Query psy9094
Match_columns 185
No_of_seqs 115 out of 607
Neff 7.0
Searched_HMMs 46136
Date Fri Aug 16 18:43:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9094.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9094hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK04011 peptide chain release 100.0 1E-43 2.2E-48 315.3 18.5 182 2-185 192-404 (411)
2 TIGR03676 aRF1/eRF1 peptide ch 100.0 1.3E-43 2.8E-48 313.8 18.9 182 2-185 184-396 (403)
3 TIGR00108 eRF peptide chain re 100.0 1.1E-43 2.4E-48 314.9 18.0 182 2-185 188-400 (409)
4 COG1503 eRF1 Peptide chain rel 100.0 7.7E-40 1.7E-44 286.3 14.2 181 2-185 191-402 (411)
5 KOG0688|consensus 100.0 4.7E-36 1E-40 254.1 6.2 184 1-185 191-405 (431)
6 TIGR00111 pelota probable tran 100.0 8.3E-32 1.8E-36 235.1 13.0 133 2-185 177-344 (351)
7 PF03465 eRF1_3: eRF1 domain 3 100.0 3.4E-30 7.4E-35 191.9 7.3 106 55-185 1-106 (113)
8 COG1537 PelA Predicted RNA-bin 100.0 4.3E-29 9.2E-34 214.7 12.3 135 5-185 176-344 (352)
9 KOG2869|consensus 99.9 9.4E-26 2E-30 191.7 9.9 141 2-185 180-363 (379)
10 PF03464 eRF1_2: eRF1 domain 2 98.6 1.3E-08 2.8E-13 77.5 2.0 42 2-44 50-91 (133)
11 TIGR03677 rpl7ae 50S ribosomal 96.4 0.022 4.8E-07 42.5 7.8 32 71-102 22-53 (117)
12 COG1358 RPL8A Ribosomal protei 96.4 0.015 3.3E-07 43.5 6.9 63 72-177 24-86 (116)
13 PRK04175 rpl7ae 50S ribosomal 96.1 0.043 9.2E-07 41.3 8.0 38 64-102 20-57 (122)
14 PRK13600 putative ribosomal pr 96.1 0.027 5.9E-07 39.8 6.4 58 75-176 13-70 (84)
15 PRK13602 putative ribosomal pr 96.1 0.032 6.9E-07 39.1 6.7 66 67-177 4-69 (82)
16 PRK06683 hypothetical protein; 95.9 0.044 9.5E-07 38.4 6.7 62 72-177 8-69 (82)
17 PRK07714 hypothetical protein; 95.4 0.062 1.3E-06 38.8 6.2 33 70-102 13-45 (100)
18 PF01248 Ribosomal_L7Ae: Ribos 95.3 0.093 2E-06 37.0 6.7 71 63-177 4-74 (95)
19 PRK13601 putative L7Ae-like ri 95.3 0.077 1.7E-06 37.2 6.1 60 73-176 6-65 (82)
20 PRK07283 hypothetical protein; 94.8 0.12 2.6E-06 37.3 6.3 34 69-102 12-45 (98)
21 PRK01018 50S ribosomal protein 94.8 0.13 2.8E-06 37.2 6.5 32 71-102 12-43 (99)
22 PRK05583 ribosomal protein L7A 94.6 0.21 4.5E-06 36.5 7.2 33 70-102 12-44 (104)
23 PF08032 SpoU_sub_bind: RNA 2' 94.4 0.14 3E-06 34.4 5.4 51 76-170 1-52 (76)
24 PRK00398 rpoP DNA-directed RNA 94.2 0.037 8E-07 34.3 2.0 39 106-150 2-40 (46)
25 PTZ00106 60S ribosomal protein 93.9 0.32 6.9E-06 35.8 6.8 41 62-103 13-53 (108)
26 TIGR00373 conserved hypothetic 93.7 0.052 1.1E-06 42.6 2.5 47 105-156 107-153 (158)
27 PRK06266 transcription initiat 93.0 0.09 1.9E-06 42.1 2.9 48 105-157 115-162 (178)
28 smart00531 TFIIE Transcription 90.7 0.13 2.8E-06 39.7 1.4 45 105-150 97-142 (147)
29 COG1911 RPL30 Ribosomal protei 90.4 3.1 6.8E-05 30.1 8.1 30 72-101 16-45 (100)
30 PTZ00222 60S ribosomal protein 90.3 0.84 1.8E-05 38.6 5.9 29 74-102 131-159 (263)
31 PF09723 Zn-ribbon_8: Zinc rib 90.2 0.51 1.1E-05 28.7 3.5 31 106-139 4-34 (42)
32 smart00834 CxxC_CXXC_SSSS Puta 90.2 0.51 1.1E-05 27.9 3.5 32 106-140 4-35 (41)
33 PRK09190 hypothetical protein; 90.2 2 4.4E-05 35.6 8.1 42 62-103 96-139 (220)
34 COG1675 TFA1 Transcription ini 88.5 0.34 7.4E-06 38.8 2.3 47 107-158 113-159 (176)
35 COG1592 Rubrerythrin [Energy p 88.3 0.39 8.5E-06 38.1 2.5 55 62-140 104-158 (166)
36 TIGR02605 CxxC_CxxC_SSSS putat 88.2 0.8 1.7E-05 28.7 3.5 31 106-139 4-34 (52)
37 PTZ00365 60S ribosomal protein 87.6 1.4 3E-05 37.4 5.5 62 71-175 128-189 (266)
38 PF10116 Host_attach: Protein 85.8 1.3 2.8E-05 33.4 4.1 47 3-54 70-116 (138)
39 smart00659 RPOLCX RNA polymera 83.4 0.85 1.8E-05 28.2 1.7 33 106-145 1-33 (44)
40 COG1198 PriA Primosomal protei 82.5 3.2 6.9E-05 40.2 6.0 68 105-173 442-518 (730)
41 PF13397 DUF4109: Domain of un 82.3 1.7 3.8E-05 31.9 3.3 38 101-140 22-59 (105)
42 PF13248 zf-ribbon_3: zinc-rib 80.4 0.79 1.7E-05 24.9 0.7 25 107-141 2-26 (26)
43 PF13240 zinc_ribbon_2: zinc-r 79.6 0.99 2.1E-05 24.0 0.9 8 133-140 15-22 (23)
44 cd00729 rubredoxin_SM Rubredox 78.9 2.1 4.5E-05 24.8 2.2 26 107-140 2-27 (34)
45 COG2888 Predicted Zn-ribbon RN 77.9 1.8 4E-05 28.5 1.9 8 131-138 27-34 (61)
46 PRK12496 hypothetical protein; 77.7 1.7 3.8E-05 34.2 2.2 29 105-141 125-153 (164)
47 PRK12380 hydrogenase nickel in 77.6 2.6 5.6E-05 31.1 3.0 26 107-140 70-95 (113)
48 PRK14892 putative transcriptio 76.6 5.6 0.00012 28.9 4.4 64 107-174 21-90 (99)
49 COG1852 Uncharacterized conser 76.0 3.1 6.7E-05 33.9 3.1 34 130-171 110-143 (209)
50 TIGR00416 sms DNA repair prote 75.8 1.7 3.6E-05 39.7 1.8 27 105-141 5-31 (454)
51 COG1439 Predicted nucleic acid 74.9 3.1 6.8E-05 33.3 2.9 28 105-142 137-164 (177)
52 PRK11823 DNA repair protein Ra 74.9 1.9 4.1E-05 39.2 1.9 30 106-145 6-35 (446)
53 TIGR02098 MJ0042_CXXC MJ0042 f 73.9 2.6 5.6E-05 24.6 1.7 33 107-141 2-35 (38)
54 TIGR00100 hypA hydrogenase nic 73.6 3.1 6.7E-05 30.8 2.5 26 107-140 70-95 (115)
55 COG2051 RPS27A Ribosomal prote 73.4 3.2 6.9E-05 28.0 2.2 41 107-167 19-59 (67)
56 TIGR00354 polC DNA polymerase, 72.1 8.4 0.00018 38.4 5.6 42 81-143 607-649 (1095)
57 PF01976 DUF116: Protein of un 71.6 4.6 0.0001 31.6 3.2 37 131-175 64-100 (158)
58 PRK00415 rps27e 30S ribosomal 71.3 5.9 0.00013 26.1 3.1 42 107-168 11-52 (59)
59 PRK03824 hypA hydrogenase nick 71.1 5.5 0.00012 30.3 3.4 10 106-115 69-78 (135)
60 cd01121 Sms Sms (bacterial rad 70.8 2.1 4.6E-05 38.0 1.2 28 108-145 1-28 (372)
61 PF07295 DUF1451: Protein of u 70.0 4.4 9.5E-05 31.5 2.7 52 79-140 88-139 (146)
62 PF01155 HypA: Hydrogenase exp 69.2 2.7 5.8E-05 31.0 1.3 26 107-140 70-95 (113)
63 TIGR01206 lysW lysine biosynth 68.4 1.3 2.8E-05 28.7 -0.5 38 107-148 2-39 (54)
64 PF08271 TF_Zn_Ribbon: TFIIB z 67.8 3.7 8.1E-05 24.8 1.5 29 108-141 1-29 (43)
65 COG1996 RPC10 DNA-directed RNA 67.3 3.1 6.8E-05 26.4 1.1 34 106-145 5-38 (49)
66 COG5257 GCD11 Translation init 67.2 2.4 5.2E-05 37.5 0.8 36 107-151 57-92 (415)
67 PHA00626 hypothetical protein 67.2 4.4 9.5E-05 26.5 1.8 30 109-140 2-32 (59)
68 cd03769 SR_IS607_transposase_l 67.1 18 0.0004 27.0 5.6 22 78-99 49-70 (134)
69 PRK03681 hypA hydrogenase nick 66.9 4.9 0.00011 29.7 2.3 27 107-140 70-96 (114)
70 cd00350 rubredoxin_like Rubred 66.6 5.6 0.00012 22.7 2.0 25 108-140 2-26 (33)
71 PF03604 DNA_RNApol_7kD: DNA d 66.1 6.1 0.00013 22.7 2.1 26 108-140 1-26 (32)
72 PRK14873 primosome assembly pr 65.9 7.6 0.00016 37.2 3.9 89 78-170 357-462 (665)
73 TIGR00595 priA primosomal prot 65.5 21 0.00045 33.0 6.6 42 131-173 253-296 (505)
74 PF11023 DUF2614: Protein of u 64.9 3.2 7E-05 30.8 1.0 30 107-144 69-98 (114)
75 PF13727 CoA_binding_3: CoA-bi 64.7 10 0.00022 28.5 3.9 51 75-168 125-175 (175)
76 TIGR03844 cysteate_syn cysteat 63.6 4.5 9.8E-05 36.2 1.9 30 106-144 1-30 (398)
77 PRK06450 threonine synthase; V 63.5 4.4 9.6E-05 35.4 1.7 30 106-144 2-31 (338)
78 COG2956 Predicted N-acetylgluc 62.7 4.1 8.9E-05 36.0 1.3 24 106-139 353-376 (389)
79 PRK14715 DNA polymerase II lar 62.6 9 0.00019 39.6 3.8 45 80-144 655-699 (1627)
80 PRK11788 tetratricopeptide rep 62.4 4.1 8.8E-05 35.0 1.3 24 107-140 354-377 (389)
81 PRK11032 hypothetical protein; 62.1 7.3 0.00016 30.7 2.5 40 94-140 112-151 (160)
82 PF10263 SprT-like: SprT-like 61.6 6.6 0.00014 29.8 2.2 67 73-143 79-155 (157)
83 PRK04351 hypothetical protein; 60.9 8.5 0.00018 29.9 2.7 38 103-144 108-145 (149)
84 PF09538 FYDLN_acid: Protein o 60.5 4.6 0.0001 29.8 1.1 28 108-143 10-38 (108)
85 PRK00564 hypA hydrogenase nick 60.2 6 0.00013 29.4 1.7 26 107-140 71-97 (117)
86 PRK14890 putative Zn-ribbon RN 57.8 4.7 0.0001 26.6 0.7 32 106-138 24-55 (59)
87 PRK00464 nrdR transcriptional 57.6 5.2 0.00011 31.3 1.0 9 108-116 29-37 (154)
88 PRK08270 anaerobic ribonucleos 57.1 4.9 0.00011 38.5 1.0 26 108-144 627-652 (656)
89 PTZ00083 40S ribosomal protein 56.4 16 0.00036 25.7 3.3 44 107-170 35-78 (85)
90 smart00440 ZnF_C2C2 C2C2 Zinc 55.9 8.4 0.00018 23.1 1.5 33 109-141 2-38 (40)
91 PLN00209 ribosomal protein S27 55.9 16 0.00036 25.8 3.2 44 107-170 36-79 (86)
92 COG1212 KdsB CMP-2-keto-3-deox 55.7 28 0.0006 29.3 5.0 23 153-175 55-77 (247)
93 PRK06260 threonine synthase; V 55.3 6.5 0.00014 35.0 1.4 30 107-144 3-32 (397)
94 COG1212 KdsB CMP-2-keto-3-deox 54.0 23 0.00049 29.8 4.3 45 140-184 21-65 (247)
95 PHA02998 RNA polymerase subuni 53.2 8.8 0.00019 30.9 1.7 38 107-144 143-184 (195)
96 cd00338 Ser_Recombinase Serine 52.8 42 0.00092 24.3 5.3 24 79-102 53-76 (137)
97 COG1110 Reverse gyrase [DNA re 52.0 17 0.00036 36.8 3.7 59 107-177 694-752 (1187)
98 PRK07591 threonine synthase; V 52.0 10 0.00022 34.2 2.0 29 107-144 18-46 (421)
99 PRK05580 primosome assembly pr 51.8 24 0.00051 33.9 4.6 41 131-172 421-463 (679)
100 PF05191 ADK_lid: Adenylate ki 51.4 10 0.00023 22.2 1.4 30 108-141 2-31 (36)
101 PF14353 CpXC: CpXC protein 51.4 9.7 0.00021 28.3 1.6 9 132-140 39-47 (128)
102 PF01096 TFIIS_C: Transcriptio 50.8 7.8 0.00017 23.1 0.8 33 109-141 2-38 (39)
103 PF07960 CBP4: CBP4; InterPro 50.5 29 0.00063 26.4 4.0 24 29-54 17-46 (128)
104 TIGR02300 FYDLN_acid conserved 50.3 10 0.00023 28.8 1.6 27 108-142 10-37 (129)
105 cd03770 SR_TndX_transposase Se 50.3 58 0.0013 24.3 5.8 22 78-99 55-76 (140)
106 PF14319 Zn_Tnp_IS91: Transpos 49.3 27 0.00059 25.6 3.7 43 106-158 41-83 (111)
107 PRK00420 hypothetical protein; 49.1 11 0.00024 28.0 1.5 28 109-143 25-52 (112)
108 PF13717 zinc_ribbon_4: zinc-r 48.8 16 0.00035 21.3 2.0 30 108-140 3-34 (36)
109 PF13719 zinc_ribbon_5: zinc-r 48.2 15 0.00033 21.5 1.8 32 107-141 2-35 (37)
110 PRK13130 H/ACA RNA-protein com 47.5 14 0.00031 24.0 1.7 25 108-144 6-30 (56)
111 COG4079 Uncharacterized protei 47.4 23 0.00049 30.1 3.3 43 28-72 120-165 (293)
112 COG2331 Uncharacterized protei 47.4 5.4 0.00012 27.7 -0.3 34 105-141 10-43 (82)
113 PRK14714 DNA polymerase II lar 46.8 12 0.00027 38.3 1.9 8 108-115 668-675 (1337)
114 PRK11181 23S rRNA (guanosine-2 46.0 52 0.0011 27.3 5.3 27 75-101 3-31 (244)
115 TIGR01384 TFS_arch transcripti 45.8 17 0.00036 25.9 2.1 36 106-141 61-100 (104)
116 PF04423 Rad50_zn_hook: Rad50 44.6 16 0.00035 23.0 1.6 24 133-156 22-45 (54)
117 COG1066 Sms Predicted ATP-depe 44.2 14 0.00031 33.6 1.7 31 107-147 7-37 (456)
118 PF10058 DUF2296: Predicted in 43.9 9.2 0.0002 24.6 0.4 36 102-139 17-52 (54)
119 PF07754 DUF1610: Domain of un 43.5 14 0.00031 19.8 1.1 8 107-114 16-23 (24)
120 PF14803 Nudix_N_2: Nudix N-te 43.4 18 0.00039 21.0 1.5 9 130-138 21-29 (34)
121 COG1150 HdrC Heterodisulfide r 43.0 22 0.00048 28.9 2.5 63 76-164 57-119 (195)
122 PRK04023 DNA polymerase II lar 42.6 23 0.00051 35.6 3.0 16 132-147 664-679 (1121)
123 PRK00762 hypA hydrogenase nick 42.2 17 0.00037 27.2 1.7 9 132-140 93-101 (124)
124 COG1327 Predicted transcriptio 42.1 13 0.00027 29.2 0.9 42 109-150 2-47 (156)
125 PRK07111 anaerobic ribonucleos 41.8 12 0.00027 36.3 1.0 21 108-139 681-701 (735)
126 COG1867 TRM1 N2,N2-dimethylgua 41.6 29 0.00063 31.1 3.3 48 105-159 238-293 (380)
127 PRK12775 putative trifunctiona 41.6 20 0.00044 36.0 2.6 34 107-147 821-854 (1006)
128 COG1545 Predicted nucleic-acid 40.8 23 0.0005 27.1 2.2 24 107-140 29-52 (140)
129 COG0566 SpoU rRNA methylases [ 40.6 1.5E+02 0.0033 24.8 7.4 31 72-102 19-50 (260)
130 PRK05978 hypothetical protein; 40.6 17 0.00037 28.3 1.5 34 107-145 33-66 (148)
131 smart00857 Resolvase Resolvase 39.7 89 0.0019 22.9 5.4 24 79-102 53-76 (148)
132 PF13597 NRDD: Anaerobic ribon 39.1 11 0.00023 35.3 0.2 23 107-140 491-513 (546)
133 PRK08351 DNA-directed RNA poly 38.5 27 0.00059 23.1 2.0 8 133-140 17-24 (61)
134 PRK02935 hypothetical protein; 38.5 19 0.00042 26.5 1.4 28 108-143 71-98 (110)
135 COG2093 DNA-directed RNA polym 38.3 39 0.00085 22.5 2.7 8 133-140 20-27 (64)
136 PF03485 Arg_tRNA_synt_N: Argi 38.0 38 0.00083 23.0 2.9 28 9-38 54-81 (85)
137 COG1083 NeuA CMP-N-acetylneura 38.0 46 0.001 27.7 3.7 26 74-100 27-52 (228)
138 PRK12286 rpmF 50S ribosomal pr 37.9 23 0.00049 23.0 1.6 21 108-139 28-48 (57)
139 KOG2593|consensus 37.8 9.6 0.00021 34.6 -0.3 37 105-142 126-164 (436)
140 KOG2907|consensus 37.4 13 0.00029 27.6 0.4 33 108-140 75-111 (116)
141 TIGR02487 NrdD anaerobic ribon 37.4 46 0.00099 31.4 4.1 39 85-140 509-547 (579)
142 PF08772 NOB1_Zn_bind: Nin one 37.3 27 0.00059 23.9 1.9 27 105-140 7-33 (73)
143 PF01667 Ribosomal_S27e: Ribos 37.2 42 0.00091 21.7 2.7 29 107-140 7-35 (55)
144 PRK14704 anaerobic ribonucleos 36.9 17 0.00036 34.7 1.1 23 107-140 559-581 (618)
145 TIGR00244 transcriptional regu 36.8 20 0.00043 27.9 1.3 39 109-147 2-44 (147)
146 TIGR00186 rRNA_methyl_3 rRNA m 36.6 1.1E+02 0.0023 25.2 5.8 24 75-100 2-25 (237)
147 COG0675 Transposase and inacti 36.2 35 0.00075 28.5 2.9 52 89-160 295-346 (364)
148 TIGR01385 TFSII transcription 36.0 20 0.00043 31.1 1.3 35 108-142 259-297 (299)
149 PF14599 zinc_ribbon_6: Zinc-r 35.9 37 0.00081 22.4 2.4 37 97-140 20-57 (61)
150 smart00731 SprT SprT homologue 35.8 29 0.00063 26.3 2.1 63 77-142 80-144 (146)
151 COG2260 Predicted Zn-ribbon RN 35.8 27 0.00059 22.9 1.6 12 133-144 19-30 (59)
152 PF14488 DUF4434: Domain of un 35.2 1.6E+02 0.0034 23.0 6.3 63 82-169 24-86 (166)
153 COG2401 ABC-type ATPase fused 35.2 15 0.00033 33.8 0.5 31 107-147 130-160 (593)
154 COG1379 PHP family phosphoeste 34.9 15 0.00032 32.5 0.4 22 131-153 265-286 (403)
155 PRK14810 formamidopyrimidine-D 34.6 30 0.00065 29.3 2.2 27 108-138 245-271 (272)
156 PRK06393 rpoE DNA-directed RNA 33.4 31 0.00067 23.1 1.6 29 133-175 19-48 (64)
157 PF06044 DRP: Dam-replacing fa 33.3 17 0.00036 30.7 0.4 38 108-148 32-70 (254)
158 PF05991 NYN_YacP: YacP-like N 33.3 2.1E+02 0.0046 22.2 6.7 36 147-183 80-115 (166)
159 TIGR00375 conserved hypothetic 33.3 23 0.00051 31.6 1.4 67 79-155 212-281 (374)
160 PRK10445 endonuclease VIII; Pr 33.0 34 0.00074 28.8 2.3 40 90-138 223-262 (263)
161 smart00661 RPOL9 RNA polymeras 32.4 27 0.00058 21.4 1.2 9 131-139 20-28 (52)
162 TIGR01031 rpmF_bact ribosomal 32.3 29 0.00063 22.3 1.3 21 108-139 27-47 (55)
163 KOG1497|consensus 31.8 25 0.00054 31.2 1.3 30 25-54 227-256 (399)
164 TIGR00577 fpg formamidopyrimid 31.7 37 0.0008 28.7 2.3 26 109-138 247-272 (272)
165 COG2179 Predicted hydrolase of 31.7 71 0.0015 25.6 3.7 24 149-173 51-74 (175)
166 COG1997 RPL43A Ribosomal prote 31.1 33 0.00071 24.4 1.6 27 107-139 35-61 (89)
167 COG1594 RPB9 DNA-directed RNA 31.0 28 0.00061 25.7 1.3 35 108-142 73-111 (113)
168 PF05876 Terminase_GpA: Phage 31.0 27 0.00059 32.7 1.5 38 105-142 198-240 (557)
169 COG1198 PriA Primosomal protei 30.6 74 0.0016 31.1 4.3 47 80-143 410-456 (730)
170 cd01675 RNR_III Class III ribo 30.5 66 0.0014 30.2 3.9 22 109-140 520-541 (555)
171 PRK01103 formamidopyrimidine/5 30.3 40 0.00087 28.5 2.3 27 109-139 247-273 (274)
172 TIGR00354 polC DNA polymerase, 30.1 38 0.00082 34.0 2.3 33 105-146 1010-1043(1095)
173 PF07191 zinc-ribbons_6: zinc- 29.9 39 0.00084 23.0 1.7 26 107-143 17-42 (70)
174 COG4972 PilM Tfp pilus assembl 29.8 75 0.0016 28.2 3.9 42 2-43 259-304 (354)
175 PRK14811 formamidopyrimidine-D 29.8 40 0.00086 28.5 2.2 27 109-139 237-263 (269)
176 PRK13945 formamidopyrimidine-D 29.7 40 0.00087 28.6 2.2 26 109-138 256-281 (282)
177 PRK08271 anaerobic ribonucleos 29.7 31 0.00066 33.0 1.6 34 5-38 442-476 (623)
178 PF03833 PolC_DP2: DNA polymer 29.7 18 0.00038 35.7 0.0 11 81-91 636-646 (900)
179 PRK10220 hypothetical protein; 29.5 35 0.00077 25.2 1.5 30 109-145 5-34 (111)
180 COG0375 HybF Zn finger protein 29.4 37 0.0008 25.3 1.7 27 106-140 69-95 (115)
181 COG2176 PolC DNA polymerase II 29.3 42 0.00092 34.6 2.5 32 107-141 914-949 (1444)
182 PF00301 Rubredoxin: Rubredoxi 29.0 75 0.0016 19.7 2.8 11 130-140 33-43 (47)
183 TIGR00686 phnA alkylphosphonat 29.0 36 0.00078 25.2 1.5 29 109-144 4-32 (109)
184 PF01780 Ribosomal_L37ae: Ribo 28.6 38 0.00082 24.2 1.5 27 107-139 35-61 (90)
185 COG1571 Predicted DNA-binding 28.5 39 0.00086 30.7 2.0 69 63-142 310-378 (421)
186 COG0777 AccD Acetyl-CoA carbox 28.2 25 0.00055 30.3 0.7 35 108-147 29-63 (294)
187 PF12172 DUF35_N: Rubredoxin-l 28.1 45 0.00098 19.1 1.6 24 107-140 11-34 (37)
188 PF01783 Ribosomal_L32p: Ribos 27.8 54 0.0012 21.0 2.1 20 108-138 27-46 (56)
189 cd00730 rubredoxin Rubredoxin; 27.8 63 0.0014 20.3 2.3 11 130-140 33-43 (50)
190 PF14205 Cys_rich_KTR: Cystein 27.6 62 0.0013 21.0 2.2 32 108-140 5-37 (55)
191 PRK00448 polC DNA polymerase I 27.5 29 0.00062 36.4 1.0 31 107-141 908-943 (1437)
192 TIGR02827 RNR_anaer_Bdell anae 27.5 36 0.00077 32.3 1.6 23 108-140 533-555 (586)
193 cd02982 PDI_b'_family Protein 27.2 94 0.002 21.1 3.4 36 147-182 28-63 (103)
194 PF09567 RE_MamI: MamI restric 27.1 32 0.00069 29.3 1.1 66 59-140 37-105 (314)
195 COG3357 Predicted transcriptio 27.0 28 0.00062 25.0 0.7 28 108-141 59-86 (97)
196 PRK14715 DNA polymerase II lar 26.9 45 0.00098 34.8 2.3 43 105-156 1540-1582(1627)
197 TIGR02180 GRX_euk Glutaredoxin 26.5 48 0.001 21.6 1.8 23 74-96 62-84 (84)
198 PRK14714 DNA polymerase II lar 26.3 52 0.0011 34.1 2.5 35 105-147 1251-1285(1337)
199 PF09845 DUF2072: Zn-ribbon co 26.2 36 0.00078 26.0 1.1 6 134-139 22-27 (131)
200 CHL00174 accD acetyl-CoA carbo 26.0 19 0.00042 31.1 -0.4 43 108-156 39-81 (296)
201 PHA02546 47 endonuclease subun 25.8 2.7E+02 0.0059 24.1 6.8 61 80-174 28-89 (340)
202 KOG3507|consensus 25.4 54 0.0012 21.6 1.7 29 105-140 18-46 (62)
203 COG1712 Predicted dinucleotide 25.1 1.9E+02 0.004 24.5 5.2 23 148-170 99-121 (255)
204 PRK10966 exonuclease subunit S 25.1 2.3E+02 0.005 25.4 6.3 60 82-176 30-89 (407)
205 COG1961 PinR Site-specific rec 24.8 1.7E+02 0.0036 23.5 5.0 58 79-177 52-114 (222)
206 PF08792 A2L_zn_ribbon: A2L zi 24.8 78 0.0017 18.1 2.1 27 108-140 4-30 (33)
207 TIGR00619 sbcd exonuclease Sbc 24.6 2.9E+02 0.0062 22.8 6.4 61 81-176 29-90 (253)
208 PRK04023 DNA polymerase II lar 24.6 58 0.0013 33.0 2.5 33 105-146 1035-1068(1121)
209 PF03811 Zn_Tnp_IS1: InsA N-te 24.4 79 0.0017 18.5 2.1 12 106-117 4-15 (36)
210 COG0266 Nei Formamidopyrimidin 24.3 58 0.0013 27.9 2.2 26 109-138 247-272 (273)
211 PRK14056 phenylalanine 4-monoo 24.2 2.8E+02 0.006 26.4 6.7 48 55-106 274-321 (578)
212 PRK05580 primosome assembly pr 23.8 99 0.0021 29.7 3.9 11 81-91 357-367 (679)
213 TIGR00515 accD acetyl-CoA carb 23.7 25 0.00054 30.2 -0.2 48 97-155 21-68 (285)
214 cd03031 GRX_GRX_like Glutaredo 23.7 50 0.0011 25.5 1.6 39 74-114 68-106 (147)
215 PRK00432 30S ribosomal protein 23.7 46 0.001 20.9 1.1 9 131-139 37-45 (50)
216 PRK10864 putative methyltransf 23.5 2.2E+02 0.0047 25.2 5.7 28 74-101 108-137 (346)
217 COG3677 Transposase and inacti 22.9 62 0.0014 24.4 1.9 12 130-141 52-63 (129)
218 TIGR00155 pqiA_fam integral me 22.8 49 0.0011 29.8 1.6 30 108-142 14-44 (403)
219 PF09818 ABC_ATPase: Predicted 22.7 1.6E+02 0.0034 27.1 4.7 68 81-171 331-398 (448)
220 PRK09263 anaerobic ribonucleos 22.5 46 0.001 32.3 1.4 27 108-140 642-668 (711)
221 PF09526 DUF2387: Probable met 22.3 56 0.0012 22.2 1.4 7 108-114 9-15 (71)
222 PF12760 Zn_Tnp_IS1595: Transp 22.3 79 0.0017 19.1 2.0 26 108-138 19-44 (46)
223 TIGR03826 YvyF flagellar opero 22.1 2.5E+02 0.0054 21.5 5.1 70 55-141 25-104 (137)
224 PF08274 PhnA_Zn_Ribbon: PhnA 22.1 57 0.0012 18.4 1.2 11 130-140 18-28 (30)
225 PRK06091 membrane protein FdrA 21.9 4.2E+02 0.0092 25.1 7.5 71 28-98 32-124 (555)
226 PRK15103 paraquat-inducible me 21.5 55 0.0012 29.6 1.6 31 108-143 11-42 (419)
227 KOG0023|consensus 21.5 1.2E+02 0.0026 26.9 3.6 30 154-183 198-227 (360)
228 TIGR01405 polC_Gram_pos DNA po 21.5 53 0.0011 33.9 1.6 9 107-115 683-691 (1213)
229 PRK05654 acetyl-CoA carboxylas 21.2 27 0.00058 30.1 -0.5 48 97-155 22-69 (292)
230 PRK14873 primosome assembly pr 21.0 67 0.0014 30.9 2.1 15 29-43 295-309 (665)
231 COG1908 FrhD Coenzyme F420-red 20.9 3.2E+02 0.0069 20.8 5.2 44 24-73 51-94 (132)
232 TIGR00411 redox_disulf_1 small 20.8 1.3E+02 0.0029 19.3 3.1 32 151-182 19-50 (82)
233 COG0420 SbcD DNA repair exonuc 20.7 2.1E+02 0.0045 25.1 5.1 61 81-176 30-90 (390)
234 PRK08579 anaerobic ribonucleos 20.7 54 0.0012 31.3 1.4 23 108-140 569-591 (625)
235 COG1645 Uncharacterized Zn-fin 20.5 48 0.001 25.3 0.9 8 133-140 46-53 (131)
236 PRK05906 lipid A biosynthesis 20.2 6.6E+02 0.014 23.0 8.3 41 60-100 175-219 (454)
No 1
>PRK04011 peptide chain release factor 1; Provisional
Probab=100.00 E-value=1e-43 Score=315.29 Aligned_cols=182 Identities=27% Similarity=0.460 Sum_probs=166.8
Q ss_pred hhhhHHHHHHHHHHHHhhhhcCCCCccEEEEeCChhhHHhhcccCCCCHhhhc---------------------------
Q psy9094 2 EKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPVRFS--------------------------- 54 (185)
Q Consensus 2 ~~~~~f~k~va~~~~~~f~~~~~~~i~~lIIaGPg~~k~~f~~~~~L~~~l~~--------------------------- 54 (185)
+++++||++||+.+.++|++.++.++++|||||||++|++|.+++||++++++
T Consensus 192 ~~~~~f~k~Vae~~~~~f~~~~~~~v~~IvlaGpg~~K~~f~~~~~L~~~l~~~vv~~~~~s~~~~~Gl~E~l~~~~~~L 271 (411)
T PRK04011 192 QAAHEFYKRVGEKANEAFLPLLEGKLKGILIGGPGPTKEEFLEGDYLHYELKKKILGLFDVSYTGESGLRELVDKASDLL 271 (411)
T ss_pred HHHHHHHHHHHHHHHHHHhhhccccccEEEEECChhHHHHHhhhhhhhHHHHhheEEEEecCCCCccCHHHHHHHHHHHH
Confidence 46889999999999999986445789999999999999999988899998764
Q ss_pred ----hHHHHHHHHHHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCC
Q psy9094 55 ----PLKNKNKMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKS 130 (185)
Q Consensus 55 ----~~~E~~lve~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~ 130 (185)
+.+|+++|++||+++++++|++|||+++|++|+++|||+||||+|+|.+.|++++|++|+...+.+..+.+.. .
