Query psy8226
Match_columns 115
No_of_seqs 107 out of 208
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 21:55:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8226.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8226hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3490|consensus 100.0 8.5E-35 1.8E-39 211.4 3.0 68 46-114 7-74 (111)
2 cd07973 Spt4 Transcription elo 100.0 3.5E-34 7.6E-39 203.7 4.9 68 47-114 3-70 (98)
3 PF06093 Spt4: Spt4/RpoE2 zinc 100.0 4.1E-34 8.9E-39 195.6 1.5 66 48-114 2-67 (77)
4 COG5204 SPT4 Transcription elo 99.9 4.5E-28 9.7E-33 175.5 0.3 69 45-114 7-75 (112)
5 PRK06393 rpoE DNA-directed RNA 99.8 1.4E-21 3E-26 130.9 3.6 51 46-113 4-54 (64)
6 PRK08351 DNA-directed RNA poly 99.7 2.3E-18 5E-23 114.3 3.5 49 48-113 4-52 (61)
7 COG2093 DNA-directed RNA polym 99.5 2.2E-14 4.8E-19 96.3 2.9 53 46-113 3-55 (64)
8 PRK00398 rpoP DNA-directed RNA 90.6 0.11 2.3E-06 31.6 0.7 34 48-81 4-38 (46)
9 PF09845 DUF2072: Zn-ribbon co 88.2 0.2 4.4E-06 37.9 0.8 24 49-72 3-27 (131)
10 PRK11788 tetratricopeptide rep 88.0 0.26 5.6E-06 38.7 1.3 28 43-73 350-377 (389)
11 PF02591 DUF164: Putative zinc 87.2 0.23 4.9E-06 31.2 0.4 27 48-74 23-56 (56)
12 COG3364 Zn-ribbon containing p 87.1 0.22 4.7E-06 36.9 0.4 25 49-73 4-29 (112)
13 PF07754 DUF1610: Domain of un 85.8 0.4 8.6E-06 26.8 0.9 22 50-71 1-23 (24)
14 COG0675 Transposase and inacti 85.3 0.58 1.3E-05 35.7 1.9 35 35-73 297-331 (364)
15 TIGR02605 CxxC_CxxC_SSSS putat 82.9 0.89 1.9E-05 27.6 1.7 29 44-72 2-34 (52)
16 PF13248 zf-ribbon_3: zinc-rib 81.0 0.59 1.3E-05 25.6 0.3 20 49-72 4-24 (26)
17 COG1579 Zn-ribbon protein, pos 78.8 0.83 1.8E-05 37.3 0.7 31 44-74 194-231 (239)
18 PF07282 OrfB_Zn_ribbon: Putat 78.7 1.5 3.3E-05 27.8 1.8 38 35-72 16-54 (69)
19 PRK12496 hypothetical protein; 77.7 1.6 3.6E-05 33.1 1.9 48 22-75 107-154 (164)
20 smart00531 TFIIE Transcription 75.7 1.1 2.5E-05 32.9 0.6 35 48-82 100-141 (147)
21 PRK03681 hypA hydrogenase nick 75.6 1.5 3.2E-05 31.5 1.1 33 48-80 71-104 (114)
22 PRK03824 hypA hydrogenase nick 73.8 1.7 3.7E-05 32.0 1.1 34 48-81 71-125 (135)
23 COG1110 Reverse gyrase [DNA re 72.4 1.6 3.4E-05 42.8 0.8 40 27-72 677-716 (1187)
24 PRK12380 hydrogenase nickel in 72.0 1.7 3.8E-05 31.1 0.8 25 48-73 71-95 (113)
25 TIGR00373 conserved hypothetic 69.7 1.2 2.7E-05 33.5 -0.5 35 48-82 110-146 (158)
26 PRK06266 transcription initiat 68.6 1.5 3.3E-05 33.7 -0.2 34 49-82 119-154 (178)
27 cd00350 rubredoxin_like Rubred 66.6 3.5 7.5E-05 23.6 1.1 23 49-72 3-25 (33)
28 PRK00564 hypA hydrogenase nick 66.0 2.9 6.3E-05 30.1 0.9 60 2-73 37-97 (117)
29 PRK00420 hypothetical protein; 64.5 2.6 5.6E-05 30.9 0.4 31 48-78 24-54 (112)
30 PF15645 Tox-PLDMTX: Dermonecr 62.9 2.4 5.2E-05 31.9 -0.0 33 79-111 54-90 (135)
31 PF01155 HypA: Hydrogenase exp 62.6 1.7 3.7E-05 30.9 -0.8 25 48-73 71-95 (113)
32 PRK14890 putative Zn-ribbon RN 62.3 3.9 8.5E-05 27.3 0.9 25 49-73 9-34 (59)
33 PHA02942 putative transposase; 61.5 6.3 0.00014 33.5 2.3 30 39-72 318-350 (383)
34 TIGR00375 conserved hypothetic 60.8 2.7 5.8E-05 36.2 -0.1 36 49-86 242-279 (374)
35 TIGR02827 RNR_anaer_Bdell anae 60.3 6.6 0.00014 35.7 2.3 44 47-106 532-575 (586)
36 PRK13130 H/ACA RNA-protein com 60.3 5.2 0.00011 26.2 1.2 25 44-73 2-26 (56)
37 smart00834 CxxC_CXXC_SSSS Puta 60.0 6.1 0.00013 22.5 1.4 29 44-72 2-34 (41)
38 KOG1315|consensus 60.0 7.9 0.00017 32.6 2.5 69 4-77 69-137 (307)
39 COG1996 RPC10 DNA-directed RNA 58.9 3.7 7.9E-05 26.4 0.3 29 46-74 5-34 (49)
40 PF09723 Zn-ribbon_8: Zinc rib 57.3 7.1 0.00015 23.4 1.4 30 43-72 1-34 (42)
41 TIGR00100 hypA hydrogenase nic 56.9 5.1 0.00011 28.7 0.8 58 3-73 38-95 (115)
42 COG2888 Predicted Zn-ribbon RN 55.2 5.4 0.00012 26.9 0.7 24 49-72 11-35 (61)
43 PRK07591 threonine synthase; V 55.2 5.9 0.00013 33.7 1.1 33 45-79 16-48 (421)
44 PF13597 NRDD: Anaerobic ribon 55.1 2.7 5.8E-05 37.3 -1.0 45 48-109 492-536 (546)
45 PF10114 PocR: Sensory domain 54.3 11 0.00024 27.1 2.2 60 22-88 20-82 (173)
46 PF10571 UPF0547: Uncharacteri 54.0 7.7 0.00017 21.6 1.1 21 49-72 2-22 (26)
47 smart00661 RPOL9 RNA polymeras 54.0 7.6 0.00017 23.2 1.1 23 50-72 3-28 (52)
48 COG0375 HybF Zn finger protein 53.8 5.7 0.00012 29.4 0.6 23 49-72 72-94 (115)
49 COG4357 Zinc finger domain con 53.7 4.3 9.3E-05 29.9 -0.0 38 36-73 51-89 (105)
50 PRK14873 primosome assembly pr 53.5 4.2 9.1E-05 37.2 -0.1 42 48-94 411-454 (665)
51 cd00729 rubredoxin_SM Rubredox 53.4 7.7 0.00017 22.5 1.1 24 48-72 3-26 (34)
52 PRK08271 anaerobic ribonucleos 52.6 5 0.00011 36.7 0.2 42 48-105 567-608 (623)
53 PF13240 zinc_ribbon_2: zinc-r 52.3 5.9 0.00013 21.4 0.4 19 50-72 2-21 (23)
54 PF02150 RNA_POL_M_15KD: RNA p 51.9 9 0.00019 22.4 1.2 14 49-62 22-35 (35)
55 PRK15103 paraquat-inducible me 48.1 9.4 0.0002 33.0 1.2 26 47-75 221-246 (419)
56 TIGR00155 pqiA_fam integral me 47.2 11 0.00023 32.5 1.4 28 48-75 14-44 (403)
57 COG1096 Predicted RNA-binding 46.8 7.5 0.00016 31.1 0.4 23 49-72 150-173 (188)
58 PF14311 DUF4379: Domain of un 46.6 13 0.00029 22.9 1.4 36 35-70 14-55 (55)
59 COG1198 PriA Primosomal protei 46.5 10 0.00023 35.4 1.3 8 49-56 437-444 (730)
60 PRK02935 hypothetical protein; 46.2 10 0.00022 28.2 0.9 22 67-88 73-94 (110)
61 TIGR02487 NrdD anaerobic ribon 45.4 11 0.00023 33.9 1.2 22 48-72 525-546 (579)
62 PF12773 DZR: Double zinc ribb 45.3 14 0.00031 22.0 1.4 30 43-72 8-37 (50)
63 PRK15103 paraquat-inducible me 45.1 11 0.00025 32.5 1.2 28 48-75 11-41 (419)
64 PRK11823 DNA repair protein Ra 44.7 13 0.00029 32.0 1.6 24 47-73 7-30 (446)
65 PRK08579 anaerobic ribonucleos 44.4 5.4 0.00012 36.4 -0.9 22 48-72 569-590 (625)
66 TIGR00412 redox_disulf_2 small 44.2 10 0.00022 24.5 0.6 13 61-73 4-16 (76)
67 PF01529 zf-DHHC: DHHC palmito 43.9 16 0.00034 26.2 1.7 23 48-70 49-71 (174)
68 COG3357 Predicted transcriptio 43.5 14 0.0003 26.9 1.3 24 49-72 60-84 (97)
69 PRK07111 anaerobic ribonucleos 43.1 12 0.00026 34.8 1.1 21 48-72 681-701 (735)
70 TIGR00595 priA primosomal prot 43.0 14 0.00031 32.3 1.5 41 49-93 242-284 (505)
71 PF03604 DNA_RNApol_7kD: DNA d 42.6 14 0.00031 21.5 1.0 24 49-72 2-25 (32)
72 COG1198 PriA Primosomal protei 42.3 6.9 0.00015 36.6 -0.5 55 46-104 461-518 (730)
73 PRK06260 threonine synthase; V 41.1 13 0.00028 31.1 1.0 31 48-79 4-34 (397)
74 PRK00481 NAD-dependent deacety 40.8 17 0.00036 28.5 1.5 27 48-74 123-152 (242)
75 smart00659 RPOLCX RNA polymera 40.7 12 0.00027 22.9 0.6 30 48-77 3-32 (44)
76 TIGR00155 pqiA_fam integral me 40.5 14 0.00031 31.7 1.2 27 47-75 215-241 (403)
77 cd02973 TRX_GRX_like Thioredox 40.0 14 0.00031 22.3 0.8 15 60-74 4-18 (67)
78 PF08772 NOB1_Zn_bind: Nin one 39.1 14 0.00031 25.2 0.8 24 45-72 7-32 (73)
79 PF11023 DUF2614: Protein of u 38.7 14 0.0003 27.6 0.7 31 50-81 72-102 (114)
80 TIGR00515 accD acetyl-CoA carb 38.6 12 0.00026 31.0 0.4 30 47-76 26-57 (285)
81 PF06620 DUF1150: Protein of u 38.3 44 0.00096 22.9 3.1 24 19-42 33-56 (76)
82 CHL00174 accD acetyl-CoA carbo 37.9 12 0.00027 31.4 0.4 30 48-77 39-70 (296)
83 cd01121 Sms Sms (bacterial rad 36.9 17 0.00036 30.9 1.0 22 49-73 2-23 (372)
84 PRK07218 replication factor A; 36.7 21 0.00045 31.3 1.5 33 36-73 286-318 (423)
85 TIGR00416 sms DNA repair prote 35.7 21 0.00045 31.0 1.4 23 48-73 8-30 (454)
86 COG1867 TRM1 N2,N2-dimethylgua 35.5 19 0.00042 31.5 1.2 31 48-78 241-271 (380)
87 PF13719 zinc_ribbon_5: zinc-r 35.4 10 0.00022 22.2 -0.4 14 66-79 4-17 (37)
88 PRK00762 hypA hydrogenase nick 35.3 18 0.00038 26.3 0.8 33 48-81 71-110 (124)
89 cd01675 RNR_III Class III ribo 34.7 32 0.00069 30.7 2.4 38 29-72 503-540 (555)
90 PF12172 DUF35_N: Rubredoxin-l 34.4 14 0.00029 21.2 0.1 21 49-72 13-33 (37)
91 PRK05654 acetyl-CoA carboxylas 33.6 16 0.00034 30.4 0.3 30 48-77 28-59 (292)
92 COG1592 Rubrerythrin [Energy p 33.3 25 0.00053 27.4 1.3 23 48-72 135-157 (166)
93 PF13453 zf-TFIIB: Transcripti 31.8 21 0.00045 21.0 0.6 23 50-72 2-27 (41)
94 PF05495 zf-CHY: CHY zinc fing 31.8 14 0.00031 24.4 -0.2 29 44-72 38-69 (71)
95 PF09567 RE_MamI: MamI restric 30.8 33 0.00072 29.3 1.8 58 16-78 52-109 (314)
96 cd00272 Chemokine_CC Chemokine 30.5 26 0.00056 21.8 0.9 16 94-110 39-54 (57)
97 COG1379 PHP family phosphoeste 30.5 11 0.00023 33.3 -1.2 41 49-90 248-290 (403)
98 COG1439 Predicted nucleic acid 29.8 23 0.0005 28.0 0.7 24 48-74 140-163 (177)
99 PF13510 Fer2_4: 2Fe-2S iron-s 29.6 22 0.00047 23.8 0.4 62 34-98 9-79 (82)
100 PRK05580 primosome assembly pr 29.4 32 0.00069 31.3 1.6 28 66-93 423-452 (679)
101 COG0846 SIR2 NAD-dependent pro 29.0 28 0.00061 28.4 1.1 25 48-72 123-154 (250)
102 PRK11032 hypothetical protein; 28.6 28 0.00061 26.9 0.9 26 47-72 124-150 (160)
103 PF13192 Thioredoxin_3: Thiore 28.1 22 0.00048 22.7 0.3 12 64-75 7-18 (76)
104 COG0266 Nei Formamidopyrimidin 27.9 34 0.00074 28.6 1.4 23 49-71 247-272 (273)
105 KOG0594|consensus 27.3 33 0.00072 29.3 1.2 18 1-18 174-191 (323)
106 COG1645 Uncharacterized Zn-fin 27.1 31 0.00067 26.1 0.9 19 49-71 30-51 (131)
107 TIGR03844 cysteate_syn cysteat 26.7 33 0.00072 29.2 1.1 30 48-79 3-32 (398)
108 cd00730 rubredoxin Rubredoxin; 26.5 36 0.00077 21.5 1.0 12 49-60 3-14 (50)
109 cd01410 SIRT7 SIRT7: Eukaryoti 25.9 30 0.00066 26.7 0.7 27 48-74 96-130 (206)
110 PRK06386 replication factor A; 25.2 38 0.00083 29.2 1.2 32 36-72 225-256 (358)
111 PRK08270 anaerobic ribonucleos 25.0 38 0.00082 31.1 1.3 22 47-72 626-647 (656)
112 cd01411 SIR2H SIR2H: Uncharact 24.7 48 0.0011 25.8 1.6 27 48-74 119-146 (225)
113 COG4260 Membrane protease subu 24.6 30 0.00066 30.0 0.5 24 48-71 316-341 (345)
114 PF00048 IL8: Small cytokines 24.2 36 0.00078 21.3 0.7 18 93-110 45-62 (64)
115 COG3880 Modulator of heat shoc 24.0 18 0.00039 28.8 -0.9 24 48-73 75-101 (176)
116 COG1675 TFA1 Transcription ini 23.9 40 0.00086 26.5 1.0 35 48-82 114-150 (176)
117 PF07295 DUF1451: Protein of u 23.8 39 0.00085 25.5 1.0 26 47-72 112-138 (146)
118 PF11845 DUF3365: Protein of u 23.8 48 0.001 24.2 1.4 61 26-100 125-187 (188)
119 PF12898 Stc1: Stc1 domain; I 23.7 36 0.00078 23.2 0.7 21 44-64 47-67 (84)
120 PF12647 RNHCP: RNHCP domain; 23.7 58 0.0012 23.4 1.7 30 48-77 5-37 (92)
121 PF14255 Cys_rich_CPXG: Cystei 23.7 33 0.00072 21.9 0.5 10 67-76 3-12 (52)
122 PRK04023 DNA polymerase II lar 23.2 41 0.0009 33.3 1.2 27 41-72 620-646 (1121)
123 KOG2324|consensus 22.8 54 0.0012 29.4 1.7 35 38-72 217-255 (457)
124 cd03026 AhpF_NTD_C TRX-GRX-lik 22.6 40 0.00086 22.6 0.7 19 59-77 16-34 (89)
125 PRK00448 polC DNA polymerase I 22.4 54 0.0012 33.1 1.8 31 47-83 908-950 (1437)
126 PF14939 DCAF15_WD40: DDB1-and 22.2 80 0.0017 25.7 2.5 65 30-98 121-188 (211)
127 PRK14704 anaerobic ribonucleos 22.2 46 0.001 30.5 1.2 21 48-72 560-580 (618)
128 PRK09263 anaerobic ribonucleos 22.0 53 0.0011 30.5 1.6 25 47-72 641-667 (711)
129 PF15288 zf-CCHC_6: Zinc knuck 21.5 36 0.00078 21.0 0.3 26 66-95 3-28 (40)
130 PRK08402 replication factor A; 21.5 62 0.0014 27.7 1.8 50 45-97 210-260 (355)
131 COG4031 Predicted metal-bindin 21.2 41 0.00089 27.6 0.6 19 49-72 2-20 (227)
132 PF04216 FdhE: Protein involve 20.8 41 0.0009 27.1 0.6 40 24-72 180-219 (290)
133 COG2260 Predicted Zn-ribbon RN 20.3 54 0.0012 22.0 0.9 21 48-73 6-26 (59)
134 cd00169 Chemokine Chemokine: s 20.3 55 0.0012 20.3 0.9 16 94-110 41-56 (59)
No 1
>KOG3490|consensus
Probab=100.00 E-value=8.5e-35 Score=211.35 Aligned_cols=68 Identities=50% Similarity=0.943 Sum_probs=66.1
Q ss_pred ccccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhccccC
Q psy8226 46 ASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRRT 114 (115)
Q Consensus 46 ~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k~ 114 (115)
+..||+-|++|||.++|.++|||||+ +|+|+||.++|+||||+||+|+||+|+|.+|||||||||++|
T Consensus 7 ~lRACllCs~Vkt~~~F~~dGC~Nc~-~l~mkgn~e~V~ecTS~nF~GiIa~m~Pt~SWVakWqri~~f 74 (111)
T KOG3490|consen 7 KLRACLLCSIVKTLNGFRKDGCENCP-MLNMKGNVENVYECTSPNFDGIIAMMSPTESWVAKWQRIGRF 74 (111)
T ss_pred hhhhhhhhhhhhhhhhhhhcCCCCch-hhhhccCcceeEEecCCCccceeeeeCccHHHHHHHHhhccc
Confidence 45689999999999999999999999 999999999999999999999999999999999999999998
No 2
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=100.00 E-value=3.5e-34 Score=203.69 Aligned_cols=68 Identities=51% Similarity=0.970 Sum_probs=65.9
Q ss_pred cccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhccccC
Q psy8226 47 SAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRRT 114 (115)
Q Consensus 47 ~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k~ 114 (115)
.+||++|++|+|.+||..+|||||+.+|+|+|++++|+||||++|+|+|+||||++|||||||||++|
T Consensus 3 lrAC~~C~~I~~~~qf~~~gCpnC~~~l~~~g~~~~v~~~tT~~f~G~i~i~dP~~SwVAk~l~i~~~ 70 (98)
T cd07973 3 LRACLLCSLIKTEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFEGIIALMDPEKSWVARWQRIDKF 70 (98)
T ss_pred CchhccCCcccccccccCCCCCCCcchhccCCCccccccccCCCcceEEEEECCchhHHHHHhCCCCC
Confidence 46899999999999999999999998999999999999999999999999999999999999999976
No 3
>PF06093 Spt4: Spt4/RpoE2 zinc finger; InterPro: IPR022800 This entry consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 []. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles []. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in []. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery. ; PDB: 2EXU_A 3H7H_A 3LPE_F 3P8B_A 1RYQ_A 3QQC_E.
