Query 047170
Match_columns 89
No_of_seqs 109 out of 351
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 08:24:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047170.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047170hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2768 Translation initiation 100.0 8.5E-34 1.8E-38 212.7 5.0 85 1-87 132-230 (231)
2 smart00653 eIF2B_5 domain pres 100.0 7.4E-31 1.6E-35 178.8 7.2 68 1-70 31-102 (110)
3 PF01873 eIF-5_eIF-2B: Domain 100.0 7.1E-30 1.5E-34 177.1 4.2 68 1-70 44-115 (125)
4 TIGR00311 aIF-2beta translatio 100.0 2.4E-29 5.3E-34 176.2 6.9 67 1-70 49-119 (133)
5 PRK03988 translation initiatio 100.0 3.5E-29 7.5E-34 176.3 7.1 67 1-70 54-124 (138)
6 PRK12336 translation initiatio 99.9 1.2E-27 2.5E-32 176.0 7.0 67 1-70 50-120 (201)
7 COG1601 GCD7 Translation initi 99.9 1.1E-23 2.3E-28 150.7 2.1 68 1-70 56-127 (151)
8 KOG2767 Translation initiation 99.8 7.7E-21 1.7E-25 151.1 3.4 63 1-65 46-113 (400)
9 TIGR00100 hypA hydrogenase nic 92.6 0.092 2E-06 35.6 2.1 60 10-70 43-108 (115)
10 PRK00564 hypA hydrogenase nick 92.4 0.1 2.3E-06 35.5 2.2 60 10-70 43-110 (117)
11 PRK03681 hypA hydrogenase nick 91.5 0.14 2.9E-06 34.8 1.9 59 10-69 43-108 (114)
12 PRK00762 hypA hydrogenase nick 91.0 0.18 3.9E-06 34.6 2.2 59 10-70 43-114 (124)
13 PRK03824 hypA hydrogenase nick 90.9 0.17 3.8E-06 35.2 2.1 22 48-69 107-128 (135)
14 PRK12380 hydrogenase nickel in 90.8 0.18 3.8E-06 34.2 2.0 59 10-69 43-107 (113)
15 TIGR02159 PA_CoA_Oxy4 phenylac 88.9 0.23 4.9E-06 35.3 1.4 17 48-64 105-121 (146)
16 PRK00464 nrdR transcriptional 87.2 0.35 7.6E-06 34.8 1.5 14 50-63 2-15 (154)
17 PF12677 DUF3797: Domain of un 86.6 0.33 7.1E-06 29.3 0.9 14 43-56 8-21 (49)
18 COG0375 HybF Zn finger protein 86.4 0.73 1.6E-05 32.0 2.7 60 10-70 43-108 (115)
19 PF01155 HypA: Hydrogenase exp 86.3 0.76 1.6E-05 30.9 2.7 23 48-70 86-108 (113)
20 cd00474 SUI1_eIF1 The SUI1/eIF 82.6 1.4 3.1E-05 28.1 2.6 38 9-47 30-67 (77)
21 TIGR01160 SUI1_MOF2 translatio 81.1 2.4 5.2E-05 29.1 3.4 41 9-49 55-100 (110)
22 PF14353 CpXC: CpXC protein 80.5 1.7 3.8E-05 29.1 2.6 45 29-73 16-69 (128)
23 COG2093 DNA-directed RNA polym 79.6 0.85 1.9E-05 28.8 0.8 21 49-69 19-39 (64)
24 TIGR01158 SUI1_rel translation 78.2 2.9 6.2E-05 27.9 3.0 34 10-44 56-89 (101)
25 PRK00939 translation initiatio 76.8 3.1 6.8E-05 27.8 2.9 32 9-41 54-85 (99)
26 PRK09019 translation initiatio 75.7 4 8.7E-05 27.9 3.2 38 9-47 62-99 (108)
27 TIGR00244 transcriptional regu 75.4 1.7 3.7E-05 31.4 1.4 14 50-63 2-15 (147)
28 PF06676 DUF1178: Protein of u 75.3 2.1 4.5E-05 30.8 1.8 26 33-58 15-42 (148)
29 PF01253 SUI1: Translation ini 74.9 5.6 0.00012 25.1 3.6 38 9-46 35-76 (83)
30 PF14205 Cys_rich_KTR: Cystein 73.5 2.2 4.7E-05 26.3 1.3 9 48-56 4-12 (55)
31 PRK06824 translation initiatio 72.2 5.5 0.00012 27.6 3.3 38 9-47 72-109 (118)
32 PRK07451 translation initiatio 68.0 7.8 0.00017 26.8 3.3 37 9-46 69-105 (115)
33 PF09526 DUF2387: Probable met 67.5 6.1 0.00013 25.0 2.5 22 49-70 9-31 (71)
34 PF14446 Prok-RING_1: Prokaryo 67.3 3.1 6.7E-05 25.4 1.1 10 48-57 21-30 (54)
35 PF14599 zinc_ribbon_6: Zinc-r 65.3 3.1 6.7E-05 25.8 0.8 13 48-60 48-60 (61)
36 TIGR02443 conserved hypothetic 64.7 7.8 0.00017 24.1 2.5 30 49-79 10-40 (59)
37 PRK11788 tetratricopeptide rep 64.7 3.3 7.2E-05 31.0 1.0 15 48-62 368-382 (389)
38 COG5319 Uncharacterized protei 64.3 4.4 9.5E-05 29.1 1.5 26 33-58 15-42 (142)
39 COG1327 Predicted transcriptio 63.7 4.1 8.9E-05 29.7 1.3 14 50-63 2-15 (156)
40 COG2835 Uncharacterized conser 62.3 13 0.00028 23.2 3.1 30 48-78 8-42 (60)
41 COG0023 SUI1 Translation initi 61.4 9.9 0.00021 25.9 2.8 37 9-46 57-93 (104)
42 PF02701 zf-Dof: Dof domain, z 61.2 4.8 0.0001 25.4 1.1 16 48-63 5-20 (63)
43 PRK06393 rpoE DNA-directed RNA 60.5 5.6 0.00012 25.0 1.3 21 50-70 19-39 (64)
44 PF02591 DUF164: Putative zinc 60.2 9.5 0.00021 22.3 2.3 22 35-56 31-54 (56)
45 PRK08351 DNA-directed RNA poly 59.9 4.3 9.3E-05 25.3 0.7 9 50-58 17-25 (61)
46 PF14949 ARF7EP_C: ARF7 effect 58.6 5.4 0.00012 27.1 1.1 45 22-70 47-97 (103)
47 PRK00420 hypothetical protein; 56.6 7.2 0.00016 26.8 1.5 21 48-69 23-43 (112)
48 COG3741 HutG N-formylglutamate 55.9 4.3 9.3E-05 32.0 0.3 55 1-57 77-155 (272)
49 TIGR01159 DRP1 density-regulat 55.1 11 0.00024 27.7 2.3 40 9-48 119-162 (173)
50 PF05046 Img2: Mitochondrial l 54.9 22 0.00047 22.9 3.5 36 9-45 44-82 (87)
51 COG1326 Uncharacterized archae 54.4 3.7 8E-05 31.1 -0.3 17 48-64 6-24 (201)
52 PF03811 Zn_Tnp_IS1: InsA N-te 53.8 8 0.00017 21.5 1.1 11 48-58 5-15 (36)
53 PF08209 Sgf11: Sgf11 (transcr 53.2 6.6 0.00014 21.6 0.7 10 48-57 4-13 (33)
54 PF03119 DNA_ligase_ZBD: NAD-d 52.3 6 0.00013 20.7 0.4 8 50-57 1-8 (28)
55 PF09723 Zn-ribbon_8: Zinc rib 51.8 8.4 0.00018 21.6 1.0 12 48-59 26-37 (42)
56 TIGR02605 CxxC_CxxC_SSSS putat 51.8 15 0.00033 20.8 2.1 15 48-62 26-41 (52)
57 PF14354 Lar_restr_allev: Rest 51.3 16 0.00035 21.3 2.2 16 50-65 5-20 (61)
58 PRK02048 4-hydroxy-3-methylbut 51.3 14 0.0003 32.2 2.6 32 25-56 479-526 (611)
59 COG2956 Predicted N-acetylgluc 50.2 17 0.00036 30.0 2.8 52 1-60 309-380 (389)
60 PRK02935 hypothetical protein; 48.7 5.3 0.00011 27.7 -0.2 26 48-73 70-95 (110)
61 PF12760 Zn_Tnp_IS1595: Transp 48.6 23 0.0005 19.9 2.6 9 48-57 19-27 (46)
62 PF08271 TF_Zn_Ribbon: TFIIB z 47.9 18 0.00038 20.1 1.9 9 50-58 2-10 (43)
63 PF01096 TFIIS_C: Transcriptio 47.3 12 0.00027 20.7 1.2 14 49-62 1-14 (39)
64 PF13597 NRDD: Anaerobic ribon 46.9 10 0.00022 31.9 1.2 14 50-63 506-519 (546)
65 PRK11088 rrmA 23S rRNA methylt 46.1 18 0.00039 26.8 2.3 30 50-82 4-38 (272)
66 PF11023 DUF2614: Protein of u 46.0 9.9 0.00022 26.5 0.8 22 48-69 69-90 (114)
67 COG2051 RPS27A Ribosomal prote 45.8 13 0.00028 23.7 1.3 16 48-63 19-34 (67)
68 PF05180 zf-DNL: DNL zinc fing 45.4 10 0.00022 23.9 0.7 10 48-57 29-38 (66)
69 smart00440 ZnF_C2C2 C2C2 Zinc 44.9 16 0.00036 20.3 1.5 13 50-62 2-14 (40)
70 KOG1603 Copper chaperone [Inor 44.9 45 0.00098 20.3 3.6 38 10-47 22-61 (73)
71 PRK00694 4-hydroxy-3-methylbut 43.8 22 0.00047 31.0 2.7 33 25-57 472-519 (606)
72 TIGR02098 MJ0042_CXXC MJ0042 f 43.1 13 0.00028 19.9 0.8 10 48-57 25-34 (38)
73 COG1645 Uncharacterized Zn-fin 43.1 17 0.00037 25.8 1.6 30 38-69 13-47 (131)
74 PRK00415 rps27e 30S ribosomal 42.7 16 0.00035 22.6 1.3 18 48-65 11-28 (59)
75 PRK00398 rpoP DNA-directed RNA 42.4 22 0.00047 20.0 1.8 14 48-61 21-34 (46)
76 PF04423 Rad50_zn_hook: Rad50 41.6 9.2 0.0002 22.2 0.1 9 49-57 21-29 (54)
77 COG1734 DksA DnaK suppressor p 41.0 14 0.0003 25.6 0.9 18 40-57 67-89 (120)
78 cd00350 rubredoxin_like Rubred 40.5 11 0.00025 20.0 0.4 14 49-62 18-31 (33)
79 PF13408 Zn_ribbon_recom: Reco 40.5 14 0.0003 20.9 0.7 19 46-64 3-21 (58)
80 PF14376 Haem_bd: Haem-binding 39.6 11 0.00024 26.1 0.3 24 37-62 32-55 (137)
81 PF06827 zf-FPG_IleRS: Zinc fi 38.8 49 0.0011 16.8 2.7 21 50-70 3-23 (30)
82 COG3024 Uncharacterized protei 38.6 14 0.00031 23.4 0.6 13 48-60 7-19 (65)
83 PRK12286 rpmF 50S ribosomal pr 38.6 17 0.00037 22.0 1.0 11 48-58 27-37 (57)
84 smart00734 ZnF_Rad18 Rad18-lik 38.5 14 0.00031 18.9 0.6 10 48-57 1-10 (26)
85 COG1439 Predicted nucleic acid 38.1 21 0.00046 26.5 1.6 15 48-63 153-167 (177)
86 COG1579 Zn-ribbon protein, pos 36.3 23 0.00049 27.3 1.6 20 37-56 208-229 (239)
87 TIGR00416 sms DNA repair prote 36.2 17 0.00036 29.8 0.9 15 48-62 21-35 (454)
88 TIGR02420 dksA RNA polymerase- 36.2 19 0.00042 23.8 1.0 18 40-57 67-89 (110)
89 cd00729 rubredoxin_SM Rubredox 36.1 15 0.00033 19.8 0.4 13 50-62 20-32 (34)
90 COG1997 RPL43A Ribosomal prote 35.5 48 0.001 22.2 2.8 32 38-70 25-56 (89)
91 PF01667 Ribosomal_S27e: Ribos 35.4 21 0.00046 21.7 1.0 16 48-63 7-22 (55)
92 PF12172 DUF35_N: Rubredoxin-l 35.4 18 0.0004 19.3 0.7 11 49-59 26-36 (37)
93 TIGR01031 rpmF_bact ribosomal 35.1 21 0.00046 21.4 1.0 10 48-57 26-35 (55)
94 COG0766 MurA UDP-N-acetylgluco 34.9 50 0.0011 27.6 3.4 33 2-35 188-220 (421)