T Consensus 272 ~~~k~~~e~~lle~f~~~l~~d~g~avyG~~~V~~Ale~GAVetLLV~d~l~~~r~~~~c~~c~~~~~~~~~~~~~~--~ 349 (411)
T PRK04011 272 KEQELVKEKKLMEEFFKELAKDGGLAVYGEEEVRKALEMGAVDTLLISEDLRKDRVTYKCPNCGYEEEKTVKRREEL--P 349 (411)
T ss_pred HHhHHHHHHHHHHHHHHHHhcCCCcEEEcHHHHHHHHHcCCceEEEEeccccceeEEEEcCCCCcceeeeccccccc--c
Confidence 6789999999999999999999999999999999999999999999999999999999998888876665532 2
Q ss_pred ccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCCCchHHHHhhhcCCcC
Q psy9094 131 HFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185 (185)
Q Consensus 131 ~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l~~~~GGia 185 (185)
.-.||.||++++.++.+++++||+++|+++|++|+|||++|++|+||+++|||||
T Consensus 350 ~~~c~~~~~~~~~~~~~~~v~~l~e~a~~~g~~v~iis~~~e~G~qL~~~fGGIa 404 (411)
T PRK04011 350 EKTCPKCGSELEIVEEEDIIEELSELAEQSGTKVEVISTDTEEGEQLLKAFGGIA 404 (411)
T ss_pred cccCcccCcccccchhhhHHHHHHHHHHHcCCEEEEECCCChhHHHHHHcCCCEE
Confidence 3369999999999999999999999999999999999999999999999999996
No 2
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=100.00 E-value=1.3e-43 Score=313.78 Aligned_cols=182 Identities=29% Similarity=0.492 Sum_probs=166.1
Q ss_pred hhhhHHHHHHHHHHHHhhhhcCCCCccEEEEeCChhhHHhhcccCCCCHhhhc---------------------------
Q psy9094 2 EKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPVRFS--------------------------- 54 (185)
Q Consensus 2 ~~~~~f~k~va~~~~~~f~~~~~~~i~~lIIaGPg~~k~~f~~~~~L~~~l~~--------------------------- 54 (185)
+++|+||++||+.+.++|++.+..++++|||||||++|++|.+++||++++++
T Consensus 184 ~~~~~f~~~Vae~~~~~f~~~~~~~v~~lILaGpg~~K~~f~~~~~L~~~l~~kvi~~vd~s~~~~~Gl~Evl~~~~~~L 263 (403)
T TIGR03676 184 IAAHEFYKRVGEAANEAFLPLKDKKLKGILIGGPGPTKEEFAEGDYLHHELKKKILGLFDVSYTGESGLRELVEKAEDLL 263 (403)
T ss_pred HHHHHHHHHHHHHHHHHHhhcccccccEEEEeCCHHHHHHHhhhhhhhHHHHhhEEEEEecCCCCccCHHHHHHHHHHHH
Confidence 46889999999999999987444479999999999999999988899999865
Q ss_pred ----hHHHHHHHHHHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCC
Q psy9094 55 ----PLKNKNKMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKS 130 (185)
Q Consensus 55 ----~~~E~~lve~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~ 130 (185)
+.+|+++|++||++|++++|++|||+++|++|+++|||+||||+|+|...|++++|++|+...+.+..+.+....
T Consensus 264 ~~~k~~~E~~lle~f~~el~~d~g~avyG~~eV~~ALe~GAVetLLV~d~l~~~r~~~rc~~c~~~~~~~~~~~~~~~~- 342 (403)
T TIGR03676 264 KDLELMKEKKLMERFFKELVKDGGLAAYGEEEVRKALEMGAVDTLLISEDLRKIRVTFKCPNCGYEEEKTVKPEEGDKS- 342 (403)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcEEEcHHHHHHHHHhCCCcEEEEEccccceeEEEEcCCCCcceeeeccccccccc-
Confidence 678999999999999999999999999999999999999999999999999999999999888877666554222
Q ss_pred ccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCCCchHHHHhhhcCCcC
Q psy9094 131 HFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185 (185)
Q Consensus 131 ~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l~~~~GGia 185 (185)
..||.||++++.++.+++++||+++|+++||+|+|||++|++|+||+++|||||
T Consensus 343 -~~~~~~~~~~~~~~~~~~ve~L~e~a~~~Ga~V~~iS~~~eeG~ql~~~fGGIa 396 (403)
T TIGR03676 343 -EACPKCGSELEIVEEEDIIEELSELAEESGAKVEIISTDTEEGEQLLKAFGGIA 396 (403)
T ss_pred -ccCcccCcccccchhhhHHHHHHHHHHHcCCEEEEECCCChhHHHHHHcCCcEE
Confidence 459999999999999999999999999999999999999999999989999996
No 3
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=100.00 E-value=1.1e-43 Score=314.91 Aligned_cols=182 Identities=35% Similarity=0.605 Sum_probs=163.0
Q ss_pred hhhhHHHHHHHHHHHHhhhhcCCCCccEEEEeCChhhHHhhcccCCCCHhhhc---------------------------
Q psy9094 2 EKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPVRFS--------------------------- 54 (185)
Q Consensus 2 ~~~~~f~k~va~~~~~~f~~~~~~~i~~lIIaGPg~~k~~f~~~~~L~~~l~~--------------------------- 54 (185)
+++|+||++||+.+.++|++.+..++++|||||||++|++|++++||++++++
T Consensus 188 ~~~~~f~~~Vae~~~~~f~~~~~~~v~~IIlaGpg~~K~~f~~~~~l~~~l~~kvi~~vdvs~gg~~gl~E~l~~~~~~L 267 (409)
T TIGR00108 188 LAAHEFLKKVGEVANEAFLPNDDVKLKGIILGGPGHTKEEFAEGEYLHHELKKKVISTVDVSYTGEFGIRELIEKSADVL 267 (409)
T ss_pred HHHHHHHHHHHHHHHHHhhhcccccceEEEEeccHHHHHHhhhhhhHHHHhhhhEEEEEEcCCCcccCHHHHHHHHHHHH
Confidence 36799999999999999987444589999999999999999988899998854
Q ss_pred ----hHHHHHHHHHHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCC
Q psy9094 55 ----PLKNKNKMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKS 130 (185)
Q Consensus 55 ----~~~E~~lve~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~ 130 (185)
+.+|+++|++||++|++++|++|||+++|++||++|||+||||+|+|...|++++|++|+.. .+..+.+..+.+
T Consensus 268 ~~~k~~~E~~lle~F~~ei~~d~G~avyG~~eV~~ALe~GAVetLLV~d~l~~~r~~~r~~~~~~~--~~~~~~~~~~~~ 345 (409)
T TIGR00108 268 AEVDYMREKKLVQRFLKELIQEDGLACYGEDEVLKALDLGAVETLIVSEDLEYIRVTYKCAECGEV--IEKTVRELKDKK 345 (409)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcEEeCHHHHHHHHHhCCCcEEEEeccccceeEEEEcCCCCce--eecccccccccc
Confidence 67899999999999999999999999999999999999999999999999999999999973 332222222334
Q ss_pred ccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCCCchHHHHhhhcCCcC
Q psy9094 131 HFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185 (185)
Q Consensus 131 ~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l~~~~GGia 185 (185)
.+.||.||+++.+++++++++||+++|+++||+|+|||++|++|+||+++|||||
T Consensus 346 ~~~c~~~~~~~~~~~~~~~ve~L~e~a~~~Ga~V~iiS~~~eeG~ql~~~fGGIa 400 (409)
T TIGR00108 346 FAICPACGQEMDVVEERDLIEWLSELAENFGAKLEFISTESEEGAQLLTAFGGIG 400 (409)
T ss_pred cccCcccCccccchhhhhHHHHHHHHHHHcCCEEEEECCCChhHHHHHHhCCCEE
Confidence 5689999999999999999999999999999999999999999999999999996
No 4
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.7e-40 Score=286.27 Aligned_cols=181 Identities=31% Similarity=0.521 Sum_probs=163.7
Q ss_pred hhhhHHHHHHHHHHHHhhhhcCCCCccEEEEeCChhhHHhhcccCCCCHhhhc---------------------------
Q psy9094 2 EKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPVRFS--------------------------- 54 (185)
Q Consensus 2 ~~~~~f~k~va~~~~~~f~~~~~~~i~~lIIaGPg~~k~~f~~~~~L~~~l~~--------------------------- 54 (185)
++.|+||++|++.|+++|++....++++||||||+++|++|++++||+++|++
T Consensus 191 e~~h~f~k~vge~A~e~f~~~~~~~~kgIilgGp~~tk~ef~e~~yL~~~lk~kv~~lvDv~y~~esg~~eli~~A~d~L 270 (411)
T COG1503 191 EAAHEFYKKVGEAASEAFLPIAKKELKGIILGGPGPTKEEFVEGDYLHHELKKKVLGLVDVSYTGESGLRELIEKAEDAL 270 (411)
T ss_pred HHHHHHHHHHHHHHHHHhcchhhhhhcceEeeCCcccchhhhcccccchHHHHHHHhhccccccccccHHHHHHHhHHHH
Confidence 57899999999999999998544489999999999999999999999999976
Q ss_pred ----hHHHHHHHHHHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCC
Q psy9094 55 ----PLKNKNKMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKS 130 (185)
Q Consensus 55 ----~~~E~~lve~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~ 130 (185)
+.+|+++|++|++++.+++|+++||.++|++||++|||++|||++++...||+|+|+.|+........+.. ..
T Consensus 271 ~~~~~~~eK~l~e~f~~e~~~~~Gla~yG~~~vr~aL~~gaVd~llv~Edl~~~r~~~~c~~~~~e~~~t~~~~~--~~- 347 (411)
T COG1503 271 KDVDYVREKKLMEEFFKELAKDSGLAVYGEEEVREALEMGAVDTLLVSEDLEKERVTYKCPTCGYENLKSKREFE--QK- 347 (411)
T ss_pred HhhhhhcchhHHHHHHHHhccCcceeecchHHHHHHHHhcccceEEeeccccccceeecCCCcchhhhhcccccc--cc-
Confidence 67999999999999999999999999999999999999999999999999999999999964433311111 11
Q ss_pred ccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCCCchHHHHhhhcCCcC
Q psy9094 131 HFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185 (185)
Q Consensus 131 ~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l~~~~GGia 185 (185)
.+.||.||.++..+++.|+++|++++|+++|++|+|||+++++|.||+++|||+|
T Consensus 348 ~~~~~~~~~e~~~v~~~d~vd~l~e~a~~~Ga~ve~is~~~~eg~q~~~afgGi~ 402 (411)
T COG1503 348 RFRCPECGSEMEEVEVSDLVDELAELAEESGAKVEIISDDTDEGAQLLKAFGGLA 402 (411)
T ss_pred cccCccccccccchhhhhHHHHHHHHHHhcCCeEEEecCchHHHHHHHHcccchh
Confidence 3389999999999999999999999999999999999999999999999999986
No 5
>KOG0688|consensus
Probab=100.00 E-value=4.7e-36 Score=254.08 Aligned_cols=184 Identities=78% Similarity=1.170 Sum_probs=174.3
Q ss_pred ChhhhHHHHHHHHHHHHhhhhcCCCCccEEEEeCChhhHHhhcccCCCCHhhhc--------------------------
Q psy9094 1 MEKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPVRFS-------------------------- 54 (185)
Q Consensus 1 ~~~~~~f~k~va~~~~~~f~~~~~~~i~~lIIaGPg~~k~~f~~~~~L~~~l~~-------------------------- 54 (185)
++++|+|.+++|+.+.+.|+..+..++.+||+||.+++|+++.+|+.+|+||+.
T Consensus 191 ~ekRhnYVrkvae~a~q~fi~~~~~Nv~gLilaGsadfKtelsqSd~fd~rlqskvi~~vdvsyGGengfnQaIeL~aev 270 (431)
T KOG0688|consen 191 MEKRHNYVRKVAELAVQRFITNDKPNVAGLILAGSADFKTELSQSDMFDPRLQSKVLKTVDVSYGGENGFNQAIELSAEV 270 (431)
T ss_pred hhhhccceeeecccceeEEecCCCcceeEEEEecccccccccchhhhcchHHhhhHHhhhcccccchhhHHHHHHHHHhh
Confidence 578999999999999999998778999999999999999999999999999986
Q ss_pred -----hHHHHHHHHHHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccC
Q psy9094 55 -----PLKNKNKMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDK 129 (185)
Q Consensus 55 -----~~~E~~lve~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~ 129 (185)
+++|++++.+||++++.|.|+.|||+++|+.||++|||+|||||++|...||+++|+. +...+.++.|+++.++
T Consensus 271 lsnvk~vqekkli~~yfdEisqdtgky~Fgv~dTl~aLe~gavetli~~enLd~~ry~~kn~~-~~~~i~~l~~~~e~d~ 349 (431)
T KOG0688|consen 271 LSNVKFVQEKKLIGKYFDEISQDTGKYCFGVEDTLLALEMGAVETLIVWENLDIIRYELKNSD-GESVIGFLVPDEEKDK 349 (431)
T ss_pred hhcceeeehhhHHHHHhhhhhcccCcccccHHHHHHHHHcCCeeehhHhhhhhhhhhhhcccC-Cccceeeecchhhccc
Confidence 7799999999999999999999999999999999999999999999999999999987 6667777778878888
Q ss_pred CccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCCCchHHHHhhhcCCcC
Q psy9094 130 SHFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185 (185)
Q Consensus 130 ~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l~~~~GGia 185 (185)
++|.+...|-.++++|..++++|+.++++++|+.++||++.|.+|.||+++||||+
T Consensus 350 s~~~Dketg~e~elie~~pLlEw~AnnYK~FGa~LE~VTdKSqEgsQFv~GfGgiG 405 (431)
T KOG0688|consen 350 SHFTDKETGWEMELIERMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIG 405 (431)
T ss_pred ccccccccchhhhHHhhhhHHHHHHHHHhhcCeEEEEecccchhHHHHHhhcCCcc
Confidence 89999999999999999999999999999999999999999999999999999986
No 6
>TIGR00111 pelota probable translation factor pelota. This model describes the Drosophila protein Pelota, the budding yeast protein DOM34 which it can replace, and a set of closely related archaeal proteins. Members contain a proposed RNA binding motif. The meiotic defect in pelota mutants may be a complex result of a protein translation defect, as suggested in yeast by ribosomal protein RPS30A being a multicopy suppressor and by an altered polyribosome profile in DOM34 mutants rescued by RPS30A. This family is homologous to a family of peptide chain release factors. Pelota is proposed to act in protein translation.
Probab=99.97 E-value=8.3e-32 Score=235.06 Aligned_cols=133 Identities=22% Similarity=0.441 Sum_probs=116.1
Q ss_pred hhhhHHHHHHHHHHHHhhhhcCCCCccEEEEeCChhhHHhhcccCCCCHhhhc---------------------------
Q psy9094 2 EKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPVRFS--------------------------- 54 (185)
Q Consensus 2 ~~~~~f~k~va~~~~~~f~~~~~~~i~~lIIaGPg~~k~~f~~~~~L~~~l~~--------------------------- 54 (185)
+++++||++|++.+.+ | +++++||||||||+|++|++ ||+.++.+
T Consensus 177 ~~~~~Ff~~v~~~l~~-~-----~~v~~iIiaGPGf~k~~f~~--~l~~~~~~~~~k~ii~~~s~g~~~gl~EvL~~~~v 248 (351)
T TIGR00111 177 ELRKEFYKEIAKKLLN-F-----DDLKTIIVAGPGFYKNDFYD--FIFERYPEEANKAVLENCSTGGRAGINEVLKRGLV 248 (351)
T ss_pred HHHHHHHHHHHHHHhh-h-----cccCEEEEECCHHHHHHHHH--HHHHHhhhhhCCcEEEecCCCchhHHHHHHhChHH
Confidence 3578999999998753 3 47999999999999999984 66554321
Q ss_pred --------hHHHHHHHHHHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCcccc
Q psy9094 55 --------PLKNKNKMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQE 126 (185)
Q Consensus 55 --------~~~E~~lve~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~ 126 (185)
+++|+++|++||++|+++++++|||+++|.+|+++|||+||||+|+++..|
T Consensus 249 ~~~l~d~k~~~E~~~l~~f~~~l~kd~~~~~YG~~eV~~Ale~GAVetLLIsD~l~~~r--------------------- 307 (351)
T TIGR00111 249 ARILQETRYAKEIMVIDEFLEHLAKDGDKAVYGEDEVVKAAEYGAIEYLLVTDKVLVQR--------------------- 307 (351)
T ss_pred HHHHhhhhHHHHHHHHHHHHHHHhcCCCeEEECHHHHHHHHHcCCceEEEEecchhhhH---------------------
Confidence 779999999999999999999999999999999999999999999995321
Q ss_pred ccCCccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCCCchHHHHhhhcCCcC
Q psy9094 127 KDKSHFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185 (185)
Q Consensus 127 ~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l~~~~GGia 185 (185)
++ +++|++.|+++|++|+|||++|++|+|| ++|||||
T Consensus 308 --------------------~~-~~~l~~~v~~~gg~V~i~Ss~~e~G~qL-~~lgGia 344 (351)
T TIGR00111 308 --------------------EE-IEKLLDSVESMGGKVVILSTEHELGKQL-DSLGGIA 344 (351)
T ss_pred --------------------HH-HHHHHHHHHHcCCEEEEEcCCCccHHHH-hhCCCEE
Confidence 22 5679999999999999999999999999 9999996
No 7
>PF03465 eRF1_3: eRF1 domain 3; InterPro: IPR005142 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins which may also be involved in translation termination but this awaits experimental verification.; PDB: 3OBY_A 3E1Y_D 1DT9_A 2KTU_A 2KTV_A 3IR9_A 3E20_H 3OBW_A 3AGJ_F 3MCA_B ....
Probab=99.96 E-value=3.4e-30 Score=191.90 Aligned_cols=106 Identities=40% Similarity=0.639 Sum_probs=94.6
Q ss_pred hHHHHHHHHHHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCcccc
Q psy9094 55 PLKNKNKMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTD 134 (185)
Q Consensus 55 ~~~E~~lve~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c 134 (185)
+++|+++|++||+++.+++++++||+++|++|+++|||+||||+|++.+.+++.+| .|
T Consensus 1 ~~~E~~~ve~f~~~l~k~~~~~~yG~~eV~~Al~~GaV~~LlI~d~l~~~~~~~r~----------------------~~ 58 (113)
T PF03465_consen 1 IIKEKKLVEEFFEELAKDPGLAVYGIEEVKKALEMGAVETLLISDDLFRSRDVERC----------------------KC 58 (113)
T ss_dssp HHHHHHHHHHHHHHHHTTCSSEEESHHHHHHHHHTT-EEEEEEEHHHHTESCHHHH----------------------HS
T ss_pred CHHHHHHHHHHHHHHhhCCCcEEECHHHHHHHHHhCCCcEEEEecccccccceecc----------------------cc
Confidence 47899999999999999999999999999999999999999999999988654444 24
Q ss_pred CccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCCCchHHHHhhhcCCcC
Q psy9094 135 KETGVELELVECQPLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185 (185)
Q Consensus 135 ~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l~~~~GGia 185 (185)
|.||++++.++ ++++|+++|+++|++|+|||++|++|+||+++|||||
T Consensus 59 ~~~~~~~~~~~---~i~~l~~~a~~~g~~v~iis~~~e~G~~L~~~~gGIa 106 (113)
T PF03465_consen 59 PECGGELEVVE---LIEELIELAEQSGAKVEIISSEHEEGEQLLKGFGGIA 106 (113)
T ss_dssp TTTHSEEEEEE---HHHHHHHHHHHTTSEEEEE-TTSHHHHHHHHCTTTEE
T ss_pred ccccchhhhHH---HHHHHHHHHHHcCCEEEEEcCCCccHHHHHhcCCcEE
Confidence 78888886665 9999999999999999999999999999999999996
No 8
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=99.96 E-value=4.3e-29 Score=214.67 Aligned_cols=135 Identities=22% Similarity=0.395 Sum_probs=117.8
Q ss_pred hHHHHHHHHHHHHhhhhcCCCCccEEEEeCChhhHHhhcccCCCCHhhhc------------------------------
Q psy9094 5 HNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPVRFS------------------------------ 54 (185)
Q Consensus 5 ~~f~k~va~~~~~~f~~~~~~~i~~lIIaGPg~~k~~f~~~~~L~~~l~~------------------------------ 54 (185)
.+||..|++.+.+++ +.+.+|||||||+|++|+ +|+..+..+
T Consensus 176 ~k~~~~i~~~~~~~~------~~~~iIvaGPGF~k~~~~--~~~~~~~p~~~~~~~~~~s~~g~~gi~EvLkr~~v~ki~ 247 (352)
T COG1537 176 RKFFDEIAKALKEYA------NLDIIIVAGPGFAKEDFY--DFLRERYPELANIVIEDTSTGGRAGINEVLKRGAVDKIL 247 (352)
T ss_pred HHHHHHHHHHHHHhh------CCCeEEEeCCchHHHHHH--HHHHHhcccccceEEEeccCcchHHHHHHHhhhhHHhHh
Confidence 589999999999776 578899999999999998 466554311
Q ss_pred ----hHHHHHHHHHHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCC
Q psy9094 55 ----PLKNKNKMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKS 130 (185)
Q Consensus 55 ----~~~E~~lve~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~ 130 (185)
+++|.++|++||+.|+++++++|||+++|++|+++|||++|||+|+++++ ++
T Consensus 248 ~e~ria~e~~~~e~fl~~iak~~~~v~YG~~eV~~A~e~GAve~LLv~De~lr~------~~------------------ 303 (352)
T COG1537 248 SETRIAEEIELVEEFLERLAKDDDKVAYGLEEVEKAAEYGAVETLLVTDELLRS------DD------------------ 303 (352)
T ss_pred hhhHHHHHHHHHHHHHHHHhcCCCceeEcHHHHHHHHhcCcceeEEeehhhhcc------cc------------------
Confidence 77999999999999999999999999999999999999999999999876 11
Q ss_pred ccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCCCchHHHHhhhcCCcC
Q psy9094 131 HFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185 (185)
Q Consensus 131 ~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l~~~~GGia 185 (185)
++.+.-++.+++.++++|++|+|||++|+.|++| ++|||||
T Consensus 304 -------------~~~re~~~~ll~~ve~~ggkV~Ivs~~he~Ge~L-k~lGGia 344 (352)
T COG1537 304 -------------VEEREDVEELLEEVESMGGKVVIVSTEHEPGERL-KALGGIA 344 (352)
T ss_pred -------------hhhHHHHHHHHHHHHHcCCeEEEEecCCcchHHH-HhccCeE
Confidence 1333456789999999999999999999999999 9999996
No 9
>KOG2869|consensus
Probab=99.93 E-value=9.4e-26 Score=191.70 Aligned_cols=141 Identities=16% Similarity=0.259 Sum_probs=120.2
Q ss_pred hhhhHHHHHHHHHHHHhhhhcCCCCccEEEEeCChhhHHhhcccCCCCHhhhc---------------------------
Q psy9094 2 EKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPVRFS--------------------------- 54 (185)
Q Consensus 2 ~~~~~f~k~va~~~~~~f~~~~~~~i~~lIIaGPg~~k~~f~~~~~L~~~l~~--------------------------- 54 (185)
+.+++||+.|.....+++ +++.++++|||+|||+++.|++ |+-....+
T Consensus 180 ~~l~kfye~V~qA~~k~v---~fd~vk~~vvASpgF~~~~~~d--~~~q~A~~~~~k~il~nk~kf~~~h~ssg~~hsln 254 (379)
T KOG2869|consen 180 EGLEKFYENVVQAILKHV---NFDVVKCVVVASPGFVKDQFMD--YLFQQAVKLDLKLILENKSKFPLVHASSGYKHSLN 254 (379)
T ss_pred HHHHHHHHHHHHHHHHhc---CcceEEEEEEcCCchhHHHHHH--HHHHHHHHhchhhhhhcccceeEEecCCchHHHHH
Confidence 457899999999888887 6889999999999999999984 43221100
Q ss_pred ----------------hHHHHHHHHHHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeE
Q psy9094 55 ----------------PLKNKNKMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRV 118 (185)
Q Consensus 55 ----------------~~~E~~lve~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~ 118 (185)
+++|.+.|++|+.+++++|++||||+++|.+|.+.|||++|||+|+++++ ++
T Consensus 255 evL~dp~v~~~l~dtK~~~EvkalddF~~~l~~~~drA~yG~khV~~A~e~~AI~tLLitD~lfr~------~D------ 322 (379)
T KOG2869|consen 255 EVLKDPAVASKLQDTKAAKEVKALDDFYVMLSKDPDRACYGPKHVEKANEYGAIETLLITDELFRS------QD------ 322 (379)
T ss_pred HHhcChHHHHHhhchhhHHHHHHHHHHHHHhccCccccccCHHHHHHHHhhcchhheehhhhhccc------cc------
Confidence 78999999999999999999999999999999999999999999999875 32
Q ss_pred EeeCccccccCCccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCCCchHHHHhhhcCCcC
Q psy9094 119 LHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185 (185)
Q Consensus 119 ~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l~~~~GGia 185 (185)
. ..++..+ .|++.++..|++|.|+|+.|.+|+|| ..++|||
T Consensus 323 -------V-----------------~tRkkyv-~lvesVk~~~gkv~Ifss~H~SGEqL-~qltGia 363 (379)
T KOG2869|consen 323 -------V-----------------ATRKKYV-RLVESVKENNGKVFIFSSLHVSGEQL-AQLTGIA 363 (379)
T ss_pred -------H-----------------HHHHHHH-HHHHHHHhcCCcEEEEehhhccHHHH-HhhcCee
Confidence 1 1333444 57899999999999999999999999 9999996
No 10
>PF03464 eRF1_2: eRF1 domain 2; InterPro: IPR005141 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins which may also be involved in translation termination ; PDB: 3AGK_A 2VGN_A 2VGM_A 3J16_A 3IZQ 3IR9_A 3OBW_A 3MCA_B 2QI2_A 3E1Y_D ....
Probab=98.63 E-value=1.3e-08 Score=77.49 Aligned_cols=42 Identities=19% Similarity=0.373 Sum_probs=37.1
Q ss_pred hhhhHHHHHHHHHHHHhhhhcCCCCccEEEEeCChhhHHhhcc
Q psy9094 2 EKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQ 44 (185)
Q Consensus 2 ~~~~~f~k~va~~~~~~f~~~~~~~i~~lIIaGPg~~k~~f~~ 44 (185)
++.++||++|++.+.++|+ .+..++++||||||||+|++|++
T Consensus 50 ~~~~~f~~~i~~~l~~~f~-~~~~~~~~iIiaGPGf~k~~f~~ 91 (133)
T PF03464_consen 50 KALEKFFKEIAEALKKYFL-VNFDDVKCIIIAGPGFTKEEFYK 91 (133)
T ss_dssp HHHHHHHHHHHHHHHHHCC-CHTTTCSEEEEEESTTHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhh-hccccccEEEEECCHHHHHHHHH
Confidence 4678999999999999976 24679999999999999999985
No 11
>TIGR03677 rpl7ae 50S ribosomal protein L7Ae. Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs. Interacts with protein L15e.
Probab=96.42 E-value=0.022 Score=42.49 Aligned_cols=32 Identities=25% Similarity=0.441 Sum_probs=29.2
Q ss_pred hCCCceEecHHHHHHHHHcCCccEEEeeccCc
Q psy9094 71 QDTGKYCFGVEDTLRALELGSVETLICWENLD 102 (185)
Q Consensus 71 ~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~ 102 (185)
...|+.++|.++|.+|+..|.+.-+|++.|..
T Consensus 22 ~ragkl~~G~~~v~kaikkgka~LVilA~D~s 53 (117)
T TIGR03677 22 RETGKIKKGTNEVTKAVERGIAKLVVIAEDVE 53 (117)
T ss_pred HHcCCEeEcHHHHHHHHHcCCccEEEEeCCCC
Confidence 36789999999999999999999999999863
No 12
>COG1358 RPL8A Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis]
Probab=96.41 E-value=0.015 Score=43.46 Aligned_cols=63 Identities=17% Similarity=0.263 Sum_probs=53.0
Q ss_pred CCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHH
Q psy9094 72 DTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLE 151 (185)
Q Consensus 72 ~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~ 151 (185)
..++..+|.++|.+|++.|.+.-++|++|.. ..+++.
