhHHhh
Q 030308 58 RYGKYKPLSEPAKCQRCTKRAVRQAYHNLCPGCAKE 93 (179)
Q Consensus 58 kY~KYKpLt~p~KC~kC~qktV~~AYh~iC~~CA~~ 93 (179)
.-|||. +|.-.+|..+....-+.+++..|+ |...
T Consensus 234 ~~GKYh-~~~c~~C~~~~~~~~~~~~~~~Cp-CG~~ 267 (374)
T TIGR00375 234 LLGKYH-QTACEACGEPAVSEDAETACANCP-CGGR 267 (374)
T ss_pred CCCccc-hhhhcccCCcCCchhhhhcCCCCC-CCCc
Confidence 346777 677778877777777777777776 6654
No 35
>PRK00420 hypothetical protein; Validated
Probab=27.07 E-value=79 Score=24.93 Aligned_cols=19 Identities=26% Similarity=0.527 Sum_probs=12.0
Q ss_pred cChhHHhh-------ccccccccCcc
Q 030308 86 LCPGCAKE-------QNVCAKCCSRV 104 (179)
Q Consensus 86 iC~~CA~~-------~~vCaKC~k~~ 104 (179)
.|+.|+.. ..+|+-||...
T Consensus 25 ~CP~Cg~pLf~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 25 HCPVCGLPLFELKDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCcceecCCCceECCCCCCee
Confidence 45555543 34799999843
No 36
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=26.66 E-value=56 Score=22.92 Aligned_cols=29 Identities=17% Similarity=0.527 Sum_probs=20.6
Q ss_pred cccccccccchhhHHHHhcChhHHhhccccccccCccceecCC
Q 030308 68 PAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRVDRVIGR 110 (179)
Q Consensus 68 p~KC~kC~qktV~~AYh~iC~~CA~~~~vCaKC~k~~~~i~~~ 110 (179)
-.+|..|+..|. ..+|+.||.+.....|.
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 457777777665 35788999887765554
No 37
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=26.48 E-value=72 Score=25.28 Aligned_cols=25 Identities=16% Similarity=0.252 Sum_probs=20.0
Q ss_pred HHHHHHHHHhhchhhchhhH-HHhhh
Q 030308 118 EQKMLEAALKNARERDRRIL-LRAVS 142 (179)
Q Consensus 118 eq~ele~~lk~l~ER~RRt~-lR~~~ 142 (179)
+...+.++|..|++++|.-| |++++
T Consensus 132 ~~~~l~~~l~~L~~~~r~vl~l~~~~ 157 (194)
T PRK09646 132 ERERVRDCLDALTDTQRESVTLAYYG 157 (194)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHc
Confidence 34568899999999999999 55554
No 38
>PHA02683 ORF078 thioredoxin-like protein; Provisional
Probab=25.74 E-value=24 Score=26.47 Aligned_cols=18 Identities=39% Similarity=1.084 Sum_probs=11.3
Q ss_pred hCCCC-CCCCccccccccc
Q 030308 59 YGKYK-PLSEPAKCQRCTK 76 (179)
Q Consensus 59 Y~KYK-pLt~p~KC~kC~q 76 (179)
|.+|+ -|.+|.+|.+|..
T Consensus 4 y~~Y~~~LdpP~rCs~C~~ 22 (75)
T PHA02683 4 YAKYNVVLDPPRRCSKCAS 22 (75)
T ss_pred hhheeeecCCCCcchHHHH
Confidence 44454 4667788877743
No 39
>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=25.69 E-value=19 Score=25.45 Aligned_cols=23 Identities=30% Similarity=0.898 Sum_probs=14.7
Q ss_pred HhcChhHHh-----hccccccccCccce
Q 030308 84 HNLCPGCAK-----EQNVCAKCCSRVDR 106 (179)
Q Consensus 84 h~iC~~CA~-----~~~vCaKC~k~~~~ 106 (179)
|++|.-|.. ....||.||-|...