95 PF01396 zf-C4_Topoisom: Topoi 34.6 17 0.00036 20.2 0.4 8 49-56 2-9 (39)
96 smart00659 RPOLCX RNA polymera 34.5 21 0.00045 20.5 0.9 9 48-56 19-27 (44)
97 smart00834 CxxC_CXXC_SSSS Puta 34.5 20 0.00044 19.0 0.8 10 48-57 26-35 (41)
98 PF04606 Ogr_Delta: Ogr/Delta- 34.4 19 0.0004 20.6 0.6 11 50-60 1-11 (47)
99 PF14690 zf-ISL3: zinc-finger 34.0 27 0.00058 19.1 1.2 10 49-58 3-12 (47)
100 PF08274 PhnA_Zn_Ribbon: PhnA 33.4 17 0.00038 19.5 0.4 11 50-60 4-14 (30)
101 cd01675 RNR_III Class III ribo 32.7 26 0.00057 29.5 1.5 13 50-62 534-546 (555)
102 PRK00115 hemE uroporphyrinogen 32.6 18 0.00038 28.0 0.4 15 48-62 317-332 (346)
103 PRK12496 hypothetical protein; 32.5 19 0.00042 25.7 0.6 9 50-58 145-153 (164)
104 smart00531 TFIIE Transcription 32.4 34 0.00075 23.6 1.8 9 48-56 99-107 (147)
105 PF05315 ICEA: ICEA Protein; 31.7 18 0.00039 27.8 0.3 56 3-63 46-116 (230)
106 PRK08477 biotin--protein ligas 31.5 29 0.00064 25.7 1.4 19 18-36 188-206 (211)
107 PF07744 SPOC: SPOC domain; I 31.3 29 0.00063 22.2 1.2 31 27-57 38-75 (119)
108 PF01927 Mut7-C: Mut7-C RNAse 31.2 33 0.00072 23.7 1.6 34 30-63 63-106 (147)
109 COG1964 Predicted Fe-S oxidore 31.0 30 0.00065 29.3 1.6 23 48-70 16-40 (475)
110 PRK10246 exonuclease subunit S 30.9 21 0.00046 32.1 0.7 12 48-59 503-514 (1047)
111 PRK09678 DNA-binding transcrip 30.6 38 0.00081 21.5 1.6 13 50-63 3-15 (72)
112 PLN02433 uroporphyrinogen deca 30.5 25 0.00053 27.3 0.9 44 14-62 272-325 (345)
113 COG5525 Bacteriophage tail ass 30.2 31 0.00066 30.1 1.5 20 38-57 211-236 (611)
114 PF14369 zf-RING_3: zinc-finge 29.6 24 0.00052 19.3 0.5 9 48-56 21-29 (35)
115 PRK11823 DNA repair protein Ra 29.6 27 0.00059 28.5 1.0 15 48-62 21-35 (446)
116 PLN00209 ribosomal protein S27 29.5 36 0.00077 22.6 1.4 19 48-66 36-54 (86)
117 PRK01343 zinc-binding protein; 29.3 27 0.00058 21.5 0.8 12 48-59 9-20 (57)
118 TIGR02890 spore_yteA sporulati 29.3 31 0.00068 24.7 1.2 18 40-57 73-95 (159)
119 COG3303 NrfA Formate-dependent 29.1 23 0.0005 29.8 0.6 25 39-63 118-154 (501)
120 cd01121 Sms Sms (bacterial rad 29.0 26 0.00057 28.0 0.9 15 48-62 14-28 (372)
121 TIGR01463 mtaA_cmuA methyltran 29.0 19 0.00042 27.5 0.1 15 48-62 311-326 (340)
122 PF03884 DUF329: Domain of unk 28.7 24 0.00052 21.6 0.5 10 49-58 3-12 (57)
123 PTZ00083 40S ribosomal protein 28.6 38 0.00083 22.4 1.5 19 48-66 35-53 (85)
124 PRK10778 dksA RNA polymerase-b 28.6 34 0.00073 24.3 1.3 19 39-57 97-120 (151)
125 COG1885 Uncharacterized protei 28.4 42 0.00091 23.3 1.7 15 48-62 49-64 (115)
126 PF13248 zf-ribbon_3: zinc-rib 28.2 25 0.00055 17.7 0.4 9 49-57 3-11 (26)
127 PRK00418 DNA gyrase inhibitor; 27.7 29 0.00062 21.7 0.7 11 48-58 6-16 (62)
128 PF13719 zinc_ribbon_5: zinc-r 27.7 34 0.00075 18.6 1.0 15 49-63 3-21 (37)
129 PF06677 Auto_anti-p27: Sjogre 27.6 50 0.0011 18.8 1.6 13 48-60 17-29 (41)
130 PF13098 Thioredoxin_2: Thiore 27.5 86 0.0019 19.3 2.9 33 13-45 73-112 (112)
131 KOG3816 Cell differentiation r 27.5 25 0.00055 29.7 0.5 16 48-63 500-515 (526)
132 TIGR02487 NrdD anaerobic ribon 27.5 28 0.00061 29.5 0.8 13 50-62 540-552 (579)
133 TIGR02827 RNR_anaer_Bdell anae 26.8 39 0.00084 29.1 1.5 13 50-62 548-560 (586)
134 PF03966 Trm112p: Trm112p-like 26.7 41 0.00089 20.3 1.3 13 45-57 4-16 (68)
135 cd03031 GRX_GRX_like Glutaredo 26.5 29 0.00062 24.5 0.6 14 48-61 110-123 (147)
136 PF02150 RNA_POL_M_15KD: RNA p 26.3 31 0.00067 18.7 0.6 8 50-57 3-10 (35)
137 PHA02776 E7 protein; Provision 26.1 78 0.0017 21.4 2.7 25 33-57 74-100 (101)
138 PF05605 zf-Di19: Drought indu 25.8 43 0.00094 19.2 1.2 9 48-56 31-39 (54)
139 cd02393 PNPase_KH Polynucleoti 25.5 1.5E+02 0.0033 17.4 4.6 34 10-44 23-56 (61)
140 smart00778 Prim_Zn_Ribbon Zinc 25.5 35 0.00076 19.0 0.7 14 49-62 4-17 (37)
141 PF02770 Acyl-CoA_dh_M: Acyl-C 25.4 83 0.0018 17.8 2.4 19 16-35 14-32 (52)
142 cd03081 TRX_Fd_NuoE_FDH_gamma 25.3 1.2E+02 0.0025 18.7 3.2 25 9-33 19-44 (80)
143 PF00013 KH_1: KH domain syndr 25.0 1.4E+02 0.003 16.8 4.4 34 10-45 21-57 (60)
144 PF14803 Nudix_N_2: Nudix N-te 24.9 69 0.0015 17.5 1.8 14 50-63 2-15 (34)
145 PF03471 CorC_HlyC: Transporte 24.6 90 0.0019 19.0 2.6 24 23-47 2-25 (81)
146 COG4338 Uncharacterized protei 24.3 25 0.00055 21.4 0.0 11 49-59 13-23 (54)
147 COG3058 FdhE Uncharacterized p 24.3 47 0.001 26.7 1.5 22 49-70 186-212 (308)
148 PF04170 NlpE: NlpE N-terminal 24.2 59 0.0013 20.6 1.7 22 49-70 5-27 (87)
149 PF04810 zf-Sec23_Sec24: Sec23 24.1 1.2E+02 0.0026 16.6 2.8 22 49-70 3-27 (40)
150 PF07196 Flagellin_IN: Flagell 23.6 1.6E+02 0.0034 16.9 3.5 26 9-34 25-54 (56)
151 PF11331 DUF3133: Protein of u 23.4 32 0.00069 20.2 0.3 9 48-56 6-14 (46)
152 PRK08271 anaerobic ribonucleos 23.4 34 0.00073 29.6 0.6 11 50-60 582-592 (623)
153 PRK13130 H/ACA RNA-protein com 23.1 39 0.00085 20.5 0.7 9 49-57 18-26 (56)
154 PF09297 zf-NADH-PPase: NADH p 23.0 35 0.00076 17.8 0.4 10 50-59 5-14 (32)
155 PF09432 THP2: Tho complex sub 22.9 82 0.0018 22.5 2.3 52 7-62 4-57 (132)
156 COG2331 Uncharacterized protei 22.8 37 0.00079 22.4 0.5 22 39-60 23-45 (82)
157 PF01783 Ribosomal_L32p: Ribos 22.8 41 0.00089 19.9 0.7 10 48-57 26-35 (56)
158 PF14569 zf-UDP: Zinc-binding 22.5 33 0.00071 22.5 0.3 10 48-57 28-37 (80)
159 PRK09263 anaerobic ribonucleos 22.4 54 0.0012 28.7 1.7 9 50-58 661-669 (711)
160 TIGR03655 anti_R_Lar restricti 22.4 62 0.0014 18.7 1.5 13 50-62 3-15 (53)
161 PF13878 zf-C2H2_3: zinc-finge 22.3 38 0.00083 18.9 0.5 9 48-56 13-21 (41)
162 cd00862 ProRS_anticodon_zinc P 22.1 42 0.00091 24.3 0.8 26 37-62 133-160 (202)
163 PF14577 SEO_C: Sieve element 22.1 46 0.00099 25.7 1.0 10 48-57 214-223 (235)
164 KOG3239 Density-regulated prot 22.1 1.4E+02 0.0029 22.6 3.5 37 9-45 131-171 (193)
165 PRK11827 hypothetical protein; 22.0 70 0.0015 19.7 1.7 30 48-78 8-42 (60)
166 PF08273 Prim_Zn_Ribbon: Zinc- 21.9 44 0.00096 18.9 0.7 15 49-63 4-18 (40)
167 PRK07111 anaerobic ribonucleos 21.8 51 0.0011 29.0 1.3 13 50-62 695-707 (735)
168 PF09180 ProRS-C_1: Prolyl-tRN 21.7 32 0.00068 21.1 0.1 23 40-62 3-27 (68)
169 PF13913 zf-C2HC_2: zinc-finge 21.7 40 0.00086 16.9 0.4 8 49-56 3-10 (25)
170 TIGR01464 hemE uroporphyrinoge 21.7 50 0.0011 25.3 1.2 43 15-62 274-327 (338)
171 PF05876 Terminase_GpA: Phage 21.6 44 0.00095 28.1 0.9 20 39-58 185-210 (557)
172 PF07635 PSCyt1: Planctomycete 21.6 47 0.001 19.6 0.8 10 51-60 1-10 (59)
173 PF14169 YdjO: Cold-inducible 21.4 43 0.00093 20.7 0.6 11 48-58 39-49 (59)
174 KOG1105 Transcription elongati 21.4 42 0.00091 26.7 0.7 9 48-56 283-291 (296)
175 COG4654 Cytochrome c551/c552 [ 21.4 34 0.00074 23.7 0.2 13 50-62 34-46 (110)
176 PF10013 DUF2256: Uncharacteri 20.7 47 0.001 19.3 0.7 11 49-59 9-19 (42)
177 PF05042 Caleosin: Caleosin re 20.7 53 0.0011 24.3 1.1 16 33-48 90-105 (174)
178 cd03308 CmuA_CmuC_like CmuA_Cm 20.5 32 0.00069 27.2 -0.1 13 48-60 350-363 (378)
179 PHA00626 hypothetical protein 20.5 45 0.00098 20.7 0.6 11 50-60 2-12 (59)
No 1
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.5e-34 Score=212.72 Aligned_cols=85 Identities=58% Similarity=1.026 Sum_probs=83.4
Q ss_pred CCCCcccHhHHHHHHHhhccceeecCCceEEEEeecCHHHHHHhhcc----ceecCCCCCCceeEEEcCcEEEE------
Q 047170 1 MHRQPENVDVVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGILHK----FVICGCCKSPDTILTNGNHLFFL------ 70 (89)
Q Consensus 1 L~R~p~h~~v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~~----yV~C~~C~sPdT~L~k~~rl~~l------ 70 (89)
|||.|+| |++||++||||+||+|+++||+|+|+|++++||++|++ ||+|..|+||||.|.+++|||||
T Consensus 132 mhR~pdH--v~~FLlAELgTsGSidg~~rLviKGrfq~kq~e~VLRrYI~eyV~C~~CkSpdt~L~kenRLfFL~C~~cg 209 (231)
T KOG2768|consen 132 MHRSPDH--VMQFLLAELGTSGSIDGQQRLVIKGRFQQKQFENVLRRYIKEYVTCKTCKSPDTILQKENRLFFLRCEKCG 209 (231)
T ss_pred hccChHH--HHHHHHHHhccccccCCCceEEEeccccHHHHHHHHHHHHHHheEeeecCChhHHhhhhcceEEEEecCCC
Confidence 7999999 99999999999999999999999999999999999999 99999999999999999999999
Q ss_pred ----EeecccceEEEeeeccc
Q 047170 71 ----IFPIKAGFVARFGRRNT 87 (89)
Q Consensus 71 ----v~~ik~g~~a~~~kr~~ 87 (89)
|++||+||+|.+|||+.