T Consensus 24 ~~~ki~~G~~e~~Kai~~g~a~LVviA~Dv~-------------------------------------------P~~~~~ 60 (116)
T COG1358 24 RAGKLKKGTNEVTKAIERGKAKLVVIAEDVS-------------------------------------------PEELVK 60 (116)
T ss_pred hcCCchhhHHHHHHHHHcCCCcEEEEecCCC-------------------------------------------HHHHHH
Confidence 5679999999999999999999999999863 133456
Q ss_pred HHHHHHHhcCCEEEEeCCCCchHHHH
Q psy9094 152 WLANNYKSFGATLEIITDKSQEGSQF 177 (185)
Q Consensus 152 ~l~e~a~~~g~~v~ivs~~~e~G~~l 177 (185)
.|..+++..+..+.+|.+..+-|..+
T Consensus 61 ~l~~lc~~~~vpyv~V~sk~~LG~a~ 86 (116)
T COG1358 61 HLPALCEEKNVPYVYVGSKKELGKAV 86 (116)
T ss_pred HHHHHHHhcCCCEEEeCCHHHHHHHh
Confidence 67788999999999999998887744
No 13
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=96.11 E-value=0.043 Score=41.30 Aligned_cols=38 Identities=29% Similarity=0.448 Sum_probs=31.8
Q ss_pred HHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCc
Q psy9094 64 KYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLD 102 (185)
Q Consensus 64 ~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~ 102 (185)
.++... ...|+.+.|.++|++|++.|.+..+++..|..
T Consensus 20 ~lL~la-~ragklv~G~~~v~kaikkgkakLVilA~D~s 57 (122)
T PRK04175 20 EAVEKA-RDTGKIKKGTNETTKAVERGIAKLVVIAEDVD 57 (122)
T ss_pred HHHHHH-HHcCCEeEcHHHHHHHHHcCCccEEEEeCCCC
Confidence 444444 35689999999999999999999999999863
No 14
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=96.10 E-value=0.027 Score=39.78 Aligned_cols=58 Identities=21% Similarity=0.392 Sum_probs=49.5
Q ss_pred ceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHH
Q psy9094 75 KYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLA 154 (185)
Q Consensus 75 ~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~ 154 (185)
..++|.++|.+|++.|.+..++|..|... .++.-|.
T Consensus 13 ~~vvG~kqt~Kai~kg~~~~v~iA~Da~~--------------------------------------------~vv~~l~ 48 (84)
T PRK13600 13 HFVVGLKETLKALKKDQVTSLIIAEDVEV--------------------------------------------YLMTRVL 48 (84)
T ss_pred CceeeHHHHHHHHhcCCceEEEEeCCCCH--------------------------------------------HHHHHHH
Confidence 34999999999999999999999998641 1456778
Q ss_pred HHHHhcCCEEEEeCCCCchHHH
Q psy9094 155 NNYKSFGATLEIITDKSQEGSQ 176 (185)
Q Consensus 155 e~a~~~g~~v~ivs~~~e~G~~ 176 (185)
..|++.|..+.+|++..+-|.-
T Consensus 49 ~lceek~Ip~v~V~s~~~LGkA 70 (84)
T PRK13600 49 SQINQKNIPVSFFKSKHALGKH 70 (84)
T ss_pred HHHHHcCCCEEEECCHHHHHHH
Confidence 8999999999999999877763
No 15
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=96.08 E-value=0.032 Score=39.06 Aligned_cols=66 Identities=21% Similarity=0.313 Sum_probs=53.7
Q ss_pred HHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhcc
Q psy9094 67 DEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVEC 146 (185)
Q Consensus 67 ~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~ 146 (185)
+.+. ..|+.+.|.++|++|++.|.+..+++..|...
T Consensus 4 ~~~~-ragkl~~G~~~v~kai~~gkaklViiA~D~~~------------------------------------------- 39 (82)
T PRK13602 4 EKVS-QAKSIVIGTKQTVKALKRGSVKEVVVAEDADP------------------------------------------- 39 (82)
T ss_pred HHHH-hcCCEEEcHHHHHHHHHcCCeeEEEEECCCCH-------------------------------------------
Confidence 4444 45899999999999999999999999988531
Q ss_pred ccHHHHHHHHHHhcCCEEEEeCCCCchHHHH
Q psy9094 147 QPLLEWLANNYKSFGATLEIITDKSQEGSQF 177 (185)
Q Consensus 147 ~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l 177 (185)
+....+...|+..+..+..+.+..+-|..+
T Consensus 40 -~~~~~i~~~c~~~~Vp~~~~~s~~eLG~a~ 69 (82)
T PRK13602 40 -RLTEKVEALANEKGVPVSKVDSMKKLGKAC 69 (82)
T ss_pred -HHHHHHHHHHHHcCCCEEEECCHHHHHHHH
Confidence 234567789999999999999888777755
No 16
>PRK06683 hypothetical protein; Provisional
Probab=95.89 E-value=0.044 Score=38.42 Aligned_cols=62 Identities=16% Similarity=0.220 Sum_probs=51.5
Q ss_pred CCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHH
Q psy9094 72 DTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLE 151 (185)
Q Consensus 72 ~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~ 151 (185)
+.|+.+.|.+.|++|+..|.+..++|..|... +...
T Consensus 8 ~agk~v~G~~~v~kaik~gkaklViiA~Da~~--------------------------------------------~~~~ 43 (82)
T PRK06683 8 NAENVVVGHKRTLEAIKNGIVKEVVIAEDADM--------------------------------------------RLTH 43 (82)
T ss_pred hCCCEEEcHHHHHHHHHcCCeeEEEEECCCCH--------------------------------------------HHHH
Confidence 66899999999999999999999999988532 1345
Q ss_pred HHHHHHHhcCCEEEEeCCCCchHHHH
Q psy9094 152 WLANNYKSFGATLEIITDKSQEGSQF 177 (185)
Q Consensus 152 ~l~e~a~~~g~~v~ivs~~~e~G~~l 177 (185)
.+.+.|+.++-.++.+++..+-|.-+
T Consensus 44 ~i~~~~~~~~Vpv~~~~t~~eLG~A~ 69 (82)
T PRK06683 44 VIIRTALQHNIPITKVESVRKLGKVA 69 (82)
T ss_pred HHHHHHHhcCCCEEEECCHHHHHHHh
Confidence 66789999999999999877766644
No 17
>PRK07714 hypothetical protein; Provisional
Probab=95.39 E-value=0.062 Score=38.82 Aligned_cols=33 Identities=18% Similarity=0.224 Sum_probs=29.7
Q ss_pred hhCCCceEecHHHHHHHHHcCCccEEEeeccCc
Q psy9094 70 SQDTGKYCFGVEDTLRALELGSVETLICWENLD 102 (185)
Q Consensus 70 ~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~ 102 (185)
+...|++++|.+.|++|+..|.+.-+|+..|..
T Consensus 13 a~raGk~v~G~~~v~~al~~g~~~lViiA~D~s 45 (100)
T PRK07714 13 ANRARKVISGEELVLKEVRSGKAKLVLLSEDAS 45 (100)
T ss_pred HHHhCCeeecHHHHHHHHHhCCceEEEEeCCCC
Confidence 446699999999999999999999999999864
No 18
>PF01248 Ribosomal_L7Ae: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; InterPro: IPR004038 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 [, ]. This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, ribosomal protein L30 from eukaryotes and archaebacteria, Gadd45 and MyD118 [].; PDB: 2CZW_A 3V7E_B 2QEX_F 1YJ9_F 1VQ8_F 1YJN_F 3I56_F 1VQ6_F 2OTJ_F 1YIJ_F ....
Probab=95.28 E-value=0.093 Score=37.04 Aligned_cols=71 Identities=17% Similarity=0.244 Sum_probs=53.4
Q ss_pred HHHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchh
Q psy9094 63 GKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELE 142 (185)
Q Consensus 63 e~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~ 142 (185)
...+.... ..++.++|.++|.++++.|.+.-++++.|....
T Consensus 4 ~~~l~~a~-~~~~lv~G~~~v~k~l~~~~~~lvilA~d~~~~-------------------------------------- 44 (95)
T PF01248_consen 4 YKLLKLAR-KAGRLVKGIKEVLKALKKGKAKLVILAEDCSPD-------------------------------------- 44 (95)
T ss_dssp HHHHHHHH-HHSEEEESHHHHHHHHHTTCESEEEEETTSSSG--------------------------------------
T ss_pred HHHHHHHH-hcCCEEEchHHHHHHHHcCCCcEEEEcCCCChh--------------------------------------
Confidence 34444443 457899999999999999999999999886321
Q ss_pred hhccccHHHHHHHHHHhcCCEEEEeCCCCchHHHH
Q psy9094 143 LVECQPLLEWLANNYKSFGATLEIITDKSQEGSQF 177 (185)
Q Consensus 143 ~~e~~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l 177 (185)
.....+...|.+.+..+..+++..+-|..+
T Consensus 45 -----~~~~~l~~~c~~~~Ip~~~~~s~~eLG~~~ 74 (95)
T PF01248_consen 45 -----SIKKHLPALCEEKNIPYVFVPSKEELGRAC 74 (95)
T ss_dssp -----HHHHHHHHHHHHTTEEEEEESHHHHHHHHT
T ss_pred -----hhcccchhheeccceeEEEECCHHHHHHHH
Confidence 122346678899999999999777666644
No 19
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=95.28 E-value=0.077 Score=37.25 Aligned_cols=60 Identities=13% Similarity=0.121 Sum_probs=49.3
Q ss_pred CCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHH
Q psy9094 73 TGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEW 152 (185)
Q Consensus 73 ~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~ 152 (185)
.|+.+.|.+.|++|++.|.+..++|..|... +....
T Consensus 6 ~GKlv~G~~~vlkaIk~gkakLViiA~Da~~--------------------------------------------~~~k~ 41 (82)
T PRK13601 6 PSKRVVGAKQTLKAITNCNVLQVYIAKDAEE--------------------------------------------HVTKK 41 (82)
T ss_pred CccEEEchHHHHHHHHcCCeeEEEEeCCCCH--------------------------------------------HHHHH
Confidence 4799999999999999999999999988532 23566
Q ss_pred HHHHHHhcCCEEEEeCCCCchHHH
Q psy9094 153 LANNYKSFGATLEIITDKSQEGSQ 176 (185)
Q Consensus 153 l~e~a~~~g~~v~ivs~~~e~G~~ 176 (185)
+.+.|+.++-.+.++.+..+-|.-
T Consensus 42 i~~~c~~~~Vpv~~~~t~~eLG~A 65 (82)
T PRK13601 42 IKELCEEKSIKIVYIDTMKELGVM 65 (82)
T ss_pred HHHHHHhCCCCEEEeCCHHHHHHH
Confidence 778899999999888877666653
No 20
>PRK07283 hypothetical protein; Provisional
Probab=94.82 E-value=0.12 Score=37.27 Aligned_cols=34 Identities=18% Similarity=0.312 Sum_probs=30.4
Q ss_pred HhhCCCceEecHHHHHHHHHcCCccEEEeeccCc
Q psy9094 69 ISQDTGKYCFGVEDTLRALELGSVETLICWENLD 102 (185)
Q Consensus 69 l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~ 102 (185)
++...|+++.|.+.|++|+..|.+.-+|+..|..
T Consensus 12 lA~raGklv~G~~~v~~aik~gk~~lVi~A~Das 45 (98)
T PRK07283 12 LAQRAGRIISGEELVVKAIQSGQAKLVFLANDAG 45 (98)
T ss_pred HHHHhCCeeEcHHHHHHHHHcCCccEEEEeCCCC
Confidence 3456799999999999999999999999999864
No 21
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=94.82 E-value=0.13 Score=37.16 Aligned_cols=32 Identities=34% Similarity=0.531 Sum_probs=28.9
Q ss_pred hCCCceEecHHHHHHHHHcCCccEEEeeccCc
Q psy9094 71 QDTGKYCFGVEDTLRALELGSVETLICWENLD 102 (185)
Q Consensus 71 ~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~ 102 (185)
...|+.+.|.++|++|+..|.+.-++|++|..
T Consensus 12 ~ragkl~~G~~~v~kai~~gkaklViiA~D~~ 43 (99)
T PRK01018 12 VDTGKVILGSKRTIKAIKLGKAKLVIVASNCP 43 (99)
T ss_pred HHcCCEEEcHHHHHHHHHcCCceEEEEeCCCC
Confidence 35689999999999999999999999999853
No 22
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=94.64 E-value=0.21 Score=36.52 Aligned_cols=33 Identities=18% Similarity=0.244 Sum_probs=29.8
Q ss_pred hhCCCceEecHHHHHHHHHcCCccEEEeeccCc
Q psy9094 70 SQDTGKYCFGVEDTLRALELGSVETLICWENLD 102 (185)
Q Consensus 70 ~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~ 102 (185)
+...|++++|.+.|++|+..|.+.-||+.+|..
T Consensus 12 A~rAGklv~G~~~v~~aik~gk~~lVI~A~D~s 44 (104)
T PRK05583 12 TKKAGKLLEGYNKCEEAIKKKKVYLIIISNDIS 44 (104)
T ss_pred HHHhCCeeecHHHHHHHHHcCCceEEEEeCCCC
Confidence 446799999999999999999999999999864
No 23
>PF08032 SpoU_sub_bind: RNA 2'-O ribose methyltransferase substrate binding; InterPro: IPR013123 Most cellular RNAs undergo a number of post-transcriptional nucleoside modifications. While the biological role of many of these modifications is unknown, some have been shown to be necessary for cell growth or for resistance to antibiotics [, ]. One of the most common modifications is 2'O-ribose methylation catalysed by the RNA 2'O-ribose methyltransferases, a large enzyme family that transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the backbone ribose []. This entry represents a substrate-binding domain found in a variety of bacterial and mitochondrial RNA 2'-O ribose methyltransferases. These include the bacterial enzyme RlmB, which specifically methylates the conserved nucleotide guanosine 2251 in 23S RNA, and PET56, which specifically methylates the equivalent guanosine in mitochondrial 21S RNA [, ]. This domain forms a four-stranded mixed beta sheet similar to that found in other RNA binding enzymes []. It shows considerable conformational flexibility which is thought to be important for its ability to bind RNA.; GO: 0008168 methyltransferase activity; PDB: 1GZ0_D 1IPA_A.
Probab=94.38 E-value=0.14 Score=34.36 Aligned_cols=51 Identities=18% Similarity=0.138 Sum_probs=38.4
Q ss_pred eEecHHHHHHHHHcCC-ccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHH
Q psy9094 76 YCFGVEDTLRALELGS-VETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLA 154 (185)
Q Consensus 76 ~~yG~~ev~~Ale~Ga-V~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~ 154 (185)
.+||...|.+|++.|. +..|+++++.... .+..+.
T Consensus 1 lieG~~~V~eaL~~~~~i~~l~~~~~~~~~--------------------------------------------~~~~i~ 36 (76)
T PF08032_consen 1 LIEGRHAVEEALKSGPRIKKLFVTEEKADK--------------------------------------------RIKEIL 36 (76)
T ss_dssp EEESHHHHHHHHHCTGGEEEEEEETT---C--------------------------------------------CTHHHH
T ss_pred CEEEHHHHHHHHcCCCCccEEEEEcCccch--------------------------------------------hHHHHH
Confidence 3799999999999987 9999999982111 024677
Q ss_pred HHHHhcCCEEEEeCCC
Q psy9094 155 NNYKSFGATLEIITDK 170 (185)
Q Consensus 155 e~a~~~g~~v~ivs~~ 170 (185)
+.+.+.|.++..+|..
T Consensus 37 ~~~~~~~i~v~~v~~~ 52 (76)
T PF08032_consen 37 KLAKKKGIPVYEVSKK 52 (76)
T ss_dssp HHHHHCT-EEEEE-HH
T ss_pred HHHHHcCCeEEEeCHH
Confidence 8999999999999874
No 24
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=94.17 E-value=0.037 Score=34.31 Aligned_cols=39 Identities=13% Similarity=0.026 Sum_probs=25.6
Q ss_pred eEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHH
Q psy9094 106 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLL 150 (185)
Q Consensus 106 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v 150 (185)
..|+|++||..... . +. .....||.||.++......++|
T Consensus 2 ~~y~C~~CG~~~~~-~-~~----~~~~~Cp~CG~~~~~~~~~~~v 40 (46)
T PRK00398 2 AEYKCARCGREVEL-D-EY----GTGVRCPYCGYRILFKERPPVV 40 (46)
T ss_pred CEEECCCCCCEEEE-C-CC----CCceECCCCCCeEEEccCCCcc
Confidence 36899999963222 1 11 1156799999988776666655
No 25
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=93.87 E-value=0.32 Score=35.85 Aligned_cols=41 Identities=27% Similarity=0.436 Sum_probs=34.0
Q ss_pred HHHHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcc
Q psy9094 62 MGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDI 103 (185)
Q Consensus 62 ve~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~ 103 (185)
++.++... ...|+.++|.+.|++|+..|.+.-++|+.|...
T Consensus 13 i~~~Lgla-~raGKlv~G~~~vlkalk~gkaklViiA~D~~~ 53 (108)
T PTZ00106 13 INSKLQLV-MKSGKYTLGTKSTLKALRNGKAKLVIISNNCPP 53 (108)
T ss_pred HHHHHHHH-HHhCCeeecHHHHHHHHHcCCeeEEEEeCCCCH
Confidence 44555444 467999999999999999999999999998753
No 26
>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=93.69 E-value=0.052 Score=42.59 Aligned_cols=47 Identities=15% Similarity=0.146 Sum_probs=32.6
Q ss_pred eeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHH
Q psy9094 105 RYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANN 156 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~ 156 (185)
..-|.||+|+. ...|.+. ....|.||.||++|+.....++++.|-+.
T Consensus 107 ~~~Y~Cp~c~~-r~tf~eA----~~~~F~Cp~Cg~~L~~~dn~~~i~~l~~~ 153 (158)
T TIGR00373 107 NMFFICPNMCV-RFTFNEA----MELNFTCPRCGAMLDYLDNSEAIEKLEEQ 153 (158)
T ss_pred CCeEECCCCCc-EeeHHHH----HHcCCcCCCCCCEeeeccCHHHHHHHHHH
Confidence 44689999993 2222211 22478999999999988888888765443
No 27
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=93.01 E-value=0.09 Score=42.09 Aligned_cols=48 Identities=15% Similarity=0.054 Sum_probs=32.6
Q ss_pred eeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHH
Q psy9094 105 RYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNY 157 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a 157 (185)
...|.||+|+. ...|.+. ....|.||.||++|+.....+.+..|-+..
T Consensus 115 ~~~Y~Cp~C~~-rytf~eA----~~~~F~Cp~Cg~~L~~~dn~~~~~~l~~~I 162 (178)
T PRK06266 115 NMFFFCPNCHI-RFTFDEA----MEYGFRCPQCGEMLEEYDNSELIKELKEQI 162 (178)
T ss_pred CCEEECCCCCc-EEeHHHH----hhcCCcCCCCCCCCeecccHHHHHHHHHHH
Confidence 44799999994 2233222 224789999999999888777776554433
No 28
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=90.72 E-value=0.13 Score=39.68 Aligned_cols=45 Identities=20% Similarity=0.126 Sum_probs=26.5
Q ss_pred eeEeecCCCCceeEEeeCcccc-ccCCccccCccCcchhhhccccHH
Q psy9094 105 RYVLKNHSTSEDRVLHLTPEQE-KDKSHFTDKETGVELELVECQPLL 150 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~~~~~~~-~~~~~~~c~~~g~~~~~~e~~~~v 150 (185)
+..|.||+|+..-. +.+.... .....|.||.||++++.......+
T Consensus 97 ~~~Y~Cp~C~~~y~-~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn~~~~ 142 (147)
T smart00531 97 NAYYKCPNCQSKYT-FLEANQLLDMDGTFTCPRCGEELEEDDNSEPI 142 (147)
T ss_pred CcEEECcCCCCEee-HHHHHHhcCCCCcEECCCCCCEEEEcCchhhH
Confidence 44799999994222 2111110 011248999999998766555444
No 29
>COG1911 RPL30 Ribosomal protein L30E [Translation, ribosomal structure and biogenesis]
Probab=90.43 E-value=3.1 Score=30.14 Aligned_cols=30 Identities=33% Similarity=0.542 Sum_probs=27.9
Q ss_pred CCCceEecHHHHHHHHHcCCccEEEeeccC
Q psy9094 72 DTGKYCFGVEDTLRALELGSVETLICWENL 101 (185)
Q Consensus 72 ~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l 101 (185)
++|+++.|.+.|++++.+|..+-+||..+.
T Consensus 16 kTGkvilG~k~tiK~lk~gkaKliiiAsN~ 45 (100)
T COG1911 16 KTGKVILGSKRTIKSLKLGKAKLIIIASNC 45 (100)
T ss_pred hcCCEEEehHHHHHHHHcCCCcEEEEecCC
Confidence 679999999999999999999999999764
No 30
>PTZ00222 60S ribosomal protein L7a; Provisional
Probab=90.29 E-value=0.84 Score=38.63 Aligned_cols=29 Identities=21% Similarity=0.291 Sum_probs=26.1
Q ss_pred CceEecHHHHHHHHHcCCccEEEeeccCc
Q psy9094 74 GKYCFGVEDTLRALELGSVETLICWENLD 102 (185)
Q Consensus 74 ~~~~yG~~ev~~Ale~GaV~~Llv~d~l~ 102 (185)
-..++|.++|..+++.|-+.-+||.+|..
T Consensus 131 ~~LvsG~n~VtkaIekkKAkLVIIA~DVs 159 (263)
T PTZ00222 131 LAVVTGLQEVTRAIEKKQARMVVIANNVD 159 (263)
T ss_pred CeeccCHHHHHHHHHcCCceEEEEeCCCC
Confidence 34789999999999999999999999863
No 31
>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=90.24 E-value=0.51 Score=28.69 Aligned_cols=31 Identities=10% Similarity=0.103 Sum_probs=20.7
Q ss_pred eEeecCCCCceeEEeeCccccccCCccccCccCc
Q psy9094 106 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGV 139 (185)
Q Consensus 106 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~ 139 (185)
|.|+|++||.....+..-.+ .....||.||+
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~---~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSISE---DDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEEcCC---CCCCcCCCCCC
Confidence 68999999965555522221 12446999998
No 32
>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=90.21 E-value=0.51 Score=27.89 Aligned_cols=32 Identities=13% Similarity=0.047 Sum_probs=20.2
Q ss_pred eEeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 106 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 106 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
|.|+|+.||..........+ .....||.||+.
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~---~~~~~CP~Cg~~ 35 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISD---DPLATCPECGGD 35 (41)
T ss_pred EEEEcCCCCCEEEEEEecCC---CCCCCCCCCCCc
Confidence 67999999974444322111 124469999984
No 33
>PRK09190 hypothetical protein; Provisional
Probab=90.18 E-value=2 Score=35.57 Aligned_cols=42 Identities=21% Similarity=0.276 Sum_probs=34.1
Q ss_pred HHHHHHHH--hhCCCceEecHHHHHHHHHcCCccEEEeeccCcc
Q psy9094 62 MGKYFDEI--SQDTGKYCFGVEDTLRALELGSVETLICWENLDI 103 (185)
Q Consensus 62 ve~f~~~l--~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~ 103 (185)
.++++..| +...|+.++|.+.|+.|+..|.+.-||+..|...
T Consensus 96 ~~ril~lLGLArRAGklVsG~~~V~~alk~gk~~Lvi~A~DaS~ 139 (220)
T PRK09190 96 ARRALDALGLARKAGQVVSGFEKVDAALRSGEAAALIHASDGAA 139 (220)
T ss_pred HHHHHHHHHHHhhhCCEeecHHHHHHHHHcCCceEEEEeccCCh
Confidence 34444443 4577999999999999999999999999999753
No 34
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=88.49 E-value=0.34 Score=38.79 Aligned_cols=47 Identities=17% Similarity=0.118 Sum_probs=31.2
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHHH
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYK 158 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~ 158 (185)
-|.|++|+. ...| +++....|.||.||+.++....-+.+..|-+...
T Consensus 113 ~y~C~~~~~-r~sf----deA~~~~F~Cp~Cg~~L~~~d~s~~i~~l~~~i~ 159 (176)
T COG1675 113 YYVCPNCHV-KYSF----DEAMELGFTCPKCGEDLEEYDSSEEIEELESELD 159 (176)
T ss_pred ceeCCCCCC-cccH----HHHHHhCCCCCCCCchhhhccchHHHHHHHHHHH
Confidence 588987773 2222 2223357889999999998877777766655444
No 35
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=88.30 E-value=0.39 Score=38.10 Aligned_cols=55 Identities=13% Similarity=-0.005 Sum_probs=31.6
Q ss_pred HHHHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 62 MGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 62 ve~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
+..+|+.++.+-..-.=-....++-++.|. +|+|+-||+.... ++ ...||.||.+
T Consensus 104 ~a~~f~~~~~~Ek~H~~~~~~~Le~~~~~~---------------~~vC~vCGy~~~g--e~-------P~~CPiCga~ 158 (166)
T COG1592 104 AARSFRAAAKAEKRHAEMFRGLLERLEEGK---------------VWVCPVCGYTHEG--EA-------PEVCPICGAP 158 (166)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcCC---------------EEEcCCCCCcccC--CC-------CCcCCCCCCh
Confidence 334444554433333333444455555555 5999999974443 22 3479999976
No 36
>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=88.25 E-value=0.8 Score=28.71 Aligned_cols=31 Identities=13% Similarity=0.018 Sum_probs=19.7
Q ss_pred eEeecCCCCceeEEeeCccccccCCccccCccCc
Q psy9094 106 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGV 139 (185)
Q Consensus 106 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~ 139 (185)
|.|+|.+||........-.+ .....||.||+
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~---~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKMSD---DPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEEEecCC---CCCCCCCCCCC
Confidence 68999999964444421121 12346999997
No 37
>PTZ00365 60S ribosomal protein L7Ae-like; Provisional
Probab=87.58 E-value=1.4 Score=37.41 Aligned_cols=62 Identities=16% Similarity=0.191 Sum_probs=47.1
Q ss_pred hCCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHH
Q psy9094 71 QDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLL 150 (185)
Q Consensus 71 ~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v 150 (185)
+.|-.+.||+.+|..+++.|.+.-+||..|..- .+++
T Consensus 128 kkp~~vk~Gin~VtklIekkKAkLVIIA~DVsP-------------------------------------------~t~k 164 (266)
T PTZ00365 128 KKPFMLKYGLNHVTDLVEYKKAKLVVIAHDVDP-------------------------------------------IELV 164 (266)
T ss_pred CCchHHHhhhHHHHHHHHhCCccEEEEeCCCCH-------------------------------------------HHHH
Confidence 334457799999999999999999999998632 2234
Q ss_pred HHHHHHHHhcCCEEEEeCCCCchHH
Q psy9094 151 EWLANNYKSFGATLEIITDKSQEGS 175 (185)
Q Consensus 151 ~~l~e~a~~~g~~v~ivs~~~e~G~ 175 (185)
.+|.++|+.+|.-..++.+..+-|.
T Consensus 165 k~LP~LC~k~~VPY~iv~sK~eLG~ 189 (266)
T PTZ00365 165 CFLPALCRKKEVPYCIIKGKSRLGK 189 (266)
T ss_pred HHHHHHHhccCCCEEEECCHHHHHH
Confidence 5566788888888888887766655
No 38
>PF10116 Host_attach: Protein required for attachment to host cells; InterPro: IPR019291 Members of this family of bacterial proteins are required for the attachment of the bacterium to host cells [, ].
Probab=85.79 E-value=1.3 Score=33.45 Aligned_cols=47 Identities=15% Similarity=0.176 Sum_probs=36.7
Q ss_pred hhhHHHHHHHHHHHHhhhhcCCCCccEEEEeCChhhHHhhcccCCCCHhhhc
Q psy9094 3 KRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPVRFS 54 (185)
Q Consensus 3 ~~~~f~k~va~~~~~~f~~~~~~~i~~lIIaGPg~~k~~f~~~~~L~~~l~~ 54 (185)
..++|.++||+.+++... ...++.|||++|-.+--.+.+ .|+..+++
T Consensus 70 ~~~~Fa~~vA~~L~~~~~---~~~~~~LvlvA~p~~LG~LR~--~L~~~~~~ 116 (138)
T PF10116_consen 70 EEERFAREVADRLEKARR---AGKFDRLVLVAPPRFLGLLRE--HLSKAVRK 116 (138)
T ss_pred HHHHHHHHHHHHHHHHHH---hCCCCeEEEEECHHHHHHHHH--HhCHHHHH
Confidence 456899999999998874 467889999888877777763 67776653
No 39
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=83.38 E-value=0.85 Score=28.18 Aligned_cols=33 Identities=9% Similarity=0.124 Sum_probs=21.0
Q ss_pred eEeecCCCCceeEEeeCccccccCCccccCccCcchhhhc
Q psy9094 106 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVE 145 (185)
Q Consensus 106 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e 145 (185)
++|+|.+||.+... ++ .....||.||.+.-...
T Consensus 1 ~~Y~C~~Cg~~~~~--~~-----~~~irC~~CG~rIlyK~ 33 (44)
T smart00659 1 MIYICGECGRENEI--KS-----KDVVRCRECGYRILYKK 33 (44)
T ss_pred CEEECCCCCCEeec--CC-----CCceECCCCCceEEEEe
Confidence 36899999963332 11 12457999998754443
No 40
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=82.49 E-value=3.2 Score=40.21 Aligned_cols=68 Identities=22% Similarity=0.268 Sum_probs=41.2
Q ss_pred eeEeecCCCCceeEEeeCcccc-------ccCCccccCccCcchhhhccccHHHHHHHHHHh-c-CCEEEEeCCCCch
Q psy9094 105 RYVLKNHSTSEDRVLHLTPEQE-------KDKSHFTDKETGVELELVECQPLLEWLANNYKS-F-GATLEIITDKSQE 173 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~~~~~~~-------~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~-~-g~~v~ivs~~~e~ 173 (185)
+++..|++|+..-+........ ..+....||.||+. .++..-.=.+.+.+...+ + +++|..+++++-.