Probab=99.98 E-value=4.1e-34 Score=195.65 Aligned_cols=66 Identities=53% Similarity=0.993 Sum_probs=58.2
Q ss_pred ccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhccccC
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRRT 114 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k~ 114 (115)
+||++|++|+|.+||+++||||| .||+|+||++++.+|||++|+|+|+||||++||||||||+++|
T Consensus 2 rAC~~C~~i~t~~qF~~~gCpnC-~~l~~~~~~~~~~~~tT~~f~G~i~i~~P~~SwvAk~~rl~~~ 67 (77)
T PF06093_consen 2 RACLRCRLIKTEDQFRDEGCPNC-PFLQMKGDRDRVSDCTTPNFEGMIAIMDPEKSWVAKWQRLGKF 67 (77)
T ss_dssp EEETTT-BEECCCHHHHH--TTT-HHHH-TCHCHHCHCCEESSEEEEEEES-TTT-HHHHHTTCTTS
T ss_pred cccccCCcccCHhHccCCCCCCC-ccccccCCcCcccccCCCCCcCEEEECCCchhHHHHhhccCCC
Confidence 68999999999999999999999 5999999999999999999999999999999999999999986
No 4
>COG5204 SPT4 Transcription elongation factor SPT4 [Transcription]
Probab=99.94 E-value=4.5e-28 Score=175.54 Aligned_cols=69 Identities=42% Similarity=0.826 Sum_probs=66.4
Q ss_pred CccccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhccccC
Q psy8226 45 SASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRRT 114 (115)
Q Consensus 45 ~~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k~ 114 (115)
+.+.||+-|++|+|.+.|.++|||||+ .|.|+|+-+.+.+|||+.|+|+|||+.|.+|||||||||+.|
T Consensus 7 t~sRACl~Cgiv~t~n~F~~dGCpNc~-~l~~~~gV~~ve~~TSp~FeGvvam~~Pt~SWVakWqrid~f 75 (112)
T COG5204 7 TLSRACLGCGIVKTLNGFRKDGCPNCP-MLNMKGGVTNVEECTSPKFEGVVAMLQPTNSWVAKWQRIDEF 75 (112)
T ss_pred hhhhhhhhcceeeecccccccCCCCCc-ccccccCccceeeecCcchHHHHHHhcccHHHHHHHhhhccc
Confidence 567899999999999999999999999 799999999999999999999999999999999999999987
No 5
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=99.84 E-value=1.4e-21 Score=130.88 Aligned_cols=51 Identities=16% Similarity=0.270 Sum_probs=45.0
Q ss_pred ccccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhcccc
Q psy8226 46 ASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113 (115)
Q Consensus 46 ~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k 113 (115)
..+||++||+|.+.++ ||+|++ ++ ||++|+|+|+|+||++|||||||||+.
T Consensus 4 ~~~AC~~C~~i~~~~~-----Cp~Cgs-------~~-----~S~~w~G~v~i~dPe~S~vAk~~~i~~ 54 (64)
T PRK06393 4 QYRACKKCKRLTPEKT-----CPVHGD-------EK-----TTTEWFGFLIITEPEGSAIAKRAGITE 54 (64)
T ss_pred hhhhHhhCCcccCCCc-----CCCCCC-------Cc-----CCcCcceEEEEECCchhHHHHHhCCCC
Confidence 4579999999996554 999985 44 899999999999999999999999983
No 6
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=99.73 E-value=2.3e-18 Score=114.27 Aligned_cols=49 Identities=22% Similarity=0.344 Sum_probs=43.8
Q ss_pred ccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhcccc
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k 113 (115)
+||++|++|++.++ ||||++ ++ +|++|.|+|+|+||++|||||+++|++
T Consensus 4 kAC~~C~~i~~~~~-----CP~Cgs-------~~-----~T~~W~G~viI~dPe~S~IAk~l~i~~ 52 (61)
T PRK08351 4 KACRHCHYITTEDR-----CPVCGS-------RD-----LSDEWFDLVIIIDVENSRIAKKLGAKV 52 (61)
T ss_pred hhhhhCCcccCCCc-----CCCCcC-------Cc-----cccccccEEEEeCCcHhHHHHHhCCCC
Confidence 59999999997765 999986 33 788999999999999999999999974
No 7
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=99.47 E-value=2.2e-14 Score=96.34 Aligned_cols=53 Identities=23% Similarity=0.397 Sum_probs=47.0
Q ss_pred ccccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhhcccc
Q psy8226 46 ASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113 (115)
Q Consensus 46 ~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwqrI~k 113 (115)
..+||.+|+.|.+.|+ +-||+|++ ++ +|++|.|+|.|+||++|.+||.+++++
T Consensus 3 ~~kAC~~Ck~l~~~d~---e~CP~Cgs-------~~-----~te~W~G~~iIidpe~SeIAkrlgi~~ 55 (64)
T COG2093 3 TEKACKNCKRLTPEDT---EICPVCGS-------TD-----LTEEWFGLLIIIDPEKSEIAKRLGIKI 55 (64)
T ss_pred hhHHHhhccccCCCCC---ccCCCCCC-------cc-----cchhhccEEEEEcCcHHHHHHHhCCCC
Confidence 4579999999999887 46999985 44 899999999999999999999999874
No 8
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.63 E-value=0.11 Score=31.55 Aligned_cols=34 Identities=12% Similarity=0.159 Sum_probs=26.1
Q ss_pred ccccCCcccccccccc-cCCCCCchhhhcccCCCC
Q psy8226 48 AETINPRTTSTFDQFE-FDGCDNCDEFLHMKNSRD 81 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~-~~GCPNC~~~L~m~gd~d 81 (115)
..|.+|+...+.++.. .--||+|++-+.++..+.
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~~~ 38 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILFKERPP 38 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEEccCCC
Confidence 4699999998888765 357999998666666554
No 9
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=88.21 E-value=0.2 Score=37.89 Aligned_cols=24 Identities=13% Similarity=0.210 Sum_probs=18.5
Q ss_pred cccCCcccccccc-cccCCCCCchh
Q psy8226 49 ETINPRTTSTFDQ-FEFDGCDNCDE 72 (115)
Q Consensus 49 ACl~C~lVkT~dQ-F~~~GCPNC~~ 72 (115)
.|.+|+-+-.... -..+|||+|+.
T Consensus 3 ~Ct~Cg~~f~dgs~eil~GCP~CGg 27 (131)
T PF09845_consen 3 QCTKCGRVFEDGSKEILSGCPECGG 27 (131)
T ss_pred ccCcCCCCcCCCcHHHHccCcccCC
Confidence 5999998865443 45689999986
No 10
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=88.01 E-value=0.26 Score=38.66 Aligned_cols=28 Identities=14% Similarity=0.202 Sum_probs=22.5
Q ss_pred CCCccccccCCcccccccccccCCCCCchhh
Q psy8226 43 IPSASAETINPRTTSTFDQFEFDGCDNCDEF 73 (115)
Q Consensus 43 ~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~~ 73 (115)
.++...+|.+|+++.+.=+|. ||||+++
T Consensus 350 ~~~p~~~c~~cg~~~~~~~~~---c~~c~~~ 377 (389)
T PRK11788 350 KRKPRYRCRNCGFTARTLYWH---CPSCKAW 377 (389)
T ss_pred hCCCCEECCCCCCCCccceeE---CcCCCCc
Confidence 444457899999998887774 9999975
No 11
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=87.21 E-value=0.23 Score=31.21 Aligned_cols=27 Identities=15% Similarity=0.224 Sum_probs=20.6
Q ss_pred ccccCCccccccccccc--C-----CCCCchhhh
Q psy8226 48 AETINPRTTSTFDQFEF--D-----GCDNCDEFL 74 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~--~-----GCPNC~~~L 74 (115)
.+|..|++..+.+.+.+ . -||||+.+|
T Consensus 23 ~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 23 GTCSGCHMELPPQELNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred CccCCCCEEcCHHHHHHHHcCCCeEECcCCCccC
Confidence 37999999998886643 2 499998654
No 12
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=87.09 E-value=0.22 Score=36.91 Aligned_cols=25 Identities=12% Similarity=0.151 Sum_probs=20.1
Q ss_pred cccCCcccccc-cccccCCCCCchhh
Q psy8226 49 ETINPRTTSTF-DQFEFDGCDNCDEF 73 (115)
Q Consensus 49 ACl~C~lVkT~-dQF~~~GCPNC~~~ 73 (115)
.|.+|+-|-.. +.-...|||+|+.-
T Consensus 4 ~CtrCG~vf~~g~~~il~GCp~CG~n 29 (112)
T COG3364 4 QCTRCGEVFDDGSEEILSGCPKCGCN 29 (112)
T ss_pred eecccccccccccHHHHccCccccch
Confidence 59999988766 66666899999863
No 13
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=85.83 E-value=0.4 Score=26.78 Aligned_cols=22 Identities=14% Similarity=0.064 Sum_probs=15.2
Q ss_pred ccCCcccccccc-cccCCCCCch
Q psy8226 50 TINPRTTSTFDQ-FEFDGCDNCD 71 (115)
Q Consensus 50 Cl~C~lVkT~dQ-F~~~GCPNC~ 71 (115)
|.+|+....... ...--||||+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 678877665544 4445799997
No 14
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=85.30 E-value=0.58 Score=35.69 Aligned_cols=35 Identities=14% Similarity=0.023 Sum_probs=25.9
Q ss_pred CCceeEcCCCCccccccCCcccccccccccCCCCCchhh
Q psy8226 35 HRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEF 73 (115)
Q Consensus 35 ~~p~~i~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~~ 73 (115)
|-+..+.+...+|.-|-.|+. .....| -||+|+..
T Consensus 297 ~~~v~~~~~~~tS~~C~~cg~-~~~r~~---~C~~cg~~ 331 (364)
T COG0675 297 GIVVKVVPPYYTSKTCPCCGH-LSGRLF---KCPRCGFV 331 (364)
T ss_pred CeEEEECCCCCCcccccccCC-ccceeE---ECCCCCCe
Confidence 345566777788899999999 444445 39999964
No 15
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=82.87 E-value=0.89 Score=27.64 Aligned_cols=29 Identities=14% Similarity=0.059 Sum_probs=18.6
Q ss_pred CCccccccCCccccccccccc----CCCCCchh
Q psy8226 44 PSASAETINPRTTSTFDQFEF----DGCDNCDE 72 (115)
Q Consensus 44 ~~~~~ACl~C~lVkT~dQF~~----~GCPNC~~ 72 (115)
|.-...|..|+..-+..+-.. .-||+|++
T Consensus 2 P~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 2 PIYEYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred CCEEEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 445678999997544433211 26999995
No 16
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=81.02 E-value=0.59 Score=25.61 Aligned_cols=20 Identities=25% Similarity=0.356 Sum_probs=13.6
Q ss_pred cccCCccccc-ccccccCCCCCchh
Q psy8226 49 ETINPRTTST-FDQFEFDGCDNCDE 72 (115)
Q Consensus 49 ACl~C~lVkT-~dQF~~~GCPNC~~ 72 (115)
.|.+|+.... .+.| ||+|+.
