Query psy7787
Match_columns 463
No_of_seqs 137 out of 162
Neff 1.8
Searched_HMMs 46136
Date Fri Aug 16 18:50:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7787.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7787hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03660 PHF5: PHF5-like prote 100.0 1.5E-45 3.2E-50 312.2 -0.6 83 1-83 1-89 (106)
2 KOG1705|consensus 100.0 3.2E-44 6.8E-49 303.5 4.5 83 1-83 1-88 (110)
3 PF03660 PHF5: PHF5-like prote 100.0 1.9E-42 4E-47 293.3 -1.6 91 317-409 11-102 (106)
4 KOG1705|consensus 100.0 4.5E-41 9.8E-46 284.4 2.1 90 317-408 11-100 (110)
5 PRK11595 DNA utilization prote 82.7 0.64 1.4E-05 42.6 1.4 49 334-383 6-56 (227)
6 PRK11595 DNA utilization prote 82.2 0.68 1.5E-05 42.5 1.3 49 23-72 6-56 (227)
7 PF07191 zinc-ribbons_6: zinc- 80.8 0.44 9.5E-06 39.2 -0.3 62 334-409 2-70 (70)
8 PF12773 DZR: Double zinc ribb 78.6 1.2 2.6E-05 31.9 1.4 44 336-381 1-49 (50)
9 COG1107 Archaea-specific RecJ- 77.8 1.5 3.3E-05 48.0 2.4 64 2-75 42-106 (715)
10 PF12773 DZR: Double zinc ribb 77.7 1.3 2.8E-05 31.8 1.3 44 25-70 1-49 (50)
11 PRK14559 putative protein seri 77.7 1.5 3.2E-05 47.3 2.3 48 334-383 2-49 (645)
12 PF04216 FdhE: Protein involve 76.6 0.81 1.7E-05 43.4 -0.0 38 334-371 173-221 (290)
13 PRK14559 putative protein seri 74.9 1.9 4.1E-05 46.5 2.2 47 23-71 2-48 (645)
14 PF14446 Prok-RING_1: Prokaryo 73.2 4.4 9.5E-05 32.1 3.3 37 334-370 6-50 (54)
15 PF14446 Prok-RING_1: Prokaryo 72.6 3.8 8.2E-05 32.4 2.8 38 22-59 5-50 (54)
16 PRK05580 primosome assembly pr 71.7 2.6 5.6E-05 44.9 2.3 50 321-370 376-430 (679)
17 PRK05580 primosome assembly pr 70.6 2.4 5.2E-05 45.1 1.8 49 11-59 377-430 (679)
18 PF04216 FdhE: Protein involve 67.5 1.6 3.5E-05 41.4 -0.3 51 23-73 173-247 (290)
19 PRK14714 DNA polymerase II lar 66.1 4.4 9.6E-05 47.4 2.8 43 327-372 668-720 (1337)
20 PRK14714 DNA polymerase II lar 63.1 5.3 0.00011 46.8 2.6 7 64-70 709-715 (1337)
21 PF07191 zinc-ribbons_6: zinc- 60.3 2.1 4.5E-05 35.3 -0.8 60 23-96 2-68 (70)
22 PRK14873 primosome assembly pr 58.9 5.4 0.00012 43.1 1.7 49 11-59 379-431 (665)
23 TIGR00595 priA primosomal prot 56.9 6 0.00013 40.8 1.6 49 11-59 209-262 (505)
24 COG1592 Rubrerythrin [Energy p 56.3 6.3 0.00014 36.6 1.5 22 38-59 134-158 (166)
25 PF08274 PhnA_Zn_Ribbon: PhnA 56.0 4 8.6E-05 28.8 0.1 24 23-46 3-27 (30)
26 PRK14873 primosome assembly pr 55.5 7.7 0.00017 41.9 2.2 50 321-370 378-431 (665)
27 COG1592 Rubrerythrin [Energy p 55.0 6.8 0.00015 36.4 1.5 23 349-371 134-159 (166)
28 KOG3507|consensus 54.6 9 0.0002 31.4 1.9 30 344-382 15-44 (62)
29 PRK03564 formate dehydrogenase 54.4 12 0.00026 37.5 3.2 37 333-369 187-234 (309)
30 PF00628 PHD: PHD-finger; Int 53.9 14 0.00029 26.3 2.6 43 335-382 1-49 (51)
31 TIGR00595 priA primosomal prot 53.3 9.1 0.0002 39.6 2.2 50 321-370 208-262 (505)
32 PF10571 UPF0547: Uncharacteri 53.1 7.2 0.00016 26.5 1.0 22 335-358 2-23 (26)
33 PRK04023 DNA polymerase II lar 51.8 7 0.00015 45.1 1.2 36 37-73 625-660 (1121)
34 PRK13130 H/ACA RNA-protein com 50.8 9.2 0.0002 30.2 1.4 27 36-62 3-29 (56)
35 PRK04023 DNA polymerase II lar 50.7 7.5 0.00016 44.8 1.2 42 348-391 625-666 (1121)
36 KOG3507|consensus 50.0 12 0.00026 30.7 1.9 30 33-71 15-44 (62)
37 PRK13130 H/ACA RNA-protein com 49.6 10 0.00022 30.0 1.4 26 347-372 3-28 (56)
38 COG1198 PriA Primosomal protei 49.5 10 0.00023 41.8 2.0 49 11-59 431-484 (730)
39 PRK03564 formate dehydrogenase 46.8 21 0.00046 35.8 3.5 51 22-72 187-260 (309)
40 PRK10220 hypothetical protein; 46.7 12 0.00025 33.5 1.5 28 24-51 5-33 (111)
41 COG1107 Archaea-specific RecJ- 46.4 14 0.0003 41.0 2.3 54 325-386 52-106 (715)
42 COG1198 PriA Primosomal protei 46.2 14 0.00031 40.8 2.5 83 322-414 431-518 (730)
43 PF03833 PolC_DP2: DNA polymer 45.7 6.9 0.00015 44.3 0.0 35 37-72 654-688 (900)
44 TIGR00686 phnA alkylphosphonat 45.0 11 0.00024 33.5 1.2 28 24-51 4-32 (109)
45 PF03833 PolC_DP2: DNA polymer 39.3 9.9 0.00021 43.1 0.0 31 350-381 656-686 (900)
46 cd00729 rubredoxin_SM Rubredox 37.5 19 0.00041 25.4 1.2 22 38-59 2-27 (34)
47 KOG0825|consensus 37.4 15 0.00033 41.9 1.0 60 23-89 216-279 (1134)
48 PF07649 C1_3: C1-like domain; 36.8 22 0.00048 23.8 1.4 11 36-46 13-23 (30)
49 COG4068 Uncharacterized protei 34.8 11 0.00023 31.1 -0.4 31 361-391 8-40 (64)
50 cd00350 rubredoxin_like Rubred 34.6 21 0.00044 24.7 1.0 21 39-59 2-26 (33)
51 smart00661 RPOL9 RNA polymeras 33.6 33 0.00072 24.4 2.0 26 335-360 2-31 (52)
52 PF08271 TF_Zn_Ribbon: TFIIB z 33.5 24 0.00053 25.2 1.2 22 335-356 2-26 (43)
53 PF03107 C1_2: C1 domain; Int 32.3 40 0.00087 22.8 2.1 22 335-357 2-23 (30)
54 KOG1813|consensus 32.0 26 0.00055 35.9 1.5 36 24-59 243-284 (313)
55 KOG1813|consensus 31.8 24 0.00053 36.1 1.4 35 335-369 243-283 (313)
56 COG1034 NuoG NADH dehydrogenas 30.4 31 0.00066 38.1 1.9 114 325-458 87-221 (693)
57 PHA00626 hypothetical protein 29.6 32 0.00069 28.1 1.4 25 335-359 2-33 (59)
58 KOG0825|consensus 28.6 27 0.00058 40.1 1.1 158 234-429 140-325 (1134)
59 PF07282 OrfB_Zn_ribbon: Putat 28.2 41 0.00089 25.4 1.8 24 335-358 30-55 (69)
60 PF09963 DUF2197: Uncharacteri 28.0 21 0.00045 28.6 0.1 8 335-342 4-11 (56)
61 PF08792 A2L_zn_ribbon: A2L zi 26.6 25 0.00054 25.0 0.3 23 361-383 3-29 (33)
62 PRK10220 hypothetical protein; 25.9 40 0.00087 30.3 1.5 28 335-362 5-33 (111)
63 TIGR01562 FdhE formate dehydro 25.7 50 0.0011 33.1 2.3 38 333-370 184-233 (305)
64 COG2260 Predicted Zn-ribbon RN 25.7 28 0.00061 28.3 0.5 25 348-372 4-28 (59)
65 PRK05766 rps14P 30S ribosomal 25.2 45 0.00099 25.9 1.5 29 44-72 8-40 (52)
66 smart00249 PHD PHD zinc finger 24.9 64 0.0014 21.1 2.0 44 25-70 2-47 (47)
67 PRK14810 formamidopyrimidine-D 24.8 31 0.00067 33.1 0.7 26 46-71 240-271 (272)
68 COG2260 Predicted Zn-ribbon RN 24.8 29 0.00062 28.3 0.4 26 37-62 4-29 (59)
69 PRK00432 30S ribosomal protein 24.2 42 0.00091 25.6 1.2 24 336-359 23-47 (50)
70 PF13453 zf-TFIIB: Transcripti 24.2 59 0.0013 23.1 1.9 21 335-355 1-25 (41)
71 PRK14289 chaperone protein Dna 24.0 34 0.00073 34.1 0.8 22 361-382 197-218 (386)
72 PRK14282 chaperone protein Dna 23.5 37 0.00079 33.8 0.9 9 326-334 152-160 (369)
73 PRK14282 chaperone protein Dna 23.1 37 0.0008 33.7 0.9 22 50-71 195-216 (369)
74 TIGR00686 phnA alkylphosphonat 23.1 42 0.00092 30.0 1.1 27 335-361 4-31 (109)
75 PF10235 Cript: Microtubule-as 23.0 43 0.00092 28.8 1.1 25 46-70 40-65 (90)
76 PRK11823 DNA repair protein Ra 22.9 49 0.0011 33.8 1.7 28 36-63 5-34 (446)
77 PTZ00218 40S ribosomal protein 22.9 56 0.0012 26.1 1.7 28 45-72 11-42 (54)
78 TIGR00570 cdk7 CDK-activating 22.4 51 0.0011 33.5 1.7 39 333-371 3-53 (309)
79 PRK06393 rpoE DNA-directed RNA 22.4 39 0.00083 27.7 0.7 26 39-64 6-31 (64)
80 PF02132 RecR: RecR protein; 22.3 16 0.00035 26.3 -1.3 26 35-60 14-39 (41)
81 COG4098 comFA Superfamily II D 22.2 42 0.0009 35.7 1.1 16 375-390 60-75 (441)
82 TIGR01384 TFS_arch transcripti 22.2 61 0.0013 26.4 1.8 23 335-357 2-24 (104)
83 PRK14811 formamidopyrimidine-D 22.2 39 0.00084 32.5 0.8 28 46-73 231-264 (269)
84 smart00547 ZnF_RBZ Zinc finger 21.7 54 0.0012 20.9 1.1 20 40-59 4-25 (26)
85 TIGR00354 polC DNA polymerase, 21.5 50 0.0011 38.5 1.5 31 37-68 624-654 (1095)
86 TIGR00570 cdk7 CDK-activating 21.2 55 0.0012 33.3 1.6 20 130-149 90-109 (309)
87 PF12025 Phage_C: Phage protei 21.2 30 0.00065 28.8 -0.2 22 132-153 30-51 (68)
88 COG4098 comFA Superfamily II D 21.1 80 0.0017 33.6 2.8 17 64-80 60-76 (441)
89 TIGR02349 DnaJ_bact chaperone 20.7 48 0.001 32.5 1.1 51 15-71 143-207 (354)
90 PRK14284 chaperone protein Dna 20.5 51 0.0011 33.1 1.3 51 15-71 158-218 (391)
91 KOG0801|consensus 20.5 58 0.0013 31.5 1.6 33 296-346 119-151 (205)
92 PRK00432 30S ribosomal protein 20.4 55 0.0012 25.0 1.1 26 24-49 22-48 (50)
93 PF09986 DUF2225: Uncharacteri 20.4 78 0.0017 29.5 2.4 8 335-342 7-14 (214)
94 PRK14289 chaperone protein Dna 20.4 43 0.00094 33.4 0.7 22 50-71 197-218 (386)
95 KOG0978|consensus 20.2 12 0.00027 41.3 -3.3 38 24-63 645-692 (698)
96 PRK14284 chaperone protein Dna 20.2 54 0.0012 32.9 1.3 51 326-382 158-218 (391)
97 KOG1100|consensus 20.1 44 0.00096 31.5 0.7 23 327-349 180-205 (207)
98 TIGR00615 recR recombination p 20.0 55 0.0012 31.2 1.3 34 35-68 50-83 (195)
99 TIGR02349 DnaJ_bact chaperone 20.0 52 0.0011 32.2 1.2 12 423-434 274-285 (354)
No 1
>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=100.00 E-value=1.5e-45 Score=312.16 Aligned_cols=83 Identities=67% Similarity=1.306 Sum_probs=56.1
Q ss_pred CCCCCCcccc-----hhhhhhccccCCCccccccCCCCccceeEecCCCCCCCcCCeeEEeC-CCCccccccchhhhhcc
Q psy7787 1 MELFHPTIFH-----ISAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICG-GPGVSDAYYCKECTIQE 74 (463)
Q Consensus 1 MSRHqpDLIm-----Gt~IGrLCeKCDGKCPICDSyVRP~tkVRICDeCSfGs~~~RCIICG-~pGvsDAYYC~ECv~LE 74 (463)
|||||||||| |++||+||++||||||||||||||+++|||||+||||++++|||||| ++|++|||||+||++||
T Consensus 1 MsrH~~DLvmC~KqpG~~iG~lC~kCdGkCpiCDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~~g~sdAYYC~eC~~lE 80 (106)
T PF03660_consen 1 MSRHQPDLVMCRKQPGTAIGRLCEKCDGKCPICDSYVRPCTKVRICDECSFGSLQGRCIICGSGPGVSDAYYCWECVRLE 80 (106)
T ss_dssp -SS--TT--B----EEEEE-EE-GGGTT--TTT-------EE-EEEHHHHTSSTTSB-TTTSSSB--EE-EE-HHHHHHT
T ss_pred CCccChhHhhhccCCcchhhhhhhhcCCcccccCCccCCcceEEECCcCCCCCcCceEEEecCCCCcccceehhhhHhhh