T Consensus 442 g~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~-~L~~~G~GterieeeL~~~FP~~rv~r~d~Dtt~ 518 (730)
T COG1198 442 GYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE-HLRAVGPGTERIEEELKRLFPGARIIRIDSDTTR 518 (730)
T ss_pred CCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC-eeEEecccHHHHHHHHHHHCCCCcEEEEcccccc
Confidence 4467777777322222222211 23446679999987 344444445666666655 3 8999999988875
No 41
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=82.33 E-value=1.7 Score=31.86 Aligned_cols=38 Identities=13% Similarity=0.038 Sum_probs=26.4
Q ss_pred CcceeeEeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 101 LDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 101 l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
..+.+|+|.|++.+...+.|... +..+..+.|+.||.+
T Consensus 22 apR~~v~Y~C~~Gh~~~v~Fa~e--AevP~~WeC~~cG~~ 59 (105)
T PF13397_consen 22 APRQRVSYWCPNGHETEVPFAAE--AEVPATWECPRCGLP 59 (105)
T ss_pred cCceEEEEECCCCCEEecccccc--CCCCCceeCCCCCCc
Confidence 35667899999977666666332 234457889999954
No 42
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=80.44 E-value=0.79 Score=24.91 Aligned_cols=25 Identities=12% Similarity=0.157 Sum_probs=14.9
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcch
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVEL 141 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~ 141 (185)
...|++||.. + .+ ..-.||.||.+|
T Consensus 2 ~~~Cp~Cg~~-~---~~------~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAE-I---DP------DAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCc-C---Cc------ccccChhhCCCC
Confidence 3579999951 1 11 122599999753
No 43
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=79.61 E-value=0.99 Score=23.97 Aligned_cols=8 Identities=13% Similarity=0.023 Sum_probs=6.1
Q ss_pred ccCccCcc
Q psy9094 133 TDKETGVE 140 (185)
Q Consensus 133 ~c~~~g~~ 140 (185)
.|+.||.+
T Consensus 15 fC~~CG~~ 22 (23)
T PF13240_consen 15 FCPNCGTP 22 (23)
T ss_pred chhhhCCc
Confidence 48888865
No 44
>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=78.87 E-value=2.1 Score=24.84 Aligned_cols=26 Identities=8% Similarity=-0.287 Sum_probs=17.1
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
.|+|..||+.... .. ....||.||.+
T Consensus 2 ~~~C~~CG~i~~g-~~-------~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEG-EE-------APEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeEC-Cc-------CCCcCcCCCCc
Confidence 5899999963321 11 12369999975
No 45
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=77.87 E-value=1.8 Score=28.54 Aligned_cols=8 Identities=25% Similarity=0.455 Sum_probs=3.7
Q ss_pred ccccCccC
Q psy9094 131 HFTDKETG 138 (185)
Q Consensus 131 ~~~c~~~g 138 (185)
.|.||+||
T Consensus 27 ~F~CPnCG 34 (61)
T COG2888 27 KFPCPNCG 34 (61)
T ss_pred EeeCCCCC
Confidence 34444444
No 46
>PRK12496 hypothetical protein; Provisional
Probab=77.74 E-value=1.7 Score=34.19 Aligned_cols=29 Identities=7% Similarity=-0.056 Sum_probs=18.3
Q ss_pred eeEeecCCCCceeEEeeCccccccCCccccCccCcch
Q psy9094 105 RYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVEL 141 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~ 141 (185)
+|.++|+.|+. .|.. +.....||.||.++
T Consensus 125 ~w~~~C~gC~~---~~~~-----~~~~~~C~~CG~~~ 153 (164)
T PRK12496 125 KWRKVCKGCKK---KYPE-----DYPDDVCEICGSPV 153 (164)
T ss_pred eeeEECCCCCc---cccC-----CCCCCcCCCCCChh
Confidence 45689999994 2211 01123599999986
No 47
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=77.57 E-value=2.6 Score=31.13 Aligned_cols=26 Identities=8% Similarity=-0.177 Sum_probs=16.9
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
.++|.+||..... ....+.||.||++
T Consensus 70 ~~~C~~Cg~~~~~--------~~~~~~CP~Cgs~ 95 (113)
T PRK12380 70 QAWCWDCSQVVEI--------HQHDAQCPHCHGE 95 (113)
T ss_pred EEEcccCCCEEec--------CCcCccCcCCCCC
Confidence 4889999942111 1235569999975
No 48
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=76.61 E-value=5.6 Score=28.90 Aligned_cols=64 Identities=6% Similarity=0.037 Sum_probs=41.4
Q ss_pred EeecCCCCceeEEe-eCccccccCCccccCccCcc-----hhhhccccHHHHHHHHHHhcCCEEEEeCCCCchH
Q psy9094 107 VLKNHSTSEDRVLH-LTPEQEKDKSHFTDKETGVE-----LELVECQPLLEWLANNYKSFGATLEIITDKSQEG 174 (185)
Q Consensus 107 ~~~c~~~~~~~~~~-~~~~~~~~~~~~~c~~~g~~-----~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~~e~G 174 (185)
.+.|++|+...+.. ... .+.+..|+.||-. ..+.+..|+-...++.+.+-...+.+...+.+++
T Consensus 21 ~f~CP~Cge~~v~v~~~k----~~~h~~C~~CG~y~~~~V~~l~epIDVY~~wiD~~~eg~i~~~~~~~~~~~~ 90 (99)
T PRK14892 21 IFECPRCGKVSISVKIKK----NIAIITCGNCGLYTEFEVPSVYDEVDVYNKFIDLYLEGKIEIKERKNEETEE 90 (99)
T ss_pred EeECCCCCCeEeeeecCC----CcceEECCCCCCccCEECCccccchhhHHHHHHHHHhcCCCccccCcccccc
Confidence 47899999544432 111 2235579999932 2234667887788888888777777776666554
No 49
>COG1852 Uncharacterized conserved protein [Function unknown]
Probab=75.96 E-value=3.1 Score=33.95 Aligned_cols=34 Identities=15% Similarity=0.224 Sum_probs=28.7
Q ss_pred CccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCCC
Q psy9094 130 SHFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDKS 171 (185)
Q Consensus 130 ~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~~ 171 (185)
+.+.|..||.= ++-++.+.|++.|-+|.|+|+.|
T Consensus 110 ~G~~Ck~CgkC--------vi~ei~e~ae~~gykvfIvpGgs 143 (209)
T COG1852 110 TGYECKKCGKC--------VIGEIKEIAEKYGYKVFIVPGGS 143 (209)
T ss_pred ccceecccCCe--------ehHHHHHHHHHhCcEEEEecChH
Confidence 47789999853 36678999999999999999976
No 50
>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=75.85 E-value=1.7 Score=39.67 Aligned_cols=27 Identities=7% Similarity=-0.173 Sum_probs=19.1
Q ss_pred eeEeecCCCCceeEEeeCccccccCCccccCccCcch
Q psy9094 105 RYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVEL 141 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~ 141 (185)
+..|+|.+||+. +.++.+.||.|+.-.
T Consensus 5 ~~~y~C~~Cg~~----------~~~~~g~Cp~C~~w~ 31 (454)
T TIGR00416 5 KSKFVCQHCGAD----------SPKWQGKCPACHAWN 31 (454)
T ss_pred CCeEECCcCCCC----------CccccEECcCCCCcc
Confidence 346999999962 233566899998643
No 51
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=74.92 E-value=3.1 Score=33.33 Aligned_cols=28 Identities=18% Similarity=0.254 Sum_probs=19.0
Q ss_pred eeEeecCCCCceeEEeeCccccccCCccccCccCcchh
Q psy9094 105 RYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELE 142 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~ 142 (185)
+|.++|..|+. .|..| +-.||.||+++.
T Consensus 137 ~w~~rC~GC~~---~f~~~-------~~~Cp~CG~~~~ 164 (177)
T COG1439 137 KWRLRCHGCKR---IFPEP-------KDFCPICGSPLK 164 (177)
T ss_pred eeeEEEecCce---ecCCC-------CCcCCCCCCceE
Confidence 46789999995 22222 336999999853
No 52
>PRK11823 DNA repair protein RadA; Provisional
Probab=74.88 E-value=1.9 Score=39.17 Aligned_cols=30 Identities=20% Similarity=0.003 Sum_probs=20.5
Q ss_pred eEeecCCCCceeEEeeCccccccCCccccCccCcchhhhc
Q psy9094 106 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVE 145 (185)
Q Consensus 106 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e 145 (185)
..|+|++||+.. .++...||.|++---++|
T Consensus 6 ~~y~C~~Cg~~~----------~~~~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 6 TAYVCQECGAES----------PKWLGRCPECGAWNTLVE 35 (446)
T ss_pred CeEECCcCCCCC----------cccCeeCcCCCCccceee
Confidence 469999999622 234668999996544444
No 53
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=73.88 E-value=2.6 Score=24.60 Aligned_cols=33 Identities=6% Similarity=-0.044 Sum_probs=18.6
Q ss_pred EeecCCCCceeEEeeCccccc-cCCccccCccCcch
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEK-DKSHFTDKETGVEL 141 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~-~~~~~~c~~~g~~~ 141 (185)
.+.||+|+..- . ..+++.. ......||.||..+
T Consensus 2 ~~~CP~C~~~~-~-v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 2 RIQCPNCKTSF-R-VVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEE-E-eCHHHcCCCCCEEECCCCCCEE
Confidence 36799999521 1 2222211 12256799999765
No 54
>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=73.64 E-value=3.1 Score=30.79 Aligned_cols=26 Identities=8% Similarity=-0.084 Sum_probs=17.0
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
..+|++|+..... ....+.||.||++
T Consensus 70 ~~~C~~Cg~~~~~--------~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 70 ECECEDCSEEVSP--------EIDLYRCPKCHGI 95 (115)
T ss_pred EEEcccCCCEEec--------CCcCccCcCCcCC
Confidence 4789999942111 1124579999986
No 55
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=73.42 E-value=3.2 Score=27.97 Aligned_cols=41 Identities=15% Similarity=0.092 Sum_probs=29.0
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEe
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSFGATLEII 167 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~iv 167 (185)
-.+|++|+..++.|-.+.. .-.|..||.. +|+-+||+-.+.
T Consensus 19 ~VkCpdC~N~q~vFshast-----~V~C~~CG~~---------------l~~PTGGka~i~ 59 (67)
T COG2051 19 RVKCPDCGNEQVVFSHAST-----VVTCLICGTT---------------LAEPTGGKAKIS 59 (67)
T ss_pred EEECCCCCCEEEEeccCce-----EEEecccccE---------------EEecCCCeEEee
Confidence 3689999999998844432 3369999964 466777776554
No 56
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=72.11 E-value=8.4 Score=38.40 Aligned_cols=42 Identities=14% Similarity=0.138 Sum_probs=27.3
Q ss_pred HHHHHHHHcC-CccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhh
Q psy9094 81 EDTLRALELG-SVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELEL 143 (185)
Q Consensus 81 ~ev~~Ale~G-aV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~ 143 (185)
..+.+|.+.| .++.= +. ..+|++||..+. .+.||.||+..++
T Consensus 607 R~i~~A~~~g~~i~ve-----v~----~RKCPkCG~yTl------------k~rCP~CG~~Te~ 649 (1095)
T TIGR00354 607 RDIKNAINYTKEIEVE-----IA----IRKCPQCGKESF------------WLKCPVCGELTEQ 649 (1095)
T ss_pred hhHHHHhccCCeeEEE-----EE----EEECCCCCcccc------------cccCCCCCCcccc
Confidence 4688999888 43221 11 258999995221 4479999988543
No 57
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=71.57 E-value=4.6 Score=31.64 Aligned_cols=37 Identities=16% Similarity=0.108 Sum_probs=28.5
Q ss_pred ccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCCCchHH
Q psy9094 131 HFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDKSQEGS 175 (185)
Q Consensus 131 ~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~~e~G~ 175 (185)
.+.|..||.= .|..+.+.++++|-+|.|+++.|-.-+
T Consensus 64 g~~C~~Cg~C--------~Ig~l~~lae~~g~~v~i~~Ggt~ar~ 100 (158)
T PF01976_consen 64 GYNCKRCGKC--------DIGDLKKLAEKYGYKVYIATGGTLARK 100 (158)
T ss_pred CCcCCCCCCC--------chhHHHHHHHHcCCEEEEEcChHHHHH
Confidence 4468888732 256788999999999999999876544
No 58
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=71.35 E-value=5.9 Score=26.11 Aligned_cols=42 Identities=12% Similarity=0.064 Sum_probs=29.0
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeC
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSFGATLEIIT 168 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs 168 (185)
-.+|++|+.+++.|-.+. +.-.|..||.. +++-+|++..|..
T Consensus 11 ~VkCp~C~n~q~vFsha~-----t~V~C~~Cg~~---------------L~~PtGGKa~i~~ 52 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHAS-----TVVRCLVCGKT---------------LAEPTGGKAKIKG 52 (59)
T ss_pred EEECCCCCCeEEEEecCC-----cEEECcccCCC---------------cccCCCcceeeeh
Confidence 478999999888883222 13369999975 4566777766543
No 59
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=71.05 E-value=5.5 Score=30.33 Aligned_cols=10 Identities=30% Similarity=0.298 Sum_probs=8.3
Q ss_pred eEeecCCCCc
Q psy9094 106 YVLKNHSTSE 115 (185)
Q Consensus 106 ~~~~c~~~~~ 115 (185)
..++|++||.
T Consensus 69 ~~~~C~~CG~ 78 (135)
T PRK03824 69 AVLKCRNCGN 78 (135)
T ss_pred eEEECCCCCC
Confidence 3589999995
No 60
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=70.80 E-value=2.1 Score=38.04 Aligned_cols=28 Identities=21% Similarity=-0.111 Sum_probs=17.0
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcchhhhc
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVE 145 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e 145 (185)
|+|++||+.+ .++...||.||.-..++|
T Consensus 1 ~~c~~cg~~~----------~~~~g~cp~c~~w~~~~e 28 (372)
T cd01121 1 YVCSECGYVS----------PKWLGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCCCC----------CCccEECcCCCCceeeee
Confidence 5788888622 234557888885444444
No 61
>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=70.05 E-value=4.4 Score=31.45 Aligned_cols=52 Identities=13% Similarity=0.036 Sum_probs=30.6
Q ss_pred cHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 79 GVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 79 G~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
-..++.+-++... +.-+-+....+ +++|.+||...... .|+. -..||.||+.
T Consensus 88 Ew~el~~d~~h~g---~Y~sGE~~g~G-~l~C~~Cg~~~~~~-~~~~-----l~~Cp~C~~~ 139 (146)
T PF07295_consen 88 EWAELAQDLEHHG---VYHSGEVVGPG-TLVCENCGHEVELT-HPER-----LPPCPKCGHT 139 (146)
T ss_pred HHHHHHHHHHhcC---CeecCcEecCc-eEecccCCCEEEec-CCCc-----CCCCCCCCCC
Confidence 3345555554433 45555555555 69999999644433 3332 2259999975
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=69.24 E-value=2.7 Score=30.97 Aligned_cols=26 Identities=12% Similarity=0.100 Sum_probs=15.7
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
..+|.+||..... +...+.||.||++
T Consensus 70 ~~~C~~Cg~~~~~--------~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 70 RARCRDCGHEFEP--------DEFDFSCPRCGSP 95 (113)
T ss_dssp EEEETTTS-EEEC--------HHCCHH-SSSSSS
T ss_pred cEECCCCCCEEec--------CCCCCCCcCCcCC
Confidence 4889999952211 1124579999986
No 63
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=68.42 E-value=1.3 Score=28.68 Aligned_cols=38 Identities=24% Similarity=0.304 Sum_probs=19.4
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhhcccc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQP 148 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~ 148 (185)
.+.||.||.. +.+..+ .. -.-..||.||..+++++..+
T Consensus 2 ~~~CP~CG~~-iev~~~--~~-GeiV~Cp~CGaeleVv~~~p 39 (54)
T TIGR01206 2 QFECPDCGAE-IELENP--EL-GELVICDECGAELEVVSLDP 39 (54)
T ss_pred ccCCCCCCCE-EecCCC--cc-CCEEeCCCCCCEEEEEeCCC
Confidence 3578888852 222110 00 01225788887777665544
No 64
>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=67.83 E-value=3.7 Score=24.78 Aligned_cols=29 Identities=14% Similarity=0.331 Sum_probs=16.3
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcch
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVEL 141 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~ 141 (185)
++||.|+...+.+- + .+..+.|+.||.-+
T Consensus 1 m~Cp~Cg~~~~~~D-~----~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 1 MKCPNCGSKEIVFD-P----ERGELVCPNCGLVL 29 (43)
T ss_dssp ESBTTTSSSEEEEE-T----TTTEEEETTT-BBE
T ss_pred CCCcCCcCCceEEc-C----CCCeEECCCCCCEe
Confidence 46889986553331 1 12345799998643
No 65
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=67.31 E-value=3.1 Score=26.37 Aligned_cols=34 Identities=12% Similarity=0.081 Sum_probs=21.2
Q ss_pred eEeecCCCCceeEEeeCccccccCCccccCccCcchhhhc
Q psy9094 106 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVE 145 (185)
Q Consensus 106 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e 145 (185)
+.|+|.+||...... +......||.||.+.-+.+
T Consensus 5 ~~Y~C~~Cg~~~~~~------~~~~~irCp~Cg~rIl~K~ 38 (49)
T COG1996 5 MEYKCARCGREVELD------QETRGIRCPYCGSRILVKE 38 (49)
T ss_pred EEEEhhhcCCeeehh------hccCceeCCCCCcEEEEec
Confidence 479999999643211 1123457999998754443
No 66
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=67.24 E-value=2.4 Score=37.54 Aligned_cols=36 Identities=17% Similarity=0.182 Sum_probs=24.1
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHH
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLE 151 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~ 151 (185)
.|+|++|....... ....||.||.+.++.....+||
T Consensus 57 i~kC~~c~~~~~y~---------~~~~C~~cg~~~~l~R~VSfVD 92 (415)
T COG5257 57 IYKCPECYRPECYT---------TEPKCPNCGAETELVRRVSFVD 92 (415)
T ss_pred eEeCCCCCCCcccc---------cCCCCCCCCCCccEEEEEEEee
Confidence 68999999421111 1336999999887777766654
No 67
>PHA00626 hypothetical protein
Probab=67.19 E-value=4.4 Score=26.46 Aligned_cols=30 Identities=3% Similarity=0.119 Sum_probs=16.9
Q ss_pred ecCCCCceeEEeeCcccccc-CCccccCccCcc
Q psy9094 109 KNHSTSEDRVLHLTPEQEKD-KSHFTDKETGVE 140 (185)
Q Consensus 109 ~c~~~~~~~~~~~~~~~~~~-~~~~~c~~~g~~ 140 (185)
.||+||...+.- ...... +..|.||.||-.
T Consensus 2 ~CP~CGS~~Ivr--cg~cr~~snrYkCkdCGY~ 32 (59)
T PHA00626 2 SCPKCGSGNIAK--EKTMRGWSDDYVCCDCGYN 32 (59)
T ss_pred CCCCCCCceeee--eceecccCcceEcCCCCCe
Confidence 488888633321 111112 347889999954
No 68
>cd03769 SR_IS607_transposase_like Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. This subfamily is composed of proteins that catalyze the transposition of insertion sequence (IS) elements such as IS607 from Helicobacter and IS1535 from Mycobacterium, and similar proteins from other bacteria and several archaeal species. IS elements are DNA segments that move to new sites in prokaryotic and eukaryotic genomes causing insertion mutations and gene rearrangements.
Probab=67.06 E-value=18 Score=27.04 Aligned_cols=22 Identities=23% Similarity=0.222 Sum_probs=18.8
Q ss_pred ecHHHHHHHHHcCCccEEEeec
Q psy9094 78 FGVEDTLRALELGSVETLICWE 99 (185)
Q Consensus 78 yG~~ev~~Ale~GaV~~Llv~d 99 (185)
=|+...+++++.|.|++|||++
T Consensus 49 p~l~~ll~~i~~g~~d~lvV~~ 70 (134)
T cd03769 49 KGLLKLLEDVLAGKVERVVITY 70 (134)
T ss_pred HHHHHHHHHHHcCCCCEEEEEe
Confidence 4677888999999999999976
No 69
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=66.88 E-value=4.9 Score=29.68 Aligned_cols=27 Identities=4% Similarity=-0.209 Sum_probs=16.7
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
.++|.+||..... . ....+.||.||+.
T Consensus 70 ~~~C~~Cg~~~~~---~----~~~~~~CP~Cgs~ 96 (114)
T PRK03681 70 ECWCETCQQYVTL---L----TQRVRRCPQCHGD 96 (114)
T ss_pred EEEcccCCCeeec---C----CccCCcCcCcCCC
Confidence 4899999952111 1 1113569999975
No 70
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=66.58 E-value=5.6 Score=22.70 Aligned_cols=25 Identities=8% Similarity=-0.132 Sum_probs=16.3
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
|+|..||.... +. ...+.||.||.+
T Consensus 2 ~~C~~CGy~y~----~~----~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYD----GE----EAPWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEEC----CC----cCCCcCcCCCCc
Confidence 78999996211 11 125579999975
No 71
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=66.10 E-value=6.1 Score=22.69 Aligned_cols=26 Identities=15% Similarity=0.118 Sum_probs=15.3
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
|.|.+||.... +++. ....|+.||.+
T Consensus 1 Y~C~~Cg~~~~--~~~~-----~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVE--LKPG-----DPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE---BSTS-----STSSBSSSS-S
T ss_pred CCCCcCCCeeE--cCCC-----CcEECCcCCCe
Confidence 57888995433 2222 24479999976
No 72
>PRK14873 primosome assembly protein PriA; Provisional
Probab=65.91 E-value=7.6 Score=37.25 Aligned_cols=89 Identities=12% Similarity=0.065 Sum_probs=46.3
Q ss_pred ecHHHHHHHHHcCCccEEEeeccCcce--------eeEeecCCCCceeEEe-eCcccc------ccCCccccCccCcchh
Q psy9094 78 FGVEDTLRALELGSVETLICWENLDIQ--------RYVLKNHSTSEDRVLH-LTPEQE------KDKSHFTDKETGVELE 142 (185)
Q Consensus 78 yG~~ev~~Ale~GaV~~Llv~d~l~~~--------r~~~~c~~~~~~~~~~-~~~~~~------~~~~~~~c~~~g~~~~ 142 (185)
.-.+.+.++++.| ..||...---.. +++.+|++|+- ...+ ...... .....+.||.||+..
T Consensus 357 ~l~~~i~~~L~~g--qvll~lnRrGyap~l~C~~Cg~~~~C~~C~~-~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~~- 432 (665)
T PRK14873 357 LAFRAARDALEHG--PVLVQVPRRGYVPSLACARCRTPARCRHCTG-PLGLPSAGGTPRCRWCGRAAPDWRCPRCGSDR- 432 (665)
T ss_pred HHHHHHHHHHhcC--cEEEEecCCCCCCeeEhhhCcCeeECCCCCC-ceeEecCCCeeECCCCcCCCcCccCCCCcCCc-
Confidence 4567888889999 776665432111 44677777772 2222 211111 112355799999752
Q ss_pred hhccccHHHHHHHHHHh-c-CCEEEEeCCC
Q psy9094 143 LVECQPLLEWLANNYKS-F-GATLEIITDK 170 (185)
Q Consensus 143 ~~e~~~~v~~l~e~a~~-~-g~~v~ivs~~ 170 (185)
+....-=.+.+.+...+ + ++.|..++.+
T Consensus 433 l~~~g~Gter~eeeL~~~FP~~~V~r~d~d 462 (665)
T PRK14873 433 LRAVVVGARRTAEELGRAFPGVPVVTSGGD 462 (665)
T ss_pred ceeeeccHHHHHHHHHHHCCCCCEEEEChH
Confidence 11222223444443333 3 5667766655
No 73
>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=65.48 E-value=21 Score=33.01 Aligned_cols=42 Identities=21% Similarity=0.120 Sum_probs=24.6
Q ss_pred ccccCccCcchhhhccccHHHHHHHHHHhc--CCEEEEeCCCCch
Q psy9094 131 HFTDKETGVELELVECQPLLEWLANNYKSF--GATLEIITDKSQE 173 (185)
Q Consensus 131 ~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~--g~~v~ivs~~~e~ 173 (185)
...||.||+.. +...---++.+.+...+. +++|..+++++..
T Consensus 253 ~~~Cp~C~s~~-l~~~g~Gte~~~e~l~~~fp~~~v~~~d~d~~~ 296 (505)
T TIGR00595 253 PKTCPQCGSED-LVYKGYGTEQVEEELAKLFPGARIARIDSDTTS 296 (505)
T ss_pred CCCCCCCCCCe-eEeecccHHHHHHHHHhhCCCCcEEEEeccccc
Confidence 34699998742 111111245555555554 7789988887654
No 74
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=64.86 E-value=3.2 Score=30.81 Aligned_cols=30 Identities=7% Similarity=-0.115 Sum_probs=19.4
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhh
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELV 144 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~ 144 (185)
...||+|+..+... -. ...|..|+.|+-+.
T Consensus 69 ~V~CP~C~K~TKmL-Gr-------~D~CM~C~~pLTLd 98 (114)
T PF11023_consen 69 QVECPNCGKQTKML-GR-------VDACMHCKEPLTLD 98 (114)
T ss_pred eeECCCCCChHhhh-ch-------hhccCcCCCcCccC
Confidence 56899999644333 11 12599999987543
No 75
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=64.67 E-value=10 Score=28.47 Aligned_cols=51 Identities=6% Similarity=0.120 Sum_probs=32.5
Q ss_pred ceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHH
Q psy9094 75 KYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLA 154 (185)
Q Consensus 75 ~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~ 154 (185)
++....++..+.+..+.||.++|...... .+.+..++
T Consensus 125 ~~lg~~~~l~~~~~~~~id~v~ial~~~~-------------------------------------------~~~i~~ii 161 (175)
T PF13727_consen 125 PVLGDLDDLPELVREHDIDEVIIALPWSE-------------------------------------------EEQIKRII 161 (175)
T ss_dssp EEE--GGGHHHHHHHHT--EEEE--TTS--------------------------------------------HHHHHHHH
T ss_pred eeEcCHHHHHHHHHhCCCCEEEEEcCccC-------------------------------------------HHHHHHHH
Confidence 33445799999999999999999864321 22466788
Q ss_pred HHHHhcCCEEEEeC
Q psy9094 155 NNYKSFGATLEIIT 168 (185)
Q Consensus 155 e~a~~~g~~v~ivs 168 (185)
+.+++.|.+|.+||
T Consensus 162 ~~~~~~~v~v~~vP 175 (175)
T PF13727_consen 162 EELENHGVRVRVVP 175 (175)
T ss_dssp HHHHTTT-EEEE--
T ss_pred HHHHhCCCEEEEeC
Confidence 99999999999986
No 76
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=63.63 E-value=4.5 Score=36.23 Aligned_cols=30 Identities=17% Similarity=0.020 Sum_probs=19.9
Q ss_pred eEeecCCCCceeEEeeCccccccCCccccCccCcchhhh
Q psy9094 106 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELV 144 (185)
Q Consensus 106 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~ 144 (185)
|+++|.+||.. |. +...+.||.|++++.+.
T Consensus 1 ~~l~C~~Cg~~---~~------~~~~~~C~~c~g~l~~~ 30 (398)
T TIGR03844 1 YTLRCPGCGEV---LP------DHYTLSCPLDCGLLRAE 30 (398)
T ss_pred CEEEeCCCCCc---cC------CccccCCCCCCCceEEe
Confidence 47899999952 21 11246799998877655
No 77
>PRK06450 threonine synthase; Validated
Probab=63.52 E-value=4.4 Score=35.42 Aligned_cols=30 Identities=10% Similarity=0.032 Sum_probs=20.4
Q ss_pred eEeecCCCCceeEEeeCccccccCCccccCccCcchhhh
Q psy9094 106 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELV 144 (185)
Q Consensus 106 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~ 144 (185)
+.++|.+||.. +. ....+.||.||+++++.
T Consensus 2 ~~~~C~~Cg~~---~~------~~~~~~C~~cg~~l~~~ 31 (338)
T PRK06450 2 VKEVCMKCGKE---RE------SIYEIRCKKCGGPFEIL 31 (338)
T ss_pred ceeEECCcCCc---CC------CcccccCCcCCCEeEEe
Confidence 35899999952 20 01245799999998765
No 78
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=62.72 E-value=4.1 Score=36.02 Aligned_cols=24 Identities=0% Similarity=-0.216 Sum_probs=17.5
Q ss_pred eEeecCCCCceeEEeeCccccccCCccccCccCc
Q psy9094 106 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGV 139 (185)
Q Consensus 106 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~ 139 (185)
.-|+|.+||+....+ .|.||.|..
T Consensus 353 ~~YRC~~CGF~a~~l----------~W~CPsC~~ 376 (389)
T COG2956 353 PRYRCQNCGFTAHTL----------YWHCPSCRA 376 (389)
T ss_pred CCceecccCCcceee----------eeeCCCccc
Confidence 358999999644433 457999984
No 79
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=62.60 E-value=9 Score=39.57 Aligned_cols=45 Identities=16% Similarity=0.063 Sum_probs=31.5
Q ss_pred HHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhh
Q psy9094 80 VEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELV 144 (185)
Q Consensus 80 ~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~ 144 (185)
...+.+|++.|.++.+=|. -.+||+||..+. ...||.||.+.+..
T Consensus 655 ~R~i~~A~~~g~~~~vei~--------~~~Cp~Cg~~~~------------~~~Cp~CG~~~~~~ 699 (1627)
T PRK14715 655 VRLINKAVEENKTDDIEIA--------FFKCPKCGKVGL------------YHVCPFCGTRVELK 699 (1627)
T ss_pred hhhHHHHhhcCCcceEEEE--------eeeCCCCCCccc------------cccCcccCCcccCC
Confidence 3568999999998755444 258999996222 33699999765443
No 80
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=62.45 E-value=4.1 Score=34.95 Aligned_cols=24 Identities=0% Similarity=-0.245 Sum_probs=17.1
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
.|.|+.||+.+.. ..+.||.||+-
T Consensus 354 ~~~c~~cg~~~~~----------~~~~c~~c~~~ 377 (389)
T PRK11788 354 RYRCRNCGFTART----------LYWHCPSCKAW 377 (389)
T ss_pred CEECCCCCCCCcc----------ceeECcCCCCc
Confidence 4789999974332 35579999963
No 81
>PRK11032 hypothetical protein; Provisional
Probab=62.12 E-value=7.3 Score=30.75 Aligned_cols=40 Identities=13% Similarity=-0.053 Sum_probs=24.5
Q ss_pred EEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 94 TLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 94 ~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
-+..+-+.-..+ +++|.+||.....+ .|+. -..||.||+.
T Consensus 112 g~Y~sGEvvg~G-~LvC~~Cg~~~~~~-~p~~-----i~pCp~C~~~ 151 (160)
T PRK11032 112 GVYHSGEVVGLG-NLVCEKCHHHLAFY-TPEV-----LPLCPKCGHD 151 (160)
T ss_pred Ceeecceeeecc-eEEecCCCCEEEec-CCCc-----CCCCCCCCCC
Confidence 345555554444 68999999654433 3321 1259999974
No 82
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=61.57 E-value=6.6 Score=29.83 Aligned_cols=67 Identities=16% Similarity=0.189 Sum_probs=38.3
Q ss_pred CCceEecHHHHHHHHHcCCcc-----EEEeeccCcc-----eeeEeecCCCCceeEEeeCccccccCCccccCccCcchh
Q psy9094 73 TGKYCFGVEDTLRALELGSVE-----TLICWENLDI-----QRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELE 142 (185)
Q Consensus 73 ~~~~~yG~~ev~~Ale~GaV~-----~Llv~d~l~~-----~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~ 142 (185)
.+...-|.+=-..|-..|..- ..=...++.. .++.|+|+.|+......... ....+.|+.|++++.