T Consensus 4 ~Cp~Cg~~~~~~~~f----C~~CG~ 24 (26)
T PF13248_consen 4 FCPNCGAEIDPDAKF----CPNCGA 24 (26)
T ss_pred CCcccCCcCCccccc----ChhhCC
Confidence 5888888533 3345 999984
No 17
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=78.79 E-value=0.83 Score=37.31 Aligned_cols=31 Identities=13% Similarity=0.100 Sum_probs=22.3
Q ss_pred CCccccccCCccccccccccc-------CCCCCchhhh
Q psy8226 44 PSASAETINPRTTSTFDQFEF-------DGCDNCDEFL 74 (115)
Q Consensus 44 ~~~~~ACl~C~lVkT~dQF~~-------~GCPNC~~~L 74 (115)
+....+|-.|+++.+...... --||+|+.||
T Consensus 194 pl~g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRIL 231 (239)
T COG1579 194 PLEGRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRIL 231 (239)
T ss_pred eecCCcccCCeeeecHHHHHHHhcCCCCccCCccchHH
Confidence 445678999999987653211 1599999887
No 18
>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=78.70 E-value=1.5 Score=27.84 Aligned_cols=38 Identities=11% Similarity=-0.107 Sum_probs=24.4
Q ss_pred CCceeEcCCCCccccccCCccccccc-ccccCCCCCchh
Q psy8226 35 HRPWTIDPIPSASAETINPRTTSTFD-QFEFDGCDNCDE 72 (115)
Q Consensus 35 ~~p~~i~p~~~~~~ACl~C~lVkT~d-QF~~~GCPNC~~ 72 (115)
|.+...++..-.|..|-.|+.+.... .-..--||+|+.
T Consensus 16 G~~v~~v~~~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 16 GIQVVEVDEAYTSQTCPRCGHRNKKRRSGRVFTCPNCGF 54 (69)
T ss_pred CCEEEEECCCCCccCccCcccccccccccceEEcCCCCC
Confidence 33333444455789999999987761 212235999984
No 19
>PRK12496 hypothetical protein; Provisional
Probab=77.70 E-value=1.6 Score=33.08 Aligned_cols=48 Identities=10% Similarity=0.079 Sum_probs=27.7
Q ss_pred cccceEEEeecCCCCceeEcCCCCccccccCCcccccccccccCCCCCchhhhc
Q psy8226 22 LAGLKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEFLH 75 (115)
Q Consensus 22 ~~~~~~~~~~~e~~~p~~i~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~ 75 (115)
.-|++|.|++.+-+.=.. .-.+.|..|+-.-+.+- ..+-||.|++-|.
T Consensus 107 ~lgi~v~~~~~~~i~~~~-----~w~~~C~gC~~~~~~~~-~~~~C~~CG~~~~ 154 (164)
T PRK12496 107 KLNIKFENIKTKGIKKVI-----KWRKVCKGCKKKYPEDY-PDDVCEICGSPVK 154 (164)
T ss_pred HcCCeEeccccccchhhe-----eeeEECCCCCccccCCC-CCCcCCCCCChhh
Confidence 357888888744322111 11257999996654221 1123999997554
No 20
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=75.72 E-value=1.1 Score=32.92 Aligned_cols=35 Identities=20% Similarity=0.248 Sum_probs=23.7
Q ss_pred ccccCCcccccccccccC-------CCCCchhhhcccCCCCc
Q psy8226 48 AETINPRTTSTFDQFEFD-------GCDNCDEFLHMKNSRDN 82 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~-------GCPNC~~~L~m~gd~d~ 82 (115)
..|.+|+..-+.+..... -||+|+..|....|.+.
T Consensus 100 Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn~~~ 141 (147)
T smart00531 100 YKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDDNSEP 141 (147)
T ss_pred EECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcCchhh
Confidence 358899977666543222 39999988877766553
No 21
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=75.63 E-value=1.5 Score=31.50 Aligned_cols=33 Identities=12% Similarity=0.098 Sum_probs=21.1
Q ss_pred ccccCCcccccccccccCCCCCchhh-hcccCCC
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEF-LHMKNSR 80 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~-L~m~gd~ 80 (115)
..|..|+..-+..++....||.|++. +++.+.+
T Consensus 71 ~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~~G~ 104 (114)
T PRK03681 71 CWCETCQQYVTLLTQRVRRCPQCHGDMLRIVADD 104 (114)
T ss_pred EEcccCCCeeecCCccCCcCcCcCCCCcEEccCC
Confidence 45999997766654433459999974 3344333
No 22
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=73.82 E-value=1.7 Score=32.00 Aligned_cols=34 Identities=15% Similarity=0.303 Sum_probs=21.7
Q ss_pred ccccCCcccccccc--------------------cccCCCCCchhh-hcccCCCC
Q psy8226 48 AETINPRTTSTFDQ--------------------FEFDGCDNCDEF-LHMKNSRD 81 (115)
Q Consensus 48 ~ACl~C~lVkT~dQ--------------------F~~~GCPNC~~~-L~m~gd~d 81 (115)
..|..|+.+-+.++ ....-||+|++. +++.+.++
T Consensus 71 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~e 125 (135)
T PRK03824 71 LKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKGRG 125 (135)
T ss_pred EECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecCce
Confidence 46999998877762 112359999974 34444443
No 23
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=72.37 E-value=1.6 Score=42.75 Aligned_cols=40 Identities=20% Similarity=0.287 Sum_probs=32.3
Q ss_pred EEEeecCCCCceeEcCCCCccccccCCcccccccccccCCCCCchh
Q psy8226 27 VVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 27 ~~~~~~e~~~p~~i~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
+-||-..|+. ..|+=+.-++|+.|+..-+.++ +-||+|++
T Consensus 677 ~hGvl~~~~~---~vPvY~tIKrC~dcg~q~~~~~---~~cP~Cgs 716 (1187)
T COG1110 677 VHGVLVKDGK---YVPVYDTIKRCRDCGEQFVDSE---DKCPRCGS 716 (1187)
T ss_pred cceeeccCCc---eEehHHHHHHHhhcCceecccc---ccCCCCCC
Confidence 4567777776 4788899999999999888774 36999996
No 24
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=71.98 E-value=1.7 Score=31.06 Aligned_cols=25 Identities=16% Similarity=0.218 Sum_probs=17.8
Q ss_pred ccccCCcccccccccccCCCCCchhh
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEF 73 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~ 73 (115)
..|..|+..-..+++.. -||+|++.
T Consensus 71 ~~C~~Cg~~~~~~~~~~-~CP~Cgs~ 95 (113)
T PRK12380 71 AWCWDCSQVVEIHQHDA-QCPHCHGE 95 (113)
T ss_pred EEcccCCCEEecCCcCc-cCcCCCCC
Confidence 46999997666654433 39999963
No 25
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=69.66 E-value=1.2 Score=33.45 Aligned_cols=35 Identities=17% Similarity=0.191 Sum_probs=23.7
Q ss_pred ccccCCcccccccccccC--CCCCchhhhcccCCCCc
Q psy8226 48 AETINPRTTSTFDQFEFD--GCDNCDEFLHMKNSRDN 82 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~--GCPNC~~~L~m~gd~d~ 82 (115)
..|.+|+.--|.+.=... -||+|++.|...+|++.
T Consensus 110 Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~~~dn~~~ 146 (158)
T TIGR00373 110 FICPNMCVRFTFNEAMELNFTCPRCGAMLDYLDNSEA 146 (158)
T ss_pred EECCCCCcEeeHHHHHHcCCcCCCCCCEeeeccCHHH
Confidence 358889977666632111 49999998876666653
No 26
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=68.65 E-value=1.5 Score=33.75 Aligned_cols=34 Identities=24% Similarity=0.255 Sum_probs=23.5
Q ss_pred cccCCcccccccccccC--CCCCchhhhcccCCCCc
Q psy8226 49 ETINPRTTSTFDQFEFD--GCDNCDEFLHMKNSRDN 82 (115)
Q Consensus 49 ACl~C~lVkT~dQF~~~--GCPNC~~~L~m~gd~d~ 82 (115)
.|.+|+.--|.+.=... -||+|++.|...+|++.
T Consensus 119 ~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~dn~~~ 154 (178)
T PRK06266 119 FCPNCHIRFTFDEAMEYGFRCPQCGEMLEEYDNSEL 154 (178)
T ss_pred ECCCCCcEEeHHHHhhcCCcCCCCCCCCeecccHHH
Confidence 59999987776632111 49999998876666553
No 27
>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=66.63 E-value=3.5 Score=23.57 Aligned_cols=23 Identities=9% Similarity=-0.122 Sum_probs=16.8
Q ss_pred cccCCcccccccccccCCCCCchh
Q psy8226 49 ETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 49 ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
.|..|++|-..+. ...-||.|+.
T Consensus 3 ~C~~CGy~y~~~~-~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGYIYDGEE-APWVCPVCGA 25 (33)
T ss_pred ECCCCCCEECCCc-CCCcCcCCCC
Confidence 5999999966553 2236999984
No 28
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=66.03 E-value=2.9 Score=30.10 Aligned_cols=60 Identities=12% Similarity=0.151 Sum_probs=34.3
Q ss_pred cccCCcceEEEecCCCCCC-ccccceEEEeecCCCCceeEcCCCCccccccCCcccccccccccCCCCCchhh
Q psy8226 2 RTIDPGLLTLYYRPPPKPS-TLAGLKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEF 73 (115)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~e~~~p~~i~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~~ 73 (115)
..|+|..|..+|.---+-+ .++|.++.-. ..| ....|..|+..-+.+++...-||.|++.
T Consensus 37 s~V~pe~L~faf~~~~~~T~~~ega~L~Ie---------~vp---~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 37 SGMDKSLFVSAFETFREESLVCKDAILDIV---------DEK---VELECKDCSHVFKPNALDYGVCEKCHSK 97 (117)
T ss_pred cCcCHHHHHHHHHHHhcCCcccCCCEEEEE---------ecC---CEEEhhhCCCccccCCccCCcCcCCCCC
Confidence 4566666666664433323 2456554311 111 2245999997777765433359999974
No 29
>PRK00420 hypothetical protein; Validated
Probab=64.53 E-value=2.6 Score=30.95 Aligned_cols=31 Identities=6% Similarity=-0.260 Sum_probs=20.2
Q ss_pred ccccCCcccccccccccCCCCCchhhhcccC
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEFLHMKN 78 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~g 78 (115)
..|-.|+..+....=-..-||||+.++..++
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYIVKS 54 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeeeecc
Confidence 4699999876652111234999998665544
No 30
>PF15645 Tox-PLDMTX: Dermonecrotoxin of the Papain-like fold
Probab=62.94 E-value=2.4 Score=31.91 Aligned_cols=33 Identities=21% Similarity=0.572 Sum_probs=26.1
Q ss_pred CCCccccccccccceEE----EEeCCCchHHHhhhcc
Q psy8226 79 SRDNVYNCTSSNFDGMI----ALMDPKDSWVAKWQRI 111 (115)
Q Consensus 79 d~d~v~dCTT~nF~G~I----aImdP~kSWVAKwqrI 111 (115)
+.+-|.|-|...|.+.- -++.|+++|+.|||.-
T Consensus 54 g~eyV~D~Ta~QF~~~~~~~~p~i~~~~~W~~~~~~~ 90 (135)
T PF15645_consen 54 GKEYVFDPTAHQFSNKGNDNGPIILPEDAWKKRYQQA 90 (135)
T ss_pred CEEEEEeCcHHHhhccCCCCCceEecHHHHHHHHHHH
Confidence 34557777888888776 6789999999999863
No 31
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=62.64 E-value=1.7 Score=30.93 Aligned_cols=25 Identities=20% Similarity=0.295 Sum_probs=18.6
Q ss_pred ccccCCcccccccccccCCCCCchhh
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEF 73 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~ 73 (115)
..|..|+..-+.+++. .-||+|++.
T Consensus 71 ~~C~~Cg~~~~~~~~~-~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFD-FSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EEECHHCC-HH-SSSSSS
T ss_pred EECCCCCCEEecCCCC-CCCcCCcCC
Confidence 4599999999888875 459999974
No 32
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=62.25 E-value=3.9 Score=27.26 Aligned_cols=25 Identities=16% Similarity=0.084 Sum_probs=17.6
Q ss_pred cccCCcccccccc-cccCCCCCchhh
Q psy8226 49 ETINPRTTSTFDQ-FEFDGCDNCDEF 73 (115)
Q Consensus 49 ACl~C~lVkT~dQ-F~~~GCPNC~~~ 73 (115)
.|.+|+....... ...-.||||+..
T Consensus 9 ~CtSCg~~i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 9 KCTSCGIEIAPREKAVKFLCPNCGEV 34 (59)
T ss_pred cccCCCCcccCCCccCEeeCCCCCCe
Confidence 5999998877443 333369999853
No 33
>PHA02942 putative transposase; Provisional
Probab=61.53 E-value=6.3 Score=33.51 Aligned_cols=30 Identities=17% Similarity=0.243 Sum_probs=20.6
Q ss_pred eEcCCCCccccccCCcccccc---cccccCCCCCchh
Q psy8226 39 TIDPIPSASAETINPRTTSTF---DQFEFDGCDNCDE 72 (115)
Q Consensus 39 ~i~p~~~~~~ACl~C~lVkT~---dQF~~~GCPNC~~ 72 (115)
.|.|.- +|..|-.|+.+... ..| -|++|+.
T Consensus 318 ~V~p~y-TSq~Cs~CG~~~~~l~~r~f---~C~~CG~ 350 (383)
T PHA02942 318 FVNPSY-SSVSCPKCGHKMVEIAHRYF---HCPSCGY 350 (383)
T ss_pred EECCCC-CCccCCCCCCccCcCCCCEE---ECCCCCC
Confidence 345554 78899999977532 334 3999994
No 34
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=60.81 E-value=2.7 Score=36.23 Aligned_cols=36 Identities=14% Similarity=0.142 Sum_probs=25.0
Q ss_pred cccCCccccccccccc--CCCCCchhhhcccCCCCccccc
Q psy8226 49 ETINPRTTSTFDQFEF--DGCDNCDEFLHMKNSRDNVYNC 86 (115)
Q Consensus 49 ACl~C~lVkT~dQF~~--~GCPNC~~~L~m~gd~d~v~dC 86 (115)
+|++|+...+.++=.. .-|| |++- =.+|-.+||.+=
T Consensus 242 ~c~~C~~~~~~~~~~~~~~~Cp-CG~~-i~~GV~~Rv~eL 279 (374)
T TIGR00375 242 ACEACGEPAVSEDAETACANCP-CGGR-IKKGVSDRLREL 279 (374)
T ss_pred hhcccCCcCCchhhhhcCCCCC-CCCc-ceechHHHHHHH
Confidence 6999999999877221 2499 9975 345666665543
No 35
>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=60.34 E-value=6.6 Score=35.73 Aligned_cols=44 Identities=7% Similarity=0.065 Sum_probs=29.5
Q ss_pred cccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHH
Q psy8226 47 SAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVA 106 (115)
Q Consensus 47 ~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVA 106 (115)
.-.|..|+.+.....| -||.|++ . ..+.++=+++.+.|-++|-.
T Consensus 532 ~siC~~CGy~~g~~~~---~CP~CGs-------~------~~ev~sRv~GYl~~v~~wN~ 575 (586)
T TIGR02827 532 ITICNDCHHIDKRTLH---RCPVCGS-------A------NIDYGTRVIGYLKRVSAFSK 575 (586)
T ss_pred CeecCCCCCcCCCcCC---cCcCCCC-------c------cceEEEeecceecCcccccc
Confidence 3469999996433323 4999984 2 24467777777788777754
No 36
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=60.29 E-value=5.2 Score=26.15 Aligned_cols=25 Identities=12% Similarity=0.076 Sum_probs=18.3
Q ss_pred CCccccccCCcccccccccccCCCCCchhh
Q psy8226 44 PSASAETINPRTTSTFDQFEFDGCDNCDEF 73 (115)
Q Consensus 44 ~~~~~ACl~C~lVkT~dQF~~~GCPNC~~~ 73 (115)
.++-..|-.|+...-.++ ||+|++.