Confidence 9999999999 99999999999999999999999999999999999999999999999 88999999999999999
Q ss_pred cccCCCccc
Q psy7787 75 KDVSTVEPQ 83 (463)
Q Consensus 75 KDRDGc~~~ 83 (463)
|||||||.-
T Consensus 81 KdRDGCPri 89 (106)
T PF03660_consen 81 KDRDGCPRI 89 (106)
T ss_dssp STTS----B
T ss_pred ccccCCcee
Confidence 999999864
No 2
>KOG1705|consensus
Probab=100.00 E-value=3.2e-44 Score=303.49 Aligned_cols=83 Identities=78% Similarity=1.433 Sum_probs=81.6
Q ss_pred CCCCCCcccc-----hhhhhhccccCCCccccccCCCCccceeEecCCCCCCCcCCeeEEeCCCCccccccchhhhhccc
Q psy7787 1 MELFHPTIFH-----ISAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSDAYYCKECTIQEK 75 (463)
Q Consensus 1 MSRHqpDLIm-----Gt~IGrLCeKCDGKCPICDSyVRP~tkVRICDeCSfGs~~~RCIICG~pGvsDAYYC~ECv~LEK 75 (463)
|||||||||| |+++|+||||||||||||||||||+|+|||||+|+||+++++|||||++|++||||||||+++||
T Consensus 1 MskHhpDLi~CrkQPGi~~G~LCEkCDgkC~ICDS~VRP~tlVRiC~eC~~Gs~q~~ciic~~~gV~d~~yc~ectr~ek 80 (110)
T KOG1705|consen 1 MAKHHPDLIMCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGVGVSDAYYCKECTRQEK 80 (110)
T ss_pred CCCcCCcEEEEecCCCchhhhhHHhcCCcccccccccccceeeeeehhcCCccccCceEEecCCcccchHHHHHHHhhcc
Confidence 9999999999 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCccc
Q psy7787 76 DVSTVEPQ 83 (463)
Q Consensus 76 DRDGc~~~ 83 (463)
||||||.-
T Consensus 81 drdgCpri 88 (110)
T KOG1705|consen 81 DRDGCPKI 88 (110)
T ss_pred ccccChhh
Confidence 99999863
No 3
>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=100.00 E-value=1.9e-42 Score=293.30 Aligned_cols=91 Identities=62% Similarity=1.258 Sum_probs=57.6
Q ss_pred CCCCCcchhccccccCCCccccccCCCCccceeEecCCCCCCCcCCeeEEeC-CCCccccccchhhhhccccccccccee
Q psy7787 317 HSHSLGLTIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICG-GPGVSDAYYCKECTIQEKDVSTVEPQF 395 (463)
Q Consensus 317 ~~~~PGt~IGrLCeKCDGKCPICDSyVRP~tkVRICdeCSfGs~~~RCIICG-~pGvsdAYYC~ECvrLEKDRD~c~~~~ 395 (463)
=+||||++||+||+|||||||||||||||+++|||||+||||++++|||||| ++|++|||||+||++||||||+| |.+
T Consensus 11 C~KqpG~~iG~lC~kCdGkCpiCDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~~g~sdAYYC~eC~~lEKdRDGC-Pri 89 (106)
T PF03660_consen 11 CRKQPGTAIGRLCEKCDGKCPICDSYVRPCTKVRICDECSFGSLQGRCIICGSGPGVSDAYYCWECVRLEKDRDGC-PRI 89 (106)
T ss_dssp ----EEEEE-EE-GGGTT--TTT-------EE-EEEHHHHTSSTTSB-TTTSSSB--EE-EE-HHHHHHTSTTS-----B
T ss_pred hccCCcchhhhhhhhcCCcccccCCccCCcceEEECCcCCCCCcCceEEEecCCCCcccceehhhhHhhhccccCC-cee
Confidence 4799999999999999999999999999999999999999999999999999 89999999999999999999999 999
Q ss_pred eeeccccceeEEee
Q psy7787 396 YELIGTKGCSIVFQ 409 (463)
Q Consensus 396 ~~l~~~~~~s~~~~ 409 (463)
+|+ |+.+....|.
T Consensus 90 iN~-Gs~r~d~~~~ 102 (106)
T PF03660_consen 90 INV-GSSRTDRFYE 102 (106)
T ss_dssp -S--SS-SSTT---
T ss_pred Eec-cchhhhHHHH
Confidence 999 8776654443
No 4
>KOG1705|consensus
Probab=100.00 E-value=4.5e-41 Score=284.36 Aligned_cols=90 Identities=72% Similarity=1.413 Sum_probs=85.1
Q ss_pred CCCCCcchhccccccCCCccccccCCCCccceeEecCCCCCCCcCCeeEEeCCCCccccccchhhhhcccccccccceee
Q psy7787 317 HSHSLGLTIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSDAYYCKECTIQEKDVSTVEPQFY 396 (463)
Q Consensus 317 ~~~~PGt~IGrLCeKCDGKCPICDSyVRP~tkVRICdeCSfGs~~~RCIICG~pGvsdAYYC~ECvrLEKDRD~c~~~~~ 396 (463)
-+||||++||+||||||||||||||||||+++|||||+|+||+++++|||||++|++||||||||+++|||||+| |.+.
T Consensus 11 CrkQPGi~~G~LCEkCDgkC~ICDS~VRP~tlVRiC~eC~~Gs~q~~ciic~~~gV~d~~yc~ectr~ekdrdgC-pri~ 89 (110)
T KOG1705|consen 11 CRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGVGVSDAYYCKECTRQEKDRDGC-PKIV 89 (110)
T ss_pred EecCCCchhhhhHHhcCCcccccccccccceeeeeehhcCCccccCceEEecCCcccchHHHHHHHhhccccccC-hhhh
Confidence 479999999999999999999999999999999999999999999999999999999999999999999999999 9999
Q ss_pred eeccccceeEEe
Q psy7787 397 ELIGTKGCSIVF 408 (463)
Q Consensus 397 ~l~~~~~~s~~~ 408 (463)
|| ||.+..+-|
T Consensus 90 nl-gS~r~d~~~ 100 (110)
T KOG1705|consen 90 NL-GSSKTDLFY 100 (110)
T ss_pred hc-ccccchHHH
Confidence 99 776665433
No 5
>PRK11595 DNA utilization protein GntX; Provisional
Probab=82.71 E-value=0.64 Score=42.61 Aligned_cols=49 Identities=24% Similarity=0.580 Sum_probs=33.8
Q ss_pred CccccccCCCCccceeEecCCCCCC--CcCCeeEEeCCCCccccccchhhhh
Q psy7787 334 GKCVICDSYVRPCTLVRICDECNYG--SYQGRCVICGGPGVSDAYYCKECTI 383 (463)
Q Consensus 334 GKCPICDSyVRP~tkVRICdeCSfG--s~~~RCIICG~pGvsdAYYC~ECvr 383 (463)
.+|++|+..+.+. +..||+.|.-. .....|..||.+.....+.|.+|..
T Consensus 6 ~~C~~C~~~~~~~-~~~lC~~C~~~l~~~~~~C~~Cg~~~~~~~~~C~~C~~ 56 (227)
T PRK11595 6 GLCWLCRMPLALS-HWGICSVCSRALRTLKTCCPQCGLPATHPHLPCGRCLQ 56 (227)
T ss_pred CcCccCCCccCCC-CCcccHHHHhhCCcccCcCccCCCcCCCCCCCcHHHHc
Confidence 4799999776432 23499999522 2346899999865444567999954
No 6
>PRK11595 DNA utilization protein GntX; Provisional
Probab=82.15 E-value=0.68 Score=42.47 Aligned_cols=49 Identities=24% Similarity=0.570 Sum_probs=33.8
Q ss_pred CccccccCCCCccceeEecCCCCC--CCcCCeeEEeCCCCccccccchhhhh
Q psy7787 23 GKCVICDSYVRPCTLVRICDECNY--GSYQGRCVICGGPGVSDAYYCKECTI 72 (463)
Q Consensus 23 GKCPICDSyVRP~tkVRICDeCSf--Gs~~~RCIICG~pGvsDAYYC~ECv~ 72 (463)
.+|++|+-.+.+. ...||+.|.- ......|..||.+.....+.|.+|..
T Consensus 6 ~~C~~C~~~~~~~-~~~lC~~C~~~l~~~~~~C~~Cg~~~~~~~~~C~~C~~ 56 (227)
T PRK11595 6 GLCWLCRMPLALS-HWGICSVCSRALRTLKTCCPQCGLPATHPHLPCGRCLQ 56 (227)
T ss_pred CcCccCCCccCCC-CCcccHHHHhhCCcccCcCccCCCcCCCCCCCcHHHHc
Confidence 5799999776432 2349999952 22246899999875444567999944
No 7
>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=80.84 E-value=0.44 Score=39.17 Aligned_cols=62 Identities=26% Similarity=0.522 Sum_probs=34.6
Q ss_pred CccccccCCCCccceeEecCCCCCC-CcCCeeEEeCCCC------ccccccchhhhhcccccccccceeeeeccccceeE
Q psy7787 334 GKCVICDSYVRPCTLVRICDECNYG-SYQGRCVICGGPG------VSDAYYCKECTIQEKDVSTVEPQFYELIGTKGCSI 406 (463)
Q Consensus 334 GKCPICDSyVRP~tkVRICdeCSfG-s~~~RCIICG~pG------vsdAYYC~ECvrLEKDRD~c~~~~~~l~~~~~~s~ 406 (463)
-.||.|+..+.+....+.|+.|.-- .....|.-||.+- ...-|.|..| -+||+.+|..|
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c--------------~gLiSKkrV~f 67 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHC--------------HGLISKKRVRF 67 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTT--------------T-EE-TTTSEE
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcccceeeccC--------------CceeecceEEE
Confidence 3688999888888888888888743 2244555555432 1345777765 26888888888
Q ss_pred Eee
Q psy7787 407 VFQ 409 (463)
Q Consensus 407 ~~~ 409 (463)
+||
T Consensus 68 ~~q 70 (70)
T PF07191_consen 68 EFQ 70 (70)
T ss_dssp EE-
T ss_pred EeC
Confidence 875
No 8
>PF12773 DZR: Double zinc ribbon
Probab=78.61 E-value=1.2 Score=31.94 Aligned_cols=44 Identities=23% Similarity=0.619 Sum_probs=28.7
Q ss_pred cccccCCCCccceeEecCCCCCCCc-----CCeeEEeCCCCccccccchhh
Q psy7787 336 CVICDSYVRPCTLVRICDECNYGSY-----QGRCVICGGPGVSDAYYCKEC 381 (463)
Q Consensus 336 CPICDSyVRP~tkVRICdeCSfGs~-----~~RCIICG~pGvsdAYYC~EC 381 (463)
||.|...+.+. .+.|..|+.--. ...|..||.....+|-||..|
T Consensus 1 Cp~Cg~~~~~~--~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~C 49 (50)
T PF12773_consen 1 CPHCGTPNPDD--AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPNC 49 (50)
T ss_pred CCCcCCcCCcc--ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCcc
Confidence 55666555444 466666665322 346888888777788888877
No 9
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=77.76 E-value=1.5 Score=47.96 Aligned_cols=64 Identities=28% Similarity=0.449 Sum_probs=46.7
Q ss_pred CCCCCcccchhhhhhccccCCCccccccCCCCccceeEecCCCCCCCcCCeeEEeCCC-Cccccccchhhhhccc
Q psy7787 2 ELFHPTIFHISAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGP-GVSDAYYCKECTIQEK 75 (463)
Q Consensus 2 SRHqpDLImGt~IGrLCeKCDGKCPICDSyVRP~tkVRICDeCSfGs~~~RCIICG~p-GvsDAYYC~ECv~LEK 75 (463)
++-++|+.++. +-.|++|+||= .-+.-.-|++|+=.-.-.+|-+||.. ....-|.|.||-+.+|
T Consensus 42 ~~~~~D~~~~~--~~pc~~c~gkG--------~V~v~~~c~~c~G~gkv~~c~~cG~~~~~~~~~lc~~c~~~~~ 106 (715)
T COG1107 42 SRETVDLFASF--EIPCPKCRGKG--------TVTVYDTCPECGGTGKVLTCDICGDIIVPWEEGLCPECRRKPK 106 (715)
T ss_pred hhccccccccC--CCCCCeeccce--------eEEEEeecccCCCceeEEeeccccceecCcccccChhHhhCCc
Confidence 46677777643 33799999873 23455678999866667899999975 4455568999999888
No 10
>PF12773 DZR: Double zinc ribbon
Probab=77.66 E-value=1.3 Score=31.78 Aligned_cols=44 Identities=23% Similarity=0.619 Sum_probs=29.4
Q ss_pred cccccCCCCccceeEecCCCCCCCc-----CCeeEEeCCCCccccccchhh
Q psy7787 25 CVICDSYVRPCTLVRICDECNYGSY-----QGRCVICGGPGVSDAYYCKEC 70 (463)
Q Consensus 25 CPICDSyVRP~tkVRICDeCSfGs~-----~~RCIICG~pGvsDAYYC~EC 70 (463)
||.|...+.+. ++.|..|+.--. ...|..||.+...+|-||..|
T Consensus 1 Cp~Cg~~~~~~--~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~C 49 (50)
T PF12773_consen 1 CPHCGTPNPDD--AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPNC 49 (50)
T ss_pred CCCcCCcCCcc--ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCcc
Confidence 56666655544 566777765333 346888888877778888877
No 11
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=77.65 E-value=1.5 Score=47.32 Aligned_cols=48 Identities=23% Similarity=0.471 Sum_probs=38.8
Q ss_pred CccccccCCCCccceeEecCCCCCCCcCCeeEEeCCCCccccccchhhhh
Q psy7787 334 GKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSDAYYCKECTI 383 (463)
Q Consensus 334 GKCPICDSyVRP~tkVRICdeCSfGs~~~RCIICG~pGvsdAYYC~ECvr 383 (463)
.+||-|...+.+.. +-|.+|+..-....|.-||.+-..+|-+|.+|..