T Consensus 79 ~~~~~Hg~~fk~~~~~ig~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~r~~~~----~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 79 GRRRGHGKEFKQWARRIGASPPRGRPNPTTCHSYEIEGKEYKKYVYRCPSCGREYKRHRRS----KRKRYRCGRCGGPLV 154 (157)
T ss_pred CCCCCCCHHHHHHHHHHCCcccccccccccccccccccccccceEEEcCCCCCEeeeeccc----chhhEECCCCCCEEE
Confidence 345566765555555666622 2233333333 46789999999543332111 123567999999875
Q ss_pred h
Q psy9094 143 L 143 (185)
Q Consensus 143 ~ 143 (185)
.
T Consensus 155 ~ 155 (157)
T PF10263_consen 155 Q 155 (157)
T ss_pred E
Confidence 3
No 83
>PRK04351 hypothetical protein; Provisional
Probab=60.85 E-value=8.5 Score=29.89 Aligned_cols=38 Identities=11% Similarity=0.201 Sum_probs=25.1
Q ss_pred ceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhh
Q psy9094 103 IQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELV 144 (185)
Q Consensus 103 ~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~ 144 (185)
..++.|+|.+||...... ..- +...+.|..|++.|..+
T Consensus 108 ~~~y~Y~C~~Cg~~~~r~-Rr~---n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 108 KKNYLYECQSCGQQYLRK-RRI---NTKRYRCGKCRGKLKLI 145 (149)
T ss_pred CceEEEECCCCCCEeeee-eec---CCCcEEeCCCCcEeeec
Confidence 346899999999532222 111 23478899999988655
No 84
>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=60.51 E-value=4.6 Score=29.75 Aligned_cols=28 Identities=14% Similarity=0.097 Sum_probs=17.8
Q ss_pred eecCCCCceeEEe-eCccccccCCccccCccCcchhh
Q psy9094 108 LKNHSTSEDRVLH-LTPEQEKDKSHFTDKETGVELEL 143 (185)
Q Consensus 108 ~~c~~~~~~~~~~-~~~~~~~~~~~~~c~~~g~~~~~ 143 (185)
..|++||.. +| +.. ....||.||..+.+
T Consensus 10 R~Cp~CG~k--FYDLnk------~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 10 RTCPSCGAK--FYDLNK------DPIVCPKCGTEFPP 38 (108)
T ss_pred ccCCCCcch--hccCCC------CCccCCCCCCccCc
Confidence 479999951 22 322 24469999976543
No 85
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=60.23 E-value=6 Score=29.36 Aligned_cols=26 Identities=8% Similarity=-0.032 Sum_probs=16.0
Q ss_pred EeecCCCCceeEEeeCccccccCCcc-ccCccCcc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHF-TDKETGVE 140 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~-~c~~~g~~ 140 (185)
..+|.+||..... ....+ .||.||++
T Consensus 71 ~~~C~~Cg~~~~~--------~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 71 ELECKDCSHVFKP--------NALDYGVCEKCHSK 97 (117)
T ss_pred EEEhhhCCCcccc--------CCccCCcCcCCCCC
Confidence 4789999942111 11233 49999985
No 86
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=57.83 E-value=4.7 Score=26.55 Aligned_cols=32 Identities=13% Similarity=0.110 Sum_probs=17.1
Q ss_pred eEeecCCCCceeEEeeCccccccCCccccCccC
Q psy9094 106 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETG 138 (185)
Q Consensus 106 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g 138 (185)
+.+.||+||...+.. -...-.....|.||+||
T Consensus 24 ~~F~CPnCG~~~I~R-C~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 24 VKFLCPNCGEVIIYR-CEKCRKQSNPYTCPKCG 55 (59)
T ss_pred CEeeCCCCCCeeEee-chhHHhcCCceECCCCC
Confidence 468889988632222 00000122367789888
No 87
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=57.56 E-value=5.2 Score=31.33 Aligned_cols=9 Identities=0% Similarity=-0.101 Sum_probs=5.1
Q ss_pred eecCCCCce
Q psy9094 108 LKNHSTSED 116 (185)
Q Consensus 108 ~~c~~~~~~ 116 (185)
+.|++||..
T Consensus 29 ~~c~~c~~~ 37 (154)
T PRK00464 29 RECLACGKR 37 (154)
T ss_pred eeccccCCc
Confidence 556666643
No 88
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=57.14 E-value=4.9 Score=38.47 Aligned_cols=26 Identities=15% Similarity=-0.082 Sum_probs=17.6
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcchhhh
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELV 144 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~ 144 (185)
-+|+.||+.. ...+.||.||.++++.
T Consensus 627 ~~C~~CG~~~-----------g~~~~CP~CG~~~~v~ 652 (656)
T PRK08270 627 SICPKHGYLS-----------GEHEFCPKCGEETEVY 652 (656)
T ss_pred cccCCCCCcC-----------CCCCCCcCCcCccceE
Confidence 4699999621 1156899999875443
No 89
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=56.40 E-value=16 Score=25.74 Aligned_cols=44 Identities=7% Similarity=-0.021 Sum_probs=31.8
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCC
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDK 170 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~ 170 (185)
-.+|+.|+.+.+.|--+. +.-.|..||.. +++-+||+..|..+-
T Consensus 35 ~VkCp~C~n~q~VFShA~-----t~V~C~~Cg~~---------------L~~PTGGKa~l~~gc 78 (85)
T PTZ00083 35 DVKCPGCSQITTVFSHAQ-----TVVLCGGCSSQ---------------LCQPTGGKAKLTEGC 78 (85)
T ss_pred EEECCCCCCeeEEEecCc-----eEEEccccCCE---------------eeccCCCCeEecCCc
Confidence 378999999888882222 12259999964 577888888887664
No 90
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=55.94 E-value=8.4 Score=23.06 Aligned_cols=33 Identities=6% Similarity=0.058 Sum_probs=19.9
Q ss_pred ecCCCCceeEEeeC----ccccccCCccccCccCcch
Q psy9094 109 KNHSTSEDRVLHLT----PEQEKDKSHFTDKETGVEL 141 (185)
Q Consensus 109 ~c~~~~~~~~~~~~----~~~~~~~~~~~c~~~g~~~ 141 (185)
.|++||.....|.+ ..++.....|.|.+||..+
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 58889865555521 1223333466899998654
No 91
>PLN00209 ribosomal protein S27; Provisional
Probab=55.87 E-value=16 Score=25.80 Aligned_cols=44 Identities=5% Similarity=-0.065 Sum_probs=31.6
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCC
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDK 170 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~ 170 (185)
-.+|++|+.+.+.|-.+. +.-.|..||.. +++-+||+-.|..+.
T Consensus 36 ~VkCp~C~n~q~VFShA~-----t~V~C~~Cg~~---------------L~~PTGGKa~l~~gc 79 (86)
T PLN00209 36 DVKCQGCFNITTVFSHSQ-----TVVVCGSCQTV---------------LCQPTGGKARLTEGC 79 (86)
T ss_pred EEECCCCCCeeEEEecCc-----eEEEccccCCE---------------eeccCCCCeEecCCc
Confidence 478999999888883222 12259999964 577888888877654
No 92
>COG1212 KdsB CMP-2-keto-3-deoxyoctulosonic acid synthetase [Cell envelope biogenesis, outer membrane]
Probab=55.74 E-value=28 Score=29.30 Aligned_cols=23 Identities=22% Similarity=0.485 Sum_probs=16.5
Q ss_pred HHHHHHhcCCEEEEeCCCCchHH
Q psy9094 153 LANNYKSFGATLEIITDKSQEGS 175 (185)
Q Consensus 153 l~e~a~~~g~~v~ivs~~~e~G~ 175 (185)
+.+.+..+|+++..-|.+|++|.
T Consensus 55 I~~av~~~G~~avmT~~~h~SGT 77 (247)
T COG1212 55 IAEAVQAFGGEAVMTSKDHQSGT 77 (247)
T ss_pred HHHHHHHhCCEEEecCCCCCCcc
Confidence 45667777777777777777773
No 93
>PRK06260 threonine synthase; Validated
Probab=55.28 E-value=6.5 Score=34.98 Aligned_cols=30 Identities=30% Similarity=0.310 Sum_probs=19.4
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhh
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELV 144 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~ 144 (185)
.++|.+||.. |. + +...+.||.||+++++.
T Consensus 3 ~~~C~~cg~~---~~-~----~~~~~~Cp~cg~~l~~~ 32 (397)
T PRK06260 3 WLKCIECGKE---YD-P----DEIIYTCPECGGLLEVI 32 (397)
T ss_pred EEEECCCCCC---CC-C----CCccccCCCCCCeEEEE
Confidence 5899999951 10 0 11245799999987654
No 94
>COG1212 KdsB CMP-2-keto-3-deoxyoctulosonic acid synthetase [Cell envelope biogenesis, outer membrane]
Probab=53.99 E-value=23 Score=29.79 Aligned_cols=45 Identities=20% Similarity=0.321 Sum_probs=35.9
Q ss_pred chhhhccccHHHHHHHHHHhcCCEEEEeCCCCchHHHHhhhcCCc
Q psy9094 140 ELELVECQPLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGI 184 (185)
Q Consensus 140 ~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l~~~~GGi 184 (185)
||.-..-+.+|.+..+.|.+.|++=.+|-+++|.=..-+.+|||-
T Consensus 21 PLadI~GkpmI~rV~e~a~~s~~~rvvVATDde~I~~av~~~G~~ 65 (247)
T COG1212 21 PLADIGGKPMIVRVAERALKSGADRVVVATDDERIAEAVQAFGGE 65 (247)
T ss_pred chhhhCCchHHHHHHHHHHHcCCCeEEEEcCCHHHHHHHHHhCCE
Confidence 333344455688999999999999999999999877778999984
No 95
>PHA02998 RNA polymerase subunit; Provisional
Probab=53.25 E-value=8.8 Score=30.91 Aligned_cols=38 Identities=5% Similarity=-0.070 Sum_probs=25.4
Q ss_pred EeecCCCCceeEEe---eCc-cccccCCccccCccCcchhhh
Q psy9094 107 VLKNHSTSEDRVLH---LTP-EQEKDKSHFTDKETGVELELV 144 (185)
Q Consensus 107 ~~~c~~~~~~~~~~---~~~-~~~~~~~~~~c~~~g~~~~~~ 144 (185)
...|+.|+.....+ +.+ .++.....+.|..||..+.+.
T Consensus 143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCCc
Confidence 46799999766665 222 234444577899999887654
No 96
>cd00338 Ser_Recombinase Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are protei
Probab=52.84 E-value=42 Score=24.27 Aligned_cols=24 Identities=13% Similarity=0.281 Sum_probs=20.3
Q ss_pred cHHHHHHHHHcCCccEEEeeccCc
Q psy9094 79 GVEDTLRALELGSVETLICWENLD 102 (185)
Q Consensus 79 G~~ev~~Ale~GaV~~Llv~d~l~ 102 (185)
|+...++++..|.+++|||++-=.
T Consensus 53 ~~~~ll~~~~~~~~d~ivv~~~~R 76 (137)
T cd00338 53 GLQRLLADVKAGKIDVVLVEKLDR 76 (137)
T ss_pred HHHHHHHHHHcCCCCEEEEEecch
Confidence 788889999999999999987543
No 97
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=52.03 E-value=17 Score=36.76 Aligned_cols=59 Identities=17% Similarity=0.045 Sum_probs=35.3
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCCCchHHHH
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDKSQEGSQF 177 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l 177 (185)
+.+|.+||...+.. ...||.||++.. ......|+.|-+.|-. --+|.|=++...+|+.+
T Consensus 694 IKrC~dcg~q~~~~----------~~~cP~Cgs~~v-~d~~~~ve~lRelA~E-vDeVlIgTDPDtEGEKI 752 (1187)
T COG1110 694 IKRCRDCGEQFVDS----------EDKCPRCGSRNV-EDKTETVEALRELALE-VDEILIGTDPDTEGEKI 752 (1187)
T ss_pred HHHHhhcCceeccc----------cccCCCCCCccc-cccHHHHHHHHHHHhh-cCEEEEcCCCCCccchh
Confidence 45799999744321 125999998642 2334556655555543 33566666666677643
No 98
>PRK07591 threonine synthase; Validated
Probab=52.00 E-value=10 Score=34.18 Aligned_cols=29 Identities=17% Similarity=0.019 Sum_probs=19.8
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhh
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELV 144 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~ 144 (185)
.++|.+||.. |. . . ..+.||.||+.|++.
T Consensus 18 ~l~C~~Cg~~---~~----~-~-~~~~C~~cg~~l~~~ 46 (421)
T PRK07591 18 ALKCRECGAE---YP----L-G-PIHVCEECFGPLEVA 46 (421)
T ss_pred EEEeCCCCCc---CC----C-C-CCccCCCCCCeEEEE
Confidence 5899999951 21 0 1 136799999998755
No 99
>PRK05580 primosome assembly protein PriA; Validated
Probab=51.80 E-value=24 Score=33.88 Aligned_cols=41 Identities=22% Similarity=0.157 Sum_probs=26.4
Q ss_pred ccccCccCcchhhhccccHHHHHHHHHHhc--CCEEEEeCCCCc
Q psy9094 131 HFTDKETGVELELVECQPLLEWLANNYKSF--GATLEIITDKSQ 172 (185)
Q Consensus 131 ~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~--g~~v~ivs~~~e 172 (185)
...||.||+.. +....--++.+.+...+. +.+|..+++++.
T Consensus 421 ~~~Cp~Cg~~~-l~~~g~G~e~~~e~l~~~fp~~~v~~~~~d~~ 463 (679)
T PRK05580 421 PKACPECGSTD-LVPVGPGTERLEEELAELFPEARILRIDRDTT 463 (679)
T ss_pred CCCCCCCcCCe-eEEeeccHHHHHHHHHHhCCCCcEEEEecccc
Confidence 34699998752 223233456666666665 788888887764
No 100
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=51.42 E-value=10 Score=22.25 Aligned_cols=30 Identities=13% Similarity=0.032 Sum_probs=16.9
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcch
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVEL 141 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~ 141 (185)
+.|+.||..-.....|.. ..-.|+.||++|
T Consensus 2 r~C~~Cg~~Yh~~~~pP~----~~~~Cd~cg~~L 31 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPK----VEGVCDNCGGEL 31 (36)
T ss_dssp EEETTTTEEEETTTB--S----STTBCTTTTEBE
T ss_pred cCcCCCCCccccccCCCC----CCCccCCCCCee
Confidence 579999953222222221 133699999865
No 101
>PF14353 CpXC: CpXC protein
Probab=51.38 E-value=9.7 Score=28.25 Aligned_cols=9 Identities=33% Similarity=0.416 Sum_probs=5.3
Q ss_pred cccCccCcc
Q psy9094 132 FTDKETGVE 140 (185)
Q Consensus 132 ~~c~~~g~~ 140 (185)
+.||.||..
T Consensus 39 ~~CP~Cg~~ 47 (128)
T PF14353_consen 39 FTCPSCGHK 47 (128)
T ss_pred EECCCCCCc
Confidence 346777654
No 102
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=50.80 E-value=7.8 Score=23.05 Aligned_cols=33 Identities=12% Similarity=0.116 Sum_probs=16.8
Q ss_pred ecCCCCceeEEee---Cc-cccccCCccccCccCcch
Q psy9094 109 KNHSTSEDRVLHL---TP-EQEKDKSHFTDKETGVEL 141 (185)
Q Consensus 109 ~c~~~~~~~~~~~---~~-~~~~~~~~~~c~~~g~~~ 141 (185)
.||+||.....+. .. .|+.....|.|..||..+
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 5889996655552 11 223233356788888653
No 103
>PF07960 CBP4: CBP4; InterPro: IPR012420 The CBP4 gene in Saccharomyces cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase [, ]. This family appears to be fungal specific.
Probab=50.47 E-value=29 Score=26.39 Aligned_cols=24 Identities=29% Similarity=0.263 Sum_probs=18.4
Q ss_pred EEEEeCChhhH------HhhcccCCCCHhhhc
Q psy9094 29 GLILAGSADFK------TELSQSDMFDPVRFS 54 (185)
Q Consensus 29 ~lIIaGPg~~k------~~f~~~~~L~~~l~~ 54 (185)
+||++||..++ ++++. -|++.|+.
T Consensus 17 ~ii~~G~~l~~y~tPTeEeL~~--r~sPELrk 46 (128)
T PF07960_consen 17 VIIGGGPALVKYTTPTEEELFK--RYSPELRK 46 (128)
T ss_pred eeEeechHHheecCCCHHHHHH--hcCHHHHH
Confidence 68899999776 67774 57888776
No 104
>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=50.33 E-value=10 Score=28.79 Aligned_cols=27 Identities=15% Similarity=0.060 Sum_probs=17.2
Q ss_pred eecCCCCceeEEe-eCccccccCCccccCccCcchh
Q psy9094 108 LKNHSTSEDRVLH-LTPEQEKDKSHFTDKETGVELE 142 (185)
Q Consensus 108 ~~c~~~~~~~~~~-~~~~~~~~~~~~~c~~~g~~~~ 142 (185)
..|++||.. .| +.. ....||.||..+.
T Consensus 10 r~Cp~cg~k--FYDLnk------~p~vcP~cg~~~~ 37 (129)
T TIGR02300 10 RICPNTGSK--FYDLNR------RPAVSPYTGEQFP 37 (129)
T ss_pred ccCCCcCcc--ccccCC------CCccCCCcCCccC
Confidence 479999952 22 322 2446999997653
No 105
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=50.32 E-value=58 Score=24.33 Aligned_cols=22 Identities=18% Similarity=0.424 Sum_probs=18.5
Q ss_pred ecHHHHHHHHHcCCccEEEeec
Q psy9094 78 FGVEDTLRALELGSVETLICWE 99 (185)
Q Consensus 78 yG~~ev~~Ale~GaV~~Llv~d 99 (185)
-|+...++.+..|.|++|+|++
T Consensus 55 p~l~~ll~~~~~g~vd~vvv~~ 76 (140)
T cd03770 55 PGFNRMIEDIEAGKIDIVIVKD 76 (140)
T ss_pred HHHHHHHHHHHcCCCCEEEEec
Confidence 4667788889999999999987
No 106
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=49.26 E-value=27 Score=25.60 Aligned_cols=43 Identities=5% Similarity=0.006 Sum_probs=24.4
Q ss_pred eEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHHH
Q psy9094 106 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYK 158 (185)
Q Consensus 106 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~ 158 (185)
..+.|++||.....+.+= + .-.||.||.. .....++...+..-
T Consensus 41 ~~~~C~~Cg~~~~~~~SC-----k-~R~CP~C~~~----~~~~W~~~~~~~ll 83 (111)
T PF14319_consen 41 HRYRCEDCGHEKIVYNSC-----K-NRHCPSCQAK----ATEQWIEKQREDLL 83 (111)
T ss_pred ceeecCCCCceEEecCcc-----c-CcCCCCCCCh----HHHHHHHHHHhhCC
Confidence 368999999765544111 1 2259999975 33444444444333
No 107
>PRK00420 hypothetical protein; Validated
Probab=49.07 E-value=11 Score=27.98 Aligned_cols=28 Identities=4% Similarity=-0.188 Sum_probs=17.5
Q ss_pred ecCCCCceeEEeeCccccccCCccccCccCcchhh
Q psy9094 109 KNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELEL 143 (185)
Q Consensus 109 ~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~ 143 (185)
.||.||..-..+ . .....||.||....+
T Consensus 25 ~CP~Cg~pLf~l-k------~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 25 HCPVCGLPLFEL-K------DGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCCcceec-C------CCceECCCCCCeeee
Confidence 499999533322 1 124479999986654
No 108
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=48.78 E-value=16 Score=21.28 Aligned_cols=30 Identities=7% Similarity=0.005 Sum_probs=16.3
Q ss_pred eecCCCCceeEEe-eCcccc-ccCCccccCccCcc
Q psy9094 108 LKNHSTSEDRVLH-LTPEQE-KDKSHFTDKETGVE 140 (185)
Q Consensus 108 ~~c~~~~~~~~~~-~~~~~~-~~~~~~~c~~~g~~ 140 (185)
..|++|+. .| ...+.. .......|+.||..
T Consensus 3 i~Cp~C~~---~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 3 ITCPNCQA---KYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred EECCCCCC---EEeCCHHHCCCCCcEEECCCCCCE
Confidence 57888885 34 222222 12224568888753
No 109
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=48.21 E-value=15 Score=21.48 Aligned_cols=32 Identities=6% Similarity=0.092 Sum_probs=17.6
Q ss_pred EeecCCCCceeEEeeCc-ccc-ccCCccccCccCcch
Q psy9094 107 VLKNHSTSEDRVLHLTP-EQE-KDKSHFTDKETGVEL 141 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~-~~~-~~~~~~~c~~~g~~~ 141 (185)
...||+|+. .|.-+ ++. .......|+.|+..+
T Consensus 2 ~i~CP~C~~---~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCPNCQT---RFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCc---eEEcCHHHcccCCcEEECCCCCcEe
Confidence 357899985 34222 221 122355788888643
No 110
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=47.47 E-value=14 Score=23.97 Aligned_cols=25 Identities=8% Similarity=-0.203 Sum_probs=16.2
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcchhhh
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELV 144 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~ 144 (185)
.+|++||.-+. +..||.||+++...
T Consensus 6 r~C~~CgvYTL------------k~~CP~CG~~t~~~ 30 (56)
T PRK13130 6 RKCPKCGVYTL------------KEICPVCGGKTKNP 30 (56)
T ss_pred eECCCCCCEEc------------cccCcCCCCCCCCC
Confidence 57999993111 23589999876544
No 111
>COG4079 Uncharacterized protein conserved in archaea [Function unknown]
Probab=47.41 E-value=23 Score=30.09 Aligned_cols=43 Identities=12% Similarity=0.167 Sum_probs=33.3
Q ss_pred cEEEEeCChhhHHhhcccCCCCHhhhc---hHHHHHHHHHHHHHHhhC
Q psy9094 28 AGLILAGSADFKTELSQSDMFDPVRFS---PLKNKNKMGKYFDEISQD 72 (185)
Q Consensus 28 ~~lIIaGPg~~k~~f~~~~~L~~~l~~---~~~E~~lve~f~~~l~~~ 72 (185)
-+||+-||-|+|+-.. .+|+.+|.. +++-.+++.++|+.+++.
T Consensus 120 ~aiIv~Gnk~~Ke~an--eflk~~l~~k~~lqd~~dal~elfe~vss~ 165 (293)
T COG4079 120 SAIIVFGNKFTKEVAN--EFLKDNLTKKSKLQDAVDALMELFETVSSK 165 (293)
T ss_pred ceEEEECcHHHHHHHH--HHHHhhccCCCCHHHHHHHHHHHHHHhhcC
Confidence 5899999999997665 356666654 777888889999998753
No 112
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.37 E-value=5.4 Score=27.69 Aligned_cols=34 Identities=18% Similarity=0.130 Sum_probs=19.2
Q ss_pred eeEeecCCCCceeEEeeCccccccCCccccCccCcch
Q psy9094 105 RYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVEL 141 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~ 141 (185)
-|.|+|..|+......+.- ++...-.||.||+++
T Consensus 10 tY~Y~c~~cg~~~dvvq~~---~ddplt~ce~c~a~~ 43 (82)
T COG2331 10 TYSYECTECGNRFDVVQAM---TDDPLTTCEECGARL 43 (82)
T ss_pred ceEEeecccchHHHHHHhc---ccCccccChhhChHH
Confidence 3579999999532222110 111233599999875
No 113
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=46.82 E-value=12 Score=38.33 Aligned_cols=8 Identities=13% Similarity=-0.014 Sum_probs=5.0
Q ss_pred eecCCCCc
Q psy9094 108 LKNHSTSE 115 (185)
Q Consensus 108 ~~c~~~~~ 115 (185)
.+||+||.
T Consensus 668 rkCPkCG~ 675 (1337)
T PRK14714 668 RRCPSCGT 675 (1337)
T ss_pred EECCCCCC
Confidence 45777664
No 114
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=45.97 E-value=52 Score=27.32 Aligned_cols=27 Identities=11% Similarity=0.166 Sum_probs=21.6
Q ss_pred ceEecHHHHHHHHHc-C-CccEEEeeccC
Q psy9094 75 KYCFGVEDTLRALEL-G-SVETLICWENL 101 (185)
Q Consensus 75 ~~~yG~~ev~~Ale~-G-aV~~Llv~d~l 101 (185)
..+||...|.+|++. + .+.+|++..+.
T Consensus 3 ~~i~G~~~v~eal~~~~~~~~~l~~~~~~ 31 (244)
T PRK11181 3 EIIYGIHAVQALLERAPERFIEVFVLKGR 31 (244)
T ss_pred cEEEehHHHHHHHhCCCCceeEEEEECCC
Confidence 468999999999975 3 68888887653
No 115
>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=45.77 E-value=17 Score=25.93 Aligned_cols=36 Identities=6% Similarity=0.045 Sum_probs=23.5
Q ss_pred eEeecCCCCceeEEeeC---c-cccccCCccccCccCcch
Q psy9094 106 YVLKNHSTSEDRVLHLT---P-EQEKDKSHFTDKETGVEL 141 (185)
Q Consensus 106 ~~~~c~~~~~~~~~~~~---~-~~~~~~~~~~c~~~g~~~ 141 (185)
....|++||.....|.+ + .++.....|.|.+||..+
T Consensus 61 ~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w 100 (104)
T TIGR01384 61 TRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVW 100 (104)
T ss_pred ccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCee
Confidence 35789999977766621 1 223333477899999765
No 116
>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=44.61 E-value=16 Score=23.00 Aligned_cols=24 Identities=17% Similarity=0.069 Sum_probs=12.9
Q ss_pred ccCccCcchhhhccccHHHHHHHH
Q psy9094 133 TDKETGVELELVECQPLLEWLANN 156 (185)
Q Consensus 133 ~c~~~g~~~~~~e~~~~v~~l~e~ 156 (185)
.||-|+.++..-...+++..+-..
T Consensus 22 ~CPlC~r~l~~e~~~~li~~~~~~ 45 (54)
T PF04423_consen 22 CCPLCGRPLDEEHRQELIKKYKSE 45 (54)
T ss_dssp E-TTT--EE-HHHHHHHHHHHHHH
T ss_pred cCCCCCCCCCHHHHHHHHHHHHHH
Confidence 599999988766666666554433
No 117
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=44.17 E-value=14 Score=33.65 Aligned_cols=31 Identities=13% Similarity=-0.197 Sum_probs=19.6
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhhccc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQ 147 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~ 147 (185)
.|.|++||+.+.+ +.=+||.||.-..++|..
T Consensus 7 ~f~C~~CG~~s~K----------W~GkCp~Cg~Wns~vE~~ 37 (456)
T COG1066 7 AFVCQECGYVSPK----------WLGKCPACGAWNTLVEEV 37 (456)
T ss_pred EEEcccCCCCCcc----------ccccCCCCCCccceEEee
Confidence 5899999963221 222799999654444433
No 118
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=43.90 E-value=9.2 Score=24.58 Aligned_cols=36 Identities=17% Similarity=0.160 Sum_probs=21.2
Q ss_pred cceeeEeecCCCCceeEEeeCccccccCCccccCccCc
Q psy9094 102 DIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGV 139 (185)
Q Consensus 102 ~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~ 139 (185)
..+|+.+.|++|..-.=.+. ..+.....|.|+.||.
T Consensus 17 ~~~r~aLIC~~C~~hNGla~--~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 17 PSNRYALICSKCFSHNGLAP--KEEFEEIQYRCPYCGA 52 (54)
T ss_pred ccCceeEECcccchhhcccc--cccCCceEEEcCCCCC
Confidence 45688899999984222221 1111223678999985
No 119
>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=43.48 E-value=14 Score=19.83 Aligned_cols=8 Identities=0% Similarity=-0.101 Sum_probs=4.6
Q ss_pred EeecCCCC
Q psy9094 107 VLKNHSTS 114 (185)
Q Consensus 107 ~~~c~~~~ 114 (185)
.|.||+||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 45666555
No 120
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=43.42 E-value=18 Score=21.03 Aligned_cols=9 Identities=11% Similarity=0.191 Sum_probs=4.9
Q ss_pred CccccCccC
Q psy9094 130 SHFTDKETG 138 (185)
Q Consensus 130 ~~~~c~~~g 138 (185)
....|+.||
T Consensus 21 ~R~vC~~Cg 29 (34)
T PF14803_consen 21 ERLVCPACG 29 (34)
T ss_dssp -EEEETTTT
T ss_pred cceECCCCC
Confidence 344566666
No 121
>COG1150 HdrC Heterodisulfide reductase, subunit C [Energy production and conversion]
Probab=42.99 E-value=22 Score=28.95 Aligned_cols=63 Identities=14% Similarity=0.052 Sum_probs=44.2
Q ss_pred eEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHH
Q psy9094 76 YCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLAN 155 (185)
Q Consensus 76 ~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e 155 (185)
-.|++.++.+-+..|-++.++.++++ |.|..|.+ =...||... ...++|-.|-+
T Consensus 57 t~y~pR~ii~~~~~g~~d~il~~~~l------W~C~tCyt--------------C~eRCPr~v------~i~~vv~~lR~ 110 (195)
T COG1150 57 TDYSPRKIIRKARLGLVDLILSSESL------WACVTCYT--------------CTERCPRGV------KIVEVVKALRN 110 (195)
T ss_pred CCCCHHHHHHHHHcccHHHHhcCCcc------eeeeechh--------------hhhhCCCCC------CHHHHHHHHHH
Confidence 46999999999999999955555543 88988773 022588643 44566766777
Q ss_pred HHHhcCCEE
Q psy9094 156 NYKSFGATL 164 (185)
Q Consensus 156 ~a~~~g~~v 164 (185)
.|-+.|-..