T Consensus 2 ks~mr~C~~CgvYTLk~~-----CP~CG~~ 26 (56)
T PRK13130 2 KSKIRKCPKCGVYTLKEI-----CPVCGGK 26 (56)
T ss_pred CccceECCCCCCEEcccc-----CcCCCCC
Confidence 345567999998866444 9999963
No 37
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=59.99 E-value=6.1 Score=22.45 Aligned_cols=29 Identities=17% Similarity=0.141 Sum_probs=18.9
Q ss_pred CCccccccCCcccccccccc----cCCCCCchh
Q psy8226 44 PSASAETINPRTTSTFDQFE----FDGCDNCDE 72 (115)
Q Consensus 44 ~~~~~ACl~C~lVkT~dQF~----~~GCPNC~~ 72 (115)
+.-..+|..|+..-+..+-. ...||+|++
T Consensus 2 p~Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 2 PIYEYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred CCEEEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 44456899999865544321 246999985
No 38
>KOG1315|consensus
Probab=59.96 E-value=7.9 Score=32.65 Aligned_cols=69 Identities=22% Similarity=0.265 Sum_probs=41.7
Q ss_pred cCCcceEEEecCCCCCCccccceEEEeecCCCCceeEcCCCCccccccCCcccccccccccCCCCCchhhhccc
Q psy8226 4 IDPGLLTLYYRPPPKPSTLAGLKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEFLHMK 77 (115)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~p~~i~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~ 77 (115)
+|||-....|||...+....+- |+-+|...|-+..-...+.+-|.+|+.+|...-=-=.-|.-| +|.|+
T Consensus 69 ~~pg~vp~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rC--vLKmD 137 (307)
T KOG1315|consen 69 TDPGRVPDSYRPSVEDEDSLEN---GSDNERDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRC--VLKMD 137 (307)
T ss_pred ecCCCCccccCCCcCccccccc---cCcccccceeeEecCCCCceeecccccccCCccccchhhhhh--hhccc
Confidence 5889888889887655443322 223344445555555556666999999998775321234444 45554
No 39
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=58.95 E-value=3.7 Score=26.39 Aligned_cols=29 Identities=14% Similarity=0.119 Sum_probs=21.4
Q ss_pred ccccccCCccccccccccc-CCCCCchhhh
Q psy8226 46 ASAETINPRTTSTFDQFEF-DGCDNCDEFL 74 (115)
Q Consensus 46 ~~~ACl~C~lVkT~dQF~~-~GCPNC~~~L 74 (115)
.+..|.+|+-..+.+|-.. .-||+|++-.
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCcEE
Confidence 4567999999887665443 4799999643
No 40
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=57.27 E-value=7.1 Score=23.36 Aligned_cols=30 Identities=10% Similarity=0.146 Sum_probs=18.3
Q ss_pred CCCccccccCCcccc----cccccccCCCCCchh
Q psy8226 43 IPSASAETINPRTTS----TFDQFEFDGCDNCDE 72 (115)
Q Consensus 43 ~~~~~~ACl~C~lVk----T~dQF~~~GCPNC~~ 72 (115)
+|.-..+|..|+-.- +..+-...-||+|++
T Consensus 1 MP~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 1 MPIYEYRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred CCCEEEEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 345567899999332 333311237999985
No 41
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=56.91 E-value=5.1 Score=28.67 Aligned_cols=58 Identities=14% Similarity=0.226 Sum_probs=32.1
Q ss_pred ccCCcceEEEecCCCCCCccccceEEEeecCCCCceeEcCCCCccccccCCcccccccccccCCCCCchhh
Q psy8226 3 TIDPGLLTLYYRPPPKPSTLAGLKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEF 73 (115)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~p~~i~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~~ 73 (115)
.++|..|...|.---+-+-++|.++.- ...|. ...|..|+..-+.+++. .-||.|++.
T Consensus 38 ~V~p~~L~faf~~~~~~t~~ega~L~I---------~~~p~---~~~C~~Cg~~~~~~~~~-~~CP~Cgs~ 95 (115)
T TIGR00100 38 CVNPSQLQFAFEVVREGTVAEGAKLNI---------EDEPV---ECECEDCSEEVSPEIDL-YRCPKCHGI 95 (115)
T ss_pred ccCHHHHHHHHHHHhCCCccCCCEEEE---------EeeCc---EEEcccCCCEEecCCcC-ccCcCCcCC
Confidence 456666666554433333344544321 11121 24599999777766542 359999974
No 42
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=55.23 E-value=5.4 Score=26.86 Aligned_cols=24 Identities=17% Similarity=0.079 Sum_probs=17.0
Q ss_pred cccCCcccc-cccccccCCCCCchh
Q psy8226 49 ETINPRTTS-TFDQFEFDGCDNCDE 72 (115)
Q Consensus 49 ACl~C~lVk-T~dQF~~~GCPNC~~ 72 (115)
.|.+|+.+. ..+.+..--||||++
T Consensus 11 ~CtSCg~~i~p~e~~v~F~CPnCGe 35 (61)
T COG2888 11 VCTSCGREIAPGETAVKFPCPNCGE 35 (61)
T ss_pred eeccCCCEeccCCceeEeeCCCCCc
Confidence 599999998 444333346999984
No 43
>PRK07591 threonine synthase; Validated
Probab=55.18 E-value=5.9 Score=33.68 Aligned_cols=33 Identities=9% Similarity=0.175 Sum_probs=25.0
Q ss_pred CccccccCCcccccccccccCCCCCchhhhcccCC
Q psy8226 45 SASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNS 79 (115)
Q Consensus 45 ~~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd 79 (115)
...+.|.+|+..-..+.. ..||.|++.|+..-|
T Consensus 16 ~~~l~C~~Cg~~~~~~~~--~~C~~cg~~l~~~y~ 48 (421)
T PRK07591 16 AVALKCRECGAEYPLGPI--HVCEECFGPLEVAYD 48 (421)
T ss_pred eeEEEeCCCCCcCCCCCC--ccCCCCCCeEEEEec
Confidence 345789999988776643 689999988876644
No 44
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=55.10 E-value=2.7 Score=37.33 Aligned_cols=45 Identities=11% Similarity=0.187 Sum_probs=16.5
Q ss_pred ccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHHHhhh
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQ 109 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWVAKwq 109 (115)
-.|..|+.+-.. .+ -||+|++ ++ +..+.=+++.+.|-++|-+=.|
T Consensus 492 ~~C~~CG~~~~~-~~---~CP~CGs-------~~------~~~~~Rv~GYl~~v~~~n~gK~ 536 (546)
T PF13597_consen 492 DICPDCGYIGGE-GD---KCPKCGS-------EN------IEVYSRVTGYLRPVSRWNKGKQ 536 (546)
T ss_dssp EEETTT---S---EE---E-CCC-----------------EEEEB-SSSS-BTTS-------
T ss_pred ccccCCCcCCCC-CC---CCCCCCC-------cc------cceEEEeeccccCccccCHHHH
Confidence 369999998776 44 4999996 22 2333334444448888865443
No 45
>PF10114 PocR: Sensory domain found in PocR; InterPro: IPR018771 This entry is thought to act as a sensory domain in histidine kinases catalysing the reaction: ATP + protein L-histidine = ADP + protein N- phospho-L-histidine.
Probab=54.34 E-value=11 Score=27.13 Aligned_cols=60 Identities=22% Similarity=0.314 Sum_probs=35.7
Q ss_pred cccceEEEeecCCCCceeEcCCCCccccccCCcccccccccccCCCCCchhhhc---ccCCCCccccccc
Q psy8226 22 LAGLKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEFLH---MKNSRDNVYNCTS 88 (115)
Q Consensus 22 ~~~~~~~~~~~e~~~p~~i~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~---m~gd~d~v~dCTT 88 (115)
+.|+.+ .++|.+|+|.. ..+.-|.-|+++++...- ...|..|...+. ++.+...++.|-.
T Consensus 20 ~tgl~~-~i~d~~G~~l~-----~~~~~~~fC~~~~~~~~~-~~~C~~~~~~~~~~a~~~~~~~i~~C~~ 82 (173)
T PF10114_consen 20 ATGLSI-VIVDPDGNPLT-----QPSNFCPFCKLIRSSPEG-RERCRESDRRLAEQAMKKGEPYIYRCHA 82 (173)
T ss_pred HHCCcE-EEEeCCCCEEe-----eCCCchhhhhHHhcCCcc-cccCHHHHHHHHHHhhccCCCEEEEcCc
Confidence 345554 47899999984 223557888888876652 224666655442 2333555677743
No 46
>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=54.02 E-value=7.7 Score=21.60 Aligned_cols=21 Identities=10% Similarity=0.094 Sum_probs=14.8
Q ss_pred cccCCcccccccccccCCCCCchh
Q psy8226 49 ETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 49 ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
.|-.|+-+.+.+. .-||+|+.
T Consensus 2 ~CP~C~~~V~~~~---~~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPESA---KFCPHCGY 22 (26)
T ss_pred cCCCCcCCchhhc---CcCCCCCC
Confidence 4778887776665 23999984
No 47
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=53.99 E-value=7.6 Score=23.17 Aligned_cols=23 Identities=9% Similarity=-0.068 Sum_probs=13.2
Q ss_pred ccCCcccccccccc---cCCCCCchh
Q psy8226 50 TINPRTTSTFDQFE---FDGCDNCDE 72 (115)
Q Consensus 50 Cl~C~lVkT~dQF~---~~GCPNC~~ 72 (115)
|-.|+-++...+.. ..-||.|+.
T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCccccccCCCCCEEECCcCCC
Confidence 66776666554331 234888873
No 48
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=53.83 E-value=5.7 Score=29.38 Aligned_cols=23 Identities=9% Similarity=0.497 Sum_probs=18.1
Q ss_pred cccCCcccccccccccCCCCCchh
Q psy8226 49 ETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 49 ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
.|+.|+-..+.+.+... ||.|++
T Consensus 72 ~C~~C~~~~~~e~~~~~-CP~C~s 94 (115)
T COG0375 72 WCLDCGQEVELEELDYR-CPKCGS 94 (115)
T ss_pred EeccCCCeecchhheeE-CCCCCC
Confidence 59999777777776554 999995
No 49
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=53.71 E-value=4.3 Score=29.88 Aligned_cols=38 Identities=16% Similarity=0.338 Sum_probs=26.2
Q ss_pred CceeEcCCCCccccccCCccccccccccc-CCCCCchhh
Q psy8226 36 RPWTIDPIPSASAETINPRTTSTFDQFEF-DGCDNCDEF 73 (115)
Q Consensus 36 ~p~~i~p~~~~~~ACl~C~lVkT~dQF~~-~GCPNC~~~ 73 (115)
.||...-.+.+---|-.|+-.+|.+++.. ..||||.+-
T Consensus 51 ~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~sp 89 (105)
T COG4357 51 EPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQSP 89 (105)
T ss_pred ccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcCCC
Confidence 45554222222234999999999999985 679999863
No 50
>PRK14873 primosome assembly protein PriA; Provisional
Probab=53.48 E-value=4.2 Score=37.19 Aligned_cols=42 Identities=12% Similarity=0.066 Sum_probs=23.7
Q ss_pred ccccCCcccccccccccCCCCCchhh-hcccC-CCCccccccccccceE
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEF-LHMKN-SRDNVYNCTSSNFDGM 94 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~-L~m~g-d~d~v~dCTT~nF~G~ 94 (115)
+.|..|+.-.. ..-||+|++. |...| ..+++.+-....|-|.
T Consensus 411 l~Ch~CG~~~~-----p~~Cp~Cgs~~l~~~g~Gter~eeeL~~~FP~~ 454 (665)
T PRK14873 411 PRCRWCGRAAP-----DWRCPRCGSDRLRAVVVGARRTAEELGRAFPGV 454 (665)
T ss_pred eECCCCcCCCc-----CccCCCCcCCcceeeeccHHHHHHHHHHHCCCC
Confidence 45777776432 1248888763 44333 4566666666666553
No 51
>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=53.42 E-value=7.7 Score=22.51 Aligned_cols=24 Identities=8% Similarity=-0.013 Sum_probs=17.2
Q ss_pred ccccCCcccccccccccCCCCCchh
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
..|..|++|-..+. .-+-||.|+.
T Consensus 3 ~~C~~CG~i~~g~~-~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEGEE-APEKCPICGA 26 (34)
T ss_pred EECCCCCCEeECCc-CCCcCcCCCC
Confidence 36999999966543 1246999984
No 52
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=52.64 E-value=5 Score=36.71 Aligned_cols=42 Identities=7% Similarity=0.163 Sum_probs=26.3
Q ss_pred ccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCCCchHH
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWV 105 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP~kSWV 105 (115)
-.|..|+.+-+...+ -||+|++ ++ ++.++=+++.+.|-++|-
T Consensus 567 ~iC~~CG~~~~g~~~---~CP~CGs-------~~------~ev~~RV~GYl~~v~~wN 608 (623)
T PRK08271 567 TICNDCHHIDKRTGK---RCPICGS-------EN------IDYYTRVIGYLKRVSAFS 608 (623)
T ss_pred ccCCCCCCcCCCCCc---CCcCCCC-------cc------hhHHHHHhhhhcCccccc
Confidence 369999998444443 5999984 21 234555555556655554
No 53
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=52.28 E-value=5.9 Score=21.36 Aligned_cols=19 Identities=26% Similarity=0.440 Sum_probs=11.4
Q ss_pred ccCCcccccc-cccccCCCCCchh
Q psy8226 50 TINPRTTSTF-DQFEFDGCDNCDE 72 (115)
Q Consensus 50 Cl~C~lVkT~-dQF~~~GCPNC~~ 72 (115)
|.+|+--... .+| |++|+.
T Consensus 2 Cp~CG~~~~~~~~f----C~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIEDDAKF----CPNCGT 21 (23)
T ss_pred CcccCCCCCCcCcc----hhhhCC
Confidence 6667654443 345 888873
No 54
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=51.89 E-value=9 Score=22.42 Aligned_cols=14 Identities=14% Similarity=0.074 Sum_probs=6.7
Q ss_pred cccCCccccccccc
Q psy8226 49 ETINPRTTSTFDQF 62 (115)
Q Consensus 49 ACl~C~lVkT~dQF 62 (115)
+|+.|+++...++|
T Consensus 22 ~C~~C~Y~~~~~~~ 35 (35)
T PF02150_consen 22 ACRTCGYEEPISQF 35 (35)
T ss_dssp EESSSS-EEE-SS-
T ss_pred CCCCCCCccCCCCC
Confidence 56666666655554
No 55
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=48.09 E-value=9.4 Score=33.02 Aligned_cols=26 Identities=15% Similarity=0.031 Sum_probs=19.5
Q ss_pred cccccCCcccccccccccCCCCCchhhhc
Q psy8226 47 SAETINPRTTSTFDQFEFDGCDNCDEFLH 75 (115)
Q Consensus 47 ~~ACl~C~lVkT~dQF~~~GCPNC~~~L~ 75 (115)
..+|..|+++...++ .-||.|++.|.
T Consensus 221 l~~C~~Cd~l~~~~~---a~CpRC~~~L~ 246 (419)
T PRK15103 221 LRSCSCCTAILPADQ---PVCPRCHTKGY 246 (419)
T ss_pred CCcCCCCCCCCCCCC---CCCCCCCCcCc
Confidence 346999999975443 36999998773
No 56
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=47.24 E-value=11 Score=32.51 Aligned_cols=28 Identities=14% Similarity=0.221 Sum_probs=20.4
Q ss_pred ccccCCcccccccccccC---CCCCchhhhc
Q psy8226 48 AETINPRTTSTFDQFEFD---GCDNCDEFLH 75 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~---GCPNC~~~L~ 75 (115)
.+|..|..+......... -||.|++.|.
