Query 037283
Match_columns 136
No_of_seqs 83 out of 85
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 10:39:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037283.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037283hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1705 Uncharacterized conser 100.0 4.8E-67 1E-71 388.9 5.8 108 29-136 3-110 (110)
2 PF03660 PHF5: PHF5-like prote 100.0 1E-67 2.2E-72 392.2 -0.3 103 29-131 3-106 (106)
3 PF04216 FdhE: Protein involve 91.2 0.06 1.3E-06 44.0 -0.1 79 54-132 173-281 (290)
4 PRK11595 DNA utilization prote 87.9 0.26 5.6E-06 39.0 1.3 49 54-103 6-56 (227)
5 PF12773 DZR: Double zinc ribb 87.4 0.3 6.4E-06 30.1 1.0 44 56-101 1-49 (50)
6 PF14446 Prok-RING_1: Prokaryo 85.2 0.97 2.1E-05 30.6 2.7 38 54-91 6-51 (54)
7 PRK04023 DNA polymerase II lar 84.3 0.58 1.2E-05 46.7 1.8 44 68-113 625-668 (1121)
8 PRK14559 putative protein seri 82.5 0.82 1.8E-05 42.7 2.0 48 54-103 2-49 (645)
9 PF03833 PolC_DP2: DNA polymer 81.0 0.49 1.1E-05 46.3 0.0 43 69-113 655-697 (900)
10 PRK03564 formate dehydrogenase 80.7 2.2 4.9E-05 36.8 3.9 77 53-129 187-292 (309)
11 PRK05580 primosome assembly pr 79.1 1.5 3.2E-05 40.5 2.4 51 40-90 375-430 (679)
12 PRK14714 DNA polymerase II lar 74.8 2.5 5.4E-05 43.2 2.8 28 47-77 668-700 (1337)
13 PF10571 UPF0547: Uncharacteri 74.6 1.5 3.3E-05 25.4 0.8 22 55-78 2-23 (26)
14 COG1592 Rubrerythrin [Energy p 74.6 1.8 3.9E-05 34.6 1.5 23 69-91 134-159 (166)
15 PF08274 PhnA_Zn_Ribbon: PhnA 73.5 1 2.2E-05 27.1 -0.1 24 54-77 3-27 (30)
16 PRK13130 H/ACA RNA-protein com 73.0 2.1 4.6E-05 28.9 1.3 27 67-93 3-29 (56)
17 TIGR01562 FdhE formate dehydro 72.9 4.9 0.00011 34.6 3.8 77 53-129 184-292 (305)
18 PF00628 PHD: PHD-finger; Int 71.2 4.1 8.9E-05 24.7 2.2 43 55-102 1-49 (51)
19 KOG3507 DNA-directed RNA polym 70.3 3.8 8.2E-05 28.8 2.1 30 64-102 15-44 (62)
20 PF07649 C1_3: C1-like domain; 68.9 1.3 2.8E-05 25.4 -0.4 19 83-101 2-21 (30)
21 PRK10220 hypothetical protein; 66.0 3.5 7.7E-05 31.6 1.4 28 55-82 5-33 (111)
22 TIGR00686 phnA alkylphosphonat 64.5 3.2 7E-05 31.7 0.9 28 55-82 4-32 (109)
23 PRK14873 primosome assembly pr 62.5 5.4 0.00012 37.3 2.2 54 38-91 375-432 (665)
24 TIGR00595 priA primosomal prot 60.8 6.3 0.00014 35.2 2.2 51 41-91 208-263 (505)
25 cd00729 rubredoxin_SM Rubredox 58.0 6.2 0.00013 23.7 1.2 23 69-91 2-28 (34)
26 COG1107 Archaea-specific RecJ- 58.0 7.4 0.00016 37.5 2.2 54 45-106 52-106 (715)
27 PF10764 Gin: Inhibitor of sig 57.9 11 0.00025 24.2 2.5 35 83-126 1-40 (46)
28 smart00661 RPOL9 RNA polymeras 57.5 8.9 0.00019 23.4 1.9 27 55-81 2-32 (52)
29 cd00350 rubredoxin_like Rubred 56.5 6.2 0.00014 23.2 1.0 21 70-90 2-26 (33)
30 PF03107 C1_2: C1 domain; Int 54.5 13 0.00029 21.4 2.1 21 56-77 3-23 (30)
31 KOG0825 PHD Zn-finger protein 53.0 6.7 0.00015 39.2 1.2 49 54-106 216-268 (1134)
32 COG1198 PriA Primosomal protei 50.5 12 0.00026 35.8 2.4 51 40-90 429-484 (730)
33 PF08271 TF_Zn_Ribbon: TFIIB z 50.0 7.4 0.00016 23.8 0.6 22 55-76 2-26 (43)
34 PF08792 A2L_zn_ribbon: A2L zi 49.6 6.4 0.00014 23.8 0.3 23 81-103 3-29 (33)
35 PF07191 zinc-ribbons_6: zinc- 48.2 2.8 6.1E-05 29.7 -1.6 51 54-104 2-59 (70)
36 PF07282 OrfB_Zn_ribbon: Putat 46.8 15 0.00032 23.7 1.7 26 54-79 29-56 (69)
37 PHA00626 hypothetical protein 45.2 13 0.00028 25.9 1.3 26 55-80 2-34 (59)
38 COG2260 Predicted Zn-ribbon RN 44.0 8.9 0.00019 26.6 0.3 26 68-93 4-29 (59)
39 PRK06393 rpoE DNA-directed RNA 43.9 11 0.00023 26.4 0.7 27 70-96 6-32 (64)
40 PRK00432 30S ribosomal protein 43.8 13 0.00028 24.2 1.0 26 55-80 22-48 (50)
41 PTZ00218 40S ribosomal protein 43.5 18 0.0004 24.5 1.8 28 76-103 11-42 (54)
42 PRK14714 DNA polymerase II lar 42.9 19 0.00041 37.1 2.5 31 70-101 668-698 (1337)
43 PRK11823 DNA repair protein Ra 41.7 17 0.00036 32.1 1.7 28 67-94 5-34 (446)
44 PF02132 RecR: RecR protein; 41.3 5.2 0.00011 24.6 -1.0 26 66-91 14-39 (41)
45 KOG1813 Predicted E3 ubiquitin 40.7 15 0.00033 32.5 1.3 36 55-90 243-284 (313)
46 TIGR01384 TFS_arch transcripti 40.6 20 0.00044 25.0 1.7 26 55-80 2-27 (104)
47 PF03833 PolC_DP2: DNA polymer 40.0 9.5 0.00021 37.7 0.0 44 47-93 656-704 (900)
48 smart00249 PHD PHD zinc finger 38.9 30 0.00065 19.3 2.0 44 56-101 2-47 (47)
49 smart00547 ZnF_RBZ Zinc finger 38.5 21 0.00045 19.3 1.2 20 71-90 4-25 (26)
50 cd01675 RNR_III Class III ribo 38.3 17 0.00037 33.1 1.3 26 66-91 515-542 (555)
51 smart00261 FU Furin-like repea 37.8 28 0.0006 20.7 1.8 35 47-86 2-38 (46)
52 PRK05766 rps14P 30S ribosomal 37.7 23 0.00049 23.5 1.5 29 75-103 8-40 (52)
53 PF09963 DUF2197: Uncharacteri 36.4 22 0.00048 24.3 1.3 9 94-102 30-38 (56)
54 PF06906 DUF1272: Protein of u 36.4 11 0.00023 26.1 -0.2 36 55-90 7-50 (57)
55 KOG1100 Predicted E3 ubiquitin 35.9 16 0.00034 29.6 0.7 33 56-90 161-198 (207)
56 PF10235 Cript: Microtubule-as 35.7 19 0.00042 26.4 1.0 32 55-89 46-77 (90)
57 PF13248 zf-ribbon_3: zinc-rib 35.5 19 0.00041 20.2 0.8 20 83-102 4-23 (26)
58 PF13453 zf-TFIIB: Transcripti 35.0 34 0.00073 20.7 1.9 11 55-65 1-11 (41)
59 TIGR00570 cdk7 CDK-activating 34.9 24 0.00052 30.9 1.6 23 53-76 3-27 (309)
60 TIGR00615 recR recombination p 34.8 24 0.00052 28.9 1.5 34 66-99 50-83 (195)
61 smart00440 ZnF_C2C2 C2C2 Zinc 34.5 42 0.0009 20.6 2.3 13 65-77 24-36 (40)
62 PRK04023 DNA polymerase II lar 34.4 31 0.00068 35.1 2.5 42 54-101 627-669 (1121)
63 PF09986 DUF2225: Uncharacteri 33.0 38 0.00082 27.1 2.4 14 68-81 47-60 (214)
64 PF01753 zf-MYND: MYND finger; 32.8 19 0.00042 21.1 0.5 23 72-100 1-23 (37)
65 smart00132 LIM Zinc-binding do 32.6 59 0.0013 17.6 2.5 12 55-66 1-12 (39)
66 PRK14282 chaperone protein Dna 32.3 18 0.0004 30.9 0.5 10 45-54 151-160 (369)
67 TIGR00416 sms DNA repair prote 31.3 32 0.00069 30.5 1.8 27 68-94 6-34 (454)
68 PRK08270 anaerobic ribonucleos 31.1 28 0.00061 32.7 1.5 26 65-90 622-648 (656)
69 TIGR00354 polC DNA polymerase, 30.9 27 0.00059 35.4 1.5 30 68-98 624-653 (1095)
70 TIGR02827 RNR_anaer_Bdell anae 30.8 30 0.00065 32.4 1.7 26 66-91 529-556 (586)
71 KOG0801 Predicted E3 ubiquitin 30.4 32 0.0007 28.7 1.6 12 54-65 139-150 (205)
72 PRK00076 recR recombination pr 29.2 33 0.00073 28.0 1.5 34 66-99 50-83 (196)
73 PRK07111 anaerobic ribonucleos 29.1 27 0.00058 33.3 1.1 28 63-90 674-702 (735)
74 PRK14285 chaperone protein Dna 28.3 28 0.0006 29.9 0.9 51 46-102 146-206 (365)
75 PF04134 DUF393: Protein of un 28.2 8.4 0.00018 26.5 -1.8 12 53-64 4-15 (114)
76 PRK13844 recombination protein 28.2 35 0.00076 28.1 1.5 33 66-98 54-86 (200)
77 COG4098 comFA Superfamily II D 28.0 35 0.00075 31.5 1.6 16 93-108 58-73 (441)
78 PRK12286 rpmF 50S ribosomal pr 28.0 44 0.00096 22.3 1.7 22 54-78 28-49 (57)
79 PRK08271 anaerobic ribonucleos 26.7 27 0.00058 32.9 0.6 30 62-91 559-590 (623)
80 PRK14284 chaperone protein Dna 26.6 30 0.00066 29.9 0.9 51 45-101 157-217 (391)
81 cd03031 GRX_GRX_like Glutaredo 26.5 59 0.0013 25.0 2.4 30 48-77 112-141 (147)
82 PRK12496 hypothetical protein; 26.5 42 0.0009 26.1 1.6 23 69-91 127-153 (164)
83 PF09180 ProRS-C_1: Prolyl-tRN 26.4 20 0.00043 24.1 -0.2 20 78-97 45-64 (68)
84 cd01121 Sms Sms (bacterial rad 26.3 31 0.00066 30.0 0.9 25 70-94 1-27 (372)
85 PRK14289 chaperone protein Dna 26.1 25 0.00055 30.1 0.3 22 81-102 197-218 (386)
86 PRK14890 putative Zn-ribbon RN 26.1 37 0.0008 23.5 1.1 43 55-101 9-54 (59)
87 PRK11788 tetratricopeptide rep 25.8 43 0.00094 26.5 1.6 25 68-92 353-379 (389)
88 PF06689 zf-C4_ClpX: ClpX C4-t 25.7 74 0.0016 19.6 2.3 31 71-104 3-33 (41)
89 PRK08351 DNA-directed RNA poly 25.6 33 0.00072 23.6 0.8 21 71-91 5-25 (61)
90 PF01783 Ribosomal_L32p: Ribos 25.5 26 0.00056 22.9 0.2 21 54-77 27-47 (56)
91 PF04184 ST7: ST7 protein; In 25.5 20 0.00044 33.7 -0.4 29 5-36 146-175 (539)
92 PRK14283 chaperone protein Dna 25.4 54 0.0012 28.2 2.2 52 42-93 142-215 (378)
93 TIGR02349 DnaJ_bact chaperone 25.3 31 0.00068 29.0 0.7 12 44-55 141-152 (354)
94 TIGR01031 rpmF_bact ribosomal 24.6 45 0.00097 22.0 1.2 21 54-77 27-47 (55)
95 PF03119 DNA_ligase_ZBD: NAD-d 24.4 21 0.00046 20.7 -0.3 10 55-64 1-10 (28)
96 PF00641 zf-RanBP: Zn-finger i 24.2 15 0.00033 20.8 -0.9 20 71-90 6-27 (30)
97 PRK14286 chaperone protein Dna 24.0 21 0.00045 30.7 -0.6 10 46-55 150-159 (372)
98 COG2824 PhnA Uncharacterized Z 23.8 34 0.00074 26.4 0.6 26 55-80 5-31 (112)
99 PRK14294 chaperone protein Dna 23.6 23 0.0005 30.2 -0.3 22 81-102 183-204 (366)
100 PF04423 Rad50_zn_hook: Rad50 23.4 24 0.00053 22.3 -0.2 12 53-64 20-31 (54)
101 PRK14291 chaperone protein Dna 23.2 55 0.0012 28.2 1.8 12 44-55 154-165 (382)
102 TIGR02487 NrdD anaerobic ribon 23.2 37 0.0008 31.2 0.8 30 62-91 517-548 (579)
103 PF09297 zf-NADH-PPase: NADH p 23.0 28 0.00062 20.1 0.0 23 55-77 5-29 (32)
104 smart00782 PhnA_Zn_Ribbon PhnA 23.0 46 0.001 21.6 1.0 13 50-62 4-16 (47)
105 PF06827 zf-FPG_IleRS: Zinc fi 23.0 37 0.0008 19.2 0.5 10 55-64 3-12 (30)
106 COG4068 Uncharacterized protei 22.2 31 0.00067 24.4 0.1 28 82-109 9-38 (64)
107 PRK14704 anaerobic ribonucleos 22.1 55 0.0012 30.7 1.7 26 66-91 556-582 (618)
108 COG5270 PUA domain (predicted 21.8 51 0.0011 27.7 1.3 26 66-91 11-36 (202)
109 PF14471 DUF4428: Domain of un 21.6 36 0.00079 22.1 0.3 20 83-102 1-27 (51)
110 PF09889 DUF2116: Uncharacteri 21.6 39 0.00085 23.0 0.5 21 82-102 4-25 (59)
111 PF13597 NRDD: Anaerobic ribon 21.6 24 0.00053 32.1 -0.7 30 62-91 484-514 (546)
112 PF01096 TFIIS_C: Transcriptio 21.4 60 0.0013 19.8 1.3 13 65-77 24-36 (39)
113 PF14447 Prok-RING_4: Prokaryo 21.3 40 0.00087 23.0 0.5 22 69-90 27-48 (55)
114 PRK14288 chaperone protein Dna 21.1 36 0.00078 29.3 0.3 11 45-55 139-149 (369)
115 KOG2813 Predicted molecular ch 21.1 62 0.0013 29.6 1.8 38 55-93 219-257 (406)