T Consensus 210 s~~sv~~Iktgf~A~~~kr~~ 230 (231)
T KOG2768|consen 210 SRCSVASIKTGFQAVVGKRAM 230 (231)
T ss_pred CeeeeeeeecccEEecccccc
Confidence 99999999999999974
No 2
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=99.97 E-value=7.4e-31 Score=178.82 Aligned_cols=68 Identities=49% Similarity=0.981 Sum_probs=66.6
Q ss_pred CCCCcccHhHHHHHHHhhccceeecCCceEEEEeecCHHHHHHhhcc----ceecCCCCCCceeEEEcCcEEEE
Q 047170 1 MHRQPENVDVVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGILHK----FVICGCCKSPDTILTNGNHLFFL 70 (89)
Q Consensus 1 L~R~p~h~~v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~~----yV~C~~C~sPdT~L~k~~rl~~l 70 (89)
|||+|+| |+|||++||||+|++|++|+|+|+|+|++++||++|++ ||+|++|+||||.|++++|+++|
T Consensus 31 L~R~p~h--v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~l~~yI~~yVlC~~C~spdT~l~k~~r~~~l 102 (110)
T smart00653 31 LNRPPDH--VLKFLLAELGTQGSIDGKGRLIVNGRFTPKKLQDLLRRYIKEYVLCPECGSPDTELIKENRLFFL 102 (110)
T ss_pred HCCCHHH--HHHHHHHHhCCceeECCCCeEEEEEeeCHHHHHHHHHHHHHhcEECCCCCCCCcEEEEeCCeEEE
Confidence 7999999 99999999999999999889999999999999999999 99999999999999999999998
No 3
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=99.96 E-value=7.1e-30 Score=177.11 Aligned_cols=68 Identities=46% Similarity=0.898 Sum_probs=66.4
Q ss_pred CCCCcccHhHHHHHHHhhccceeecCCceEEEEeecCHHHHHHhhcc----ceecCCCCCCceeEEEcCcEEEE
Q 047170 1 MHRQPENVDVVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGILHK----FVICGCCKSPDTILTNGNHLFFL 70 (89)
Q Consensus 1 L~R~p~h~~v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~~----yV~C~~C~sPdT~L~k~~rl~~l 70 (89)
|||+|+| +++||++||||+|++|++++|||||+|++++||++|++ ||+|++|+||||.|+++++++++
T Consensus 44 L~R~p~~--~~ky~~~ELgt~~~id~~~~lii~G~~~~~~i~~~L~~fI~~yVlC~~C~spdT~l~k~~r~~~l 115 (125)
T PF01873_consen 44 LNRDPEH--VLKYFGKELGTQGSIDGKGRLIINGRFSSKQIQDLLDKFIKEYVLCPECGSPDTELIKEGRLIFL 115 (125)
T ss_dssp HTSSHHH--HHHHHHHHSSSEEEEETTTEEEEESSSSCCHHHHHHHHHHCHHSSCTSTSSSSEEEEEETTCCEE
T ss_pred HCCCHHH--HHHHHHHHHCCceEECCCCEEEEEEecCHHHHHHHHHHHHHHEEEcCCCCCCccEEEEcCCEEEE
Confidence 6999999 99999999999999999789999999999999999999 99999999999999999999998
No 4
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=99.96 E-value=2.4e-29 Score=176.18 Aligned_cols=67 Identities=30% Similarity=0.729 Sum_probs=65.1
Q ss_pred CCCCcccHhHHHHHHHhhccceeecCCceEEEEeecCHHHHHHhhcc----ceecCCCCCCceeEEEcCcEEEE
Q 047170 1 MHRQPENVDVVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGILHK----FVICGCCKSPDTILTNGNHLFFL 70 (89)
Q Consensus 1 L~R~p~h~~v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~~----yV~C~~C~sPdT~L~k~~rl~~l 70 (89)
|||+|+| ++|||++||||+|++|+ |+++|||+|++++||++|++ ||+|++|+||||.|+|++|+++|
T Consensus 49 L~R~~~~--v~ky~~~ELgt~g~i~~-~rlii~G~~~~~~i~~~L~~yI~~yVlC~~C~sPdT~l~k~~r~~~l 119 (133)
T TIGR00311 49 LNRDEQH--LLKYLLKELGTAGNLEG-GRLILQGKFTHFLLNERIEDYVRKYVICRECNRPDTRIIKEGRVSLL 119 (133)
T ss_pred HCCCHHH--HHHHHHHHhCCCceecC-CEEEEEeecCHHHHHHHHHHHHhheEECCCCCCCCcEEEEeCCeEEE
Confidence 7999999 99999999999999985 79999999999999999999 99999999999999999999998
No 5
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=99.96 E-value=3.5e-29 Score=176.32 Aligned_cols=67 Identities=36% Similarity=0.815 Sum_probs=65.3
Q ss_pred CCCCcccHhHHHHHHHhhccceeecCCceEEEEeecCHHHHHHhhcc----ceecCCCCCCceeEEEcCcEEEE
Q 047170 1 MHRQPENVDVVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGILHK----FVICGCCKSPDTILTNGNHLFFL 70 (89)
Q Consensus 1 L~R~p~h~~v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~~----yV~C~~C~sPdT~L~k~~rl~~l 70 (89)
|||+|+| ++|||++||||+|+++ +|+++|+|+|++++||++|++ ||+|++|+||||.|+|++|+++|
T Consensus 54 L~R~~~h--v~ky~~~ELgt~g~i~-~~~lii~G~~~~~~i~~~L~~yI~~yVlC~~C~spdT~l~k~~r~~~l 124 (138)
T PRK03988 54 LNRDPKH--VAKFLLKELGTAGNIE-GGRLILQGKFSPRVINEKIDRYVKEYVICPECGSPDTKLIKEGRIWVL 124 (138)
T ss_pred HCCCHHH--HHHHHHHHhCCceeec-CCEEEEEEeeCHHHHHHHHHHHHHhcEECCCCCCCCcEEEEcCCeEEE
Confidence 7999999 9999999999999996 589999999999999999999 99999999999999999999999
No 6
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=99.94 E-value=1.2e-27 Score=176.00 Aligned_cols=67 Identities=33% Similarity=0.766 Sum_probs=65.3
Q ss_pred CCCCcccHhHHHHHHHhhccceeecCCceEEEEeecCHHHHHHhhcc----ceecCCCCCCceeEEEcCcEEEE
Q 047170 1 MHRQPENVDVVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGILHK----FVICGCCKSPDTILTNGNHLFFL 70 (89)
Q Consensus 1 L~R~p~h~~v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~~----yV~C~~C~sPdT~L~k~~rl~~l 70 (89)
|||+|+| ++|||++||||+|++|+ ++++|||+|++++||++|++ ||+|++|+||||.|++++|+++|
T Consensus 50 l~R~~~~--~~ky~~~ELgt~~~~~~-~~~ii~G~~~~~~i~~~l~~yi~~yV~C~~C~~pdT~l~k~~~~~~l 120 (201)
T PRK12336 50 LNRDPDH--LMKFLQRELGTAGKIEG-GRAVFNGKFTEEDIQAAIDAYVDEYVICSECGLPDTRLVKEDRVLML 120 (201)
T ss_pred HCCCHHH--HHHHHHHHhCCcceecC-CEEEEEeeeCHHHHHHHHHHHHHheEECCCCCCCCcEEEEcCCeEEE
Confidence 7999999 99999999999999985 59999999999999999999 99999999999999999999999
No 7
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=1.1e-23 Score=150.69 Aligned_cols=68 Identities=43% Similarity=0.828 Sum_probs=66.8
Q ss_pred CCCCcccHhHHHHHHHhhccceeecCCceEEEEeecCHHHHHHhhcc----ceecCCCCCCceeEEEcCcEEEE
Q 047170 1 MHRQPENVDVVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGILHK----FVICGCCKSPDTILTNGNHLFFL 70 (89)
Q Consensus 1 L~R~p~h~~v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~~----yV~C~~C~sPdT~L~k~~rl~~l 70 (89)
|||||+| +++||.+||||+|++|++++|+++|+|+++.|++.|++ ||.|++|+||||.|++++|+|+|
T Consensus 56 l~rDp~h--~~k~l~kel~t~g~~d~~~rlvl~g~f~~~~i~~~i~~yi~~yv~C~~c~s~dt~l~~~~R~~~l 127 (151)
T COG1601 56 LNRDPEH--LVKFLKKELGTAGSIDGKGRLVLQGKFSDSEIVNEIERYIAEYVKCKECGSPDTELIKEERLLFL 127 (151)
T ss_pred hcCCHHH--HHHHHHHHhccccccCCcceEEEEecccHHHHHHHHHHHHHheeEeccCCCCchhhhhhhhhHhh
Confidence 6999999 99999999999999999889999999999999999999 99999999999999999999999
No 8
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=99.81 E-value=7.7e-21 Score=151.13 Aligned_cols=63 Identities=24% Similarity=0.515 Sum_probs=60.4
Q ss_pred CCCCcccHhHHHHHHHhhccceeecC-CceEEEEeecCHHHHHHhhcc----ceecCCCCCCceeEEEcC
Q 047170 1 MHRQPENVDVVTFLLSEMGTSGSLDG-QQHLVVKGRFASKYIEGILHK----FVICGCCKSPDTILTNGN 65 (89)
Q Consensus 1 L~R~p~h~~v~kyl~~ELgt~g~id~-~~rlii~G~~~~~~i~~~L~~----yV~C~~C~sPdT~L~k~~ 65 (89)
|+|||-| ++|||++|||+|+++|. +||+++||.|++.+||++|+. ||+||+|++|+|.|+..+
T Consensus 46 L~RPp~Y--~tKyFGcELGAQT~fd~kn~ryiVNG~Hd~~KLqdlLdgFIkKFVlC~~C~NPETel~itk 113 (400)
T KOG2767|consen 46 LGRPPLY--PTKYFGCELGAQTKFDVKNGRYIVNGAHEASKLQDLLDGFIKKFVLCPSCENPETELIITK 113 (400)
T ss_pred hCCCCCc--ccccceeeccccccccccCCeeeecccccHHHHHHHHHHHHHHheeCcCCCCCceeEEecc
Confidence 7999999 99999999999999998 999999999999999999999 999999999999999654
No 9
>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=92.59 E-value=0.092 Score=35.60 Aligned_cols=60 Identities=12% Similarity=0.152 Sum_probs=34.9
Q ss_pred HHHHHHHhhccceeecCCceEEEEe---ecCHHH---HHHhhccceecCCCCCCceeEEEcCcEEEE
Q 047170 10 VVTFLLSEMGTSGSLDGQQHLVVKG---RFASKY---IEGILHKFVICGCCKSPDTILTNGNHLFFL 70 (89)
Q Consensus 10 v~kyl~~ELgt~g~id~~~rlii~G---~~~~~~---i~~~L~~yV~C~~C~sPdT~L~k~~rl~~l 70 (89)
.++|-.. +-+.+++-++-+|.|.= ++.-.+ .-...+.+..||.|+|+++.++..+.+.+.
T Consensus 43 ~L~faf~-~~~~~t~~ega~L~I~~~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~~i~~G~El~I~ 108 (115)
T TIGR00100 43 QLQFAFE-VVREGTVAEGAKLNIEDEPVECECEDCSEEVSPEIDLYRCPKCHGIMLQVRAGKELNLK 108 (115)
T ss_pred HHHHHHH-HHhCCCccCCCEEEEEeeCcEEEcccCCCEEecCCcCccCcCCcCCCcEEecCCeEEEE
Confidence 4555544 44666665566888761 111100 000111177899999999999987766654
No 10
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=92.42 E-value=0.1 Score=35.47 Aligned_cols=60 Identities=18% Similarity=0.213 Sum_probs=35.2
Q ss_pred HHHHHHHhhcccee-ecCCceEEEE---eecCHHHHH--Hhhc-c-ceecCCCCCCceeEEEcCcEEEE
Q 047170 10 VVTFLLSEMGTSGS-LDGQQHLVVK---GRFASKYIE--GILH-K-FVICGCCKSPDTILTNGNHLFFL 70 (89)
Q Consensus 10 v~kyl~~ELgt~g~-id~~~rlii~---G~~~~~~i~--~~L~-~-yV~C~~C~sPdT~L~k~~rl~~l 70 (89)
.++|-... -+.++ +-++-+|.|. +++.-.+=. --+. . |..||.|+||+..++..+.+++-
T Consensus 43 ~L~faf~~-~~~~T~~~ega~L~Ie~vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~~G~El~I~ 110 (117)
T PRK00564 43 LFVSAFET-FREESLVCKDAILDIVDEKVELECKDCSHVFKPNALDYGVCEKCHSKNVIITQGNEMRLL 110 (117)
T ss_pred HHHHHHHH-HhcCCcccCCCEEEEEecCCEEEhhhCCCccccCCccCCcCcCCCCCceEEecCCEEEEE
Confidence 45555544 46666 6556688876 222211111 1111 2 55699999999999987766543
No 11
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=91.51 E-value=0.14 Score=34.78 Aligned_cols=59 Identities=12% Similarity=0.189 Sum_probs=34.7
Q ss_pred HHHHHHHhhccceeecCCceEEEE---eecCHHHH---HHhhcc-ceecCCCCCCceeEEEcCcEEE
Q 047170 10 VVTFLLSEMGTSGSLDGQQHLVVK---GRFASKYI---EGILHK-FVICGCCKSPDTILTNGNHLFF 69 (89)
Q Consensus 10 v~kyl~~ELgt~g~id~~~rlii~---G~~~~~~i---~~~L~~-yV~C~~C~sPdT~L~k~~rl~~ 69 (89)
.++|-.. .-+.|++-++-+|.|. +++.-.+= -..... +..||.|+|+++.++..+.+.+
T Consensus 43 ~L~f~f~-~~~~~t~~egA~L~i~~~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~~G~El~i 108 (114)
T PRK03681 43 SLAFCFD-LVCRGTVAEGCKLHLEEQEAECWCETCQQYVTLLTQRVRRCPQCHGDMLRIVADDGLQI 108 (114)
T ss_pred HHHHHHH-HHhCCCccCCCEEEEEeeCcEEEcccCCCeeecCCccCCcCcCcCCCCcEEccCCeEEE
Confidence 4555443 4566777556688876 22221111 111112 4779999999999998776654
No 12
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=91.02 E-value=0.18 Score=34.62 Aligned_cols=59 Identities=17% Similarity=0.339 Sum_probs=34.6
Q ss_pred HHHHHHHhhccceeecCCceEEEE---eec--------CHHHHHHhhcc--ceecCCCCCCceeEEEcCcEEEE
Q 047170 10 VVTFLLSEMGTSGSLDGQQHLVVK---GRF--------ASKYIEGILHK--FVICGCCKSPDTILTNGNHLFFL 70 (89)
Q Consensus 10 v~kyl~~ELgt~g~id~~~rlii~---G~~--------~~~~i~~~L~~--yV~C~~C~sPdT~L~k~~rl~~l 70 (89)
.++|-. |+-+.|++-++-.|.|. +++ +... ....+. |..||.|+|++..++..+.+.+-
T Consensus 43 ~L~faf-~~~~~gT~~egA~L~I~~vp~~~~C~Cg~~~~~~~-~~~~~~~~~~~CP~Cgs~~~~i~~G~El~i~ 114 (124)
T PRK00762 43 QLRFML-DVLAEGTIAEDADLIVEMIPVEIECECGYEGVVDE-DEIDHYAAVIECPVCGNKRAHILGGRECNVK 114 (124)
T ss_pred HHHHHH-HHHhCCCCcCCCEEEEEecCeeEEeeCcCcccccc-cchhccccCCcCcCCCCCCCEEecCCeEEEE
Confidence 445444 34566777555577775 111 1110 111112 46899999999999987766654
No 13
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=90.95 E-value=0.17 Score=35.19 Aligned_cols=22 Identities=27% Similarity=0.641 Sum_probs=18.4
Q ss_pred ceecCCCCCCceeEEEcCcEEE
Q 047170 48 FVICGCCKSPDTILTNGNHLFF 69 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k~~rl~~ 69 (89)
|..||.|+|++..++..+.+++
T Consensus 107 ~~~CP~Cgs~~~~i~~G~el~i 128 (135)
T PRK03824 107 FLKCPKCGSRDFEIVKGRGVYI 128 (135)
T ss_pred CcCCcCCCCCCcEEecCceEEE
Confidence 7789999999999998766554
No 14
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=90.82 E-value=0.18 Score=34.17 Aligned_cols=59 Identities=17% Similarity=0.211 Sum_probs=34.0
Q ss_pred HHHHHHHhhccceeecCCceEEEE---eecCHHH--HHHhhc-cceecCCCCCCceeEEEcCcEEE
Q 047170 10 VVTFLLSEMGTSGSLDGQQHLVVK---GRFASKY--IEGILH-KFVICGCCKSPDTILTNGNHLFF 69 (89)
Q Consensus 10 v~kyl~~ELgt~g~id~~~rlii~---G~~~~~~--i~~~L~-~yV~C~~C~sPdT~L~k~~rl~~ 69 (89)
.++|-. |+-+.|++-++-+|.|. +++.-.+ -+--+. .+..||.|+|++..++....+++
T Consensus 43 ~L~f~f-~~~~~~T~~egA~L~I~~vp~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~~i~~G~El~i 107 (113)
T PRK12380 43 AVRFSF-EIVCHGTVAQGCDLHIVYKPAQAWCWDCSQVVEIHQHDAQCPHCHGERLRVDTGDSLIV 107 (113)
T ss_pred HHHHHH-HHHhCCCccCCCEEEEEeeCcEEEcccCCCEEecCCcCccCcCCCCCCcEEccCCeEEE
Confidence 455544 45566666555588876 1111110 011111 25569999999999998776654
No 15
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=88.94 E-value=0.23 Score=35.26 Aligned_cols=17 Identities=41% Similarity=0.542 Sum_probs=14.8
Q ss_pred ceecCCCCCCceeEEEc
Q 047170 48 FVICGCCKSPDTILTNG 64 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k~ 64 (89)
-|.||.|+|.+|+++..
T Consensus 105 ~~~cp~c~s~~t~~~s~ 121 (146)
T TIGR02159 105 SVQCPRCGSADTTITSI 121 (146)
T ss_pred CCcCCCCCCCCcEeecC
Confidence 38999999999999853
No 16
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=87.21 E-value=0.35 Score=34.75 Aligned_cols=14 Identities=36% Similarity=0.778 Sum_probs=12.8
Q ss_pred ecCCCCCCceeEEE
Q 047170 50 ICGCCKSPDTILTN 63 (89)
Q Consensus 50 ~C~~C~sPdT~L~k 63 (89)
.||.|++|+|..+.