T Consensus 14 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 14 ILCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eeCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 469999999865543332 3999998774
No 57
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=46.81 E-value=7.5 Score=31.09 Aligned_cols=23 Identities=17% Similarity=0.229 Sum_probs=17.0
Q ss_pred c-ccCCcccccccccccCCCCCchh
Q psy8226 49 E-TINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 49 A-Cl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
| |.+|+-.+-. ....--||||+.
T Consensus 150 A~CsrC~~~L~~-~~~~l~Cp~Cg~ 173 (188)
T COG1096 150 ARCSRCRAPLVK-KGNMLKCPNCGN 173 (188)
T ss_pred EEccCCCcceEE-cCcEEECCCCCC
Confidence 5 9999987766 333446999983
No 58
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=46.63 E-value=13 Score=22.91 Aligned_cols=36 Identities=14% Similarity=0.277 Sum_probs=21.2
Q ss_pred CCceeEcCCCCccc--cccCCcc--ccccccc--ccCCCCCc
Q psy8226 35 HRPWTIDPIPSASA--ETINPRT--TSTFDQF--EFDGCDNC 70 (115)
Q Consensus 35 ~~p~~i~p~~~~~~--ACl~C~l--VkT~dQF--~~~GCPNC 70 (115)
..|..|.+.|.+.. .|..|+. -.+...- ...|||.|
T Consensus 14 ~~p~~v~~~s~~~v~W~C~~Cgh~w~~~v~~R~~~~~~CP~C 55 (55)
T PF14311_consen 14 LDPSEVTPGSNKKVWWKCPKCGHEWKASVNDRTRRGKGCPYC 55 (55)
T ss_pred CCHHHhCcCCCCEEEEECCCCCCeeEccHhhhccCCCCCCCC
Confidence 46666666555544 3999954 3333332 23689988
No 59
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=46.54 E-value=10 Score=35.41 Aligned_cols=8 Identities=0% Similarity=-0.417 Sum_probs=4.2
Q ss_pred cccCCccc
Q psy8226 49 ETINPRTT 56 (115)
Q Consensus 49 ACl~C~lV 56 (115)
.|.+|+.+
T Consensus 437 ~C~~Cg~v 444 (730)
T COG1198 437 LCRDCGYI 444 (730)
T ss_pred ecccCCCc
Confidence 35555554
No 60
>PRK02935 hypothetical protein; Provisional
Probab=46.23 E-value=10 Score=28.20 Aligned_cols=22 Identities=23% Similarity=0.616 Sum_probs=11.4
Q ss_pred CCCchhhhcccCCCCccccccc
Q psy8226 67 CDNCDEFLHMKNSRDNVYNCTS 88 (115)
Q Consensus 67 CPNC~~~L~m~gd~d~v~dCTT 88 (115)
||||+..-.|-|..|....|-+
T Consensus 73 CP~C~K~TKmLGrvD~CM~C~~ 94 (110)
T PRK02935 73 CPSCEKPTKMLGRVDACMHCNQ 94 (110)
T ss_pred CCCCCchhhhccceeecCcCCC
Confidence 5555555555555554444433
No 61
>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=45.44 E-value=11 Score=33.86 Aligned_cols=22 Identities=18% Similarity=0.185 Sum_probs=15.2
Q ss_pred ccccCCcccccccccccCCCCCchh
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
-.|..|+++-.... .-||.|++
T Consensus 525 ~~C~~CG~~g~~~~---~~CP~Cgs 546 (579)
T TIGR02487 525 DVCEDCGYTGEGLN---DKCPKCGS 546 (579)
T ss_pred ccCCCCCCCCCCCC---CcCcCCCC
Confidence 46999998544332 34999985
No 62
>PF12773 DZR: Double zinc ribbon
Probab=45.26 E-value=14 Score=21.98 Aligned_cols=30 Identities=17% Similarity=0.106 Sum_probs=17.7
Q ss_pred CCCccccccCCcccccccccccCCCCCchh
Q psy8226 43 IPSASAETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 43 ~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
++...+.|..|+.-+..+.-...-|++|+.
T Consensus 8 ~~~~~~fC~~CG~~l~~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 8 NPDDAKFCPHCGTPLPPPDQSKKICPNCGA 37 (50)
T ss_pred CCccccCChhhcCChhhccCCCCCCcCCcC
Confidence 344455688888877722222234888875
No 63
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=45.13 E-value=11 Score=32.52 Aligned_cols=28 Identities=14% Similarity=0.250 Sum_probs=20.1
Q ss_pred ccccCCccccccccccc---CCCCCchhhhc
Q psy8226 48 AETINPRTTSTFDQFEF---DGCDNCDEFLH 75 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~---~GCPNC~~~L~ 75 (115)
.+|..|+++.....-.. --||.|++.|.
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 41 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTLT 41 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCCc
Confidence 57999999986553322 23999998773
No 64
>PRK11823 DNA repair protein RadA; Provisional
Probab=44.74 E-value=13 Score=32.01 Aligned_cols=24 Identities=13% Similarity=0.069 Sum_probs=18.5
Q ss_pred cccccCCcccccccccccCCCCCchhh
Q psy8226 47 SAETINPRTTSTFDQFEFDGCDNCDEF 73 (115)
Q Consensus 47 ~~ACl~C~lVkT~dQF~~~GCPNC~~~ 73 (115)
...|.+|++....=++ .||+|++-
T Consensus 7 ~y~C~~Cg~~~~~~~g---~Cp~C~~w 30 (446)
T PRK11823 7 AYVCQECGAESPKWLG---RCPECGAW 30 (446)
T ss_pred eEECCcCCCCCcccCe---eCcCCCCc
Confidence 3579999998766665 49999863
No 65
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=44.42 E-value=5.4 Score=36.41 Aligned_cols=22 Identities=14% Similarity=0.096 Sum_probs=15.7
Q ss_pred ccccCCcccccccccccCCCCCchh
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
-.|..|+.+.....| -||+|++
T Consensus 569 ~~C~~CG~~~~g~~~---~CP~CGs 590 (625)
T PRK08579 569 TVCNKCGRSTTGLYT---RCPRCGS 590 (625)
T ss_pred ccCCCCCCccCCCCC---cCcCCCC
Confidence 469999985444443 5999985
No 66
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=44.20 E-value=10 Score=24.45 Aligned_cols=13 Identities=38% Similarity=0.657 Sum_probs=10.1
Q ss_pred ccccCCCCCchhh
Q psy8226 61 QFEFDGCDNCDEF 73 (115)
Q Consensus 61 QF~~~GCPNC~~~ 73 (115)
+|+..|||+|...
T Consensus 4 ~~~a~~C~~C~~~ 16 (76)
T TIGR00412 4 QIYGTGCANCQMT 16 (76)
T ss_pred EEECCCCcCHHHH
Confidence 4666899999854
No 67
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=43.91 E-value=16 Score=26.20 Aligned_cols=23 Identities=9% Similarity=0.164 Sum_probs=15.3
Q ss_pred ccccCCcccccccccccCCCCCc
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNC 70 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC 70 (115)
+-|..|++.+......-.-|..|
T Consensus 49 ~~C~~C~~~kp~Rs~HC~~C~~C 71 (174)
T PF01529_consen 49 KYCSTCKIIKPPRSHHCRVCNRC 71 (174)
T ss_pred EECcccCCcCCCcceeccccccc
Confidence 34999999988877553344444
No 68
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=43.51 E-value=14 Score=26.95 Aligned_cols=24 Identities=13% Similarity=0.184 Sum_probs=19.0
Q ss_pred cccCCccccccccccc-CCCCCchh
Q psy8226 49 ETINPRTTSTFDQFEF-DGCDNCDE 72 (115)
Q Consensus 49 ACl~C~lVkT~dQF~~-~GCPNC~~ 72 (115)
+|..|+++-..+.-.. .-||-|.+
T Consensus 60 ~CkkCGfef~~~~ik~pSRCP~CKS 84 (97)
T COG3357 60 RCKKCGFEFRDDKIKKPSRCPKCKS 84 (97)
T ss_pred hhcccCccccccccCCcccCCcchh
Confidence 6999999877666553 57999985
No 69
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=43.06 E-value=12 Score=34.80 Aligned_cols=21 Identities=14% Similarity=0.297 Sum_probs=15.5
Q ss_pred ccccCCcccccccccccCCCCCchh
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
-.|..|++..... .-||+|++
T Consensus 681 ~~C~~CG~~~~~~----~~CP~CG~ 701 (735)
T PRK07111 681 DRCPVCGYLGVIE----DKCPKCGS 701 (735)
T ss_pred eecCCCCCCCCcC----ccCcCCCC
Confidence 4699999865542 35999984
No 70
>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=43.01 E-value=14 Score=32.32 Aligned_cols=41 Identities=17% Similarity=0.230 Sum_probs=23.6
Q ss_pred cccCCcccccccccccCCCCCchhh-hcccC-CCCccccccccccce
Q psy8226 49 ETINPRTTSTFDQFEFDGCDNCDEF-LHMKN-SRDNVYNCTSSNFDG 93 (115)
Q Consensus 49 ACl~C~lVkT~dQF~~~GCPNC~~~-L~m~g-d~d~v~dCTT~nF~G 93 (115)
.|..|+....... -||+|++. |...| ..+++.+-....|-|
T Consensus 242 ~Ch~Cg~~~~~~~----~Cp~C~s~~l~~~g~Gte~~~e~l~~~fp~ 284 (505)
T TIGR00595 242 RCHYCGYQEPIPK----TCPQCGSEDLVYKGYGTEQVEEELAKLFPG 284 (505)
T ss_pred EcCCCcCcCCCCC----CCCCCCCCeeEeecccHHHHHHHHHhhCCC
Confidence 3555555544333 49999862 33333 356666666667765
No 71
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=42.58 E-value=14 Score=21.49 Aligned_cols=24 Identities=8% Similarity=0.050 Sum_probs=15.6
Q ss_pred cccCCcccccccccccCCCCCchh
Q psy8226 49 ETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 49 ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
.|.+|+...+.+.-..--|++|+.
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCCcCCCeeEcCCCCcEECCcCCC
Confidence 488888887755433347999984
No 72
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=42.31 E-value=6.9 Score=36.57 Aligned_cols=55 Identities=15% Similarity=0.208 Sum_probs=32.9
Q ss_pred ccccccCCcccccccccccCCCCCchhh-hcccC-CCCccccccccccceE-EEEeCCCchH
Q psy8226 46 ASAETINPRTTSTFDQFEFDGCDNCDEF-LHMKN-SRDNVYNCTSSNFDGM-IALMDPKDSW 104 (115)
Q Consensus 46 ~~~ACl~C~lVkT~dQF~~~GCPNC~~~-L~m~g-d~d~v~dCTT~nF~G~-IaImdP~kSW 104 (115)
..+.|..|+.-...-+ -||+|++. |.-.| ..++|.+-...-|-+. |+-||-+..+
T Consensus 461 ~~L~CH~Cg~~~~~p~----~Cp~Cgs~~L~~~G~GterieeeL~~~FP~~rv~r~d~Dtt~ 518 (730)
T COG1198 461 GQLRCHYCGYQEPIPQ----SCPECGSEHLRAVGPGTERIEEELKRLFPGARIIRIDSDTTR 518 (730)
T ss_pred CeeEeCCCCCCCCCCC----CCCCCCCCeeEEecccHHHHHHHHHHHCCCCcEEEEcccccc
Confidence 4456888888755444 39999976 33333 4666777666667443 4445544433
No 73
>PRK06260 threonine synthase; Validated
Probab=41.08 E-value=13 Score=31.11 Aligned_cols=31 Identities=16% Similarity=0.248 Sum_probs=24.1
Q ss_pred ccccCCcccccccccccCCCCCchhhhcccCC
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEFLHMKNS 79 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd 79 (115)
+.|.+|+..-..+.+. ..||.|+..|+..-|
T Consensus 4 ~~C~~cg~~~~~~~~~-~~Cp~cg~~l~~~y~ 34 (397)
T PRK06260 4 LKCIECGKEYDPDEII-YTCPECGGLLEVIYD 34 (397)
T ss_pred EEECCCCCCCCCCCcc-ccCCCCCCeEEEEec
Confidence 6799999888777653 579999987766644
No 74
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=40.79 E-value=17 Score=28.48 Aligned_cols=27 Identities=22% Similarity=0.397 Sum_probs=19.2
Q ss_pred ccccCCcccccccccccC---CCCCchhhh
Q psy8226 48 AETINPRTTSTFDQFEFD---GCDNCDEFL 74 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~---GCPNC~~~L 74 (115)
..|..|+..-..+..... -||+|++.|
T Consensus 123 ~~C~~C~~~~~~~~~~~~~~p~C~~Cgg~l 152 (242)
T PRK00481 123 ARCTKCGQTYDLDEYLKPEPPRCPKCGGIL 152 (242)
T ss_pred eeeCCCCCCcChhhhccCCCCCCCCCCCcc
Confidence 459999987665554442 399998755
No 75
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=40.71 E-value=12 Score=22.94 Aligned_cols=30 Identities=10% Similarity=0.073 Sum_probs=19.7
Q ss_pred ccccCCcccccccccccCCCCCchhhhccc
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEFLHMK 77 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~ 77 (115)
..|.+|+.-.+.+.-..--||+|++-.-++
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~rIlyK 32 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGYRILYK 32 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCceEEEE
Confidence 458999987776632223699999644333
No 76
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=40.47 E-value=14 Score=31.69 Aligned_cols=27 Identities=22% Similarity=0.076 Sum_probs=19.1
Q ss_pred cccccCCcccccccccccCCCCCchhhhc
Q psy8226 47 SAETINPRTTSTFDQFEFDGCDNCDEFLH 75 (115)
Q Consensus 47 ~~ACl~C~lVkT~dQF~~~GCPNC~~~L~ 75 (115)
-.+|..|+++....+ +--||.|++.|.
T Consensus 215 ~~~C~~Cd~~~~~~~--~a~CpRC~~~L~ 241 (403)
T TIGR00155 215 LRSCSACHTTILPAQ--EPVCPRCSTPLY 241 (403)
T ss_pred CCcCCCCCCccCCCC--CcCCcCCCCccc
Confidence 346999999665443 235999998763
No 77
>cd02973 TRX_GRX_like Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacteri
Probab=39.96 E-value=14 Score=22.31 Aligned_cols=15 Identities=20% Similarity=0.536 Sum_probs=11.6
Q ss_pred cccccCCCCCchhhh
Q psy8226 60 DQFEFDGCDNCDEFL 74 (115)
Q Consensus 60 dQF~~~GCPNC~~~L 74 (115)
.-|...+||.|....
T Consensus 4 ~~f~~~~C~~C~~~~ 18 (67)
T cd02973 4 EVFVSPTCPYCPDAV 18 (67)
T ss_pred EEEECCCCCCcHHHH
Confidence 457788999998643
No 78
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=39.11 E-value=14 Score=25.17 Aligned_cols=24 Identities=17% Similarity=0.279 Sum_probs=11.7
Q ss_pred CccccccCCccccc--ccccccCCCCCchh
Q psy8226 45 SASAETINPRTTST--FDQFEFDGCDNCDE 72 (115)
Q Consensus 45 ~~~~ACl~C~lVkT--~dQF~~~GCPNC~~ 72 (115)
+.-++|..|--+.. ..+| ||+|+.
