Query 026747
Match_columns 234
No_of_seqs 27 out of 29
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 12:07:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026747.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026747hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3490 Transcription elongati 91.2 0.074 1.6E-06 43.7 0.5 26 160-185 7-32 (111)
2 COG5204 SPT4 Transcription elo 90.6 0.13 2.9E-06 42.1 1.4 26 160-185 8-33 (112)
3 PF09297 zf-NADH-PPase: NADH p 89.3 0.076 1.6E-06 33.6 -0.7 25 162-186 4-29 (32)
4 COG1645 Uncharacterized Zn-fin 88.4 0.2 4.3E-06 42.0 0.9 26 164-190 31-56 (131)
5 PF14803 Nudix_N_2: Nudix N-te 87.0 0.13 2.8E-06 34.1 -0.8 24 162-185 1-29 (34)
6 PF08274 PhnA_Zn_Ribbon: PhnA 86.7 0.27 5.9E-06 31.9 0.6 24 163-186 4-27 (30)
7 PF15559 DUF4660: Domain of un 86.4 0.51 1.1E-05 38.7 2.2 29 54-83 30-58 (108)
8 PRK00420 hypothetical protein; 84.1 0.52 1.1E-05 38.4 1.2 31 164-194 26-56 (112)
9 COG1096 Predicted RNA-binding 83.5 0.17 3.6E-06 44.7 -2.0 30 157-187 145-174 (188)
10 cd07973 Spt4 Transcription elo 82.6 0.6 1.3E-05 37.1 1.0 25 161-185 3-27 (98)
11 PRK12496 hypothetical protein; 82.0 0.57 1.2E-05 39.3 0.7 23 162-186 128-151 (164)
12 PRK03824 hypA hydrogenase nick 79.7 0.81 1.8E-05 37.3 0.9 27 162-190 71-119 (135)
13 PRK12380 hydrogenase nickel in 77.2 1.2 2.6E-05 35.4 1.1 25 163-189 72-97 (113)
14 TIGR00100 hypA hydrogenase nic 76.3 1.2 2.5E-05 35.4 0.8 26 162-189 71-97 (115)
15 PF07282 OrfB_Zn_ribbon: Putat 74.5 1.2 2.7E-05 31.3 0.5 25 163-187 30-55 (69)
16 PF06677 Auto_anti-p27: Sjogre 72.8 1.6 3.5E-05 30.0 0.7 22 164-185 20-41 (41)
17 COG1675 TFA1 Transcription ini 71.6 0.89 1.9E-05 39.5 -0.9 28 163-190 115-144 (176)
18 PRK09521 exosome complex RNA-b 71.2 1.6 3.4E-05 36.6 0.5 29 159-187 147-175 (189)
19 PF12773 DZR: Double zinc ribb 70.3 1.7 3.7E-05 28.9 0.4 27 161-187 12-38 (50)
20 COG2816 NPY1 NTP pyrophosphohy 70.2 1.6 3.4E-05 40.6 0.3 26 162-187 112-138 (279)
21 COG1592 Rubrerythrin [Energy p 66.6 2.4 5.1E-05 36.6 0.6 24 162-187 135-158 (166)
22 PRK12495 hypothetical protein; 65.0 4.7 0.0001 36.7 2.2 27 162-189 43-69 (226)
23 TIGR02682 cas_csx11 CRISPR-ass 65.0 3.3 7.1E-05 43.9 1.4 13 179-191 385-397 (918)
24 TIGR00373 conserved hypothetic 65.0 1.2 2.6E-05 37.0 -1.4 26 164-189 112-139 (158)
25 PRK00398 rpoP DNA-directed RNA 64.7 2.6 5.7E-05 28.2 0.4 26 164-189 6-32 (46)
26 PF09845 DUF2072: Zn-ribbon co 64.3 2.6 5.7E-05 35.5 0.5 23 163-187 3-28 (131)
27 PRK00241 nudC NADH pyrophospha 63.9 2.7 5.8E-05 37.3 0.5 26 163-188 101-127 (256)
28 COG2093 DNA-directed RNA polym 63.1 5.9 0.00013 30.1 2.1 27 161-190 4-30 (64)
29 smart00661 RPOL9 RNA polymeras 62.5 2.6 5.6E-05 28.0 0.1 28 163-190 2-32 (52)
30 PRK06266 transcription initiat 62.4 1.5 3.3E-05 37.3 -1.3 28 164-191 120-149 (178)
31 PF08792 A2L_zn_ribbon: A2L zi 62.0 2.2 4.8E-05 28.0 -0.3 26 161-186 3-29 (33)
32 COG3058 FdhE Uncharacterized p 61.5 6.4 0.00014 37.3 2.5 16 176-191 183-198 (308)
33 PF09538 FYDLN_acid: Protein o 61.5 3 6.4E-05 33.5 0.2 29 162-190 10-38 (108)
34 PRK03681 hypA hydrogenase nick 59.1 4.8 0.0001 32.0 1.1 25 163-189 72-98 (114)
35 PF13248 zf-ribbon_3: zinc-rib 59.0 3.8 8.3E-05 25.0 0.4 20 164-186 5-24 (26)
36 PF07754 DUF1610: Domain of un 58.5 4.1 8.9E-05 25.5 0.5 23 164-186 1-24 (24)
37 smart00659 RPOLCX RNA polymera 57.3 4.3 9.2E-05 28.0 0.4 26 164-189 5-30 (44)
38 PF04423 Rad50_zn_hook: Rad50 57.3 3.9 8.5E-05 28.1 0.3 9 176-185 19-27 (54)
39 TIGR01031 rpmF_bact ribosomal 55.2 4.3 9.4E-05 29.1 0.2 21 161-185 26-46 (55)
40 PRK00762 hypA hydrogenase nick 54.1 5.7 0.00012 32.0 0.7 24 163-189 72-103 (124)
41 COG0675 Transposase and inacti 53.8 4.5 9.8E-05 33.7 0.1 27 163-193 311-340 (364)
42 PF04161 Arv1: Arv1-like famil 53.5 5.2 0.00011 34.4 0.4 23 164-186 3-32 (208)
43 PRK00564 hypA hydrogenase nick 53.4 8.4 0.00018 30.7 1.6 27 161-189 71-99 (117)
44 PRK12286 rpmF 50S ribosomal pr 53.3 5 0.00011 29.0 0.3 21 161-185 27-47 (57)
45 cd00350 rubredoxin_like Rubred 52.5 5.6 0.00012 25.4 0.4 22 164-187 4-26 (33)
46 TIGR00375 conserved hypothetic 52.4 6.7 0.00014 37.4 1.0 34 153-187 232-267 (374)
47 cd00729 rubredoxin_SM Rubredox 52.1 5 0.00011 26.1 0.1 23 163-187 4-27 (34)
48 TIGR02300 FYDLN_acid conserved 52.0 6.1 0.00013 33.4 0.6 28 162-189 10-37 (129)
49 PF02318 FYVE_2: FYVE-type zin 50.5 7.5 0.00016 30.6 0.9 25 163-187 56-80 (118)
50 PF06093 Spt4: Spt4/RpoE2 zinc 49.6 0.63 1.4E-05 35.5 -5.1 24 161-184 1-24 (77)
51 PF05924 SAMP: SAMP Motif; In 49.5 13 0.00029 22.7 1.6 16 159-174 4-19 (20)
52 COG1996 RPC10 DNA-directed RNA 49.4 9.4 0.0002 27.5 1.1 26 164-189 9-35 (49)
53 smart00834 CxxC_CXXC_SSSS Puta 47.3 8 0.00017 24.4 0.5 23 164-186 8-34 (41)
54 PRK08270 anaerobic ribonucleos 47.2 8 0.00017 39.1 0.7 32 150-185 597-646 (656)
55 PRK08351 DNA-directed RNA poly 47.0 16 0.00035 27.2 2.1 23 162-189 4-26 (61)
56 PF03604 DNA_RNApol_7kD: DNA d 46.0 9.4 0.0002 25.0 0.7 24 164-187 3-26 (32)
57 PF08271 TF_Zn_Ribbon: TFIIB z 45.4 7.1 0.00015 25.8 0.0 23 164-186 3-27 (43)
58 KOG4602 Nanos and related prot 45.4 8 0.00017 36.6 0.4 14 177-190 267-280 (318)
59 TIGR02487 NrdD anaerobic ribon 45.3 9.8 0.00021 37.7 1.0 21 164-188 527-548 (579)
60 cd01675 RNR_III Class III ribo 44.3 11 0.00023 37.2 1.1 21 164-188 521-542 (555)
61 TIGR02605 CxxC_CxxC_SSSS putat 43.2 8 0.00017 25.9 0.0 26 164-189 8-37 (52)
62 PF01155 HypA: Hydrogenase exp 42.4 4.7 0.0001 31.8 -1.4 25 163-188 72-96 (113)
63 PRK07111 anaerobic ribonucleos 42.2 11 0.00023 38.8 0.7 37 150-186 652-701 (735)
64 PF04216 FdhE: Protein involve 41.9 8.6 0.00019 34.2 0.0 13 178-190 172-184 (290)
65 PF10609 ParA: ParA/MinD ATPas 41.9 14 0.0003 28.6 1.2 33 155-187 40-74 (81)
66 TIGR00686 phnA alkylphosphonat 41.4 9.9 0.00021 31.4 0.3 27 163-189 4-30 (109)
67 PF01783 Ribosomal_L32p: Ribos 40.7 7.5 0.00016 27.6 -0.4 19 163-185 28-46 (56)
68 TIGR01374 soxD sarcosine oxida 40.6 11 0.00024 29.6 0.4 13 179-191 2-14 (84)
69 PF13597 NRDD: Anaerobic ribon 40.5 7.2 0.00016 38.3 -0.7 33 151-187 463-513 (546)
70 PRK14559 putative protein seri 40.1 15 0.00034 37.3 1.5 23 162-189 16-38 (645)
71 cd00730 rubredoxin Rubredoxin; 39.1 13 0.00029 26.3 0.6 8 179-186 35-42 (50)
72 COG4260 Membrane protease subu 38.3 7.7 0.00017 37.2 -0.9 26 161-186 315-342 (345)
73 PRK14873 primosome assembly pr 38.2 10 0.00023 38.3 -0.0 26 163-188 394-420 (665)
74 COG2260 Predicted Zn-ribbon RN 37.6 13 0.00029 27.8 0.4 27 160-191 4-30 (59)
75 TIGR00595 priA primosomal prot 37.1 13 0.00027 36.1 0.3 27 163-189 224-251 (505)
76 PRK10220 hypothetical protein; 36.6 13 0.00028 30.8 0.3 25 163-187 5-29 (111)
77 COG3809 Uncharacterized protei 36.3 16 0.00034 29.3 0.7 9 178-186 1-9 (88)
78 PRK03564 formate dehydrogenase 36.2 15 0.00033 34.3 0.7 13 178-190 187-199 (309)
79 KOG2767 Translation initiation 35.9 26 0.00056 34.4 2.2 46 143-191 71-131 (400)
80 PRK05580 primosome assembly pr 35.6 13 0.00028 37.3 0.1 25 163-187 392-417 (679)
81 PRK06393 rpoE DNA-directed RNA 35.4 29 0.00062 26.2 1.9 24 161-189 5-28 (64)
82 TIGR01562 FdhE formate dehydro 35.4 16 0.00034 34.1 0.6 12 179-190 185-196 (305)
83 PRK08271 anaerobic ribonucleos 35.3 16 0.00034 37.2 0.7 18 164-185 569-587 (623)
84 PRK09263 anaerobic ribonucleos 35.1 19 0.0004 36.9 1.2 22 164-185 644-666 (711)
85 PF12760 Zn_Tnp_IS1595: Transp 35.0 18 0.00039 24.3 0.8 11 177-187 17-27 (46)
86 PRK01110 rpmF 50S ribosomal pr 35.0 13 0.00028 27.1 0.0 21 161-186 27-47 (60)
87 PRK14704 anaerobic ribonucleos 34.8 19 0.0004 36.5 1.1 35 150-188 531-582 (618)
88 KOG2879 Predicted E3 ubiquitin 34.6 26 0.00057 33.2 1.9 15 164-178 242-256 (298)
89 PRK06450 threonine synthase; V 34.4 16 0.00034 33.5 0.5 21 164-186 6-26 (338)
90 PRK00085 recO DNA repair prote 34.2 29 0.00062 29.3 2.0 23 163-185 151-177 (247)
91 COG0419 SbcC ATPase involved i 34.0 21 0.00046 36.5 1.4 14 177-191 456-469 (908)
92 PF00301 Rubredoxin: Rubredoxi 33.6 16 0.00035 25.6 0.3 9 179-187 35-43 (47)
93 PRK13130 H/ACA RNA-protein com 33.6 7.8 0.00017 28.3 -1.3 25 161-190 5-29 (56)
94 KOG4218 Nuclear hormone recept 33.0 20 0.00043 35.4 0.9 16 173-188 10-25 (475)
95 KOG1597 Transcription initiati 32.7 18 0.00039 34.4 0.6 27 164-191 3-38 (308)
96 TIGR02827 RNR_anaer_Bdell anae 32.6 19 0.00042 36.3 0.8 19 164-185 535-553 (586)
97 TIGR01384 TFS_arch transcripti 32.6 14 0.0003 28.0 -0.1 24 163-187 2-25 (104)
98 PF09723 Zn-ribbon_8: Zinc rib 32.2 17 0.00038 24.2 0.3 25 164-188 8-36 (42)
99 smart00653 eIF2B_5 domain pres 32.1 12 0.00025 30.2 -0.7 44 144-187 56-110 (110)
100 PRK12860 transcriptional activ 31.9 27 0.00058 30.9 1.5 22 164-185 137-161 (189)
101 PRK08579 anaerobic ribonucleos 31.9 20 0.00044 36.3 0.9 19 164-185 571-589 (625)
102 COG2824 PhnA Uncharacterized Z 31.2 10 0.00023 31.5 -1.1 29 161-189 3-31 (112)
103 PRK05452 anaerobic nitric oxid 30.8 22 0.00047 34.3 0.8 23 163-187 427-467 (479)
104 COG0375 HybF Zn finger protein 30.5 17 0.00038 29.9 0.1 24 162-186 71-94 (115)
105 PF09526 DUF2387: Probable met 29.6 27 0.00058 26.4 1.0 12 178-189 8-19 (71)
106 PHA02942 putative transposase; 29.5 22 0.00048 33.5 0.6 8 179-186 326-333 (383)
107 PRK06260 threonine synthase; V 29.1 22 0.00049 32.8 0.6 21 164-186 6-27 (397)
108 PF07295 DUF1451: Protein of u 28.9 26 0.00057 29.4 0.9 24 163-186 114-138 (146)
109 PRK06835 DNA replication prote 28.6 42 0.00091 31.0 2.2 28 162-190 83-110 (329)
110 COG5270 PUA domain (predicted 28.6 31 0.00066 31.2 1.3 20 162-186 15-34 (202)
111 PRK07591 threonine synthase; V 28.1 25 0.00055 33.1 0.7 22 163-186 20-41 (421)
112 TIGR02443 conserved hypothetic 28.0 30 0.00065 25.9 0.9 18 170-189 3-20 (59)
113 smart00540 LEM in nuclear memb 27.3 48 0.001 23.2 1.8 15 157-171 8-22 (44)
114 PRK10246 exonuclease subunit S 27.0 27 0.00058 36.8 0.8 11 178-188 503-513 (1047)
115 TIGR00613 reco DNA repair prot 26.4 20 0.00044 30.1 -0.2 25 164-188 150-178 (241)
116 COG1545 Predicted nucleic-acid 26.0 31 0.00067 28.4 0.8 22 164-188 32-53 (140)
117 COG1439 Predicted nucleic acid 25.9 26 0.00057 30.9 0.4 21 164-187 142-162 (177)
118 TIGR00416 sms DNA repair prote 25.7 25 0.00055 33.7 0.3 25 163-190 9-33 (454)
119 TIGR03831 YgiT_finger YgiT-typ 25.3 37 0.00081 21.5 0.9 13 175-187 29-41 (46)
120 PF14634 zf-RING_5: zinc-RING 24.5 31 0.00067 22.6 0.5 20 163-185 24-43 (44)
121 smart00531 TFIIE Transcription 24.3 17 0.00037 29.6 -1.0 27 164-190 102-135 (147)