T Consensus 2 ~cp~c~~~~~~~~~ 15 (154)
T PRK00464 2 RCPFCGHPDTRVID 15 (154)
T ss_pred cCCCCCCCCCEeEe
Confidence 69999999999886
No 17
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=86.61 E-value=0.33 Score=29.26 Aligned_cols=14 Identities=21% Similarity=0.605 Sum_probs=11.2
Q ss_pred HhhccceecCCCCC
Q 047170 43 GILHKFVICGCCKS 56 (89)
Q Consensus 43 ~~L~~yV~C~~C~s 56 (89)
.++.+|+.||.|+|
T Consensus 8 ~L~~kY~~Cp~CGN 21 (49)
T PF12677_consen 8 KLSNKYCKCPKCGN 21 (49)
T ss_pred chhhhhccCcccCC
Confidence 44555999999997
No 18
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=86.45 E-value=0.73 Score=31.96 Aligned_cols=60 Identities=17% Similarity=0.204 Sum_probs=33.7
Q ss_pred HHHHHHHhhccceeecCCceEEEEee---cCHHHHHH--hhcc-ceecCCCCCCceeEEEcCcEEEE
Q 047170 10 VVTFLLSEMGTSGSLDGQQHLVVKGR---FASKYIEG--ILHK-FVICGCCKSPDTILTNGNHLFFL 70 (89)
Q Consensus 10 v~kyl~~ELgt~g~id~~~rlii~G~---~~~~~i~~--~L~~-yV~C~~C~sPdT~L~k~~rl~~l 70 (89)
.++| ..|.-+.|++-++.++.|.=. +--.+=+. .++. ...||.|+|++.++...+.+.+.
T Consensus 43 ~l~F-aFev~~egT~aega~l~Ie~~p~~~~C~~C~~~~~~e~~~~~CP~C~s~~~~i~~G~el~i~ 108 (115)
T COG0375 43 ALRF-AFEVVAEGTIAEGAELHIEEEPAECWCLDCGQEVELEELDYRCPKCGSINLRIIGGDELIIK 108 (115)
T ss_pred HHHH-HHHHHhccCcccCCEEEEEEeccEEEeccCCCeecchhheeECCCCCCCceEEecCCeeEEE
Confidence 3443 445566677755658877411 10000000 0011 34499999999999988877654
No 19
>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=86.32 E-value=0.76 Score=30.91 Aligned_cols=23 Identities=30% Similarity=0.491 Sum_probs=15.8
Q ss_pred ceecCCCCCCceeEEEcCcEEEE
Q 047170 48 FVICGCCKSPDTILTNGNHLFFL 70 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k~~rl~~l 70 (89)
+..||.|+|++..++..+.+.+.
T Consensus 86 ~~~CP~Cgs~~~~i~~G~el~i~ 108 (113)
T PF01155_consen 86 DFSCPRCGSPDVEIISGRELRIK 108 (113)
T ss_dssp CHH-SSSSSS-EEEEESS-EEEE
T ss_pred CCCCcCCcCCCcEEccCCeEEEE
Confidence 45699999999999987766653
No 20
>cd00474 SUI1_eIF1 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two antiparallel alpha helices packed against the same side of a five-strand beta sheet, is structurally similar to other RNA-binding domains suggesting that SUI1/eIF1 may bind RNA. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown.
Probab=82.64 E-value=1.4 Score=28.05 Aligned_cols=38 Identities=13% Similarity=0.199 Sum_probs=30.9
Q ss_pred hHHHHHHHhhccceeecCCceEEEEeecCHHHHHHhhcc
Q 047170 9 DVVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGILHK 47 (89)
Q Consensus 9 ~v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~~ 47 (89)
++++.|.+.+|+.|++.+ +.+.|+|.+...-.+-+++.
T Consensus 30 ~l~k~lKk~~~cggtv~~-~~I~lQGD~r~~v~~~L~~~ 67 (77)
T cd00474 30 KLAKELKKKCACGGTVKD-EVIELQGDQRKKIKEFLIKM 67 (77)
T ss_pred HHHHHHHHHcCCCcEEec-CEEEEeCcHHHHHHHHHHHc
Confidence 389999999999999985 59999999987766544443
No 21
>TIGR01160 SUI1_MOF2 translation initiation factor SUI1, eukaryotic. Alternate name: MOF2. A similar protein family (see TIGRFAMs model TIGR01158) is found in prokaryotes. The human proteins complements a yeast SUI1 mutatation.
Probab=81.08 E-value=2.4 Score=29.07 Aligned_cols=41 Identities=15% Similarity=0.265 Sum_probs=32.6
Q ss_pred hHHHHHHHhhccceeecC----CceEEEEeecCHHHHHHhhcc-ce
Q 047170 9 DVVTFLLSEMGTSGSLDG----QQHLVVKGRFASKYIEGILHK-FV 49 (89)
Q Consensus 9 ~v~kyl~~ELgt~g~id~----~~rlii~G~~~~~~i~~~L~~-yV 49 (89)
.++|.|.+.+|+.|++-+ ++.+.|+|.+..+-.+-+... ||
T Consensus 55 ~l~K~lKkk~~cGGsVk~~~~~~~~IelQGD~re~v~~~L~~~g~~ 100 (110)
T TIGR01160 55 KIVKALKKEFACNGTVIEDPEMGEVIQLQGDQRKNVCEFLISQGLL 100 (110)
T ss_pred HHHHHHHHHhCCCceEEeCCCCCCEEEEeCcHHHHHHHHHHHcCCC
Confidence 589999999999999943 357999999988766655555 54
No 22
>PF14353 CpXC: CpXC protein
Probab=80.52 E-value=1.7 Score=29.10 Aligned_cols=45 Identities=18% Similarity=0.319 Sum_probs=31.9
Q ss_pred eEEEEeecCHHHHHHhhcc---ceecCCCCC---CceeEE--E-cCcEEEEEee
Q 047170 29 HLVVKGRFASKYIEGILHK---FVICGCCKS---PDTILT--N-GNHLFFLIFP 73 (89)
Q Consensus 29 rlii~G~~~~~~i~~~L~~---yV~C~~C~s---PdT~L~--k-~~rl~~lv~~ 73 (89)
--+|+..-+++-.+.+|+. -+.||.|+. .+..+. - +.+++++..|
T Consensus 16 ~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~~~~~i~~~P 69 (128)
T PF14353_consen 16 WTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPEKKFMIYYFP 69 (128)
T ss_pred EeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCCCCEEEEEcC
Confidence 4578889999999999988 889999995 333333 2 3455555433
No 23
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=79.64 E-value=0.85 Score=28.83 Aligned_cols=21 Identities=29% Similarity=0.324 Sum_probs=13.5
Q ss_pred eecCCCCCCceeEEEcCcEEE
Q 047170 49 VICGCCKSPDTILTNGNHLFF 69 (89)
Q Consensus 49 V~C~~C~sPdT~L~k~~rl~~ 69 (89)
-+||.|+|+|+.-.=.+=+.+
T Consensus 19 e~CP~Cgs~~~te~W~G~~iI 39 (64)
T COG2093 19 EICPVCGSTDLTEEWFGLLII 39 (64)
T ss_pred ccCCCCCCcccchhhccEEEE
Confidence 469999999875433333333
No 24
>TIGR01158 SUI1_rel translation initation factor SUI1, putative, prokaryotic. This family of archaeal and bacterial proteins is homologous to the eukaryotic translation intiation factor SUI1 involved in directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met.
Probab=78.18 E-value=2.9 Score=27.94 Aligned_cols=34 Identities=15% Similarity=0.291 Sum_probs=28.3
Q ss_pred HHHHHHHhhccceeecCCceEEEEeecCHHHHHHh
Q 047170 10 VVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGI 44 (89)
Q Consensus 10 v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~ 44 (89)
+++.|.+.+|+.|++. ++.+.|+|.|...-.+-+
T Consensus 56 l~k~LKk~~gcGgtvk-~~~IeiQGD~~~~v~~~L 89 (101)
T TIGR01158 56 LAKELKSKCGCGGTVK-DGVIEIQGDHRDRVKDLL 89 (101)
T ss_pred HHHHHHHHhcCCeeEe-CCEEEEeCcHHHHHHHHH
Confidence 8899999999999997 559999999987654333
No 25
>PRK00939 translation initiation factor Sui1; Reviewed
Probab=76.82 E-value=3.1 Score=27.79 Aligned_cols=32 Identities=13% Similarity=0.309 Sum_probs=27.3
Q ss_pred hHHHHHHHhhccceeecCCceEEEEeecCHHHH
Q 047170 9 DVVTFLLSEMGTSGSLDGQQHLVVKGRFASKYI 41 (89)
Q Consensus 9 ~v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i 41 (89)
++++.|.+.+|+.|++.+ +.+.|+|.+...-.
T Consensus 54 ~l~k~lKk~~gcGgsvk~-~~I~iQGD~r~~v~ 85 (99)
T PRK00939 54 ELAKKLKSKLACGGTVKD-GRIELQGDHRERVK 85 (99)
T ss_pred HHHHHHHHHhCCCceEEC-CEEEEeCcHHHHHH
Confidence 388999999999999974 47999999977654
No 26
>PRK09019 translation initiation factor Sui1; Validated
Probab=75.70 E-value=4 Score=27.94 Aligned_cols=38 Identities=13% Similarity=0.155 Sum_probs=30.4
Q ss_pred hHHHHHHHhhccceeecCCceEEEEeecCHHHHHHhhcc
Q 047170 9 DVVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGILHK 47 (89)
Q Consensus 9 ~v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~~ 47 (89)
.++|.|-+.+|+-|++-+ +.+.|+|.+..+-.+-+...
T Consensus 62 ~l~K~lKkk~gcGGtvk~-~~IelQGD~r~~v~~~L~~~ 99 (108)
T PRK09019 62 KLAAELKKKCGCGGAVKD-GVIEIQGDKRDLLKSLLEAK 99 (108)
T ss_pred HHHHHHHHHhcCCCeEEc-CEEEEcCcHHHHHHHHHHHC
Confidence 489999999999999984 58999999987655544433
No 27
>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=75.36 E-value=1.7 Score=31.36 Aligned_cols=14 Identities=21% Similarity=0.562 Sum_probs=12.5
Q ss_pred ecCCCCCCceeEEE
Q 047170 50 ICGCCKSPDTILTN 63 (89)
Q Consensus 50 ~C~~C~sPdT~L~k 63 (89)
.||-|+++||..+-
T Consensus 2 ~CP~C~~~dtkViD 15 (147)
T TIGR00244 2 HCPFCQHHNTRVLD 15 (147)
T ss_pred CCCCCCCCCCEeee
Confidence 59999999999884
No 28
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=75.27 E-value=2.1 Score=30.77 Aligned_cols=26 Identities=27% Similarity=0.542 Sum_probs=20.3
Q ss_pred EeecC-HHHHHHhhcc-ceecCCCCCCc
Q 047170 33 KGRFA-SKYIEGILHK-FVICGCCKSPD 58 (89)
Q Consensus 33 ~G~~~-~~~i~~~L~~-yV~C~~C~sPd 58 (89)
-|=|. ++.++....+ .|.||.|+|.+
T Consensus 15 EgWF~ss~~fd~Q~~~glv~CP~Cgs~~ 42 (148)
T PF06676_consen 15 EGWFRSSAAFDRQQARGLVSCPVCGSTE 42 (148)
T ss_pred ceecCCHHHHHHHHHcCCccCCCCCCCe
Confidence 35555 6678888777 99999999965
No 29
>PF01253 SUI1: Translation initiation factor SUI1; InterPro: IPR001950 In Saccharomyces cerevisiae (Baker's yeast), SUI1 is a translation initiation factor that functions in concert with eIF-2 and the initiator tRNA-Met in directing the ribosome to the proper start site of translation []. SUI1 is a protein of 108 residues. Close homologs of SUI1 have been found [] in mammals, insects and plants. SUI1 is also evolutionary related to hypothetical proteins from Escherichia coli (yciH), Haemophilus influenzae (HI1225) and Methanococcus vannielii.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2OGH_A 1D1R_A 2IF1_A 2XZN_F 2XZM_F.
Probab=74.89 E-value=5.6 Score=25.11 Aligned_cols=38 Identities=11% Similarity=0.267 Sum_probs=27.4
Q ss_pred hHHHHHHHhhccceeec----CCceEEEEeecCHHHHHHhhc
Q 047170 9 DVVTFLLSEMGTSGSLD----GQQHLVVKGRFASKYIEGILH 46 (89)
Q Consensus 9 ~v~kyl~~ELgt~g~id----~~~rlii~G~~~~~~i~~~L~ 46 (89)
++++.|.+.+|++|++. .+..+.|+|.+...-.+-++.
T Consensus 35 ~lak~lkk~~ac~~sv~~~~~k~~~I~iQGd~~~~i~~~L~~ 76 (83)
T PF01253_consen 35 ELAKELKKKFACGGSVTKDPGKGEEIQIQGDHRDEIKDLLVE 76 (83)
T ss_dssp HHHHHHHHHHTS-EEEEE-TTTSSEEEEESS-HHHHHHHHHH
T ss_pred HHHHHHHHhccCceEEeecCCCCCEEEECCcHHHHHHHHHHH
Confidence 38999999999999993 145699999998774444433
No 30
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=73.53 E-value=2.2 Score=26.27 Aligned_cols=9 Identities=22% Similarity=1.095 Sum_probs=7.9
Q ss_pred ceecCCCCC
Q 047170 48 FVICGCCKS 56 (89)
Q Consensus 48 yV~C~~C~s 56 (89)
.++||.|++
T Consensus 4 Wi~CP~Cgn 12 (55)
T PF14205_consen 4 WILCPICGN 12 (55)
T ss_pred EEECCCCCC
Confidence 689999996
No 31
>PRK06824 translation initiation factor Sui1; Validated
Probab=72.22 E-value=5.5 Score=27.61 Aligned_cols=38 Identities=18% Similarity=0.387 Sum_probs=30.5
Q ss_pred hHHHHHHHhhccceeecCCceEEEEeecCHHHHHHhhcc
Q 047170 9 DVVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGILHK 47 (89)
Q Consensus 9 ~v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~~ 47 (89)
+++|.|.+.+|+.|++- ++.+.|+|.+..+-.+-+...
T Consensus 72 ~l~K~LKkk~gcGGtvk-d~~IeiQGD~r~~v~~~L~~~ 109 (118)
T PRK06824 72 ELAKELKRRCGTGGTLK-DGVIEIQGDHVELLLAELLKR 109 (118)
T ss_pred HHHHHHHHHhcCCceEe-cCEEEEcCcHHHHHHHHHHHC
Confidence 48999999999999997 459999999987655544443
No 32
>PRK07451 translation initiation factor Sui1; Validated
Probab=68.04 E-value=7.8 Score=26.78 Aligned_cols=37 Identities=16% Similarity=0.433 Sum_probs=29.4
Q ss_pred hHHHHHHHhhccceeecCCceEEEEeecCHHHHHHhhc
Q 047170 9 DVVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGILH 46 (89)
Q Consensus 9 ~v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~ 46 (89)
.++|.|-..+|+.|++. ++.+.|+|.+..+-.+-+..