T Consensus 7 ~~vlrC~aCf~~t~~~~k~F----Cp~CGn 32 (73)
T PF08772_consen 7 TWVLRCHACFKITKDMTKQF----CPKCGN 32 (73)
T ss_dssp -EEEE-SSS--EES-SS--S-----SSS--
T ss_pred eeeEEccccccCcCCCCcee----CcccCC
Confidence 34478999998875 4577 999994
No 79
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=38.66 E-value=14 Score=27.57 Aligned_cols=31 Identities=23% Similarity=0.334 Sum_probs=18.0
Q ss_pred ccCCcccccccccccCCCCCchhhhcccCCCC
Q psy8226 50 TINPRTTSTFDQFEFDGCDNCDEFLHMKNSRD 81 (115)
Q Consensus 50 Cl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d 81 (115)
|-+|+-..-.=- +.+.|.+|.+-|.++-+-|
T Consensus 72 CP~C~K~TKmLG-r~D~CM~C~~pLTLd~~le 102 (114)
T PF11023_consen 72 CPNCGKQTKMLG-RVDACMHCKEPLTLDPSLE 102 (114)
T ss_pred CCCCCChHhhhc-hhhccCcCCCcCccCchhh
Confidence 888876531100 1146888888776665443
No 80
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=38.61 E-value=12 Score=30.99 Aligned_cols=30 Identities=17% Similarity=0.287 Sum_probs=24.2
Q ss_pred cccccCCccccccccccc--CCCCCchhhhcc
Q psy8226 47 SAETINPRTTSTFDQFEF--DGCDNCDEFLHM 76 (115)
Q Consensus 47 ~~ACl~C~lVkT~dQF~~--~GCPNC~~~L~m 76 (115)
-..|-.|+-+.-.+++.+ .-||+|+..+.|
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMRM 57 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcCcC
Confidence 346999999998887755 489999987665
No 81
>PF06620 DUF1150: Protein of unknown function (DUF1150); InterPro: IPR009531 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=38.31 E-value=44 Score=22.93 Aligned_cols=24 Identities=25% Similarity=0.383 Sum_probs=19.4
Q ss_pred CCccccceEEEeecCCCCceeEcC
Q psy8226 19 PSTLAGLKVVGVHNEDHRPWTIDP 42 (115)
Q Consensus 19 ~~~~~~~~~~~~~~e~~~p~~i~p 42 (115)
|..-.|..+..||++||.|+-+..
T Consensus 33 ~~~~~~~~l~Avh~AdG~~lal~~ 56 (76)
T PF06620_consen 33 PQIDPGETLYAVHAADGTPLALVD 56 (76)
T ss_pred cccCCCceEEEEecCCCCEEEEEC
Confidence 445568899999999999998654
No 82
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=37.85 E-value=12 Score=31.43 Aligned_cols=30 Identities=17% Similarity=0.218 Sum_probs=24.6
Q ss_pred ccccCCccccccccccc--CCCCCchhhhccc
Q psy8226 48 AETINPRTTSTFDQFEF--DGCDNCDEFLHMK 77 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~--~GCPNC~~~L~m~ 77 (115)
..|-.|+-+.-.+++.+ .-||+|+..+.|.
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICEQCGYHLKMS 70 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCCCCCCCcCCC
Confidence 46999999999998866 4899999766554
No 83
>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=36.92 E-value=17 Score=30.88 Aligned_cols=22 Identities=18% Similarity=0.110 Sum_probs=17.3
Q ss_pred cccCCcccccccccccCCCCCchhh
Q psy8226 49 ETINPRTTSTFDQFEFDGCDNCDEF 73 (115)
Q Consensus 49 ACl~C~lVkT~dQF~~~GCPNC~~~ 73 (115)
.|..|++....=++ .||+|+.-
T Consensus 2 ~c~~cg~~~~~~~g---~cp~c~~w 23 (372)
T cd01121 2 VCSECGYVSPKWLG---KCPECGEW 23 (372)
T ss_pred CCCCCCCCCCCccE---ECcCCCCc
Confidence 59999998766665 39999864
No 84
>PRK07218 replication factor A; Provisional
Probab=36.66 E-value=21 Score=31.30 Aligned_cols=33 Identities=6% Similarity=-0.044 Sum_probs=24.5
Q ss_pred CceeEcCCCCccccccCCcccccccccccCCCCCchhh
Q psy8226 36 RPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEF 73 (115)
Q Consensus 36 ~p~~i~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~~ 73 (115)
+...|-+-|-.-.+|-.|+.+.+.-+ ||.|+.+
T Consensus 286 ~Iv~i~~gsgli~rCP~C~r~v~~~~-----C~~hG~v 318 (423)
T PRK07218 286 NIISVRDGSGLIERCPECGRVIQKGQ-----CRSHGAV 318 (423)
T ss_pred EEEEeccCCcceecCcCccccccCCc-----CCCCCCc
Confidence 44555566666689999999996644 9999963
No 85
>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=35.69 E-value=21 Score=31.00 Aligned_cols=23 Identities=17% Similarity=0.108 Sum_probs=18.1
Q ss_pred ccccCCcccccccccccCCCCCchhh
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEF 73 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~ 73 (115)
..|..|++-...=++ .||.|++-
T Consensus 8 y~C~~Cg~~~~~~~g---~Cp~C~~w 30 (454)
T TIGR00416 8 FVCQHCGADSPKWQG---KCPACHAW 30 (454)
T ss_pred EECCcCCCCCccccE---ECcCCCCc
Confidence 579999998666665 39999864
No 86
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=35.46 E-value=19 Score=31.53 Aligned_cols=31 Identities=10% Similarity=0.055 Sum_probs=20.8
Q ss_pred ccccCCcccccccccccCCCCCchhhhcccC
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEFLHMKN 78 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~g 78 (115)
.-|.+|+.+.....-.+.-||+|++.+++.|
T Consensus 241 ~~c~~cg~~~~~~~~~~~~c~~Cg~~~~~~G 271 (380)
T COG1867 241 YHCSRCGEIVGSFREVDEKCPHCGGKVHLAG 271 (380)
T ss_pred EEcccccceecccccccccCCcccccceecc
Confidence 3599998444444444568999997665554
No 87
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=35.42 E-value=10 Score=22.18 Aligned_cols=14 Identities=21% Similarity=0.688 Sum_probs=10.5
Q ss_pred CCCCchhhhcccCC
Q psy8226 66 GCDNCDEFLHMKNS 79 (115)
Q Consensus 66 GCPNC~~~L~m~gd 79 (115)
-||||+..+++.++
T Consensus 4 ~CP~C~~~f~v~~~ 17 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD 17 (37)
T ss_pred ECCCCCceEEcCHH
Confidence 49999987766644
No 88
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=35.33 E-value=18 Score=26.27 Aligned_cols=33 Identities=18% Similarity=0.266 Sum_probs=18.4
Q ss_pred ccccCCccccccccc-----c-cCCCCCchhh-hcccCCCC
Q psy8226 48 AETINPRTTSTFDQF-----E-FDGCDNCDEF-LHMKNSRD 81 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF-----~-~~GCPNC~~~-L~m~gd~d 81 (115)
..| .|+..-+.+.+ . ...||.|++. +++.+.++
T Consensus 71 ~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~E 110 (124)
T PRK00762 71 IEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGGRE 110 (124)
T ss_pred EEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecCCe
Confidence 459 99966443322 1 2359999952 34444333
No 89
>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=34.70 E-value=32 Score=30.70 Aligned_cols=38 Identities=11% Similarity=0.148 Sum_probs=22.9
Q ss_pred EeecCCCCceeEcCCCCccccccCCcccccccccccCCCCCchh
Q psy8226 29 GVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 29 ~~~~e~~~p~~i~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
..+++..++..+. ...+ .|..|+.+.....+ -||.|++
T Consensus 503 ~a~~~~~~y~~~~--~p~~-~C~~CG~~~~~~~~---~CP~CGs 540 (555)
T cd01675 503 KAAKRGVIYFGIN--TPID-ICNDCGYIGEGEGF---KCPKCGS 540 (555)
T ss_pred HHHHcCCceEEEe--cCCc-cCCCCCCCCcCCCC---CCcCCCC
Confidence 3455555553322 1222 89999997644443 4999985
No 90
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=34.39 E-value=14 Score=21.20 Aligned_cols=21 Identities=10% Similarity=0.164 Sum_probs=10.8
Q ss_pred cccCCcccccccccccCCCCCchh
Q psy8226 49 ETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 49 ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
+|..|+.+.=.-+ .-||+|++
T Consensus 13 rC~~Cg~~~~pPr---~~Cp~C~s 33 (37)
T PF12172_consen 13 RCRDCGRVQFPPR---PVCPHCGS 33 (37)
T ss_dssp E-TTT--EEES-----SEETTTT-
T ss_pred EcCCCCCEecCCC---cCCCCcCc
Confidence 5999998843222 35999974
No 91
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=33.56 E-value=16 Score=30.39 Aligned_cols=30 Identities=10% Similarity=0.248 Sum_probs=25.0
Q ss_pred ccccCCcccccccccccC--CCCCchhhhccc
Q psy8226 48 AETINPRTTSTFDQFEFD--GCDNCDEFLHMK 77 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~--GCPNC~~~L~m~ 77 (115)
..|-.|+-+.-..++.++ -||.|+..+.|.
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCPKCGHHMRIS 59 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCCCCCCCeeCC
Confidence 469999999998888664 799999877664
No 92
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=33.34 E-value=25 Score=27.43 Aligned_cols=23 Identities=13% Similarity=-0.120 Sum_probs=17.0
Q ss_pred ccccCCcccccccccccCCCCCchh
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
..|..|+++.-. ---.-||.|+.
T Consensus 135 ~vC~vCGy~~~g--e~P~~CPiCga 157 (166)
T COG1592 135 WVCPVCGYTHEG--EAPEVCPICGA 157 (166)
T ss_pred EEcCCCCCcccC--CCCCcCCCCCC
Confidence 459999998755 23356999984
No 93
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=31.85 E-value=21 Score=20.96 Aligned_cols=23 Identities=22% Similarity=0.271 Sum_probs=11.6
Q ss_pred ccCCccccccccc---ccCCCCCchh
Q psy8226 50 TINPRTTSTFDQF---EFDGCDNCDE 72 (115)
Q Consensus 50 Cl~C~lVkT~dQF---~~~GCPNC~~ 72 (115)
|-+|+..+...++ .-+.|++|+.
T Consensus 2 CP~C~~~l~~~~~~~~~id~C~~C~G 27 (41)
T PF13453_consen 2 CPRCGTELEPVRLGDVEIDVCPSCGG 27 (41)
T ss_pred cCCCCcccceEEECCEEEEECCCCCe
Confidence 4555554443333 2245777764
No 94
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=31.76 E-value=14 Score=24.36 Aligned_cols=29 Identities=21% Similarity=0.313 Sum_probs=16.7
Q ss_pred CCccccccCCcccccccccccC---CCCCchh
Q psy8226 44 PSASAETINPRTTSTFDQFEFD---GCDNCDE 72 (115)
Q Consensus 44 ~~~~~ACl~C~lVkT~dQF~~~---GCPNC~~ 72 (115)
+.+...|..|+..++.++..-. -||+|..
T Consensus 38 ~~~~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~ 69 (71)
T PF05495_consen 38 PVKRVICGKCRTEQPIDEYSCGADYFCPICGL 69 (71)
T ss_dssp T--EEEETTT--EEES-SBTT--SEEETTTTE
T ss_pred cccCeECCCCCCccChhhhhcCCCccCcCcCC
Confidence 3334559999999999885222 4888874
No 95
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=30.82 E-value=33 Score=29.31 Aligned_cols=58 Identities=16% Similarity=0.142 Sum_probs=29.7
Q ss_pred CCCCCccccceEEEeecCCCCceeEcCCCCccccccCCcccccccccccCCCCCchhhhcccC
Q psy8226 16 PPKPSTLAGLKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEFLHMKN 78 (115)
Q Consensus 16 ~~~~~~~~~~~~~~~~~e~~~p~~i~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~g 78 (115)
|-+-|-..|-..|---++-.+.|. +-.-+-...|.+|+-....=| ..||||++ -++++
T Consensus 52 PG~~SGARG~DL~~~n~d~sEiKs-C~rvDQl~~C~~CGa~V~~~e---~~Cp~C~S-tnI~r 109 (314)
T PF09567_consen 52 PGGGSGARGDDLVMNNDDGSEIKS-CYRVDQLGKCNNCGANVSRLE---ESCPNCGS-TNIKR 109 (314)
T ss_pred CCCccccccccccccCCCcchhhh-hhhhhhhhhhccccceeeehh---hcCCCCCc-ccccc
Confidence 334444445444322222223332 333333346999997665433 35999995 34443
No 96
>cd00272 Chemokine_CC Chemokine_CC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; some members (e.g. 2HCC) contain an additional disulfide bond which is thought to compensate for the highly conserved Trp missing in these; chemotatic for monocytes, macrophages, eosinophils, basophils, and T cells, but not neutrophils; exist as monomers and dimers, but are believed to be functional as monomers; found only in vertebrates and a few viruses; a subgroup of CC, identified by an N-terminal DCCL motif (Exodus-1, Exodus-2, and Exodus-3), has been shown to inhibit specific types of human cancer cell growth in a mouse model. See CDs: Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CXC (cd00273), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for the additional chemokine subgroups, and Chemokine_C
Probab=30.53 E-value=26 Score=21.81 Aligned_cols=16 Identities=31% Similarity=0.891 Sum_probs=12.7
Q ss_pred EEEEeCCCchHHHhhhc
Q psy8226 94 MIALMDPKDSWVAKWQR 110 (115)
Q Consensus 94 ~IaImdP~kSWVAKwqr 110 (115)
.+.+ ||++.||-+.++
T Consensus 39 ~iC~-dP~~~WVk~~i~ 54 (57)
T cd00272 39 EVCA-DPKQKWVQRYMK 54 (57)
T ss_pred EEeC-CCChHHHHHHHH
Confidence 4444 999999999874
No 97
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=30.47 E-value=11 Score=33.26 Aligned_cols=41 Identities=15% Similarity=0.178 Sum_probs=28.6
Q ss_pred cccCCccccccccccc--CCCCCchhhhcccCCCCccccccccc
Q psy8226 49 ETINPRTTSTFDQFEF--DGCDNCDEFLHMKNSRDNVYNCTSSN 90 (115)
Q Consensus 49 ACl~C~lVkT~dQF~~--~GCPNC~~~L~m~gd~d~v~dCTT~n 90 (115)
||.+|+..-+.+.=.. --||+|+. .=-+|-+|||.+-.+.+
T Consensus 248 AC~rC~t~y~le~A~~~~wrCpkCGg-~ikKGV~dRv~ELad~~ 290 (403)
T COG1379 248 ACSRCYTRYSLEEAKSLRWRCPKCGG-KIKKGVSDRVLELADTE 290 (403)
T ss_pred HHHHhhhccCcchhhhhcccCccccc-chhhhHHHHHHHhhccC
Confidence 7999997666554322 36999997 33478888887765543
No 98
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=29.78 E-value=23 Score=28.00 Aligned_cols=24 Identities=17% Similarity=0.066 Sum_probs=17.7
Q ss_pred ccccCCcccccccccccCCCCCchhhh
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEFL 74 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~L 74 (115)
++|..|+.+-+.+ .+-||-|++-+
T Consensus 140 ~rC~GC~~~f~~~---~~~Cp~CG~~~ 163 (177)
T COG1439 140 LRCHGCKRIFPEP---KDFCPICGSPL 163 (177)
T ss_pred EEEecCceecCCC---CCcCCCCCCce
Confidence 5799999998822 23499999743
No 99
>PF13510 Fer2_4: 2Fe-2S iron-sulfur cluster binding domain; PDB: 1Y56_A 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 2GAG_A 2GAH_A.