122 COG1198 PriA Primosomal protei 24.3 28 0.00062 36.1 0.4 24 164-187 447-471 (730)
123 PRK03988 translation initiatio 24.1 55 0.0012 27.3 1.9 87 102-189 29-134 (138)
124 PRK14892 putative transcriptio 23.7 27 0.00059 27.9 0.1 24 164-187 24-51 (99)
125 KOG4334 Uncharacterized conser 23.7 40 0.00087 34.7 1.2 15 160-174 480-494 (650)
126 PRK12722 transcriptional activ 23.7 42 0.00091 29.7 1.2 33 154-186 117-162 (187)
127 PF09396 Thrombin_light: Throm 23.6 53 0.0011 24.0 1.5 25 178-207 16-40 (49)
128 PHA00626 hypothetical protein 23.4 36 0.00078 25.7 0.6 9 179-187 1-9 (59)
129 PRK01103 formamidopyrimidine/5 22.2 31 0.00066 30.7 0.1 74 107-187 159-254 (274)
130 PRK14811 formamidopyrimidine-D 22.2 39 0.00085 30.2 0.8 9 178-186 235-243 (269)
131 PF14447 Prok-RING_4: Prokaryo 21.8 45 0.00098 24.6 0.9 25 164-188 22-49 (55)
132 cd00202 ZnF_GATA Zinc finger D 21.6 24 0.00052 25.0 -0.5 24 164-187 2-30 (54)
133 TIGR03830 CxxCG_CxxCG_HTH puta 21.0 36 0.00078 25.7 0.3 16 175-190 28-43 (127)
134 PRK11823 DNA repair protein Ra 20.8 38 0.00081 32.4 0.4 24 163-189 9-32 (446)
135 PF09986 DUF2225: Uncharacteri 20.6 40 0.00087 29.3 0.5 13 178-190 48-60 (214)
136 smart00734 ZnF_Rad18 Rad18-lik 20.5 45 0.00098 20.6 0.6 8 180-187 3-10 (26)
137 COG1867 TRM1 N2,N2-dimethylgua 20.5 59 0.0013 31.8 1.6 40 145-186 218-265 (380)
138 PRK13945 formamidopyrimidine-D 20.4 1E+02 0.0023 27.7 3.1 76 104-186 165-262 (282)
139 PRK14890 putative Zn-ribbon RN 20.3 53 0.0011 24.6 1.0 25 162-186 8-33 (59)
140 PRK11032 hypothetical protein; 20.2 45 0.00098 28.7 0.7 24 163-186 126-150 (160)
141 PF05741 zf-nanos: Nanos RNA b 20.1 37 0.00081 24.8 0.2 12 177-188 32-43 (55)
No 1
>KOG3490 consensus Transcription elongation factor SPT4 [Transcription]
Probab=91.24 E-value=0.074 Score=43.74 Aligned_cols=26 Identities=42% Similarity=0.752 Sum_probs=24.6
Q ss_pred HHHHHHhcCCCccccCCCCccccCCC
Q 026747 160 LLRMCLQCGIPKTFSNTRGMVCPVCS 185 (234)
Q Consensus 160 lLrMclqcgiPKt~s~argmvcPvcg 185 (234)
-||.||.|||=||+..-+--+||.|+
T Consensus 7 ~lRACllCs~Vkt~~~F~~dGC~Nc~ 32 (111)
T KOG3490|consen 7 KLRACLLCSIVKTLNGFRKDGCENCP 32 (111)
T ss_pred hhhhhhhhhhhhhhhhhhhcCCCCch
Confidence 48999999999999999999999998
No 2
>COG5204 SPT4 Transcription elongation factor SPT4 [Transcription]
Probab=90.59 E-value=0.13 Score=42.14 Aligned_cols=26 Identities=50% Similarity=0.943 Sum_probs=23.9
Q ss_pred HHHHHHhcCCCccccCCCCccccCCC
Q 026747 160 LLRMCLQCGIPKTFSNTRGMVCPVCS 185 (234)
Q Consensus 160 lLrMclqcgiPKt~s~argmvcPvcg 185 (234)
+-|.||.|||=||.+.-+--.||.|-
T Consensus 8 ~sRACl~Cgiv~t~n~F~~dGCpNc~ 33 (112)
T COG5204 8 LSRACLGCGIVKTLNGFRKDGCPNCP 33 (112)
T ss_pred hhhhhhhcceeeecccccccCCCCCc
Confidence 45899999999999999999999995
No 3
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=89.35 E-value=0.076 Score=33.56 Aligned_cols=25 Identities=32% Similarity=0.812 Sum_probs=16.1
Q ss_pred HHHHhcCCCccccCC-CCccccCCCC
Q 026747 162 RMCLQCGIPKTFSNT-RGMVCPVCSD 186 (234)
Q Consensus 162 rMclqcgiPKt~s~a-rgmvcPvcgd 186 (234)
|.|-.||.|-....+ ..|+||.||-
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred cccCcCCccccCCCCcCEeECCCCcC
Confidence 458899999888776 6999999984
No 4
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=88.43 E-value=0.2 Score=42.02 Aligned_cols=26 Identities=35% Similarity=0.827 Sum_probs=20.3
Q ss_pred HHhcCCCccccCCCCccccCCCCCCCC
Q 026747 164 CLQCGIPKTFSNTRGMVCPVCSDRPPA 190 (234)
Q Consensus 164 clqcgiPKt~s~argmvcPvcgdRp~~ 190 (234)
|--||.|.-=-.+ --+||+||-+=..
T Consensus 31 Cp~Cg~PLF~KdG-~v~CPvC~~~~~~ 56 (131)
T COG1645 31 CPKCGTPLFRKDG-EVFCPVCGYREVV 56 (131)
T ss_pred CcccCCcceeeCC-eEECCCCCceEEE
Confidence 9999999977434 4899999976544
No 5
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=87.00 E-value=0.13 Score=34.06 Aligned_cols=24 Identities=42% Similarity=0.973 Sum_probs=13.4
Q ss_pred HHHHhcCCCccccCC----C-CccccCCC
Q 026747 162 RMCLQCGIPKTFSNT----R-GMVCPVCS 185 (234)
Q Consensus 162 rMclqcgiPKt~s~a----r-gmvcPvcg 185 (234)
+.|-+||-|-.+.-- | -+|||.||
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACG 29 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTT
T ss_pred CccccccChhhhhcCCCCCccceECCCCC
Confidence 358899988777533 2 48999998
No 6
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=86.66 E-value=0.27 Score=31.91 Aligned_cols=24 Identities=33% Similarity=0.840 Sum_probs=14.7
Q ss_pred HHHhcCCCccccCCCCccccCCCC
Q 026747 163 MCLQCGIPKTFSNTRGMVCPVCSD 186 (234)
Q Consensus 163 MclqcgiPKt~s~argmvcPvcgd 186 (234)
-|-+||-.-||...-.||||-|+.
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----EE-SSSEEETTTTE
T ss_pred CCCCCCCcceeccCCEEeCCcccc
Confidence 488999999999999999999983
No 7
>PF15559 DUF4660: Domain of unknown function (DUF4660)
Probab=86.43 E-value=0.51 Score=38.72 Aligned_cols=29 Identities=31% Similarity=0.524 Sum_probs=25.5
Q ss_pred CCCCCCChhhhhccccCCcccccchhhhhc
Q 026747 54 VDSGLPSAFDVFSQISGPPRFLNNSLEVKA 83 (234)
Q Consensus 54 ~~S~LPSA~DaFseIsGPP~FLnn~v~e~~ 83 (234)
..-.||...++|.-|+- |-||-|...+++
T Consensus 30 ~~~~LP~PDeLFrsVsr-PaFLyNPlnKqI 58 (108)
T PF15559_consen 30 KAERLPGPDELFRSVSR-PAFLYNPLNKQI 58 (108)
T ss_pred ccCcCCCHHHHHhhcCc-cccccCcccccc
Confidence 34489999999999999 899999998874
No 8
>PRK00420 hypothetical protein; Validated
Probab=84.12 E-value=0.52 Score=38.39 Aligned_cols=31 Identities=26% Similarity=0.479 Sum_probs=24.1
Q ss_pred HHhcCCCccccCCCCccccCCCCCCCCCCch
Q 026747 164 CLQCGIPKTFSNTRGMVCPVCSDRPPADISN 194 (234)
Q Consensus 164 clqcgiPKt~s~argmvcPvcgdRp~~~~~~ 194 (234)
|--||.|-+-......+||+||........+
T Consensus 26 CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~~~e 56 (112)
T PRK00420 26 CPVCGLPLFELKDGEVVCPVHGKVYIVKSDE 56 (112)
T ss_pred CCCCCCcceecCCCceECCCCCCeeeeccHH
Confidence 8889999997666679999999966654433
No 9
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=83.55 E-value=0.17 Score=44.70 Aligned_cols=30 Identities=20% Similarity=0.546 Sum_probs=25.3
Q ss_pred HHHHHHHHHhcCCCccccCCCCccccCCCCC
Q 026747 157 AAELLRMCLQCGIPKTFSNTRGMVCPVCSDR 187 (234)
Q Consensus 157 aadlLrMclqcgiPKt~s~argmvcPvcgdR 187 (234)
-+=++++|..||-|--+ ..+.|.||.||..
T Consensus 145 lGVI~A~CsrC~~~L~~-~~~~l~Cp~Cg~t 174 (188)
T COG1096 145 LGVIYARCSRCRAPLVK-KGNMLKCPNCGNT 174 (188)
T ss_pred ceEEEEEccCCCcceEE-cCcEEECCCCCCE
Confidence 34457899999999999 7888999999953
No 10
>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=82.62 E-value=0.6 Score=37.13 Aligned_cols=25 Identities=40% Similarity=0.753 Sum_probs=22.0
Q ss_pred HHHHHhcCCCccccCCCCccccCCC
Q 026747 161 LRMCLQCGIPKTFSNTRGMVCPVCS 185 (234)
Q Consensus 161 LrMclqcgiPKt~s~argmvcPvcg 185 (234)
||.|+.|++=+|+..-..-+||.|+
T Consensus 3 lrAC~~C~~I~~~~qf~~~gCpnC~ 27 (98)
T cd07973 3 LRACLLCSLIKTEDQFERDGCPNCE 27 (98)
T ss_pred CchhccCCcccccccccCCCCCCCc
Confidence 6899999999998876678999994
No 11
>PRK12496 hypothetical protein; Provisional
Probab=82.04 E-value=0.57 Score=39.32 Aligned_cols=23 Identities=26% Similarity=0.853 Sum_probs=17.6
Q ss_pred HHHHhcCCCccccCC-CCccccCCCC
Q 026747 162 RMCLQCGIPKTFSNT-RGMVCPVCSD 186 (234)
Q Consensus 162 rMclqcgiPKt~s~a-rgmvcPvcgd 186 (234)
.+|..|| +.|... -+.+||+||-
T Consensus 128 ~~C~gC~--~~~~~~~~~~~C~~CG~ 151 (164)
T PRK12496 128 KVCKGCK--KKYPEDYPDDVCEICGS 151 (164)
T ss_pred EECCCCC--ccccCCCCCCcCCCCCC
Confidence 4599999 778553 3689999994
No 12
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=79.72 E-value=0.81 Score=37.31 Aligned_cols=27 Identities=30% Similarity=0.659 Sum_probs=19.9
Q ss_pred HHHHhcCCCccccCC----------------------CCccccCCCCCCCC
Q 026747 162 RMCLQCGIPKTFSNT----------------------RGMVCPVCSDRPPA 190 (234)
Q Consensus 162 rMclqcgiPKt~s~a----------------------rgmvcPvcgdRp~~ 190 (234)
-.|.+|| .+|+.. ..+.||.||-+...
T Consensus 71 ~~C~~CG--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~ 119 (135)
T PRK03824 71 LKCRNCG--NEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFE 119 (135)
T ss_pred EECCCCC--CEEecccccccccccccccccccccccccCcCCcCCCCCCcE
Confidence 4599999 566553 46789999987653
No 13
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=77.18 E-value=1.2 Score=35.37 Aligned_cols=25 Identities=20% Similarity=0.607 Sum_probs=19.2
Q ss_pred HHHhcCCCccccCC-CCccccCCCCCCC
Q 026747 163 MCLQCGIPKTFSNT-RGMVCPVCSDRPP 189 (234)
Q Consensus 163 MclqcgiPKt~s~a-rgmvcPvcgdRp~ 189 (234)
-|.+|| .+|... ..+.||.||-...
T Consensus 72 ~C~~Cg--~~~~~~~~~~~CP~Cgs~~~ 97 (113)
T PRK12380 72 WCWDCS--QVVEIHQHDAQCPHCHGERL 97 (113)
T ss_pred EcccCC--CEEecCCcCccCcCCCCCCc
Confidence 499999 666664 5688999997654
No 14
>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=76.31 E-value=1.2 Score=35.43 Aligned_cols=26 Identities=23% Similarity=0.443 Sum_probs=20.1
Q ss_pred HHHHhcCCCccccCC-CCccccCCCCCCC
Q 026747 162 RMCLQCGIPKTFSNT-RGMVCPVCSDRPP 189 (234)
Q Consensus 162 rMclqcgiPKt~s~a-rgmvcPvcgdRp~ 189 (234)
--|.+|| ++|... ....||.||-...
T Consensus 71 ~~C~~Cg--~~~~~~~~~~~CP~Cgs~~~ 97 (115)
T TIGR00100 71 CECEDCS--EEVSPEIDLYRCPKCHGIML 97 (115)
T ss_pred EEcccCC--CEEecCCcCccCcCCcCCCc
Confidence 3599999 777664 4788999997654
No 15
>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=74.46 E-value=1.2 Score=31.27 Aligned_cols=25 Identities=28% Similarity=0.667 Sum_probs=19.8
Q ss_pred HHHhcCCCccc-cCCCCccccCCCCC
Q 026747 163 MCLQCGIPKTF-SNTRGMVCPVCSDR 187 (234)
Q Consensus 163 MclqcgiPKt~-s~argmvcPvcgdR 187 (234)
.|-.||..... .+.|.++||.||-.
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCcccccccccccceEEcCCCCCE
Confidence 38888888777 77788999999853
No 16
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=72.80 E-value=1.6 Score=29.96 Aligned_cols=22 Identities=27% Similarity=0.765 Sum_probs=18.7
Q ss_pred HHhcCCCccccCCCCccccCCC
Q 026747 164 CLQCGIPKTFSNTRGMVCPVCS 185 (234)
Q Consensus 164 clqcgiPKt~s~argmvcPvcg 185 (234)
|-.||+|-.-+.....+||+|+
T Consensus 20 Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 20 CPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred cCCCCCeeEEecCCCEECCCCC
Confidence 8899999988666679999996
No 17
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=71.62 E-value=0.89 Score=39.46 Aligned_cols=28 Identities=25% Similarity=0.808 Sum_probs=23.6
Q ss_pred HHHhcCCCccccCCC--CccccCCCCCCCC
Q 026747 163 MCLQCGIPKTFSNTR--GMVCPVCSDRPPA 190 (234)
Q Consensus 163 MclqcgiPKt~s~ar--gmvcPvcgdRp~~ 190 (234)
+|.+|.++-||-.|- |..||.||..=..