T Consensus 69 ~LaK~LK~k~gcGGtvk-d~~IelQGD~r~~v~~~L~~ 105 (115)
T PRK07451 69 KLLKQLKTQCGSGGTVK-DNTIEIQGDHRQKILEILIK 105 (115)
T ss_pred HHHHHHHHHhcCCceEc-CCEEEEcCcHHHHHHHHHHH
Confidence 48899999999999996 44899999997765544433
No 33
>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=67.54 E-value=6.1 Score=25.03 Aligned_cols=22 Identities=27% Similarity=0.638 Sum_probs=17.1
Q ss_pred eecCCCCCCceeEE-EcCcEEEE
Q 047170 49 VICGCCKSPDTILT-NGNHLFFL 70 (89)
Q Consensus 49 V~C~~C~sPdT~L~-k~~rl~~l 70 (89)
..||.|++-||... +++.+-++
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~v 31 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYV 31 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEE
Confidence 57999999999877 56665544
No 34
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=67.26 E-value=3.1 Score=25.37 Aligned_cols=10 Identities=40% Similarity=1.115 Sum_probs=9.2
Q ss_pred ceecCCCCCC
Q 047170 48 FVICGCCKSP 57 (89)
Q Consensus 48 yV~C~~C~sP 57 (89)
-|.||.|+.|
T Consensus 21 iVvCp~Cgap 30 (54)
T PF14446_consen 21 IVVCPECGAP 30 (54)
T ss_pred EEECCCCCCc
Confidence 7999999987
No 35
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=65.30 E-value=3.1 Score=25.75 Aligned_cols=13 Identities=31% Similarity=0.337 Sum_probs=5.3
Q ss_pred ceecCCCCCCcee
Q 047170 48 FVICGCCKSPDTI 60 (89)
Q Consensus 48 yV~C~~C~sPdT~ 60 (89)
+..|+.|+|.+|.
T Consensus 48 g~KC~~C~SYNT~ 60 (61)
T PF14599_consen 48 GHKCSHCGSYNTR 60 (61)
T ss_dssp ----TTTS---EE
T ss_pred hhcCCCCCCcccC
Confidence 7899999999985
No 36
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=64.74 E-value=7.8 Score=24.08 Aligned_cols=30 Identities=20% Similarity=0.570 Sum_probs=20.6
Q ss_pred eecCCCCCCceeEE-EcCcEEEEEeecccceE
Q 047170 49 VICGCCKSPDTILT-NGNHLFFLIFPIKAGFV 79 (89)
Q Consensus 49 V~C~~C~sPdT~L~-k~~rl~~lv~~ik~g~~ 79 (89)
..||.|+..||... +++.+-. +.=|.=||+
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~-vECv~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIEL-VECVECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceE-EEeccCCCc
Confidence 57999999999866 5666543 444555554
No 37
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=64.67 E-value=3.3 Score=30.98 Aligned_cols=15 Identities=33% Similarity=0.629 Sum_probs=12.7
Q ss_pred ceecCCCCCCceeEE
Q 047170 48 FVICGCCKSPDTILT 62 (89)
Q Consensus 48 yV~C~~C~sPdT~L~ 62 (89)
+-.||.|++.+|..-
T Consensus 368 ~~~c~~c~~~~~~~~ 382 (389)
T PRK11788 368 YWHCPSCKAWETIKP 382 (389)
T ss_pred eeECcCCCCccCcCC
Confidence 778999999999654
No 38
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.30 E-value=4.4 Score=29.10 Aligned_cols=26 Identities=27% Similarity=0.571 Sum_probs=19.9
Q ss_pred EeecC-HHHHHHhhcc-ceecCCCCCCc
Q 047170 33 KGRFA-SKYIEGILHK-FVICGCCKSPD 58 (89)
Q Consensus 33 ~G~~~-~~~i~~~L~~-yV~C~~C~sPd 58 (89)
-|-|. +.++++-..+ .|.||.|+|-+
T Consensus 15 EGWF~ssaDfd~Q~~rgLv~CPvCgs~~ 42 (142)
T COG5319 15 EGWFGSSADFDRQRERGLVTCPVCGSTE 42 (142)
T ss_pred cccccCchhHHHHHHcCceeCCCCCcHH
Confidence 45564 5678887777 99999999943
No 39
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=63.75 E-value=4.1 Score=29.74 Aligned_cols=14 Identities=29% Similarity=0.600 Sum_probs=12.4
Q ss_pred ecCCCCCCceeEEE
Q 047170 50 ICGCCKSPDTILTN 63 (89)
Q Consensus 50 ~C~~C~sPdT~L~k 63 (89)
.||.|+++||..+-
T Consensus 2 ~CPfC~~~~tkViD 15 (156)
T COG1327 2 KCPFCGHEDTKVID 15 (156)
T ss_pred CCCCCCCCCCeeee
Confidence 59999999999873
No 40
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=62.30 E-value=13 Score=23.20 Aligned_cols=30 Identities=23% Similarity=0.701 Sum_probs=20.1
Q ss_pred ceecCCCCCCceeEEEcCcEEEE-----Eeecccce
Q 047170 48 FVICGCCKSPDTILTNGNHLFFL-----IFPIKAGF 78 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k~~rl~~l-----v~~ik~g~ 78 (89)
-+-||.|+.| -.+..++...+- ..||..|-
T Consensus 8 iLaCP~~kg~-L~~~~~~~~L~c~~~~~aYpI~dGI 42 (60)
T COG2835 8 ILACPVCKGP-LVYDEEKQELICPRCKLAYPIRDGI 42 (60)
T ss_pred eeeccCcCCc-ceEeccCCEEEecccCceeecccCc
Confidence 4789999999 444455554443 77777774
No 41
>COG0023 SUI1 Translation initiation factor 1 (eIF-1/SUI1) and related proteins [Translation, ribosomal structure and biogenesis]
Probab=61.42 E-value=9.9 Score=25.93 Aligned_cols=37 Identities=14% Similarity=0.256 Sum_probs=30.7
Q ss_pred hHHHHHHHhhccceeecCCceEEEEeecCHHHHHHhhc
Q 047170 9 DVVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGILH 46 (89)
Q Consensus 9 ~v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~ 46 (89)
.+++.|-+.+|+.|++-++ ...|+|.|..+-.+=++.
T Consensus 57 ~Lak~LKk~cacGGtvk~~-~IeiQGdhr~~v~~~L~~ 93 (104)
T COG0023 57 KLAKELKKKCACGGTVKDG-EIEIQGDHRDKVKELLIK 93 (104)
T ss_pred HHHHHHHHHcCCCceecCC-EEEEeChHHHHHHHHHHH
Confidence 3899999999999999845 999999998776655544
No 42
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=61.25 E-value=4.8 Score=25.37 Aligned_cols=16 Identities=25% Similarity=0.420 Sum_probs=13.5
Q ss_pred ceecCCCCCCceeEEE
Q 047170 48 FVICGCCKSPDTILTN 63 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k 63 (89)
-+.||-|.|.+|++-=
T Consensus 5 ~~~CPRC~S~nTKFcY 20 (63)
T PF02701_consen 5 PLPCPRCDSTNTKFCY 20 (63)
T ss_pred CCCCCCcCCCCCEEEe
Confidence 3579999999999873
No 43
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=60.47 E-value=5.6 Score=25.02 Aligned_cols=21 Identities=14% Similarity=0.067 Sum_probs=14.8
Q ss_pred ecCCCCCCceeEEEcCcEEEE
Q 047170 50 ICGCCKSPDTILTNGNHLFFL 70 (89)
Q Consensus 50 ~C~~C~sPdT~L~k~~rl~~l 70 (89)
.||.|+|.+|.-.=++=+.++
T Consensus 19 ~Cp~Cgs~~~S~~w~G~v~i~ 39 (64)
T PRK06393 19 TCPVHGDEKTTTEWFGFLIIT 39 (64)
T ss_pred cCCCCCCCcCCcCcceEEEEE
Confidence 499999998765555555444
No 44
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=60.20 E-value=9.5 Score=22.31 Aligned_cols=22 Identities=18% Similarity=0.452 Sum_probs=17.5
Q ss_pred ecCHHHHHHhhcc--ceecCCCCC
Q 047170 35 RFASKYIEGILHK--FVICGCCKS 56 (89)
Q Consensus 35 ~~~~~~i~~~L~~--yV~C~~C~s 56 (89)
..++..++++... -+.||+|+.
T Consensus 31 ~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 31 ELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred EcCHHHHHHHHcCCCeEECcCCCc
Confidence 4567788888666 999999985
No 45
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=59.95 E-value=4.3 Score=25.27 Aligned_cols=9 Identities=44% Similarity=0.885 Sum_probs=8.0
Q ss_pred ecCCCCCCc
Q 047170 50 ICGCCKSPD 58 (89)
Q Consensus 50 ~C~~C~sPd 58 (89)
.||.|+|.+
T Consensus 17 ~CP~Cgs~~ 25 (61)
T PRK08351 17 RCPVCGSRD 25 (61)
T ss_pred cCCCCcCCc
Confidence 399999988
No 46
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=58.56 E-value=5.4 Score=27.10 Aligned_cols=45 Identities=18% Similarity=0.253 Sum_probs=32.2
Q ss_pred eeecCCceEEEEeecCHHHHHHhhcc-----ceecCCCCCCceeEE-EcCcEEEE
Q 047170 22 GSLDGQQHLVVKGRFASKYIEGILHK-----FVICGCCKSPDTILT-NGNHLFFL 70 (89)
Q Consensus 22 g~id~~~rlii~G~~~~~~i~~~L~~-----yV~C~~C~sPdT~L~-k~~rl~~l 70 (89)
..+|+.|+|+.+|. ++=+-|+. |--||.|+|.-=-.+ +-+|=|+.
T Consensus 47 ~~YD~~G~l~~~~~----DlCDCL~~~C~GC~~PC~~C~S~KCG~~CR~nRkw~y 97 (103)
T PF14949_consen 47 KHYDEKGRLISNGK----DLCDCLDEDCPGCHYPCPKCGSRKCGPECRCNRKWVY 97 (103)
T ss_pred ccccCCceEeeCCC----ccccccCCCCCCccccCCCCCCCccChhhCcCCceee
Confidence 44588999999994 77777777 999999999754443 34444443
No 47
>PRK00420 hypothetical protein; Validated
Probab=56.59 E-value=7.2 Score=26.82 Aligned_cols=21 Identities=19% Similarity=0.271 Sum_probs=13.6
Q ss_pred ceecCCCCCCceeEEEcCcEEE
Q 047170 48 FVICGCCKSPDTILTNGNHLFF 69 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k~~rl~~ 69 (89)
--.||.|++|=+.+ +++.++-
T Consensus 23 ~~~CP~Cg~pLf~l-k~g~~~C 43 (112)
T PRK00420 23 SKHCPVCGLPLFEL-KDGEVVC 43 (112)
T ss_pred cCCCCCCCCcceec-CCCceEC
Confidence 34688888877776 5555443
No 48
>COG3741 HutG N-formylglutamate amidohydrolase [Amino acid transport and metabolism]
Probab=55.93 E-value=4.3 Score=31.99 Aligned_cols=55 Identities=16% Similarity=0.301 Sum_probs=44.3
Q ss_pred CCCCcccHhHHHH---HHHhhccceeecCCceEEEEeecCHHHHHHhhcc---------------------ceecCCCCC
Q 047170 1 MHRQPENVDVVTF---LLSEMGTSGSLDGQQHLVVKGRFASKYIEGILHK---------------------FVICGCCKS 56 (89)
Q Consensus 1 L~R~p~h~~v~ky---l~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~~---------------------yV~C~~C~s 56 (89)
+||+|++ +.-| --..|++...+|+.+.++--|+.++.+++.-|.. |++=..|+|
T Consensus 77 vNR~p~~--~~l~~~~~ttGL~~~~~fdge~l~~~g~~~~~~e~~~Rle~~~~PYHaaL~~el~r~~a~~G~avLiDcHS 154 (272)
T COG3741 77 VNREPDG--ASLYPGRVTTGLGPVTTFDGEPLYIYGGAPTPAEALARLETLWKPYHAALRRELERLRAIFGAAVLIDCHS 154 (272)
T ss_pred cCCCCCC--CcCccccccCCccccccccCccccccCCCCCHHHHHHHHHHhhccHHHHHHHHHHHHHhhcCeEEEEeccc
Confidence 6999999 7777 4567999999999889999999998887665543 777778887
Q ss_pred C
Q 047170 57 P 57 (89)
Q Consensus 57 P 57 (89)
-
T Consensus 155 m 155 (272)
T COG3741 155 M 155 (272)
T ss_pred c
Confidence 3
No 49
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=55.10 E-value=11 Score=27.66 Aligned_cols=40 Identities=18% Similarity=0.326 Sum_probs=31.2
Q ss_pred hHHHHHHHhhccceee----cCCceEEEEeecCHHHHHHhhccc
Q 047170 9 DVVTFLLSEMGTSGSL----DGQQHLVVKGRFASKYIEGILHKF 48 (89)
Q Consensus 9 ~v~kyl~~ELgt~g~i----d~~~rlii~G~~~~~~i~~~L~~y 48 (89)
++.++|.+.+++.+++ .+++.++|+|.+..+-.+=++.+|
T Consensus 119 ~laK~lkkkfacG~SV~k~~~~~~eI~IQGD~~~~v~e~L~~~~ 162 (173)
T TIGR01159 119 KASKTFAQKFATGCSVSKSVTGKEEIVIQGDVMDDIEDYIHEKW 162 (173)
T ss_pred HHHHHHHHHhCCCCccccCCCCCCEEEecCCHHHHHHHHHHHHc
Confidence 3899999999999877 237799999999887665444445
No 50
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 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 of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=54.85 E-value=22 Score=22.91 Aligned_cols=36 Identities=19% Similarity=0.290 Sum_probs=25.2
Q ss_pred hHHHHHHHhhc--cceeecC-CceEEEEeecCHHHHHHhh
Q 047170 9 DVVTFLLSEMG--TSGSLDG-QQHLVVKGRFASKYIEGIL 45 (89)
Q Consensus 9 ~v~kyl~~ELg--t~g~id~-~~rlii~G~~~~~~i~~~L 45 (89)
|+.++|..+.. -...+.+ .++++|+|.+. +.+...|
T Consensus 44 dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~~-~~Vk~wL 82 (87)
T PF05046_consen 44 DLRKFLGEKPKKKIDVRVNELTGHIEIKGDHV-EEVKKWL 82 (87)
T ss_pred HHHHHhhhhcCCCcceEEeecCCEEEEcCccH-HHHHHHH
Confidence 46777777666 4566666 88999999994 4455444
No 51
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=54.40 E-value=3.7 Score=31.07 Aligned_cols=17 Identities=18% Similarity=0.565 Sum_probs=8.9
Q ss_pred ceecCCCCCCce--eEEEc
Q 047170 48 FVICGCCKSPDT--ILTNG 64 (89)
Q Consensus 48 yV~C~~C~sPdT--~L~k~ 64 (89)
|..||+|++-+| +++|+
T Consensus 6 y~~Cp~Cg~eev~hEVik~ 24 (201)
T COG1326 6 YIECPSCGSEEVSHEVIKE 24 (201)
T ss_pred EEECCCCCcchhhHHHHHh
Confidence 555555555555 44443
No 52
>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=53.77 E-value=8 Score=21.47 Aligned_cols=11 Identities=36% Similarity=0.679 Sum_probs=9.6
Q ss_pred ceecCCCCCCc
Q 047170 48 FVICGCCKSPD 58 (89)
Q Consensus 48 yV~C~~C~sPd 58 (89)
.|.||.|+|.+
T Consensus 5 ~v~CP~C~s~~ 15 (36)
T PF03811_consen 5 DVHCPRCQSTE 15 (36)
T ss_pred eeeCCCCCCCC
Confidence 58999999976
No 53
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=53.17 E-value=6.6 Score=21.58 Aligned_cols=10 Identities=40% Similarity=1.055 Sum_probs=7.7
Q ss_pred ceecCCCCCC
Q 047170 48 FVICGCCKSP 57 (89)
Q Consensus 48 yV~C~~C~sP 57 (89)
||.|+.|+.+
T Consensus 4 ~~~C~nC~R~ 13 (33)
T PF08209_consen 4 YVECPNCGRP 13 (33)
T ss_dssp EEE-TTTSSE
T ss_pred eEECCCCcCC
Confidence 7999999974
No 54
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=52.32 E-value=6 Score=20.72 Aligned_cols=8 Identities=38% Similarity=0.887 Sum_probs=3.8
Q ss_pred ecCCCCCC
Q 047170 50 ICGCCKSP 57 (89)
Q Consensus 50 ~C~~C~sP 57 (89)
.||.|+|+
T Consensus 1 ~CP~C~s~ 8 (28)
T PF03119_consen 1 TCPVCGSK 8 (28)
T ss_dssp B-TTT--B
T ss_pred CcCCCCCE
Confidence 49999985
No 55
>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=51.77 E-value=8.4 Score=21.57 Aligned_cols=12 Identities=33% Similarity=0.537 Sum_probs=9.7
Q ss_pred ceecCCCCCCce
Q 047170 48 FVICGCCKSPDT 59 (89)
Q Consensus 48 yV~C~~C~sPdT 59 (89)
-+.||.|++.+.