116 PRK10767 chaperone protein Dna 21.0 28 0.0006 29.7 -0.4 12 43-54 139-150 (371)
117 PF04810 zf-Sec23_Sec24: Sec23 20.9 63 0.0014 19.6 1.3 15 55-69 4-18 (40)
118 PF08421 Methyltransf_13: Puta 20.8 62 0.0013 21.3 1.3 24 56-79 18-50 (62)
119 PF12855 Ecl1: Life-span regul 20.8 28 0.00061 22.3 -0.3 24 81-104 6-33 (43)
120 TIGR00627 tfb4 transcription f 20.6 56 0.0012 27.8 1.4 20 34-54 244-263 (279)
121 TIGR00577 fpg formamidopyrimid 20.5 42 0.0009 27.7 0.5 25 77-101 241-271 (272)
122 PLN03158 methionine aminopepti 20.4 58 0.0013 28.8 1.4 32 69-101 9-43 (396)
123 PF13842 Tnp_zf-ribbon_2: DDE_ 20.1 62 0.0013 19.2 1.1 19 83-101 2-22 (32)
No 1
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=100.00 E-value=4.8e-67 Score=388.89 Aligned_cols=108 Identities=88% Similarity=1.656 Sum_probs=105.9
Q ss_pred ccCcceeeeccCCCcccccccccCCCceecccCCCCCceeeEecCCCCCCCcCCeeEEecCCCccceeeehhhhhhhccC
Q 037283 29 SIWTSSLLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQQEKDR 108 (136)
Q Consensus 29 ~~~~DLi~C~KqpG~~iG~lC~kCdGkCpICDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~g~sdAYYC~EC~~lEKDR 108 (136)
+||||||||+||||++||+||||||||||||||||||+|+||||++|+||+++++|||||++|++||||||||+++||||
T Consensus 3 kHhpDLi~CrkQPGi~~G~LCEkCDgkC~ICDS~VRP~tlVRiC~eC~~Gs~q~~ciic~~~gV~d~~yc~ectr~ekdr 82 (110)
T KOG1705|consen 3 KHHPDLIMCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGVGVSDAYYCKECTRQEKDR 82 (110)
T ss_pred CcCCcEEEEecCCCchhhhhHHhcCCcccccccccccceeeeeehhcCCccccCceEEecCCcccchHHHHHHHhhcccc
Confidence 45999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcceeccCCchhHHHHHHhhhcccCC
Q 037283 109 DGCPKIVNLGSAKTDLFYERKKYGFKKR 136 (136)
Q Consensus 109 DGCPrIiN~Gs~ktD~~yekkk~~~kk~ 136 (136)
||||||+|+||+|+|+||||||++|+++
T Consensus 83 dgCpri~nlgS~r~d~~~erkk~~~~~~ 110 (110)
T KOG1705|consen 83 DGCPKIVNLGSSKTDLFYERKKYGFKKR 110 (110)
T ss_pred ccChhhhhcccccchHHHHHHhhccccC
Confidence 9999999999999999999999999875
No 2
>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=1e-67 Score=392.22 Aligned_cols=103 Identities=71% Similarity=1.436 Sum_probs=66.3
Q ss_pred ccCcceeeeccCCCcccccccccCCCceecccCCCCCceeeEecCCCCCCCcCCeeEEec-CCCccceeeehhhhhhhcc
Q 037283 29 SIWTSSLLCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICG-GVGISDAYYCKECTQQEKD 107 (136)
Q Consensus 29 ~~~~DLi~C~KqpG~~iG~lC~kCdGkCpICDS~Vrp~~~VrICdeCs~G~~~~rCIiCg-~~g~sdAYYC~EC~~lEKD 107 (136)
+|||||||||||||++||+||++||||||||||||||+++|||||+||||++++|||||| ++|+++|||||||++||||
T Consensus 3 rH~~DLvmC~KqpG~~iG~lC~kCdGkCpiCDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~~g~sdAYYC~eC~~lEKd 82 (106)
T PF03660_consen 3 RHQPDLVMCRKQPGTAIGRLCEKCDGKCPICDSYVRPCTKVRICDECSFGSLQGRCIICGSGPGVSDAYYCWECVRLEKD 82 (106)
T ss_dssp S--TT--B----EEEEE-EE-GGGTT--TTT-------EE-EEEHHHHTSSTTSB-TTTSSSB--EE-EE-HHHHHHTST
T ss_pred ccChhHhhhccCCcchhhhhhhhcCCcccccCCccCCcceEEECCcCCCCCcCceEEEecCCCCcccceehhhhHhhhcc
Confidence 459999999999999999999999999999999999999999999999999999999999 8999999999999999999
Q ss_pred CCCCcceeccCCchhHHHHHHhhh
Q 037283 108 RDGCPKIVNLGSAKTDLFYERKKY 131 (136)
Q Consensus 108 RDGCPrIiN~Gs~ktD~~yekkk~ 131 (136)
|||||||||+||+|+|+|||+||.
T Consensus 83 RDGCPriiN~Gs~r~d~~~~~kk~ 106 (106)
T PF03660_consen 83 RDGCPRIINVGSSRTDRFYEKKKK 106 (106)
T ss_dssp TS----B-S-SS-SSTT---SSTT
T ss_pred ccCCceeEeccchhhhHHHHhhcC
Confidence 999999999999999999999874
No 3
>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=91.18 E-value=0.06 Score=44.05 Aligned_cols=79 Identities=25% Similarity=0.490 Sum_probs=47.8
Q ss_pred CceecccCC-----CCCc----eeeEecCCCCCCC--cCCeeEEecCCC-------------ccceeeehhhhh------
Q 037283 54 GKCVICDSY-----VRPC----TLVRVCDECNYGS--FQGRCVICGGVG-------------ISDAYYCKECTQ------ 103 (136)
Q Consensus 54 GkCpICDS~-----Vrp~----~~VrICdeCs~G~--~~~rCIiCg~~g-------------~sdAYYC~EC~~------ 103 (136)
|.||+|.|. |++. .+.-.|..|++.- .+.+|..||+.+ ..-++-|.+|..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd 252 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVD 252 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEE
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHh
Confidence 899999996 4443 5888999999754 467899999755 233778999943
Q ss_pred hhccCCCCcceeccCCchhHHHHHHhhhc
Q 037283 104 QEKDRDGCPKIVNLGSAKTDLFYERKKYG 132 (136)
Q Consensus 104 lEKDRDGCPrIiN~Gs~ktD~~yekkk~~ 132 (136)
+|+|.+-=|-+-+++|-.-|+..+.+-+.
T Consensus 253 ~~~~~~~~~~~dDl~tl~LD~~a~e~Gy~ 281 (290)
T PF04216_consen 253 REKDPELDPVADDLATLHLDLLAQEEGYR 281 (290)
T ss_dssp TTT-TT--HHHHHHTTHHHHHHHHHTT-E
T ss_pred hhhCcccchhhHHhhhhhHHHHHHhCCCC
Confidence 57777776777799999999988766543
No 4
>PRK11595 DNA utilization protein GntX; Provisional
Probab=87.95 E-value=0.26 Score=39.04 Aligned_cols=49 Identities=22% Similarity=0.551 Sum_probs=33.5
Q ss_pred CceecccCCCCCceeeEecCCCCCC--CcCCeeEEecCCCccceeeehhhhh
Q 037283 54 GKCVICDSYVRPCTLVRVCDECNYG--SFQGRCVICGGVGISDAYYCKECTQ 103 (136)
Q Consensus 54 GkCpICDS~Vrp~~~VrICdeCs~G--~~~~rCIiCg~~g~sdAYYC~EC~~ 103 (136)
.+|++|+-.+.+. ...||+.|.-. .....|..||.+.....+.|.+|..
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 23489999522 2346899999875544567999954
No 5
>PF12773 DZR: Double zinc ribbon
Probab=87.37 E-value=0.3 Score=30.13 Aligned_cols=44 Identities=23% Similarity=0.590 Sum_probs=27.4
Q ss_pred eecccCCCCCceeeEecCCCCCCCc-----CCeeEEecCCCccceeeehhh
Q 037283 56 CVICDSYVRPCTLVRVCDECNYGSF-----QGRCVICGGVGISDAYYCKEC 101 (136)
Q Consensus 56 CpICDS~Vrp~~~VrICdeCs~G~~-----~~rCIiCg~~g~sdAYYC~EC 101 (136)
||.|...+.+. ++.|..|+.--. ...|..||.+...+|-||..|
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 45555554443 456666654332 346888888777778888776
No 6
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=85.16 E-value=0.97 Score=30.59 Aligned_cols=38 Identities=29% Similarity=0.590 Sum_probs=31.7
Q ss_pred CceecccCCCCCceeeEecCCCCCCC------cCCeeEE--ecCCC
Q 037283 54 GKCVICDSYVRPCTLVRVCDECNYGS------FQGRCVI--CGGVG 91 (136)
Q Consensus 54 GkCpICDS~Vrp~~~VrICdeCs~G~------~~~rCIi--Cg~~g 91 (136)
++|++|...++|..-+-+|.+|+--. ..+.|++ ||.+-
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 68999999999999999999999542 3578999 87643
No 7
>PRK04023 DNA polymerase II large subunit; Validated
Probab=84.27 E-value=0.58 Score=46.71 Aligned_cols=44 Identities=32% Similarity=0.736 Sum_probs=33.8
Q ss_pred eeEecCCCCCCCcCCeeEEecCCCccceeeehhhhhhhccCCCCcc
Q 037283 68 LVRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQQEKDRDGCPK 113 (136)
Q Consensus 68 ~VrICdeCs~G~~~~rCIiCg~~g~sdAYYC~EC~~lEKDRDGCPr 113 (136)
-.|.|.+|+......+|..||.. +..+|.|.+|..+.. .+-||+
T Consensus 625 g~RfCpsCG~~t~~frCP~CG~~-Te~i~fCP~CG~~~~-~y~CPK 668 (1121)
T PRK04023 625 GRRKCPSCGKETFYRRCPFCGTH-TEPVYRCPRCGIEVE-EDECEK 668 (1121)
T ss_pred cCccCCCCCCcCCcccCCCCCCC-CCcceeCccccCcCC-CCcCCC
Confidence 45788888888888999999987 467899999966543 355775
No 8
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=82.55 E-value=0.82 Score=42.72 Aligned_cols=48 Identities=23% Similarity=0.452 Sum_probs=38.6
Q ss_pred CceecccCCCCCceeeEecCCCCCCCcCCeeEEecCCCccceeeehhhhh
Q 037283 54 GKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQ 103 (136)
Q Consensus 54 GkCpICDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~g~sdAYYC~EC~~ 103 (136)
.+||-|...+.+.. +-|.+|+..-....|.-||.+-..+|-+|.+|..
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 36899988876554 5899997765557899999988888999999954
No 9
>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=81.03 E-value=0.49 Score=46.28 Aligned_cols=43 Identities=37% Similarity=0.896 Sum_probs=0.0
Q ss_pred eEecCCCCCCCcCCeeEEecCCCccceeeehhhhhhhccCCCCcc
Q 037283 69 VRVCDECNYGSFQGRCVICGGVGISDAYYCKECTQQEKDRDGCPK 113 (136)
Q Consensus 69 VrICdeCs~G~~~~rCIiCg~~g~sdAYYC~EC~~lEKDRDGCPr 113 (136)
-|.|..|+.-+...+|-.||+.. ..-|+|..|.. +-+.+-||+
T Consensus 655 ~r~Cp~Cg~~t~~~~Cp~CG~~T-~~~~~Cp~C~~-~~~~~~C~~ 697 (900)
T PF03833_consen 655 RRRCPKCGKETFYNRCPECGSHT-EPVYVCPDCGI-EVEEDECPK 697 (900)
T ss_dssp ---------------------------------------------
T ss_pred cccCcccCCcchhhcCcccCCcc-ccceecccccc-ccCcccccc
Confidence 47888888888888998898743 44788888854 444557875
No 10
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=80.69 E-value=2.2 Score=36.82 Aligned_cols=77 Identities=26% Similarity=0.386 Sum_probs=57.9
Q ss_pred CCceecccCC-----CC----CceeeEecCCCCCCC--cCCeeEEecCCC------------ccceeeehhhh------h
Q 037283 53 DGKCVICDSY-----VR----PCTLVRVCDECNYGS--FQGRCVICGGVG------------ISDAYYCKECT------Q 103 (136)
Q Consensus 53 dGkCpICDS~-----Vr----p~~~VrICdeCs~G~--~~~rCIiCg~~g------------~sdAYYC~EC~------~ 103 (136)
.|.||+|.|. |+ ...+.-.|..|+..- .+.+|..||..+ ..-++-|.+|. -
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~~ 266 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKILY 266 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeeeecCCCcceEeeecccccccceecc
Confidence 6899999996 32 234677899999754 477899999754 12357788884 3
Q ss_pred hhccCCCCcceeccCCchhHHHHHHh
Q 037283 104 QEKDRDGCPKIVNLGSAKTDLFYERK 129 (136)
Q Consensus 104 lEKDRDGCPrIiN~Gs~ktD~~yekk 129 (136)
+|||...=|..-++.|---|+..+.+
T Consensus 267 ~~~d~~~~p~adDlatL~LDl~a~e~ 292 (309)
T PRK03564 267 QEKDPKVEAVADDLASLVLDARMEQE 292 (309)
T ss_pred cccCCCCCcchhHHhhhHhHHHHHhc
Confidence 67887767877899999999988665
No 11
>PRK05580 primosome assembly protein PriA; Validated
Probab=79.13 E-value=1.5 Score=40.45 Aligned_cols=51 Identities=27% Similarity=0.615 Sum_probs=40.9
Q ss_pred CCCcccccccccCC--CceecccCCCC--CceeeEecCCCCCCCc-CCeeEEecCC
Q 037283 40 QPGIAIGRLCEKCD--GKCVICDSYVR--PCTLVRVCDECNYGSF-QGRCVICGGV 90 (136)
Q Consensus 40 qpG~~iG~lC~kCd--GkCpICDS~Vr--p~~~VrICdeCs~G~~-~~rCIiCg~~ 90 (136)
.-|-+--.+|..|. -+||.||.... -.+..-.|..|++... ..+|..||+.