T Consensus 115 ~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~~ 144 (176)
T COG1675 115 VCPNCHVKYSFDEAMELGFTCPKCGEDLEE 144 (176)
T ss_pred eCCCCCCcccHHHHHHhCCCCCCCCchhhh
Confidence 498999999998886 8999999976544
No 18
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=71.20 E-value=1.6 Score=36.65 Aligned_cols=29 Identities=24% Similarity=0.658 Sum_probs=24.0
Q ss_pred HHHHHHHhcCCCccccCCCCccccCCCCC
Q 026747 159 ELLRMCLQCGIPKTFSNTRGMVCPVCSDR 187 (234)
Q Consensus 159 dlLrMclqcgiPKt~s~argmvcPvcgdR 187 (234)
-|...|-.||-|.+-.+-..|.||.||-+
T Consensus 147 vv~a~~~~~g~~~~~~~~~~~~c~~~~~~ 175 (189)
T PRK09521 147 VIYAMCSRCRTPLVKKGENELKCPNCGNI 175 (189)
T ss_pred EEEEEccccCCceEECCCCEEECCCCCCE
Confidence 34556888999999888788999999964
No 19
>PF12773 DZR: Double zinc ribbon
Probab=70.29 E-value=1.7 Score=28.92 Aligned_cols=27 Identities=26% Similarity=0.798 Sum_probs=22.5
Q ss_pred HHHHHhcCCCccccCCCCccccCCCCC
Q 026747 161 LRMCLQCGIPKTFSNTRGMVCPVCSDR 187 (234)
Q Consensus 161 LrMclqcgiPKt~s~argmvcPvcgdR 187 (234)
.+.|..||++-.......++||.||..
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCC
Confidence 468999999999666667899999985
No 20
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=70.19 E-value=1.6 Score=40.55 Aligned_cols=26 Identities=31% Similarity=0.732 Sum_probs=21.9
Q ss_pred HHHHhcCCCccccCCC-CccccCCCCC
Q 026747 162 RMCLQCGIPKTFSNTR-GMVCPVCSDR 187 (234)
Q Consensus 162 rMclqcgiPKt~s~ar-gmvcPvcgdR 187 (234)
|.|=.||-|.....+- .|+||.||-+
T Consensus 112 RFCg~CG~~~~~~~~g~~~~C~~cg~~ 138 (279)
T COG2816 112 RFCGRCGTKTYPREGGWARVCPKCGHE 138 (279)
T ss_pred cCCCCCCCcCccccCceeeeCCCCCCc
Confidence 4588999998887655 9999999986
No 21
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=66.59 E-value=2.4 Score=36.63 Aligned_cols=24 Identities=29% Similarity=0.729 Sum_probs=17.4
Q ss_pred HHHHhcCCCccccCCCCccccCCCCC
Q 026747 162 RMCLQCGIPKTFSNTRGMVCPVCSDR 187 (234)
Q Consensus 162 rMclqcgiPKt~s~argmvcPvcgdR 187 (234)
=+|..||..--- .---+||+||.+
T Consensus 135 ~vC~vCGy~~~g--e~P~~CPiCga~ 158 (166)
T COG1592 135 WVCPVCGYTHEG--EAPEVCPICGAP 158 (166)
T ss_pred EEcCCCCCcccC--CCCCcCCCCCCh
Confidence 469999975444 335899999964
No 22
>PRK12495 hypothetical protein; Provisional
Probab=65.04 E-value=4.7 Score=36.74 Aligned_cols=27 Identities=26% Similarity=0.603 Sum_probs=19.0
Q ss_pred HHHHhcCCCccccCCCCccccCCCCCCC
Q 026747 162 RMCLQCGIPKTFSNTRGMVCPVCSDRPP 189 (234)
Q Consensus 162 rMclqcgiPKt~s~argmvcPvcgdRp~ 189 (234)
..|..||.|-.-..+ --+||+|+..--
T Consensus 43 ~hC~~CG~PIpa~pG-~~~Cp~CQ~~~~ 69 (226)
T PRK12495 43 AHCDECGDPIFRHDG-QEFCPTCQQPVT 69 (226)
T ss_pred hhcccccCcccCCCC-eeECCCCCCccc
Confidence 349999999883322 256999996643
No 23
>TIGR02682 cas_csx11 CRISPR-associated protein, Csx11 family. Members of this uncommon, sporadically distributed protein family are large (900 amino acids) and strictly associated, so far, with CRISPR-associated (Cas) gene clusters. Nearby Cas genes always include members of the RAMP superfamily and the six-gene CRISPR-associated RAMP module. Species in which it is found, so far, include three archaea (Methanosarcina mazei, M. barkeri and Methanobacterium thermoautotrophicum) and two bacteria (Thermodesulfovibrio yellowstonii DSM 11347 and Sulfurihydrogenibium azorense).
Probab=65.04 E-value=3.3 Score=43.87 Aligned_cols=13 Identities=38% Similarity=0.772 Sum_probs=11.9
Q ss_pred ccccCCCCCCCCC
Q 026747 179 MVCPVCSDRPPAD 191 (234)
Q Consensus 179 mvcPvcgdRp~~~ 191 (234)
-||||||-||+..
T Consensus 385 ~IC~VCglR~~~~ 397 (918)
T TIGR02682 385 GICPLCRLRLIYD 397 (918)
T ss_pred eecCCcceeecCC
Confidence 8999999999874
No 24
>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=64.99 E-value=1.2 Score=37.01 Aligned_cols=26 Identities=23% Similarity=0.540 Sum_probs=20.9
Q ss_pred HHhcCCCccccCCC--CccccCCCCCCC
Q 026747 164 CLQCGIPKTFSNTR--GMVCPVCSDRPP 189 (234)
Q Consensus 164 clqcgiPKt~s~ar--gmvcPvcgdRp~ 189 (234)
|-+||+==||..|- |..||+||..=.
T Consensus 112 Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 112 CPNMCVRFTFNEAMELNFTCPRCGAMLD 139 (158)
T ss_pred CCCCCcEeeHHHHHHcCCcCCCCCCEee
Confidence 88999777777665 899999998643
No 25
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=64.75 E-value=2.6 Score=28.21 Aligned_cols=26 Identities=31% Similarity=0.754 Sum_probs=21.1
Q ss_pred HHhcCCCccccCCC-CccccCCCCCCC
Q 026747 164 CLQCGIPKTFSNTR-GMVCPVCSDRPP 189 (234)
Q Consensus 164 clqcgiPKt~s~ar-gmvcPvcgdRp~ 189 (234)
|.+||..-++.... ...||.||-+=.
T Consensus 6 C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 6 CARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred CCCCCCEEEECCCCCceECCCCCCeEE
Confidence 78899988887776 789999996543
No 26
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=64.34 E-value=2.6 Score=35.48 Aligned_cols=23 Identities=30% Similarity=0.869 Sum_probs=16.4
Q ss_pred HHHhcCCCccccCCC---CccccCCCCC
Q 026747 163 MCLQCGIPKTFSNTR---GMVCPVCSDR 187 (234)
Q Consensus 163 MclqcgiPKt~s~ar---gmvcPvcgdR 187 (234)
+|..|| ++|-.+. -.+||.||-.
T Consensus 3 ~Ct~Cg--~~f~dgs~eil~GCP~CGg~ 28 (131)
T PF09845_consen 3 QCTKCG--RVFEDGSKEILSGCPECGGN 28 (131)
T ss_pred ccCcCC--CCcCCCcHHHHccCcccCCc
Confidence 588888 4565554 5789999854
No 27
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=63.93 E-value=2.7 Score=37.35 Aligned_cols=26 Identities=38% Similarity=0.837 Sum_probs=20.2
Q ss_pred HHHhcCCCcccc-CCCCccccCCCCCC
Q 026747 163 MCLQCGIPKTFS-NTRGMVCPVCSDRP 188 (234)
Q Consensus 163 MclqcgiPKt~s-~argmvcPvcgdRp 188 (234)
.|-.||-|-... ....++||.||.+=
T Consensus 101 fC~~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 101 FCGYCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred cccccCCCCeecCCceeEECCCCCCEE
Confidence 599999997654 34489999999653
No 28
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=63.10 E-value=5.9 Score=30.11 Aligned_cols=27 Identities=26% Similarity=0.720 Sum_probs=19.6
Q ss_pred HHHHHhcCCCccccCCCCccccCCCCCCCC
Q 026747 161 LRMCLQCGIPKTFSNTRGMVCPVCSDRPPA 190 (234)
Q Consensus 161 LrMclqcgiPKt~s~argmvcPvcgdRp~~ 190 (234)
.+.|..| |.......-+||+||.....
T Consensus 4 ~kAC~~C---k~l~~~d~e~CP~Cgs~~~t 30 (64)
T COG2093 4 EKACKNC---KRLTPEDTEICPVCGSTDLT 30 (64)
T ss_pred hHHHhhc---cccCCCCCccCCCCCCcccc
Confidence 3568888 45566666789999998543
No 29
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=62.48 E-value=2.6 Score=28.01 Aligned_cols=28 Identities=25% Similarity=0.596 Sum_probs=19.5
Q ss_pred HHHhcCCCccccCCC---CccccCCCCCCCC
Q 026747 163 MCLQCGIPKTFSNTR---GMVCPVCSDRPPA 190 (234)
Q Consensus 163 MclqcgiPKt~s~ar---gmvcPvcgdRp~~ 190 (234)
.|-.||-........ -.|||.||-.-..
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEEC
Confidence 477888877666442 4899999965443
No 30
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=62.37 E-value=1.5 Score=37.31 Aligned_cols=28 Identities=32% Similarity=0.723 Sum_probs=22.7
Q ss_pred HHhcCCCccccCCC--CccccCCCCCCCCC
Q 026747 164 CLQCGIPKTFSNTR--GMVCPVCSDRPPAD 191 (234)
Q Consensus 164 clqcgiPKt~s~ar--gmvcPvcgdRp~~~ 191 (234)
|-+||+==||..|- |..||+||..-...
T Consensus 120 Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 120 CPNCHIRFTFDEAMEYGFRCPQCGEMLEEY 149 (178)
T ss_pred CCCCCcEEeHHHHhhcCCcCCCCCCCCeec
Confidence 88899777777665 89999999987654
No 31
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=61.97 E-value=2.2 Score=27.96 Aligned_cols=26 Identities=27% Similarity=0.600 Sum_probs=22.2
Q ss_pred HHHHHhcCCCccc-cCCCCccccCCCC
Q 026747 161 LRMCLQCGIPKTF-SNTRGMVCPVCSD 186 (234)
Q Consensus 161 LrMclqcgiPKt~-s~argmvcPvcgd 186 (234)
|.+|--||-+..+ +.--.+||+-||-
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCc
Confidence 5678899999999 6666999999984
No 32
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=61.55 E-value=6.4 Score=37.33 Aligned_cols=16 Identities=38% Similarity=0.802 Sum_probs=13.4
Q ss_pred CCCccccCCCCCCCCC
Q 026747 176 TRGMVCPVCSDRPPAD 191 (234)
Q Consensus 176 argmvcPvcgdRp~~~ 191 (234)
.+--+|||||-+|+..
T Consensus 183 e~~~~CPvCGS~PvaS 198 (308)
T COG3058 183 ESRQYCPVCGSMPVAS 198 (308)
T ss_pred cccccCCCcCCCCcce
Confidence 5567999999999964
No 33
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=61.46 E-value=3 Score=33.54 Aligned_cols=29 Identities=34% Similarity=0.691 Sum_probs=21.4
Q ss_pred HHHHhcCCCccccCCCCccccCCCCCCCC
Q 026747 162 RMCLQCGIPKTFSNTRGMVCPVCSDRPPA 190 (234)
Q Consensus 162 rMclqcgiPKt~s~argmvcPvcgdRp~~ 190 (234)
|.|..||.=--=++-+-.|||-||.--+.
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTEFPP 38 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCccCc
Confidence 56999997444455558899999976554
No 34
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=59.09 E-value=4.8 Score=31.99 Aligned_cols=25 Identities=24% Similarity=0.499 Sum_probs=17.9
Q ss_pred HHHhcCCCccccC-CC-CccccCCCCCCC
Q 026747 163 MCLQCGIPKTFSN-TR-GMVCPVCSDRPP 189 (234)
Q Consensus 163 MclqcgiPKt~s~-ar-gmvcPvcgdRp~ 189 (234)
-|.+|| .+|.. .. .+.||.||-...
T Consensus 72 ~C~~Cg--~~~~~~~~~~~~CP~Cgs~~~ 98 (114)
T PRK03681 72 WCETCQ--QYVTLLTQRVRRCPQCHGDML 98 (114)
T ss_pred EcccCC--CeeecCCccCCcCcCcCCCCc
Confidence 499999 45554 33 377999997654
No 35
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=58.95 E-value=3.8 Score=25.00 Aligned_cols=20 Identities=30% Similarity=0.929 Sum_probs=11.4
Q ss_pred HHhcCCCccccCCCCccccCCCC
Q 026747 164 CLQCGIPKTFSNTRGMVCPVCSD 186 (234)
Q Consensus 164 clqcgiPKt~s~argmvcPvcgd 186 (234)
|-+||.+ . ...-..||.||.
T Consensus 5 Cp~Cg~~-~--~~~~~fC~~CG~ 24 (26)
T PF13248_consen 5 CPNCGAE-I--DPDAKFCPNCGA 24 (26)
T ss_pred CcccCCc-C--CcccccChhhCC
Confidence 6667762 2 222457777774
No 36
>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=58.49 E-value=4.1 Score=25.53 Aligned_cols=23 Identities=30% Similarity=0.727 Sum_probs=15.7
Q ss_pred HHhcCCCccccC-CCCccccCCCC
Q 026747 164 CLQCGIPKTFSN-TRGMVCPVCSD 186 (234)
Q Consensus 164 clqcgiPKt~s~-argmvcPvcgd 186 (234)
|..||++-.--. +--.+||.||.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 456777766444 44588999983
No 37
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=57.34 E-value=4.3 Score=27.98 Aligned_cols=26 Identities=23% Similarity=0.519 Sum_probs=20.9
Q ss_pred HHhcCCCccccCCCCccccCCCCCCC
Q 026747 164 CLQCGIPKTFSNTRGMVCPVCSDRPP 189 (234)
Q Consensus 164 clqcgiPKt~s~argmvcPvcgdRp~ 189 (234)
|..||..-+-....+..||-||-|=.
T Consensus 5 C~~Cg~~~~~~~~~~irC~~CG~rIl 30 (44)
T smart00659 5 CGECGRENEIKSKDVVRCRECGYRIL 30 (44)
T ss_pred CCCCCCEeecCCCCceECCCCCceEE
Confidence 78899876666666899999998755
No 38
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=57.30 E-value=3.9 Score=28.14 Aligned_cols=9 Identities=44% Similarity=1.579 Sum_probs=4.8
Q ss_pred CCCccccCCC
Q 026747 176 TRGMVCPVCS 185 (234)
Q Consensus 176 argmvcPvcg 185 (234)
+.| +||+|+
T Consensus 19 ~~~-~CPlC~ 27 (54)
T PF04423_consen 19 AKG-CCPLCG 27 (54)
T ss_dssp -SE-E-TTT-
T ss_pred CCC-cCCCCC
Confidence 334 999998
No 39
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=55.19 E-value=4.3 Score=29.07 Aligned_cols=21 Identities=43% Similarity=0.849 Sum_probs=16.9
Q ss_pred HHHHHhcCCCccccCCCCccccCCC
Q 026747 161 LRMCLQCGIPKTFSNTRGMVCPVCS 185 (234)
Q Consensus 161 LrMclqcgiPKt~s~argmvcPvcg 185 (234)
|-.|-+||-++-. ..|||.||
T Consensus 26 l~~C~~cG~~~~~----H~vc~~cG 46 (55)
T TIGR01031 26 LVVCPNCGEFKLP----HRVCPSCG 46 (55)
T ss_pred ceECCCCCCcccC----eeECCccC
Confidence 4569999988754 68999998
No 40
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=54.07 E-value=5.7 Score=32.01 Aligned_cols=24 Identities=29% Similarity=0.787 Sum_probs=15.6
Q ss_pred HHHhcCCCccccCC------CC--ccccCCCCCCC
Q 026747 163 MCLQCGIPKTFSNT------RG--MVCPVCSDRPP 189 (234)
Q Consensus 163 MclqcgiPKt~s~a------rg--mvcPvcgdRp~ 189 (234)
-| .|| .+|... .. +.||.||-...