T Consensus 26 ~~~CP~Cg~~~~ 37 (42)
T PF09723_consen 26 PVPCPECGSTEV 37 (42)
T ss_pred CCcCCCCCCCce
Confidence 689999999553
No 56
>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=51.77 E-value=15 Score=20.78 Aligned_cols=15 Identities=20% Similarity=0.406 Sum_probs=11.2
Q ss_pred ceecCCCCCCce-eEE
Q 047170 48 FVICGCCKSPDT-ILT 62 (89)
Q Consensus 48 yV~C~~C~sPdT-~L~ 62 (89)
.+.||.|++.+. +++
T Consensus 26 ~~~CP~Cg~~~~~r~~ 41 (52)
T TIGR02605 26 LATCPECGGEKLRRLL 41 (52)
T ss_pred CCCCCCCCCCceeEEe
Confidence 688999999654 444
No 57
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=51.35 E-value=16 Score=21.27 Aligned_cols=16 Identities=25% Similarity=0.650 Sum_probs=11.5
Q ss_pred ecCCCCCCceeEEEcC
Q 047170 50 ICGCCKSPDTILTNGN 65 (89)
Q Consensus 50 ~C~~C~sPdT~L~k~~ 65 (89)
-||.|++++..+..+.
T Consensus 5 PCPFCG~~~~~~~~~~ 20 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDE 20 (61)
T ss_pred CCCCCCCcceEeeccc
Confidence 4999977777766543
No 58
>PRK02048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional
Probab=51.28 E-value=14 Score=32.17 Aligned_cols=32 Identities=16% Similarity=0.488 Sum_probs=20.6
Q ss_pred cC-CceEEEEee--cCHHHHHHh----hcc---------ceecCCCCC
Q 047170 25 DG-QQHLVVKGR--FASKYIEGI----LHK---------FVICGCCKS 56 (89)
Q Consensus 25 d~-~~rlii~G~--~~~~~i~~~----L~~---------yV~C~~C~s 56 (89)
|+ ++-+.|... .+.+.+.++ |+. |+-||+|+.
T Consensus 479 DGlgDgi~l~~~~~~~~~~~~~laf~ILQa~r~R~sKTEyISCPsCGR 526 (611)
T PRK02048 479 DGLCDGIFLFNQGKLSHVVVDATAFGILQAGRLRTSKTEYISCPGCGR 526 (611)
T ss_pred CcccceEEEecCCCccHHHHHHHHHHHHHHhccccccceEEECCCCCc
Confidence 66 556666644 555554432 322 999999997
No 59
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=50.18 E-value=17 Score=30.00 Aligned_cols=52 Identities=12% Similarity=0.351 Sum_probs=32.8
Q ss_pred CCCCcccHhHHHHHHHhhccceeecCCceEEEEeecCHHHHHHhhcc--------------------ceecCCCCCCcee
Q 047170 1 MHRQPENVDVVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGILHK--------------------FVICGCCKSPDTI 60 (89)
Q Consensus 1 L~R~p~h~~v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~~--------------------yV~C~~C~sPdT~ 60 (89)
|+|.|.-.-+.+++..+|.-. + +|+ ++=+-..+.+++.. |-.||+|+..+|.
T Consensus 309 l~r~Pt~~gf~rl~~~~l~da---e-eg~----~k~sL~~lr~mvge~l~~~~~YRC~~CGF~a~~l~W~CPsC~~W~Ti 380 (389)
T COG2956 309 LRRKPTMRGFHRLMDYHLADA---E-EGR----AKESLDLLRDMVGEQLRRKPRYRCQNCGFTAHTLYWHCPSCRAWETI 380 (389)
T ss_pred HhhCCcHHHHHHHHHhhhccc---c-ccc----hhhhHHHHHHHHHHHHhhcCCceecccCCcceeeeeeCCCccccccc
Confidence 456777655666666666432 2 222 55555566666543 8899999998884
No 60
>PRK02935 hypothetical protein; Provisional
Probab=48.74 E-value=5.3 Score=27.67 Aligned_cols=26 Identities=27% Similarity=0.511 Sum_probs=16.7
Q ss_pred ceecCCCCCCceeEEEcCcEEEEEee
Q 047170 48 FVICGCCKSPDTILTNGNHLFFLIFP 73 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k~~rl~~lv~~ 73 (89)
-|.||+|+.|---|=+.+.-++..+|
T Consensus 70 qV~CP~C~K~TKmLGrvD~CM~C~~P 95 (110)
T PRK02935 70 QVICPSCEKPTKMLGRVDACMHCNQP 95 (110)
T ss_pred eeECCCCCchhhhccceeecCcCCCc
Confidence 68999999875555455555444333
No 61
>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=48.62 E-value=23 Score=19.92 Aligned_cols=9 Identities=56% Similarity=1.172 Sum_probs=7.6
Q ss_pred ceecCCCCCC
Q 047170 48 FVICGCCKSP 57 (89)
Q Consensus 48 yV~C~~C~sP 57 (89)
|| ||.|++.
T Consensus 19 ~~-CP~Cg~~ 27 (46)
T PF12760_consen 19 FV-CPHCGST 27 (46)
T ss_pred CC-CCCCCCe
Confidence 55 9999997
No 62
>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=47.88 E-value=18 Score=20.10 Aligned_cols=9 Identities=33% Similarity=0.767 Sum_probs=6.7
Q ss_pred ecCCCCCCc
Q 047170 50 ICGCCKSPD 58 (89)
Q Consensus 50 ~C~~C~sPd 58 (89)
.||.|++.+
T Consensus 2 ~Cp~Cg~~~ 10 (43)
T PF08271_consen 2 KCPNCGSKE 10 (43)
T ss_dssp SBTTTSSSE
T ss_pred CCcCCcCCc
Confidence 488888866
No 63
>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=47.34 E-value=12 Score=20.69 Aligned_cols=14 Identities=14% Similarity=0.562 Sum_probs=9.1
Q ss_pred eecCCCCCCceeEE
Q 047170 49 VICGCCKSPDTILT 62 (89)
Q Consensus 49 V~C~~C~sPdT~L~ 62 (89)
+.||.|++.++...
T Consensus 1 ~~Cp~Cg~~~a~~~ 14 (39)
T PF01096_consen 1 IKCPKCGHNEAVFF 14 (39)
T ss_dssp S--SSS-SSEEEEE
T ss_pred CCCcCCCCCeEEEE
Confidence 46999999888776
No 64
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=46.90 E-value=10 Score=31.86 Aligned_cols=14 Identities=21% Similarity=0.401 Sum_probs=5.9
Q ss_pred ecCCCCCCceeEEE
Q 047170 50 ICGCCKSPDTILTN 63 (89)
Q Consensus 50 ~C~~C~sPdT~L~k 63 (89)
.||.|+|+|+....
T Consensus 506 ~CP~CGs~~~~~~~ 519 (546)
T PF13597_consen 506 KCPKCGSENIEVYS 519 (546)
T ss_dssp E-CCC----EEEEB
T ss_pred CCCCCCCcccceEE
Confidence 68888888865553
No 65
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=46.15 E-value=18 Score=26.84 Aligned_cols=30 Identities=23% Similarity=0.385 Sum_probs=19.2
Q ss_pred ecCCCCCCceeEEEcCcEEEE-----EeecccceEEEe
Q 047170 50 ICGCCKSPDTILTNGNHLFFL-----IFPIKAGFVARF 82 (89)
Q Consensus 50 ~C~~C~sPdT~L~k~~rl~~l-----v~~ik~g~~a~~ 82 (89)
+||.|++|=+ .+++-+.. .-.-|+||.-..
T Consensus 4 ~CP~C~~~l~---~~~~~~~C~~~h~fd~a~~Gy~~ll 38 (272)
T PRK11088 4 QCPLCHQPLT---LEENSWICPQNHQFDCAKEGYVNLL 38 (272)
T ss_pred cCCCCCcchh---cCCCEEEcCCCCCCccccCceEEec
Confidence 6999998853 34444444 335578886554
No 66
>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=45.98 E-value=9.9 Score=26.46 Aligned_cols=22 Identities=18% Similarity=0.311 Sum_probs=13.9
Q ss_pred ceecCCCCCCceeEEEcCcEEE
Q 047170 48 FVICGCCKSPDTILTNGNHLFF 69 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k~~rl~~ 69 (89)
-|.||+|+.+---|=+.+.-++
T Consensus 69 ~V~CP~C~K~TKmLGr~D~CM~ 90 (114)
T PF11023_consen 69 QVECPNCGKQTKMLGRVDACMH 90 (114)
T ss_pred eeECCCCCChHhhhchhhccCc
Confidence 6899999987444434444333
No 67
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=45.80 E-value=13 Score=23.67 Aligned_cols=16 Identities=19% Similarity=0.507 Sum_probs=13.4
Q ss_pred ceecCCCCCCceeEEE
Q 047170 48 FVICGCCKSPDTILTN 63 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k 63 (89)
+|.||.|++..|.+-.
T Consensus 19 ~VkCpdC~N~q~vFsh 34 (67)
T COG2051 19 RVKCPDCGNEQVVFSH 34 (67)
T ss_pred EEECCCCCCEEEEecc
Confidence 8999999998777654
No 68
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=45.43 E-value=10 Score=23.93 Aligned_cols=10 Identities=40% Similarity=0.836 Sum_probs=6.2
Q ss_pred ceecCCCCCC
Q 047170 48 FVICGCCKSP 57 (89)
Q Consensus 48 yV~C~~C~sP 57 (89)
+|.||.|++.
T Consensus 29 iv~C~gC~~~ 38 (66)
T PF05180_consen 29 IVQCPGCKNR 38 (66)
T ss_dssp EEE-TTS--E
T ss_pred EEECCCCcce
Confidence 8999999984
No 69
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=44.94 E-value=16 Score=20.31 Aligned_cols=13 Identities=15% Similarity=0.447 Sum_probs=11.2
Q ss_pred ecCCCCCCceeEE
Q 047170 50 ICGCCKSPDTILT 62 (89)
Q Consensus 50 ~C~~C~sPdT~L~ 62 (89)
.||.|++.+....
T Consensus 2 ~Cp~C~~~~a~~~ 14 (40)
T smart00440 2 PCPKCGNREATFF 14 (40)
T ss_pred cCCCCCCCeEEEE
Confidence 6999999998775
No 70
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=44.91 E-value=45 Score=20.25 Aligned_cols=38 Identities=29% Similarity=0.264 Sum_probs=30.0
Q ss_pred HHHHHHHhhc-cceeecC-CceEEEEeecCHHHHHHhhcc
Q 047170 10 VVTFLLSEMG-TSGSLDG-QQHLVVKGRFASKYIEGILHK 47 (89)
Q Consensus 10 v~kyl~~ELg-t~g~id~-~~rlii~G~~~~~~i~~~L~~ 47 (89)
+.+.|..--| -+..+|. ++++.+.|.+++..+...|.+
T Consensus 22 V~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k 61 (73)
T KOG1603|consen 22 VKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKK 61 (73)
T ss_pred HHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHh
Confidence 6677777777 4556676 889999999999998888764
No 71
>PRK00694 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated
Probab=43.76 E-value=22 Score=30.96 Aligned_cols=33 Identities=18% Similarity=0.439 Sum_probs=21.8
Q ss_pred cC-CceEEEEee-cCHHHHHHh----hcc---------ceecCCCCCC
Q 047170 25 DG-QQHLVVKGR-FASKYIEGI----LHK---------FVICGCCKSP 57 (89)
Q Consensus 25 d~-~~rlii~G~-~~~~~i~~~----L~~---------yV~C~~C~sP 57 (89)
|+ ++-+.|... .+.+.+.++ |+. |+-||+|+.-
T Consensus 472 DGlGDgi~l~~~~~~~~~~~~laf~ILQaaR~R~sKte~isCP~CgRt 519 (606)
T PRK00694 472 DGLGECVLLDLPNIKLSDVRTIAFGTLQSAGVRLVKTEYISCPGCGRT 519 (606)
T ss_pred ccCcceEEEeCCCCCHHHHHHHHHHHHHHhccccccceEEECCCCCce
Confidence 77 556677655 666555443 222 9999999974
No 72
>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=43.08 E-value=13 Score=19.88 Aligned_cols=10 Identities=40% Similarity=0.713 Sum_probs=8.4
Q ss_pred ceecCCCCCC
Q 047170 48 FVICGCCKSP 57 (89)
Q Consensus 48 yV~C~~C~sP 57 (89)
-|.||.|+++
T Consensus 25 ~v~C~~C~~~ 34 (38)
T TIGR02098 25 KVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCE
Confidence 6899999974
No 73
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=43.05 E-value=17 Score=25.77 Aligned_cols=30 Identities=23% Similarity=0.348 Sum_probs=19.7
Q ss_pred HHHHHHhhcc-----ceecCCCCCCceeEEEcCcEEE
Q 047170 38 SKYIEGILHK-----FVICGCCKSPDTILTNGNHLFF 69 (89)
Q Consensus 38 ~~~i~~~L~~-----yV~C~~C~sPdT~L~k~~rl~~ 69 (89)
.+.|.++|.. ---||.|+.|=-. |++++|-
T Consensus 13 ~k~iA~lLl~GAkML~~hCp~Cg~PLF~--KdG~v~C 47 (131)
T COG1645 13 VKKIAELLLQGAKMLAKHCPKCGTPLFR--KDGEVFC 47 (131)
T ss_pred HHHHHHHHHhhhHHHHhhCcccCCccee--eCCeEEC
Confidence 3566666666 5568888888555 6666653
No 74
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=42.74 E-value=16 Score=22.61 Aligned_cols=18 Identities=17% Similarity=0.475 Sum_probs=14.6
Q ss_pred ceecCCCCCCceeEEEcC
Q 047170 48 FVICGCCKSPDTILTNGN 65 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k~~ 65 (89)
-|.||.|++..|.+-.-.