T Consensus 2 ~~Cp~Cg~~n~~~a--kFC~~CG~~l~~~~Cp~CG~~~~~~~~fC~~CG~ 49 (645)
T PRK14559 2 LICPQCQFENPNNN--RFCQKCGTSLTHKPCPQCGTEVPVDEAHCPNCGA 49 (645)
T ss_pred CcCCCCCCcCCCCC--ccccccCCCCCCCcCCCCCCCCCcccccccccCC
Confidence 37999998876554 5899997765457899999988889999999943
No 12
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=76.61 E-value=0.81 Score=43.41 Aligned_cols=38 Identities=26% Similarity=0.572 Sum_probs=19.4
Q ss_pred CccccccCC-----CCcc----ceeEecCCCCCC--CcCCeeEEeCCCC
Q psy7787 334 GKCVICDSY-----VRPC----TLVRICDECNYG--SYQGRCVICGGPG 371 (463)
Q Consensus 334 GKCPICDSy-----VRP~----tkVRICdeCSfG--s~~~RCIICG~pG 371 (463)
|.||+|.|. +++. .+.-.|..|++. ..+.+|..||+..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~ 221 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTD 221 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---S
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCC
Confidence 889999987 4443 488899999975 4478899999743
No 13
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=74.93 E-value=1.9 Score=46.51 Aligned_cols=47 Identities=23% Similarity=0.487 Sum_probs=37.9
Q ss_pred CccccccCCCCccceeEecCCCCCCCcCCeeEEeCCCCccccccchhhh
Q psy7787 23 GKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSDAYYCKECT 71 (463)
Q Consensus 23 GKCPICDSyVRP~tkVRICDeCSfGs~~~RCIICG~pGvsDAYYC~ECv 71 (463)
.+||-|...+.+.. +-|.+|+..-....|.-||.+-..+|-+|.+|.
T Consensus 2 ~~Cp~Cg~~n~~~a--kFC~~CG~~l~~~~Cp~CG~~~~~~~~fC~~CG 48 (645)
T PRK14559 2 LICPQCQFENPNNN--RFCQKCGTSLTHKPCPQCGTEVPVDEAHCPNCG 48 (645)
T ss_pred CcCCCCCCcCCCCC--ccccccCCCCCCCcCCCCCCCCCcccccccccC
Confidence 37899988875544 589999776555789999998888899999995
No 14
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=73.16 E-value=4.4 Score=32.06 Aligned_cols=37 Identities=27% Similarity=0.695 Sum_probs=31.5
Q ss_pred CccccccCCCCccceeEecCCCCCC------CcCCeeEE--eCCC
Q psy7787 334 GKCVICDSYVRPCTLVRICDECNYG------SYQGRCVI--CGGP 370 (463)
Q Consensus 334 GKCPICDSyVRP~tkVRICdeCSfG------s~~~RCII--CG~p 370 (463)
++|++|...++|..-+-+|.+|+-- ...+.|++ ||.+
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~ 50 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTG 50 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCC
Confidence 6899999999999999999999954 23688999 8864
No 15
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=72.59 E-value=3.8 Score=32.41 Aligned_cols=38 Identities=26% Similarity=0.659 Sum_probs=31.8
Q ss_pred CCccccccCCCCccceeEecCCCCCCC------cCCeeEE--eCCC
Q psy7787 22 DGKCVICDSYVRPCTLVRICDECNYGS------YQGRCVI--CGGP 59 (463)
Q Consensus 22 DGKCPICDSyVRP~tkVRICDeCSfGs------~~~RCII--CG~p 59 (463)
.++|++|...++|..-+-+|.+|+--. ..+.|++ ||.+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~ 50 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTG 50 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCC
Confidence 368999999999999999999999532 3578999 8865
No 16
>PRK05580 primosome assembly protein PriA; Validated
Probab=71.71 E-value=2.6 Score=44.85 Aligned_cols=50 Identities=26% Similarity=0.620 Sum_probs=40.3
Q ss_pred CcchhccccccCC--CccccccCCCC--ccceeEecCCCCCCC-cCCeeEEeCCC
Q psy7787 321 LGLTIGRLCEKCD--GKCVICDSYVR--PCTLVRICDECNYGS-YQGRCVICGGP 370 (463)
Q Consensus 321 PGt~IGrLCeKCD--GKCPICDSyVR--P~tkVRICdeCSfGs-~~~RCIICG~p 370 (463)
-|-+--.+|.+|. -+||.||.... -....-.|..|++.. ...+|..||+.
T Consensus 376 rGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 376 RGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 3666678999998 68999998764 356777899999985 47899999984
No 17
>PRK05580 primosome assembly protein PriA; Validated
Probab=70.59 E-value=2.4 Score=45.09 Aligned_cols=49 Identities=27% Similarity=0.555 Sum_probs=40.1
Q ss_pred hhhhhhccccCC--CccccccCCCC--ccceeEecCCCCCCCc-CCeeEEeCCC
Q psy7787 11 ISAIGRLCEKCD--GKCVICDSYVR--PCTLVRICDECNYGSY-QGRCVICGGP 59 (463)
Q Consensus 11 Gt~IGrLCeKCD--GKCPICDSyVR--P~tkVRICDeCSfGs~-~~RCIICG~p 59 (463)
|-+--.+|..|. -+||-||.... -.+..-.|..|++... ..+|..||+.
T Consensus 377 Gy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 377 GYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 666777999997 68999998754 3566778999999865 7799999985
No 18
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=67.50 E-value=1.6 Score=41.45 Aligned_cols=51 Identities=24% Similarity=0.501 Sum_probs=27.4
Q ss_pred CccccccCC-----CCcc----ceeEecCCCCCCC--cCCeeEEeCCCCc-------------cccccchhhhhc
Q psy7787 23 GKCVICDSY-----VRPC----TLVRICDECNYGS--YQGRCVICGGPGV-------------SDAYYCKECTIQ 73 (463)
Q Consensus 23 GKCPICDSy-----VRP~----tkVRICDeCSfGs--~~~RCIICG~pGv-------------sDAYYC~ECv~L 73 (463)
|.||+|.|. +++. .+.-.|..|++.- .+.+|..||+... .-++.|.+|..-
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~Y 247 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSY 247 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTEE
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccch
Confidence 899999996 4443 4888999999743 3678999997532 225678888543
No 19
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=66.14 E-value=4.4 Score=47.37 Aligned_cols=43 Identities=26% Similarity=0.664 Sum_probs=24.1
Q ss_pred cccccCCC-----ccccccCCCCccceeEecCCCCCCCcCC-----eeEEeCCCCc
Q psy7787 327 RLCEKCDG-----KCVICDSYVRPCTLVRICDECNYGSYQG-----RCVICGGPGV 372 (463)
Q Consensus 327 rLCeKCDG-----KCPICDSyVRP~tkVRICdeCSfGs~~~-----RCIICG~pGv 372 (463)
+.|.+|.. +||.|++...| ++.|..|+.--..+ +|.-||.+.+
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~te~---vy~CPsCGaev~~des~a~~CP~CGtplv 720 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHTEP---VYVCPDCGAEVPPDESGRVECPRCDVELT 720 (1337)
T ss_pred EECCCCCCccccccCcccCCcCCC---ceeCccCCCccCCCccccccCCCCCCccc
Confidence 45777653 67777776544 44666666532222 5555555443
No 20
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=63.09 E-value=5.3 Score=46.78 Aligned_cols=7 Identities=29% Similarity=0.876 Sum_probs=3.7
Q ss_pred cccchhh
Q psy7787 64 AYYCKEC 70 (463)
Q Consensus 64 AYYC~EC 70 (463)
|..|.+|
T Consensus 709 a~~CP~C 715 (1337)
T PRK14714 709 RVECPRC 715 (1337)
T ss_pred cccCCCC
Confidence 4555555
No 21
>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=60.27 E-value=2.1 Score=35.34 Aligned_cols=60 Identities=23% Similarity=0.501 Sum_probs=35.0
Q ss_pred CccccccCCCCccceeEecCCCCCCCc-CCeeEEeCCCC------ccccccchhhhhcccccCCCccceeEeecccccee
Q psy7787 23 GKCVICDSYVRPCTLVRICDECNYGSY-QGRCVICGGPG------VSDAYYCKECTIQEKDVSTVEPQFYELIGTKGLCL 95 (463)
Q Consensus 23 GKCPICDSyVRP~tkVRICDeCSfGs~-~~RCIICG~pG------vsDAYYC~ECv~LEKDRDGc~~~~yel~~~~~l~~ 95 (463)
-.||.|+..+.+....+.|+.|.---. ...|.-||.+- ...-|.|..|- +|||.+|+.|
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c~--------------gLiSKkrV~f 67 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHCH--------------GLISKKRVRF 67 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTTT---------------EE-TTTSEE
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcccceeeccCC--------------ceeecceEEE
Confidence 368999998888888888888875322 45677777652 23469998763 6788888776
Q ss_pred c
Q psy7787 96 S 96 (463)
Q Consensus 96 s 96 (463)
+
T Consensus 68 ~ 68 (70)
T PF07191_consen 68 E 68 (70)
T ss_dssp E
T ss_pred E
Confidence 4
No 22
>PRK14873 primosome assembly protein PriA; Provisional
Probab=58.95 E-value=5.4 Score=43.05 Aligned_cols=49 Identities=20% Similarity=0.445 Sum_probs=39.7
Q ss_pred hhhhhhccccCC--CccccccCCCCc--cceeEecCCCCCCCcCCeeEEeCCC
Q psy7787 11 ISAIGRLCEKCD--GKCVICDSYVRP--CTLVRICDECNYGSYQGRCVICGGP 59 (463)
Q Consensus 11 Gt~IGrLCeKCD--GKCPICDSyVRP--~tkVRICDeCSfGs~~~RCIICG~p 59 (463)
|-+--..|.+|. -+||-||....= .+..-.|.-|++.....+|.-||+.