T Consensus 375 rrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 375 RRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 34666677899998 68999998754 3566778999999864 7899999985
No 12
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=74.77 E-value=2.5 Score=43.16 Aligned_cols=28 Identities=36% Similarity=0.949 Sum_probs=15.5
Q ss_pred cccccCCC-----ceecccCCCCCceeeEecCCCCC
Q 037283 47 RLCEKCDG-----KCVICDSYVRPCTLVRVCDECNY 77 (136)
Q Consensus 47 ~lC~kCdG-----kCpICDS~Vrp~~~VrICdeCs~ 77 (136)
+.|.+|.. +||.|++...| +..|..|+.
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~te~---vy~CPsCGa 700 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHTEP---VYVCPDCGA 700 (1337)
T ss_pred EECCCCCCccccccCcccCCcCCC---ceeCccCCC
Confidence 44666643 56666665433 345666655
No 13
>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=74.59 E-value=1.5 Score=25.38 Aligned_cols=22 Identities=27% Similarity=0.744 Sum_probs=16.0
Q ss_pred ceecccCCCCCceeeEecCCCCCC
Q 037283 55 KCVICDSYVRPCTLVRVCDECNYG 78 (136)
Q Consensus 55 kCpICDS~Vrp~~~VrICdeCs~G 78 (136)
+||-|++.| ...+++|..|+|-
T Consensus 2 ~CP~C~~~V--~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEV--PESAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCc--hhhcCcCCCCCCC
Confidence 589999888 3445778877763
No 14
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=74.55 E-value=1.8 Score=34.60 Aligned_cols=23 Identities=43% Similarity=0.937 Sum_probs=19.3
Q ss_pred eEecCCCCC---CCcCCeeEEecCCC
Q 037283 69 VRVCDECNY---GSFQGRCVICGGVG 91 (136)
Q Consensus 69 VrICdeCs~---G~~~~rCIiCg~~g 91 (136)
|.||..|+| |.--++|.|||.|.
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~k 159 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAPK 159 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCChH
Confidence 899999998 44567999999864
No 15
>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=73.46 E-value=1 Score=27.10 Aligned_cols=24 Identities=33% Similarity=0.596 Sum_probs=13.4
Q ss_pred CceecccCC-CCCceeeEecCCCCC
Q 037283 54 GKCVICDSY-VRPCTLVRVCDECNY 77 (136)
Q Consensus 54 GkCpICDS~-Vrp~~~VrICdeCs~ 77 (136)
.+||-|.|- .-+...+.||++|++
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 478999884 446778899999975
No 16
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=72.97 E-value=2.1 Score=28.91 Aligned_cols=27 Identities=26% Similarity=0.736 Sum_probs=23.0
Q ss_pred eeeEecCCCCCCCcCCeeEEecCCCcc
Q 037283 67 TLVRVCDECNYGSFQGRCVICGGVGIS 93 (136)
Q Consensus 67 ~~VrICdeCs~G~~~~rCIiCg~~g~s 93 (136)
.+.+.|..|+.-++.+.|..||++..+
T Consensus 3 s~mr~C~~CgvYTLk~~CP~CG~~t~~ 29 (56)
T PRK13130 3 SKIRKCPKCGVYTLKEICPVCGGKTKN 29 (56)
T ss_pred ccceECCCCCCEEccccCcCCCCCCCC
Confidence 467899999998999999999987643
No 17
>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=72.86 E-value=4.9 Score=34.60 Aligned_cols=77 Identities=25% Similarity=0.363 Sum_probs=57.1
Q ss_pred CCceecccCC-----CCC-----ceeeEecCCCCCCC--cCCeeEEecCCC------c--------cceeeehhhh----
Q 037283 53 DGKCVICDSY-----VRP-----CTLVRVCDECNYGS--FQGRCVICGGVG------I--------SDAYYCKECT---- 102 (136)
Q Consensus 53 dGkCpICDS~-----Vrp-----~~~VrICdeCs~G~--~~~rCIiCg~~g------~--------sdAYYC~EC~---- 102 (136)
-|.||+|.|. |+. -.+.-.|..|+..- .+-+|..||... + .-++.|.+|.
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeEeecCCCCCcceEEeeccccccchh
Confidence 4689999996 332 34677899999754 477999999754 1 1366788884
Q ss_pred --hhhccCCCCcceeccCCchhHHHHHHh
Q 037283 103 --QQEKDRDGCPKIVNLGSAKTDLFYERK 129 (136)
Q Consensus 103 --~lEKDRDGCPrIiN~Gs~ktD~~yekk 129 (136)
-+|||.+.=|..-++.|---|+..+.+
T Consensus 264 ~~~~~~d~~~~~~adDlaSL~LD~~a~e~ 292 (305)
T TIGR01562 264 ILYQEKDPHADAVADDLASLALDMRMAED 292 (305)
T ss_pred hhccccCCccCchHHHHhhhHhhHHHHhc
Confidence 368887776777799999999888655
No 18
>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=71.25 E-value=4.1 Score=24.74 Aligned_cols=43 Identities=28% Similarity=0.676 Sum_probs=29.7
Q ss_pred ceecccCCCCCceeeEecCCCCCCCcCCeeEEecCCCc------cceeeehhhh
Q 037283 55 KCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGI------SDAYYCKECT 102 (136)
Q Consensus 55 kCpICDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~g~------sdAYYC~EC~ 102 (136)
.|+||.+ ..+....-.|+.|... +-.. |=++.. ...|+|.+|.
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 4788988 7778888999999943 3333 434331 2379999985
No 19
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=70.25 E-value=3.8 Score=28.78 Aligned_cols=30 Identities=27% Similarity=0.702 Sum_probs=22.6
Q ss_pred CCceeeEecCCCCCCCcCCeeEEecCCCccceeeehhhh
Q 037283 64 RPCTLVRVCDECNYGSFQGRCVICGGVGISDAYYCKECT 102 (136)
Q Consensus 64 rp~~~VrICdeCs~G~~~~rCIiCg~~g~sdAYYC~EC~ 102 (136)
||.+..+||.+|+....-. ..|+.-|+||.
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 7789999999998755322 45788888884
No 20
>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=68.93 E-value=1.3 Score=25.40 Aligned_cols=19 Identities=42% Similarity=0.789 Sum_probs=9.2
Q ss_pred eeEEecCCCcc-ceeeehhh
Q 037283 83 RCVICGGVGIS-DAYYCKEC 101 (136)
Q Consensus 83 rCIiCg~~g~s-dAYYC~EC 101 (136)
+|-+||.++.. ..|+|.+|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~C 21 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSEC 21 (30)
T ss_dssp --TTTS----S--EEE-TTT
T ss_pred cCCcCCCcCCCCceEECccC
Confidence 46678877766 79999988
No 21
>PRK10220 hypothetical protein; Provisional
Probab=65.98 E-value=3.5 Score=31.61 Aligned_cols=28 Identities=25% Similarity=0.513 Sum_probs=22.8
Q ss_pred ceecccC-CCCCceeeEecCCCCCCCcCC
Q 037283 55 KCVICDS-YVRPCTLVRVCDECNYGSFQG 82 (136)
Q Consensus 55 kCpICDS-~Vrp~~~VrICdeCs~G~~~~ 82 (136)
.||-|+| |+-+...-.||.||+|--..+
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCcCCcc
Confidence 5899998 567777789999999977655
No 22
>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=64.53 E-value=3.2 Score=31.68 Aligned_cols=28 Identities=25% Similarity=0.522 Sum_probs=22.8
Q ss_pred ceecccC-CCCCceeeEecCCCCCCCcCC
Q 037283 55 KCVICDS-YVRPCTLVRVCDECNYGSFQG 82 (136)
Q Consensus 55 kCpICDS-~Vrp~~~VrICdeCs~G~~~~ 82 (136)
.||-|.| |+-+.....||.||+|--...
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccccccc
Confidence 5899998 577777789999999977544
No 23
>PRK14873 primosome assembly protein PriA; Provisional
Probab=62.52 E-value=5.4 Score=37.30 Aligned_cols=54 Identities=20% Similarity=0.445 Sum_probs=43.2
Q ss_pred ccCCCcccccccccCC--CceecccCCCCC--ceeeEecCCCCCCCcCCeeEEecCCC
Q 037283 38 RKQPGIAIGRLCEKCD--GKCVICDSYVRP--CTLVRVCDECNYGSFQGRCVICGGVG 91 (136)
Q Consensus 38 ~KqpG~~iG~lC~kCd--GkCpICDS~Vrp--~~~VrICdeCs~G~~~~rCIiCg~~g 91 (136)
...-|-+--.+|..|. -+||-||....= .+..-.|.-|++.....+|.-||+..
T Consensus 375 lnRrGyap~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~~ 432 (665)
T PRK14873 375 VPRRGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSDR 432 (665)
T ss_pred ecCCCCCCeeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCCc
Confidence 4556777778999997 489999977542 45577899999987788999999864
No 24
>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=60.84 E-value=6.3 Score=35.21 Aligned_cols=51 Identities=25% Similarity=0.513 Sum_probs=39.1
Q ss_pred CCcccccccccCCC--ceecccCCCC--CceeeEecCCCCCCCc-CCeeEEecCCC
Q 037283 41 PGIAIGRLCEKCDG--KCVICDSYVR--PCTLVRVCDECNYGSF-QGRCVICGGVG 91 (136)
Q Consensus 41 pG~~iG~lC~kCdG--kCpICDS~Vr--p~~~VrICdeCs~G~~-~~rCIiCg~~g 91 (136)
-|-+--.+|..|.- +||-||.... -....-.|.-|++... -.+|.-||+..
T Consensus 208 rGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~ 263 (505)
T TIGR00595 208 RGYSKNLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSED 263 (505)
T ss_pred CcCCCeeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCe
Confidence 45555678999976 5999998753 2445678999999875 77999999853
No 25
>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=58.01 E-value=6.2 Score=23.68 Aligned_cols=23 Identities=39% Similarity=0.816 Sum_probs=16.3
Q ss_pred eEecCCCCCCCc----CCeeEEecCCC
Q 037283 69 VRVCDECNYGSF----QGRCVICGGVG 91 (136)
Q Consensus 69 VrICdeCs~G~~----~~rCIiCg~~g 91 (136)
+.+|..|+|-.. -++|.+||.+.
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~~~ 28 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGAPK 28 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCCch
Confidence 467888887532 36899999753
No 26
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=57.98 E-value=7.4 Score=37.52 Aligned_cols=54 Identities=31% Similarity=0.616 Sum_probs=38.8
Q ss_pred cccccccCCCceecccCCCCCceeeEecCCCCCCCcCCeeEEecC-CCccceeeehhhhhhhc
Q 037283 45 IGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGG-VGISDAYYCKECTQQEK 106 (136)
Q Consensus 45 iG~lC~kCdGkCpICDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~-~g~sdAYYC~EC~~lEK 106 (136)
.+-.|++|+|+ ..-+.-.-|++|+=.-...+|-+||. .+...-|.|.||-+.++
T Consensus 52 ~~~pc~~c~gk--------G~V~v~~~c~~c~G~gkv~~c~~cG~~~~~~~~~lc~~c~~~~~ 106 (715)
T COG1107 52 FEIPCPKCRGK--------GTVTVYDTCPECGGTGKVLTCDICGDIIVPWEEGLCPECRRKPK 106 (715)
T ss_pred CCCCCCeeccc--------eeEEEEeecccCCCceeEEeeccccceecCcccccChhHhhCCc
Confidence 45679999887 23345567888876556778999996 33344568999988877
No 27
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=57.86 E-value=11 Score=24.24 Aligned_cols=35 Identities=34% Similarity=0.837 Sum_probs=24.3
Q ss_pred eeEEecCCC-----ccceeeehhhhhhhccCCCCcceeccCCchhHHHH
Q 037283 83 RCVICGGVG-----ISDAYYCKECTQQEKDRDGCPKIVNLGSAKTDLFY 126 (136)
Q Consensus 83 rCIiCg~~g-----~sdAYYC~EC~~lEKDRDGCPrIiN~Gs~ktD~~y 126 (136)
.||+||.+. +...|-|.+| |+ +|||+-++..+--|
T Consensus 1 ~CiiC~~~~~~GI~I~~~fIC~~C---E~------~iv~~~~~d~~Y~~ 40 (46)
T PF10764_consen 1 KCIICGKEKEEGIHIYGKFICSDC---EK------EIVNTETDDPKYEF 40 (46)
T ss_pred CeEeCCCcCCCCEEEECeEehHHH---HH------HhccCCCCCCCHHH
Confidence 499999643 4668999999 43 47777776665433
No 28
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=57.50 E-value=8.9 Score=23.39 Aligned_cols=27 Identities=26% Similarity=0.525 Sum_probs=19.8
Q ss_pred ceecccCCCCCce----eeEecCCCCCCCcC
Q 037283 55 KCVICDSYVRPCT----LVRVCDECNYGSFQ 81 (136)
Q Consensus 55 kCpICDS~Vrp~~----~VrICdeCs~G~~~ 81 (136)
-||-|.+.+-|.. ...+|..|+|....