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 445555543 56899999987653
No 40
>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=25.18 E-value=22 Score=28.19 Aligned_cols=26 Identities=31% Similarity=0.613 Sum_probs=15.8
Q ss_pred CCcccccccc-cchhhHHHHhcChhHHhh
Q 030308 66 SEPAKCQRCT-KRAVRQAYHNLCPGCAKE 93 (179)
Q Consensus 66 t~p~KC~kC~-qktV~~AYh~iC~~CA~~ 93 (179)
+...+|+.|+ ...+..||. |..|..-
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 3467899998 888899996 8888543
No 41
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=24.18 E-value=22 Score=32.47 Aligned_cols=32 Identities=19% Similarity=0.085 Sum_probs=15.6
Q ss_pred HHHHHHHHHhh----chhhchhhHHHhhhhcccccc
Q 030308 118 EQKMLEAALKN----ARERDRRILLRAVSSYTAILD 149 (179)
Q Consensus 118 eq~ele~~lk~----l~ER~RRt~lR~~~k~~~~~d 149 (179)
-+.+|.+.++. ++++-+.-+.+.++++..++-
T Consensus 191 ~~~~L~~~l~~~~~~~~~~~~~~~~~~l~~~L~d~~ 226 (391)
T PF09334_consen 191 FRDQLREWLESNPDFPPPRVREIVRNWLKEGLPDLS 226 (391)
T ss_dssp GHHHHHHHHHHSTTSSHHHHHHHHHHHHHT----EE
T ss_pred hHHHHHHHHhcCCCCCChhHHHHHHHHhhcccCcee
Confidence 33456666654 355555555577776555443
No 42
>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=24.10 E-value=15 Score=23.82 Aligned_cols=30 Identities=23% Similarity=0.753 Sum_probs=22.0
Q ss_pred cccccccchhhHHHHhcChhHHhhccccccccC
Q 030308 70 KCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCS 102 (179)
Q Consensus 70 KC~kC~qktV~~AYh~iC~~CA~~~~vCaKC~k 102 (179)
.|..|++ .+.- ++.-|..|. +..+|..|-.
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 5788877 5554 666788885 6888888854
No 43
>cd00817 ValRS_core catalytic core domain of valyl-tRNA synthetases. Valine amino-acyl tRNA synthetase (ValRS) catalytic core domain. This enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=23.90 E-value=78 Score=28.60 Aligned_cols=57 Identities=18% Similarity=0.302 Sum_probs=35.5
Q ss_pred ChhHH---hhccccccccCccceecCCCc-hhHHHHHHHHHHHHhh-----chhhchhhHHHhhhh
Q 030308 87 CPGCA---KEQNVCAKCCSRVDRVIGRDL-AEVEAEQKMLEAALKN-----ARERDRRILLRAVSS 143 (179)
Q Consensus 87 C~~CA---~~~~vCaKC~k~~~~i~~~~~-~e~e~eq~ele~~lk~-----l~ER~RRt~lR~~~k 143 (179)
|+.|. .+..+|..||.+.+.+....- -...+-+.+|.+.++. ++++-|..+++-++.
T Consensus 143 c~~~~t~l~~~evc~~cg~~~~~~~~~qwf~~l~~~~~~l~~~~~~~~~~~~P~~~~~~~~~~l~~ 208 (382)
T cd00817 143 CPKLRTAISDIEVCSRSGDVIEPLLKPQWFVKVKDLAKKALEAVKEGDIKFVPERMEKRYENWLEN 208 (382)
T ss_pred cCCcCCCCCcchhcccCCCeEEEEecCeeEEehHHHHHHHHHHHhcCCcEEEChHHHHHHHHHHhh
Confidence 77776 566789999987765432210 1123344566666765 567777777777765
No 44
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=23.75 E-value=12 Score=26.38 Aligned_cols=19 Identities=37% Similarity=0.934 Sum_probs=12.9
Q ss_pred CCCccCcchhhHHHHHHHH
Q 030308 39 YPEITGVCPRCKDQIDWKR 57 (179)
Q Consensus 39 ~~~~~gvCqRC~eiIeWK~ 57 (179)
..++.|-|+.|...|.|+.