T Consensus 72 ~C-~Cg--~~~~~~~~~~~~~~~~~~CP~Cgs~~~ 103 (124)
T PRK00762 72 EC-ECG--YEGVVDEDEIDHYAAVIECPVCGNKRA 103 (124)
T ss_pred Ee-eCc--CcccccccchhccccCCcCcCCCCCCC
Confidence 49 999 444321 22 67999996554
No 41
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=53.83 E-value=4.5 Score=33.75 Aligned_cols=27 Identities=30% Similarity=0.534 Sum_probs=19.5
Q ss_pred HHHhcCCCccccCCCCccccCCCC---CCCCCCc
Q 026747 163 MCLQCGIPKTFSNTRGMVCPVCSD---RPPADIS 193 (234)
Q Consensus 163 MclqcgiPKt~s~argmvcPvcgd---Rp~~~~~ 193 (234)
.|--||. .+.|-..||.||- |+.|...
T Consensus 311 ~C~~cg~----~~~r~~~C~~cg~~~~rD~naa~ 340 (364)
T COG0675 311 TCPCCGH----LSGRLFKCPRCGFVHDRDVNAAL 340 (364)
T ss_pred cccccCC----ccceeEECCCCCCeehhhHHHHH
Confidence 4777887 5566788999985 7777433
No 42
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=53.52 E-value=5.2 Score=34.41 Aligned_cols=23 Identities=39% Similarity=1.083 Sum_probs=18.4
Q ss_pred HHhcCCC-----ccccCC--CCccccCCCC
Q 026747 164 CLQCGIP-----KTFSNT--RGMVCPVCSD 186 (234)
Q Consensus 164 clqcgiP-----Kt~s~a--rgmvcPvcgd 186 (234)
|+.||.| +.|+++ |=+.||.||.
T Consensus 3 CIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~ 32 (208)
T PF04161_consen 3 CIECGHPVKSLYRQYSPGNIRLTKCPNCGK 32 (208)
T ss_pred eccCCCcchhhhhccCCCcEEEeeccccCC
Confidence 9999999 467665 4689999993
No 43
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=53.38 E-value=8.4 Score=30.74 Aligned_cols=27 Identities=22% Similarity=0.512 Sum_probs=18.3
Q ss_pred HHHHHhcCCCccccCC-CC-ccccCCCCCCC
Q 026747 161 LRMCLQCGIPKTFSNT-RG-MVCPVCSDRPP 189 (234)
Q Consensus 161 LrMclqcgiPKt~s~a-rg-mvcPvcgdRp~ 189 (234)
+--|.+|| ++|.-. .. ..||.||-+..
T Consensus 71 ~~~C~~Cg--~~~~~~~~~~~~CP~Cgs~~~ 99 (117)
T PRK00564 71 ELECKDCS--HVFKPNALDYGVCEKCHSKNV 99 (117)
T ss_pred EEEhhhCC--CccccCCccCCcCcCCCCCce
Confidence 34599999 555553 23 35999997654
No 44
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=53.27 E-value=5 Score=29.05 Aligned_cols=21 Identities=48% Similarity=0.972 Sum_probs=17.5
Q ss_pred HHHHHhcCCCccccCCCCccccCCC
Q 026747 161 LRMCLQCGIPKTFSNTRGMVCPVCS 185 (234)
Q Consensus 161 LrMclqcgiPKt~s~argmvcPvcg 185 (234)
|-.|-+||-++.. -.|||.||
T Consensus 27 l~~C~~CG~~~~~----H~vC~~CG 47 (57)
T PRK12286 27 LVECPNCGEPKLP----HRVCPSCG 47 (57)
T ss_pred ceECCCCCCccCC----eEECCCCC
Confidence 4569999998875 68999999
No 45
>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=52.51 E-value=5.6 Score=25.37 Aligned_cols=22 Identities=36% Similarity=0.966 Sum_probs=14.6
Q ss_pred HHhcCCCccccCC-CCccccCCCCC
Q 026747 164 CLQCGIPKTFSNT-RGMVCPVCSDR 187 (234)
Q Consensus 164 clqcgiPKt~s~a-rgmvcPvcgdR 187 (234)
|..||- +|... ..-+||+||..
T Consensus 4 C~~CGy--~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 4 CPVCGY--IYDGEEAPWVCPVCGAP 26 (33)
T ss_pred CCCCCC--EECCCcCCCcCcCCCCc
Confidence 667773 44443 46799999874
No 46
>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=52.43 E-value=6.7 Score=37.42 Aligned_cols=34 Identities=24% Similarity=0.504 Sum_probs=25.3
Q ss_pred ChhhHHHHHHHHHhcCCCccccCCC--CccccCCCCC
Q 026747 153 NAEDAAELLRMCLQCGIPKTFSNTR--GMVCPVCSDR 187 (234)
Q Consensus 153 ~aedaadlLrMclqcgiPKt~s~ar--gmvcPvcgdR 187 (234)
.||.+-==+--|..|+++-+-..+. ++.|| ||-+
T Consensus 232 ~P~~GKYh~~~c~~C~~~~~~~~~~~~~~~Cp-CG~~ 267 (374)
T TIGR00375 232 DPLLGKYHQTACEACGEPAVSEDAETACANCP-CGGR 267 (374)
T ss_pred CcCCCccchhhhcccCCcCCchhhhhcCCCCC-CCCc
Confidence 3444444466799999998876655 78899 9976
No 47
>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=52.14 E-value=5 Score=26.10 Aligned_cols=23 Identities=26% Similarity=0.775 Sum_probs=14.5
Q ss_pred HHHhcCCCccccCC-CCccccCCCCC
Q 026747 163 MCLQCGIPKTFSNT-RGMVCPVCSDR 187 (234)
Q Consensus 163 MclqcgiPKt~s~a-rgmvcPvcgdR 187 (234)
+|.-||. +|.+. .--+||+||..
T Consensus 4 ~C~~CG~--i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 4 VCPVCGY--IHEGEEAPEKCPICGAP 27 (34)
T ss_pred ECCCCCC--EeECCcCCCcCcCCCCc
Confidence 3677883 33333 24699999974
No 48
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=52.02 E-value=6.1 Score=33.40 Aligned_cols=28 Identities=29% Similarity=0.393 Sum_probs=21.9
Q ss_pred HHHHhcCCCccccCCCCccccCCCCCCC
Q 026747 162 RMCLQCGIPKTFSNTRGMVCPVCSDRPP 189 (234)
Q Consensus 162 rMclqcgiPKt~s~argmvcPvcgdRp~ 189 (234)
|.|..||.=-.=++-+-.|||-||.-=+
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~~ 37 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQFP 37 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCccC
Confidence 6799999755556667999999998644
No 49
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=50.51 E-value=7.5 Score=30.63 Aligned_cols=25 Identities=44% Similarity=0.913 Sum_probs=20.3
Q ss_pred HHHhcCCCccccCCCCccccCCCCC
Q 026747 163 MCLQCGIPKTFSNTRGMVCPVCSDR 187 (234)
Q Consensus 163 MclqcgiPKt~s~argmvcPvcgdR 187 (234)
.|+.|+-|-+|...+|.+|..|..+
T Consensus 56 ~C~~C~~~fg~l~~~~~~C~~C~~~ 80 (118)
T PF02318_consen 56 HCARCGKPFGFLFNRGRVCVDCKHR 80 (118)
T ss_dssp B-TTTS-BCSCTSTTCEEETTTTEE
T ss_pred chhhhCCcccccCCCCCcCCcCCcc
Confidence 5999999999999999999998754
No 50
>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=49.58 E-value=0.63 Score=35.48 Aligned_cols=24 Identities=46% Similarity=0.894 Sum_probs=16.9
Q ss_pred HHHHHhcCCCccccCCCCccccCC
Q 026747 161 LRMCLQCGIPKTFSNTRGMVCPVC 184 (234)
Q Consensus 161 LrMclqcgiPKt~s~argmvcPvc 184 (234)
||.|+.|++=+|+..=+--+||.|
T Consensus 1 lrAC~~C~~i~t~~qF~~~gCpnC 24 (77)
T PF06093_consen 1 LRACLRCRLIKTEDQFRDEGCPNC 24 (77)
T ss_dssp EEEETTT-BEECCCHHHHH--TTT
T ss_pred CcccccCCcccCHhHccCCCCCCC
Confidence 577999999999876444689999
No 51
>PF05924 SAMP: SAMP Motif; InterPro: IPR009224 This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). This motif binds axin [].; GO: 0008013 beta-catenin binding, 0016055 Wnt receptor signaling pathway; PDB: 1EMU_B 2RQU_B.
Probab=49.46 E-value=13 Score=22.71 Aligned_cols=16 Identities=31% Similarity=0.698 Sum_probs=10.8
Q ss_pred HHHHHHHhcCCCcccc
Q 026747 159 ELLRMCLQCGIPKTFS 174 (234)
Q Consensus 159 dlLrMclqcgiPKt~s 174 (234)
|||+-|++-.+||-.+
T Consensus 4 eiL~~CI~sAmPk~~~ 19 (20)
T PF05924_consen 4 EILQECIGSAMPKRRR 19 (20)
T ss_dssp HHHHHHHHCTS-----
T ss_pred HHHHHHHHHhcccccC
Confidence 9999999999998654
No 52
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=49.41 E-value=9.4 Score=27.46 Aligned_cols=26 Identities=38% Similarity=0.850 Sum_probs=20.3
Q ss_pred HHhcCCCcc-ccCCCCccccCCCCCCC
Q 026747 164 CLQCGIPKT-FSNTRGMVCPVCSDRPP 189 (234)
Q Consensus 164 clqcgiPKt-~s~argmvcPvcgdRp~ 189 (234)
|.-||-.-. -+..+|-.||-||-|=.
T Consensus 9 C~~Cg~~~~~~~~~~~irCp~Cg~rIl 35 (49)
T COG1996 9 CARCGREVELDQETRGIRCPYCGSRIL 35 (49)
T ss_pred hhhcCCeeehhhccCceeCCCCCcEEE
Confidence 889997765 44667999999997643
No 53
>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=47.31 E-value=8 Score=24.41 Aligned_cols=23 Identities=26% Similarity=0.639 Sum_probs=15.4
Q ss_pred HHhcCCCccccC----CCCccccCCCC
Q 026747 164 CLQCGIPKTFSN----TRGMVCPVCSD 186 (234)
Q Consensus 164 clqcgiPKt~s~----argmvcPvcgd 186 (234)
|..||..-+... ..--+||.||.
T Consensus 8 C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 8 CEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred cCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 778887443222 44678999997
No 54
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=47.22 E-value=8 Score=39.13 Aligned_cols=32 Identities=25% Similarity=0.562 Sum_probs=23.3
Q ss_pred CCCChhhHHHHHHH------------------HHhcCCCccccCCCCccccCCC
Q 026747 150 TNPNAEDAAELLRM------------------CLQCGIPKTFSNTRGMVCPVCS 185 (234)
Q Consensus 150 ~np~aedaadlLrM------------------clqcgiPKt~s~argmvcPvcg 185 (234)
..|+++-..+|+++ |..||. ..+.+-.||.||
T Consensus 597 ~~~n~~a~~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~----~~g~~~~CP~CG 646 (656)
T PRK08270 597 AISDAEACKKLVKKALENYRLPYITITPTFSICPKHGY----LSGEHEFCPKCG 646 (656)
T ss_pred CCCCHHHHHHHHHHHHHhCCCceEEeCCCCcccCCCCC----cCCCCCCCcCCc
Confidence 34678888899885 345663 346678999999
No 55
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=46.97 E-value=16 Score=27.17 Aligned_cols=23 Identities=35% Similarity=0.764 Sum_probs=17.2
Q ss_pred HHHHhcCCCccccCCCCccccCCCCCCC
Q 026747 162 RMCLQCGIPKTFSNTRGMVCPVCSDRPP 189 (234)
Q Consensus 162 rMclqcgiPKt~s~argmvcPvcgdRp~ 189 (234)
+.|..|..=.+ +-+||+||....
T Consensus 4 kAC~~C~~i~~-----~~~CP~Cgs~~~ 26 (61)
T PRK08351 4 KACRHCHYITT-----EDRCPVCGSRDL 26 (61)
T ss_pred hhhhhCCcccC-----CCcCCCCcCCcc
Confidence 47899987653 237999999884
No 56
>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=45.97 E-value=9.4 Score=25.00 Aligned_cols=24 Identities=29% Similarity=0.787 Sum_probs=18.5
Q ss_pred HHhcCCCccccCCCCccccCCCCC
Q 026747 164 CLQCGIPKTFSNTRGMVCPVCSDR 187 (234)
Q Consensus 164 clqcgiPKt~s~argmvcPvcgdR 187 (234)
|..||..-........-||.||-|
T Consensus 3 C~~Cg~~~~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 3 CGECGAEVELKPGDPIRCPECGHR 26 (32)
T ss_dssp ESSSSSSE-BSTSSTSSBSSSS-S
T ss_pred CCcCCCeeEcCCCCcEECCcCCCe
Confidence 678998888777778899999977
No 57
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=45.43 E-value=7.1 Score=25.84 Aligned_cols=23 Identities=43% Similarity=1.086 Sum_probs=13.7
Q ss_pred HHhcCCCcc-ccCCCC-ccccCCCC
Q 026747 164 CLQCGIPKT-FSNTRG-MVCPVCSD 186 (234)
Q Consensus 164 clqcgiPKt-~s~arg-mvcPvcgd 186 (234)
|-.||...+ +-.++| +||+.||-
T Consensus 3 Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 3 CPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp BTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CcCCcCCceEEcCCCCeEECCCCCC
Confidence 556777663 333443 58888884
No 58
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=45.40 E-value=8 Score=36.62 Aligned_cols=14 Identities=36% Similarity=0.935 Sum_probs=10.8
Q ss_pred CCccccCCCCCCCC
Q 026747 177 RGMVCPVCSDRPPA 190 (234)
Q Consensus 177 rgmvcPvcgdRp~~ 190 (234)
|-||||+||.---+
T Consensus 267 R~YVCPiCGATgDn 280 (318)
T KOG4602|consen 267 RSYVCPICGATGDN 280 (318)
T ss_pred hhhcCccccccCCc
Confidence 56899999976444
No 59
>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=45.31 E-value=9.8 Score=37.69 Aligned_cols=21 Identities=29% Similarity=0.860 Sum_probs=0.0
Q ss_pred HHhcCCCccccCCCC-ccccCCCCCC
Q 026747 164 CLQCGIPKTFSNTRG-MVCPVCSDRP 188 (234)
Q Consensus 164 clqcgiPKt~s~arg-mvcPvcgdRp 188 (234)
|..|| |.+... .+||+||.+.
T Consensus 527 C~~CG----~~g~~~~~~CP~Cgs~~ 548 (579)
T TIGR02487 527 CEDCG----YTGEGLNDKCPKCGSHD 548 (579)
T ss_pred CCCCC----CCCCCCCCcCcCCCCcc
No 60
>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=44.25 E-value=11 Score=37.17 Aligned_cols=21 Identities=33% Similarity=1.055 Sum_probs=0.0
Q ss_pred HHhcCCCccccC-CCCccccCCCCCC
Q 026747 164 CLQCGIPKTFSN-TRGMVCPVCSDRP 188 (234)
Q Consensus 164 clqcgiPKt~s~-argmvcPvcgdRp 188 (234)
|..|| |.. .-+-+||+||-++
T Consensus 521 C~~CG----~~~~~~~~~CP~CGs~~ 542 (555)
T cd01675 521 CNDCG----YIGEGEGFKCPKCGSED 542 (555)
T ss_pred CCCCC----CCCcCCCCCCcCCCCcC
No 61
>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=43.16 E-value=8 Score=25.95 Aligned_cols=26 Identities=23% Similarity=0.529 Sum_probs=15.0
Q ss_pred HHhcCCCcccc---C-CCCccccCCCCCCC
Q 026747 164 CLQCGIPKTFS---N-TRGMVCPVCSDRPP 189 (234)
Q Consensus 164 clqcgiPKt~s---~-argmvcPvcgdRp~ 189 (234)
|..||.--... + ..-..||.||....