T Consensus 11 ~VkCp~C~n~q~vFsha~ 28 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHAS 28 (59)
T ss_pred EEECCCCCCeEEEEecCC
Confidence 689999999888777643
No 75
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=42.44 E-value=22 Score=19.97 Aligned_cols=14 Identities=21% Similarity=0.159 Sum_probs=9.9
Q ss_pred ceecCCCCCCceeE
Q 047170 48 FVICGCCKSPDTIL 61 (89)
Q Consensus 48 yV~C~~C~sPdT~L 61 (89)
-+.||.|++|-..-
T Consensus 21 ~~~Cp~CG~~~~~~ 34 (46)
T PRK00398 21 GVRCPYCGYRILFK 34 (46)
T ss_pred ceECCCCCCeEEEc
Confidence 36899999865543
No 76
>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=41.59 E-value=9.2 Score=22.21 Aligned_cols=9 Identities=33% Similarity=0.807 Sum_probs=4.9
Q ss_pred eecCCCCCC
Q 047170 49 VICGCCKSP 57 (89)
Q Consensus 49 V~C~~C~sP 57 (89)
-.||.|++|
T Consensus 21 ~~CPlC~r~ 29 (54)
T PF04423_consen 21 GCCPLCGRP 29 (54)
T ss_dssp EE-TTT--E
T ss_pred CcCCCCCCC
Confidence 389999986
No 77
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=41.00 E-value=14 Score=25.57 Aligned_cols=18 Identities=39% Similarity=0.813 Sum_probs=13.1
Q ss_pred HHHHhhcc-----ceecCCCCCC
Q 047170 40 YIEGILHK-----FVICGCCKSP 57 (89)
Q Consensus 40 ~i~~~L~~-----yV~C~~C~sP 57 (89)
+|+..|++ |.+|-.|+-|
T Consensus 67 ~i~~al~rIe~gtYG~Ce~cG~~ 89 (120)
T COG1734 67 KIESALDRIEEGTYGICEECGEP 89 (120)
T ss_pred HHHHHHHHHHcCCccchhccCCc
Confidence 44455554 9999999975
No 78
>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=40.52 E-value=11 Score=19.98 Aligned_cols=14 Identities=21% Similarity=0.710 Sum_probs=10.3
Q ss_pred eecCCCCCCceeEE
Q 047170 49 VICGCCKSPDTILT 62 (89)
Q Consensus 49 V~C~~C~sPdT~L~ 62 (89)
-.||.|+.|-..++
T Consensus 18 ~~CP~Cg~~~~~F~ 31 (33)
T cd00350 18 WVCPVCGAPKDKFE 31 (33)
T ss_pred CcCcCCCCcHHHcE
Confidence 37999998766554
No 79
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=40.49 E-value=14 Score=20.88 Aligned_cols=19 Identities=26% Similarity=0.406 Sum_probs=14.0
Q ss_pred ccceecCCCCCCceeEEEc
Q 047170 46 HKFVICGCCKSPDTILTNG 64 (89)
Q Consensus 46 ~~yV~C~~C~sPdT~L~k~ 64 (89)
...|.|+.|+++=+.-.+.
T Consensus 3 ~g~l~C~~CG~~m~~~~~~ 21 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRRKRK 21 (58)
T ss_pred CCcEEcccCCcEeEEEECC
Confidence 3478999999987765443
No 80
>PF14376 Haem_bd: Haem-binding domain
Probab=39.59 E-value=11 Score=26.07 Aligned_cols=24 Identities=29% Similarity=0.401 Sum_probs=18.7
Q ss_pred CHHHHHHhhccceecCCCCCCceeEE
Q 047170 37 ASKYIEGILHKFVICGCCKSPDTILT 62 (89)
Q Consensus 37 ~~~~i~~~L~~yV~C~~C~sPdT~L~ 62 (89)
.++.++.+|++ -|.-|+|++|.+-
T Consensus 32 ~p~~v~~il~~--~CydCHSn~T~~P 55 (137)
T PF14376_consen 32 APEEVKIILKN--SCYDCHSNNTRYP 55 (137)
T ss_pred chHHHHHHHHc--cccccCCCCCCCc
Confidence 46667777765 7999999999874
No 81
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=38.78 E-value=49 Score=16.84 Aligned_cols=21 Identities=14% Similarity=0.142 Sum_probs=12.4
Q ss_pred ecCCCCCCceeEEEcCcEEEE
Q 047170 50 ICGCCKSPDTILTNGNHLFFL 70 (89)
Q Consensus 50 ~C~~C~sPdT~L~k~~rl~~l 70 (89)
.|+-|+++-+.+...++-.++
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~ 23 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYL 23 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE
T ss_pred cCccCCCcceEeEecCCCCeE
Confidence 588999988777776655443
No 82
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.64 E-value=14 Score=23.37 Aligned_cols=13 Identities=31% Similarity=0.549 Sum_probs=10.2
Q ss_pred ceecCCCCCCcee
Q 047170 48 FVICGCCKSPDTI 60 (89)
Q Consensus 48 yV~C~~C~sPdT~ 60 (89)
-|-||+|+.|-.-
T Consensus 7 ~v~CP~Cgkpv~w 19 (65)
T COG3024 7 TVPCPTCGKPVVW 19 (65)
T ss_pred cccCCCCCCcccc
Confidence 5889999987543
No 83
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=38.63 E-value=17 Score=21.97 Aligned_cols=11 Identities=36% Similarity=0.893 Sum_probs=9.4
Q ss_pred ceecCCCCCCc
Q 047170 48 FVICGCCKSPD 58 (89)
Q Consensus 48 yV~C~~C~sPd 58 (89)
++.||.|+++-
T Consensus 27 l~~C~~CG~~~ 37 (57)
T PRK12286 27 LVECPNCGEPK 37 (57)
T ss_pred ceECCCCCCcc
Confidence 89999999863
No 84
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=38.47 E-value=14 Score=18.85 Aligned_cols=10 Identities=30% Similarity=0.697 Sum_probs=8.0
Q ss_pred ceecCCCCCC
Q 047170 48 FVICGCCKSP 57 (89)
Q Consensus 48 yV~C~~C~sP 57 (89)
+|.||.|...
T Consensus 1 ~v~CPiC~~~ 10 (26)
T smart00734 1 LVQCPVCFRE 10 (26)
T ss_pred CCcCCCCcCc
Confidence 4889999864
No 85
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=38.14 E-value=21 Score=26.45 Aligned_cols=15 Identities=27% Similarity=0.414 Sum_probs=10.8
Q ss_pred ceecCCCCCCceeEEE
Q 047170 48 FVICGCCKSPDTILTN 63 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k 63 (89)
.=.||.|+|| |.+..
T Consensus 153 ~~~Cp~CG~~-~~~~~ 167 (177)
T COG1439 153 KDFCPICGSP-LKRKR 167 (177)
T ss_pred CCcCCCCCCc-eEEee
Confidence 3479999999 55543
No 86
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=36.33 E-value=23 Score=27.28 Aligned_cols=20 Identities=25% Similarity=0.562 Sum_probs=14.2
Q ss_pred CHHHHHHhhcc--ceecCCCCC
Q 047170 37 ASKYIEGILHK--FVICGCCKS 56 (89)
Q Consensus 37 ~~~~i~~~L~~--yV~C~~C~s 56 (89)
++.-+..+..+ -|.||.|+.
T Consensus 208 ~~~~~~~V~~~d~iv~CP~CgR 229 (239)
T COG1579 208 PSQTLSKVRKKDEIVFCPYCGR 229 (239)
T ss_pred cHHHHHHHhcCCCCccCCccch
Confidence 44555555555 999999996
No 87
>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=36.25 E-value=17 Score=29.83 Aligned_cols=15 Identities=27% Similarity=0.399 Sum_probs=13.3
Q ss_pred ceecCCCCCCceeEE
Q 047170 48 FVICGCCKSPDTILT 62 (89)
Q Consensus 48 yV~C~~C~sPdT~L~ 62 (89)
+-.||.|++++|.-.
T Consensus 21 ~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 21 QGKCPACHAWNTITE 35 (454)
T ss_pred cEECcCCCCccccch
Confidence 679999999999876
No 88
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=36.16 E-value=19 Score=23.79 Aligned_cols=18 Identities=22% Similarity=0.541 Sum_probs=13.3
Q ss_pred HHHHhhcc-----ceecCCCCCC
Q 047170 40 YIEGILHK-----FVICGCCKSP 57 (89)
Q Consensus 40 ~i~~~L~~-----yV~C~~C~sP 57 (89)
+|+..|.+ |-.|-.|+.|
T Consensus 67 ~i~~AL~ri~~g~yG~C~~Cge~ 89 (110)
T TIGR02420 67 KIDEALKRIEDGEYGYCEECGEE 89 (110)
T ss_pred HHHHHHHHHhCCCCCchhccCCc
Confidence 44555555 9999999975
No 89
>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=36.14 E-value=15 Score=19.81 Aligned_cols=13 Identities=23% Similarity=0.667 Sum_probs=10.1
Q ss_pred ecCCCCCCceeEE
Q 047170 50 ICGCCKSPDTILT 62 (89)
Q Consensus 50 ~C~~C~sPdT~L~ 62 (89)
.||.|+.|-..++
T Consensus 20 ~CP~Cg~~~~~F~ 32 (34)
T cd00729 20 KCPICGAPKEKFE 32 (34)
T ss_pred cCcCCCCchHHcE
Confidence 7999999866554
No 90
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=35.48 E-value=48 Score=22.18 Aligned_cols=32 Identities=19% Similarity=0.243 Sum_probs=21.2
Q ss_pred HHHHHHhhccceecCCCCCCceeEEEcCcEEEE
Q 047170 38 SKYIEGILHKFVICGCCKSPDTILTNGNHLFFL 70 (89)
Q Consensus 38 ~~~i~~~L~~yV~C~~C~sPdT~L~k~~rl~~l 70 (89)
-++|+...+.--.||.|+++ |.--....+|..
T Consensus 25 v~~ie~~~~~~~~Cp~C~~~-~VkR~a~GIW~C 56 (89)
T COG1997 25 VKEIEAQQRAKHVCPFCGRT-TVKRIATGIWKC 56 (89)
T ss_pred HHHHHHHHhcCCcCCCCCCc-ceeeeccCeEEc
Confidence 34566666665579999999 433334577776
No 91
>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=35.43 E-value=21 Score=21.70 Aligned_cols=16 Identities=25% Similarity=0.492 Sum_probs=10.5
Q ss_pred ceecCCCCCCceeEEE
Q 047170 48 FVICGCCKSPDTILTN 63 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k 63 (89)
-|.||.|.+..|.+-.
T Consensus 7 ~VkCp~C~~~q~vFSh 22 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSH 22 (55)
T ss_dssp EEE-TTT-SEEEEETT
T ss_pred EEECCCCCCeeEEEec
Confidence 4899999997776654
No 92
>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=35.36 E-value=18 Score=19.32 Aligned_cols=11 Identities=27% Similarity=0.703 Sum_probs=5.6
Q ss_pred eecCCCCCCce
Q 047170 49 VICGCCKSPDT 59 (89)
Q Consensus 49 V~C~~C~sPdT 59 (89)
..||.|+|.|.
T Consensus 26 ~~Cp~C~s~~l 36 (37)
T PF12172_consen 26 PVCPHCGSDEL 36 (37)
T ss_dssp SEETTTT----
T ss_pred cCCCCcCcccc
Confidence 57888887654
No 93
>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=35.11 E-value=21 Score=21.36 Aligned_cols=10 Identities=30% Similarity=0.780 Sum_probs=8.9
Q ss_pred ceecCCCCCC
Q 047170 48 FVICGCCKSP 57 (89)
Q Consensus 48 yV~C~~C~sP 57 (89)
.|.|+.|+++
T Consensus 26 l~~C~~cG~~ 35 (55)
T TIGR01031 26 LVVCPNCGEF 35 (55)
T ss_pred ceECCCCCCc
Confidence 8999999975
No 94
>COG0766 MurA UDP-N-acetylglucosamine enolpyruvyl transferase [Cell envelope biogenesis, outer membrane]
Probab=34.90 E-value=50 Score=27.62 Aligned_cols=33 Identities=33% Similarity=0.590 Sum_probs=27.8
Q ss_pred CCCcccHhHHHHHHHhhccceeecCCceEEEEee
Q 047170 2 HRQPENVDVVTFLLSEMGTSGSLDGQQHLVVKGR 35 (89)
Q Consensus 2 ~R~p~h~~v~kyl~~ELgt~g~id~~~rlii~G~ 35 (89)
-|+||-+|+..|| +.+|+.-+=.+.+++.|.|.
T Consensus 188 A~EPEIvDLa~~L-n~MGA~I~GaGT~~I~I~GV 220 (421)
T COG0766 188 AREPEIVDLANFL-NKMGAKIEGAGTSTITIEGV 220 (421)
T ss_pred ccCchHHHHHHHH-HHcCCeeEEcCCCeEEEecc
Confidence 4899999999976 56899888888889999984
No 95
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=34.61 E-value=17 Score=20.18 Aligned_cols=8 Identities=25% Similarity=0.580 Sum_probs=6.6
Q ss_pred eecCCCCC
Q 047170 49 VICGCCKS 56 (89)
Q Consensus 49 V~C~~C~s 56 (89)
+.||.|++
T Consensus 2 ~~CP~Cg~ 9 (39)
T PF01396_consen 2 EKCPKCGG 9 (39)
T ss_pred cCCCCCCc
Confidence 47999995
No 96
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=34.55 E-value=21 Score=20.47 Aligned_cols=9 Identities=33% Similarity=0.634 Sum_probs=8.2
Q ss_pred ceecCCCCC
Q 047170 48 FVICGCCKS 56 (89)
Q Consensus 48 yV~C~~C~s 56 (89)
=|.||.|++
T Consensus 19 ~irC~~CG~ 27 (44)
T smart00659 19 VVRCRECGY 27 (44)
T ss_pred ceECCCCCc
Confidence 689999998
No 97
>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=34.52 E-value=20 Score=19.03 Aligned_cols=10 Identities=20% Similarity=0.617 Sum_probs=8.5
Q ss_pred ceecCCCCCC
Q 047170 48 FVICGCCKSP 57 (89)
Q Consensus 48 yV~C~~C~sP 57 (89)
-+.||.|+++
T Consensus 26 ~~~CP~Cg~~ 35 (41)
T smart00834 26 LATCPECGGD 35 (41)
T ss_pred CCCCCCCCCc
Confidence 6789999994
No 98
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=34.38 E-value=19 Score=20.57 Aligned_cols=11 Identities=36% Similarity=0.658 Sum_probs=8.4
Q ss_pred ecCCCCCCcee
Q 047170 50 ICGCCKSPDTI 60 (89)
Q Consensus 50 ~C~~C~sPdT~ 60 (89)
.||.|+++-..