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEEC
Confidence 3888888876643 36889999987653
No 29
>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=56.49 E-value=6.2 Score=23.21 Aligned_cols=21 Identities=33% Similarity=0.713 Sum_probs=13.7
Q ss_pred EecCCCCCCC----cCCeeEEecCC
Q 037283 70 RVCDECNYGS----FQGRCVICGGV 90 (136)
Q Consensus 70 rICdeCs~G~----~~~rCIiCg~~ 90 (136)
.+|..|+|-. -..+|.+||.+
T Consensus 2 ~~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCcCCCcCcCCCCc
Confidence 5677777642 34588888864
No 30
>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=54.50 E-value=13 Score=21.37 Aligned_cols=21 Identities=24% Similarity=0.727 Sum_probs=12.6
Q ss_pred eecccCCCCCceeeEecCCCCC
Q 037283 56 CVICDSYVRPCTLVRVCDECNY 77 (136)
Q Consensus 56 CpICDS~Vrp~~~VrICdeCs~ 77 (136)
|-+|...+.+.. ++.|++|.|
T Consensus 3 C~~C~~~~~~~~-~Y~C~~c~f 23 (30)
T PF03107_consen 3 CDVCRRKIDGFY-FYHCSECCF 23 (30)
T ss_pred CCCCCCCcCCCE-eEEeCCCCC
Confidence 555666666655 666666664
No 31
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=53.03 E-value=6.7 Score=39.17 Aligned_cols=49 Identities=29% Similarity=0.716 Sum_probs=37.3
Q ss_pred CceecccCCCCCceeeEecCCCCCCCcCCeeEEecCCCc----cceeeehhhhhhhc
Q 037283 54 GKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGI----SDAYYCKECTQQEK 106 (136)
Q Consensus 54 GkCpICDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~g~----sdAYYC~EC~~lEK 106 (136)
-+|.||.+. .|....-.||.|+++.+..-|. .|.. ...+||..|..||-
T Consensus 216 ~~C~IC~~~-DpEdVLLLCDsCN~~~YH~YCL---DPdl~eiP~~eWYC~NC~dL~~ 268 (1134)
T KOG0825|consen 216 VKCDICTVH-DPEDVLLLCDSCNKVYYHVYCL---DPDLSESPVNEWYCTNCSLLEI 268 (1134)
T ss_pred ccceeeccC-ChHHhheeecccccceeecccc---CcccccccccceecCcchhhhh
Confidence 489999886 4566667899999998776554 5543 45789999988764
No 32
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=50.47 E-value=12 Score=35.84 Aligned_cols=51 Identities=31% Similarity=0.634 Sum_probs=41.0
Q ss_pred CCCcccccccccCC--CceecccCCCC--CceeeEecCCCCCC-CcCCeeEEecCC
Q 037283 40 QPGIAIGRLCEKCD--GKCVICDSYVR--PCTLVRVCDECNYG-SFQGRCVICGGV 90 (136)
Q Consensus 40 qpG~~iG~lC~kCd--GkCpICDS~Vr--p~~~VrICdeCs~G-~~~~rCIiCg~~ 90 (136)
.-|-+--.+|..|. -+||-||++.- -.+..-.|..|++- ..-.+|.-||+.
T Consensus 429 RRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 429 RRGYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cCCccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 34666677899997 48999999853 36688899999998 457899999986
No 33
>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=50.03 E-value=7.4 Score=23.76 Aligned_cols=22 Identities=36% Similarity=0.644 Sum_probs=12.0
Q ss_pred ceecccCCC---CCceeeEecCCCC
Q 037283 55 KCVICDSYV---RPCTLVRVCDECN 76 (136)
Q Consensus 55 kCpICDS~V---rp~~~VrICdeCs 76 (136)
+||.|.+.. .+.+--.||..|+
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 577777642 3444455666664
No 34
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=49.59 E-value=6.4 Score=23.80 Aligned_cols=23 Identities=39% Similarity=0.801 Sum_probs=15.9
Q ss_pred CCeeEEecCCCcc----ceeeehhhhh
Q 037283 81 QGRCVICGGVGIS----DAYYCKECTQ 103 (136)
Q Consensus 81 ~~rCIiCg~~g~s----dAYYC~EC~~ 103 (136)
..+|..||++++. +-|.|.+|..
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCc
Confidence 4578888888754 4567887754
No 35
>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=48.23 E-value=2.8 Score=29.66 Aligned_cols=51 Identities=20% Similarity=0.420 Sum_probs=28.2
Q ss_pred CceecccCCCCCceeeEecCCCCCCC-cCCeeEEecCCC------ccceeeehhhhhh
Q 037283 54 GKCVICDSYVRPCTLVRVCDECNYGS-FQGRCVICGGVG------ISDAYYCKECTQQ 104 (136)
Q Consensus 54 GkCpICDS~Vrp~~~VrICdeCs~G~-~~~rCIiCg~~g------~sdAYYC~EC~~l 104 (136)
-.||.|...+.+....+.|+.|.--- ....|.-|+.+- .+.-|.|..|-.|
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c~gL 59 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHCHGL 59 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTTT-E
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcccceeeccCCce
Confidence 35888888888877778888887532 245666666543 3456889877544
No 36
>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=46.84 E-value=15 Score=23.75 Aligned_cols=26 Identities=19% Similarity=0.506 Sum_probs=18.8
Q ss_pred CceecccCCCCC--ceeeEecCCCCCCC
Q 037283 54 GKCVICDSYVRP--CTLVRVCDECNYGS 79 (136)
Q Consensus 54 GkCpICDS~Vrp--~~~VrICdeCs~G~ 79 (136)
-.||.|+..++. ...+..|..|++..
T Consensus 29 q~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 29 QTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred cCccCcccccccccccceEEcCCCCCEE
Confidence 358888887655 77788888887643
No 37
>PHA00626 hypothetical protein
Probab=45.17 E-value=13 Score=25.92 Aligned_cols=26 Identities=27% Similarity=0.548 Sum_probs=15.1
Q ss_pred ceecccCC--CC-----CceeeEecCCCCCCCc
Q 037283 55 KCVICDSY--VR-----PCTLVRVCDECNYGSF 80 (136)
Q Consensus 55 kCpICDS~--Vr-----p~~~VrICdeCs~G~~ 80 (136)
.||.|.|- +| -.+--+.|..|+|--+
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 57888872 33 3344566777766443
No 38
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=44.01 E-value=8.9 Score=26.63 Aligned_cols=26 Identities=31% Similarity=0.839 Sum_probs=20.7
Q ss_pred eeEecCCCCCCCcCCeeEEecCCCcc
Q 037283 68 LVRVCDECNYGSFQGRCVICGGVGIS 93 (136)
Q Consensus 68 ~VrICdeCs~G~~~~rCIiCg~~g~s 93 (136)
+.|.|..|+-=+.+++|..||+...+
T Consensus 4 ~~rkC~~cg~YTLke~Cp~CG~~t~~ 29 (59)
T COG2260 4 LIRKCPKCGRYTLKEKCPVCGGDTKV 29 (59)
T ss_pred hhhcCcCCCceeecccCCCCCCcccc
Confidence 45778888888888999999986643
No 39
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=43.85 E-value=11 Score=26.38 Aligned_cols=27 Identities=19% Similarity=0.524 Sum_probs=20.4
Q ss_pred EecCCCCCCCcCCeeEEecCCCcccee
Q 037283 70 RVCDECNYGSFQGRCVICGGVGISDAY 96 (136)
Q Consensus 70 rICdeCs~G~~~~rCIiCg~~g~sdAY 96 (136)
+-|..|.+-...+.|.+||+...++-+
T Consensus 6 ~AC~~C~~i~~~~~Cp~Cgs~~~S~~w 32 (64)
T PRK06393 6 RACKKCKRLTPEKTCPVHGDEKTTTEW 32 (64)
T ss_pred hhHhhCCcccCCCcCCCCCCCcCCcCc
Confidence 467888887777889999987766543
No 40
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=43.83 E-value=13 Score=24.19 Aligned_cols=26 Identities=27% Similarity=0.639 Sum_probs=18.7
Q ss_pred ceecccC-CCCCceeeEecCCCCCCCc
Q 037283 55 KCVICDS-YVRPCTLVRVCDECNYGSF 80 (136)
Q Consensus 55 kCpICDS-~Vrp~~~VrICdeCs~G~~ 80 (136)
-||-|.+ +..+......|..|+|-.+
T Consensus 22 fCP~Cg~~~m~~~~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 22 FCPRCGSGFMAEHLDRWHCGKCGYTEF 48 (50)
T ss_pred cCcCCCcchheccCCcEECCCcCCEEe
Confidence 3666777 7777777778888887554
No 41
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=43.47 E-value=18 Score=24.53 Aligned_cols=28 Identities=21% Similarity=0.667 Sum_probs=21.0
Q ss_pred CCCCcCCeeEEecCCC-c---cceeeehhhhh
Q 037283 76 NYGSFQGRCVICGGVG-I---SDAYYCKECTQ 103 (136)
Q Consensus 76 s~G~~~~rCIiCg~~g-~---sdAYYC~EC~~ 103 (136)
.||+...+|.+||.+. . ..-+.|+.|-+
T Consensus 11 ~yGkGsr~C~vCg~~~gliRkygL~~CRqCFR 42 (54)
T PTZ00218 11 TYGKGSRQCRVCSNRHGLIRKYGLNVCRQCFR 42 (54)
T ss_pred cCCCCCCeeecCCCcchhhhhcCcchhhHHHH
Confidence 4899999999999854 2 34556888754
No 42
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=42.90 E-value=19 Score=37.13 Aligned_cols=31 Identities=32% Similarity=0.909 Sum_probs=14.8
Q ss_pred EecCCCCCCCcCCeeEEecCCCccceeeehhh
Q 037283 70 RVCDECNYGSFQGRCVICGGVGISDAYYCKEC 101 (136)
Q Consensus 70 rICdeCs~G~~~~rCIiCg~~g~sdAYYC~EC 101 (136)
+.|..|+.-..+.+|-.||.+.. ..|.|..|
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~te-~vy~CPsC 698 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHTE-PVYVCPDC 698 (1337)
T ss_pred EECCCCCCccccccCcccCCcCC-CceeCccC
Confidence 45555555444445555554432 23445554
No 43
>PRK11823 DNA repair protein RadA; Provisional
Probab=41.72 E-value=17 Score=32.07 Aligned_cols=28 Identities=36% Similarity=0.611 Sum_probs=22.7
Q ss_pred eeeEecCCCCCCCc--CCeeEEecCCCccc
Q 037283 67 TLVRVCDECNYGSF--QGRCVICGGVGISD 94 (136)
Q Consensus 67 ~~VrICdeCs~G~~--~~rCIiCg~~g~sd 94 (136)
...++|.+|+|.+. .++|.-||.-+...
T Consensus 5 ~~~y~C~~Cg~~~~~~~g~Cp~C~~w~t~~ 34 (446)
T PRK11823 5 KTAYVCQECGAESPKWLGRCPECGAWNTLV 34 (446)
T ss_pred CCeEECCcCCCCCcccCeeCcCCCCcccee
Confidence 35799999999774 78999999877543
No 44
>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=41.32 E-value=5.2 Score=24.62 Aligned_cols=26 Identities=23% Similarity=0.479 Sum_probs=16.4
Q ss_pred ceeeEecCCCCCCCcCCeeEEecCCC
Q 037283 66 CTLVRVCDECNYGSFQGRCVICGGVG 91 (136)
Q Consensus 66 ~~~VrICdeCs~G~~~~rCIiCg~~g 91 (136)
...|+.|..|+.=+...-|-||..+.
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 45789999999988889999998754
No 45
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.67 E-value=15 Score=32.50 Aligned_cols=36 Identities=33% Similarity=0.859 Sum_probs=28.6
Q ss_pred ceecccCC-CCC---ceeeEecCCCCCCCcCC--eeEEecCC
Q 037283 55 KCVICDSY-VRP---CTLVRVCDECNYGSFQG--RCVICGGV 90 (136)
Q Consensus 55 kCpICDS~-Vrp---~~~VrICdeCs~G~~~~--rCIiCg~~ 90 (136)
+|-||-.+ ++| .-.-+.|..|+..+++. +|++|+..
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 47788764 555 55889999999999865 99999963
No 46
>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=40.63 E-value=20 Score=24.96 Aligned_cols=26 Identities=35% Similarity=0.660 Sum_probs=19.4
Q ss_pred ceecccCCCCCceeeEecCCCCCCCc
Q 037283 55 KCVICDSYVRPCTLVRVCDECNYGSF 80 (136)
Q Consensus 55 kCpICDS~Vrp~~~VrICdeCs~G~~ 80 (136)
-||-|.+.+.|......|..|++-..
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~~~ 27 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYEKE 27 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCccc
Confidence 48888888877666777888887543
No 47
>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=39.98 E-value=9.5 Score=37.75 Aligned_cols=44 Identities=34% Similarity=0.732 Sum_probs=0.0
Q ss_pred cccccCC-----CceecccCCCCCceeeEecCCCCCCCcCCeeEEecCCCcc
Q 037283 47 RLCEKCD-----GKCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGGVGIS 93 (136)
Q Consensus 47 ~lC~kCd-----GkCpICDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~g~s 93 (136)
|.|.+|. -+||.|.+. ++.++.|..|..-...+.|--||.+..+
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG~~---T~~~~~Cp~C~~~~~~~~C~~C~~~~~~ 704 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECGSH---TEPVYVCPDCGIEVEEDECPKCGRETTS 704 (900)
T ss_dssp ----------------------------------------------------
T ss_pred ccCcccCCcchhhcCcccCCc---cccceeccccccccCccccccccccCcc
Confidence 5688885 589999875 4567899999998888899999976543
No 48
>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 smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=38.47 E-value=21 Score=19.31 Aligned_cols=20 Identities=25% Similarity=0.865 Sum_probs=12.8
Q ss_pred ecCCCCCCC--cCCeeEEecCC
Q 037283 71 VCDECNYGS--FQGRCVICGGV 90 (136)
Q Consensus 71 ICdeCs~G~--~~~rCIiCg~~ 90 (136)
+|..|.+-. .+..|.+|+.|
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred cCCCCCCcChhhhccccccCCc
Confidence 566675543 35678888764
No 50
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=38.28 E-value=17 Score=33.07 Aligned_cols=26 Identities=31% Similarity=0.824 Sum_probs=20.0
Q ss_pred ceeeEecCCCCC-C-CcCCeeEEecCCC
Q 037283 66 CTLVRVCDECNY-G-SFQGRCVICGGVG 91 (136)
Q Consensus 66 ~~~VrICdeCs~-G-~~~~rCIiCg~~g 91 (136)
-+.+-||.+|+| + .....|..||+..
T Consensus 515 ~~p~~~C~~CG~~~~~~~~~CP~CGs~~ 542 (555)
T cd01675 515 NTPIDICNDCGYIGEGEGFKCPKCGSED 542 (555)
T ss_pred ecCCccCCCCCCCCcCCCCCCcCCCCcC
Confidence 345559999999 4 4578999999854
No 51
>smart00261 FU Furin-like repeats.