T Consensus 111 ~a~k~G~~~ 119 (195)
T COG1150 111 IAVKEGLIE 119 (195)
T ss_pred HHHHhcccc
Confidence 777777654
No 122
>PRK04023 DNA polymerase II large subunit; Validated
Probab=42.60 E-value=23 Score=35.64 Aligned_cols=16 Identities=13% Similarity=-0.093 Sum_probs=8.7
Q ss_pred cccCccCcchhhhccc
Q psy9094 132 FTDKETGVELELVECQ 147 (185)
Q Consensus 132 ~~c~~~g~~~~~~e~~ 147 (185)
+.||+||..+.....+
T Consensus 664 y~CPKCG~El~~~s~~ 679 (1121)
T PRK04023 664 DECEKCGREPTPYSKR 679 (1121)
T ss_pred CcCCCCCCCCCccceE
Confidence 3466777555444443
No 123
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.23 E-value=17 Score=27.21 Aligned_cols=9 Identities=11% Similarity=0.014 Sum_probs=7.2
Q ss_pred cccCccCcc
Q psy9094 132 FTDKETGVE 140 (185)
Q Consensus 132 ~~c~~~g~~ 140 (185)
+.||.||+.
T Consensus 93 ~~CP~Cgs~ 101 (124)
T PRK00762 93 IECPVCGNK 101 (124)
T ss_pred CcCcCCCCC
Confidence 569999964
No 124
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=42.13 E-value=13 Score=29.21 Aligned_cols=42 Identities=12% Similarity=0.014 Sum_probs=24.3
Q ss_pred ecCCCCceeEEee-Cccc---cccCCccccCccCcchhhhccccHH
Q psy9094 109 KNHSTSEDRVLHL-TPEQ---EKDKSHFTDKETGVELELVECQPLL 150 (185)
Q Consensus 109 ~c~~~~~~~~~~~-~~~~---~~~~~~~~c~~~g~~~~~~e~~~~v 150 (185)
+||.|++..+++. +... .+.+..-+|+.||.++--.|...+.
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~ 47 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELR 47 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeec
Confidence 5888887666662 2221 1233344689999876555554443
No 125
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=41.75 E-value=12 Score=36.28 Aligned_cols=21 Identities=10% Similarity=-0.201 Sum_probs=14.7
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCc
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGV 139 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~ 139 (185)
-+|+.||.... ..+.||.||+
T Consensus 681 ~~C~~CG~~~~-----------~~~~CP~CG~ 701 (735)
T PRK07111 681 DRCPVCGYLGV-----------IEDKCPKCGS 701 (735)
T ss_pred eecCCCCCCCC-----------cCccCcCCCC
Confidence 57999995221 1457999995
No 126
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=41.64 E-value=29 Score=31.07 Aligned_cols=48 Identities=13% Similarity=-0.035 Sum_probs=27.6
Q ss_pred eeEeecCCCCceeEEeeCccccccCCccccCccC------cchhhhc--cccHHHHHHHHHHh
Q psy9094 105 RYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETG------VELELVE--CQPLLEWLANNYKS 159 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g------~~~~~~e--~~~~v~~l~e~a~~ 159 (185)
.+++.|+.|++....+ .+. ..+||.|| +|+++=. .+++++.+++.+++
T Consensus 238 g~~~~c~~cg~~~~~~-~~~------~~~c~~Cg~~~~~~GPlW~GpL~d~~f~e~~l~~~~~ 293 (380)
T COG1867 238 GYIYHCSRCGEIVGSF-REV------DEKCPHCGGKVHLAGPLWLGPLHDEEFIEEMLEIAEG 293 (380)
T ss_pred CcEEEcccccceeccc-ccc------cccCCcccccceeccCcccCcccCHHHHHHHHHHhhc
Confidence 3468899998322221 111 23699999 6655433 34567777766653
No 127
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=41.63 E-value=20 Score=35.99 Aligned_cols=34 Identities=9% Similarity=-0.001 Sum_probs=23.0
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhhccc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQ 147 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~ 147 (185)
-|+|++|+..+.-|.-|.. -||-||+.++..++.
T Consensus 821 ~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~ 854 (1006)
T PRK12775 821 QWRCDDCGKVSEGFAFPYG-------MCPACGGKLQALDRR 854 (1006)
T ss_pred eeehhhhccccccccCCcC-------cCcccccchhhhhcc
Confidence 4899999975555433321 499999987665443
No 128
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=40.77 E-value=23 Score=27.07 Aligned_cols=24 Identities=13% Similarity=-0.063 Sum_probs=15.8
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
..+|.+||... | +....||.||++
T Consensus 29 g~kC~~CG~v~--~--------PPr~~Cp~C~~~ 52 (140)
T COG1545 29 GTKCKKCGRVY--F--------PPRAYCPKCGSE 52 (140)
T ss_pred EEEcCCCCeEE--c--------CCcccCCCCCCC
Confidence 46899999522 1 123359999986
No 129
>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis]
Probab=40.65 E-value=1.5e+02 Score=24.82 Aligned_cols=31 Identities=19% Similarity=0.116 Sum_probs=27.0
Q ss_pred CCCceEecHHHHHHHHHcC-CccEEEeeccCc
Q psy9094 72 DTGKYCFGVEDTLRALELG-SVETLICWENLD 102 (185)
Q Consensus 72 ~~~~~~yG~~ev~~Ale~G-aV~~Llv~d~l~ 102 (185)
..-..+||...|..|+++| .+..++++++..
T Consensus 19 ~~~~~~~G~~~v~~al~~~~~i~~i~~~~~~~ 50 (260)
T COG0566 19 AGEFLIEGEHAVLEALASGPKIVRILVTEGRL 50 (260)
T ss_pred cCcEEEeeHHHHHHHHhcCCCceEEEEecccc
Confidence 3348899999999999999 999999998754
No 130
>PRK05978 hypothetical protein; Provisional
Probab=40.56 E-value=17 Score=28.30 Aligned_cols=34 Identities=9% Similarity=-0.080 Sum_probs=19.4
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhhc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVE 145 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e 145 (185)
.-+||+||.-.. |..- -+-...|+.||.+++...
T Consensus 33 ~grCP~CG~G~L-F~g~----Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 33 RGRCPACGEGKL-FRAF----LKPVDHCAACGEDFTHHR 66 (148)
T ss_pred cCcCCCCCCCcc-cccc----cccCCCccccCCccccCC
Confidence 457999994222 1100 111336999998876543
No 131
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=39.71 E-value=89 Score=22.94 Aligned_cols=24 Identities=21% Similarity=0.457 Sum_probs=18.5
Q ss_pred cHHHHHHHHHcCCccEEEeeccCc
Q psy9094 79 GVEDTLRALELGSVETLICWENLD 102 (185)
Q Consensus 79 G~~ev~~Ale~GaV~~Llv~d~l~ 102 (185)
++...++.++.|.+++|||++-=.
T Consensus 53 ~l~~ll~~~~~g~~~~ivv~~~~R 76 (148)
T smart00857 53 GLQRLLADLRAGDIDVLVVYKLDR 76 (148)
T ss_pred HHHHHHHHHHcCCCCEEEEeccch
Confidence 567788888999998888876543
No 132
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=39.13 E-value=11 Score=35.29 Aligned_cols=23 Identities=9% Similarity=-0.226 Sum_probs=10.7
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
.-+|++||.... ..+.||.||++
T Consensus 491 ~~~C~~CG~~~~-----------~~~~CP~CGs~ 513 (546)
T PF13597_consen 491 IDICPDCGYIGG-----------EGDKCPKCGSE 513 (546)
T ss_dssp EEEETTT---S-------------EEE-CCC---
T ss_pred cccccCCCcCCC-----------CCCCCCCCCCc
Confidence 467999996221 14579999987
No 133
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=38.54 E-value=27 Score=23.09 Aligned_cols=8 Identities=13% Similarity=-0.014 Sum_probs=6.5
Q ss_pred ccCccCcc
Q psy9094 133 TDKETGVE 140 (185)
Q Consensus 133 ~c~~~g~~ 140 (185)
.||.||+.
T Consensus 17 ~CP~Cgs~ 24 (61)
T PRK08351 17 RCPVCGSR 24 (61)
T ss_pred cCCCCcCC
Confidence 59999975
No 134
>PRK02935 hypothetical protein; Provisional
Probab=38.45 E-value=19 Score=26.47 Aligned_cols=28 Identities=11% Similarity=-0.028 Sum_probs=17.9
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcchhh
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELEL 143 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~ 143 (185)
..||+|+..+... -+.| .|..|+.|+.+
T Consensus 71 V~CP~C~K~TKmL-GrvD-------~CM~C~~PLTL 98 (110)
T PRK02935 71 VICPSCEKPTKML-GRVD-------ACMHCNQPLTL 98 (110)
T ss_pred eECCCCCchhhhc-ccee-------ecCcCCCcCCc
Confidence 5799999633332 2221 49999998754
No 135
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=38.32 E-value=39 Score=22.52 Aligned_cols=8 Identities=13% Similarity=-0.051 Sum_probs=6.6
Q ss_pred ccCccCcc
Q psy9094 133 TDKETGVE 140 (185)
Q Consensus 133 ~c~~~g~~ 140 (185)
.||.||++
T Consensus 20 ~CP~Cgs~ 27 (64)
T COG2093 20 ICPVCGST 27 (64)
T ss_pred cCCCCCCc
Confidence 49999985
No 136
>PF03485 Arg_tRNA_synt_N: Arginyl tRNA synthetase N terminal domain; InterPro: IPR005148 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found at the N terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested that this domain will be involved in tRNA recognition [].; GO: 0000166 nucleotide binding, 0004814 arginine-tRNA ligase activity, 0005524 ATP binding, 0006420 arginyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1F7V_A 1F7U_A 1BS2_A 2ZUE_A 2ZUF_A 1IQ0_A 3GDZ_B.
Probab=37.99 E-value=38 Score=23.03 Aligned_cols=28 Identities=25% Similarity=0.302 Sum_probs=20.6
Q ss_pred HHHHHHHHHhhhhcCCCCccEEEEeCChhh
Q psy9094 9 RKVAEVATTLFITNDKPNIAGLILAGSADF 38 (185)
Q Consensus 9 k~va~~~~~~f~~~~~~~i~~lIIaGPg~~ 38 (185)
.++|+.+.+.+.. .+.++.+=++||||.
T Consensus 54 ~~iA~~i~~~l~~--~~~i~~vev~gpGFi 81 (85)
T PF03485_consen 54 REIAEEIAEKLEK--SPIIEKVEVAGPGFI 81 (85)
T ss_dssp HHHHHHHHHCHCT--TTTEEEEEEETTTEE
T ss_pred HHHHHHHHHhcCC--CCCEEEEEEcCCcEE
Confidence 4677777766643 334999999999985
No 137
>COG1083 NeuA CMP-N-acetylneuraminic acid synthetase [Cell envelope biogenesis, outer membrane]
Probab=37.97 E-value=46 Score=27.70 Aligned_cols=26 Identities=19% Similarity=0.201 Sum_probs=20.2
Q ss_pred CceEecHHHHHHHHHcCCccEEEeecc
Q psy9094 74 GKYCFGVEDTLRALELGSVETLICWEN 100 (185)
Q Consensus 74 ~~~~yG~~ev~~Ale~GaV~~Llv~d~ 100 (185)
|+--+|. -+..|++.+-++.++||.|
T Consensus 27 gkpLi~~-~I~aA~ns~~fd~VviSsD 52 (228)
T COG1083 27 GKPLIGY-TIEAALNSKLFDKVVISSD 52 (228)
T ss_pred CcchHHH-HHHHHhcCCccceEEEcCC
Confidence 4555553 4788999999999999865
No 138
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=37.91 E-value=23 Score=23.01 Aligned_cols=21 Identities=14% Similarity=0.110 Sum_probs=14.1
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCc
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGV 139 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~ 139 (185)
..|++||.. .+++..|+.||-
T Consensus 28 ~~C~~CG~~-----------~~~H~vC~~CG~ 48 (57)
T PRK12286 28 VECPNCGEP-----------KLPHRVCPSCGY 48 (57)
T ss_pred eECCCCCCc-----------cCCeEECCCCCc
Confidence 468999842 234557999984
No 139
>KOG2593|consensus
Probab=37.80 E-value=9.6 Score=34.58 Aligned_cols=37 Identities=16% Similarity=0.057 Sum_probs=21.7
Q ss_pred eeEeecCCCCceeEEeeCcccc--ccCCccccCccCcchh
Q psy9094 105 RYVLKNHSTSEDRVLHLTPEQE--KDKSHFTDKETGVELE 142 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~~~~~~~--~~~~~~~c~~~g~~~~ 142 (185)
+-.|+||.|+..-.. ++..+. .....|.|..|+++++
T Consensus 126 ~~~Y~Cp~C~kkyt~-Lea~~L~~~~~~~F~C~~C~gelv 164 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTS-LEALQLLDNETGEFHCENCGGELV 164 (436)
T ss_pred cccccCCccccchhh-hHHHHhhcccCceEEEecCCCchh
Confidence 336899999953221 222111 1224678999998875
No 140
>KOG2907|consensus
Probab=37.43 E-value=13 Score=27.63 Aligned_cols=33 Identities=12% Similarity=0.073 Sum_probs=19.5
Q ss_pred eecCCCCceeEEeeC----ccccccCCccccCccCcc
Q psy9094 108 LKNHSTSEDRVLHLT----PEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~----~~~~~~~~~~~c~~~g~~ 140 (185)
-+||.||+..-.|.. .-|+-+.-.|.||+|+-.
T Consensus 75 ~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k 111 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYK 111 (116)
T ss_pred ccCcccCCchhhhhhhhcccccCCceEEEEcCcccee
Confidence 479999977666611 112212226679998854
No 141
>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=37.38 E-value=46 Score=31.41 Aligned_cols=39 Identities=8% Similarity=-0.078 Sum_probs=22.9
Q ss_pred HHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 85 RALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 85 ~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
.|.+.| +.-.=+.-.+ -+|.+||+... ...+.||.||+.
T Consensus 509 ~a~~~~-i~Y~~~n~~~------~~C~~CG~~g~----------~~~~~CP~Cgs~ 547 (579)
T TIGR02487 509 KAMKNG-IGYFGINPPV------DVCEDCGYTGE----------GLNDKCPKCGSH 547 (579)
T ss_pred HHHhcC-CceEEeccCC------ccCCCCCCCCC----------CCCCcCcCCCCc
Confidence 344555 5555555444 46999996211 112579999964
No 142
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=37.33 E-value=27 Score=23.90 Aligned_cols=27 Identities=19% Similarity=0.167 Sum_probs=11.2
Q ss_pred eeEeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 105 RYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
+|+++|..|-.... +-++..||.||..
T Consensus 7 ~~vlrC~aCf~~t~---------~~~k~FCp~CGn~ 33 (73)
T PF08772_consen 7 TWVLRCHACFKITK---------DMTKQFCPKCGNA 33 (73)
T ss_dssp -EEEE-SSS--EES----------SS--S-SSS--S
T ss_pred eeeEEccccccCcC---------CCCceeCcccCCC
Confidence 56889988874211 2235569999954
No 143
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=37.24 E-value=42 Score=21.73 Aligned_cols=29 Identities=7% Similarity=-0.064 Sum_probs=16.9
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
-.+|++|+..++.|-.+. +.-.|..||..
T Consensus 7 ~VkCp~C~~~q~vFSha~-----t~V~C~~Cg~~ 35 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQ-----TVVKCVVCGTV 35 (55)
T ss_dssp EEE-TTT-SEEEEETT-S-----S-EE-SSSTSE
T ss_pred EEECCCCCCeeEEEecCC-----eEEEcccCCCE
Confidence 368999999888882222 12359999875
No 144
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=36.91 E-value=17 Score=34.68 Aligned_cols=23 Identities=22% Similarity=0.007 Sum_probs=15.4
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
.-+|+.||.... -.+.||.||..
T Consensus 559 ~~~C~~CGy~g~-----------~~~~CP~CG~~ 581 (618)
T PRK14704 559 VDRCKCCSYHGV-----------IGNECPSCGNE 581 (618)
T ss_pred CeecCCCCCCCC-----------cCccCcCCCCC
Confidence 357999995211 13579999964
No 145
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=36.85 E-value=20 Score=27.92 Aligned_cols=39 Identities=5% Similarity=-0.181 Sum_probs=18.6
Q ss_pred ecCCCCceeEEe-eCccc---cccCCccccCccCcchhhhccc
Q psy9094 109 KNHSTSEDRVLH-LTPEQ---EKDKSHFTDKETGVELELVECQ 147 (185)
Q Consensus 109 ~c~~~~~~~~~~-~~~~~---~~~~~~~~c~~~g~~~~~~e~~ 147 (185)
+||.|+...+++ -+... .+.+..-+|+.||.++--.|..
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErv 44 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERA 44 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeec
Confidence 477777555555 22211 1222233577777665444433
No 146
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=36.59 E-value=1.1e+02 Score=25.22 Aligned_cols=24 Identities=21% Similarity=0.365 Sum_probs=18.4
Q ss_pred ceEecHHHHHHHHHcCCccEEEeecc
Q psy9094 75 KYCFGVEDTLRALELGSVETLICWEN 100 (185)
Q Consensus 75 ~~~yG~~ev~~Ale~GaV~~Llv~d~ 100 (185)
..+||...|.+|++.| ..+++...
T Consensus 2 ~~i~G~~~v~eal~~~--~~~~~~~~ 25 (237)
T TIGR00186 2 EYLYGKNAVLEALLNQ--QRVFILKG 25 (237)
T ss_pred cEEEehHHHHHHHhCC--CEEEEEec
Confidence 4679999999999998 55555443
No 147
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=36.22 E-value=35 Score=28.49 Aligned_cols=52 Identities=10% Similarity=-0.020 Sum_probs=29.6
Q ss_pred cCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHHHhc
Q psy9094 89 LGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSF 160 (185)
Q Consensus 89 ~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~ 160 (185)
.|.+-..++.+..- + -.|+.||. + ....+.||.||.. ..+|++ ..++.+...
T Consensus 295 ~~~~~v~~~~~~~t-S---~~C~~cg~-----~------~~r~~~C~~cg~~----~~rD~n-aa~Ni~~~~ 346 (364)
T COG0675 295 WGGIVVKVVPPYYT-S---KTCPCCGH-----L------SGRLFKCPRCGFV----HDRDVN-AALNIARRA 346 (364)
T ss_pred hCCeEEEECCCCCC-c---ccccccCC-----c------cceeEECCCCCCe----ehhhHH-HHHHHHHHh
Confidence 36666666653332 2 36999996 1 1235689999964 235554 334444443
No 148
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=36.05 E-value=20 Score=31.09 Aligned_cols=35 Identities=14% Similarity=0.126 Sum_probs=22.6
Q ss_pred eecCCCCceeEEee---Cc-cccccCCccccCccCcchh
Q psy9094 108 LKNHSTSEDRVLHL---TP-EQEKDKSHFTDKETGVELE 142 (185)
Q Consensus 108 ~~c~~~~~~~~~~~---~~-~~~~~~~~~~c~~~g~~~~ 142 (185)
+.|+.|+.....|. .+ .++.....|.|..||..|.
T Consensus 259 ~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 259 FTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 57999996666552 11 2333445678999998753
No 149
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=35.88 E-value=37 Score=22.37 Aligned_cols=37 Identities=8% Similarity=-0.084 Sum_probs=13.3
Q ss_pred eeccCcceeeEeecCCCCcee-EEeeCccccccCCccccCccCcc
Q psy9094 97 CWENLDIQRYVLKNHSTSEDR-VLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 97 v~d~l~~~r~~~~c~~~~~~~-~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
+++++...++...|.+|+..+ +.|.- -..+|+.||+-
T Consensus 20 mP~~Y~~~~v~IlCNDC~~~s~v~fH~-------lg~KC~~C~SY 57 (61)
T PF14599_consen 20 MPEEYRNKKVWILCNDCNAKSEVPFHF-------LGHKCSHCGSY 57 (61)
T ss_dssp --------EEEEEESSS--EEEEE--T-------T----TTTS--
T ss_pred CCHHHhCCEEEEECCCCCCccceeeeH-------hhhcCCCCCCc
Confidence 677777667888999999433 33310 12369999863
No 150
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=35.79 E-value=29 Score=26.34 Aligned_cols=63 Identities=10% Similarity=0.018 Sum_probs=31.9
Q ss_pred EecHHHHHHHHHcCCccE-EEeeccCcc-eeeEeecCCCCceeEEeeCccccccCCccccCccCcchh
Q psy9094 77 CFGVEDTLRALELGSVET-LICWENLDI-QRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELE 142 (185)
Q Consensus 77 ~yG~~ev~~Ale~GaV~~-Llv~d~l~~-~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~ 142 (185)
--|.+==..+-+.|+..- .--+-+... .++.|+|..|+...... .... +...+.|..||+.+.
T Consensus 80 ~Hg~~f~~~~~~~~~~~~~~~h~~~~~~~~~~~y~C~~C~~~~~~~-rr~~--~~~~y~C~~C~g~l~ 144 (146)
T smart00731 80 GHGDEWKRWMRQVNGLFPERCHTFLIESVKKYPYRCTGCGQRYLRV-RRSN--NVSRYRCGKCGGKLI 144 (146)
T ss_pred CcCHHHHHHHHHHcCCCcceEcCCcccccceEEEECCCCCCCCceE-cccc--CcceEEcCCCCCEEE
Confidence 556443333445666621 111111111 36799999999532211 1110 114578999998764
No 151
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=35.75 E-value=27 Score=22.94 Aligned_cols=12 Identities=8% Similarity=-0.003 Sum_probs=8.5
Q ss_pred ccCccCcchhhh
Q psy9094 133 TDKETGVELELV 144 (185)
Q Consensus 133 ~c~~~g~~~~~~ 144 (185)
.||.||+...+.
T Consensus 19 ~Cp~CG~~t~~~ 30 (59)
T COG2260 19 KCPVCGGDTKVP 30 (59)
T ss_pred cCCCCCCccccC
Confidence 589999875443
No 152
>PF14488 DUF4434: Domain of unknown function (DUF4434)
Probab=35.22 E-value=1.6e+02 Score=23.03 Aligned_cols=63 Identities=17% Similarity=0.005 Sum_probs=39.3
Q ss_pred HHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHHHhcC
Q psy9094 82 DTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSFG 161 (185)
Q Consensus 82 ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g 161 (185)
+-..++..--++|||+.+.-......+ +. +. ....|. ....|.|+.+++.|.+.|
T Consensus 24 ~~~~~m~~~GidtlIlq~~~~~~~~~y--ps------------~~---~~~~~~--------~~~~d~l~~~L~~A~~~G 78 (166)
T PF14488_consen 24 EEFRAMKAIGIDTLILQWTGYGGFAFY--PS------------KL---SPGGFY--------MPPVDLLEMILDAADKYG 78 (166)
T ss_pred HHHHHHHHcCCcEEEEEEeecCCcccC--Cc------------cc---cCcccc--------CCcccHHHHHHHHHHHcC
Confidence 456677778899999887654432100 10 00 000111 134788999999999999
Q ss_pred CEEEEeCC
Q psy9094 162 ATLEIITD 169 (185)
Q Consensus 162 ~~v~ivs~ 169 (185)
-+|.+=-.
T Consensus 79 mkv~~Gl~ 86 (166)
T PF14488_consen 79 MKVFVGLY 86 (166)
T ss_pred CEEEEeCC
Confidence 99987433
No 153
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=35.18 E-value=15 Score=33.84 Aligned_cols=31 Identities=6% Similarity=0.085 Sum_probs=19.2
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhhhccc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQ 147 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~ 147 (185)
.|+|+.||..... + ++..| .||+++++.+.+
T Consensus 130 ~w~c~~cg~~iea--------n-~kp~c-~cg~~~~~~ei~ 160 (593)
T COG2401 130 LWRCEKCGTIIEA--------N-TKPEC-KCGSHVHILEIK 160 (593)
T ss_pred EEecchhchhhhh--------c-CCccc-CCCCceEEEEee
Confidence 5889999942111 1 23369 899877665543
No 154
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=34.86 E-value=15 Score=32.53 Aligned_cols=22 Identities=9% Similarity=-0.003 Sum_probs=12.1
Q ss_pred ccccCccCcchhhhccccHHHHH
Q psy9094 131 HFTDKETGVELELVECQPLLEWL 153 (185)
Q Consensus 131 ~~~c~~~g~~~~~~e~~~~v~~l 153 (185)
.+.||+||+.. -..+.|.|.+|
T Consensus 265 ~wrCpkCGg~i-kKGV~dRv~EL 286 (403)
T COG1379 265 RWRCPKCGGKI-KKGVSDRVLEL 286 (403)
T ss_pred cccCcccccch-hhhHHHHHHHh
Confidence 46789998843 23333444333
No 155
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=34.60 E-value=30 Score=29.30 Aligned_cols=27 Identities=4% Similarity=-0.226 Sum_probs=18.0
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccC
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETG 138 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g 138 (185)
--|+.||....+.. ...|+.|.||.|+
T Consensus 245 ~pCprCG~~I~~~~----~~gR~t~~CP~CQ 271 (272)
T PRK14810 245 EPCLNCKTPIRRVV----VAGRSSHYCPHCQ 271 (272)
T ss_pred CcCCCCCCeeEEEE----ECCCccEECcCCc
Confidence 36999996444432 2346788899986
No 156
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=33.35 E-value=31 Score=23.09 Aligned_cols=29 Identities=21% Similarity=0.062 Sum_probs=17.2
Q ss_pred ccCccCcchhhhccccHHHHHHHHHHhcCCEEEEeCCC-CchHH
Q psy9094 133 TDKETGVELELVECQPLLEWLANNYKSFGATLEIITDK-SQEGS 175 (185)
Q Consensus 133 ~c~~~g~~~~~~e~~~~v~~l~e~a~~~g~~v~ivs~~-~e~G~ 175 (185)
.||.||+. +....+.|=|.|+..+ |+..+
T Consensus 19 ~Cp~Cgs~--------------~~S~~w~G~v~i~dPe~S~vAk 48 (64)
T PRK06393 19 TCPVHGDE--------------KTTTEWFGFLIITEPEGSAIAK 48 (64)
T ss_pred cCCCCCCC--------------cCCcCcceEEEEECCchhHHHH
Confidence 59999974 2345566667777433 44433
No 157
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=33.35 E-value=17 Score=30.73 Aligned_cols=38 Identities=11% Similarity=0.025 Sum_probs=15.5
Q ss_pred eecCCCCceeEE-eeCccccccCCccccCccCcchhhhcccc
Q psy9094 108 LKNHSTSEDRVL-HLTPEQEKDKSHFTDKETGVELELVECQP 148 (185)
Q Consensus 108 ~~c~~~~~~~~~-~~~~~~~~~~~~~~c~~~g~~~~~~e~~~ 148 (185)
..||+||..... |.....+ .-|.|+.|++..|+.+...
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PV---aDF~C~~C~eeyELKSk~~ 70 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPV---ADFYCPNCNEEYELKSKKK 70 (254)
T ss_dssp ---TTT--SS-EE-----------EEE-TTT--EEEEEEEES
T ss_pred CcCCCCCChhHhhccCCCcc---ceeECCCCchHHhhhhhcc
Confidence 579999965333 2211111 1467999999988877663
No 158
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=33.34 E-value=2.1e+02 Score=22.19 Aligned_cols=36 Identities=19% Similarity=0.286 Sum_probs=24.4
Q ss_pred ccHHHHHHHHHHhcCCEEEEeCCCCchHHHHhhhcCC
Q psy9094 147 QPLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGG 183 (185)
Q Consensus 147 ~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l~~~~GG 183 (185)
.++|+.++......+.+|.+||+++..=... .+.|+
T Consensus 80 D~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~-~~~GA 115 (166)
T PF05991_consen 80 DDYIERLVRELKNRPRQVTVVTSDREIQRAA-RGRGA 115 (166)
T ss_pred HHHHHHHHHHhccCCCeEEEEeCCHHHHHHH-hhCCC
Confidence 4456665555555567999999999875543 66665
No 159
>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=33.29 E-value=23 Score=31.62 Aligned_cols=67 Identities=16% Similarity=0.112 Sum_probs=36.9
Q ss_pred cHHHHHHHHHcCCccEEEeeccCcce--ee-EeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHH
Q psy9094 79 GVEDTLRALELGSVETLICWENLDIQ--RY-VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLAN 155 (185)
Q Consensus 79 G~~ev~~Ale~GaV~~Llv~d~l~~~--r~-~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e 155 (185)
+...+++|++.|.+ ..+-+++-. +| ---|.+|+. ..++.+ +.+....|| ||++ -.+-+.+.|++|.+
T Consensus 212 ~~~~~l~ai~~~~i---~~~~g~~P~~GKYh~~~c~~C~~----~~~~~~-~~~~~~~Cp-CG~~-i~~GV~~Rv~eLad 281 (374)
T TIGR00375 212 EFALALKAIDDRKI---IANYGLDPLLGKYHQTACEACGE----PAVSED-AETACANCP-CGGR-IKKGVSDRLRELSD 281 (374)
T ss_pred HHHHHHHHhhCCce---EeeeeECcCCCccchhhhcccCC----cCCchh-hhhcCCCCC-CCCc-ceechHHHHHHHhc
Confidence 46667777666643 444444321 11 124778873 122322 122246799 9999 45666677766654
No 160
>PRK10445 endonuclease VIII; Provisional
Probab=33.02 E-value=34 Score=28.81 Aligned_cols=40 Identities=3% Similarity=-0.154 Sum_probs=23.4
Q ss_pred CCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccC
Q psy9094 90 GSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETG 138 (185)
Q Consensus 90 GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g 138 (185)
|....+.|...- .-.|+.||....+.. ...|+.|.||.|.
T Consensus 223 g~~~~~~Vy~r~-----g~~Cp~Cg~~I~~~~----~~gR~t~~CP~CQ 262 (263)
T PRK10445 223 GALFRFKVFHRD-----GEACERCGGIIEKTT----LSSRPFYWCPGCQ 262 (263)
T ss_pred CCcceEEEeCCC-----CCCCCCCCCEeEEEE----ECCCCcEECCCCc
Confidence 333455555422 245999995444332 2346788899986
No 161
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=32.41 E-value=27 Score=21.39 Aligned_cols=9 Identities=22% Similarity=0.493 Sum_probs=5.2
Q ss_pred ccccCccCc
Q psy9094 131 HFTDKETGV 139 (185)
Q Consensus 131 ~~~c~~~g~ 139 (185)
.+.||.||-
T Consensus 20 ~~vC~~Cg~ 28 (52)
T smart00661 20 RFVCRKCGY 28 (52)
T ss_pred EEECCcCCC
Confidence 445666664
No 162
>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=32.28 E-value=29 Score=22.30 Aligned_cols=21 Identities=14% Similarity=0.004 Sum_probs=13.7
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCc
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGV 139 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~ 139 (185)
..|++||.. ..++..|+.||-
T Consensus 27 ~~C~~cG~~-----------~~~H~vc~~cG~ 47 (55)
T TIGR01031 27 VVCPNCGEF-----------KLPHRVCPSCGY 47 (55)
T ss_pred eECCCCCCc-----------ccCeeECCccCe
Confidence 458888841 234567888883
No 163
>KOG1497|consensus
Probab=31.83 E-value=25 Score=31.15 Aligned_cols=30 Identities=10% Similarity=0.055 Sum_probs=24.7
Q ss_pred CCccEEEEeCChhhHHhhcccCCCCHhhhc
Q psy9094 25 PNIAGLILAGSADFKTELSQSDMFDPVRFS 54 (185)
Q Consensus 25 ~~i~~lIIaGPg~~k~~f~~~~~L~~~l~~ 54 (185)
.-+.|+++|+||+....|...-|.++|.++
T Consensus 227 ~a~~CtlLA~~gpqrsr~Latlfkder~~~ 256 (399)
T KOG1497|consen 227 KALQCTLLASAGPQRSRMLATLFKDERCQK 256 (399)
T ss_pred HhHhheeecCCChHHHHHHHHHhcCccccc
Confidence 457899999999999999866677777665
No 164
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.70 E-value=37 Score=28.73 Aligned_cols=26 Identities=0% Similarity=-0.248 Sum_probs=16.5
Q ss_pred ecCCCCceeEEeeCccccccCCccccCccC
Q psy9094 109 KNHSTSEDRVLHLTPEQEKDKSHFTDKETG 138 (185)
Q Consensus 109 ~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g 138 (185)
-|+.||....+.. ...|+.|.||.|.