Probab=29.56 E-value=22 Score=23.75 Aligned_cols=62 Identities=18% Similarity=0.320 Sum_probs=31.2
Q ss_pred CCCceeEcCCCCccccccCCcccccc--------ccccc-CCCCCchhhhcccCCCCccccccccccceEEEEe
Q psy8226 34 DHRPWTIDPIPSASAETINPRTTSTF--------DQFEF-DGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALM 98 (115)
Q Consensus 34 ~~~p~~i~p~~~~~~ACl~C~lVkT~--------dQF~~-~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaIm 98 (115)
||++..+.+=.+-..|++..++-... ..|.. ..|..| ..+.+|.. .+..|+|+--+||..-.
T Consensus 9 dG~~v~~~~G~til~al~~~gi~ip~~c~~~~~r~~~~~~g~C~~C--~Vev~g~~-~v~AC~t~v~~GM~V~T 79 (82)
T PF13510_consen 9 DGKPVEVPPGETILEALLAAGIDIPRLCYHGRPRGGLCPIGSCRLC--LVEVDGEP-NVRACSTPVEDGMVVET 79 (82)
T ss_dssp TTEEEEEEET-BHHHHHHHTT--B-EETTTS-EEBSSSSSTT-SS---EEEESSEE-EEETTT-B--TTEEEE-
T ss_pred CCEEEEEcCCCHHHHHHHHCCCeEEEeeeccCcccccCCccccceE--EEEECCCc-ceEcccCCCcCCcEEEE
Confidence 56666655555555556555544332 22222 246677 45666644 37999999999998764
No 100
>PRK05580 primosome assembly protein PriA; Validated
Probab=29.40 E-value=32 Score=31.27 Aligned_cols=28 Identities=14% Similarity=0.273 Sum_probs=14.1
Q ss_pred CCCCchhh-hcccC-CCCccccccccccce
Q psy8226 66 GCDNCDEF-LHMKN-SRDNVYNCTSSNFDG 93 (115)
Q Consensus 66 GCPNC~~~-L~m~g-d~d~v~dCTT~nF~G 93 (115)
-||+|++. |...| ..+++.+-....|-|
T Consensus 423 ~Cp~Cg~~~l~~~g~G~e~~~e~l~~~fp~ 452 (679)
T PRK05580 423 ACPECGSTDLVPVGPGTERLEEELAELFPE 452 (679)
T ss_pred CCCCCcCCeeEEeeccHHHHHHHHHHhCCC
Confidence 49999753 22211 344455555555544
No 101
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=28.96 E-value=28 Score=28.38 Aligned_cols=25 Identities=20% Similarity=0.332 Sum_probs=18.3
Q ss_pred ccccCCcccccccc---cccCC----CCCchh
Q psy8226 48 AETINPRTTSTFDQ---FEFDG----CDNCDE 72 (115)
Q Consensus 48 ~ACl~C~lVkT~dQ---F~~~G----CPNC~~ 72 (115)
..|..|+-....+. +..++ ||.|++
T Consensus 123 ~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~ 154 (250)
T COG0846 123 VRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGG 154 (250)
T ss_pred eEeCCCcCccchhhhhhhcccCCCCcCccCCC
Confidence 45999987776444 44456 999997
No 102
>PRK11032 hypothetical protein; Provisional
Probab=28.60 E-value=28 Score=26.91 Aligned_cols=26 Identities=15% Similarity=0.174 Sum_probs=19.3
Q ss_pred cccccCCccccccccccc-CCCCCchh
Q psy8226 47 SAETINPRTTSTFDQFEF-DGCDNCDE 72 (115)
Q Consensus 47 ~~ACl~C~lVkT~dQF~~-~GCPNC~~ 72 (115)
-+.|.+|+.-.....-.. .-||+|++
T Consensus 124 ~LvC~~Cg~~~~~~~p~~i~pCp~C~~ 150 (160)
T PRK11032 124 NLVCEKCHHHLAFYTPEVLPLCPKCGH 150 (160)
T ss_pred eEEecCCCCEEEecCCCcCCCCCCCCC
Confidence 368999998887755433 47999984
No 103
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=28.07 E-value=22 Score=22.73 Aligned_cols=12 Identities=33% Similarity=0.886 Sum_probs=8.7
Q ss_pred cCCCCCchhhhc
Q psy8226 64 FDGCDNCDEFLH 75 (115)
Q Consensus 64 ~~GCPNC~~~L~ 75 (115)
..|||+|....+
T Consensus 7 ~~~C~~C~~~~~ 18 (76)
T PF13192_consen 7 SPGCPYCPELVQ 18 (76)
T ss_dssp CSSCTTHHHHHH
T ss_pred CCCCCCcHHHHH
Confidence 457999996544
No 104
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=27.95 E-value=34 Score=28.57 Aligned_cols=23 Identities=13% Similarity=-0.050 Sum_probs=16.3
Q ss_pred cccCCccccccccccc---CCCCCch
Q psy8226 49 ETINPRTTSTFDQFEF---DGCDNCD 71 (115)
Q Consensus 49 ACl~C~lVkT~dQF~~---~GCPNC~ 71 (115)
.|.+|+-+-....+.. ..||+|.
T Consensus 247 pC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 247 PCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 3999997766655533 2599996
No 105
>KOG0594|consensus
Probab=27.35 E-value=33 Score=29.31 Aligned_cols=18 Identities=50% Similarity=0.925 Sum_probs=15.0
Q ss_pred CcccCCcceEEEecCCCC
Q psy8226 1 MRTIDPGLLTLYYRPPPK 18 (115)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~ 18 (115)
||+..+-..||.||||--
T Consensus 174 ~~~yt~evvTlWYRaPEv 191 (323)
T KOG0594|consen 174 MRTYTPEVVTLWYRAPEV 191 (323)
T ss_pred cccccccEEEeeccCHHH
Confidence 577889999999999743
No 106
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=27.07 E-value=31 Score=26.13 Aligned_cols=19 Identities=21% Similarity=0.312 Sum_probs=14.2
Q ss_pred cccCCcccc---cccccccCCCCCch
Q psy8226 49 ETINPRTTS---TFDQFEFDGCDNCD 71 (115)
Q Consensus 49 ACl~C~lVk---T~dQF~~~GCPNC~ 71 (115)
.|-.|+..+ +-+.| ||+|+
T Consensus 30 hCp~Cg~PLF~KdG~v~----CPvC~ 51 (131)
T COG1645 30 HCPKCGTPLFRKDGEVF----CPVCG 51 (131)
T ss_pred hCcccCCcceeeCCeEE----CCCCC
Confidence 599999875 33344 99999
No 107
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=26.69 E-value=33 Score=29.25 Aligned_cols=30 Identities=10% Similarity=0.035 Sum_probs=21.3
Q ss_pred ccccCCcccccccccccCCCCCchhhhcccCC
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEFLHMKNS 79 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd 79 (115)
+.|.+|+..-. +.+ ...||.|.+.|...-|
T Consensus 3 l~C~~Cg~~~~-~~~-~~~C~~c~g~l~~~y~ 32 (398)
T TIGR03844 3 LRCPGCGEVLP-DHY-TLSCPLDCGLLRAEYA 32 (398)
T ss_pred EEeCCCCCccC-Ccc-ccCCCCCCCceEEeec
Confidence 57999998766 444 4689988777765543
No 108
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=26.49 E-value=36 Score=21.52 Aligned_cols=12 Identities=8% Similarity=-0.405 Sum_probs=8.3
Q ss_pred cccCCccccccc
Q psy8226 49 ETINPRTTSTFD 60 (115)
Q Consensus 49 ACl~C~lVkT~d 60 (115)
.|+.|++|-..+
T Consensus 3 ~C~~CgyiYd~~ 14 (50)
T cd00730 3 ECRICGYIYDPA 14 (50)
T ss_pred CCCCCCeEECCC
Confidence 477788777653
No 109
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=25.89 E-value=30 Score=26.73 Aligned_cols=27 Identities=15% Similarity=0.172 Sum_probs=18.0
Q ss_pred ccccCCcccccccccc-----c---CCCCCchhhh
Q psy8226 48 AETINPRTTSTFDQFE-----F---DGCDNCDEFL 74 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~-----~---~GCPNC~~~L 74 (115)
..|..|+..-..+.+. . --||+|++.|
T Consensus 96 ~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~l 130 (206)
T cd01410 96 EVCKSCGPEYVRDDVVETRGDKETGRRCHACGGIL 130 (206)
T ss_pred ccCCCCCCccchHHHHHHhhcCCCCCcCCCCcCcc
Confidence 4699999776554432 1 2499998754
No 110
>PRK06386 replication factor A; Reviewed
Probab=25.22 E-value=38 Score=29.16 Aligned_cols=32 Identities=3% Similarity=-0.108 Sum_probs=22.7
Q ss_pred CceeEcCCCCccccccCCcccccccccccCCCCCchh
Q psy8226 36 RPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 36 ~p~~i~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
....|-+-+-.-.+|-.|+.+.+..+ ||.|+.
T Consensus 225 ~iv~i~~gsgli~rCP~C~R~l~~g~-----C~~HG~ 256 (358)
T PRK06386 225 FIVSVGQGSRIFTKCSVCNKIIEDGV-----CKDHPD 256 (358)
T ss_pred EEEEEcCCcEeEecCcCCCeEccCCc-----CCCCCC
Confidence 33444444445578999999998644 999985
No 111
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.02 E-value=38 Score=31.14 Aligned_cols=22 Identities=18% Similarity=0.102 Sum_probs=15.8
Q ss_pred cccccCCcccccccccccCCCCCchh
Q psy8226 47 SAETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 47 ~~ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
.-.|..|+++. ..+| -||+|++
T Consensus 626 ~~~C~~CG~~~-g~~~---~CP~CG~ 647 (656)
T PRK08270 626 FSICPKHGYLS-GEHE---FCPKCGE 647 (656)
T ss_pred CcccCCCCCcC-CCCC---CCcCCcC
Confidence 34699999863 4444 5999985
No 112
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=24.68 E-value=48 Score=25.85 Aligned_cols=27 Identities=7% Similarity=0.075 Sum_probs=19.3
Q ss_pred ccccCCccccccccccc-CCCCCchhhh
Q psy8226 48 AETINPRTTSTFDQFEF-DGCDNCDEFL 74 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~-~GCPNC~~~L 74 (115)
..|..|+.....+.+.. --||+|++.|
T Consensus 119 ~~C~~C~~~~~~~~~~~~p~C~~Cgg~l 146 (225)
T cd01411 119 IYCTVCGKTVDWEEYLKSPYHAKCGGVI 146 (225)
T ss_pred eEeCCCCCccchhhcCCCCCCCCCCCEe
Confidence 45999997766555443 4699998765
No 113
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=24.61 E-value=30 Score=29.96 Aligned_cols=24 Identities=21% Similarity=0.182 Sum_probs=12.7
Q ss_pred ccccCCccccccccc--ccCCCCCch
Q psy8226 48 AETINPRTTSTFDQF--EFDGCDNCD 71 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF--~~~GCPNC~ 71 (115)
+-|++|+...+.+-= ..+=||+|+
T Consensus 316 nfc~ncG~~~t~~~~ng~a~fcp~cg 341 (345)
T COG4260 316 NFCLNCGCGTTADFDNGKAKFCPECG 341 (345)
T ss_pred ccccccCcccccCCccchhhhChhhc
Confidence 357777766665310 012277776
No 114
>PF00048 IL8: Small cytokines (intecrine/chemokine), interleukin-8 like; InterPro: IPR001811 Many low-molecular weight factors secreted by cells including fibroblasts, macrophages and endothelial cells, in response to a variety of stimuli such as growth factors, interferons, viral transformation and bacterial products, are structurally related [, , ]. Most members of this family of proteins seem to have mitogenic, chemotactic or inflammatory activities. These small cytokines are also called intercrines or chemokines. They are cationic proteins of 70 to 100 amino acid residues that share four conserved cysteine residues involved in two disulphide bonds, as shown in the following schematic representation: +------------------------------------+ | | xxxxxxxxxxxxxxxxxxxxxxCxCxxxxxxxxxxxxxxxxxxxxxxxCxxxxxxxxxxxxCxxxxx | | +-------------------------+ 'C': conserved cysteine involved in a disulphide bond. Chemokines can be sorted into main groups based on the spacing of the two amino-terminal cysteines. In the first group (see IPR001089 from INTERPRO), the two cysteines are separated by a single residue (C-x-C), while in the second group (see IPR000827 from INTERPRO), they are adjacent (C-C).; GO: 0008009 chemokine activity, 0006955 immune response, 0005576 extracellular region; PDB: 3HP3_B 2K01_A 2KEE_A 2K04_C 2J7Z_A 1QG7_A 2KED_A 2NWG_B 2KEC_A 1VMC_A ....
Probab=24.23 E-value=36 Score=21.35 Aligned_cols=18 Identities=33% Similarity=0.626 Sum_probs=13.5
Q ss_pred eEEEEeCCCchHHHhhhc
Q psy8226 93 GMIALMDPKDSWVAKWQR 110 (115)
Q Consensus 93 G~IaImdP~kSWVAKwqr 110 (115)
|--.=+||+..||-++++
T Consensus 45 g~~~C~dP~~~wvk~~ik 62 (64)
T PF00048_consen 45 GREVCADPNAPWVKKLIK 62 (64)
T ss_dssp SEEEEEETTSHHHHHHHH
T ss_pred CCcEEcCCchHHHHHHHh
Confidence 444445999999999874
No 115
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=24.05 E-value=18 Score=28.80 Aligned_cols=24 Identities=29% Similarity=0.414 Sum_probs=15.5
Q ss_pred ccccCCccccccccccc---CCCCCchhh
Q psy8226 48 AETINPRTTSTFDQFEF---DGCDNCDEF 73 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~---~GCPNC~~~ 73 (115)
++|-.|++ |.++|.. -||-+|-..
T Consensus 75 l~C~~C~~--Tfk~f~~~g~fGCaeCY~t 101 (176)
T COG3880 75 LGCHNCGM--TFKEFIQSGLFGCAECYKT 101 (176)
T ss_pred hcCccccc--cHHHHHHhcccchHHHHHH
Confidence 56777775 6666655 377777553
No 116
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=23.86 E-value=40 Score=26.47 Aligned_cols=35 Identities=26% Similarity=0.418 Sum_probs=24.5
Q ss_pred ccccCCcccccccc-cccC-CCCCchhhhcccCCCCc
Q psy8226 48 AETINPRTTSTFDQ-FEFD-GCDNCDEFLHMKNSRDN 82 (115)
Q Consensus 48 ~ACl~C~lVkT~dQ-F~~~-GCPNC~~~L~m~gd~d~ 82 (115)
..|..|+.=.|.+. |... -||-|++.|+..++++.
T Consensus 114 y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~~~d~s~~ 150 (176)
T COG1675 114 YVCPNCHVKYSFDEAMELGFTCPKCGEDLEEYDSSEE 150 (176)
T ss_pred eeCCCCCCcccHHHHHHhCCCCCCCCchhhhccchHH
Confidence 46878887777763 3322 59999999987766553
No 117
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=23.83 E-value=39 Score=25.55 Aligned_cols=26 Identities=15% Similarity=0.188 Sum_probs=18.7
Q ss_pred cccccCCccccccccccc-CCCCCchh
Q psy8226 47 SAETINPRTTSTFDQFEF-DGCDNCDE 72 (115)
Q Consensus 47 ~~ACl~C~lVkT~dQF~~-~GCPNC~~ 72 (115)
-+.|.+|+.......-.. .-||+|+.
T Consensus 112 ~l~C~~Cg~~~~~~~~~~l~~Cp~C~~ 138 (146)
T PF07295_consen 112 TLVCENCGHEVELTHPERLPPCPKCGH 138 (146)
T ss_pred eEecccCCCEEEecCCCcCCCCCCCCC
Confidence 357999998877665322 46999984
No 118
>PF11845 DUF3365: Protein of unknown function (DUF3365); InterPro: IPR021796 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 198 to 657 amino acids in length.