Probab=37.81 E-value=28 Score=20.72 Aligned_cols=35 Identities=31% Similarity=0.779 Sum_probs=19.9
Q ss_pred cccccCCCceecccCCCCCceeeEecCCCCCCCcC--CeeEE
Q 037283 47 RLCEKCDGKCVICDSYVRPCTLVRVCDECNYGSFQ--GRCVI 86 (136)
Q Consensus 47 ~lC~kCdGkCpICDS~Vrp~~~VrICdeCs~G~~~--~rCIi 86 (136)
.+|.+|+--|.+|.... ...|..|..|.+. +.|+-
T Consensus 2 ~~C~~C~~~C~~C~~~~-----~~~C~~C~~~~~l~~~~Cv~ 38 (46)
T smart00261 2 GECKPCHPECATCTGPG-----PDDCTSCKHGFFLDGGTCVS 38 (46)
T ss_pred CccccccccccccCCcC-----cCcCccCCcccCCCCCCccC
Confidence 35777877777765432 3346667665543 34443
No 52
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=37.75 E-value=23 Score=23.50 Aligned_cols=29 Identities=31% Similarity=0.812 Sum_probs=19.3
Q ss_pred CCCCCcCCeeEEecCC-Cccc---eeeehhhhh
Q 037283 75 CNYGSFQGRCVICGGV-GISD---AYYCKECTQ 103 (136)
Q Consensus 75 Cs~G~~~~rCIiCg~~-g~sd---AYYC~EC~~ 103 (136)
-+++....+|++||.+ |+.. -+.|+-|-+
T Consensus 8 ~~~~r~~nrC~~~Gr~rgvirkf~l~lcR~~FR 40 (52)
T PRK05766 8 RKYGKGARECQRCGRKQGLIRKYGLYLCRQCFR 40 (52)
T ss_pred CCCCCCCceeecCCCCceeHHhhCCcccHHHHH
Confidence 3677888999999975 4433 334666543
No 53
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=36.40 E-value=22 Score=24.26 Aligned_cols=9 Identities=44% Similarity=1.324 Sum_probs=6.6
Q ss_pred ceeeehhhh
Q 037283 94 DAYYCKECT 102 (136)
Q Consensus 94 dAYYC~EC~ 102 (136)
.-|.|.||.
T Consensus 30 ~tYmC~eC~ 38 (56)
T PF09963_consen 30 HTYMCDECK 38 (56)
T ss_pred cceeChhHH
Confidence 368888883
No 54
>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=36.37 E-value=11 Score=26.09 Aligned_cols=36 Identities=33% Similarity=0.883 Sum_probs=25.8
Q ss_pred ceecccCCCCCce-eeEecC-CCCC------CCcCCeeEEecCC
Q 037283 55 KCVICDSYVRPCT-LVRVCD-ECNY------GSFQGRCVICGGV 90 (136)
Q Consensus 55 kCpICDS~Vrp~~-~VrICd-eCs~------G~~~~rCIiCg~~ 90 (136)
.|-.||..+.|.+ .++||. ||-| ...++.|.-||+.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGe 50 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGE 50 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCc
Confidence 3667899999965 899986 4444 3457788888873
No 55
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.94 E-value=16 Score=29.64 Aligned_cols=33 Identities=27% Similarity=0.742 Sum_probs=21.7
Q ss_pred eecccCC-----CCCceeeEecCCCCCCCcCCeeEEecCC
Q 037283 56 CVICDSY-----VRPCTLVRVCDECNYGSFQGRCVICGGV 90 (136)
Q Consensus 56 CpICDS~-----Vrp~~~VrICdeCs~G~~~~rCIiCg~~ 90 (136)
|-.|..- ++|+.-.=+|..|.-+ -..|.+|-.+
T Consensus 161 Cr~C~~~~~~VlllPCrHl~lC~~C~~~--~~~CPiC~~~ 198 (207)
T KOG1100|consen 161 CRKCGEREATVLLLPCRHLCLCGICDES--LRICPICRSP 198 (207)
T ss_pred ceecCcCCceEEeecccceEeccccccc--CccCCCCcCh
Confidence 5555553 4677777778888766 3447777654
No 56
>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=35.71 E-value=19 Score=26.44 Aligned_cols=32 Identities=34% Similarity=0.891 Sum_probs=15.0
Q ss_pred ceecccCCCCCceeeEecCCCCCCCcCCeeEEecC
Q 037283 55 KCVICDSYVRPCTLVRVCDECNYGSFQGRCVICGG 89 (136)
Q Consensus 55 kCpICDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~ 89 (136)
+|-||-+-|...- .+-|..| --..+.|-+||.
T Consensus 46 ~C~~CK~~v~q~g-~~YCq~C--AYkkGiCamCGK 77 (90)
T PF10235_consen 46 KCKICKTKVHQPG-AKYCQTC--AYKKGICAMCGK 77 (90)
T ss_pred cccccccccccCC-CccChhh--hcccCcccccCC
Confidence 4555555443311 1335555 333556666664
No 57
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=35.47 E-value=19 Score=20.17 Aligned_cols=20 Identities=35% Similarity=0.747 Sum_probs=12.0
Q ss_pred eeEEecCCCccceeeehhhh
Q 037283 83 RCVICGGVGISDAYYCKECT 102 (136)
Q Consensus 83 rCIiCg~~g~sdAYYC~EC~ 102 (136)
.|.-||.+-..+|=||..|.
T Consensus 4 ~Cp~Cg~~~~~~~~fC~~CG 23 (26)
T PF13248_consen 4 FCPNCGAEIDPDAKFCPNCG 23 (26)
T ss_pred CCcccCCcCCcccccChhhC
Confidence 45566665555666666664
No 58
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=35.01 E-value=34 Score=20.66 Aligned_cols=11 Identities=36% Similarity=0.930 Sum_probs=7.7
Q ss_pred ceecccCCCCC
Q 037283 55 KCVICDSYVRP 65 (136)
Q Consensus 55 kCpICDS~Vrp 65 (136)
+||.|.....+
T Consensus 1 ~CP~C~~~l~~ 11 (41)
T PF13453_consen 1 KCPRCGTELEP 11 (41)
T ss_pred CcCCCCcccce
Confidence 58888875543
No 59
>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=34.86 E-value=24 Score=30.89 Aligned_cols=23 Identities=30% Similarity=0.660 Sum_probs=15.7
Q ss_pred CCceecccC--CCCCceeeEecCCCC
Q 037283 53 DGKCVICDS--YVRPCTLVRVCDECN 76 (136)
Q Consensus 53 dGkCpICDS--~Vrp~~~VrICdeCs 76 (136)
|-.||+|-+ |+.|..+.-|= +|+
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~-~CG 27 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVN-VCG 27 (309)
T ss_pred CCCCCcCCCCCccCcccccccC-CCC
Confidence 347999988 88897655443 443
No 60
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.81 E-value=24 Score=28.90 Aligned_cols=34 Identities=26% Similarity=0.445 Sum_probs=27.2
Q ss_pred ceeeEecCCCCCCCcCCeeEEecCCCccceeeeh
Q 037283 66 CTLVRVCDECNYGSFQGRCVICGGVGISDAYYCK 99 (136)
Q Consensus 66 ~~~VrICdeCs~G~~~~rCIiCg~~g~sdAYYC~ 99 (136)
...++.|..|++-+..+-|-||..+.....-.|-
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 4678899999988888999999887766655553
No 61
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=34.46 E-value=42 Score=20.62 Aligned_cols=13 Identities=38% Similarity=0.899 Sum_probs=11.2
Q ss_pred CceeeEecCCCCC
Q 037283 65 PCTLVRVCDECNY 77 (136)
Q Consensus 65 p~~~VrICdeCs~ 77 (136)
|+|+-++|..|++
T Consensus 24 ~mT~fy~C~~C~~ 36 (40)
T smart00440 24 PMTVFYVCTKCGH 36 (40)
T ss_pred CCeEEEEeCCCCC
Confidence 7889999988876
No 62
>PRK04023 DNA polymerase II large subunit; Validated
Probab=34.38 E-value=31 Score=35.05 Aligned_cols=42 Identities=29% Similarity=0.573 Sum_probs=17.9
Q ss_pred CceecccCCCCCceeeEecCCCCCC-CcCCeeEEecCCCccceeeehhh
Q 037283 54 GKCVICDSYVRPCTLVRVCDECNYG-SFQGRCVICGGVGISDAYYCKEC 101 (136)
Q Consensus 54 GkCpICDS~Vrp~~~VrICdeCs~G-~~~~rCIiCg~~g~sdAYYC~EC 101 (136)
-+||.|.... ....|..|+-- ....+|.-||... ..|-|..|
T Consensus 627 RfCpsCG~~t----~~frCP~CG~~Te~i~fCP~CG~~~--~~y~CPKC 669 (1121)
T PRK04023 627 RKCPSCGKET----FYRRCPFCGTHTEPVYRCPRCGIEV--EEDECEKC 669 (1121)
T ss_pred ccCCCCCCcC----CcccCCCCCCCCCcceeCccccCcC--CCCcCCCC
Confidence 3444444432 33445555432 1233555555422 23445544
No 63
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=33.03 E-value=38 Score=27.13 Aligned_cols=14 Identities=43% Similarity=1.037 Sum_probs=9.2
Q ss_pred eeEecCCCCCCCcC
Q 037283 68 LVRVCDECNYGSFQ 81 (136)
Q Consensus 68 ~VrICdeCs~G~~~ 81 (136)
.|.+|..|+|....
T Consensus 47 ~V~vCP~CgyA~~~ 60 (214)
T PF09986_consen 47 EVWVCPHCGYAAFE 60 (214)
T ss_pred eEEECCCCCCcccc
Confidence 56677777776654
No 64
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=32.79 E-value=19 Score=21.07 Aligned_cols=23 Identities=39% Similarity=1.109 Sum_probs=12.8
Q ss_pred cCCCCCCCcCCeeEEecCCCccceeeehh
Q 037283 72 CDECNYGSFQGRCVICGGVGISDAYYCKE 100 (136)
Q Consensus 72 CdeCs~G~~~~rCIiCg~~g~sdAYYC~E 100 (136)
|..|+-.... +|-.|+. +|||.+
T Consensus 1 C~~C~~~~~~-~C~~C~~-----~~YCs~ 23 (37)
T PF01753_consen 1 CAVCGKPALK-RCSRCKS-----VYYCSE 23 (37)
T ss_dssp -TTTSSCSSE-EETTTSS-----SEESSH
T ss_pred CcCCCCCcCC-cCCCCCC-----EEecCH
Confidence 3444444433 6666654 788876
No 65
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=32.62 E-value=59 Score=17.64 Aligned_cols=12 Identities=33% Similarity=0.642 Sum_probs=8.9
Q ss_pred ceecccCCCCCc
Q 037283 55 KCVICDSYVRPC 66 (136)
Q Consensus 55 kCpICDS~Vrp~ 66 (136)
+|..|+..+.+.
T Consensus 1 ~C~~C~~~i~~~ 12 (39)
T smart00132 1 KCAGCGKPIRGG 12 (39)
T ss_pred CccccCCcccCC
Confidence 577788887775
No 66
>PRK14282 chaperone protein DnaJ; Provisional
Probab=32.30 E-value=18 Score=30.87 Aligned_cols=10 Identities=30% Similarity=0.750 Sum_probs=7.1
Q ss_pred cccccccCCC
Q 037283 45 IGRLCEKCDG 54 (136)
Q Consensus 45 iG~lC~kCdG 54 (136)
.-.+|+.|+|
T Consensus 151 r~~~C~~C~G 160 (369)
T PRK14282 151 RYETCPHCGG 160 (369)
T ss_pred ecccCCCCCc
Confidence 3456888887
No 67
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=31.28 E-value=32 Score=30.54 Aligned_cols=27 Identities=30% Similarity=0.548 Sum_probs=22.3
Q ss_pred eeEecCCCCCCCc--CCeeEEecCCCccc
Q 037283 68 LVRVCDECNYGSF--QGRCVICGGVGISD 94 (136)
Q Consensus 68 ~VrICdeCs~G~~--~~rCIiCg~~g~sd 94 (136)
.+++|.+|+|.+. .++|.-|+.-+...
T Consensus 6 ~~y~C~~Cg~~~~~~~g~Cp~C~~w~t~~ 34 (454)
T TIGR00416 6 SKFVCQHCGADSPKWQGKCPACHAWNTIT 34 (454)
T ss_pred CeEECCcCCCCCccccEECcCCCCccccc
Confidence 4799999999774 78999999877554
No 68
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=31.10 E-value=28 Score=32.72 Aligned_cols=26 Identities=19% Similarity=0.446 Sum_probs=20.3
Q ss_pred CceeeEecCCCCC-CCcCCeeEEecCC
Q 037283 65 PCTLVRVCDECNY-GSFQGRCVICGGV 90 (136)
Q Consensus 65 p~~~VrICdeCs~-G~~~~rCIiCg~~ 90 (136)
-.+.+-+|.+|+| +.....|..||++
T Consensus 622 in~~~~~C~~CG~~~g~~~~CP~CG~~ 648 (656)
T PRK08270 622 ITPTFSICPKHGYLSGEHEFCPKCGEE 648 (656)
T ss_pred eCCCCcccCCCCCcCCCCCCCcCCcCc
Confidence 3567889999998 4456789999865
No 69
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=30.94 E-value=27 Score=35.36 Aligned_cols=30 Identities=33% Similarity=0.839 Sum_probs=26.0
Q ss_pred eeEecCCCCCCCcCCeeEEecCCCccceeee
Q 037283 68 LVRVCDECNYGSFQGRCVICGGVGISDAYYC 98 (136)
Q Consensus 68 ~VrICdeCs~G~~~~rCIiCg~~g~sdAYYC 98 (136)
-.|.|..|+.-+...+|..||++. ..+|+|
T Consensus 624 ~~RKCPkCG~yTlk~rCP~CG~~T-e~~~pc 653 (1095)
T TIGR00354 624 AIRKCPQCGKESFWLKCPVCGELT-EQLYYG 653 (1095)
T ss_pred EEEECCCCCcccccccCCCCCCcc-ccccce
Confidence 348899999999999999999875 558888
No 70
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=30.81 E-value=30 Score=32.38 Aligned_cols=26 Identities=23% Similarity=0.749 Sum_probs=20.3
Q ss_pred ceeeEecCCCCC--CCcCCeeEEecCCC
Q 037283 66 CTLVRVCDECNY--GSFQGRCVICGGVG 91 (136)
Q Consensus 66 ~~~VrICdeCs~--G~~~~rCIiCg~~g 91 (136)
...+-||.+|+| |.....|..||+..