T Consensus 379 Gyap~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 379 GYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred CCCCeeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 777777999995 689999987542 3457789999997778899999985
No 23
>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=56.93 E-value=6 Score=40.84 Aligned_cols=49 Identities=24% Similarity=0.464 Sum_probs=38.4
Q ss_pred hhhhhhccccCC--CccccccCCCC--ccceeEecCCCCCCCc-CCeeEEeCCC
Q psy7787 11 ISAIGRLCEKCD--GKCVICDSYVR--PCTLVRICDECNYGSY-QGRCVICGGP 59 (463)
Q Consensus 11 Gt~IGrLCeKCD--GKCPICDSyVR--P~tkVRICDeCSfGs~-~~RCIICG~p 59 (463)
|-+--.+|..|. -+||-||.... -....-.|.-|++... -.+|.-||+.
T Consensus 209 Gya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 209 GYSKNLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCeeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 666667999995 56999998753 2445668999999876 7799999985
No 24
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=56.27 E-value=6.3 Score=36.62 Aligned_cols=22 Identities=45% Similarity=1.135 Sum_probs=18.9
Q ss_pred eEecCCCCC---CCcCCeeEEeCCC
Q psy7787 38 VRICDECNY---GSYQGRCVICGGP 59 (463)
Q Consensus 38 VRICDeCSf---Gs~~~RCIICG~p 59 (463)
|.||..|+| |.--++|.|||.|
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCCh
Confidence 899999998 5446799999986
No 25
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=55.97 E-value=4 Score=28.81 Aligned_cols=24 Identities=29% Similarity=0.592 Sum_probs=13.6
Q ss_pred CccccccCC-CCccceeEecCCCCC
Q psy7787 23 GKCVICDSY-VRPCTLVRICDECNY 46 (463)
Q Consensus 23 GKCPICDSy-VRP~tkVRICDeCSf 46 (463)
.+||-|.|- .-....+.||++|.+
T Consensus 3 p~Cp~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp ---TTT-----EE-SSSEEETTTTE
T ss_pred CCCCCCCCcceeccCCEEeCCcccc
Confidence 479999984 456788899999975
No 26
>PRK14873 primosome assembly protein PriA; Provisional
Probab=55.46 E-value=7.7 Score=41.90 Aligned_cols=50 Identities=22% Similarity=0.507 Sum_probs=41.0
Q ss_pred CcchhccccccCC--CccccccCCCCc--cceeEecCCCCCCCcCCeeEEeCCC
Q psy7787 321 LGLTIGRLCEKCD--GKCVICDSYVRP--CTLVRICDECNYGSYQGRCVICGGP 370 (463)
Q Consensus 321 PGt~IGrLCeKCD--GKCPICDSyVRP--~tkVRICdeCSfGs~~~RCIICG~p 370 (463)
-|-+--.+|.+|. -+||-||....= .+..-.|.-|++.....+|.-||+.
T Consensus 378 rGyap~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 378 RGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred CCCCCeeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 4777778999997 489999977543 3557889999998778899999985
No 27
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=54.99 E-value=6.8 Score=36.38 Aligned_cols=23 Identities=43% Similarity=1.070 Sum_probs=19.0
Q ss_pred eEecCCCCC---CCcCCeeEEeCCCC
Q psy7787 349 VRICDECNY---GSYQGRCVICGGPG 371 (463)
Q Consensus 349 VRICdeCSf---Gs~~~RCIICG~pG 371 (463)
|+||..|+| |.--++|.|||.|.
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~k 159 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAPK 159 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCChH
Confidence 899999998 55678999999753
No 28
>KOG3507|consensus
Probab=54.61 E-value=9 Score=31.39 Aligned_cols=30 Identities=30% Similarity=0.720 Sum_probs=22.9
Q ss_pred CccceeEecCCCCCCCcCCeeEEeCCCCccccccchhhh
Q psy7787 344 RPCTLVRICDECNYGSYQGRCVICGGPGVSDAYYCKECT 382 (463)
Q Consensus 344 RP~tkVRICdeCSfGs~~~RCIICG~pGvsdAYYC~ECv 382 (463)
||.+..+||.+|+....-. ..|+.-|+||.
T Consensus 15 r~~~miYiCgdC~~en~lk---------~~D~irCReCG 44 (62)
T KOG3507|consen 15 RTATMIYICGDCGQENTLK---------RGDVIRCRECG 44 (62)
T ss_pred CcccEEEEecccccccccc---------CCCcEehhhcc
Confidence 6789999999998654322 46788888883
No 29
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=54.45 E-value=12 Score=37.49 Aligned_cols=37 Identities=22% Similarity=0.472 Sum_probs=20.2
Q ss_pred CCccccccCC-----CC----ccceeEecCCCCCC--CcCCeeEEeCC
Q psy7787 333 DGKCVICDSY-----VR----PCTLVRICDECNYG--SYQGRCVICGG 369 (463)
Q Consensus 333 DGKCPICDSy-----VR----P~tkVRICdeCSfG--s~~~RCIICG~ 369 (463)
.|.||+|.|. |+ .-.+.-.|..|+.. ..+-+|..||.
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 3556666655 22 12345566666653 33566777765
No 30
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=53.94 E-value=14 Score=26.27 Aligned_cols=43 Identities=33% Similarity=0.773 Sum_probs=29.9
Q ss_pred ccccccCCCCccceeEecCCCCCCCcCCeeEEeCCCCc------cccccchhhh
Q psy7787 335 KCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGV------SDAYYCKECT 382 (463)
Q Consensus 335 KCPICDSyVRP~tkVRICdeCSfGs~~~RCIICG~pGv------sdAYYC~ECv 382 (463)
.|++|.+ ..+....-.|+.|... +-.. |=++.. ...|||.+|.
T Consensus 1 ~C~vC~~-~~~~~~~i~C~~C~~~-~H~~---C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQ-SDDDGDMIQCDSCNRW-YHQE---CVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTS-SCTTSSEEEBSTTSCE-EETT---TSTSSHSHHSHHSSSBSSHHHH
T ss_pred eCcCCCC-cCCCCCeEEcCCCChh-hCcc---cCCCChhhccCCCCcEECcCCc
Confidence 4889998 7778888999999943 2333 444332 2379999985
No 31
>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=53.33 E-value=9.1 Score=39.55 Aligned_cols=50 Identities=26% Similarity=0.532 Sum_probs=39.2
Q ss_pred CcchhccccccCCC--ccccccCCCC--ccceeEecCCCCCCCc-CCeeEEeCCC
Q psy7787 321 LGLTIGRLCEKCDG--KCVICDSYVR--PCTLVRICDECNYGSY-QGRCVICGGP 370 (463)
Q Consensus 321 PGt~IGrLCeKCDG--KCPICDSyVR--P~tkVRICdeCSfGs~-~~RCIICG~p 370 (463)
-|-+--.+|..|.- +||-||.... -....-.|..|++... ..+|.-||+.
T Consensus 208 rGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 208 RGYSKNLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CcCCCeeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 36666779999986 5999997753 2455678999999854 7899999984
No 32
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=53.06 E-value=7.2 Score=26.53 Aligned_cols=22 Identities=27% Similarity=0.757 Sum_probs=16.0
Q ss_pred ccccccCCCCccceeEecCCCCCC
Q psy7787 335 KCVICDSYVRPCTLVRICDECNYG 358 (463)
Q Consensus 335 KCPICDSyVRP~tkVRICdeCSfG 358 (463)
+||-|++.| ...+++|..|+|-
T Consensus 2 ~CP~C~~~V--~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEV--PESAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCc--hhhcCcCCCCCCC
Confidence 689999888 3445677777763
No 33
>PRK04023 DNA polymerase II large subunit; Validated
Probab=51.80 E-value=7 Score=45.08 Aligned_cols=36 Identities=31% Similarity=0.781 Sum_probs=23.2
Q ss_pred eeEecCCCCCCCcCCeeEEeCCCCccccccchhhhhc
Q psy7787 37 LVRICDECNYGSYQGRCVICGGPGVSDAYYCKECTIQ 73 (463)
Q Consensus 37 kVRICDeCSfGs~~~RCIICG~pGvsDAYYC~ECv~L 73 (463)
..|.|.+|+......+|..||.. +..+|.|.+|..+
T Consensus 625 g~RfCpsCG~~t~~frCP~CG~~-Te~i~fCP~CG~~ 660 (1121)
T PRK04023 625 GRRKCPSCGKETFYRRCPFCGTH-TEPVYRCPRCGIE 660 (1121)
T ss_pred cCccCCCCCCcCCcccCCCCCCC-CCcceeCccccCc
Confidence 34567777766666777777765 3556777777443
No 34
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=50.80 E-value=9.2 Score=30.24 Aligned_cols=27 Identities=26% Similarity=0.725 Sum_probs=22.9
Q ss_pred ceeEecCCCCCCCcCCeeEEeCCCCcc
Q psy7787 36 TLVRICDECNYGSYQGRCVICGGPGVS 62 (463)
Q Consensus 36 tkVRICDeCSfGs~~~RCIICG~pGvs 62 (463)
.+.+.|..|+.-+..+.|..||.+..+
T Consensus 3 s~mr~C~~CgvYTLk~~CP~CG~~t~~ 29 (56)
T PRK13130 3 SKIRKCPKCGVYTLKEICPVCGGKTKN 29 (56)
T ss_pred ccceECCCCCCEEccccCcCCCCCCCC
Confidence 467999999999999999999987433
No 35
>PRK04023 DNA polymerase II large subunit; Validated
Probab=50.68 E-value=7.5 Score=44.84 Aligned_cols=42 Identities=26% Similarity=0.653 Sum_probs=26.9
Q ss_pred eeEecCCCCCCCcCCeeEEeCCCCccccccchhhhhcccccccc
Q psy7787 348 LVRICDECNYGSYQGRCVICGGPGVSDAYYCKECTIQEKDVSTV 391 (463)
Q Consensus 348 kVRICdeCSfGs~~~RCIICG~pGvsdAYYC~ECvrLEKDRD~c 391 (463)
..|.|.+|+......+|..||.. +..+|.|.+|....- .+.|
T Consensus 625 g~RfCpsCG~~t~~frCP~CG~~-Te~i~fCP~CG~~~~-~y~C 666 (1121)
T PRK04023 625 GRRKCPSCGKETFYRRCPFCGTH-TEPVYRCPRCGIEVE-EDEC 666 (1121)
T ss_pred cCccCCCCCCcCCcccCCCCCCC-CCcceeCccccCcCC-CCcC
Confidence 34667777766677788888865 456778888744432 3444
No 36
>KOG3507|consensus
Probab=50.03 E-value=12 Score=30.73 Aligned_cols=30 Identities=30% Similarity=0.720 Sum_probs=22.7
Q ss_pred CccceeEecCCCCCCCcCCeeEEeCCCCccccccchhhh
Q psy7787 33 RPCTLVRICDECNYGSYQGRCVICGGPGVSDAYYCKECT 71 (463)
Q Consensus 33 RP~tkVRICDeCSfGs~~~RCIICG~pGvsDAYYC~ECv 71 (463)
||.+..+||.+|+....- -..|+.-|+||.
T Consensus 15 r~~~miYiCgdC~~en~l---------k~~D~irCReCG 44 (62)
T KOG3507|consen 15 RTATMIYICGDCGQENTL---------KRGDVIRCRECG 44 (62)
T ss_pred CcccEEEEeccccccccc---------cCCCcEehhhcc
Confidence 678999999999876532 245788888883
No 37
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=49.58 E-value=10 Score=30.03 Aligned_cols=26 Identities=27% Similarity=0.741 Sum_probs=22.4
Q ss_pred ceeEecCCCCCCCcCCeeEEeCCCCc
Q psy7787 347 TLVRICDECNYGSYQGRCVICGGPGV 372 (463)
Q Consensus 347 tkVRICdeCSfGs~~~RCIICG~pGv 372 (463)
.+.+.|..|+--++.+.|..||.+..
T Consensus 3 s~mr~C~~CgvYTLk~~CP~CG~~t~ 28 (56)
T PRK13130 3 SKIRKCPKCGVYTLKEICPVCGGKTK 28 (56)
T ss_pred ccceECCCCCCEEccccCcCCCCCCC
Confidence 57899999999899999999998543
No 38
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=49.52 E-value=10 Score=41.81 Aligned_cols=49 Identities=31% Similarity=0.568 Sum_probs=40.0
Q ss_pred hhhhhhccccCC--CccccccCCCC--ccceeEecCCCCCC-CcCCeeEEeCCC
Q psy7787 11 ISAIGRLCEKCD--GKCVICDSYVR--PCTLVRICDECNYG-SYQGRCVICGGP 59 (463)
Q Consensus 11 Gt~IGrLCeKCD--GKCPICDSyVR--P~tkVRICDeCSfG-s~~~RCIICG~p 59 (463)
|-+--.+|..|. -+||-||.+.. -.+..-.|..|++- ..-.+|.-||+.