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 45
>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=23.68 E-value=78 Score=20.10 Aligned_cols=25 Identities=32% Similarity=0.327 Sum_probs=18.5
Q ss_pred HHHHHHHhhchhhchhhHHHhhhhc
Q 030308 120 KMLEAALKNARERDRRILLRAVSSY 144 (179)
Q Consensus 120 ~ele~~lk~l~ER~RRt~lR~~~k~ 144 (179)
+.++++|..|++++|.-|+-..-.|
T Consensus 2 ~~l~~~l~~L~~~~r~i~~l~~~~g 26 (54)
T PF08281_consen 2 EALQQALAQLPERQREIFLLRYFQG 26 (54)
T ss_dssp HHHHHHHHCS-HHHHHHHHHHHTS-
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4688899999999999988754444
No 46
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=23.59 E-value=39 Score=25.95 Aligned_cols=32 Identities=19% Similarity=0.432 Sum_probs=18.9
Q ss_pred CcccccccccchhhHHHHhcChhHHhhccccccccCccceec
Q 030308 67 EPAKCQRCTKRAVRQAYHNLCPGCAKEQNVCAKCCSRVDRVI 108 (179)
Q Consensus 67 ~p~KC~kC~qktV~~AYh~iC~~CA~~~~vCaKC~k~~~~i~ 108 (179)
...+|..|+...-...+ ...|+.||.+...|+
T Consensus 69 ~~~~C~~Cg~~~~~~~~----------~~~CP~Cgs~~~~i~ 100 (115)
T TIGR00100 69 VECECEDCSEEVSPEID----------LYRCPKCHGIMLQVR 100 (115)
T ss_pred cEEEcccCCCEEecCCc----------CccCcCCcCCCcEEe
Confidence 35677777744433333 346889987654444
No 47
>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=23.18 E-value=46 Score=24.20 Aligned_cols=41 Identities=27% Similarity=0.677 Sum_probs=31.8
Q ss_pred cchhhHHHHHHHHHhCCCCCCCCcccccccccch--------hhHHHHh-----cChhHHhhc
Q 030308 45 VCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTKRA--------VRQAYHN-----LCPGCAKEQ 94 (179)
Q Consensus 45 vCqRC~eiIeWK~kY~KYKpLt~p~KC~kC~qkt--------V~~AYh~-----iC~~CA~~~ 94 (179)
-|..|+.- ........+|..|+... ...|||. .|-.|=.+.
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 888886554
No 48
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=22.75 E-value=33 Score=23.30 Aligned_cols=32 Identities=19% Similarity=0.593 Sum_probs=21.4
Q ss_pred cchhhHHHHHHHHHhCCCCCCCCccccccccc
Q 030308 45 VCPRCKDQIDWKRRYGKYKPLSEPAKCQRCTK 76 (179)
Q Consensus 45 vCqRC~eiIeWK~kY~KYKpLt~p~KC~kC~q 76 (179)
+|..|-++|||=.++.=-+.-.+--+|-.|++
T Consensus 8 ~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~ 39 (46)
T PF11331_consen 8 VCSSCFELLQLPAKFSLSKKNQQKLRCGACSE 39 (46)
T ss_pred ECccHHHHHcCCCccCCCccceeEEeCCCCce
Confidence 69999999999765543333334556777754
No 49
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=22.51 E-value=56 Score=27.80 Aligned_cols=38 Identities=26% Similarity=0.600 Sum_probs=22.2
Q ss_pred CCCcccccccccchhhHHHHhcChhHHhhccc----cccccCcc
Q 030308 65 LSEPAKCQRCTKRAVRQAYHNLCPGCAKEQNV----CAKCCSRV 104 (179)
Q Consensus 65 Lt~p~KC~kC~qktV~~AYh~iC~~CA~~~~v----CaKC~k~~ 104 (179)
|..+.-|..|+..--.... +|+.|+.++.. |+.|...+
T Consensus 21 l~~~~~C~~C~~~~~~~~~--~C~~C~~~l~~~~~~~~~~~~~~ 62 (225)
T COG1040 21 LFFPGLCSGCQADLPLIGN--LCPLCGLPLSSHACRCGECLAKP 62 (225)
T ss_pred ccCCCcChhhhhchhHHHh--hhHhhhChhccccccCHHHhcCC
Confidence 3333677777554443333 78888888655 35554433
No 50
>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=22.14 E-value=66 Score=25.81 Aligned_cols=24 Identities=29% Similarity=0.322 Sum_probs=18.6
Q ss_pred HHHHHHHhhchhhchhhHHHhhhh
Q 030308 120 KMLEAALKNARERDRRILLRAVSS 143 (179)
Q Consensus 120 ~ele~~lk~l~ER~RRt~lR~~~k 143 (179)
++|+..|+.|++.+|+..+.+-+.