T Consensus 529 n~~~siC~~CGy~~g~~~~~CP~CGs~~ 556 (586)
T TIGR02827 529 NIKITICNDCHHIDKRTLHRCPVCGSAN 556 (586)
T ss_pred CCCCeecCCCCCcCCCcCCcCcCCCCcc
Confidence 557889999999 33457999999753
No 71
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.43 E-value=32 Score=28.73 Aligned_cols=12 Identities=33% Similarity=0.731 Sum_probs=10.0
Q ss_pred CceecccCCCCC
Q 037283 54 GKCVICDSYVRP 65 (136)
Q Consensus 54 GkCpICDS~Vrp 65 (136)
-|||+|...|-|
T Consensus 139 ~KCPvC~K~V~s 150 (205)
T KOG0801|consen 139 MKCPVCHKVVPS 150 (205)
T ss_pred ccCCccccccCC
Confidence 389999998877
No 72
>PRK00076 recR recombination protein RecR; Reviewed
Probab=29.20 E-value=33 Score=27.99 Aligned_cols=34 Identities=21% Similarity=0.457 Sum_probs=26.6
Q ss_pred ceeeEecCCCCCCCcCCeeEEecCCCccceeeeh
Q 037283 66 CTLVRVCDECNYGSFQGRCVICGGVGISDAYYCK 99 (136)
Q Consensus 66 ~~~VrICdeCs~G~~~~rCIiCg~~g~sdAYYC~ 99 (136)
...++.|..|++=+..+-|-||..+.......|-
T Consensus 50 ~~~i~~C~~C~~lse~~~C~IC~d~~Rd~~~icV 83 (196)
T PRK00076 50 KEKIKHCSVCGNLTEQDPCEICSDPRRDQSLICV 83 (196)
T ss_pred HHcCCcCCCCCCcCCCCcCCCCCCCCCCCCEEEE
Confidence 4567889999988888899999887766665653
No 73
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.11 E-value=27 Score=33.28 Aligned_cols=28 Identities=29% Similarity=0.672 Sum_probs=22.0
Q ss_pred CCCceeeEecCCCCC-CCcCCeeEEecCC
Q 037283 63 VRPCTLVRVCDECNY-GSFQGRCVICGGV 90 (136)
Q Consensus 63 Vrp~~~VrICdeCs~-G~~~~rCIiCg~~ 90 (136)
.-....+-+|.+|+| +.....|..||+.
T Consensus 674 ~sin~~~~~C~~CG~~~~~~~~CP~CG~~ 702 (735)
T PRK07111 674 GSINHPVDRCPVCGYLGVIEDKCPKCGST 702 (735)
T ss_pred EEeCCCCeecCCCCCCCCcCccCcCCCCc
Confidence 345678899999998 4457899999974
No 74
>PRK14285 chaperone protein DnaJ; Provisional
Probab=28.27 E-value=28 Score=29.90 Aligned_cols=51 Identities=33% Similarity=0.616 Sum_probs=26.0
Q ss_pred ccccccCCCceecccCCCCCceeeEecCCCCCC----------CcCCeeEEecCCCccceeeehhhh
Q 037283 46 GRLCEKCDGKCVICDSYVRPCTLVRVCDECNYG----------SFQGRCVICGGVGISDAYYCKECT 102 (136)
Q Consensus 46 G~lC~kCdGkCpICDS~Vrp~~~VrICdeCs~G----------~~~~rCIiCg~~g~sdAYYC~EC~ 102 (136)
-.+|+.|.|.-- .+.+....|..|+=. ..+..|--|++.|..-.--|..|.
T Consensus 146 ~~~C~~C~G~G~------~~~~~~~~C~~C~G~G~~~~~~G~~~~~~~C~~C~G~G~~~~~~C~~C~ 206 (365)
T PRK14285 146 NMLCESCLGKKS------EKGTSPSICNMCNGSGRVMQGGGFFRVTTTCPKCYGNGKIISNPCKSCK 206 (365)
T ss_pred cccCCCCCCccc------CCCCCCccCCCccCceeEEecCceeEEeeecCCCCCcccccCCCCCCCC
Confidence 457888888531 222223345555321 124456666666654444566653
No 75
>PF04134 DUF393: Protein of unknown function, DUF393; InterPro: IPR007263 The DCC family, named after the conserved N-terminal DxxCxxC motif, encompasses COG3011 from COG. Proteins in this family are predicted to have a thioredoxin-like fold which, together with the presence of an invariant catalytic cysteine residue, suggests that they are a novel group of thiol-disulphide oxidoreductases []. As some of the bacterial proteins are encoded near penicillin-binding proteins, it has been suggested that these may be involved in redox regulation of cell wall biosynthesis [].
Probab=28.19 E-value=8.4 Score=26.47 Aligned_cols=12 Identities=50% Similarity=1.129 Sum_probs=10.3
Q ss_pred CCceecccCCCC
Q 037283 53 DGKCVICDSYVR 64 (136)
Q Consensus 53 dGkCpICDS~Vr 64 (136)
||.||.|...|+
T Consensus 4 Dg~C~lC~~~~~ 15 (114)
T PF04134_consen 4 DGDCPLCRREVR 15 (114)
T ss_pred CCCCHhHHHHHH
Confidence 899999998863
No 76
>PRK13844 recombination protein RecR; Provisional
Probab=28.16 E-value=35 Score=28.10 Aligned_cols=33 Identities=21% Similarity=0.487 Sum_probs=25.4
Q ss_pred ceeeEecCCCCCCCcCCeeEEecCCCccceeee
Q 037283 66 CTLVRVCDECNYGSFQGRCVICGGVGISDAYYC 98 (136)
Q Consensus 66 ~~~VrICdeCs~G~~~~rCIiCg~~g~sdAYYC 98 (136)
.+.++.|..|++=+.++-|-||..+.....-.|
T Consensus 54 ~~~i~~C~~C~~lte~~~C~IC~d~~Rd~~~iC 86 (200)
T PRK13844 54 TANIKKCVYCQALTEDDVCNICSNTNRDDTKLC 86 (200)
T ss_pred HHhCCcCCCCCCCCCCCCCCCCCCCCCCCCEEE
Confidence 456788999988888888999988776555555
No 77
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=28.05 E-value=35 Score=31.48 Aligned_cols=16 Identities=25% Similarity=0.739 Sum_probs=13.5
Q ss_pred cceeeehhhhhhhccC
Q 037283 93 SDAYYCKECTQQEKDR 108 (136)
Q Consensus 93 sdAYYC~EC~~lEKDR 108 (136)
+-+|||++|..+.+.+
T Consensus 58 ~~~~YCr~Cl~mgRv~ 73 (441)
T COG4098 58 CGCLYCRNCLMMGRVR 73 (441)
T ss_pred cceEeehhhhhccccc
Confidence 3499999999998876
No 78
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=27.96 E-value=44 Score=22.30 Aligned_cols=22 Identities=36% Similarity=0.757 Sum_probs=17.4
Q ss_pred CceecccCCCCCceeeEecCCCCCC
Q 037283 54 GKCVICDSYVRPCTLVRVCDECNYG 78 (136)
Q Consensus 54 GkCpICDS~Vrp~~~VrICdeCs~G 78 (136)
-.||-|.++.+| -++|..|+|=
T Consensus 28 ~~C~~CG~~~~~---H~vC~~CG~Y 49 (57)
T PRK12286 28 VECPNCGEPKLP---HRVCPSCGYY 49 (57)
T ss_pred eECCCCCCccCC---eEECCCCCcC
Confidence 368899999888 4789888853
No 79
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=26.72 E-value=27 Score=32.88 Aligned_cols=30 Identities=27% Similarity=0.655 Sum_probs=23.1
Q ss_pred CCCCceeeEecCCCCCC--CcCCeeEEecCCC
Q 037283 62 YVRPCTLVRVCDECNYG--SFQGRCVICGGVG 91 (136)
Q Consensus 62 ~Vrp~~~VrICdeCs~G--~~~~rCIiCg~~g 91 (136)
|.-....+-||.+|+|. .....|..||+..
T Consensus 559 Yf~in~~~~iC~~CG~~~~g~~~~CP~CGs~~ 590 (623)
T PRK08271 559 YFAFNVKITICNDCHHIDKRTGKRCPICGSEN 590 (623)
T ss_pred eEEeCCCCccCCCCCCcCCCCCcCCcCCCCcc
Confidence 44456788999999994 3477999999754
No 80
>PRK14284 chaperone protein DnaJ; Provisional
Probab=26.63 E-value=30 Score=29.87 Aligned_cols=51 Identities=29% Similarity=0.670 Sum_probs=24.4
Q ss_pred cccccccCCCceecccCCCCCceeeEecCCCCCC----------CcCCeeEEecCCCccceeeehhh
Q 037283 45 IGRLCEKCDGKCVICDSYVRPCTLVRVCDECNYG----------SFQGRCVICGGVGISDAYYCKEC 101 (136)
Q Consensus 45 iG~lC~kCdGkCpICDS~Vrp~~~VrICdeCs~G----------~~~~rCIiCg~~g~sdAYYC~EC 101 (136)
.-..|+.|.|.-- .+.+....|..|+=. ..+..|--|++.|....=-|..|
T Consensus 157 r~~~C~~C~G~G~------~~~~~~~~C~~C~G~G~v~~~~G~~~~~~~C~~C~G~G~~~~~~C~~C 217 (391)
T PRK14284 157 GYKSCDACSGSGA------NSSQGIKVCDRCKGSGQVVQSRGFFSMASTCPECGGEGRVITDPCSVC 217 (391)
T ss_pred eeccCCCCccccc------CCCCCCeecCccCCeeEEEEEeceEEEEEECCCCCCCCcccCCcCCCC
Confidence 3556888876421 222223444444411 12345666666664333335555
No 81
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=26.52 E-value=59 Score=24.98 Aligned_cols=30 Identities=27% Similarity=0.664 Sum_probs=14.5
Q ss_pred ccccCCCceecccCCCCCceeeEecCCCCC
Q 037283 48 LCEKCDGKCVICDSYVRPCTLVRVCDECNY 77 (136)
Q Consensus 48 lC~kCdGkCpICDS~Vrp~~~VrICdeCs~ 77 (136)
+|+.|.|.|-+=....-....++-|.+||=
T Consensus 112 ~C~~C~Gs~k~~~~~~~~~~~~~rC~~Cne 141 (147)
T cd03031 112 PCSECNGSCKVFAENATAAGGFLRCPECNE 141 (147)
T ss_pred ECCCCCCcceEEeccCcccccEEECCCCCc
Confidence 455555555442222112345677777763
No 82
>PRK12496 hypothetical protein; Provisional
Probab=26.45 E-value=42 Score=26.08 Aligned_cols=23 Identities=35% Similarity=0.814 Sum_probs=16.1
Q ss_pred eEecCCCC--CCC--cCCeeEEecCCC
Q 037283 69 VRVCDECN--YGS--FQGRCVICGGVG 91 (136)
Q Consensus 69 VrICdeCs--~G~--~~~rCIiCg~~g 91 (136)
.+.|.-|+ |-. ..+.|.+||+|-
T Consensus 127 ~~~C~gC~~~~~~~~~~~~C~~CG~~~ 153 (164)
T PRK12496 127 RKVCKGCKKKYPEDYPDDVCEICGSPV 153 (164)
T ss_pred eEECCCCCccccCCCCCCcCCCCCChh
Confidence 46799998 532 346799999863
No 83
>PF09180 ProRS-C_1: Prolyl-tRNA synthetase, C-terminal; InterPro: IPR016061 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. Prolyl tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa. This domain is found at the C-terminal in archaeal and eukaryotic enzymes, as well as in certain bacterial ones.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1NJ6_A 1NJ2_A 1NJ5_A 1NJ1_A 1H4T_C 1H4S_A 1HC7_C 1H4Q_B 3IAL_B.
Probab=26.37 E-value=20 Score=24.12 Aligned_cols=20 Identities=20% Similarity=0.591 Sum_probs=10.8
Q ss_pred CCcCCeeEEecCCCccceee
Q 037283 78 GSFQGRCVICGGVGISDAYY 97 (136)
Q Consensus 78 G~~~~rCIiCg~~g~sdAYY 97 (136)
....++||+||.|....||.
T Consensus 45 ~~~~~~Ci~cgk~a~~~~~f 64 (68)
T PF09180_consen 45 EPEGGKCIVCGKPAKKWVLF 64 (68)
T ss_dssp EBTT-B-TTT-SB-SCEEEE
T ss_pred CCCCCeeecCCChhhEEEEE
Confidence 34567888888877766654
No 84
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=26.32 E-value=31 Score=29.97 Aligned_cols=25 Identities=40% Similarity=0.749 Sum_probs=20.3
Q ss_pred EecCCCCCCCc--CCeeEEecCCCccc
Q 037283 70 RVCDECNYGSF--QGRCVICGGVGISD 94 (136)
Q Consensus 70 rICdeCs~G~~--~~rCIiCg~~g~sd 94 (136)
++|.+|+|.+. .++|.-||.-+...
T Consensus 1 ~~c~~cg~~~~~~~g~cp~c~~w~~~~ 27 (372)
T cd01121 1 YVCSECGYVSPKWLGKCPECGEWNTLV 27 (372)
T ss_pred CCCCCCCCCCCCccEECcCCCCceeee
Confidence 47999999774 78999999877554
No 85
>PRK14289 chaperone protein DnaJ; Provisional
Probab=26.10 E-value=25 Score=30.14 Aligned_cols=22 Identities=36% Similarity=0.745 Sum_probs=13.0
Q ss_pred CCeeEEecCCCccceeeehhhh
Q 037283 81 QGRCVICGGVGISDAYYCKECT 102 (136)
Q Consensus 81 ~~rCIiCg~~g~sdAYYC~EC~ 102 (136)
+..|..|++.|...+--|..|.