T Consensus 431 Gys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 431 GYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred CccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 777778999995 58999999853 36678889999997 457789999985
No 39
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=46.76 E-value=21 Score=35.85 Aligned_cols=51 Identities=24% Similarity=0.479 Sum_probs=35.7
Q ss_pred CCccccccCC-----CCc----cceeEecCCCCCCC--cCCeeEEeCCCCc------------cccccchhhhh
Q psy7787 22 DGKCVICDSY-----VRP----CTLVRICDECNYGS--YQGRCVICGGPGV------------SDAYYCKECTI 72 (463)
Q Consensus 22 DGKCPICDSy-----VRP----~tkVRICDeCSfGs--~~~RCIICG~pGv------------sDAYYC~ECv~ 72 (463)
.|.||+|.|. |+. -.+.-.|..|+..- .+.+|..||..+. .-++.|.+|..
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~ 260 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGT 260 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeeeecCCCcceEeeecccccc
Confidence 6899999996 322 34667899999743 3779999997531 12467888843
No 40
>PRK10220 hypothetical protein; Provisional
Probab=46.72 E-value=12 Score=33.54 Aligned_cols=28 Identities=29% Similarity=0.543 Sum_probs=22.9
Q ss_pred ccccccC-CCCccceeEecCCCCCCCcCC
Q psy7787 24 KCVICDS-YVRPCTLVRICDECNYGSYQG 51 (463)
Q Consensus 24 KCPICDS-yVRP~tkVRICDeCSfGs~~~ 51 (463)
.||-|+| |+-+...-.||.||++--..+
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCcCCcc
Confidence 5899998 577777789999999977655
No 41
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=46.39 E-value=14 Score=40.96 Aligned_cols=54 Identities=31% Similarity=0.559 Sum_probs=39.1
Q ss_pred hccccccCCCccccccCCCCccceeEecCCCCCCCcCCeeEEeCC-CCccccccchhhhhccc
Q psy7787 325 IGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGG-PGVSDAYYCKECTIQEK 386 (463)
Q Consensus 325 IGrLCeKCDGKCPICDSyVRP~tkVRICdeCSfGs~~~RCIICG~-pGvsdAYYC~ECvrLEK 386 (463)
.+-.|++|+||=. -+.-.-|++|+=.-...+|-+||. .....-|.|.||-+.+|
T Consensus 52 ~~~pc~~c~gkG~--------V~v~~~c~~c~G~gkv~~c~~cG~~~~~~~~~lc~~c~~~~~ 106 (715)
T COG1107 52 FEIPCPKCRGKGT--------VTVYDTCPECGGTGKVLTCDICGDIIVPWEEGLCPECRRKPK 106 (715)
T ss_pred CCCCCCeecccee--------EEEEeecccCCCceeEEeeccccceecCcccccChhHhhCCc
Confidence 3568999998732 233456888886556788999996 34445568999988888
No 42
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=46.18 E-value=14 Score=40.78 Aligned_cols=83 Identities=23% Similarity=0.362 Sum_probs=56.7
Q ss_pred cchhccccccCCC--ccccccCCCC--ccceeEecCCCCCC-CcCCeeEEeCCCCccccccchhhhhcccccccccceee
Q psy7787 322 GLTIGRLCEKCDG--KCVICDSYVR--PCTLVRICDECNYG-SYQGRCVICGGPGVSDAYYCKECTIQEKDVSTVEPQFY 396 (463)
Q Consensus 322 Gt~IGrLCeKCDG--KCPICDSyVR--P~tkVRICdeCSfG-s~~~RCIICG~pGvsdAYYC~ECvrLEKDRD~c~~~~~ 396 (463)
|-+--.+|..|.- +||-||.+.. -.+..-.|..|++- ..-.+|.-||+. +--|+-..=.+.|+--..- |
T Consensus 431 Gys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~--~L~~~G~GterieeeL~~~---F- 504 (730)
T COG1198 431 GYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE--HLRAVGPGTERIEEELKRL---F- 504 (730)
T ss_pred CccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC--eeEEecccHHHHHHHHHHH---C-
Confidence 6777889999974 8999999854 36688899999997 678899999984 4444444333333322221 2
Q ss_pred eeccccceeEEeecccee
Q psy7787 397 ELIGTKGCSIVFQKNTYW 414 (463)
Q Consensus 397 ~l~~~~~~s~~~~~~~~w 414 (463)
-.+ -.+++|.++.|
T Consensus 505 ---P~~-rv~r~d~Dtt~ 518 (730)
T COG1198 505 ---PGA-RIIRIDSDTTR 518 (730)
T ss_pred ---CCC-cEEEEcccccc
Confidence 222 34578888777
No 43
>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=45.69 E-value=6.9 Score=44.32 Aligned_cols=35 Identities=31% Similarity=0.805 Sum_probs=0.0
Q ss_pred eeEecCCCCCCCcCCeeEEeCCCCccccccchhhhh
Q psy7787 37 LVRICDECNYGSYQGRCVICGGPGVSDAYYCKECTI 72 (463)
Q Consensus 37 kVRICDeCSfGs~~~RCIICG~pGvsDAYYC~ECv~ 72 (463)
--|.|..|+.-+...+|-.||..+ ..-|+|..|..
T Consensus 654 ~~r~Cp~Cg~~t~~~~Cp~CG~~T-~~~~~Cp~C~~ 688 (900)
T PF03833_consen 654 GRRRCPKCGKETFYNRCPECGSHT-EPVYVCPDCGI 688 (900)
T ss_dssp ------------------------------------
T ss_pred ecccCcccCCcchhhcCcccCCcc-ccceecccccc
Confidence 347899999999999999998753 44799999844
No 44
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=44.98 E-value=11 Score=33.48 Aligned_cols=28 Identities=29% Similarity=0.553 Sum_probs=22.9
Q ss_pred ccccccC-CCCccceeEecCCCCCCCcCC
Q psy7787 24 KCVICDS-YVRPCTLVRICDECNYGSYQG 51 (463)
Q Consensus 24 KCPICDS-yVRP~tkVRICDeCSfGs~~~ 51 (463)
.||-|.| |+-+.....||.||.|--...
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccccccc
Confidence 5899998 677777889999999976544
No 45
>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=39.31 E-value=9.9 Score=43.13 Aligned_cols=31 Identities=32% Similarity=0.957 Sum_probs=0.0
Q ss_pred EecCCCCCCCcCCeeEEeCCCCccccccchhh
Q psy7787 350 RICDECNYGSYQGRCVICGGPGVSDAYYCKEC 381 (463)
Q Consensus 350 RICdeCSfGs~~~RCIICG~pGvsdAYYC~EC 381 (463)
|.|..|+.-+...+|-.||.. +..-|+|..|
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG~~-T~~~~~Cp~C 686 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECGSH-TEPVYVCPDC 686 (900)
T ss_dssp --------------------------------
T ss_pred ccCcccCCcchhhcCcccCCc-cccceecccc
Confidence 556666666666666666652 2335666665
No 46
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=37.47 E-value=19 Score=25.38 Aligned_cols=22 Identities=41% Similarity=1.025 Sum_probs=16.3
Q ss_pred eEecCCCCCCCc----CCeeEEeCCC
Q psy7787 38 VRICDECNYGSY----QGRCVICGGP 59 (463)
Q Consensus 38 VRICDeCSfGs~----~~RCIICG~p 59 (463)
+.+|..|+|-.. -++|.+||.+
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCCc
Confidence 578888887532 3589999985
No 47
>KOG0825|consensus
Probab=37.43 E-value=15 Score=41.94 Aligned_cols=60 Identities=28% Similarity=0.650 Sum_probs=41.9
Q ss_pred CccccccCCCCccceeEecCCCCCCCcCCeeEEeCCCCc----cccccchhhhhcccccCCCccceeEeec
Q psy7787 23 GKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGV----SDAYYCKECTIQEKDVSTVEPQFYELIG 89 (463)
Q Consensus 23 GKCPICDSyVRP~tkVRICDeCSfGs~~~RCIICG~pGv----sDAYYC~ECv~LEKDRDGc~~~~yel~~ 89 (463)
-+|.||.+.- |....-.||.|+++.|.--|. .|.. ...+||..|..|+---+. .+|+++.
T Consensus 216 ~~C~IC~~~D-pEdVLLLCDsCN~~~YH~YCL---DPdl~eiP~~eWYC~NC~dL~~~eh~---~~~~~~~ 279 (1134)
T KOG0825|consen 216 VKCDICTVHD-PEDVLLLCDSCNKVYYHVYCL---DPDLSESPVNEWYCTNCSLLEITEHK---DFTLKTE 279 (1134)
T ss_pred ccceeeccCC-hHHhheeecccccceeecccc---CcccccccccceecCcchhhhhhhhh---HHHHHHH
Confidence 4799998764 455667899999998876654 5533 347899999988754443 3455443
No 48
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=36.83 E-value=22 Score=23.78 Aligned_cols=11 Identities=27% Similarity=0.863 Sum_probs=3.0
Q ss_pred ceeEecCCCCC
Q psy7787 36 TLVRICDECNY 46 (463)
Q Consensus 36 tkVRICDeCSf 46 (463)
..++.|.+|+|
T Consensus 13 ~~~Y~C~~Cdf 23 (30)
T PF07649_consen 13 GWFYRCSECDF 23 (30)
T ss_dssp --EEE-TTT--
T ss_pred CceEECccCCC
Confidence 34444554444
No 49
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=34.75 E-value=11 Score=31.08 Aligned_cols=31 Identities=32% Similarity=0.681 Sum_probs=24.1
Q ss_pred CCeeEEeCCCCccccccchh-hh-hcccccccc
Q psy7787 361 QGRCVICGGPGVSDAYYCKE-CT-IQEKDVSTV 391 (463)
Q Consensus 361 ~~RCIICG~pGvsdAYYC~E-Cv-rLEKDRD~c 391 (463)
...|++||.+=--|.-.|.| |. .|+|+|.+.
T Consensus 8 H~HC~VCg~aIp~de~~CSe~C~eil~ker~R~ 40 (64)
T COG4068 8 HRHCVVCGKAIPPDEQVCSEECGEILNKERKRQ 40 (64)
T ss_pred CccccccCCcCCCccchHHHHHHHHHHHHHHHH
Confidence 36799999876777788888 53 489998875
No 50
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=34.61 E-value=21 Score=24.71 Aligned_cols=21 Identities=33% Similarity=0.858 Sum_probs=14.1
Q ss_pred EecCCCCCCC----cCCeeEEeCCC
Q psy7787 39 RICDECNYGS----YQGRCVICGGP 59 (463)
Q Consensus 39 RICDeCSfGs----~~~RCIICG~p 59 (463)
++|..|+|-. -..+|.+||.+
T Consensus 2 ~~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCcCCCcCcCCCCc
Confidence 5777777642 24588888874
No 51
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=33.59 E-value=33 Score=24.44 Aligned_cols=26 Identities=23% Similarity=0.575 Sum_probs=17.8
Q ss_pred ccccccCCCCccc----eeEecCCCCCCCc
Q psy7787 335 KCVICDSYVRPCT----LVRICDECNYGSY 360 (463)
Q Consensus 335 KCPICDSyVRP~t----kVRICdeCSfGs~ 360 (463)
-||-|.+.+-|.. ...+|..|+|...
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEE
Confidence 3788888776642 3677888887644
No 52
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=33.48 E-value=24 Score=25.20 Aligned_cols=22 Identities=32% Similarity=0.640 Sum_probs=12.4
Q ss_pred ccccccCCC---CccceeEecCCCC
Q psy7787 335 KCVICDSYV---RPCTLVRICDECN 356 (463)
Q Consensus 335 KCPICDSyV---RP~tkVRICdeCS 356 (463)
+||.|.+.. .+.+--.||..|+
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG 26 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCG 26 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-
T ss_pred CCcCCcCCceEEcCCCCeEECCCCC
Confidence 577777752 3445555666664
No 53
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=32.29 E-value=40 Score=22.81 Aligned_cols=22 Identities=23% Similarity=0.638 Sum_probs=13.5
Q ss_pred ccccccCCCCccceeEecCCCCC
Q psy7787 335 KCVICDSYVRPCTLVRICDECNY 357 (463)
Q Consensus 335 KCPICDSyVRP~tkVRICdeCSf 357 (463)
+|-+|...+.+.. ++.|++|.|
T Consensus 2 ~C~~C~~~~~~~~-~Y~C~~c~f 23 (30)
T PF03107_consen 2 WCDVCRRKIDGFY-FYHCSECCF 23 (30)
T ss_pred CCCCCCCCcCCCE-eEEeCCCCC
Confidence 3556666666655 666666664
No 54
>KOG1813|consensus
Probab=32.03 E-value=26 Score=35.91 Aligned_cols=36 Identities=36% Similarity=0.904 Sum_probs=29.2
Q ss_pred ccccccCC-CCc---cceeEecCCCCCCCcCC--eeEEeCCC
Q psy7787 24 KCVICDSY-VRP---CTLVRICDECNYGSYQG--RCVICGGP 59 (463)
Q Consensus 24 KCPICDSy-VRP---~tkVRICDeCSfGs~~~--RCIICG~p 59 (463)
+|-||-.+ ++| .-.-+.|..|+..+++. +|++|+..