T Consensus 8 C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~ 37 (52)
T TIGR02605 8 CTACGHRFEVLQKMSDDPLATCPECGGEKL 37 (52)
T ss_pred eCCCCCEeEEEEecCCCCCCCCCCCCCCce
Confidence 77788522111 1 22457999998544
No 62
>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=42.37 E-value=4.7 Score=31.75 Aligned_cols=25 Identities=24% Similarity=0.589 Sum_probs=16.9
Q ss_pred HHHhcCCCccccCCCCccccCCCCCC
Q 026747 163 MCLQCGIPKTFSNTRGMVCPVCSDRP 188 (234)
Q Consensus 163 MclqcgiPKt~s~argmvcPvcgdRp 188 (234)
-|..||---+..... ..||.||-..
T Consensus 72 ~C~~Cg~~~~~~~~~-~~CP~Cgs~~ 96 (113)
T PF01155_consen 72 RCRDCGHEFEPDEFD-FSCPRCGSPD 96 (113)
T ss_dssp EETTTS-EEECHHCC-HH-SSSSSS-
T ss_pred ECCCCCCEEecCCCC-CCCcCCcCCC
Confidence 499999766555555 8899999764
No 63
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=42.21 E-value=11 Score=38.75 Aligned_cols=37 Identities=16% Similarity=0.284 Sum_probs=23.4
Q ss_pred CCCChhhHHHHHHHHHhcCCCcc-------------ccCCCCccccCCCC
Q 026747 150 TNPNAEDAAELLRMCLQCGIPKT-------------FSNTRGMVCPVCSD 186 (234)
Q Consensus 150 ~np~aedaadlLrMclqcgiPKt-------------~s~argmvcPvcgd 186 (234)
..++++-..+|++.+..-|||=- |.....-+||.||-
T Consensus 652 ~~~n~eal~~lvk~~~~~~i~Y~sin~~~~~C~~CG~~~~~~~~CP~CG~ 701 (735)
T PRK07111 652 PSKNVEAFEIIVKAMKNTNIGYGSINHPVDRCPVCGYLGVIEDKCPKCGS 701 (735)
T ss_pred cCCCHHHHHHHHHHHHhCCCceEEeCCCCeecCCCCCCCCcCccCcCCCC
Confidence 34688888888887655444431 33333468888885
No 64
>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=41.90 E-value=8.6 Score=34.20 Aligned_cols=13 Identities=38% Similarity=0.846 Sum_probs=6.8
Q ss_pred CccccCCCCCCCC
Q 026747 178 GMVCPVCSDRPPA 190 (234)
Q Consensus 178 gmvcPvcgdRp~~ 190 (234)
..+|||||..|.-
T Consensus 172 ~g~CPvCGs~P~~ 184 (290)
T PF04216_consen 172 RGYCPVCGSPPVL 184 (290)
T ss_dssp -SS-TTT---EEE
T ss_pred CCcCCCCCCcCce
Confidence 3699999999975
No 65
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=41.90 E-value=14 Score=28.57 Aligned_cols=33 Identities=27% Similarity=0.497 Sum_probs=22.2
Q ss_pred hhHHHHHHHHHhcCCCcccc--CCCCccccCCCCC
Q 026747 155 EDAAELLRMCLQCGIPKTFS--NTRGMVCPVCSDR 187 (234)
Q Consensus 155 edaadlLrMclqcgiPKt~s--~argmvcPvcgdR 187 (234)
.|+...++||.+=+||---. |-.+.+||.||.+
T Consensus 40 ~dv~r~~~~~~~~~vpilGvVENMs~~~Cp~Cg~~ 74 (81)
T PF10609_consen 40 ADVRRAIDMFRKLNVPILGVVENMSYFVCPHCGER 74 (81)
T ss_dssp HHHHHHHHHHHCTT-EEEEEEECT-EEE-TTT--E
T ss_pred HHHHHHHHHHHhcCCCcEEEEECCCccCCCCCCCe
Confidence 57777889999999997654 3448899999964
No 66
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=41.38 E-value=9.9 Score=31.39 Aligned_cols=27 Identities=22% Similarity=0.595 Sum_probs=23.4
Q ss_pred HHHhcCCCccccCCCCccccCCCCCCC
Q 026747 163 MCLQCGIPKTFSNTRGMVCPVCSDRPP 189 (234)
Q Consensus 163 MclqcgiPKt~s~argmvcPvcgdRp~ 189 (234)
-|-+|+---||....-+|||-|+--=.
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~EW~ 30 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYEWN 30 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccccc
Confidence 388999999999999999999986433
No 67
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=40.72 E-value=7.5 Score=27.56 Aligned_cols=19 Identities=47% Similarity=1.050 Sum_probs=13.8
Q ss_pred HHHhcCCCccccCCCCccccCCC
Q 026747 163 MCLQCGIPKTFSNTRGMVCPVCS 185 (234)
Q Consensus 163 MclqcgiPKt~s~argmvcPvcg 185 (234)
-|-+||-++.. ..|||.||
T Consensus 28 ~c~~cg~~~~~----H~vc~~cG 46 (56)
T PF01783_consen 28 KCPNCGEPKLP----HRVCPSCG 46 (56)
T ss_dssp ESSSSSSEEST----TSBCTTTB
T ss_pred eeccCCCEecc----cEeeCCCC
Confidence 37778865543 58999997
No 68
>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form
Probab=40.60 E-value=11 Score=29.61 Aligned_cols=13 Identities=38% Similarity=1.137 Sum_probs=10.9
Q ss_pred ccccCCCCCCCCC
Q 026747 179 MVCPVCSDRPPAD 191 (234)
Q Consensus 179 mvcPvcgdRp~~~ 191 (234)
.-||.||.|+..+
T Consensus 2 I~CP~CG~R~~~E 14 (84)
T TIGR01374 2 IPCPYCGPRPEEE 14 (84)
T ss_pred ccCCCCCCccHhh
Confidence 4699999998876
No 69
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=40.55 E-value=7.2 Score=38.31 Aligned_cols=33 Identities=33% Similarity=0.851 Sum_probs=17.2
Q ss_pred CCChhhHHHHHHHHHh------------------cCCCccccCCCCccccCCCCC
Q 026747 151 NPNAEDAAELLRMCLQ------------------CGIPKTFSNTRGMVCPVCSDR 187 (234)
Q Consensus 151 np~aedaadlLrMclq------------------cgiPKt~s~argmvcPvcgdR 187 (234)
.|+++...+|++.+.. || |....+-.||.||-.
T Consensus 463 ~~n~~al~~lv~~~~~~~~i~Y~~in~~~~~C~~CG----~~~~~~~~CP~CGs~ 513 (546)
T PF13597_consen 463 KPNPEALEKLVRYAMENTGIPYFTINPPIDICPDCG----YIGGEGDKCPKCGSE 513 (546)
T ss_dssp -T-HHHHHHHHHHHHH--H-SEEEEE--EEEETTT-------S--EEE-CCC---
T ss_pred CCCHHHHHHHHHHHHHhCCCCeEEEecCcccccCCC----cCCCCCCCCCCCCCc
Confidence 4578888888887554 66 344448899999976
No 70
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=40.11 E-value=15 Score=37.27 Aligned_cols=23 Identities=39% Similarity=0.990 Sum_probs=16.2
Q ss_pred HHHHhcCCCccccCCCCccccCCCCCCC
Q 026747 162 RMCLQCGIPKTFSNTRGMVCPVCSDRPP 189 (234)
Q Consensus 162 rMclqcgiPKt~s~argmvcPvcgdRp~ 189 (234)
++|-+||.+-+. ..||.||..-+
T Consensus 16 kFC~~CG~~l~~-----~~Cp~CG~~~~ 38 (645)
T PRK14559 16 RFCQKCGTSLTH-----KPCPQCGTEVP 38 (645)
T ss_pred ccccccCCCCCC-----CcCCCCCCCCC
Confidence 688889888652 46777777633
No 71
>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=39.06 E-value=13 Score=26.28 Aligned_cols=8 Identities=63% Similarity=1.518 Sum_probs=6.6
Q ss_pred ccccCCCC
Q 026747 179 MVCPVCSD 186 (234)
Q Consensus 179 mvcPvcgd 186 (234)
-+||+||.
T Consensus 35 w~CP~C~a 42 (50)
T cd00730 35 WVCPVCGA 42 (50)
T ss_pred CCCCCCCC
Confidence 48999986
No 72
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=38.34 E-value=7.7 Score=37.19 Aligned_cols=26 Identities=42% Similarity=1.053 Sum_probs=19.4
Q ss_pred HHHHHhcCCCcc--ccCCCCccccCCCC
Q 026747 161 LRMCLQCGIPKT--FSNTRGMVCPVCSD 186 (234)
Q Consensus 161 LrMclqcgiPKt--~s~argmvcPvcgd 186 (234)
|..|+.||.-+| |-++.--+||.||-
T Consensus 315 ~nfc~ncG~~~t~~~~ng~a~fcp~cgq 342 (345)
T COG4260 315 LNFCLNCGCGTTADFDNGKAKFCPECGQ 342 (345)
T ss_pred cccccccCcccccCCccchhhhChhhcC
Confidence 447999996555 45666789999985
No 73
>PRK14873 primosome assembly protein PriA; Provisional
Probab=38.20 E-value=10 Score=38.33 Aligned_cols=26 Identities=19% Similarity=0.460 Sum_probs=20.0
Q ss_pred HHHhcCCCccccCCC-CccccCCCCCC
Q 026747 163 MCLQCGIPKTFSNTR-GMVCPVCSDRP 188 (234)
Q Consensus 163 MclqcgiPKt~s~ar-gmvcPvcgdRp 188 (234)
+|-.|++|-||.... -+.|.-||..-
T Consensus 394 ~C~~C~~~L~~h~~~~~l~Ch~CG~~~ 420 (665)
T PRK14873 394 RCRHCTGPLGLPSAGGTPRCRWCGRAA 420 (665)
T ss_pred ECCCCCCceeEecCCCeeECCCCcCCC
Confidence 588889999996543 57899998754
No 74
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=37.60 E-value=13 Score=27.84 Aligned_cols=27 Identities=33% Similarity=0.859 Sum_probs=19.1
Q ss_pred HHHHHHhcCCCccccCCCCccccCCCCCCCCC
Q 026747 160 LLRMCLQCGIPKTFSNTRGMVCPVCSDRPPAD 191 (234)
Q Consensus 160 lLrMclqcgiPKt~s~argmvcPvcgdRp~~~ 191 (234)
++|-|-.||+ |.-. -.||+||-.....
T Consensus 4 ~~rkC~~cg~---YTLk--e~Cp~CG~~t~~~ 30 (59)
T COG2260 4 LIRKCPKCGR---YTLK--EKCPVCGGDTKVP 30 (59)
T ss_pred hhhcCcCCCc---eeec--ccCCCCCCccccC
Confidence 6788999987 2221 5799999876543
No 75
>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=37.08 E-value=13 Score=36.09 Aligned_cols=27 Identities=22% Similarity=0.709 Sum_probs=19.2
Q ss_pred HHHhcCCCccccCCC-CccccCCCCCCC
Q 026747 163 MCLQCGIPKTFSNTR-GMVCPVCSDRPP 189 (234)
Q Consensus 163 MclqcgiPKt~s~ar-gmvcPvcgdRp~ 189 (234)
+|-.|++|-||.... .+.|..||..-+
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcCcCC
Confidence 378899999996544 566777776643
No 76
>PRK10220 hypothetical protein; Provisional
Probab=36.61 E-value=13 Score=30.81 Aligned_cols=25 Identities=24% Similarity=0.752 Sum_probs=22.6
Q ss_pred HHHhcCCCccccCCCCccccCCCCC
Q 026747 163 MCLQCGIPKTFSNTRGMVCPVCSDR 187 (234)
Q Consensus 163 MclqcgiPKt~s~argmvcPvcgdR 187 (234)
-|-||+---||-..--+|||-|+--
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hE 29 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHE 29 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCc
Confidence 3899999999999999999999854
No 77
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.34 E-value=16 Score=29.32 Aligned_cols=9 Identities=33% Similarity=1.195 Sum_probs=6.9
Q ss_pred CccccCCCC
Q 026747 178 GMVCPVCSD 186 (234)
Q Consensus 178 gmvcPvcgd 186 (234)
+|+||+||-
T Consensus 1 ~llCP~C~v 9 (88)
T COG3809 1 MLLCPICGV 9 (88)
T ss_pred CcccCcCCc
Confidence 478888875
No 78
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=36.23 E-value=15 Score=34.34 Aligned_cols=13 Identities=38% Similarity=0.979 Sum_probs=11.3
Q ss_pred CccccCCCCCCCC
Q 026747 178 GMVCPVCSDRPPA 190 (234)
Q Consensus 178 gmvcPvcgdRp~~ 190 (234)
--+|||||-.|+-
T Consensus 187 ~~~CPvCGs~P~~ 199 (309)
T PRK03564 187 RQFCPVCGSMPVS 199 (309)
T ss_pred CCCCCCCCCcchh
Confidence 4799999999985
No 79
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=35.91 E-value=26 Score=34.39 Aligned_cols=46 Identities=26% Similarity=0.430 Sum_probs=34.6
Q ss_pred cccccccCCCChhhHHHHHHH----------HHhcCCCccccCCC-----CccccCCCCCCCCC
Q 026747 143 VKRVATATNPNAEDAAELLRM----------CLQCGIPKTFSNTR-----GMVCPVCSDRPPAD 191 (234)
Q Consensus 143 ~kR~~~a~np~aedaadlLrM----------clqcgiPKt~s~ar-----gmvcPvcgdRp~~~ 191 (234)
..|-+ -+|+-|+..|--| |--|+-|-|...-. ++-|-.||-|-.-+
T Consensus 71 n~ryi---VNG~Hd~~KLqdlLdgFIkKFVlC~~C~NPETel~itk~q~i~~~CkACG~r~~~d 131 (400)
T KOG2767|consen 71 NGRYI---VNGAHEASKLQDLLDGFIKKFVLCPSCENPETELIITKKQTISLKCKACGFRSDMD 131 (400)
T ss_pred CCeee---ecccccHHHHHHHHHHHHHHheeCcCCCCCceeEEecccchhhhHHHHcCCccccc
Confidence 44555 5777787766544 88999999987665 47899999887655
No 80
>PRK05580 primosome assembly protein PriA; Validated
Probab=35.56 E-value=13 Score=37.30 Aligned_cols=25 Identities=24% Similarity=0.608 Sum_probs=17.4
Q ss_pred HHHhcCCCccccC-CCCccccCCCCC
Q 026747 163 MCLQCGIPKTFSN-TRGMVCPVCSDR 187 (234)
Q Consensus 163 MclqcgiPKt~s~-argmvcPvcgdR 187 (234)
+|-.|++|-||.. .+.+.|..||-.
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQ 417 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCC
Confidence 5777889999864 335666666665
No 81
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=35.39 E-value=29 Score=26.22 Aligned_cols=24 Identities=29% Similarity=0.623 Sum_probs=17.9
Q ss_pred HHHHHhcCCCccccCCCCccccCCCCCCC
Q 026747 161 LRMCLQCGIPKTFSNTRGMVCPVCSDRPP 189 (234)
Q Consensus 161 LrMclqcgiPKt~s~argmvcPvcgdRp~ 189 (234)
++.|..|..=.+ +-+||+||....