T Consensus 8 ~~L~~~L~~lp~~e~~e~l~~Y~e 31 (181)
T PF08006_consen 8 NELEKYLKKLPEEEREEILEYYEE 31 (181)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHH
Confidence 468888888888888888776554
No 51
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=21.61 E-value=1.2e+02 Score=23.54 Aligned_cols=25 Identities=24% Similarity=0.276 Sum_probs=20.1
Q ss_pred HHHHHHHHhhchhhchhhHH-Hhhhh
Q 030308 119 QKMLEAALKNARERDRRILL-RAVSS 143 (179)
Q Consensus 119 q~ele~~lk~l~ER~RRt~l-R~~~k 143 (179)
...|+++|..|++++|+.|+ ++++.
T Consensus 126 ~~~l~~~l~~L~~~~r~vl~l~~~~~ 151 (186)
T PRK13919 126 RTRLGRALKALSPEERRVIEVLYYQG 151 (186)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcC
Confidence 34688999999999999996 55553
No 52
>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=21.30 E-value=44 Score=31.60 Aligned_cols=33 Identities=30% Similarity=0.736 Sum_probs=22.4
Q ss_pred ccccccccchhhHHHH-----hcChhHHhhc---cccccccCcc
Q 030308 69 AKCQRCTKRAVRQAYH-----NLCPGCAKEQ---NVCAKCCSRV 104 (179)
Q Consensus 69 ~KC~kC~qktV~~AYh-----~iC~~CA~~~---~vCaKC~k~~ 104 (179)
.+|..|. +.-.|| -.|.-|.... ..|+.||...
T Consensus 223 ~~C~~C~---~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~ 263 (505)
T TIGR00595 223 LCCPNCD---VSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSED 263 (505)
T ss_pred cCCCCCC---CceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCe
Confidence 4677774 344454 3688888775 4899998754
No 53
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=21.02 E-value=1.1e+02 Score=23.87 Aligned_cols=24 Identities=25% Similarity=0.267 Sum_probs=19.0
Q ss_pred HHHHHHHhhchhhchhhH-HHhhhh
Q 030308 120 KMLEAALKNARERDRRIL-LRAVSS 143 (179)
Q Consensus 120 ~ele~~lk~l~ER~RRt~-lR~~~k 143 (179)
..+.++|..|+++.|..| |++++.
T Consensus 123 ~~l~~~l~~L~~~~r~vl~l~~~~~ 147 (189)
T PRK12515 123 AALRACLAKLSPAHREIIDLVYYHE 147 (189)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcC
Confidence 457888999999999999 555543
No 54
>PF00816 Histone_HNS: H-NS histone family Partial NMR structure.; InterPro: IPR001801 The histone-like nucleoid-structuring (H-NS) protein belongs to a family of bacterial proteins that play a role in the formation of nucleoid structure and affect gene expression under certain conditions [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2LEV_A 1HNS_A 1LR1_B 1HNR_A 1NI8_A 1OV9_A 2JR1_A 3NR7_A 2L93_A 2L92_A.