T Consensus 243 ~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~ 284 (313)
T KOG1813|consen 243 KCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQ 284 (313)
T ss_pred cccccccccccchhhcCCceeehhhhccccccCCcceecccc
Confidence 57888764 555 55889999999999965 99999975
No 55
>KOG1813|consensus
Probab=31.83 E-value=24 Score=36.06 Aligned_cols=35 Identities=37% Similarity=0.934 Sum_probs=27.9
Q ss_pred ccccccCC-CCc---cceeEecCCCCCCCcC--CeeEEeCC
Q psy7787 335 KCVICDSY-VRP---CTLVRICDECNYGSYQ--GRCVICGG 369 (463)
Q Consensus 335 KCPICDSy-VRP---~tkVRICdeCSfGs~~--~RCIICG~ 369 (463)
+|-||-.+ ++| .-.-+.|..|+..+++ .+|++|+.
T Consensus 243 ~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~ 283 (313)
T KOG1813|consen 243 KCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQ 283 (313)
T ss_pred cccccccccccchhhcCCceeehhhhccccccCCcceeccc
Confidence 46788754 555 5688999999998875 49999996
No 56
>COG1034 NuoG NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion]
Probab=30.39 E-value=31 Score=38.15 Aligned_cols=114 Identities=21% Similarity=0.268 Sum_probs=63.8
Q ss_pred hccccccCCCccccccCC----------------CCc---cceeEecCCCCCC-CcCCeeEEeCCCCccccccchhhhhc
Q psy7787 325 IGRLCEKCDGKCVICDSY----------------VRP---CTLVRICDECNYG-SYQGRCVICGGPGVSDAYYCKECTIQ 384 (463)
Q Consensus 325 IGrLCeKCDGKCPICDSy----------------VRP---~tkVRICdeCSfG-s~~~RCIICG~pGvsdAYYC~ECvrL 384 (463)
+-.|+.++--.|||||.- .|. ++.+.-=+.=++- ...+|||.|+ .|+|.
T Consensus 87 mE~LLiNHPlDCpiCD~gGeCeLQD~a~~~G~~~sr~~~~kr~~~~~~~gp~v~~dm~RCI~C~-----------RCVR~ 155 (693)
T COG1034 87 MEFLLINHPLDCPVCDKGGECELQDLAVKYGVSHSRYRETKRTHRDKDLGPLVKYDMNRCILCT-----------RCVRF 155 (693)
T ss_pred HHHHHhcCCCCCCccCCCCCchhHHHHHHhCCCcccccccccccccccccchhhcccccceech-----------hhHHh
Confidence 456788888899999943 222 1111111111111 4468999987 58887
Q ss_pred ccccccccceeeeeccccceeEEeeccceeeeeeeh-hchhhHhhhhcCccccccccchhhhhhccccccceeeE
Q psy7787 385 EKDVSTVEPQFYELIGTKGCSIVFQKNTYWDIFVNT-LSTLSIATCLNGFGTCAEFMSVEYCYQRNWHKQAVTSV 458 (463)
Q Consensus 385 EKDRD~c~~~~~~l~~~~~~s~~~~~~~~w~i~v~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 458 (463)
=||.-+ ...+.+++. ......-++|+-.+-. +|-=-|+.|--|-=|---| --++|.|..+..-|+
T Consensus 156 c~eiaG--~~~l~~~~r---g~~~~i~t~~~~~l~se~cGncv~vCPvGALt~K~~----~~~ar~wEl~k~~si 221 (693)
T COG1034 156 CKEIAG--THELGVIKR---GENSEIGTYLDQPLESELCGNCVDVCPVGALTSKPF----AFTARKWELKKTPSI 221 (693)
T ss_pred hhhhcC--ccccceeec---CCCceeecccccccccccccceeeeccccccccChH----HhhhccchhccCcee
Confidence 777665 233444442 2344556777766554 4444455555443333222 237899988766554
No 57
>PHA00626 hypothetical protein
Probab=29.57 E-value=32 Score=28.08 Aligned_cols=25 Identities=24% Similarity=0.603 Sum_probs=14.7
Q ss_pred ccccccCC--CC-----ccceeEecCCCCCCC
Q psy7787 335 KCVICDSY--VR-----PCTLVRICDECNYGS 359 (463)
Q Consensus 335 KCPICDSy--VR-----P~tkVRICdeCSfGs 359 (463)
.||.|.|. +| -.+.-+.|.+|+|--
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 58888873 32 234456666666644
No 58
>KOG0825|consensus
Probab=28.57 E-value=27 Score=40.11 Aligned_cols=158 Identities=27% Similarity=0.418 Sum_probs=87.7
Q ss_pred hcccccch---hhhhHhhhhccccc----cccccccceeeeecccceEEEEEeeecCCCCcc--cccccccccccccccc
Q psy7787 234 NHIHTRHY---SVIDSFFKAQQEDE----IFGSSKTKAIKYSSSITSVHIFRLHPVKNGQTS--SGFDLLSKTSRRSCPL 304 (463)
Q Consensus 234 ~~~~~~~~---~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~ 304 (463)
..+|+-|| +-|+++-+-.|-+- +|+- |+---|.++--++|.-|+..-+.+ -|-|--..+
T Consensus 140 ~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~-----v~V~eS~~~~~~vR~lP~EEs~~~~e~~~d~~~d~------- 207 (1134)
T KOG0825|consen 140 SEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGE-----VKVLESTGIEANVRCLPSEESENILEKGGDEKQDQ------- 207 (1134)
T ss_pred cccccccccHHHHhhhhhhhcccCchhhhhhhe-----eeeeccccccceeEecchhhhhhhhhhcccccccc-------
Confidence 34666666 56888888777654 3442 333345555567777777544321 111110000
Q ss_pred ccccceeeeeccCCCCCcchhccccccCCCccccccCCCCccceeEecCCCCCCCcCCeeEEeCCCCc----cccccchh
Q psy7787 305 SLGKILKLRLEPHSHSLGLTIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGV----SDAYYCKE 380 (463)
Q Consensus 305 ~~~~~~~~~~~~~~~~PGt~IGrLCeKCDGKCPICDSyVRP~tkVRICdeCSfGs~~~RCIICG~pGv----sdAYYC~E 380 (463)
++ -++.. .-+|.||.+. .|....-.||.|+++.+..-|. .|.. ...+||..
T Consensus 208 ----~~---------~~~~E--------~~~C~IC~~~-DpEdVLLLCDsCN~~~YH~YCL---DPdl~eiP~~eWYC~N 262 (1134)
T KOG0825|consen 208 ----IS---------GLSQE--------EVKCDICTVH-DPEDVLLLCDSCNKVYYHVYCL---DPDLSESPVNEWYCTN 262 (1134)
T ss_pred ----cc---------Ccccc--------cccceeeccC-ChHHhheeecccccceeecccc---CcccccccccceecCc
Confidence 00 01111 2379999875 3455667899999997776654 4433 45789999
Q ss_pred hhhccc--cccccccee-------------eeeccccceeEEeeccceeeeeeehhchhhHhhh
Q psy7787 381 CTIQEK--DVSTVEPQF-------------YELIGTKGCSIVFQKNTYWDIFVNTLSTLSIATC 429 (463)
Q Consensus 381 CvrLEK--DRD~c~~~~-------------~~l~~~~~~s~~~~~~~~w~i~v~~~~~~~~~~~ 429 (463)
|..||- |++-. -++ -+|+-+.-.-.+-|.--.|.--+++.-.=.|++|
T Consensus 263 C~dL~~~eh~~~~-~~~~~~~~~~~~~~R~g~~~~tR~r~~~~Q~~~~~lR~~~~eR~RA~~~~ 325 (1134)
T KOG0825|consen 263 CSLLEITEHKDFT-LKTEELIESPKLESREGEIIQTRDRQSVKQPEVQLLRHVETERVRAIATC 325 (1134)
T ss_pred chhhhhhhhhHHH-HHHHHHhhhhhhhhhcccchhhhhhhhhccccHHHHHHhhhHHHHHHHHH
Confidence 988764 33322 011 1112222222245566677777777777777777
No 59
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=28.20 E-value=41 Score=25.37 Aligned_cols=24 Identities=21% Similarity=0.573 Sum_probs=17.0
Q ss_pred ccccccCCCCc--cceeEecCCCCCC
Q psy7787 335 KCVICDSYVRP--CTLVRICDECNYG 358 (463)
Q Consensus 335 KCPICDSyVRP--~tkVRICdeCSfG 358 (463)
.||.|+..++. ...+..|..|++-
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCcccccccccccceEEcCCCCCE
Confidence 37777777654 6677888887764
No 60
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=28.03 E-value=21 Score=28.58 Aligned_cols=8 Identities=50% Similarity=1.448 Sum_probs=5.1
Q ss_pred ccccccCC
Q psy7787 335 KCVICDSY 342 (463)
Q Consensus 335 KCPICDSy 342 (463)
+|.|||.-
T Consensus 4 kC~lCdk~ 11 (56)
T PF09963_consen 4 KCILCDKK 11 (56)
T ss_pred EEEecCCE
Confidence 56777654
No 61
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=26.64 E-value=25 Score=24.99 Aligned_cols=23 Identities=35% Similarity=0.778 Sum_probs=15.7
Q ss_pred CCeeEEeCCCCcc----ccccchhhhh
Q psy7787 361 QGRCVICGGPGVS----DAYYCKECTI 383 (463)
Q Consensus 361 ~~RCIICG~pGvs----dAYYC~ECvr 383 (463)
..+|..||++++. +-|.|.+|..
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCc
Confidence 4578888887765 3566887743
No 62
>PRK10220 hypothetical protein; Provisional
Probab=25.94 E-value=40 Score=30.25 Aligned_cols=28 Identities=29% Similarity=0.543 Sum_probs=21.9
Q ss_pred ccccccC-CCCccceeEecCCCCCCCcCC
Q psy7787 335 KCVICDS-YVRPCTLVRICDECNYGSYQG 362 (463)
Q Consensus 335 KCPICDS-yVRP~tkVRICdeCSfGs~~~ 362 (463)
.||-|+| |+-+...-.||.||++--..+
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCcCCcc
Confidence 5899987 466777789999999875444
No 63
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=25.71 E-value=50 Score=33.12 Aligned_cols=38 Identities=24% Similarity=0.419 Sum_probs=27.3
Q ss_pred CCccccccCC-----CCc-----cceeEecCCCCCC--CcCCeeEEeCCC
Q psy7787 333 DGKCVICDSY-----VRP-----CTLVRICDECNYG--SYQGRCVICGGP 370 (463)
Q Consensus 333 DGKCPICDSy-----VRP-----~tkVRICdeCSfG--s~~~RCIICG~p 370 (463)
-|.||+|.|. |+. -.+.-.|..|+.. ..+-+|..||+.
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence 3589999976 332 3467789999874 447889999963
No 64
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=25.71 E-value=28 Score=28.32 Aligned_cols=25 Identities=32% Similarity=0.889 Sum_probs=20.1
Q ss_pred eeEecCCCCCCCcCCeeEEeCCCCc
Q psy7787 348 LVRICDECNYGSYQGRCVICGGPGV 372 (463)
Q Consensus 348 kVRICdeCSfGs~~~RCIICG~pGv 372 (463)
+.|.|..|.-=+++++|..||+...
T Consensus 4 ~~rkC~~cg~YTLke~Cp~CG~~t~ 28 (59)
T COG2260 4 LIRKCPKCGRYTLKEKCPVCGGDTK 28 (59)
T ss_pred hhhcCcCCCceeecccCCCCCCccc
Confidence 4577888888888899999998554
No 65
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=25.23 E-value=45 Score=25.93 Aligned_cols=29 Identities=31% Similarity=0.792 Sum_probs=20.9
Q ss_pred CCCCCcCCeeEEeCCC-Cccccc---cchhhhh
Q psy7787 44 CNYGSYQGRCVICGGP-GVSDAY---YCKECTI 72 (463)
Q Consensus 44 CSfGs~~~RCIICG~p-GvsDAY---YC~ECv~ 72 (463)
-+++...++|++||.+ |+..-| .|+-|-+
T Consensus 8 ~~~~r~~nrC~~~Gr~rgvirkf~l~lcR~~FR 40 (52)
T PRK05766 8 RKYGKGARECQRCGRKQGLIRKYGLYLCRQCFR 40 (52)
T ss_pred CCCCCCCceeecCCCCceeHHhhCCcccHHHHH
Confidence 3678889999999987 666544 4666644
No 66
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.78 E-value=31 Score=33.08 Aligned_cols=26 Identities=27% Similarity=0.723 Sum_probs=20.2
Q ss_pred CCCcCCeeEEeCCC------Cccccccchhhh
Q psy7787 46 YGSYQGRCVICGGP------GVSDAYYCKECT 71 (463)
Q Consensus 46 fGs~~~RCIICG~p------GvsDAYYC~ECv 71 (463)
||..+..|..||.+ +.-.+|||..|-
T Consensus 240 y~R~g~pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 240 YQRTGEPCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred cCCCCCcCCCCCCeeEEEEECCCccEECcCCc
Confidence 57777889999976 334599999983
No 68
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=24.77 E-value=29 Score=28.27 Aligned_cols=26 Identities=31% Similarity=0.842 Sum_probs=20.8
Q ss_pred eeEecCCCCCCCcCCeeEEeCCCCcc
Q psy7787 37 LVRICDECNYGSYQGRCVICGGPGVS 62 (463)
Q Consensus 37 kVRICDeCSfGs~~~RCIICG~pGvs 62 (463)
+.|.|..|+-=+.+++|..||+...+
T Consensus 4 ~~rkC~~cg~YTLke~Cp~CG~~t~~ 29 (59)
T COG2260 4 LIRKCPKCGRYTLKEKCPVCGGDTKV 29 (59)
T ss_pred hhhcCcCCCceeecccCCCCCCcccc
Confidence 45778889888888999999986543
No 69
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=24.16 E-value=42 Score=25.58 Aligned_cols=24 Identities=25% Similarity=0.638 Sum_probs=16.0
Q ss_pred cccccC-CCCccceeEecCCCCCCC
Q psy7787 336 CVICDS-YVRPCTLVRICDECNYGS 359 (463)
Q Consensus 336 CPICDS-yVRP~tkVRICdeCSfGs 359 (463)
||-|.+ +..+...-..|..|+|-.