T Consensus 5 ~~AC~~C~~i~~-----~~~Cp~Cgs~~~ 28 (64)
T PRK06393 5 YRACKKCKRLTP-----EKTCPVHGDEKT 28 (64)
T ss_pred hhhHhhCCcccC-----CCcCCCCCCCcC
Confidence 567999986552 349999999873
No 82
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=35.37 E-value=16 Score=34.14 Aligned_cols=12 Identities=42% Similarity=1.113 Sum_probs=10.5
Q ss_pred ccccCCCCCCCC
Q 026747 179 MVCPVCSDRPPA 190 (234)
Q Consensus 179 mvcPvcgdRp~~ 190 (234)
.+|||||-.|+-
T Consensus 185 ~~CPvCGs~P~~ 196 (305)
T TIGR01562 185 TLCPACGSPPVA 196 (305)
T ss_pred CcCCCCCChhhh
Confidence 589999999974
No 83
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=35.35 E-value=16 Score=37.16 Aligned_cols=18 Identities=33% Similarity=1.023 Sum_probs=0.0
Q ss_pred HHhcCCCcccc-CCCCccccCCC
Q 026747 164 CLQCGIPKTFS-NTRGMVCPVCS 185 (234)
Q Consensus 164 clqcgiPKt~s-~argmvcPvcg 185 (234)
|..|| |. ...+-.||.||
T Consensus 569 C~~CG----~~~~g~~~~CP~CG 587 (623)
T PRK08271 569 CNDCH----HIDKRTGKRCPICG 587 (623)
T ss_pred CCCCC----CcCCCCCcCCcCCC
No 84
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=35.11 E-value=19 Score=36.93 Aligned_cols=22 Identities=36% Similarity=1.194 Sum_probs=0.0
Q ss_pred HHhcCCCccc-cCCCCccccCCC
Q 026747 164 CLQCGIPKTF-SNTRGMVCPVCS 185 (234)
Q Consensus 164 clqcgiPKt~-s~argmvcPvcg 185 (234)
|..||.---. ...+|-.||.||
T Consensus 644 C~~CG~~Ge~~~~~~~~~CP~CG 666 (711)
T PRK09263 644 CYECGFTGEFECTEKGFTCPKCG 666 (711)
T ss_pred cCCCCCCccccCCCCCCcCcCCC
No 85
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=35.05 E-value=18 Score=24.28 Aligned_cols=11 Identities=45% Similarity=1.229 Sum_probs=9.1
Q ss_pred CCccccCCCCC
Q 026747 177 RGMVCPVCSDR 187 (234)
Q Consensus 177 rgmvcPvcgdR 187 (234)
.|.|||-||-.
T Consensus 17 ~g~~CP~Cg~~ 27 (46)
T PF12760_consen 17 DGFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCCe
Confidence 37999999965
No 86
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=34.98 E-value=13 Score=27.12 Aligned_cols=21 Identities=19% Similarity=-0.012 Sum_probs=16.4
Q ss_pred HHHHHhcCCCccccCCCCccccCCCC
Q 026747 161 LRMCLQCGIPKTFSNTRGMVCPVCSD 186 (234)
Q Consensus 161 LrMclqcgiPKt~s~argmvcPvcgd 186 (234)
|-.|-+||.++.. ..||| ||-
T Consensus 27 ~~~c~~cg~~~~p----H~vc~-cG~ 47 (60)
T PRK01110 27 LSVDKTTGEYHLP----HHVSP-KGY 47 (60)
T ss_pred eeEcCCCCceecc----ceecC-Ccc
Confidence 4569999988765 46799 994
No 87
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=34.82 E-value=19 Score=36.45 Aligned_cols=35 Identities=20% Similarity=0.548 Sum_probs=22.6
Q ss_pred CCCChhhHHHHHHH-----------------HHhcCCCccccCCCCccccCCCCCC
Q 026747 150 TNPNAEDAAELLRM-----------------CLQCGIPKTFSNTRGMVCPVCSDRP 188 (234)
Q Consensus 150 ~np~aedaadlLrM-----------------clqcgiPKt~s~argmvcPvcgdRp 188 (234)
..++++-..+|.+. |..||. .+.-+-.||.||-++
T Consensus 531 ~~~n~~Al~~lvk~~~~~~i~Y~sin~~~~~C~~CGy----~g~~~~~CP~CG~~d 582 (618)
T PRK14704 531 AMHNKKALKQIVQAMAEHGVGYGSINHPVDRCKCCSY----HGVIGNECPSCGNED 582 (618)
T ss_pred cCCCHHHHHHHHHHHHhcCCceEEeCCCCeecCCCCC----CCCcCccCcCCCCCC
Confidence 34688888888776 445552 223345899999654
No 88
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.59 E-value=26 Score=33.24 Aligned_cols=15 Identities=40% Similarity=0.875 Sum_probs=9.9
Q ss_pred HHhcCCCccccCCCC
Q 026747 164 CLQCGIPKTFSNTRG 178 (234)
Q Consensus 164 clqcgiPKt~s~arg 178 (234)
|.-||.|-|--+--|
T Consensus 242 C~~Cg~~PtiP~~~~ 256 (298)
T KOG2879|consen 242 CPVCGEPPTIPHVIG 256 (298)
T ss_pred eeccCCCCCCCeeec
Confidence 777887777555444
No 89
>PRK06450 threonine synthase; Validated
Probab=34.40 E-value=16 Score=33.53 Aligned_cols=21 Identities=29% Similarity=0.847 Sum_probs=15.4
Q ss_pred HHhcCCCccccCCCCccccCCCC
Q 026747 164 CLQCGIPKTFSNTRGMVCPVCSD 186 (234)
Q Consensus 164 clqcgiPKt~s~argmvcPvcgd 186 (234)
|+.|| ++|....--.||.||-
T Consensus 6 C~~Cg--~~~~~~~~~~C~~cg~ 26 (338)
T PRK06450 6 CMKCG--KERESIYEIRCKKCGG 26 (338)
T ss_pred ECCcC--CcCCCcccccCCcCCC
Confidence 88999 5676543467999973
No 90
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=34.24 E-value=29 Score=29.35 Aligned_cols=23 Identities=43% Similarity=1.032 Sum_probs=17.4
Q ss_pred HHHhcCCCcc---ccCCC-CccccCCC
Q 026747 163 MCLQCGIPKT---FSNTR-GMVCPVCS 185 (234)
Q Consensus 163 MclqcgiPKt---~s~ar-gmvcPvcg 185 (234)
-|.-||-|.. |+-.. |.+|..|+
T Consensus 151 ~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 151 HCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hHhcCCCCCCceEEecccCCccccccc
Confidence 3999998744 54333 89999998
No 91
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=33.98 E-value=21 Score=36.52 Aligned_cols=14 Identities=36% Similarity=0.914 Sum_probs=11.7
Q ss_pred CCccccCCCCCCCCC
Q 026747 177 RGMVCPVCSDRPPAD 191 (234)
Q Consensus 177 rgmvcPvcgdRp~~~ 191 (234)
.|-.||||| +|...
T Consensus 456 ~~~~CPvCg-~~l~~ 469 (908)
T COG0419 456 AGEKCPVCG-QELPE 469 (908)
T ss_pred CCCCCCCCC-CCCCc
Confidence 578999999 88864
No 92
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=33.64 E-value=16 Score=25.60 Aligned_cols=9 Identities=56% Similarity=1.317 Sum_probs=5.6
Q ss_pred ccccCCCCC
Q 026747 179 MVCPVCSDR 187 (234)
Q Consensus 179 mvcPvcgdR 187 (234)
-+||+|+..
T Consensus 35 w~CP~C~a~ 43 (47)
T PF00301_consen 35 WVCPVCGAP 43 (47)
T ss_dssp -B-TTTSSB
T ss_pred CcCcCCCCc
Confidence 489999863
No 93
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=33.64 E-value=7.8 Score=28.31 Aligned_cols=25 Identities=32% Similarity=1.039 Sum_probs=17.9
Q ss_pred HHHHHhcCCCccccCCCCccccCCCCCCCC
Q 026747 161 LRMCLQCGIPKTFSNTRGMVCPVCSDRPPA 190 (234)
Q Consensus 161 LrMclqcgiPKt~s~argmvcPvcgdRp~~ 190 (234)
+|-|-+||+ |+- ..+||+||..-.+
T Consensus 5 mr~C~~Cgv---YTL--k~~CP~CG~~t~~ 29 (56)
T PRK13130 5 IRKCPKCGV---YTL--KEICPVCGGKTKN 29 (56)
T ss_pred ceECCCCCC---EEc--cccCcCCCCCCCC
Confidence 456788885 444 6899999976554
No 94
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=32.97 E-value=20 Score=35.44 Aligned_cols=16 Identities=38% Similarity=1.055 Sum_probs=12.0
Q ss_pred ccCCCCccccCCCCCC
Q 026747 173 FSNTRGMVCPVCSDRP 188 (234)
Q Consensus 173 ~s~argmvcPvcgdRp 188 (234)
|-+--|-.||||||+-
T Consensus 10 ydedl~ElCPVCGDkV 25 (475)
T KOG4218|consen 10 YDEDLGELCPVCGDKV 25 (475)
T ss_pred CccccccccccccCcc
Confidence 3444588899999974
No 95
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=32.72 E-value=18 Score=34.38 Aligned_cols=27 Identities=30% Similarity=0.598 Sum_probs=20.4
Q ss_pred HHhcCCCcc-----ccCCCCccccCCC----CCCCCC
Q 026747 164 CLQCGIPKT-----FSNTRGMVCPVCS----DRPPAD 191 (234)
Q Consensus 164 clqcgiPKt-----~s~argmvcPvcg----dRp~~~ 191 (234)
|+.|..+.. |+.+ -+||+.|| ||...+
T Consensus 3 c~~C~~~~~~~V~d~~~g-dtvC~~CGlVl~~r~Id~ 38 (308)
T KOG1597|consen 3 CPDCKRHPENLVEDHSAG-DTVCSECGLVLEDRIIDE 38 (308)
T ss_pred CCCCCCCCCCeeeeccCC-ceecccCCeeeccccccc
Confidence 889998876 4444 49999997 677664
No 96
>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=32.57 E-value=19 Score=36.29 Aligned_cols=19 Identities=32% Similarity=0.805 Sum_probs=0.0
Q ss_pred HHhcCCCccccCCCCccccCCC
Q 026747 164 CLQCGIPKTFSNTRGMVCPVCS 185 (234)
Q Consensus 164 clqcgiPKt~s~argmvcPvcg 185 (234)
|..||. ..+.-+-.||.||
T Consensus 535 C~~CGy---~~g~~~~~CP~CG 553 (586)
T TIGR02827 535 CNDCHH---IDKRTLHRCPVCG 553 (586)
T ss_pred cCCCCC---cCCCcCCcCcCCC
No 97
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=32.55 E-value=14 Score=27.96 Aligned_cols=24 Identities=38% Similarity=0.749 Sum_probs=19.0
Q ss_pred HHHhcCCCccccCCCCccccCCCCC
Q 026747 163 MCLQCGIPKTFSNTRGMVCPVCSDR 187 (234)
Q Consensus 163 MclqcgiPKt~s~argmvcPvcgdR 187 (234)
+|-.||-+-...+. .++|+.||-.
T Consensus 2 fC~~Cg~~l~~~~~-~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKNG-VYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccCCC-eEECcCCCCc
Confidence 58889988876554 5999999965
No 98
>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=32.22 E-value=17 Score=24.21 Aligned_cols=25 Identities=28% Similarity=0.796 Sum_probs=15.4
Q ss_pred HHhcCCC----ccccCCCCccccCCCCCC
Q 026747 164 CLQCGIP----KTFSNTRGMVCPVCSDRP 188 (234)
Q Consensus 164 clqcgiP----Kt~s~argmvcPvcgdRp 188 (234)
|..||.. -.++..-...||.||...
T Consensus 8 C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (42)
T PF09723_consen 8 CEECGHEFEVLQSISEDDPVPCPECGSTE 36 (42)
T ss_pred eCCCCCEEEEEEEcCCCCCCcCCCCCCCc
Confidence 5567722 223334578999999843
No 99
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=32.07 E-value=12 Score=30.16 Aligned_cols=44 Identities=30% Similarity=0.577 Sum_probs=32.5
Q ss_pred ccccccCCCChhhHHHHHH-------HHHhcCCCccccCC--C--CccccCCCCC
Q 026747 144 KRVATATNPNAEDAAELLR-------MCLQCGIPKTFSNT--R--GMVCPVCSDR 187 (234)
Q Consensus 144 kR~~~a~np~aedaadlLr-------MclqcgiPKt~s~a--r--gmvcPvcgdR 187 (234)
-|.+--..=.+.+-.++|+ +|-.||-|-|...- | -+.|-+||.+
T Consensus 56 ~rlii~G~~~~~~i~~~l~~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 110 (110)
T smart00653 56 GRLIVNGRFTPKKLQDLLRRYIKEYVLCPECGSPDTELIKENRLFFLKCEACGAR 110 (110)
T ss_pred CeEEEEEeeCHHHHHHHHHHHHHhcEECCCCCCCCcEEEEeCCeEEEEccccCCC
Confidence 3444344555778888886 49999999998875 3 5779999975
No 100
>PRK12860 transcriptional activator FlhC; Provisional
Probab=31.91 E-value=27 Score=30.94 Aligned_cols=22 Identities=27% Similarity=0.724 Sum_probs=16.4
Q ss_pred HHhcCCCcc---ccCCCCccccCCC
Q 026747 164 CLQCGIPKT---FSNTRGMVCPVCS 185 (234)
Q Consensus 164 clqcgiPKt---~s~argmvcPvcg 185 (234)
|-.||-.=. +-...+.+||.|.
T Consensus 137 C~~Cgg~fv~~~~e~~~~f~CplC~ 161 (189)
T PRK12860 137 CCRCGGKFVTHAHDLRHNFVCGLCQ 161 (189)
T ss_pred CCCCCCCeeccccccCCCCcCCCCC
Confidence 899998743 3223489999999
No 101
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=31.88 E-value=20 Score=36.25 Aligned_cols=19 Identities=32% Similarity=0.782 Sum_probs=0.0
Q ss_pred HHhcCCCccccCCCCccccCCC
Q 026747 164 CLQCGIPKTFSNTRGMVCPVCS 185 (234)
Q Consensus 164 clqcgiPKt~s~argmvcPvcg 185 (234)
|..||. ++ .+-+-+||+||
T Consensus 571 C~~CG~--~~-~g~~~~CP~CG 589 (625)
T PRK08579 571 CNKCGR--ST-TGLYTRCPRCG 589 (625)
T ss_pred CCCCCC--cc-CCCCCcCcCCC
No 102
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=31.20 E-value=10 Score=31.47 Aligned_cols=29 Identities=24% Similarity=0.648 Sum_probs=24.8
Q ss_pred HHHHHhcCCCccccCCCCccccCCCCCCC
Q 026747 161 LRMCLQCGIPKTFSNTRGMVCPVCSDRPP 189 (234)
Q Consensus 161 LrMclqcgiPKt~s~argmvcPvcgdRp~ 189 (234)
|-||-+|.---||-.+-.|+||-|+--=.
T Consensus 3 lp~cp~c~sEytYed~~~~~cpec~~ew~ 31 (112)
T COG2824 3 LPPCPKCNSEYTYEDGGQLICPECAHEWN 31 (112)
T ss_pred CCCCCccCCceEEecCceEeCchhccccc
Confidence 45799999999999999999999986543
No 103
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=30.79 E-value=22 Score=34.28 Aligned_cols=23 Identities=30% Similarity=0.829 Sum_probs=18.1
Q ss_pred HHHhcCCCccccCCCC------------------ccccCCCCC
Q 026747 163 MCLQCGIPKTFSNTRG------------------MVCPVCSDR 187 (234)
Q Consensus 163 MclqcgiPKt~s~arg------------------mvcPvcgdR 187 (234)
+|.-|| -.|..+.| -+||+||..