Probab=23.79 E-value=48 Score=24.20 Aligned_cols=61 Identities=20% Similarity=0.295 Sum_probs=33.6
Q ss_pred eEEEeecCCCCceeEc--CCCCccccccCCcccccccccccCCCCCchhhhcccCCCCccccccccccceEEEEeCC
Q psy8226 26 KVVGVHNEDHRPWTID--PIPSASAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDP 100 (115)
Q Consensus 26 ~~~~~~~e~~~p~~i~--p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaImdP 100 (115)
.++.+ +.||++.+.. |+.. ...|+.||= +.++=-. ..+.. .+.-.+..-.+..|+++|.=|
T Consensus 125 ~~~~~-~~~g~~~~ry~~pi~~-~~~CL~CHg--~~~~~~~-------~~~~~---~~~~~~~k~GDlrG~~si~iP 187 (188)
T PF11845_consen 125 EYVEV-EINGKPYFRYARPIRV-EESCLSCHG--DPDQAPP-------EIIKK---GDPAFGYKVGDLRGAISITIP 187 (188)
T ss_pred eeeee-ccCCCceEEEEeehhc-chHHHHccC--Ccccchh-------hhhcc---ccccCCCCccceEEEEEEEee
Confidence 34455 6778887554 5444 556999998 2222000 01111 222244556778899888644
No 119
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=23.74 E-value=36 Score=23.19 Aligned_cols=21 Identities=14% Similarity=0.091 Sum_probs=15.3
Q ss_pred CCccccccCCccccccccccc
Q psy8226 44 PSASAETINPRTTSTFDQFEF 64 (115)
Q Consensus 44 ~~~~~ACl~C~lVkT~dQF~~ 64 (115)
+...+.|..|+.+++.++|.+
T Consensus 47 q~~El~C~~C~~~k~ld~FSK 67 (84)
T PF12898_consen 47 QVVELTCSPCGKTKPLDEFSK 67 (84)
T ss_pred CcCcCEeccCCCCcCHHHHhH
Confidence 334456888888888888865
No 120
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=23.68 E-value=58 Score=23.40 Aligned_cols=30 Identities=17% Similarity=0.173 Sum_probs=21.4
Q ss_pred ccccCCccccccccc---ccCCCCCchhhhccc
Q psy8226 48 AETINPRTTSTFDQF---EFDGCDNCDEFLHMK 77 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF---~~~GCPNC~~~L~m~ 77 (115)
-.|..|++..+...- ..+=||+|=.-++..
T Consensus 5 F~C~~CG~~V~p~~~g~~~RNHCP~CL~S~Hvd 37 (92)
T PF12647_consen 5 FTCVHCGLTVSPLAAGSAHRNHCPSCLSSLHVD 37 (92)
T ss_pred cCccccCCCcccCCCCCCccCcCcccccccccC
Confidence 469999996655332 347899998777655
No 121
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=23.67 E-value=33 Score=21.94 Aligned_cols=10 Identities=30% Similarity=0.883 Sum_probs=6.6
Q ss_pred CCCchhhhcc
Q psy8226 67 CDNCDEFLHM 76 (115)
Q Consensus 67 CPNC~~~L~m 76 (115)
||+|++.++|
T Consensus 3 CPyCge~~~~ 12 (52)
T PF14255_consen 3 CPYCGEPIEI 12 (52)
T ss_pred CCCCCCeeEE
Confidence 7777765543
No 122
>PRK04023 DNA polymerase II large subunit; Validated
Probab=23.23 E-value=41 Score=33.30 Aligned_cols=27 Identities=7% Similarity=0.132 Sum_probs=17.3
Q ss_pred cCCCCccccccCCcccccccccccCCCCCchh
Q psy8226 41 DPIPSASAETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 41 ~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
+.++.....|..|+..... | -||+|+.
T Consensus 620 ~eVEVg~RfCpsCG~~t~~--f---rCP~CG~ 646 (1121)
T PRK04023 620 IEVEIGRRKCPSCGKETFY--R---RCPFCGT 646 (1121)
T ss_pred eeecccCccCCCCCCcCCc--c---cCCCCCC
Confidence 4555566678888887422 2 3888874
No 123
>KOG2324|consensus
Probab=22.84 E-value=54 Score=29.45 Aligned_cols=35 Identities=14% Similarity=0.411 Sum_probs=25.5
Q ss_pred eeEcCCCCccc-cccCCcccccccccccC---CCCCchh
Q psy8226 38 WTIDPIPSASA-ETINPRTTSTFDQFEFD---GCDNCDE 72 (115)
Q Consensus 38 ~~i~p~~~~~~-ACl~C~lVkT~dQF~~~---GCPNC~~ 72 (115)
-.+.|+---.+ -|-+|++-++.+.+... -||+|.+
T Consensus 217 hl~~~vgED~l~~C~~C~~s~n~e~~~~sk~~~Cp~C~~ 255 (457)
T KOG2324|consen 217 HLIHPVGEDTLMSCPSCGYSKNSEDLDLSKIASCPKCNE 255 (457)
T ss_pred eccCccCccceeecCcCCccCchhhhcCCccccCCcccC
Confidence 34455544444 49999999999987664 5999985
No 124
>cd03026 AhpF_NTD_C TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then reduces hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD containing two contiguous TRX-fold subdomains similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The catalytic CXXC motif of the NTD of AhpF is contained in its C-terminal TRX subdomain.
Probab=22.59 E-value=40 Score=22.62 Aligned_cols=19 Identities=21% Similarity=0.632 Sum_probs=13.7
Q ss_pred ccccccCCCCCchhhhccc
Q psy8226 59 FDQFEFDGCDNCDEFLHMK 77 (115)
Q Consensus 59 ~dQF~~~GCPNC~~~L~m~ 77 (115)
...|...+|++|....++-
T Consensus 16 i~~F~~~~C~~C~~~~~~~ 34 (89)
T cd03026 16 FETYVSLSCHNCPDVVQAL 34 (89)
T ss_pred EEEEECCCCCCcHHHHHHH
Confidence 3467778999999755444
No 125
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=22.42 E-value=54 Score=33.06 Aligned_cols=31 Identities=16% Similarity=0.330 Sum_probs=19.8
Q ss_pred cccccCCccccccccccc------------CCCCCchhhhcccCCCCcc
Q psy8226 47 SAETINPRTTSTFDQFEF------------DGCDNCDEFLHMKNSRDNV 83 (115)
Q Consensus 47 ~~ACl~C~lVkT~dQF~~------------~GCPNC~~~L~m~gd~d~v 83 (115)
+..|-+|+.. +|.. +-||+|+.- |.+|...+
T Consensus 908 hy~C~~C~~~----ef~~~~~~~sG~Dlpdk~Cp~Cg~~--~~kdg~~l 950 (1437)
T PRK00448 908 HYVCPNCKYS----EFFTDGSVGSGFDLPDKDCPKCGTK--LKKDGHDI 950 (1437)
T ss_pred cccCcccccc----cccccccccccccCccccCcccccc--ccccCCCc
Confidence 4678888754 3332 359999974 55665544
No 126
>PF14939 DCAF15_WD40: DDB1-and CUL4-substrate receptor 15, WD repeat
Probab=22.21 E-value=80 Score=25.69 Aligned_cols=65 Identities=12% Similarity=0.096 Sum_probs=43.9
Q ss_pred eecCCCCceeEcCCCCcccc-ccCCccccc--ccccccCCCCCchhhhcccCCCCccccccccccceEEEEe
Q psy8226 30 VHNEDHRPWTIDPIPSASAE-TINPRTTST--FDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALM 98 (115)
Q Consensus 30 ~~~e~~~p~~i~p~~~~~~A-Cl~C~lVkT--~dQF~~~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaIm 98 (115)
..+|+++=-+|.-..--++. |+.|+-+.. ...+....|-+|+-.++++=+. .-+-+.|+.-+.+-
T Consensus 121 ~s~~e~~~~YiTiv~vP~l~~C~~C~~~~~~~~~~~~~~~CL~H~~tiHtkY~~----~~p~P~F~P~~~Lk 188 (211)
T PF14939_consen 121 ASDEESRDSYITIVAVPPLGPCLDCKKLADSHPGDPYRASCLEHGFTIHTKYQV----VSPFPTFQPKVSLK 188 (211)
T ss_pred cCcccCccEEEEEEcCCCcchhhhhhhhhhccCCcccccchhcCccEEEEEEEe----cCCCCCcCCceecc
Confidence 77889998888888888888 999998874 2334444699999767776321 11334566555443
No 127
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.15 E-value=46 Score=30.45 Aligned_cols=21 Identities=10% Similarity=0.162 Sum_probs=14.5
Q ss_pred ccccCCcccccccccccCCCCCchh
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
-.|..|++ ....+ .-||+|++
T Consensus 560 ~~C~~CGy-~g~~~---~~CP~CG~ 580 (618)
T PRK14704 560 DRCKCCSY-HGVIG---NECPSCGN 580 (618)
T ss_pred eecCCCCC-CCCcC---ccCcCCCC
Confidence 36999998 33322 35999985
No 128
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.01 E-value=53 Score=30.54 Aligned_cols=25 Identities=16% Similarity=0.029 Sum_probs=14.4
Q ss_pred cccccCCcccccccccc--cCCCCCchh
Q psy8226 47 SAETINPRTTSTFDQFE--FDGCDNCDE 72 (115)
Q Consensus 47 ~~ACl~C~lVkT~dQF~--~~GCPNC~~ 72 (115)
.-.|..|++- -+-... ..-||+|++
T Consensus 641 ~~~C~~CG~~-Ge~~~~~~~~~CP~CG~ 667 (711)
T PRK09263 641 IDECYECGFT-GEFECTEKGFTCPKCGN 667 (711)
T ss_pred CcccCCCCCC-ccccCCCCCCcCcCCCC
Confidence 3469999982 111011 124999985
No 129
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=21.48 E-value=36 Score=21.05 Aligned_cols=26 Identities=31% Similarity=0.833 Sum_probs=18.8
Q ss_pred CCCCchhhhcccCCCCccccccccccceEE
Q psy8226 66 GCDNCDEFLHMKNSRDNVYNCTSSNFDGMI 95 (115)
Q Consensus 66 GCPNC~~~L~m~gd~d~v~dCTT~nF~G~I 95 (115)
-|-||+.|=||+.|+. |.-..|.|..
T Consensus 3 kC~~CG~~GH~~t~k~----CP~~~~~~a~ 28 (40)
T PF15288_consen 3 KCKNCGAFGHMRTNKR----CPMYCWSGAL 28 (40)
T ss_pred cccccccccccccCcc----CCCCCCCCCC
Confidence 3899998888888875 6666665543
No 130
>PRK08402 replication factor A; Reviewed
Probab=21.47 E-value=62 Score=27.66 Aligned_cols=50 Identities=12% Similarity=0.076 Sum_probs=27.8
Q ss_pred CccccccCCccccccccccc-CCCCCchhhhcccCCCCccccccccccceEEEE
Q psy8226 45 SASAETINPRTTSTFDQFEF-DGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIAL 97 (115)
Q Consensus 45 ~~~~ACl~C~lVkT~dQF~~-~GCPNC~~~L~m~gd~d~v~dCTT~nF~G~IaI 97 (115)
+.-.||..|+-..+.++-.. -.|++|+. -+....-++.+.=.++.|.+-+
T Consensus 210 ~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~---v~p~~ryil~~~l~D~TG~~~v 260 (355)
T PRK08402 210 LVYDACPECRRKVDYDPATDTWICPEHGE---VEPIKITILDFGLDDGTGYIRV 260 (355)
T ss_pred eeEecCCCCCeEEEEecCCCCEeCCCCCC---cCcceeEEEEEEEEcCCCcEEE
Confidence 34468999999887543221 24999974 1233333444444445554443
No 131
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=21.23 E-value=41 Score=27.63 Aligned_cols=19 Identities=21% Similarity=0.343 Sum_probs=15.5
Q ss_pred cccCCcccccccccccCCCCCchh
Q psy8226 49 ETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 49 ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
.| +|+.-++.-.| |+||+.
T Consensus 2 ~C-rCG~~l~~p~~----Cl~Cg~ 20 (227)
T COG4031 2 IC-RCGAELSSPAF----CLNCGR 20 (227)
T ss_pred cc-ccCCcccccch----hcccCC
Confidence 48 89988877777 999985
No 132
>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=20.77 E-value=41 Score=27.05 Aligned_cols=40 Identities=18% Similarity=0.072 Sum_probs=16.5
Q ss_pred cceEEEeecCCCCceeEcCCCCccccccCCcccccccccccCCCCCchh
Q psy8226 24 GLKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDE 72 (115)
Q Consensus 24 ~~~~~~~~~e~~~p~~i~p~~~~~~ACl~C~lVkT~dQF~~~GCPNC~~ 72 (115)
+..++++..+.++. --+.+.|..|+. .=.|.+-+||+|+.
T Consensus 180 s~P~~s~l~~~~~~------G~R~L~Cs~C~t---~W~~~R~~Cp~Cg~ 219 (290)
T PF04216_consen 180 SPPVLSVLRGGERE------GKRYLHCSLCGT---EWRFVRIKCPYCGN 219 (290)
T ss_dssp --EEEEEEE------------EEEEEETTT-----EEE--TTS-TTT--
T ss_pred CcCceEEEecCCCC------ccEEEEcCCCCC---eeeecCCCCcCCCC
Confidence 34566666555321 123456888874 44555568999985
No 133
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=20.31 E-value=54 Score=21.95 Aligned_cols=21 Identities=10% Similarity=0.131 Sum_probs=15.4
Q ss_pred ccccCCcccccccccccCCCCCchhh
Q psy8226 48 AETINPRTTSTFDQFEFDGCDNCDEF 73 (115)
Q Consensus 48 ~ACl~C~lVkT~dQF~~~GCPNC~~~ 73 (115)
..|.+|+.-.=.|. ||.|++.
T Consensus 6 rkC~~cg~YTLke~-----Cp~CG~~ 26 (59)
T COG2260 6 RKCPKCGRYTLKEK-----CPVCGGD 26 (59)
T ss_pred hcCcCCCceeeccc-----CCCCCCc
Confidence 45999998744444 9999963
No 134
>cd00169 Chemokine Chemokine: small cytokines, including a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; distinguished from other cytokines by their receptors, which are G-protein coupled receptors; divided into 4 subfamilies based on the arrangement of the two N-terminal cysteines; some members can bind multiple receptors and many chemokine receptors can bind more than one chemokine; this redundancy allows precise control in stimulating the immune system and in contributing to the homeostasis of a cell; when expressed inappropriately, chemokines play a role in autoimmune diseases, vascular irregularities, graft rejection, neoplasia, and allergies; exist as monomers, dimers and multimers, but are believed to function as monomers; found only in vertebrates and a few viruses. See CDs: Chemokine_CXC (cd00273), Chemokine_CC (cd00272), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for chemokine subgroups.
Probab=20.25 E-value=55 Score=20.34 Aligned_cols=16 Identities=31% Similarity=0.765 Sum_probs=12.2
Q ss_pred EEEEeCCCchHHHhhhc
Q psy8226 94 MIALMDPKDSWVAKWQR 110 (115)
Q Consensus 94 ~IaImdP~kSWVAKwqr 110 (115)
.+. +||++.||-|.++
T Consensus 41 ~iC-~dP~~~WV~~~i~ 56 (59)
T cd00169 41 KVC-ADPKEPWVKDLIQ 56 (59)
T ss_pred EEE-CCCCcHHHHHHHH
Confidence 444 4999999988764
Done!