T Consensus 23 CP~Cg~~~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 23 CPRCGSGFMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred CcCCCcchheccCCcEECCCcCCEE
Confidence 555666 666666677777777654
No 70
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=24.16 E-value=59 Score=23.07 Aligned_cols=21 Identities=29% Similarity=0.893 Sum_probs=12.2
Q ss_pred ccccccCCCCcc----ceeEecCCC
Q psy7787 335 KCVICDSYVRPC----TLVRICDEC 355 (463)
Q Consensus 335 KCPICDSyVRP~----tkVRICdeC 355 (463)
+||.|.....+. ..|..|..|
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C 25 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSC 25 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCC
Confidence 689998765442 244445444
No 71
>PRK14289 chaperone protein DnaJ; Provisional
Probab=24.02 E-value=34 Score=34.12 Aligned_cols=22 Identities=36% Similarity=0.773 Sum_probs=13.6
Q ss_pred CCeeEEeCCCCccccccchhhh
Q psy7787 361 QGRCVICGGPGVSDAYYCKECT 382 (463)
Q Consensus 361 ~~RCIICG~pGvsdAYYC~ECv 382 (463)
+..|.-|++.|...+--|..|.
T Consensus 197 ~~~C~~C~G~G~~~~~~C~~C~ 218 (386)
T PRK14289 197 QSTCPTCNGEGKIIKKKCKKCG 218 (386)
T ss_pred EEecCCCCccccccCcCCCCCC
Confidence 4556666666665555666663
No 72
>PRK14282 chaperone protein DnaJ; Provisional
Probab=23.48 E-value=37 Score=33.75 Aligned_cols=9 Identities=33% Similarity=0.922 Sum_probs=6.3
Q ss_pred ccccccCCC
Q psy7787 326 GRLCEKCDG 334 (463)
Q Consensus 326 GrLCeKCDG 334 (463)
-.+|+.|+|
T Consensus 152 ~~~C~~C~G 160 (369)
T PRK14282 152 YETCPHCGG 160 (369)
T ss_pred cccCCCCCc
Confidence 356888877
No 73
>PRK14282 chaperone protein DnaJ; Provisional
Probab=23.13 E-value=37 Score=33.71 Aligned_cols=22 Identities=41% Similarity=1.008 Sum_probs=13.8
Q ss_pred CCeeEEeCCCCccccccchhhh
Q psy7787 50 QGRCVICGGPGVSDAYYCKECT 71 (463)
Q Consensus 50 ~~RCIICG~pGvsDAYYC~ECv 71 (463)
+..|--|++.|..-.-.|..|.
T Consensus 195 ~~~C~~C~G~G~~~~~~C~~C~ 216 (369)
T PRK14282 195 ERTCERCGGTGKIPGEYCHECG 216 (369)
T ss_pred EEECCCCCCcceeCCCCCCCCC
Confidence 3456777776655555677773
No 74
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=23.11 E-value=42 Score=29.97 Aligned_cols=27 Identities=30% Similarity=0.568 Sum_probs=21.4
Q ss_pred ccccccC-CCCccceeEecCCCCCCCcC
Q psy7787 335 KCVICDS-YVRPCTLVRICDECNYGSYQ 361 (463)
Q Consensus 335 KCPICDS-yVRP~tkVRICdeCSfGs~~ 361 (463)
.||-|.| |+-+.....||.||+|--..
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~EW~~ 31 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYEWNE 31 (109)
T ss_pred cCCcCCCcceEecCCeeECccccccccc
Confidence 5899987 46677788999999986443
No 75
>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=22.98 E-value=43 Score=28.84 Aligned_cols=25 Identities=36% Similarity=0.930 Sum_probs=12.9
Q ss_pred CCCcCCeeEEeCCCCcc-ccccchhh
Q psy7787 46 YGSYQGRCVICGGPGVS-DAYYCKEC 70 (463)
Q Consensus 46 fGs~~~RCIICG~pGvs-DAYYC~EC 70 (463)
|+.+..+|.+|...-.- ++.||..|
T Consensus 40 y~~~~~~C~~CK~~v~q~g~~YCq~C 65 (90)
T PF10235_consen 40 YAPYSSKCKICKTKVHQPGAKYCQTC 65 (90)
T ss_pred ccccCccccccccccccCCCccChhh
Confidence 34444566666544222 45666665
No 76
>PRK11823 DNA repair protein RadA; Provisional
Probab=22.91 E-value=49 Score=33.84 Aligned_cols=28 Identities=32% Similarity=0.595 Sum_probs=22.4
Q ss_pred ceeEecCCCCCCCc--CCeeEEeCCCCccc
Q psy7787 36 TLVRICDECNYGSY--QGRCVICGGPGVSD 63 (463)
Q Consensus 36 tkVRICDeCSfGs~--~~RCIICG~pGvsD 63 (463)
...++|.+|+|.+. .++|.-||.-+...
T Consensus 5 ~~~y~C~~Cg~~~~~~~g~Cp~C~~w~t~~ 34 (446)
T PRK11823 5 KTAYVCQECGAESPKWLGRCPECGAWNTLV 34 (446)
T ss_pred CCeEECCcCCCCCcccCeeCcCCCCcccee
Confidence 35799999999766 78999999865543
No 77
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=22.88 E-value=56 Score=26.09 Aligned_cols=28 Identities=25% Similarity=0.727 Sum_probs=21.5
Q ss_pred CCCCcCCeeEEeCCC-Cccc---cccchhhhh
Q psy7787 45 NYGSYQGRCVICGGP-GVSD---AYYCKECTI 72 (463)
Q Consensus 45 SfGs~~~RCIICG~p-GvsD---AYYC~ECv~ 72 (463)
+||+...+|.+||.+ |... -+-|+.|-+
T Consensus 11 ~yGkGsr~C~vCg~~~gliRkygL~~CRqCFR 42 (54)
T PTZ00218 11 TYGKGSRQCRVCSNRHGLIRKYGLNVCRQCFR 42 (54)
T ss_pred cCCCCCCeeecCCCcchhhhhcCcchhhHHHH
Confidence 589999999999987 5444 446888854
No 78
>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=22.45 E-value=51 Score=33.50 Aligned_cols=39 Identities=28% Similarity=0.732 Sum_probs=25.7
Q ss_pred CCccccccC--CCCccceeEe-------cCCCC---CCCcCCeeEEeCCCC
Q psy7787 333 DGKCVICDS--YVRPCTLVRI-------CDECN---YGSYQGRCVICGGPG 371 (463)
Q Consensus 333 DGKCPICDS--yVRP~tkVRI-------CdeCS---fGs~~~RCIICG~pG 371 (463)
|-.||+|-+ |+.|..+..| |..|- |......|..|+.+-
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~l 53 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPL 53 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCcc
Confidence 347999988 8899765544 44442 344556788888643
No 79
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=22.42 E-value=39 Score=27.66 Aligned_cols=26 Identities=19% Similarity=0.515 Sum_probs=20.1
Q ss_pred EecCCCCCCCcCCeeEEeCCCCcccc
Q psy7787 39 RICDECNYGSYQGRCVICGGPGVSDA 64 (463)
Q Consensus 39 RICDeCSfGs~~~RCIICG~pGvsDA 64 (463)
+-|..|.+-...+.|.+||+...++-
T Consensus 6 ~AC~~C~~i~~~~~Cp~Cgs~~~S~~ 31 (64)
T PRK06393 6 RACKKCKRLTPEKTCPVHGDEKTTTE 31 (64)
T ss_pred hhHhhCCcccCCCcCCCCCCCcCCcC
Confidence 46888888888889999998665543
No 80
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=22.34 E-value=16 Score=26.34 Aligned_cols=26 Identities=27% Similarity=0.626 Sum_probs=16.5
Q ss_pred cceeEecCCCCCCCcCCeeEEeCCCC
Q psy7787 35 CTLVRICDECNYGSYQGRCVICGGPG 60 (463)
Q Consensus 35 ~tkVRICDeCSfGs~~~RCIICG~pG 60 (463)
...|+.|..|+.=+...-|-||..+.
T Consensus 14 ~~~i~~C~~C~nlse~~~C~IC~d~~ 39 (41)
T PF02132_consen 14 KENIKFCSICGNLSEEDPCEICSDPK 39 (41)
T ss_dssp HHH-EE-SSS--EESSSS-HHHH-TT
T ss_pred HHcCCccCCCCCcCCCCcCcCCCCCC
Confidence 45789999999988899999997754
No 81
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=22.25 E-value=42 Score=35.65 Aligned_cols=16 Identities=25% Similarity=0.715 Sum_probs=14.4
Q ss_pred cccchhhhhccccccc
Q psy7787 375 AYYCKECTIQEKDVST 390 (463)
Q Consensus 375 AYYC~ECvrLEKDRD~ 390 (463)
+|||++|..+.|.|.-
T Consensus 60 ~~YCr~Cl~mgRv~sd 75 (441)
T COG4098 60 CLYCRNCLMMGRVRSD 75 (441)
T ss_pred eEeehhhhhccccccc
Confidence 9999999999998864
No 82
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=22.18 E-value=61 Score=26.40 Aligned_cols=23 Identities=35% Similarity=0.808 Sum_probs=13.3
Q ss_pred ccccccCCCCccceeEecCCCCC
Q psy7787 335 KCVICDSYVRPCTLVRICDECNY 357 (463)
Q Consensus 335 KCPICDSyVRP~tkVRICdeCSf 357 (463)
-||-|.+...|......|..|++
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~ 24 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGY 24 (104)
T ss_pred CCcccCcccccCCCeEECcCCCC
Confidence 36677776666544455555554
No 83
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=22.16 E-value=39 Score=32.48 Aligned_cols=28 Identities=32% Similarity=0.799 Sum_probs=21.0
Q ss_pred CCCcCCeeEEeCCC------Cccccccchhhhhc
Q psy7787 46 YGSYQGRCVICGGP------GVSDAYYCKECTIQ 73 (463)
Q Consensus 46 fGs~~~RCIICG~p------GvsDAYYC~ECv~L 73 (463)
||..+..|..||.+ +.-..|||..|-.+
T Consensus 231 y~R~g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 231 YGREGQPCPRCGTPIEKIVVGGRGTHFCPQCQPL 264 (269)
T ss_pred cCCCcCCCCcCCCeeEEEEECCCCcEECCCCcCC
Confidence 67767789999976 34459999999543
No 84
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=21.70 E-value=54 Score=20.90 Aligned_cols=20 Identities=30% Similarity=1.139 Sum_probs=12.7
Q ss_pred ecCCCCCCCc--CCeeEEeCCC
Q psy7787 40 ICDECNYGSY--QGRCVICGGP 59 (463)
Q Consensus 40 ICDeCSfGs~--~~RCIICG~p 59 (463)
+|..|.+-.. +.+|.+|+.|
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred cCCCCCCcChhhhccccccCCc
Confidence 5666755333 5678888764
No 85
>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=21.47 E-value=50 Score=38.50 Aligned_cols=31 Identities=32% Similarity=0.777 Sum_probs=26.6
Q ss_pred eeEecCCCCCCCcCCeeEEeCCCCccccccch
Q psy7787 37 LVRICDECNYGSYQGRCVICGGPGVSDAYYCK 68 (463)
Q Consensus 37 kVRICDeCSfGs~~~RCIICG~pGvsDAYYC~ 68 (463)
-.|.|..|+.-+...+|..||++. ..+|+|+
T Consensus 624 ~~RKCPkCG~yTlk~rCP~CG~~T-e~~~pc~ 654 (1095)
T TIGR00354 624 AIRKCPQCGKESFWLKCPVCGELT-EQLYYGK 654 (1095)
T ss_pred EEEECCCCCcccccccCCCCCCcc-cccccee
Confidence 358999999999999999999875 5589993
No 86
>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=21.19 E-value=55 Score=33.27 Aligned_cols=20 Identities=20% Similarity=0.483 Sum_probs=15.5
Q ss_pred CCChhhhhhhhhhhhhhhee
Q psy7787 130 PGPPEWRNALSGFEKQMFEI 149 (463)
Q Consensus 130 ~~~~~~~~~~~~~~~~~~~~ 149 (463)
|.-++|-+-|.-+|--.|.+
T Consensus 90 ~~l~~yNdYLE~vEdii~nL 109 (309)
T TIGR00570 90 PSLREYNDYLEEVEDIVYNL 109 (309)
T ss_pred CCHHHHHHHHHHHHHHHHHh
Confidence 36789999998888777754
No 87
>PF12025 Phage_C: Phage protein C; InterPro: IPR016407 This family of phage proteins is functionally uncharacterised. Proteins in this family are typically between 68 to 86 amino acids in length.; GO: 0019073 viral DNA genome packaging
Probab=21.17 E-value=30 Score=28.81 Aligned_cols=22 Identities=32% Similarity=0.554 Sum_probs=19.8
Q ss_pred Chhhhhhhhhhhhhhheeecee
Q psy7787 132 PPEWRNALSGFEKQMFEIEQHR 153 (463)
Q Consensus 132 ~~~~~~~~~~~~~~~~~~~~~~ 153 (463)
...|-|++-.+-||-|.+|+|-
T Consensus 30 eEKwLNm~G~llkdWFryE~hf 51 (68)
T PF12025_consen 30 EEKWLNMLGALLKDWFRYEDHF 51 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3579999999999999999984
No 88
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=21.07 E-value=80 Score=33.65 Aligned_cols=17 Identities=24% Similarity=0.643 Sum_probs=15.2
Q ss_pred cccchhhhhcccccCCC
Q psy7787 64 AYYCKECTIQEKDVSTV 80 (463)
Q Consensus 64 AYYC~ECv~LEKDRDGc 80 (463)
+|||++|..+.|.+.-.