T Consensus 247 pC~~Cg~~I~~~~----~~gR~t~~CP~CQ 272 (272)
T TIGR00577 247 PCRRCGTPIEKIK----VGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCeeEEEE----ECCCCCEECCCCC
Confidence 5888885444432 2246777898884
No 165
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=31.68 E-value=71 Score=25.56 Aligned_cols=24 Identities=25% Similarity=0.596 Sum_probs=19.5
Q ss_pred HHHHHHHHHHhcCCEEEEeCCCCch
Q psy9094 149 LLEWLANNYKSFGATLEIITDKSQE 173 (185)
Q Consensus 149 ~v~~l~e~a~~~g~~v~ivs~~~e~ 173 (185)
+.+|+. ..+..|.++.|+|++++.
T Consensus 51 ~~~W~~-e~k~~gi~v~vvSNn~e~ 74 (175)
T COG2179 51 LRAWLA-ELKEAGIKVVVVSNNKES 74 (175)
T ss_pred HHHHHH-HHHhcCCEEEEEeCCCHH
Confidence 456644 778899999999999886
No 166
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=31.07 E-value=33 Score=24.41 Aligned_cols=27 Identities=7% Similarity=0.028 Sum_probs=16.4
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGV 139 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~ 139 (185)
.+.||.|+...+...... -|.|..||.
T Consensus 35 ~~~Cp~C~~~~VkR~a~G------IW~C~kCg~ 61 (89)
T COG1997 35 KHVCPFCGRTTVKRIATG------IWKCRKCGA 61 (89)
T ss_pred CCcCCCCCCcceeeeccC------eEEcCCCCC
Confidence 467888886544432222 456888874
No 167
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=30.98 E-value=28 Score=25.67 Aligned_cols=35 Identities=9% Similarity=0.080 Sum_probs=23.5
Q ss_pred eecCCCCceeEEeeCc----cccccCCccccCccCcchh
Q psy9094 108 LKNHSTSEDRVLHLTP----EQEKDKSHFTDKETGVELE 142 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~----~~~~~~~~~~c~~~g~~~~ 142 (185)
..|+.||.....|+.. .|+.....|.|..||-.+.
T Consensus 73 ~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 73 EKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred ccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEee
Confidence 5699999877777222 2334444678999997653
No 168
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=30.97 E-value=27 Score=32.70 Aligned_cols=38 Identities=21% Similarity=0.407 Sum_probs=23.6
Q ss_pred eeEeecCCCCceeEEe-----eCccccccCCccccCccCcchh
Q psy9094 105 RYVLKNHSTSEDRVLH-----LTPEQEKDKSHFTDKETGVELE 142 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~-----~~~~~~~~~~~~~c~~~g~~~~ 142 (185)
|+-+.||.||..+..- ..+++......|.||.||....
T Consensus 198 ~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 198 RYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred EEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCC
Confidence 6678899999644432 1111122334778999998753
No 169
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=30.55 E-value=74 Score=31.05 Aligned_cols=47 Identities=17% Similarity=0.032 Sum_probs=28.6
Q ss_pred HHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhh
Q psy9094 80 VEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELEL 143 (185)
Q Consensus 80 ~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~ 143 (185)
++.+.+.++.|.--.|.+.---... ...|.+||+ -+.||+|..+|..
T Consensus 410 l~~i~~~l~~geQ~llflnRRGys~--~l~C~~Cg~---------------v~~Cp~Cd~~lt~ 456 (730)
T COG1198 410 LEAIRKTLERGEQVLLFLNRRGYAP--LLLCRDCGY---------------IAECPNCDSPLTL 456 (730)
T ss_pred HHHHHHHHhcCCeEEEEEccCCccc--eeecccCCC---------------cccCCCCCcceEE
Confidence 5666777777776555554322222 467999995 3457777665543
No 170
>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=30.54 E-value=66 Score=30.18 Aligned_cols=22 Identities=14% Similarity=-0.009 Sum_probs=15.2
Q ss_pred ecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 109 KNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 109 ~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
+|.+||...+ ...+.||.||+.
T Consensus 520 ~C~~CG~~~~----------~~~~~CP~CGs~ 541 (555)
T cd01675 520 ICNDCGYIGE----------GEGFKCPKCGSE 541 (555)
T ss_pred cCCCCCCCCc----------CCCCCCcCCCCc
Confidence 6999996221 125689999964
No 171
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=30.26 E-value=40 Score=28.48 Aligned_cols=27 Identities=7% Similarity=-0.122 Sum_probs=17.9
Q ss_pred ecCCCCceeEEeeCccccccCCccccCccCc
Q psy9094 109 KNHSTSEDRVLHLTPEQEKDKSHFTDKETGV 139 (185)
Q Consensus 109 ~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~ 139 (185)
-|+.||....+.. ...|+.|.||.|..
T Consensus 247 pC~~Cg~~I~~~~----~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 247 PCRRCGTPIEKIK----QGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCeeEEEE----ECCCCcEECcCCCC
Confidence 5999995433331 23467888999974
No 172
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=30.14 E-value=38 Score=34.05 Aligned_cols=33 Identities=15% Similarity=0.016 Sum_probs=20.7
Q ss_pred eeEeecCCCCceeEEe-eCccccccCCccccCccCcchhhhcc
Q psy9094 105 RYVLKNHSTSEDRVLH-LTPEQEKDKSHFTDKETGVELELVEC 146 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~-~~~~~~~~~~~~~c~~~g~~~~~~e~ 146 (185)
|=.++|.+|+. +| .-|- .=.|+.||+.+.++--
T Consensus 1010 rQ~fRC~kC~~---kYRR~PL------~G~C~kCGg~lilTV~ 1043 (1095)
T TIGR00354 1010 RQEVRCTKCNT---KYRRIPL------VGKCLKCGNNLTLTVS 1043 (1095)
T ss_pred ccceeecccCC---ccccCCC------CCcccccCCeEEEEEe
Confidence 44689999995 33 1111 1159999998766533
No 173
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=29.94 E-value=39 Score=23.01 Aligned_cols=26 Identities=15% Similarity=0.087 Sum_probs=12.5
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcchhh
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELEL 143 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~ 143 (185)
.|.|+.|+..-.. ...||+|+.+|+.
T Consensus 17 ~~~C~~C~~~~~~-----------~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 17 HYHCEACQKDYKK-----------EAFCPDCGQPLEV 42 (70)
T ss_dssp EEEETTT--EEEE-----------EEE-TTT-SB-EE
T ss_pred EEECcccccccee-----------cccCCCcccHHHH
Confidence 4778888842211 2249999988753
No 174
>COG4972 PilM Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=29.84 E-value=75 Score=28.19 Aligned_cols=42 Identities=14% Similarity=0.308 Sum_probs=30.5
Q ss_pred hhhhHHHHHHHHHHHHh---hhh-cCCCCccEEEEeCChhhHHhhc
Q psy9094 2 EKRHNYVRKVAEVATTL---FIT-NDKPNIAGLILAGSADFKTELS 43 (185)
Q Consensus 2 ~~~~~f~k~va~~~~~~---f~~-~~~~~i~~lIIaGPg~~k~~f~ 43 (185)
+.+.+|..++.+.+++. |.+ -....|++|+++|||-.-..+.
T Consensus 259 ~vl~~f~~~l~~ei~Rslqfy~~~s~~~~id~i~LaGggA~l~gL~ 304 (354)
T COG4972 259 EVLRPFLGELTQEIRRSLQFYLSQSEMVDIDQILLAGGGASLEGLA 304 (354)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccccceeeEEEEecCCcchhhHH
Confidence 45678888888877654 443 2246899999999998776664
No 175
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.83 E-value=40 Score=28.54 Aligned_cols=27 Identities=0% Similarity=-0.234 Sum_probs=18.5
Q ss_pred ecCCCCceeEEeeCccccccCCccccCccCc
Q psy9094 109 KNHSTSEDRVLHLTPEQEKDKSHFTDKETGV 139 (185)
Q Consensus 109 ~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~ 139 (185)
-|+.||....+.. ...|+.|.||.|..
T Consensus 237 pC~~Cg~~I~~~~----~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 237 PCPRCGTPIEKIV----VGGRGTHFCPQCQP 263 (269)
T ss_pred CCCcCCCeeEEEE----ECCCCcEECCCCcC
Confidence 5999996444432 22467888999985
No 176
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.74 E-value=40 Score=28.65 Aligned_cols=26 Identities=4% Similarity=-0.252 Sum_probs=17.1
Q ss_pred ecCCCCceeEEeeCccccccCCccccCccC
Q psy9094 109 KNHSTSEDRVLHLTPEQEKDKSHFTDKETG 138 (185)
Q Consensus 109 ~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g 138 (185)
-|+.||....+.. ...|+.|.||.|.
T Consensus 256 pC~~Cg~~I~~~~----~~gR~t~~CP~CQ 281 (282)
T PRK13945 256 PCRKCGTPIERIK----LAGRSTHWCPNCQ 281 (282)
T ss_pred CCCcCCCeeEEEE----ECCCccEECCCCc
Confidence 6999995444331 2346788899886
No 177
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.69 E-value=31 Score=32.99 Aligned_cols=34 Identities=12% Similarity=-0.031 Sum_probs=18.4
Q ss_pred hHHHHHHHHHHHHhhhhc-CCCCccEEEEeCChhh
Q psy9094 5 HNYVRKVAEVATTLFITN-DKPNIAGLILAGSADF 38 (185)
Q Consensus 5 ~~f~k~va~~~~~~f~~~-~~~~i~~lIIaGPg~~ 38 (185)
.+|-.+|.+.+++....- ......-=+-+-|++.
T Consensus 442 ~~f~~~il~~mr~~~~~~~~etG~~fnle~TPAEs 476 (623)
T PRK08271 442 KDFVQEVLKVIYEANEKASKEYGFTFNTEFVPAEN 476 (623)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCceEEEECCcch
Confidence 456666666666444320 1234444567788754
No 178
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=29.66 E-value=18 Score=35.73 Aligned_cols=11 Identities=27% Similarity=0.383 Sum_probs=0.0
Q ss_pred HHHHHHHHcCC
Q psy9094 81 EDTLRALELGS 91 (185)
Q Consensus 81 ~ev~~Ale~Ga 91 (185)
.++.+|.+.+.
T Consensus 636 R~i~~A~~~~~ 646 (900)
T PF03833_consen 636 RDIQKAAKKGK 646 (900)
T ss_dssp -----------
T ss_pred ccHHHHHhcCC
Confidence 45666666664
No 179
>PRK10220 hypothetical protein; Provisional
Probab=29.47 E-value=35 Score=25.24 Aligned_cols=30 Identities=13% Similarity=0.040 Sum_probs=17.9
Q ss_pred ecCCCCceeEEeeCccccccCCccccCccCcchhhhc
Q psy9094 109 KNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVE 145 (185)
Q Consensus 109 ~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e 145 (185)
.||.|+.+- .|. +...+.||.|+..|...+
T Consensus 5 ~CP~C~sey-tY~------d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 5 HCPKCNSEY-TYE------DNGMYICPECAHEWNDAE 34 (111)
T ss_pred cCCCCCCcc-eEc------CCCeEECCcccCcCCccc
Confidence 478888422 222 223567999998775544
No 180
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=29.36 E-value=37 Score=25.33 Aligned_cols=27 Identities=4% Similarity=-0.065 Sum_probs=16.5
Q ss_pred eEeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 106 YVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 106 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
...+|.+|+... ++ +...+.||.||+.
T Consensus 69 ~~~~C~~C~~~~----~~----e~~~~~CP~C~s~ 95 (115)
T COG0375 69 AECWCLDCGQEV----EL----EELDYRCPKCGSI 95 (115)
T ss_pred cEEEeccCCCee----cc----hhheeECCCCCCC
Confidence 368899997311 11 1124459999964
No 181
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=29.30 E-value=42 Score=34.59 Aligned_cols=32 Identities=6% Similarity=-0.127 Sum_probs=17.6
Q ss_pred EeecCCCCceeEEe----eCccccccCCccccCccCcch
Q psy9094 107 VLKNHSTSEDRVLH----LTPEQEKDKSHFTDKETGVEL 141 (185)
Q Consensus 107 ~~~c~~~~~~~~~~----~~~~~~~~~~~~~c~~~g~~~ 141 (185)
-|+||+|++....- -++-+.. .-.||.||.++
T Consensus 914 HY~Cp~Cky~Ef~~d~svgsGfDLp---dK~CPkCg~pl 949 (1444)
T COG2176 914 HYLCPECKYSEFIDDGSVGSGFDLP---DKDCPKCGTPL 949 (1444)
T ss_pred cccCCCCceeeeecCCCcCCCCCCC---CCCCCcCCCcc
Confidence 38999999532211 1111111 11499999886
No 182
>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=28.99 E-value=75 Score=19.74 Aligned_cols=11 Identities=9% Similarity=0.138 Sum_probs=6.7
Q ss_pred CccccCccCcc
Q psy9094 130 SHFTDKETGVE 140 (185)
Q Consensus 130 ~~~~c~~~g~~ 140 (185)
..|.||.|+.+
T Consensus 33 ~~w~CP~C~a~ 43 (47)
T PF00301_consen 33 DDWVCPVCGAP 43 (47)
T ss_dssp TT-B-TTTSSB
T ss_pred CCCcCcCCCCc
Confidence 35679999875
No 183
>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=28.96 E-value=36 Score=25.15 Aligned_cols=29 Identities=7% Similarity=-0.117 Sum_probs=17.3
Q ss_pred ecCCCCceeEEeeCccccccCCccccCccCcchhhh
Q psy9094 109 KNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELV 144 (185)
Q Consensus 109 ~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~ 144 (185)
.||.|+.+- .|. +...+-||.|+..|...
T Consensus 4 ~CP~C~sey-tY~------dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEY-TYH------DGTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcc-eEe------cCCeeECcccccccccc
Confidence 488888422 222 22356799999876443
No 184
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=28.56 E-value=38 Score=24.18 Aligned_cols=27 Identities=11% Similarity=0.056 Sum_probs=16.1
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGV 139 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~ 139 (185)
.|.||.||...+....-+ -|.|..||.
T Consensus 35 ky~Cp~Cgk~~vkR~a~G------IW~C~~C~~ 61 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATG------IWKCKKCGK 61 (90)
T ss_dssp -BEESSSSSSEEEEEETT------EEEETTTTE
T ss_pred CCcCCCCCCceeEEeeeE------EeecCCCCC
Confidence 467888886655542222 356888873
No 185
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=28.46 E-value=39 Score=30.70 Aligned_cols=69 Identities=9% Similarity=0.031 Sum_probs=37.1
Q ss_pred HHHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchh
Q psy9094 63 GKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELE 142 (185)
Q Consensus 63 e~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~ 142 (185)
....+.|..++.-.+||- +..-. =+|+++.|..=....+..=+||.||..- . ...++.|.|++||.+..
T Consensus 310 r~~a~~L~pGD~i~~~G~--~~~~~--~n~ek~~v~~l~~~~~~~p~Cp~Cg~~m---~----S~G~~g~rC~kCg~~~~ 378 (421)
T COG1571 310 RELARKLIPGDEITVYGS--VKPGT--LNLEKFQVLKLARYERVNPVCPRCGGRM---K----SAGRNGFRCKKCGTRAR 378 (421)
T ss_pred hHHHHhcCCCCEEEEecC--ccccc--eeEEEEEEEEeeeeEEcCCCCCccCCch---h----hcCCCCcccccccccCC
Confidence 344566666655668883 22211 2344444432222223345899999311 1 12344889999997653
No 186
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=28.18 E-value=25 Score=30.26 Aligned_cols=35 Identities=14% Similarity=0.075 Sum_probs=20.8
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcchhhhccc
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQ 147 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~ 147 (185)
.+||.|+. ..|.+.- .+..+.||.|+.-+++...+
T Consensus 29 ~KCp~c~~--~~y~~eL---~~n~~vcp~c~~h~ri~A~~ 63 (294)
T COG0777 29 TKCPSCGE--MLYRKEL---ESNLKVCPKCGHHMRISARE 63 (294)
T ss_pred eECCCccc--eeeHHHH---HhhhhcccccCcccccCHHH
Confidence 57999994 3332221 12355799999877665433
No 187
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=28.11 E-value=45 Score=19.12 Aligned_cols=24 Identities=4% Similarity=-0.083 Sum_probs=10.8
Q ss_pred EeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
.-+|.+||.. .| .....||.|++.
T Consensus 11 ~~rC~~Cg~~--~~--------pPr~~Cp~C~s~ 34 (37)
T PF12172_consen 11 GQRCRDCGRV--QF--------PPRPVCPHCGSD 34 (37)
T ss_dssp EEE-TTT--E--EE--------S--SEETTTT--
T ss_pred EEEcCCCCCE--ec--------CCCcCCCCcCcc
Confidence 4579999952 22 112359999864
No 188
>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=27.84 E-value=54 Score=20.95 Aligned_cols=20 Identities=20% Similarity=0.167 Sum_probs=14.1
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccC
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETG 138 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g 138 (185)
..|+.||.. ...+..|+.||
T Consensus 27 ~~c~~cg~~-----------~~~H~vc~~cG 46 (56)
T PF01783_consen 27 VKCPNCGEP-----------KLPHRVCPSCG 46 (56)
T ss_dssp EESSSSSSE-----------ESTTSBCTTTB
T ss_pred eeeccCCCE-----------ecccEeeCCCC
Confidence 578999942 23466799997
No 189
>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=27.83 E-value=63 Score=20.34 Aligned_cols=11 Identities=9% Similarity=0.129 Sum_probs=8.4
Q ss_pred CccccCccCcc
Q psy9094 130 SHFTDKETGVE 140 (185)
Q Consensus 130 ~~~~c~~~g~~ 140 (185)
..|.||.||.+
T Consensus 33 ~~w~CP~C~a~ 43 (50)
T cd00730 33 DDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCc
Confidence 35679999975
No 190
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=27.57 E-value=62 Score=20.97 Aligned_cols=32 Identities=3% Similarity=-0.122 Sum_probs=16.5
Q ss_pred eecCCCCcee-EEeeCccccccCCccccCccCcc
Q psy9094 108 LKNHSTSEDR-VLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 108 ~~c~~~~~~~-~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
+.||.||... +++ .++.+-..-...||+|...
T Consensus 5 i~CP~CgnKTR~ki-r~DT~LkNfPlyCpKCK~E 37 (55)
T PF14205_consen 5 ILCPICGNKTRLKI-REDTVLKNFPLYCPKCKQE 37 (55)
T ss_pred EECCCCCCccceee-ecCceeccccccCCCCCce
Confidence 5699999432 332 2222211123469999753
No 191
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=27.49 E-value=29 Score=36.42 Aligned_cols=31 Identities=13% Similarity=0.045 Sum_probs=17.2
Q ss_pred EeecCCCCceeEEeeCccccccCCcc-----ccCccCcch
Q psy9094 107 VLKNHSTSEDRVLHLTPEQEKDKSHF-----TDKETGVEL 141 (185)
Q Consensus 107 ~~~c~~~~~~~~~~~~~~~~~~~~~~-----~c~~~g~~~ 141 (185)
-|+|++|++.... ..++ ..+.| .||.||.++
T Consensus 908 hy~C~~C~~~ef~-~~~~---~~sG~Dlpdk~Cp~Cg~~~ 943 (1437)
T PRK00448 908 HYVCPNCKYSEFF-TDGS---VGSGFDLPDKDCPKCGTKL 943 (1437)
T ss_pred cccCccccccccc-cccc---ccccccCccccCccccccc
Confidence 4899999953221 1111 11122 499999765
No 192
>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=27.46 E-value=36 Score=32.32 Aligned_cols=23 Identities=4% Similarity=-0.129 Sum_probs=14.9
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
-+|+.||.. ..+ ..+.||.||+.
T Consensus 533 siC~~CGy~-----~g~-----~~~~CP~CGs~ 555 (586)
T TIGR02827 533 TICNDCHHI-----DKR-----TLHRCPVCGSA 555 (586)
T ss_pred eecCCCCCc-----CCC-----cCCcCcCCCCc
Confidence 479999961 110 13579999953
No 193
>cd02982 PDI_b'_family Protein Disulfide Isomerase (PDIb') family, redox inactive TRX-like domain b'; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI, calsequestrin and other PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5 and PDIR. PDI, ERp57, ERp72, P5 and PDIR are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and one or more redox inactive TRX-like (b) domains. The molecular structure of PDI is abb'a'. Also included in this family is the PDI-related protein ERp27, w
Probab=27.24 E-value=94 Score=21.06 Aligned_cols=36 Identities=19% Similarity=0.269 Sum_probs=27.3
Q ss_pred ccHHHHHHHHHHhcCCEEEEeCCCCchHHHHhhhcC
Q psy9094 147 QPLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFG 182 (185)
Q Consensus 147 ~~~v~~l~e~a~~~g~~v~ivs~~~e~G~~l~~~~G 182 (185)
..+.+.+-+.|+++.+++.++.-+.+....+.+.||
T Consensus 28 ~~~~~~~~~vA~~~~~~v~f~~vd~~~~~~~~~~~~ 63 (103)
T cd02982 28 EELRERFKEVAKKFKGKLLFVVVDADDFGRHLEYFG 63 (103)
T ss_pred HHHHHHHHHHHHHhCCeEEEEEEchHhhHHHHHHcC
Confidence 345566778889998999998888877666767775
No 194
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=27.12 E-value=32 Score=29.35 Aligned_cols=66 Identities=9% Similarity=0.067 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHhh---CCCceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccC
Q psy9094 59 KNKMGKYFDEISQ---DTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDK 135 (185)
Q Consensus 59 ~~lve~f~~~l~~---~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~ 135 (185)
+-.+.+++-.+.. +++-++-|-+=++.-=+.+-|++--=.|.|. +|.+||..... ...+||
T Consensus 37 ~GYigQHLaSlVTG~PG~~SGARG~DL~~~n~d~sEiKsC~rvDQl~------~C~~CGa~V~~----------~e~~Cp 100 (314)
T PF09567_consen 37 MGYIGQHLASLVTGYPGGGSGARGDDLVMNNDDGSEIKSCYRVDQLG------KCNNCGANVSR----------LEESCP 100 (314)
T ss_pred hccHHHhhhhheecCCCCccccccccccccCCCcchhhhhhhhhhhh------hhccccceeee----------hhhcCC
Confidence 3455555555543 3346788877665555666666666666663 68999952221 133699
Q ss_pred ccCcc
Q psy9094 136 ETGVE 140 (185)
Q Consensus 136 ~~g~~ 140 (185)
.||+.
T Consensus 101 ~C~St 105 (314)
T PF09567_consen 101 NCGST 105 (314)
T ss_pred CCCcc
Confidence 99975
No 195
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=26.95 E-value=28 Score=24.96 Aligned_cols=28 Identities=11% Similarity=-0.129 Sum_probs=16.1
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcch
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVEL 141 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~ 141 (185)
.+|.+||+..-. . ..+..-.||.|.+.+
T Consensus 59 a~CkkCGfef~~----~--~ik~pSRCP~CKSE~ 86 (97)
T COG3357 59 ARCKKCGFEFRD----D--KIKKPSRCPKCKSEW 86 (97)
T ss_pred hhhcccCccccc----c--ccCCcccCCcchhhc
Confidence 469999963221 1 112233699998753
No 196
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=26.92 E-value=45 Score=34.78 Aligned_cols=43 Identities=12% Similarity=-0.056 Sum_probs=24.3
Q ss_pred eeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHH
Q psy9094 105 RYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANN 156 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~ 156 (185)
|=.++| +|+. +|..+. -.=.||.||+.+.++--+--|+.-++.
T Consensus 1540 rQ~~RC-kC~~---kyRR~P-----L~G~C~kCGg~~ilTV~kGsv~KYl~~ 1582 (1627)
T PRK14715 1540 RQEFRC-KCGA---KYRRVP-----LKGKCPKCGSKLILTVSKGAVEKYMPV 1582 (1627)
T ss_pred ccceee-cCCC---ccccCC-----CCCcCcccCCeEEEEEecchHHHHHHH
Confidence 447899 9995 331111 011599999987766444444333333
No 197
>TIGR02180 GRX_euk Glutaredoxin. This model represents eukaryotic glutaredoxins and includes sequences from fungi, plants and metazoans as well as viruses.
Probab=26.52 E-value=48 Score=21.61 Aligned_cols=23 Identities=30% Similarity=0.512 Sum_probs=20.2
Q ss_pred CceEecHHHHHHHHHcCCccEEE
Q psy9094 74 GKYCFGVEDTLRALELGSVETLI 96 (185)
Q Consensus 74 ~~~~yG~~ev~~Ale~GaV~~Ll 96 (185)
|..+.|.++++++.+.|....+|
T Consensus 62 g~~igg~~~~~~~~~~g~l~~~~ 84 (84)
T TIGR02180 62 GKFIGGCSDLLALYKSGKLAELL 84 (84)
T ss_pred CEEEcCHHHHHHHHHcCChhhhC
Confidence 78899999999999999877654
No 198
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.27 E-value=52 Score=34.06 Aligned_cols=35 Identities=9% Similarity=-0.084 Sum_probs=21.3
Q ss_pred eeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccc
Q psy9094 105 RYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQ 147 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~ 147 (185)
|=.++|.+|+. +|..+. -.=.|+.||+.+.++--+
T Consensus 1251 rQ~~RC~kC~~---kyRR~P-----L~G~C~kCGg~iilTv~~ 1285 (1337)
T PRK14714 1251 RQEFRCLKCGT---KYRRMP-----LAGKCRKCGGRIILTVHE 1285 (1337)
T ss_pred ccceeecccCc---ccccCC-----CCCcccccCCeEEEEEec
Confidence 44689999995 331110 011599999987665433
No 199
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=26.17 E-value=36 Score=25.99 Aligned_cols=6 Identities=33% Similarity=0.147 Sum_probs=3.4
Q ss_pred cCccCc
Q psy9094 134 DKETGV 139 (185)
Q Consensus 134 c~~~g~ 139 (185)
||.||+
T Consensus 22 CP~CGg 27 (131)
T PF09845_consen 22 CPECGG 27 (131)
T ss_pred CcccCC
Confidence 555653
No 200
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=25.97 E-value=19 Score=31.14 Aligned_cols=43 Identities=9% Similarity=-0.019 Sum_probs=25.5
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHH
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANN 156 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~ 156 (185)
.+|++|+.. .+.+.- .+..+.||.||.-+.+..+ +.++.|++.
T Consensus 39 ~kc~~C~~~--~~~~~l---~~~~~vcp~c~~h~rltAr-eRI~~L~D~ 81 (296)
T CHL00174 39 VQCENCYGL--NYKKFL---KSKMNICEQCGYHLKMSSS-DRIELLIDP 81 (296)
T ss_pred eECCCccch--hhHHHH---HHcCCCCCCCCCCcCCCHH-HHHHHHccC
Confidence 479999942 111111 1235679999987776654 345566653
No 201
>PHA02546 47 endonuclease subunit; Provisional
Probab=25.83 E-value=2.7e+02 Score=24.07 Aligned_cols=61 Identities=11% Similarity=0.066 Sum_probs=38.3
Q ss_pred HHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHH-HHHHHH
Q psy9094 80 VEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEW-LANNYK 158 (185)
Q Consensus 80 ~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~-l~e~a~ 158 (185)
++.+.+.+..-.++.||++=|++-.+. . + + ......+.. +.....
T Consensus 28 l~~ii~~a~~~~vD~VliaGDlfD~~~---~------------------------~----~---~~~~~~~~~~l~~~L~ 73 (340)
T PHA02546 28 IKQAIEYSKAHGITTWIQLGDTFDVRK---A------------------------I----T---QNTMNFVREKIFDLLK 73 (340)
T ss_pred HHHHHHHHHHcCCCEEEECCcccCCCC---C------------------------C----C---HHHHHHHHHHHHHHHH
Confidence 455666666778999999999975410 0 0 0 011122323 344455
Q ss_pred hcCCEEEEeCCCCchH
Q psy9094 159 SFGATLEIITDKSQEG 174 (185)
Q Consensus 159 ~~g~~v~ivs~~~e~G 174 (185)
+.|..|++|+++|..+
T Consensus 74 ~~gi~v~~I~GNHD~~ 89 (340)
T PHA02546 74 EAGITLHVLVGNHDMY 89 (340)
T ss_pred HCCCeEEEEccCCCcc
Confidence 6799999999999963
No 202
>KOG3507|consensus
Probab=25.36 E-value=54 Score=21.63 Aligned_cols=29 Identities=10% Similarity=0.153 Sum_probs=18.0
Q ss_pred eeEeecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 105 RYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
-++|.|.+|+..-+ +++.+ .+.|..||-+
T Consensus 18 ~miYiCgdC~~en~--lk~~D-----~irCReCG~R 46 (62)
T KOG3507|consen 18 TMIYICGDCGQENT--LKRGD-----VIRCRECGYR 46 (62)
T ss_pred cEEEEecccccccc--ccCCC-----cEehhhcchH
Confidence 35799999994211 12221 4579999965
No 203
>COG1712 Predicted dinucleotide-utilizing enzyme [General function prediction only]
Probab=25.10 E-value=1.9e+02 Score=24.52 Aligned_cols=23 Identities=26% Similarity=0.128 Sum_probs=18.9
Q ss_pred cHHHHHHHHHHhcCCEEEEeCCC
Q psy9094 148 PLLEWLANNYKSFGATLEIITDK 170 (185)
Q Consensus 148 ~~v~~l~e~a~~~g~~v~ivs~~ 170 (185)
.+.+-+-+.++..|+++++.|+-
T Consensus 99 ~l~erl~~lak~~~~rv~~pSGA 121 (255)
T COG1712 99 GLRERLRELAKCGGARVYLPSGA 121 (255)
T ss_pred HHHHHHHHHHhcCCcEEEecCcc
Confidence 35677778999999999998874
No 204
>PRK10966 exonuclease subunit SbcD; Provisional
Probab=25.06 E-value=2.3e+02 Score=25.43 Aligned_cols=60 Identities=12% Similarity=0.115 Sum_probs=36.8
Q ss_pred HHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHHHhcC
Q psy9094 82 DTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSFG 161 (185)
Q Consensus 82 ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~g 161 (185)
.+...+..-.++.|||+=|+.-.. . |. .........++....+.+
T Consensus 30 ~l~~~i~~~~~D~viIaGDifD~~-----~-----------------------p~-------~~a~~~~~~~l~~L~~~~ 74 (407)
T PRK10966 30 WLLEQVQEHQVDAIIVAGDIFDTG-----S-----------------------PP-------SYARELYNRFVVNLQQTG 74 (407)
T ss_pred HHHHHHHhcCCCEEEECCccccCC-----C-----------------------Cc-------HHHHHHHHHHHHHHHhcC
Confidence 344455566899999999986431 0 00 011222334444445668
Q ss_pred CEEEEeCCCCchHHH
Q psy9094 162 ATLEIITDKSQEGSQ 176 (185)
Q Consensus 162 ~~v~ivs~~~e~G~~ 176 (185)
..|++|+++|+....