T Consensus 427 ~c~~c~--~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 427 QCSVCQ--WIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred EECCCC--eEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 599999 56777665 599999975
No 104
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=30.50 E-value=17 Score=29.90 Aligned_cols=24 Identities=29% Similarity=0.732 Sum_probs=17.4
Q ss_pred HHHHhcCCCccccCCCCccccCCCC
Q 026747 162 RMCLQCGIPKTFSNTRGMVCPVCSD 186 (234)
Q Consensus 162 rMclqcgiPKt~s~argmvcPvcgd 186 (234)
--|++|+-+-+----+.. ||.||-
T Consensus 71 ~~C~~C~~~~~~e~~~~~-CP~C~s 94 (115)
T COG0375 71 CWCLDCGQEVELEELDYR-CPKCGS 94 (115)
T ss_pred EEeccCCCeecchhheeE-CCCCCC
Confidence 359999877665555544 999994
No 105
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=29.65 E-value=27 Score=26.36 Aligned_cols=12 Identities=42% Similarity=0.994 Sum_probs=10.1
Q ss_pred CccccCCCCCCC
Q 026747 178 GMVCPVCSDRPP 189 (234)
Q Consensus 178 gmvcPvcgdRp~ 189 (234)
|-+||.|+.++.
T Consensus 8 Ga~CP~C~~~D~ 19 (71)
T PF09526_consen 8 GAVCPKCQAMDT 19 (71)
T ss_pred CccCCCCcCccE
Confidence 779999998874
No 106
>PHA02942 putative transposase; Provisional
Probab=29.47 E-value=22 Score=33.47 Aligned_cols=8 Identities=38% Similarity=1.261 Sum_probs=4.1
Q ss_pred ccccCCCC
Q 026747 179 MVCPVCSD 186 (234)
Q Consensus 179 mvcPvcgd 186 (234)
-.||.||-
T Consensus 326 q~Cs~CG~ 333 (383)
T PHA02942 326 VSCPKCGH 333 (383)
T ss_pred ccCCCCCC
Confidence 34555554
No 107
>PRK06260 threonine synthase; Validated
Probab=29.10 E-value=22 Score=32.85 Aligned_cols=21 Identities=33% Similarity=1.059 Sum_probs=15.2
Q ss_pred HHhcCCCccccCCC-CccccCCCC
Q 026747 164 CLQCGIPKTFSNTR-GMVCPVCSD 186 (234)
Q Consensus 164 clqcgiPKt~s~ar-gmvcPvcgd 186 (234)
|+.|| ++|.... -..||.||-
T Consensus 6 C~~cg--~~~~~~~~~~~Cp~cg~ 27 (397)
T PRK06260 6 CIECG--KEYDPDEIIYTCPECGG 27 (397)
T ss_pred ECCCC--CCCCCCCccccCCCCCC
Confidence 88999 5676432 467999984
No 108
>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=28.88 E-value=26 Score=29.45 Aligned_cols=24 Identities=25% Similarity=0.707 Sum_probs=19.8
Q ss_pred HHHhcCCCccccCCC-CccccCCCC
Q 026747 163 MCLQCGIPKTFSNTR-GMVCPVCSD 186 (234)
Q Consensus 163 MclqcgiPKt~s~ar-gmvcPvcgd 186 (234)
.|.+||-=-+|.+.- -.-||.||-
T Consensus 114 ~C~~Cg~~~~~~~~~~l~~Cp~C~~ 138 (146)
T PF07295_consen 114 VCENCGHEVELTHPERLPPCPKCGH 138 (146)
T ss_pred ecccCCCEEEecCCCcCCCCCCCCC
Confidence 499999888877765 778999985
No 109
>PRK06835 DNA replication protein DnaC; Validated
Probab=28.64 E-value=42 Score=31.05 Aligned_cols=28 Identities=21% Similarity=0.571 Sum_probs=22.9
Q ss_pred HHHHhcCCCccccCCCCccccCCCCCCCC
Q 026747 162 RMCLQCGIPKTFSNTRGMVCPVCSDRPPA 190 (234)
Q Consensus 162 rMclqcgiPKt~s~argmvcPvcgdRp~~ 190 (234)
++...=|+|.-|..-. ..||.|+|.---
T Consensus 83 ~lL~~~g~~~dyl~~~-y~Cp~C~dtG~i 110 (329)
T PRK06835 83 ELLVSNGYPPDYLEMK-YTCPKCKDTGFI 110 (329)
T ss_pred HHHHHcCCChhhcCCC-CCCCCCCCCCCc
Confidence 3456679999999776 889999999775
No 110
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=28.59 E-value=31 Score=31.24 Aligned_cols=20 Identities=35% Similarity=0.948 Sum_probs=17.5
Q ss_pred HHHHhcCCCccccCCCCccccCCCC
Q 026747 162 RMCLQCGIPKTFSNTRGMVCPVCSD 186 (234)
Q Consensus 162 rMclqcgiPKt~s~argmvcPvcgd 186 (234)
-.|..|-+|-+ |..|++||+
T Consensus 15 yWCe~cNlPl~-----~~~c~~cg~ 34 (202)
T COG5270 15 YWCEKCNLPLL-----GRRCSVCGS 34 (202)
T ss_pred eehhhCCCccc-----cccccccCC
Confidence 35999999988 789999996
No 111
>PRK07591 threonine synthase; Validated
Probab=28.10 E-value=25 Score=33.06 Aligned_cols=22 Identities=27% Similarity=0.655 Sum_probs=15.3
Q ss_pred HHHhcCCCccccCCCCccccCCCC
Q 026747 163 MCLQCGIPKTFSNTRGMVCPVCSD 186 (234)
Q Consensus 163 MclqcgiPKt~s~argmvcPvcgd 186 (234)
-|+.|| ++|....-..||.||-
T Consensus 20 ~C~~Cg--~~~~~~~~~~C~~cg~ 41 (421)
T PRK07591 20 KCRECG--AEYPLGPIHVCEECFG 41 (421)
T ss_pred EeCCCC--CcCCCCCCccCCCCCC
Confidence 399999 4554333378999983
No 112
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=27.97 E-value=30 Score=25.89 Aligned_cols=18 Identities=44% Similarity=0.927 Sum_probs=12.9
Q ss_pred CccccCCCCccccCCCCCCC
Q 026747 170 PKTFSNTRGMVCPVCSDRPP 189 (234)
Q Consensus 170 PKt~s~argmvcPvcgdRp~ 189 (234)
.|-|.. |-|||.|+.++.
T Consensus 3 kKRFIA--GA~CP~C~~~Dt 20 (59)
T TIGR02443 3 KKRFIA--GAVCPACSAQDT 20 (59)
T ss_pred cceEec--cccCCCCcCccE
Confidence 344544 779999998864
No 113
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=27.31 E-value=48 Score=23.16 Aligned_cols=15 Identities=40% Similarity=0.443 Sum_probs=12.8
Q ss_pred HHHHHHHHHhcCCCc
Q 026747 157 AAELLRMCLQCGIPK 171 (234)
Q Consensus 157 aadlLrMclqcgiPK 171 (234)
-++|.++|.++|+|-
T Consensus 8 d~eL~~~L~~~G~~~ 22 (44)
T smart00540 8 DAELRAELKQYGLPP 22 (44)
T ss_pred HHHHHHHHHHcCCCC
Confidence 368999999999873
No 114
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=27.01 E-value=27 Score=36.76 Aligned_cols=11 Identities=36% Similarity=1.129 Sum_probs=7.5
Q ss_pred CccccCCCCCC
Q 026747 178 GMVCPVCSDRP 188 (234)
Q Consensus 178 gmvcPvcgdRp 188 (234)
|.-|||||-.-
T Consensus 503 GePCPVCGS~~ 513 (1047)
T PRK10246 503 GQPCPLCGSTS 513 (1047)
T ss_pred CCCcCCCCccc
Confidence 66788887543
No 115
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=26.41 E-value=20 Score=30.13 Aligned_cols=25 Identities=36% Similarity=0.832 Sum_probs=17.9
Q ss_pred HHhcCCC---ccccCC-CCccccCCCCCC
Q 026747 164 CLQCGIP---KTFSNT-RGMVCPVCSDRP 188 (234)
Q Consensus 164 clqcgiP---Kt~s~a-rgmvcPvcgdRp 188 (234)
|.-||-. ..|+-. .|.+|+.|+..+
T Consensus 150 C~~cg~~~~~~~fs~~~gg~~C~~c~~~~ 178 (241)
T TIGR00613 150 CAVCGSKEDLIYFSMTYGGALCRQCGEKD 178 (241)
T ss_pred cCCCCCcCCCceEchhcCeEEChhhCccC
Confidence 8889852 345543 489999999754
No 116
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=26.02 E-value=31 Score=28.35 Aligned_cols=22 Identities=27% Similarity=0.842 Sum_probs=16.1
Q ss_pred HHhcCCCccccCCCCccccCCCCCC
Q 026747 164 CLQCGIPKTFSNTRGMVCPVCSDRP 188 (234)
Q Consensus 164 clqcgiPKt~s~argmvcPvcgdRp 188 (234)
|-.||- .|--- .+.||.||.+.
T Consensus 32 C~~CG~--v~~PP-r~~Cp~C~~~~ 53 (140)
T COG1545 32 CKKCGR--VYFPP-RAYCPKCGSET 53 (140)
T ss_pred cCCCCe--EEcCC-cccCCCCCCCC
Confidence 888883 33333 48999999986
No 117
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=25.88 E-value=26 Score=30.86 Aligned_cols=21 Identities=29% Similarity=0.907 Sum_probs=14.8
Q ss_pred HHhcCCCccccCCCCccccCCCCC
Q 026747 164 CLQCGIPKTFSNTRGMVCPVCSDR 187 (234)
Q Consensus 164 clqcgiPKt~s~argmvcPvcgdR 187 (234)
|..|+ +.|. .-+-+||+||-+
T Consensus 142 C~GC~--~~f~-~~~~~Cp~CG~~ 162 (177)
T COG1439 142 CHGCK--RIFP-EPKDFCPICGSP 162 (177)
T ss_pred EecCc--eecC-CCCCcCCCCCCc
Confidence 66665 3444 557899999987
No 118
>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=25.68 E-value=25 Score=33.70 Aligned_cols=25 Identities=24% Similarity=0.583 Sum_probs=16.6
Q ss_pred HHHhcCCCccccCCCCccccCCCCCCCC
Q 026747 163 MCLQCGIPKTFSNTRGMVCPVCSDRPPA 190 (234)
Q Consensus 163 MclqcgiPKt~s~argmvcPvcgdRp~~ 190 (234)
.|.+||.--.-- -.-||.|+.--.-
T Consensus 9 ~C~~Cg~~~~~~---~g~Cp~C~~w~t~ 33 (454)
T TIGR00416 9 VCQHCGADSPKW---QGKCPACHAWNTI 33 (454)
T ss_pred ECCcCCCCCccc---cEECcCCCCcccc
Confidence 399999643333 3459999876543
No 119
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=25.26 E-value=37 Score=21.52 Aligned_cols=13 Identities=38% Similarity=1.081 Sum_probs=10.0
Q ss_pred CCCCccccCCCCC
Q 026747 175 NTRGMVCPVCSDR 187 (234)
Q Consensus 175 ~argmvcPvcgdR 187 (234)
+--+++|+.||..
T Consensus 29 ~vp~~~C~~CGE~ 41 (46)
T TIGR03831 29 NVPALVCPQCGEE 41 (46)
T ss_pred CCCccccccCCCE
Confidence 4457899999975
No 120
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=24.51 E-value=31 Score=22.60 Aligned_cols=20 Identities=25% Similarity=0.826 Sum_probs=12.9
Q ss_pred HHHhcCCCccccCCCCccccCCC
Q 026747 163 MCLQCGIPKTFSNTRGMVCPVCS 185 (234)
Q Consensus 163 MclqcgiPKt~s~argmvcPvcg 185 (234)
+|..|-.-.. ....+||+|+
T Consensus 24 ~C~~C~~~~~---~~~~~CP~C~ 43 (44)
T PF14634_consen 24 FCEKCLKKLK---GKSVKCPICR 43 (44)
T ss_pred HHHHHHHhhc---CCCCCCcCCC
Confidence 4555544433 5678999997
No 121
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=24.35 E-value=17 Score=29.57 Aligned_cols=27 Identities=26% Similarity=0.637 Sum_probs=16.9
Q ss_pred HHhcCCCccccCCC--C-----ccccCCCCCCCC
Q 026747 164 CLQCGIPKTFSNTR--G-----MVCPVCSDRPPA 190 (234)
Q Consensus 164 clqcgiPKt~s~ar--g-----mvcPvcgdRp~~ 190 (234)
|-.||.==||..+- . .+||.||..-..
T Consensus 102 Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 102 CPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred CcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEE
Confidence 77777443433222 2 899999987654
No 122
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=24.26 E-value=28 Score=36.10 Aligned_cols=24 Identities=25% Similarity=0.700 Sum_probs=20.5
Q ss_pred HHhcCCCccccCCC-CccccCCCCC
Q 026747 164 CLQCGIPKTFSNTR-GMVCPVCSDR 187 (234)
Q Consensus 164 clqcgiPKt~s~ar-gmvcPvcgdR 187 (234)
|-+|.++-||...+ .|.|.-||-.
T Consensus 447 Cp~Cd~~lt~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 447 CPNCDSPLTLHKATGQLRCHYCGYQ 471 (730)
T ss_pred CCCCCcceEEecCCCeeEeCCCCCC
Confidence 77888999998776 8999999977
No 123
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=24.06 E-value=55 Score=27.35 Aligned_cols=87 Identities=17% Similarity=0.277 Sum_probs=51.4
Q ss_pred CCCCCcceEeecceee----ccchhhcccccCC----CCCCCCCccccccccccccCCCChhhHHHHHHH-------HHh
Q 026747 102 KELPAGAVMEAKAQLV----GIHDRVRSDMEGD----QPPASVSSTTQGVKRVATATNPNAEDAAELLRM-------CLQ 166 (234)
Q Consensus 102 K~~P~gAVveAKpqlv----~i~eRvrsd~~g~----~~p~s~s~~~~~~kR~~~a~np~aedaadlLrM-------clq 166 (234)
+.+|+-+..+.|=+++ -|-+.+..|..-. ..+=++.+.- ++-|.+--..=.+.+-.++|+- |-.
T Consensus 29 ~~p~~~v~~eG~kTvi~Nf~~I~~~L~R~~~hv~ky~~~ELgt~g~i-~~~~lii~G~~~~~~i~~~L~~yI~~yVlC~~ 107 (138)
T PRK03988 29 EVPKPDVRIEGNRTIIRNFKEIADRLNRDPKHVAKFLLKELGTAGNI-EGGRLILQGKFSPRVINEKIDRYVKEYVICPE 107 (138)
T ss_pred eCCCCeEEEEcCcEEEecHHHHHHHHCCCHHHHHHHHHHHhCCceee-cCCEEEEEEeeCHHHHHHHHHHHHHhcEECCC
Confidence 3555667777765533 3445555442111 0111111112 3355554445567888888885 999
Q ss_pred cCCCccccCCC----CccccCCCCCCC
Q 026747 167 CGIPKTFSNTR----GMVCPVCSDRPP 189 (234)
Q Consensus 167 cgiPKt~s~ar----gmvcPvcgdRp~ 189 (234)
||-|-|...-. -+.|-+||.+-+
T Consensus 108 C~spdT~l~k~~r~~~l~C~ACGa~~~ 134 (138)
T PRK03988 108 CGSPDTKLIKEGRIWVLKCEACGAETP 134 (138)
T ss_pred CCCCCcEEEEcCCeEEEEcccCCCCCc
Confidence 99999988653 467999998654
No 124
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=23.70 E-value=27 Score=27.87 Aligned_cols=24 Identities=21% Similarity=0.503 Sum_probs=14.1
Q ss_pred HHhcCCCcc---ccCCC-CccccCCCCC
Q 026747 164 CLQCGIPKT---FSNTR-GMVCPVCSDR 187 (234)
Q Consensus 164 clqcgiPKt---~s~ar-gmvcPvcgdR 187 (234)
|-+||-++. ....+ -.+||+||-.