Probab=20.93 E-value=1e+02 Score=22.28 Aligned_cols=29 Identities=24% Similarity=0.425 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHhhchhhchhhHHHhhhh
Q 030308 115 VEAEQKMLEAALKNARERDRRILLRAVSS 143 (179)
Q Consensus 115 ~e~eq~ele~~lk~l~ER~RRt~lR~~~k 143 (179)
.+++..+++..+...+.++|...+..+.+
T Consensus 3 L~~~~~~l~~~~~~~~~~e~~~~~~~i~~ 31 (93)
T PF00816_consen 3 LEAQIKELEKEIEERRKQEREEAIAEIRE 31 (93)
T ss_dssp HHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455667766776666666666655544
No 55
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=20.72 E-value=19 Score=25.82 Aligned_cols=36 Identities=33% Similarity=0.798 Sum_probs=22.4
Q ss_pred cccccccccchh--hHHHHhcChhHHhh-ccccccccCc
Q 030308 68 PAKCQRCTKRAV--RQAYHNLCPGCAKE-QNVCAKCCSR 103 (179)
Q Consensus 68 p~KC~kC~qktV--~~AYh~iC~~CA~~-~~vCaKC~k~ 103 (179)
+-+|++|+..-. -.+=+-.|+.|.++ -..|++|.+-
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~ 45 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQ 45 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhc
Confidence 446777764332 22455578888777 6777777653
No 56
>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=20.56 E-value=23 Score=23.84 Aligned_cols=32 Identities=22% Similarity=0.747 Sum_probs=23.5
Q ss_pred cccccccchhhHHHHhcChhHHh-hccccccccC
Q 030308 70 KCQRCTKRAVRQAYHNLCPGCAK-EQNVCAKCCS 102 (179)
Q Consensus 70 KC~kC~qktV~~AYh~iC~~CA~-~~~vCaKC~k 102 (179)
+|..|++.+|. -.+--|..|.. ...+|..|-.
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 55666888875 6888888843
No 57
>PF13945 NST1: Salt tolerance down-regulator
Probab=20.39 E-value=86 Score=26.84 Aligned_cols=24 Identities=25% Similarity=0.450 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHhhchhhchhhHHH
Q 030308 116 EAEQKMLEAALKNARERDRRILLR 139 (179)
Q Consensus 116 e~eq~ele~~lk~l~ER~RRt~lR 139 (179)
++|+..|.+.-.+|.|-+||.||+
T Consensus 101 ~eEre~LkeFW~SL~eeERr~LVk 124 (190)
T PF13945_consen 101 QEEREKLKEFWESLSEEERRSLVK 124 (190)
T ss_pred HHHHHHHHHHHHccCHHHHHHHHH
Confidence 456667888889999999999886
No 58
>PRK12496 hypothetical protein; Provisional
Probab=20.29 E-value=30 Score=28.25 Aligned_cols=20 Identities=45% Similarity=1.046 Sum_probs=14.0
Q ss_pred cChhHHhhc------cccccccCccc
Q 030308 86 LCPGCAKEQ------NVCAKCCSRVD 105 (179)
Q Consensus 86 iC~~CA~~~------~vCaKC~k~~~ 105 (179)
.|..|.... ..|+.||.+..
T Consensus 129 ~C~gC~~~~~~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 129 VCKGCKKKYPEDYPDDVCEICGSPVK 154 (164)
T ss_pred ECCCCCccccCCCCCCcCCCCCChhh
Confidence 577777655 46999997654
No 59
>PF13376 OmdA: Bacteriocin-protection, YdeI or OmpD-Associated
Probab=20.23 E-value=76 Score=21.64 Aligned_cols=39 Identities=15% Similarity=0.118 Sum_probs=26.1
Q ss_pred eecCCCchhHHHHHHHHHHHHhhchhhchhhHHHhhhhc
Q 030308 106 RVIGRDLAEVEAEQKMLEAALKNARERDRRILLRAVSSY 144 (179)
Q Consensus 106 ~i~~~~~~e~e~eq~ele~~lk~l~ER~RRt~lR~~~k~ 144 (179)
.++|.+..+.-++..+..+....|+.-.||.+++.+...
T Consensus 4 ~~vP~dl~~aL~~~p~a~~~f~~l~~~~rr~~i~wi~~A 42 (63)
T PF13376_consen 4 VEVPEDLEAALEANPEAKEFFESLTPSYRREYIRWINSA 42 (63)
T ss_pred CCCCHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHc
Confidence 344444433333444566778889999999999988753
Done!