T Consensus 75 ~~v~~I~GNHD~~~~ 89 (407)
T PRK10966 75 CQLVVLAGNHDSVAT 89 (407)
T ss_pred CcEEEEcCCCCChhh
Confidence 899999999997654
No 205
>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]
Probab=24.82 E-value=1.7e+02 Score=23.46 Aligned_cols=58 Identities=28% Similarity=0.377 Sum_probs=38.8
Q ss_pred cHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHHH
Q psy9094 79 GVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYK 158 (185)
Q Consensus 79 G~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~ 158 (185)
|+.+.++.++.|. ++|||++ +.+- .+ ...++. .+++...
T Consensus 52 ~l~~ll~~i~~g~-d~lvV~~-lDRL------~R--------------------------------~~~~~~-~~~~~l~ 90 (222)
T COG1961 52 GLQRLLEDIEEGK-DTLVVYK-LDRL------GR--------------------------------SLSDLL-QLLELLA 90 (222)
T ss_pred HHHHHHHHHHcCC-cEEEEEE-echh------hc--------------------------------CHHHHH-HHHHHHH
Confidence 6788999999999 8888875 3221 00 112233 5778899
Q ss_pred hcCCEEEEeCCC-----CchHHHH
Q psy9094 159 SFGATLEIITDK-----SQEGSQF 177 (185)
Q Consensus 159 ~~g~~v~ivs~~-----~e~G~~l 177 (185)
..|..+..+.+. ++.|..+
T Consensus 91 ~~gv~~~~~~~~~~d~~s~~~~l~ 114 (222)
T COG1961 91 EKGITLISLAENIFDTSSPMGRLM 114 (222)
T ss_pred HCCCEEEEecCCcccCCCccHHHH
Confidence 999999988743 4566633
No 206
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=24.79 E-value=78 Score=18.11 Aligned_cols=27 Identities=7% Similarity=-0.032 Sum_probs=15.2
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
+.|+.|+...+... ++.-+.|++||..
T Consensus 4 ~~C~~C~~~~i~~~------~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 4 KKCSKCGGNGIVNK------EDDYEVCIFCGSS 30 (33)
T ss_pred eEcCCCCCCeEEEe------cCCeEEcccCCcE
Confidence 46777775444321 2224468888853
No 207
>TIGR00619 sbcd exonuclease SbcD. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.62 E-value=2.9e+02 Score=22.81 Aligned_cols=61 Identities=15% Similarity=0.209 Sum_probs=36.9
Q ss_pred HHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHHHhc
Q psy9094 81 EDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSF 160 (185)
Q Consensus 81 ~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~ 160 (185)
+.+...+....++.||++=|+.-.+ . |. .....++...+....+.
T Consensus 29 ~~l~~~~~~~~~D~lli~GDi~d~~----~------------------------p~-------~~~~~~~~~~l~~l~~~ 73 (253)
T TIGR00619 29 DDLLEFAKAEQIDALLVAGDVFDTA----N------------------------PP-------AEAQELFNAFFRNLSDA 73 (253)
T ss_pred HHHHHHHHHcCCCEEEECCccCCCC----C------------------------CC-------HHHHHHHHHHHHHHHhc
Confidence 4455555556799999999987431 0 10 01122233344444455
Q ss_pred C-CEEEEeCCCCchHHH
Q psy9094 161 G-ATLEIITDKSQEGSQ 176 (185)
Q Consensus 161 g-~~v~ivs~~~e~G~~ 176 (185)
+ ..|++|+++|+....
T Consensus 74 ~~i~v~~i~GNHD~~~~ 90 (253)
T TIGR00619 74 NPIPIVVISGNHDSAQR 90 (253)
T ss_pred CCceEEEEccCCCChhh
Confidence 6 899999999997643
No 208
>PRK04023 DNA polymerase II large subunit; Validated
Probab=24.61 E-value=58 Score=32.98 Aligned_cols=33 Identities=15% Similarity=0.002 Sum_probs=20.8
Q ss_pred eeEeecCCCCceeEEe-eCccccccCCccccCccCcchhhhcc
Q psy9094 105 RYVLKNHSTSEDRVLH-LTPEQEKDKSHFTDKETGVELELVEC 146 (185)
Q Consensus 105 r~~~~c~~~~~~~~~~-~~~~~~~~~~~~~c~~~g~~~~~~e~ 146 (185)
|=.++|.+|+. +| .-|- .=.|+.||+.+.++--
T Consensus 1035 rQ~fRC~kC~~---kYRR~PL------~G~C~kCGg~lilTVh 1068 (1121)
T PRK04023 1035 RQEFRCTKCGA---KYRRPPL------SGKCPKCGGNLILTVH 1068 (1121)
T ss_pred ccceeecccCc---ccccCCC------CCcCccCCCeEEEEEe
Confidence 44689999995 33 1111 1159999998766533
No 209
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=24.37 E-value=79 Score=18.51 Aligned_cols=12 Identities=0% Similarity=-0.108 Sum_probs=7.9
Q ss_pred eEeecCCCCcee
Q psy9094 106 YVLKNHSTSEDR 117 (185)
Q Consensus 106 ~~~~c~~~~~~~ 117 (185)
+...||.|+...
T Consensus 4 i~v~CP~C~s~~ 15 (36)
T PF03811_consen 4 IDVHCPRCQSTE 15 (36)
T ss_pred EeeeCCCCCCCC
Confidence 456788888533
No 210
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=24.31 E-value=58 Score=27.90 Aligned_cols=26 Identities=8% Similarity=-0.188 Sum_probs=15.8
Q ss_pred ecCCCCceeEEeeCccccccCCccccCccC
Q psy9094 109 KNHSTSEDRVLHLTPEQEKDKSHFTDKETG 138 (185)
Q Consensus 109 ~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g 138 (185)
-|..||....+.. ...|+.|.||.|.
T Consensus 247 pC~~CGt~I~k~~----~~gR~t~~CP~CQ 272 (273)
T COG0266 247 PCRRCGTPIEKIK----LGGRSTFYCPVCQ 272 (273)
T ss_pred CCCccCCEeEEEE----EcCCcCEeCCCCC
Confidence 3888885444431 2345677788885
No 211
>PRK14056 phenylalanine 4-monooxygenase; Provisional
Probab=24.25 E-value=2.8e+02 Score=26.39 Aligned_cols=48 Identities=17% Similarity=0.181 Sum_probs=41.7
Q ss_pred hHHHHHHHHHHHHHHhhCCCceEecHHHHHHHHHcCCccEEEeeccCcceee
Q psy9094 55 PLKNKNKMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRY 106 (185)
Q Consensus 55 ~~~E~~lve~f~~~l~~~~~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~ 106 (185)
+.+-.+.+++|...++-..| |.+-+.+|++.+.+.|+..+..+..+++
T Consensus 274 fe~L~~~l~ef~~~m~~r~G----G~~gl~kai~s~~~~t~~lssGlqvsG~ 321 (578)
T PRK14056 274 FEELSEVLEEFAETMAFRTG----GLEGLEKAIRSENLATAELSSGLQITGT 321 (578)
T ss_pred HHHHHHHHHHHHHhhhhhcC----CHHHHHHHHhcCCCceEEecCCcEEEEE
Confidence 66778899999998876655 7888999999999999999999988865
No 212
>PRK05580 primosome assembly protein PriA; Validated
Probab=23.83 E-value=99 Score=29.71 Aligned_cols=11 Identities=36% Similarity=0.416 Sum_probs=5.8
Q ss_pred HHHHHHHHcCC
Q psy9094 81 EDTLRALELGS 91 (185)
Q Consensus 81 ~ev~~Ale~Ga 91 (185)
+.+.+.++.|.
T Consensus 357 ~~i~~~l~~g~ 367 (679)
T PRK05580 357 EAIKQRLERGE 367 (679)
T ss_pred HHHHHHHHcCC
Confidence 34555565554
No 213
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=23.74 E-value=25 Score=30.25 Aligned_cols=48 Identities=10% Similarity=-0.047 Sum_probs=27.9
Q ss_pred eeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHH
Q psy9094 97 CWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLAN 155 (185)
Q Consensus 97 v~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e 155 (185)
+.++|- .+|+.|+.. .+.+.- .+..+.||.||.-+.+..+ +.++.|++
T Consensus 21 ~~~~~~-----~~c~~c~~~--~~~~~l---~~~~~vc~~c~~h~rl~ar-eRi~~L~D 68 (285)
T TIGR00515 21 VPEGVW-----TKCPKCGQV--LYTKEL---ERNLEVCPKCDHHMRMDAR-ERIESLLD 68 (285)
T ss_pred CCCCCe-----eECCCCcch--hhHHHH---HhhCCCCCCCCCcCcCCHH-HHHHHcee
Confidence 566653 479999941 111111 1235679999987765543 45556665
No 214
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=23.71 E-value=50 Score=25.48 Aligned_cols=39 Identities=23% Similarity=0.229 Sum_probs=27.9
Q ss_pred CceEecHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCC
Q psy9094 74 GKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTS 114 (185)
Q Consensus 74 ~~~~yG~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~ 114 (185)
|+.+-|.+++.+..+.|-...||=. +....-...|..||
T Consensus 68 G~~IGG~del~~L~e~G~L~~lL~~--~~~~~~~~~C~~Cg 106 (147)
T cd03031 68 GRYLGGAEEVLRLNESGELRKLLKG--IRARAGGGVCEGCG 106 (147)
T ss_pred CEEEecHHHHHHHHHcCCHHHHHhh--cccccCCCCCCCCC
Confidence 6788899999999999999888743 22211124577777
No 215
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=23.70 E-value=46 Score=20.91 Aligned_cols=9 Identities=11% Similarity=0.217 Sum_probs=5.3
Q ss_pred ccccCccCc
Q psy9094 131 HFTDKETGV 139 (185)
Q Consensus 131 ~~~c~~~g~ 139 (185)
.+.|+.||-
T Consensus 37 r~~C~~Cgy 45 (50)
T PRK00432 37 RWHCGKCGY 45 (50)
T ss_pred cEECCCcCC
Confidence 445776663
No 216
>PRK10864 putative methyltransferase; Provisional
Probab=23.51 E-value=2.2e+02 Score=25.24 Aligned_cols=28 Identities=4% Similarity=0.070 Sum_probs=23.3
Q ss_pred CceEecHHHHHHHHHc--CCccEEEeeccC
Q psy9094 74 GKYCFGVEDTLRALEL--GSVETLICWENL 101 (185)
Q Consensus 74 ~~~~yG~~ev~~Ale~--GaV~~Llv~d~l 101 (185)
...+||...|.+|++. ..|..|++.++.
T Consensus 108 ~~~I~G~~aV~ealk~~~~~i~~l~~~~~~ 137 (346)
T PRK10864 108 ETRVYGENACQALFQSRPEAIVRAWFIQSV 137 (346)
T ss_pred CcEEEEHHHHHHHHhCCCCceeEEEEecCc
Confidence 5778999999999986 468898888764
No 217
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.85 E-value=62 Score=24.39 Aligned_cols=12 Identities=17% Similarity=0.368 Sum_probs=7.3
Q ss_pred CccccCccCcch
Q psy9094 130 SHFTDKETGVEL 141 (185)
Q Consensus 130 ~~~~c~~~g~~~ 141 (185)
..|.|+.|+..+
T Consensus 52 qRyrC~~C~~tf 63 (129)
T COG3677 52 QRYKCKSCGSTF 63 (129)
T ss_pred cccccCCcCcce
Confidence 356677777543
No 218
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=22.79 E-value=49 Score=29.76 Aligned_cols=30 Identities=13% Similarity=0.050 Sum_probs=18.9
Q ss_pred eecCCCCceeEEe-eCccccccCCccccCccCcchh
Q psy9094 108 LKNHSTSEDRVLH-LTPEQEKDKSHFTDKETGVELE 142 (185)
Q Consensus 108 ~~c~~~~~~~~~~-~~~~~~~~~~~~~c~~~g~~~~ 142 (185)
..|+.|+.....- ..+++ ...||.||..+.
T Consensus 14 ~~C~~Cd~l~~~~~l~~g~-----~a~CpRCg~~L~ 44 (403)
T TIGR00155 14 ILCSQCDMLVALPRIESGQ-----KAACPRCGTTLT 44 (403)
T ss_pred eeCCCCCCcccccCCCCCC-----eeECCCCCCCCc
Confidence 4699999643322 22222 446999999875
No 219
>PF09818 ABC_ATPase: Predicted ATPase of the ABC class; InterPro: IPR019195 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry consists of various predicted ABC transporter class ATPases.
Probab=22.73 E-value=1.6e+02 Score=27.14 Aligned_cols=68 Identities=15% Similarity=0.336 Sum_probs=42.2
Q ss_pred HHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHHHhc
Q psy9094 81 EDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSF 160 (185)
Q Consensus 81 ~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~ 160 (185)
-.+.+|+|.| .+.|||.||......-+++...+. ... +.. + ...++++.+-.+.++.
T Consensus 331 AnI~EAlE~G-a~~LLiDEDtsATNfmiRD~rMq~----Lv~--------k~k-----E-----PITPfidrvr~l~~~~ 387 (448)
T PF09818_consen 331 ANIMEALEAG-ARLLLIDEDTSATNFMIRDERMQA----LVS--------KEK-----E-----PITPFIDRVRSLYEKL 387 (448)
T ss_pred HHHHHHHHcC-CCEEEEcCcccchheeehhHHHHH----hhc--------cCC-----C-----CcchHHHHHHHHHHHc
Confidence 3688999999 588999998755432222221110 000 000 0 1245788888888999
Q ss_pred CCEEEEeCCCC
Q psy9094 161 GATLEIITDKS 171 (185)
Q Consensus 161 g~~v~ivs~~~ 171 (185)
|--..+|.+.+
T Consensus 388 GvStIlV~Ggs 398 (448)
T PF09818_consen 388 GVSTILVVGGS 398 (448)
T ss_pred CceEEEEeccc
Confidence 99999888765
No 220
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.45 E-value=46 Score=32.28 Aligned_cols=27 Identities=11% Similarity=-0.032 Sum_probs=15.8
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
-+|+.||+....- .....+.||.||+.
T Consensus 642 ~~C~~CG~~Ge~~------~~~~~~~CP~CG~~ 668 (711)
T PRK09263 642 DECYECGFTGEFE------CTEKGFTCPKCGNH 668 (711)
T ss_pred cccCCCCCCcccc------CCCCCCcCcCCCCC
Confidence 4799999621110 01113679999964
No 221
>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=22.33 E-value=56 Score=22.16 Aligned_cols=7 Identities=0% Similarity=-0.282 Sum_probs=4.0
Q ss_pred eecCCCC
Q psy9094 108 LKNHSTS 114 (185)
Q Consensus 108 ~~c~~~~ 114 (185)
.+||.|+
T Consensus 9 a~CP~C~ 15 (71)
T PF09526_consen 9 AVCPKCQ 15 (71)
T ss_pred ccCCCCc
Confidence 3566666
No 222
>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=22.28 E-value=79 Score=19.10 Aligned_cols=26 Identities=8% Similarity=0.129 Sum_probs=14.2
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccC
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETG 138 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g 138 (185)
+.||.||......... +..|.|..|+
T Consensus 19 ~~CP~Cg~~~~~~~~~-----~~~~~C~~C~ 44 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKT-----RGRYRCKACR 44 (46)
T ss_pred CCCCCCCCeeeEEeCC-----CCeEECCCCC
Confidence 5688888542222222 2356677765
No 223
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=22.09 E-value=2.5e+02 Score=21.47 Aligned_cols=70 Identities=9% Similarity=-0.007 Sum_probs=38.8
Q ss_pred hHHHHHHHHHHHHHHhhCCCceEe----------cHHHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCcc
Q psy9094 55 PLKNKNKMGKYFDEISQDTGKYCF----------GVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPE 124 (185)
Q Consensus 55 ~~~E~~lve~f~~~l~~~~~~~~y----------G~~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~ 124 (185)
..++.+..++..+.|.+++++.+= -.+.+..-+..|+ |.+++.-. +.+.|.+||..
T Consensus 25 ~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGR---L~~~~~~n---l~~~CE~CG~~-------- 90 (137)
T TIGR03826 25 YEEEEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGR---LQLKHFPN---LGYPCERCGTS-------- 90 (137)
T ss_pred hHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCC---eeccCCCC---CcCcccccCCc--------
Confidence 344455555555666666653331 2334444456665 45555332 24789999951
Q ss_pred ccccCCccccCccCcch
Q psy9094 125 QEKDKSHFTDKETGVEL 141 (185)
Q Consensus 125 ~~~~~~~~~c~~~g~~~ 141 (185)
.++.-.|+.|-..+
T Consensus 91 ---I~~Gr~C~~C~~~l 104 (137)
T TIGR03826 91 ---IREGRLCDSCAGEL 104 (137)
T ss_pred ---CCCCCccHHHHHHH
Confidence 23455699887543
No 224
>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=22.09 E-value=57 Score=18.39 Aligned_cols=11 Identities=27% Similarity=0.238 Sum_probs=7.1
Q ss_pred CccccCccCcc
Q psy9094 130 SHFTDKETGVE 140 (185)
Q Consensus 130 ~~~~c~~~g~~ 140 (185)
..+.||.|+..
T Consensus 18 ~~~vCp~C~~e 28 (30)
T PF08274_consen 18 ELLVCPECGHE 28 (30)
T ss_dssp SSEEETTTTEE
T ss_pred CEEeCCccccc
Confidence 35568887754
No 225
>PRK06091 membrane protein FdrA; Validated
Probab=21.89 E-value=4.2e+02 Score=25.11 Aligned_cols=71 Identities=11% Similarity=0.077 Sum_probs=46.2
Q ss_pred cEEEEeCChhhHHhhcccCCCCHhhhc-----------h--------HHHHHHHHHHHHHHhhCCCc--eEecHHHHHHH
Q psy9094 28 AGLILAGSADFKTELSQSDMFDPVRFS-----------P--------LKNKNKMGKYFDEISQDTGK--YCFGVEDTLRA 86 (185)
Q Consensus 28 ~~lIIaGPg~~k~~f~~~~~L~~~l~~-----------~--------~~E~~lve~f~~~l~~~~~~--~~yG~~ev~~A 86 (185)
+..|..|....|+-|....+++..+.+ . ..-...+++|++..+...+. ..++..-+..|
T Consensus 32 ~~~v~MgT~~Nk~i~~~~G~~~~e~~~a~pnDl~i~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~t~~~a 111 (555)
T PRK06091 32 DVSVMMGTPANKALLDTTGFWHDDFNNATPNDICVAIRTEAADAGIAQAIMQQLEEALKQLAQGSGSSQSLTQVRRWDSA 111 (555)
T ss_pred hhhhhhcCHHHHHHHHhCCCCChhhccCCCCCEEEEEEcCCcchHHHHHHHHHHHHHhhccccccCCcCCCcccccHHHH
Confidence 346778999999999888887777744 1 11146677777765533223 56777777777
Q ss_pred HH-cCCccEEEee
Q psy9094 87 LE-LGSVETLICW 98 (185)
Q Consensus 87 le-~GaV~~Llv~ 98 (185)
+. ...++..||+
T Consensus 112 ~~~lpe~DLAvIs 124 (555)
T PRK06091 112 CQKLPDANLALIS 124 (555)
T ss_pred HhcCCCCCEEEEe
Confidence 74 4445766665
No 226
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=21.51 E-value=55 Score=29.62 Aligned_cols=31 Identities=16% Similarity=0.055 Sum_probs=19.1
Q ss_pred eecCCCCceeEEe-eCccccccCCccccCccCcchhh
Q psy9094 108 LKNHSTSEDRVLH-LTPEQEKDKSHFTDKETGVELEL 143 (185)
Q Consensus 108 ~~c~~~~~~~~~~-~~~~~~~~~~~~~c~~~g~~~~~ 143 (185)
..|+.|+.....- +.+++ ...||.||..+.-
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~-----~a~CpRCg~~L~~ 42 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQ-----KAACPRCGTTLTV 42 (419)
T ss_pred ccCCCCCceeecCCCCCCC-----eeECCCCCCCCcC
Confidence 4599999643322 22221 3469999998843
No 227
>KOG0023|consensus
Probab=21.49 E-value=1.2e+02 Score=26.93 Aligned_cols=30 Identities=17% Similarity=0.422 Sum_probs=23.5
Q ss_pred HHHHHhcCCEEEEeCCCCchHHHHhhhcCC
Q psy9094 154 ANNYKSFGATLEIITDKSQEGSQFVRGFGG 183 (185)
Q Consensus 154 ~e~a~~~g~~v~ivs~~~e~G~~l~~~~GG 183 (185)
+..|+.+|.+|..||+.+..=+..++.||+
T Consensus 198 Vq~AKAMG~rV~vis~~~~kkeea~~~LGA 227 (360)
T KOG0023|consen 198 VQYAKAMGMRVTVISTSSKKKEEAIKSLGA 227 (360)
T ss_pred HHHHHHhCcEEEEEeCCchhHHHHHHhcCc
Confidence 457899999999999987554556688875
No 228
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=21.48 E-value=53 Score=33.93 Aligned_cols=9 Identities=0% Similarity=-0.337 Sum_probs=7.2
Q ss_pred EeecCCCCc
Q psy9094 107 VLKNHSTSE 115 (185)
Q Consensus 107 ~~~c~~~~~ 115 (185)
-|+|++|++
T Consensus 683 hy~c~~c~~ 691 (1213)
T TIGR01405 683 HYLCPNCKY 691 (1213)
T ss_pred cccCccccc
Confidence 378999985
No 229
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=21.19 E-value=27 Score=30.14 Aligned_cols=48 Identities=17% Similarity=0.039 Sum_probs=28.2
Q ss_pred eeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHH
Q psy9094 97 CWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLAN 155 (185)
Q Consensus 97 v~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e 155 (185)
+.++|- .+|+.|+.. .|.+.- .+..+.||.||.-+++..+ +.++.|++
T Consensus 22 ~~~~~~-----~~c~~c~~~--~~~~~l---~~~~~vc~~c~~h~rl~ar-eRi~~L~D 69 (292)
T PRK05654 22 VPEGLW-----TKCPSCGQV--LYRKEL---EANLNVCPKCGHHMRISAR-ERLDLLLD 69 (292)
T ss_pred CCCCCe-----eECCCccch--hhHHHH---HhcCCCCCCCCCCeeCCHH-HHHHHHcc
Confidence 556653 479999941 111111 1124579999988776544 45666665
No 230
>PRK14873 primosome assembly protein PriA; Provisional
Probab=21.00 E-value=67 Score=30.94 Aligned_cols=15 Identities=20% Similarity=0.355 Sum_probs=9.8
Q ss_pred EEEEeCChhhHHhhc
Q psy9094 29 GLILAGSADFKTELS 43 (185)
Q Consensus 29 ~lIIaGPg~~k~~f~ 43 (185)
.||++|..+.-+.++
T Consensus 295 ~lvLgSaTPSles~~ 309 (665)
T PRK14873 295 ALLIGGHARTAEAQA 309 (665)
T ss_pred cEEEECCCCCHHHHH
Confidence 467777776666653
No 231
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=20.87 E-value=3.2e+02 Score=20.79 Aligned_cols=44 Identities=9% Similarity=0.187 Sum_probs=25.1
Q ss_pred CCCccEEEEeCChhhHHhhcccCCCCHhhhchHHHHHHHHHHHHHHhhCC
Q psy9094 24 KPNIAGLILAGSADFKTELSQSDMFDPVRFSPLKNKNKMGKYFDEISQDT 73 (185)
Q Consensus 24 ~~~i~~lIIaGPg~~k~~f~~~~~L~~~l~~~~~E~~lve~f~~~l~~~~ 73 (185)
+...+|++|+|-..--=.|..++|. ..+-++++.++++++.-++
T Consensus 51 ~~GaDGV~v~GC~~geCHy~~GN~k------a~rR~~~lke~l~elgie~ 94 (132)
T COG1908 51 RKGADGVLVAGCKIGECHYISGNYK------AKRRMELLKELLKELGIEP 94 (132)
T ss_pred HcCCCeEEEecccccceeeeccchH------HHHHHHHHHHHHHHhCCCc
Confidence 4689999999975443333333321 2223456667777765443
No 232
>TIGR00411 redox_disulf_1 small redox-active disulfide protein 1. This protein is homologous to a family of proteins that includes thioredoxins, glutaredoxins, protein-disulfide isomerases, and others, some of which have several such domains. The sequence of this protein at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although its overall sequence seems closer to thioredoxins. It is suggested to be a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.
Probab=20.80 E-value=1.3e+02 Score=19.27 Aligned_cols=32 Identities=19% Similarity=0.210 Sum_probs=13.7
Q ss_pred HHHHHHHHhcCCEEEEeCCCCchHHHHhhhcC
Q psy9094 151 EWLANNYKSFGATLEIITDKSQEGSQFVRGFG 182 (185)
Q Consensus 151 ~~l~e~a~~~g~~v~ivs~~~e~G~~l~~~~G 182 (185)
..+-+.+..++.++.++.-+.+....+.+.+|
T Consensus 19 ~~l~~l~~~~~~~~~~~~vd~~~~~~~~~~~~ 50 (82)
T TIGR00411 19 RVVEEVAKEMGDAVEVEYINVMENPQKAMEYG 50 (82)
T ss_pred HHHHHHHHHhcCceEEEEEeCccCHHHHHHcC
Confidence 33444555555544433333222233445443
No 233
>COG0420 SbcD DNA repair exonuclease [DNA replication, recombination, and repair]
Probab=20.70 E-value=2.1e+02 Score=25.05 Aligned_cols=61 Identities=15% Similarity=0.157 Sum_probs=40.0
Q ss_pred HHHHHHHHcCCccEEEeeccCcceeeEeecCCCCceeEEeeCccccccCCccccCccCcchhhhccccHHHHHHHHHHhc
Q psy9094 81 EDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSF 160 (185)
Q Consensus 81 ~ev~~Ale~GaV~~Llv~d~l~~~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~~~~v~~l~e~a~~~ 160 (185)
+++++.+..-+||-+|+.=||+-.. . |+ + ......-..+......
T Consensus 30 ~~~l~~a~~~~vD~vliAGDlFd~~-----~-----------Ps----------~---------~a~~~~~~~l~~l~~~ 74 (390)
T COG0420 30 DELLEIAKEEKVDFVLIAGDLFDTN-----N-----------PS----------P---------RALKLFLEALRRLKDA 74 (390)
T ss_pred HHHHHHHHHccCCEEEEccccccCC-----C-----------CC----------H---------HHHHHHHHHHHHhccC
Confidence 4566666667789999999997541 0 10 0 1122233445555667
Q ss_pred CCEEEEeCCCCchHHH
Q psy9094 161 GATLEIITDKSQEGSQ 176 (185)
Q Consensus 161 g~~v~ivs~~~e~G~~ 176 (185)
|..|++|+++|+.-.+
T Consensus 75 ~Ipv~~I~GNHD~~~~ 90 (390)
T COG0420 75 GIPVVVIAGNHDSPSR 90 (390)
T ss_pred CCcEEEecCCCCchhc
Confidence 8999999999997653
No 234
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.68 E-value=54 Score=31.35 Aligned_cols=23 Identities=9% Similarity=-0.075 Sum_probs=15.2
Q ss_pred eecCCCCceeEEeeCccccccCCccccCccCcc
Q psy9094 108 LKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVE 140 (185)
Q Consensus 108 ~~c~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~ 140 (185)
-+|+.||.... ...+.||.||+.
T Consensus 569 ~~C~~CG~~~~----------g~~~~CP~CGs~ 591 (625)
T PRK08579 569 TVCNKCGRSTT----------GLYTRCPRCGSE 591 (625)
T ss_pred ccCCCCCCccC----------CCCCcCcCCCCc
Confidence 47999996210 124579999964
No 235
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=20.46 E-value=48 Score=25.30 Aligned_cols=8 Identities=13% Similarity=-0.101 Sum_probs=5.1
Q ss_pred ccCccCcc
Q psy9094 133 TDKETGVE 140 (185)
Q Consensus 133 ~c~~~g~~ 140 (185)
.||.||..
T Consensus 46 ~CPvC~~~ 53 (131)
T COG1645 46 FCPVCGYR 53 (131)
T ss_pred ECCCCCce
Confidence 47777743
No 236
>PRK05906 lipid A biosynthesis lauroyl acyltransferase; Provisional
Probab=20.17 E-value=6.6e+02 Score=23.02 Aligned_cols=41 Identities=20% Similarity=0.283 Sum_probs=29.2
Q ss_pred HHHHHHHHHHhhCCCceEe----cHHHHHHHHHcCCccEEEeecc
Q psy9094 60 NKMGKYFDEISQDTGKYCF----GVEDTLRALELGSVETLICWEN 100 (185)
Q Consensus 60 ~lve~f~~~l~~~~~~~~y----G~~ev~~Ale~GaV~~Llv~d~ 100 (185)
..+++++..+....|.-.. |...+.+|+..|.+=-+|...+
T Consensus 175 p~ld~li~~~R~r~G~~lI~~~~giR~liraLk~G~~vgiL~DQ~ 219 (454)
T PRK05906 175 RRLNKKIFSLRESFKGKIVPPKNGINQALRALHQGEVVGIVGDQA 219 (454)
T ss_pred HHHHHHHHHHHHhcCCeeecCchHHHHHHHHHhcCCEEEEEeCCC
Confidence 5788888888775555556 7889999999998544444333
Done!