T Consensus 24 CP~Cge~~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 24 CPRCGKVSISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred CCCCCCeEeeeecCCCcceEECCCCCCc
Confidence 888883211 11122 4689999965
No 125
>KOG4334 consensus Uncharacterized conserved protein, contains double-stranded RNA-binding motif and WW domain [General function prediction only]
Probab=23.69 E-value=40 Score=34.67 Aligned_cols=15 Identities=33% Similarity=1.105 Sum_probs=12.8
Q ss_pred HHHHHHhcCCCcccc
Q 026747 160 LLRMCLQCGIPKTFS 174 (234)
Q Consensus 160 lLrMclqcgiPKt~s 174 (234)
+..||-+||||++|-
T Consensus 480 v~e~ctk~~~psPy~ 494 (650)
T KOG4334|consen 480 VVEMCTKCAIPSPYN 494 (650)
T ss_pred HHHHhhhcCCCCHHH
Confidence 457999999999984
No 126
>PRK12722 transcriptional activator FlhC; Provisional
Probab=23.67 E-value=42 Score=29.66 Aligned_cols=33 Identities=27% Similarity=0.517 Sum_probs=22.6
Q ss_pred hhhHHHHHHH----------HHhcCCCcc---ccCCCCccccCCCC
Q 026747 154 AEDAAELLRM----------CLQCGIPKT---FSNTRGMVCPVCSD 186 (234)
Q Consensus 154 aedaadlLrM----------clqcgiPKt---~s~argmvcPvcgd 186 (234)
+.-|-.|+|. |-.||-.=. +--....+||.|+-
T Consensus 117 ~tRAw~LvRf~~s~~L~l~~C~~Cgg~fv~~~~e~~~~f~CplC~~ 162 (187)
T PRK12722 117 LTRAWTLVRFVDSGMLQLSSCNCCGGHFVTHAHDPVGSFVCGLCQP 162 (187)
T ss_pred HHHHHHHHHHHhcCcEeeccCCCCCCCeeccccccCCCCcCCCCCC
Confidence 4456666664 999998733 32334899999985
No 127
>PF09396 Thrombin_light: Thrombin light chain; InterPro: IPR018992 Thrombin is a Na+-activated, allosteric serine protease that functions in blood homeostasis, inflammation and wound healing []. Thrombin (or coagulation factor II) is an enzyme that cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, and (in complex with thrombomodulin) protein C []. Sodium binding is the major driving force behind the procoagulant, prothrombotic and signaling functions of the enzyme, but is dispensable for cleavage of the anticoagulant protein C []. Prothrombin is activated on the surface of a phospholipid membrane where factor Xa removes the activation peptide and cleaves the remaining part into light and heavy chains. This domain corresponds to the light chain of thrombin. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis, 0007596 blood coagulation, 0005576 extracellular region; PDB: 3HKI_D 2OCV_A 3EDX_A 3HK6_C 2PV9_A 2PUX_A 3HK3_A 1HRT_L 1TOC_G 1ETT_L ....
Probab=23.59 E-value=53 Score=23.99 Aligned_cols=25 Identities=28% Similarity=0.279 Sum_probs=12.8
Q ss_pred CccccCCCCCCCCCCchhhhhcCCchhHHH
Q 026747 178 GMVCPVCSDRPPADISNESKKKGSIIKDRE 207 (234)
Q Consensus 178 gmvcPvcgdRp~~~~~~~~kk~g~~~kd~e 207 (234)
|-.=-.||-||.- +||...+..++|
T Consensus 16 G~GEadCG~RPlF-----Ekk~~~D~~E~E 40 (49)
T PF09396_consen 16 GSGEADCGLRPLF-----EKKSKKDKTEKE 40 (49)
T ss_dssp TSSGTTTT--TTT-----GGGT---TTHHH
T ss_pred cCcccccCcchhh-----hhhcccccCHHH
Confidence 4455789999996 445554555554
No 128
>PHA00626 hypothetical protein
Probab=23.40 E-value=36 Score=25.66 Aligned_cols=9 Identities=44% Similarity=1.187 Sum_probs=6.0
Q ss_pred ccccCCCCC
Q 026747 179 MVCPVCSDR 187 (234)
Q Consensus 179 mvcPvcgdR 187 (234)
|.||.||-+
T Consensus 1 m~CP~CGS~ 9 (59)
T PHA00626 1 MSCPKCGSG 9 (59)
T ss_pred CCCCCCCCc
Confidence 567777764
No 129
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=22.22 E-value=31 Score=30.73 Aligned_cols=74 Identities=15% Similarity=0.228 Sum_probs=37.2
Q ss_pred cceEeecceeeccchhhcccccCCC--CCCC-CCcccc-ccccccccCCCChhhHHHHHHHHHhcCCC------------
Q 026747 107 GAVMEAKAQLVGIHDRVRSDMEGDQ--PPAS-VSSTTQ-GVKRVATATNPNAEDAAELLRMCLQCGIP------------ 170 (234)
Q Consensus 107 gAVveAKpqlv~i~eRvrsd~~g~~--~p~s-~s~~~~-~~kR~~~a~np~aedaadlLrMclqcgiP------------ 170 (234)
++++-=...+.||-.=|.+.+-=.+ .|.. +++-+. +-+++ .+...++|+.++..|--
T Consensus 159 k~~LLDQ~~iaGiGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L-------~~~~~~vl~~ai~~gg~t~~~~~~~~g~~ 231 (274)
T PRK01103 159 KPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERL-------VDAIKAVLAEAIEQGGTTLRDYVNADGKP 231 (274)
T ss_pred HHHhhcCCeEecccHhHHHHHHHHcCCCccCccccCCHHHHHHH-------HHHHHHHHHHHHHcCCCccccccccCCCC
Confidence 4444333456677555554432111 4444 222222 23333 45667777777775421
Q ss_pred cc-----ccCCC-CccccCCCCC
Q 026747 171 KT-----FSNTR-GMVCPVCSDR 187 (234)
Q Consensus 171 Kt-----~s~ar-gmvcPvcgdR 187 (234)
.. +-+.| |.-||+||..
T Consensus 232 g~~~~~l~Vy~R~g~pC~~Cg~~ 254 (274)
T PRK01103 232 GYFQQSLQVYGREGEPCRRCGTP 254 (274)
T ss_pred CCccceeEEcCCCCCCCCCCCCe
Confidence 11 23455 7889999854
No 130
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=22.21 E-value=39 Score=30.24 Aligned_cols=9 Identities=44% Similarity=1.213 Sum_probs=5.3
Q ss_pred CccccCCCC
Q 026747 178 GMVCPVCSD 186 (234)
Q Consensus 178 gmvcPvcgd 186 (234)
|.-||+||.
T Consensus 235 g~pC~~Cg~ 243 (269)
T PRK14811 235 GQPCPRCGT 243 (269)
T ss_pred cCCCCcCCC
Confidence 556666663
No 131
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=21.80 E-value=45 Score=24.61 Aligned_cols=25 Identities=36% Similarity=0.699 Sum_probs=19.1
Q ss_pred HHhcC--CC-ccccCCCCccccCCCCCC
Q 026747 164 CLQCG--IP-KTFSNTRGMVCPVCSDRP 188 (234)
Q Consensus 164 clqcg--iP-Kt~s~argmvcPvcgdRp 188 (234)
-+.|| || .||-..|--.||.||-|=
T Consensus 22 ~~pCgH~I~~~~f~~~rYngCPfC~~~~ 49 (55)
T PF14447_consen 22 VLPCGHLICDNCFPGERYNGCPFCGTPF 49 (55)
T ss_pred cccccceeeccccChhhccCCCCCCCcc
Confidence 35666 45 478899999999999763
No 132
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=21.59 E-value=24 Score=25.01 Aligned_cols=24 Identities=25% Similarity=0.578 Sum_probs=17.6
Q ss_pred HHhcCCCcccc-----CCCCccccCCCCC
Q 026747 164 CLQCGIPKTFS-----NTRGMVCPVCSDR 187 (234)
Q Consensus 164 clqcgiPKt~s-----~argmvcPvcgdR 187 (234)
|..||+.+|.. +..+++|-.||-+
T Consensus 2 C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~ 30 (54)
T cd00202 2 CSNCGTTTTPLWRRGPSGGSTLCNACGLY 30 (54)
T ss_pred CCCCCCCCCcccccCCCCcchHHHHHHHH
Confidence 77899988752 3556889999854
No 133
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=21.05 E-value=36 Score=25.75 Aligned_cols=16 Identities=25% Similarity=0.694 Sum_probs=12.0
Q ss_pred CCCCccccCCCCCCCC
Q 026747 175 NTRGMVCPVCSDRPPA 190 (234)
Q Consensus 175 ~argmvcPvcgdRp~~ 190 (234)
..-+.+||.||..=..
T Consensus 28 ~~~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 28 GVPGWYCPACGEELLD 43 (127)
T ss_pred eeeeeECCCCCCEEEc
Confidence 4558899999986443
No 134
>PRK11823 DNA repair protein RadA; Provisional
Probab=20.80 E-value=38 Score=32.38 Aligned_cols=24 Identities=25% Similarity=0.558 Sum_probs=15.9
Q ss_pred HHHhcCCCccccCCCCccccCCCCCCC
Q 026747 163 MCLQCGIPKTFSNTRGMVCPVCSDRPP 189 (234)
Q Consensus 163 MclqcgiPKt~s~argmvcPvcgdRp~ 189 (234)
.|.+||.=-..- ..-||.|+.--.
T Consensus 9 ~C~~Cg~~~~~~---~g~Cp~C~~w~t 32 (446)
T PRK11823 9 VCQECGAESPKW---LGRCPECGAWNT 32 (446)
T ss_pred ECCcCCCCCccc---CeeCcCCCCccc
Confidence 389999533322 456999987654
No 135
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=20.57 E-value=40 Score=29.27 Aligned_cols=13 Identities=31% Similarity=0.544 Sum_probs=9.6
Q ss_pred CccccCCCCCCCC
Q 026747 178 GMVCPVCSDRPPA 190 (234)
Q Consensus 178 gmvcPvcgdRp~~ 190 (234)
-.|||.||=-=.+
T Consensus 48 V~vCP~CgyA~~~ 60 (214)
T PF09986_consen 48 VWVCPHCGYAAFE 60 (214)
T ss_pred EEECCCCCCcccc
Confidence 4799999965444
No 136
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=20.48 E-value=45 Score=20.57 Aligned_cols=8 Identities=50% Similarity=1.240 Sum_probs=6.6
Q ss_pred cccCCCCC
Q 026747 180 VCPVCSDR 187 (234)
Q Consensus 180 vcPvcgdR 187 (234)
-||+|+.+
T Consensus 3 ~CPiC~~~ 10 (26)
T smart00734 3 QCPVCFRE 10 (26)
T ss_pred cCCCCcCc
Confidence 49999876
No 137
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=20.47 E-value=59 Score=31.79 Aligned_cols=40 Identities=33% Similarity=0.639 Sum_probs=28.2
Q ss_pred cccccCCCChhhHHHHHHH------HHhcCCCccccCCC--CccccCCCC
Q 026747 145 RVATATNPNAEDAAELLRM------CLQCGIPKTFSNTR--GMVCPVCSD 186 (234)
Q Consensus 145 R~~~a~np~aedaadlLrM------clqcgiPKt~s~ar--gmvcPvcgd 186 (234)
|+---...+++.|.+++.+ |..|| +.+...+ ---||.||-
T Consensus 218 Rvfv~v~rga~~ad~~~e~~g~~~~c~~cg--~~~~~~~~~~~~c~~Cg~ 265 (380)
T COG1867 218 RVFVEVRRGARRADKLLENLGYIYHCSRCG--EIVGSFREVDEKCPHCGG 265 (380)
T ss_pred EEEEEEccCchhHHHHHHhcCcEEEccccc--ceecccccccccCCcccc
Confidence 4445556778888888765 99999 5444444 356999994
No 138
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.45 E-value=1e+02 Score=27.66 Aligned_cols=76 Identities=16% Similarity=0.288 Sum_probs=43.4
Q ss_pred CCCcceEeecceeeccchhhcccccCCC--CCCC-CCccccc-cccccccCCCChhhHHHHHHHHHhcCCC---------
Q 026747 104 LPAGAVMEAKAQLVGIHDRVRSDMEGDQ--PPAS-VSSTTQG-VKRVATATNPNAEDAAELLRMCLQCGIP--------- 170 (234)
Q Consensus 104 ~P~gAVveAKpqlv~i~eRvrsd~~g~~--~p~s-~s~~~~~-~kR~~~a~np~aedaadlLrMclqcgiP--------- 170 (234)
.|-++++-=.-.+.||=.=|++.+-=.+ .|.. +.+.+.. -+|. .+...++|+.++..|--
T Consensus 165 ~~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~~Ls~~~~~~L-------~~~i~~vl~~ai~~gg~~~~~~~~~~ 237 (282)
T PRK13945 165 RSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERL-------REAIIEVLKTSIGAGGTTFSDFRDLE 237 (282)
T ss_pred ccHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccccCCHHHHHHH-------HHHHHHHHHHHHHcCCCccccccccC
Confidence 3446666666678888666665532221 4444 2222222 2333 46778888888887632
Q ss_pred ---cc-----ccCCC-CccccCCCC
Q 026747 171 ---KT-----FSNTR-GMVCPVCSD 186 (234)
Q Consensus 171 ---Kt-----~s~ar-gmvcPvcgd 186 (234)
.. +-..| |.-||.||.
T Consensus 238 g~~g~~~~~~~Vy~R~g~pC~~Cg~ 262 (282)
T PRK13945 238 GVNGNYGGQAWVYRRTGKPCRKCGT 262 (282)
T ss_pred CCCCcccceEEEeCCCcCCCCcCCC
Confidence 22 23455 789999995
No 139
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=20.27 E-value=53 Score=24.59 Aligned_cols=25 Identities=28% Similarity=0.767 Sum_probs=18.6
Q ss_pred HHHHhcCCCccccC-CCCccccCCCC
Q 026747 162 RMCLQCGIPKTFSN-TRGMVCPVCSD 186 (234)
Q Consensus 162 rMclqcgiPKt~s~-argmvcPvcgd 186 (234)
..|.-||++-+-.+ +--..||.||.
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~ 33 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGE 33 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCC
Confidence 35888998877444 55688999986
No 140
>PRK11032 hypothetical protein; Provisional
Probab=20.22 E-value=45 Score=28.71 Aligned_cols=24 Identities=25% Similarity=0.665 Sum_probs=20.1
Q ss_pred HHHhcCCCccccCCC-CccccCCCC
Q 026747 163 MCLQCGIPKTFSNTR-GMVCPVCSD 186 (234)
Q Consensus 163 MclqcgiPKt~s~ar-gmvcPvcgd 186 (234)
.|.+||-=.+|.+.- ---||.||-
T Consensus 126 vC~~Cg~~~~~~~p~~i~pCp~C~~ 150 (160)
T PRK11032 126 VCEKCHHHLAFYTPEVLPLCPKCGH 150 (160)
T ss_pred EecCCCCEEEecCCCcCCCCCCCCC
Confidence 499999998888754 778999985
No 141
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=20.13 E-value=37 Score=24.81 Aligned_cols=12 Identities=42% Similarity=1.077 Sum_probs=4.3
Q ss_pred CCccccCCCCCC
Q 026747 177 RGMVCPVCSDRP 188 (234)
Q Consensus 177 rgmvcPvcgdRp 188 (234)
|..+||.||..-
T Consensus 32 r~y~Cp~CgAtG 43 (55)
T PF05741_consen 32 RKYVCPICGATG 43 (55)
T ss_dssp GG---TTT---G
T ss_pred hcCcCCCCcCcC
Confidence 457999999763
Done!