T Consensus 197 ~~~C~~C~G~G~~~~~~C~~C~ 218 (386)
T PRK14289 197 QSTCPTCNGEGKIIKKKCKKCG 218 (386)
T ss_pred EEecCCCCccccccCcCCCCCC
Confidence 4456666666655555566663
No 86
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=26.06 E-value=37 Score=23.49 Aligned_cols=43 Identities=33% Similarity=0.816 Sum_probs=23.8
Q ss_pred ceecccCCCCCc--eeeEecCCCCCCCc-CCeeEEecCCCccceeeehhh
Q 037283 55 KCVICDSYVRPC--TLVRVCDECNYGSF-QGRCVICGGVGISDAYYCKEC 101 (136)
Q Consensus 55 kCpICDS~Vrp~--~~VrICdeCs~G~~-~~rCIiCg~~g~sdAYYC~EC 101 (136)
+|..|...+-|. ...-.|..| |.. -.||.-|.. -++.|-|.+|
T Consensus 9 ~CtSCg~~i~~~~~~~~F~CPnC--G~~~I~RC~~CRk--~~~~Y~CP~C 54 (59)
T PRK14890 9 KCTSCGIEIAPREKAVKFLCPNC--GEVIIYRCEKCRK--QSNPYTCPKC 54 (59)
T ss_pred cccCCCCcccCCCccCEeeCCCC--CCeeEeechhHHh--cCCceECCCC
Confidence 455666655552 345566666 333 456666655 3456666665
No 87
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=25.83 E-value=43 Score=26.53 Aligned_cols=25 Identities=16% Similarity=0.368 Sum_probs=19.6
Q ss_pred eeEecCCCCCCCc--CCeeEEecCCCc
Q 037283 68 LVRVCDECNYGSF--QGRCVICGGVGI 92 (136)
Q Consensus 68 ~VrICdeCs~G~~--~~rCIiCg~~g~ 92 (136)
.+.+|+.|++.+. .-.|..||+.++
T Consensus 353 p~~~c~~cg~~~~~~~~~c~~c~~~~~ 379 (389)
T PRK11788 353 PRYRCRNCGFTARTLYWHCPSCKAWET 379 (389)
T ss_pred CCEECCCCCCCCccceeECcCCCCccC
Confidence 4478999999874 668999998664
No 88
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=25.67 E-value=74 Score=19.59 Aligned_cols=31 Identities=32% Similarity=0.636 Sum_probs=15.7
Q ss_pred ecCCCCCCCcCCeeEEecCCCccceeeehhhhhh
Q 037283 71 VCDECNYGSFQGRCVICGGVGISDAYYCKECTQQ 104 (136)
Q Consensus 71 ICdeCs~G~~~~rCIiCg~~g~sdAYYC~EC~~l 104 (136)
.|..|+-...+.+=+|= + ..+||-|.+|+.+
T Consensus 3 ~CSFCgr~~~~v~~li~-g--~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLIS-G--PNGAYICDECVEQ 33 (41)
T ss_dssp B-TTT--BTTTSSSEEE-E--S-SEEEEHHHHHH
T ss_pred CccCCCCCHHHHhceec-C--CCCcEECHHHHHH
Confidence 45555555544444442 2 2349999999754
No 89
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=25.61 E-value=33 Score=23.61 Aligned_cols=21 Identities=33% Similarity=0.998 Sum_probs=16.9
Q ss_pred ecCCCCCCCcCCeeEEecCCC
Q 037283 71 VCDECNYGSFQGRCVICGGVG 91 (136)
Q Consensus 71 ICdeCs~G~~~~rCIiCg~~g 91 (136)
-|..|.+-...++|.+||+..
T Consensus 5 AC~~C~~i~~~~~CP~Cgs~~ 25 (61)
T PRK08351 5 ACRHCHYITTEDRCPVCGSRD 25 (61)
T ss_pred hhhhCCcccCCCcCCCCcCCc
Confidence 678888877777899998855
No 90
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=25.55 E-value=26 Score=22.91 Aligned_cols=21 Identities=43% Similarity=0.899 Sum_probs=15.1
Q ss_pred CceecccCCCCCceeeEecCCCCC
Q 037283 54 GKCVICDSYVRPCTLVRVCDECNY 77 (136)
Q Consensus 54 GkCpICDS~Vrp~~~VrICdeCs~ 77 (136)
..||.|..+..|. ++|..|+|
T Consensus 27 ~~c~~cg~~~~~H---~vc~~cG~ 47 (56)
T PF01783_consen 27 VKCPNCGEPKLPH---RVCPSCGY 47 (56)
T ss_dssp EESSSSSSEESTT---SBCTTTBB
T ss_pred eeeccCCCEeccc---EeeCCCCe
Confidence 3578888776665 78888853
No 91
>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene. The molecular function of this protein is uncertain.
Probab=25.55 E-value=20 Score=33.74 Aligned_cols=29 Identities=28% Similarity=0.448 Sum_probs=23.7
Q ss_pred hhh-hhhhhhhccccceeeecccccccCcceee
Q 037283 5 TYY-KTLSLLIRSNLNIFFSKQADVSIWTSSLL 36 (136)
Q Consensus 5 ~~~-~~~~~~~~~~~~~~~~~~~~~~~~~DLi~ 36 (136)
||| ||||. .||--||+-++|-..+.|-||
T Consensus 146 TyYDMNLSA---QDHQtfFtcd~D~~r~Aq~IM 175 (539)
T PF04184_consen 146 TYYDMNLSA---QDHQTFFTCDTDALRPAQEIM 175 (539)
T ss_pred ccccCCccc---cccceeEecCCCccCHHHHHH
Confidence 455 89999 999999999999877777665
No 92
>PRK14283 chaperone protein DnaJ; Provisional
Probab=25.42 E-value=54 Score=28.18 Aligned_cols=52 Identities=25% Similarity=0.680 Sum_probs=30.3
Q ss_pred CcccccccccCCCc----------eecccCCCC----------CceeeEecCCCC-CCCc-CCeeEEecCCCcc
Q 037283 42 GIAIGRLCEKCDGK----------CVICDSYVR----------PCTLVRVCDECN-YGSF-QGRCVICGGVGIS 93 (136)
Q Consensus 42 G~~iG~lC~kCdGk----------CpICDS~Vr----------p~~~VrICdeCs-~G~~-~~rCIiCg~~g~s 93 (136)
.+.....|+.|.|. |+.|.-.=. ....+..|+.|. .|.. ...|-.|.+.|+.
T Consensus 142 ~~~r~~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~~~~~~g~~~~~~~C~~C~G~G~~~~~~C~~C~G~g~v 215 (378)
T PRK14283 142 KVRHTKKCPVCNGSRAEPGSEVKTCPTCGGTGQVKQVRNTILGQMMNVTTCPDCQGEGKIVEKPCSNCHGKGVV 215 (378)
T ss_pred EeeeeccCCCCCccccCCCCCCccCCCcCCccEEEEEEeccCceEEEEEECCCCCccceecCCCCCCCCCceee
Confidence 34446679999883 777766421 122356677775 2322 4567777766643
No 93
>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=25.30 E-value=31 Score=29.04 Aligned_cols=12 Identities=33% Similarity=0.803 Sum_probs=8.2
Q ss_pred ccccccccCCCc
Q 037283 44 AIGRLCEKCDGK 55 (136)
Q Consensus 44 ~iG~lC~kCdGk 55 (136)
..-.+|..|+|.
T Consensus 141 ~r~~~C~~C~G~ 152 (354)
T TIGR02349 141 PRKESCETCHGT 152 (354)
T ss_pred ecCCcCCCCCCC
Confidence 335678888885
No 94
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=24.62 E-value=45 Score=22.01 Aligned_cols=21 Identities=38% Similarity=0.952 Sum_probs=16.3
Q ss_pred CceecccCCCCCceeeEecCCCCC
Q 037283 54 GKCVICDSYVRPCTLVRVCDECNY 77 (136)
Q Consensus 54 GkCpICDS~Vrp~~~VrICdeCs~ 77 (136)
..||.|.++.+|- ++|..|+|
T Consensus 27 ~~C~~cG~~~~~H---~vc~~cG~ 47 (55)
T TIGR01031 27 VVCPNCGEFKLPH---RVCPSCGY 47 (55)
T ss_pred eECCCCCCcccCe---eECCccCe
Confidence 4688899888775 78888875
No 95
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=24.39 E-value=21 Score=20.71 Aligned_cols=10 Identities=30% Similarity=0.813 Sum_probs=4.1
Q ss_pred ceecccCCCC
Q 037283 55 KCVICDSYVR 64 (136)
Q Consensus 55 kCpICDS~Vr 64 (136)
.||+|+|.+.
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 3777777653
No 96
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=24.18 E-value=15 Score=20.78 Aligned_cols=20 Identities=30% Similarity=0.941 Sum_probs=10.2
Q ss_pred ecCCCCCCC--cCCeeEEecCC
Q 037283 71 VCDECNYGS--FQGRCVICGGV 90 (136)
Q Consensus 71 ICdeCs~G~--~~~rCIiCg~~ 90 (136)
.|..|.+-. ...+|+.||.+
T Consensus 6 ~C~~C~~~N~~~~~~C~~C~~~ 27 (30)
T PF00641_consen 6 KCPSCTFMNPASRSKCVACGAP 27 (30)
T ss_dssp EETTTTEEEESSSSB-TTT--B
T ss_pred cCCCCcCCchHHhhhhhCcCCC
Confidence 566666543 35577777764
No 97
>PRK14286 chaperone protein DnaJ; Provisional
Probab=23.99 E-value=21 Score=30.73 Aligned_cols=10 Identities=30% Similarity=0.813 Sum_probs=7.2
Q ss_pred ccccccCCCc
Q 037283 46 GRLCEKCDGK 55 (136)
Q Consensus 46 G~lC~kCdGk 55 (136)
-.+|+.|+|.
T Consensus 150 ~~~C~~C~G~ 159 (372)
T PRK14286 150 LESCVDCNGS 159 (372)
T ss_pred cccCCCCcCC
Confidence 4568888883
No 98
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=23.84 E-value=34 Score=26.42 Aligned_cols=26 Identities=27% Similarity=0.453 Sum_probs=19.5
Q ss_pred ceecccC-CCCCceeeEecCCCCCCCc
Q 037283 55 KCVICDS-YVRPCTLVRVCDECNYGSF 80 (136)
Q Consensus 55 kCpICDS-~Vrp~~~VrICdeCs~G~~ 80 (136)
.||.|.| |+--.....||++|.+--.
T Consensus 5 ~cp~c~sEytYed~~~~~cpec~~ew~ 31 (112)
T COG2824 5 PCPKCNSEYTYEDGGQLICPECAHEWN 31 (112)
T ss_pred CCCccCCceEEecCceEeCchhccccc
Confidence 5888855 6666666999999998654
No 99
>PRK14294 chaperone protein DnaJ; Provisional
Probab=23.60 E-value=23 Score=30.22 Aligned_cols=22 Identities=32% Similarity=0.709 Sum_probs=13.4
Q ss_pred CCeeEEecCCCccceeeehhhh
Q 037283 81 QGRCVICGGVGISDAYYCKECT 102 (136)
Q Consensus 81 ~~rCIiCg~~g~sdAYYC~EC~ 102 (136)
+..|--|++.|..-.--|..|.
T Consensus 183 ~~~C~~C~G~G~~~~~~C~~C~ 204 (366)
T PRK14294 183 RTTCPRCRGMGKVIVSPCKTCH 204 (366)
T ss_pred EeeCCCCCCcCeecCcCCCCCC
Confidence 4466667766655555566664
No 100
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=23.40 E-value=24 Score=22.29 Aligned_cols=12 Identities=25% Similarity=0.739 Sum_probs=5.6
Q ss_pred CCceecccCCCC
Q 037283 53 DGKCVICDSYVR 64 (136)
Q Consensus 53 dGkCpICDS~Vr 64 (136)
+|+||.|.+...
T Consensus 20 ~~~CPlC~r~l~ 31 (54)
T PF04423_consen 20 KGCCPLCGRPLD 31 (54)
T ss_dssp SEE-TTT--EE-
T ss_pred CCcCCCCCCCCC
Confidence 458999987543
No 101
>PRK14291 chaperone protein DnaJ; Provisional
Probab=23.25 E-value=55 Score=28.23 Aligned_cols=12 Identities=33% Similarity=0.628 Sum_probs=8.5
Q ss_pred ccccccccCCCc
Q 037283 44 AIGRLCEKCDGK 55 (136)
Q Consensus 44 ~iG~lC~kCdGk 55 (136)
..-.+|..|+|.
T Consensus 154 ~r~~~C~~C~G~ 165 (382)
T PRK14291 154 PRYVPCEACGGT 165 (382)
T ss_pred eeeccCCCCccc
Confidence 345678888884
No 102
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=23.23 E-value=37 Score=31.20 Aligned_cols=30 Identities=30% Similarity=0.720 Sum_probs=22.1
Q ss_pred CCCCceeeEecCCCCCCCcC--CeeEEecCCC
Q 037283 62 YVRPCTLVRVCDECNYGSFQ--GRCVICGGVG 91 (136)
Q Consensus 62 ~Vrp~~~VrICdeCs~G~~~--~rCIiCg~~g 91 (136)
|.--...+-||.+|+|.... ..|..||+..
T Consensus 517 Y~~~n~~~~~C~~CG~~g~~~~~~CP~Cgs~~ 548 (579)
T TIGR02487 517 YFGINPPVDVCEDCGYTGEGLNDKCPKCGSHD 548 (579)
T ss_pred eEEeccCCccCCCCCCCCCCCCCcCcCCCCcc
Confidence 34456778999999984433 5899999754
No 103
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=23.05 E-value=28 Score=20.05 Aligned_cols=23 Identities=26% Similarity=0.611 Sum_probs=12.5
Q ss_pred ceecccCCCCC--ceeeEecCCCCC
Q 037283 55 KCVICDSYVRP--CTLVRVCDECNY 77 (136)
Q Consensus 55 kCpICDS~Vrp--~~~VrICdeCs~ 77 (136)
-|+-|.+...+ ...++.|..|+.
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-
T ss_pred ccCcCCccccCCCCcCEeECCCCcC
Confidence 47777776554 557888888865
No 104
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised 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 characterised phosphonoacetate hydrolase designated PhnA.
Probab=23.04 E-value=46 Score=21.62 Aligned_cols=13 Identities=38% Similarity=1.124 Sum_probs=9.7
Q ss_pred ccCCCceecccCC
Q 037283 50 EKCDGKCVICDSY 62 (136)
Q Consensus 50 ~kCdGkCpICDS~ 62 (136)
+++.++|..|.+.