T Consensus 60 ~~YCr~Cl~mgRv~sd~ 76 (441)
T COG4098 60 CLYCRNCLMMGRVRSDQ 76 (441)
T ss_pred eEeehhhhhcccccccc
Confidence 99999999999988763
No 89
>TIGR02349 DnaJ_bact chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
Probab=20.72 E-value=48 Score=32.47 Aligned_cols=51 Identities=31% Similarity=0.675 Sum_probs=28.4
Q ss_pred hhccccCCCccccccCCCCccceeEecCCCCCC--------------CcCCeeEEeCCCCccccccchhhh
Q psy7787 15 GRLCEKCDGKCVICDSYVRPCTLVRICDECNYG--------------SYQGRCVICGGPGVSDAYYCKECT 71 (463)
Q Consensus 15 GrLCeKCDGKCPICDSyVRP~tkVRICDeCSfG--------------s~~~RCIICG~pGvsDAYYC~ECv 71 (463)
-.+|..|+|..- ++......|..|+=. ..+..|--|++.|..-.--|..|.
T Consensus 143 ~~~C~~C~G~G~------~~~~~~~~C~~C~G~G~~~~~~~~~~g~~~~~~~C~~C~G~G~~~~~~C~~C~ 207 (354)
T TIGR02349 143 KESCETCHGTGA------KPGTDPKTCPTCGGTGQVRRQQGTPFGFFQQQQTCPTCGGEGKIIKEPCSTCK 207 (354)
T ss_pred CCcCCCCCCCCC------CCCCCCccCCCCCCeeEEEEEEeccCCceEEEEecCCCCCcceecCCCCCCCC
Confidence 457888888542 112223446666521 123467777777665555677774
No 90
>PRK14284 chaperone protein DnaJ; Provisional
Probab=20.52 E-value=51 Score=33.07 Aligned_cols=51 Identities=27% Similarity=0.696 Sum_probs=29.1
Q ss_pred hhccccCCCccccccCCCCccceeEecCCCCCC----------CcCCeeEEeCCCCccccccchhhh
Q psy7787 15 GRLCEKCDGKCVICDSYVRPCTLVRICDECNYG----------SYQGRCVICGGPGVSDAYYCKECT 71 (463)
Q Consensus 15 GrLCeKCDGKCPICDSyVRP~tkVRICDeCSfG----------s~~~RCIICG~pGvsDAYYC~ECv 71 (463)
-..|+.|.|.-- ++.+..+.|..|+=. ..+..|--|++.|....=.|..|.
T Consensus 158 ~~~C~~C~G~G~------~~~~~~~~C~~C~G~G~v~~~~G~~~~~~~C~~C~G~G~~~~~~C~~C~ 218 (391)
T PRK14284 158 YKSCDACSGSGA------NSSQGIKVCDRCKGSGQVVQSRGFFSMASTCPECGGEGRVITDPCSVCR 218 (391)
T ss_pred eccCCCCccccc------CCCCCCeecCccCCeeEEEEEeceEEEEEECCCCCCCCcccCCcCCCCC
Confidence 456888876532 333334556666521 123467777777655555577774
No 91
>KOG0801|consensus
Probab=20.50 E-value=58 Score=31.52 Aligned_cols=33 Identities=36% Similarity=0.502 Sum_probs=21.2
Q ss_pred cccccccccccccceeeeeccCCCCCcchhccccccCCCccccccCCCCcc
Q psy7787 296 KTSRRSCPLSLGKILKLRLEPHSHSLGLTIGRLCEKCDGKCVICDSYVRPC 346 (463)
Q Consensus 296 ~~~~~~~~~~~~~~~~~~~~~~~~~PGt~IGrLCeKCDGKCPICDSyVRP~ 346 (463)
-.|||+ |..-|-+-+-+|+- -|||+|...|-|.
T Consensus 119 l~sRrs----la~slP~hi~~~~g--------------~KCPvC~K~V~sD 151 (205)
T KOG0801|consen 119 LGSRRS----LADSLPVHIMDHSG--------------MKCPVCHKVVPSD 151 (205)
T ss_pred hhhhhh----hhhccceeeeccCC--------------ccCCccccccCCC
Confidence 346774 34445555566541 3899999999873
No 92
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.45 E-value=55 Score=24.95 Aligned_cols=26 Identities=23% Similarity=0.612 Sum_probs=17.5
Q ss_pred ccccccC-CCCccceeEecCCCCCCCc
Q psy7787 24 KCVICDS-YVRPCTLVRICDECNYGSY 49 (463)
Q Consensus 24 KCPICDS-yVRP~tkVRICDeCSfGs~ 49 (463)
-||-|.+ +..+......|..|+|-.+
T Consensus 22 fCP~Cg~~~m~~~~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 22 FCPRCGSGFMAEHLDRWHCGKCGYTEF 48 (50)
T ss_pred cCcCCCcchheccCCcEECCCcCCEEe
Confidence 3666777 7777666777877776543
No 93
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=20.44 E-value=78 Score=29.55 Aligned_cols=8 Identities=25% Similarity=0.912 Sum_probs=5.5
Q ss_pred ccccccCC
Q psy7787 335 KCVICDSY 342 (463)
Q Consensus 335 KCPICDSy 342 (463)
+||+|+.-
T Consensus 7 ~CPvC~~~ 14 (214)
T PF09986_consen 7 TCPVCGKE 14 (214)
T ss_pred ECCCCCCe
Confidence 57888754
No 94
>PRK14289 chaperone protein DnaJ; Provisional
Probab=20.41 E-value=43 Score=33.37 Aligned_cols=22 Identities=36% Similarity=0.773 Sum_probs=16.8
Q ss_pred CCeeEEeCCCCccccccchhhh
Q psy7787 50 QGRCVICGGPGVSDAYYCKECT 71 (463)
Q Consensus 50 ~~RCIICG~pGvsDAYYC~ECv 71 (463)
+..|.-|++.|...+--|..|.
T Consensus 197 ~~~C~~C~G~G~~~~~~C~~C~ 218 (386)
T PRK14289 197 QSTCPTCNGEGKIIKKKCKKCG 218 (386)
T ss_pred EEecCCCCccccccCcCCCCCC
Confidence 5578888888877777788884
No 95
>KOG0978|consensus
Probab=20.21 E-value=12 Score=41.35 Aligned_cols=38 Identities=37% Similarity=0.868 Sum_probs=28.2
Q ss_pred ccccccCCCCccceeE------ecCCCC---CCCcCCeeEEeCCC-Cccc
Q psy7787 24 KCVICDSYVRPCTLVR------ICDECN---YGSYQGRCVICGGP-GVSD 63 (463)
Q Consensus 24 KCPICDSyVRP~tkVR------ICDeCS---fGs~~~RCIICG~p-GvsD 63 (463)
+||.|+ .||...|- -|.+|= |..-+.+|..||.+ |++|
T Consensus 645 kCs~Cn--~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 645 KCSVCN--TRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred eCCCcc--CchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 799999 78865443 367775 45558899999977 7776
No 96
>PRK14284 chaperone protein DnaJ; Provisional
Probab=20.16 E-value=54 Score=32.93 Aligned_cols=51 Identities=27% Similarity=0.696 Sum_probs=26.0
Q ss_pred ccccccCCCccccccCCCCccceeEecCCCCCC----------CcCCeeEEeCCCCccccccchhhh
Q psy7787 326 GRLCEKCDGKCVICDSYVRPCTLVRICDECNYG----------SYQGRCVICGGPGVSDAYYCKECT 382 (463)
Q Consensus 326 GrLCeKCDGKCPICDSyVRP~tkVRICdeCSfG----------s~~~RCIICG~pGvsdAYYC~ECv 382 (463)
-..|+.|.|.-- ++.+....|..|.=. ..+..|--|++.|....=.|..|.
T Consensus 158 ~~~C~~C~G~G~------~~~~~~~~C~~C~G~G~v~~~~G~~~~~~~C~~C~G~G~~~~~~C~~C~ 218 (391)
T PRK14284 158 YKSCDACSGSGA------NSSQGIKVCDRCKGSGQVVQSRGFFSMASTCPECGGEGRVITDPCSVCR 218 (391)
T ss_pred eccCCCCccccc------CCCCCCeecCccCCeeEEEEEeceEEEEEECCCCCCCCcccCCcCCCCC
Confidence 457888876431 222233445555411 123456666666654444466664
No 97
>KOG1100|consensus
Probab=20.11 E-value=44 Score=31.55 Aligned_cols=23 Identities=39% Similarity=0.680 Sum_probs=13.4
Q ss_pred cccccCCC---ccccccCCCCcccee
Q psy7787 327 RLCEKCDG---KCVICDSYVRPCTLV 349 (463)
Q Consensus 327 rLCeKCDG---KCPICDSyVRP~tkV 349 (463)
-+|.-|++ .||||.+.+.....|
T Consensus 180 ~lC~~C~~~~~~CPiC~~~~~s~~~v 205 (207)
T KOG1100|consen 180 CLCGICDESLRICPICRSPKTSSVEV 205 (207)
T ss_pred EecccccccCccCCCCcChhhceeec
Confidence 35666665 477777665544443
No 98
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.04 E-value=55 Score=31.22 Aligned_cols=34 Identities=26% Similarity=0.473 Sum_probs=28.4
Q ss_pred cceeEecCCCCCCCcCCeeEEeCCCCccccccch
Q psy7787 35 CTLVRICDECNYGSYQGRCVICGGPGVSDAYYCK 68 (463)
Q Consensus 35 ~tkVRICDeCSfGs~~~RCIICG~pGvsDAYYC~ 68 (463)
...++.|..|++-+..+-|-||..+.....--|-
T Consensus 50 ~~~i~~C~~C~~lse~~~C~IC~d~~Rd~~~iCV 83 (195)
T TIGR00615 50 KENLRTCSVCGAISDQEVCNICSDERRDNSVICV 83 (195)
T ss_pred HHcCCcCCCCCCCCCCCcCCCCCCCCCCCCEEEE
Confidence 5678999999999999999999988776666664
No 99
>TIGR02349 DnaJ_bact chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
Probab=20.01 E-value=52 Score=32.25 Aligned_cols=12 Identities=17% Similarity=0.213 Sum_probs=8.0
Q ss_pred hhhHhhhhcCcc
Q psy7787 423 TLSIATCLNGFG 434 (463)
Q Consensus 423 ~~~~~~~~~~~~ 434 (463)
.+|+...|.|+-
T Consensus 274 ~isl~eAl~G~~ 285 (354)
T TIGR02349 274 PISFTQAILGGE 285 (354)
T ss_pred EeCHHHHhCCCe
Confidence 456677777764
Done!