T Consensus 4 ~Rs~~kCELC~a~ 16 (47)
T smart00782 4 ARCESKCELCGSD 16 (47)
T ss_pred HHcCCcccCcCCC
Confidence 3567888888874
No 105
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=23.02 E-value=37 Score=19.16 Aligned_cols=10 Identities=40% Similarity=0.966 Sum_probs=3.9
Q ss_pred ceecccCCCC
Q 037283 55 KCVICDSYVR 64 (136)
Q Consensus 55 kCpICDS~Vr 64 (136)
+|+.|..++.
T Consensus 3 ~C~rC~~~~~ 12 (30)
T PF06827_consen 3 KCPRCWNYIE 12 (30)
T ss_dssp B-TTT--BBE
T ss_pred cCccCCCcce
Confidence 4666666543
No 106
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=22.21 E-value=31 Score=24.37 Aligned_cols=28 Identities=36% Similarity=0.762 Sum_probs=20.7
Q ss_pred CeeEEecCCCccceeeehh-hh-hhhccCC
Q 037283 82 GRCVICGGVGISDAYYCKE-CT-QQEKDRD 109 (136)
Q Consensus 82 ~rCIiCg~~g~sdAYYC~E-C~-~lEKDRD 109 (136)
..|++||.+=--|.-.|.| |. .|||+|.
T Consensus 9 ~HC~VCg~aIp~de~~CSe~C~eil~ker~ 38 (64)
T COG4068 9 RHCVVCGKAIPPDEQVCSEECGEILNKERK 38 (64)
T ss_pred ccccccCCcCCCccchHHHHHHHHHHHHHH
Confidence 5799999877777888887 53 3676653
No 107
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.15 E-value=55 Score=30.70 Aligned_cols=26 Identities=27% Similarity=0.627 Sum_probs=19.9
Q ss_pred ceeeEecCCCCCC-CcCCeeEEecCCC
Q 037283 66 CTLVRVCDECNYG-SFQGRCVICGGVG 91 (136)
Q Consensus 66 ~~~VrICdeCs~G-~~~~rCIiCg~~g 91 (136)
...+-+|.+|+|. .....|..||+..
T Consensus 556 n~~~~~C~~CGy~g~~~~~CP~CG~~d 582 (618)
T PRK14704 556 NHPVDRCKCCSYHGVIGNECPSCGNED 582 (618)
T ss_pred CCCCeecCCCCCCCCcCccCcCCCCCC
Confidence 5678899999983 3346899999754
No 108
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=21.79 E-value=51 Score=27.70 Aligned_cols=26 Identities=27% Similarity=0.644 Sum_probs=22.0
Q ss_pred ceeeEecCCCCCCCcCCeeEEecCCC
Q 037283 66 CTLVRVCDECNYGSFQGRCVICGGVG 91 (136)
Q Consensus 66 ~~~VrICdeCs~G~~~~rCIiCg~~g 91 (136)
.-.++-|..||.--...+|..||+..
T Consensus 11 k~~iyWCe~cNlPl~~~~c~~cg~~~ 36 (202)
T COG5270 11 KFPIYWCEKCNLPLLGRRCSVCGSKV 36 (202)
T ss_pred ccceeehhhCCCccccccccccCCcc
Confidence 34578899999999999999999643
No 109
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=21.61 E-value=36 Score=22.08 Aligned_cols=20 Identities=50% Similarity=1.217 Sum_probs=14.5
Q ss_pred eeEEecCCC-------ccceeeehhhh
Q 037283 83 RCVICGGVG-------ISDAYYCKECT 102 (136)
Q Consensus 83 rCIiCg~~g-------~sdAYYC~EC~ 102 (136)
+|.|||.+- .+|.|-|..|-
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~ 27 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCL 27 (51)
T ss_pred CCCccccccccccceeccCccchHHHH
Confidence 367777532 67889999995
No 110
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=21.60 E-value=39 Score=22.98 Aligned_cols=21 Identities=29% Similarity=0.838 Sum_probs=15.7
Q ss_pred CeeEEecCCCccceeeeh-hhh
Q 037283 82 GRCVICGGVGISDAYYCK-ECT 102 (136)
Q Consensus 82 ~rCIiCg~~g~sdAYYC~-EC~ 102 (136)
..|++||.|=..+-=+|. +|.
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~ 25 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCR 25 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHH
Confidence 579999987777777785 573
No 111
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=21.56 E-value=24 Score=32.11 Aligned_cols=30 Identities=23% Similarity=0.637 Sum_probs=15.1
Q ss_pred CCCCceeeEecCCCCCCCc-CCeeEEecCCC
Q 037283 62 YVRPCTLVRVCDECNYGSF-QGRCVICGGVG 91 (136)
Q Consensus 62 ~Vrp~~~VrICdeCs~G~~-~~rCIiCg~~g 91 (136)
|......+-+|.+|++-.. ...|..||++.
T Consensus 484 Y~~in~~~~~C~~CG~~~~~~~~CP~CGs~~ 514 (546)
T PF13597_consen 484 YFTINPPIDICPDCGYIGGEGDKCPKCGSEN 514 (546)
T ss_dssp EEEEE--EEEETTT---S--EEE-CCC----
T ss_pred eEEEecCcccccCCCcCCCCCCCCCCCCCcc
Confidence 4556778899999998443 56899999875
No 112
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=21.35 E-value=60 Score=19.76 Aligned_cols=13 Identities=46% Similarity=0.866 Sum_probs=10.5
Q ss_pred CceeeEecCCCCC
Q 037283 65 PCTLVRVCDECNY 77 (136)
Q Consensus 65 p~~~VrICdeCs~ 77 (136)
|+|+-+.|-.|++
T Consensus 24 ~~T~fy~C~~C~~ 36 (39)
T PF01096_consen 24 PMTLFYVCCNCGH 36 (39)
T ss_dssp SSEEEEEESSSTE
T ss_pred CCeEEEEeCCCCC
Confidence 7888888888874
No 113
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=21.26 E-value=40 Score=22.97 Aligned_cols=22 Identities=32% Similarity=0.735 Sum_probs=19.3
Q ss_pred eEecCCCCCCCcCCeeEEecCC
Q 037283 69 VRVCDECNYGSFQGRCVICGGV 90 (136)
Q Consensus 69 VrICdeCs~G~~~~rCIiCg~~ 90 (136)
--||+.|.-|+.-+-|.+||.|
T Consensus 27 H~I~~~~f~~~rYngCPfC~~~ 48 (55)
T PF14447_consen 27 HLICDNCFPGERYNGCPFCGTP 48 (55)
T ss_pred ceeeccccChhhccCCCCCCCc
Confidence 3699999999988899999975
No 114
>PRK14288 chaperone protein DnaJ; Provisional
Probab=21.14 E-value=36 Score=29.26 Aligned_cols=11 Identities=45% Similarity=1.150 Sum_probs=7.7
Q ss_pred cccccccCCCc
Q 037283 45 IGRLCEKCDGK 55 (136)
Q Consensus 45 iG~lC~kCdGk 55 (136)
...+|+.|+|.
T Consensus 139 r~~~C~~C~G~ 149 (369)
T PRK14288 139 YQSVCESCDGT 149 (369)
T ss_pred eeccCCCCCCc
Confidence 34578888884
No 115
>KOG2813 consensus Predicted molecular chaperone, contains DnaJ domain [Posttranslational modification, protein turnover, chaperones]
Probab=21.13 E-value=62 Score=29.56 Aligned_cols=38 Identities=26% Similarity=0.615 Sum_probs=26.0
Q ss_pred ceecccCCCCC-ceeeEecCCCCCCCcCCeeEEecCCCcc
Q 037283 55 KCVICDSYVRP-CTLVRVCDECNYGSFQGRCVICGGVGIS 93 (136)
Q Consensus 55 kCpICDS~Vrp-~~~VrICdeCs~G~~~~rCIiCg~~g~s 93 (136)
+|+.|--.+.| ...-+||.+|+ |+...+|-.|.+.|.-
T Consensus 219 ~c~sc~G~~~~k~gt~~~C~~C~-G~G~~~C~tC~grG~k 257 (406)
T KOG2813|consen 219 HCMSCTGVPPPKIGTHDLCYMCH-GRGIKECHTCKGRGKK 257 (406)
T ss_pred ecccccCCCCCCCCccchhhhcc-CCCcccCCcccCCCCc
Confidence 57777665555 44668999995 6666777777766643
No 116
>PRK10767 chaperone protein DnaJ; Provisional
Probab=21.01 E-value=28 Score=29.69 Aligned_cols=12 Identities=33% Similarity=0.800 Sum_probs=8.6
Q ss_pred cccccccccCCC
Q 037283 43 IAIGRLCEKCDG 54 (136)
Q Consensus 43 ~~iG~lC~kCdG 54 (136)
+....+|+.|+|
T Consensus 139 ~~r~~~C~~C~G 150 (371)
T PRK10767 139 IPTLVTCDTCHG 150 (371)
T ss_pred eeecccCCCCCC
Confidence 444567888888
No 117
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=20.89 E-value=63 Score=19.64 Aligned_cols=15 Identities=27% Similarity=0.817 Sum_probs=7.9
Q ss_pred ceecccCCCCCceee
Q 037283 55 KCVICDSYVRPCTLV 69 (136)
Q Consensus 55 kCpICDS~Vrp~~~V 69 (136)
||.-|.+|+.|...+
T Consensus 4 rC~~C~aylNp~~~~ 18 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQF 18 (40)
T ss_dssp B-TTT--BS-TTSEE
T ss_pred ccCCCCCEECCcceE
Confidence 688899999885544
No 118
>PF08421 Methyltransf_13: Putative zinc binding domain; InterPro: IPR013630 This domain is found at the N terminus of bacterial methyltransferases. ; PDB: 4E2X_A 3NDJ_A 3NDI_A 4E32_A 4E33_A 4E31_A 4E2Y_A 4E2W_A 4E2Z_A 4E30_A.
Probab=20.80 E-value=62 Score=21.29 Aligned_cols=24 Identities=21% Similarity=0.575 Sum_probs=11.0
Q ss_pred eecccCCCCC---------ceeeEecCCCCCCC
Q 037283 56 CVICDSYVRP---------CTLVRVCDECNYGS 79 (136)
Q Consensus 56 CpICDS~Vrp---------~~~VrICdeCs~G~ 79 (136)
=|++++++++ .-.+..|+.|++-.
T Consensus 18 ~Pl~~~f~~~~~~~~e~~~pL~l~~C~~CglvQ 50 (62)
T PF08421_consen 18 QPLANSFLKPELDEPEPRYPLDLYVCEDCGLVQ 50 (62)
T ss_dssp EE-TT--B-TTS-S---EEEEEEEEETTT--EE
T ss_pred CCccccccChhhCCCceEECCEEEECCCCCchh
Confidence 3778888777 11567777776543
No 119
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=20.77 E-value=28 Score=22.34 Aligned_cols=24 Identities=25% Similarity=0.740 Sum_probs=15.9
Q ss_pred CCeeEEecCCC---ccceeeehh-hhhh
Q 037283 81 QGRCVICGGVG---ISDAYYCKE-CTQQ 104 (136)
Q Consensus 81 ~~rCIiCg~~g---~sdAYYC~E-C~~l 104 (136)
.+-|++|+..- ...+-||.| |-+.
T Consensus 6 ~~yC~~Cdk~~~~~~~~~lYCSe~Cr~~ 33 (43)
T PF12855_consen 6 NDYCIVCDKQIDPPDDGSLYCSEECRLK 33 (43)
T ss_pred hhHHHHhhccccCCCCCccccCHHHHhH
Confidence 45688887533 566888887 6543
No 120
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.65 E-value=56 Score=27.80 Aligned_cols=20 Identities=35% Similarity=0.785 Sum_probs=14.9
Q ss_pred eeeeccCCCcccccccccCCC
Q 037283 34 SLLCRKQPGIAIGRLCEKCDG 54 (136)
Q Consensus 34 Li~C~KqpG~~iG~lC~kCdG 54 (136)
+-+|.+.+ +.+|.+|..|-.
T Consensus 244 ~CfCh~k~-v~~GyvCs~Cls 263 (279)
T TIGR00627 244 SCFCHHQL-VSIGFVCSVCLS 263 (279)
T ss_pred eeeecCcc-ccceEECCCccC
Confidence 56678776 668999888743
No 121
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.50 E-value=42 Score=27.67 Aligned_cols=25 Identities=32% Similarity=0.801 Sum_probs=15.6
Q ss_pred CCCcCCeeEEecCC------Cccceeeehhh
Q 037283 77 YGSFQGRCVICGGV------GISDAYYCKEC 101 (136)
Q Consensus 77 ~G~~~~rCIiCg~~------g~sdAYYC~EC 101 (136)
||..+..|..||.+ +.-..|||..|
T Consensus 241 y~r~g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 241 YGRKGEPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred eCCCCCCCCCCCCeeEEEEECCCCCEECCCC
Confidence 34445567777653 23458999887
No 122
>PLN03158 methionine aminopeptidase; Provisional
Probab=20.36 E-value=58 Score=28.76 Aligned_cols=32 Identities=22% Similarity=0.668 Sum_probs=24.3
Q ss_pred eEecCCCCCCCcCCeeEEecCCCcc--ceeeehh-h
Q 037283 69 VRVCDECNYGSFQGRCVICGGVGIS--DAYYCKE-C 101 (136)
Q Consensus 69 VrICdeCs~G~~~~rCIiCg~~g~s--dAYYC~E-C 101 (136)
-++|..|+--. .-+|.+|-..|+. .+|+|.+ |
T Consensus 9 ~~~c~~c~~~a-~l~Cp~C~k~~~~~~~s~fCsq~C 43 (396)
T PLN03158 9 PLACARCSKPA-HLQCPKCLELKLPREGASFCSQDC 43 (396)
T ss_pred cccccCCCCcc-cccCccchhcCCCCCCceeECHHH
Confidence 35588887654 4789999888864 7999985 7
No 123
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=20.06 E-value=62 Score=19.20 Aligned_cols=19 Identities=32% Similarity=0.964 Sum_probs=13.1
Q ss_pred eeEEecCCCc--cceeeehhh
Q 037283 83 RCVICGGVGI--SDAYYCKEC 101 (136)
Q Consensus 83 rCIiCg~~g~--sdAYYC~EC 101 (136)
+|.+|...+. ...|+|.+|
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C 22 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKC 22 (32)
T ss_pred CCeECCcCCccceeEEEccCC
Confidence 5777765432 468999888
Done!