T Consensus 1 ~CP~Cg~~a~i 11 (47)
T PF04606_consen 1 RCPHCGSKARI 11 (47)
T ss_pred CcCCCCCeeEE
Confidence 39999997643
No 99
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=34.01 E-value=27 Score=19.15 Aligned_cols=10 Identities=40% Similarity=0.836 Sum_probs=8.5
Q ss_pred eecCCCCCCc
Q 047170 49 VICGCCKSPD 58 (89)
Q Consensus 49 V~C~~C~sPd 58 (89)
..||.|+++.
T Consensus 3 ~~Cp~Cg~~~ 12 (47)
T PF14690_consen 3 PRCPHCGSPS 12 (47)
T ss_pred ccCCCcCCCc
Confidence 3699999988
No 100
>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=33.36 E-value=17 Score=19.47 Aligned_cols=11 Identities=36% Similarity=0.528 Sum_probs=3.6
Q ss_pred ecCCCCCCcee
Q 047170 50 ICGCCKSPDTI 60 (89)
Q Consensus 50 ~C~~C~sPdT~ 60 (89)
.||.|+|..|-
T Consensus 4 ~Cp~C~se~~y 14 (30)
T PF08274_consen 4 KCPLCGSEYTY 14 (30)
T ss_dssp --TTT-----E
T ss_pred CCCCCCCccee
Confidence 69999998886
No 101
>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=32.72 E-value=26 Score=29.46 Aligned_cols=13 Identities=31% Similarity=0.521 Sum_probs=9.5
Q ss_pred ecCCCCCCceeEE
Q 047170 50 ICGCCKSPDTILT 62 (89)
Q Consensus 50 ~C~~C~sPdT~L~ 62 (89)
.||.|+|.|+...
T Consensus 534 ~CP~CGs~~~~~~ 546 (555)
T cd01675 534 KCPKCGSEDVEVI 546 (555)
T ss_pred CCcCCCCcCceEE
Confidence 6888988875544
No 102
>PRK00115 hemE uroporphyrinogen decarboxylase; Validated
Probab=32.60 E-value=18 Score=28.02 Aligned_cols=15 Identities=13% Similarity=-0.011 Sum_probs=12.1
Q ss_pred ceecCCCCC-CceeEE
Q 047170 48 FVICGCCKS-PDTILT 62 (89)
Q Consensus 48 yV~C~~C~s-PdT~L~ 62 (89)
|++.+.|+- |+|.++
T Consensus 317 fIl~~Gc~i~~~tp~e 332 (346)
T PRK00115 317 HIFNLGHGILPETPPE 332 (346)
T ss_pred eeeecCCcCCCCcCHH
Confidence 999999995 577654
No 103
>PRK12496 hypothetical protein; Provisional
Probab=32.48 E-value=19 Score=25.66 Aligned_cols=9 Identities=44% Similarity=1.110 Sum_probs=6.9
Q ss_pred ecCCCCCCc
Q 047170 50 ICGCCKSPD 58 (89)
Q Consensus 50 ~C~~C~sPd 58 (89)
.||.||||=
T Consensus 145 ~C~~CG~~~ 153 (164)
T PRK12496 145 VCEICGSPV 153 (164)
T ss_pred cCCCCCChh
Confidence 488899873
No 104
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=32.42 E-value=34 Score=23.63 Aligned_cols=9 Identities=33% Similarity=0.932 Sum_probs=8.0
Q ss_pred ceecCCCCC
Q 047170 48 FVICGCCKS 56 (89)
Q Consensus 48 yV~C~~C~s 56 (89)
|..||.|+.
T Consensus 99 ~Y~Cp~C~~ 107 (147)
T smart00531 99 YYKCPNCQS 107 (147)
T ss_pred EEECcCCCC
Confidence 889999984
No 105
>PF05315 ICEA: ICEA Protein; InterPro: IPR007979 This family consists of several ICEA proteins from Helicobacter pylori, infection of which causes gastritis and peptic ulcer disease, and the bacteria is classified as a definite carcinogen of gastric cancer. ICEA1 is speculated to be associated with peptic ulcer disease and may have endonuclease activity [].
Probab=31.69 E-value=18 Score=27.84 Aligned_cols=56 Identities=18% Similarity=0.323 Sum_probs=39.8
Q ss_pred CCcccHhHHHHHHHhhcc----ceeecCCceEEEEeecCHHHHHHhhcc----------ceecCCCCC-CceeEEE
Q 047170 3 RQPENVDVVTFLLSEMGT----SGSLDGQQHLVVKGRFASKYIEGILHK----------FVICGCCKS-PDTILTN 63 (89)
Q Consensus 3 R~p~h~~v~kyl~~ELgt----~g~id~~~rlii~G~~~~~~i~~~L~~----------yV~C~~C~s-PdT~L~k 63 (89)
|.... +.|++--|++- ..+|| ++.+||--+...++.-|++ -|+|..|++ ..|.|..
T Consensus 46 R~~Ss--Lak~y~lEfdk~~~~gnsId---~IRLnG~n~~~~fnq~Ir~dIk~~yk~q~Cvm~g~~g~sent~iei 116 (230)
T PF05315_consen 46 RSSSS--LAKEYILEFDKRQTSGNSID---RIRLNGFNTEKVFNQNIRQDIKNYYKQQCCVMCGVRGNSENTKIEI 116 (230)
T ss_pred CCchH--HHHHhhcccccccCCCccHH---HHHHcCcCchhhhhhHHHHHHHHHHHhcCeeeecccCCCccceeee
Confidence 45555 77777666653 33445 8888998888777777766 799999996 5577775
No 106
>PRK08477 biotin--protein ligase; Provisional
Probab=31.48 E-value=29 Score=25.72 Aligned_cols=19 Identities=11% Similarity=0.158 Sum_probs=15.3
Q ss_pred hccceeecCCceEEEEeec
Q 047170 18 MGTSGSLDGQQHLVVKGRF 36 (89)
Q Consensus 18 Lgt~g~id~~~rlii~G~~ 36 (89)
-|+.-.||++|+|+|+|+-
T Consensus 188 ~g~a~~I~~~G~L~v~~~~ 206 (211)
T PRK08477 188 SLKDAELLEDGSILINGKK 206 (211)
T ss_pred EEEEeeECCCCeEEECCEE
Confidence 3566778999999999974
No 107
>PF07744 SPOC: SPOC domain; InterPro: IPR012921 Spen (split end) proteins regulate the expression of key transcriptional effectors in diverse signalling pathways. They are large proteins characterised by N-terminal RNA-binding motifs and a highly conserved C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The function of the SPOC domain is unknown, but the SPOC domain of the SHARP Spen protein has been implicated in the interaction of SHARP with the SMRT/NcoR corepressor, where SHARP plays an essential role in the repressor complex []. The SPOC domain is folded into a single compact domain consisting of a beta-barrel with seven strands framed by six alpha helices. A number of deep grooves and clefts in the surface, plus two nonpolar loops, render the SPOC domain well suited to protein-protein interactions; most of the conserved residues occur on the protein surface rather than in the core. Other proteins containing a SPOC domain include drosophila Split ends, which promotes sclerite development in the head and restricts it in the thorax, and mouse MINT (homologue of SHARP), which is involved in skeletal and neuronal development via its repression of Msx2.; PDB: 1OW1_A.
Probab=31.29 E-value=29 Score=22.22 Aligned_cols=31 Identities=19% Similarity=0.300 Sum_probs=20.9
Q ss_pred CceEEEEeecCHHHHHHhhcc-------ceecCCCCCC
Q 047170 27 QQHLVVKGRFASKYIEGILHK-------FVICGCCKSP 57 (89)
Q Consensus 27 ~~rlii~G~~~~~~i~~~L~~-------yV~C~~C~sP 57 (89)
-..+.+.||.+.+.+++.|.+ +|+|-.+.+|
T Consensus 38 p~~i~i~gRl~~~~~~~yl~~i~~s~~~~v~v~~~~~~ 75 (119)
T PF07744_consen 38 PKKIDIRGRLDPEKVWDYLRQIRKSRSKDVCVVALSSP 75 (119)
T ss_dssp -EEE-EEEE-SHHHHHHHHHHTSSTTT-EEEEEEE-SS
T ss_pred CcEEEEEeecCHHHHHHHHHhcccCCCceEEEEEEcCC
Confidence 348899999999999999876 5555555444
No 108
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=31.19 E-value=33 Score=23.66 Aligned_cols=34 Identities=15% Similarity=0.461 Sum_probs=24.0
Q ss_pred EEEEeecCHHHHHHhhcc----------ceecCCCCCCceeEEE
Q 047170 30 LVVKGRFASKYIEGILHK----------FVICGCCKSPDTILTN 63 (89)
Q Consensus 30 lii~G~~~~~~i~~~L~~----------yV~C~~C~sPdT~L~k 63 (89)
+.+...-..+++..+++. |-.|+.|++|=..+.+
T Consensus 63 ~li~~~~~~~QL~ev~~~~~l~~~~~~~~sRC~~CN~~L~~v~~ 106 (147)
T PF01927_consen 63 ILIRSDDPEEQLREVLERFGLKLRLDPIFSRCPKCNGPLRPVSK 106 (147)
T ss_pred EEEcCCCHHHHHHHHHHHcCCccccCCCCCccCCCCcEeeechh
Confidence 445666667788888766 7899999995444444
No 109
>COG1964 Predicted Fe-S oxidoreductases [General function prediction only]
Probab=31.02 E-value=30 Score=29.29 Aligned_cols=23 Identities=13% Similarity=0.481 Sum_probs=20.2
Q ss_pred ceecCCCCC--CceeEEEcCcEEEE
Q 047170 48 FVICGCCKS--PDTILTNGNHLFFL 70 (89)
Q Consensus 48 yV~C~~C~s--PdT~L~k~~rl~~l 70 (89)
.-+||+|.. |-+..++++++|+-
T Consensus 16 ~SlCP~C~~~v~A~v~e~~gkv~i~ 40 (475)
T COG1964 16 KSLCPECLRVVPAVVFEEDGKVWIR 40 (475)
T ss_pred hccChhhhccccceEEecCCeEEEE
Confidence 779999996 88888888999987
No 110
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=30.90 E-value=21 Score=32.07 Aligned_cols=12 Identities=25% Similarity=0.335 Sum_probs=9.2
Q ss_pred ceecCCCCCCce
Q 047170 48 FVICGCCKSPDT 59 (89)
Q Consensus 48 yV~C~~C~sPdT 59 (89)
=--||.|||++=
T Consensus 503 GePCPVCGS~~H 514 (1047)
T PRK10246 503 GQPCPLCGSTSH 514 (1047)
T ss_pred CCCcCCCCcccC
Confidence 667999999653
No 111
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=30.59 E-value=38 Score=21.54 Aligned_cols=13 Identities=15% Similarity=0.409 Sum_probs=10.0
Q ss_pred ecCCCCCCceeEEE
Q 047170 50 ICGCCKSPDTILTN 63 (89)
Q Consensus 50 ~C~~C~sPdT~L~k 63 (89)
.||.|++++ .+.+
T Consensus 3 ~CP~Cg~~a-~irt 15 (72)
T PRK09678 3 HCPLCQHAA-HART 15 (72)
T ss_pred cCCCCCCcc-EEEE
Confidence 599999999 4443
No 112
>PLN02433 uroporphyrinogen decarboxylase
Probab=30.47 E-value=25 Score=27.32 Aligned_cols=44 Identities=23% Similarity=0.239 Sum_probs=24.9
Q ss_pred HHHhhccceeecCCceEEEEeecCHHHHH----Hhhcc-----ceecCCCCC-CceeEE
Q 047170 14 LLSEMGTSGSLDGQQHLVVKGRFASKYIE----GILHK-----FVICGCCKS-PDTILT 62 (89)
Q Consensus 14 l~~ELgt~g~id~~~rlii~G~~~~~~i~----~~L~~-----yV~C~~C~s-PdT~L~ 62 (89)
+....-.+|++|. ..++|. +++|+ ++|+. |++++.|+- |+|.++
T Consensus 272 ~g~~~~l~GNi~p---~ll~gt--~e~i~~~v~~~i~~~~~~g~Il~~Gc~i~~~tp~e 325 (345)
T PLN02433 272 LGSDVAVQGNVDP---AVLFGS--KEAIEKEVRDVVKKAGPQGHILNLGHGVLVGTPEE 325 (345)
T ss_pred hCCCeEEEeCCCc---hhhCCC--HHHHHHHHHHHHHHcCCCCeEEecCCCCCCCCCHH
Confidence 3333445666663 233453 34343 34443 899999996 588654
No 113
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=30.18 E-value=31 Score=30.12 Aligned_cols=20 Identities=25% Similarity=0.516 Sum_probs=16.0
Q ss_pred HHHHHHhhcc------ceecCCCCCC
Q 047170 38 SKYIEGILHK------FVICGCCKSP 57 (89)
Q Consensus 38 ~~~i~~~L~~------yV~C~~C~sP 57 (89)
...|++.+.. ||.||.|+..
T Consensus 211 ts~Ie~~y~~gd~rr~yvpCPHCGe~ 236 (611)
T COG5525 211 TTTIERAYNAGDQRRFYVPCPHCGEE 236 (611)
T ss_pred chHHHHHhhhccceeEEeeCCCCCch
Confidence 5677777766 9999999963
No 114
>PF14369 zf-RING_3: zinc-finger
Probab=29.64 E-value=24 Score=19.26 Aligned_cols=9 Identities=33% Similarity=0.678 Sum_probs=7.6
Q ss_pred ceecCCCCC
Q 047170 48 FVICGCCKS 56 (89)
Q Consensus 48 yV~C~~C~s 56 (89)
.|.||.|++
T Consensus 21 ~~~CP~C~~ 29 (35)
T PF14369_consen 21 DVACPRCHG 29 (35)
T ss_pred CcCCcCCCC
Confidence 568999997
No 115
>PRK11823 DNA repair protein RadA; Provisional
Probab=29.60 E-value=27 Score=28.46 Aligned_cols=15 Identities=20% Similarity=0.421 Sum_probs=13.6
Q ss_pred ceecCCCCCCceeEE
Q 047170 48 FVICGCCKSPDTILT 62 (89)
Q Consensus 48 yV~C~~C~sPdT~L~ 62 (89)
+-.||.|++++|.-+
T Consensus 21 ~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 21 LGRCPECGAWNTLVE 35 (446)
T ss_pred CeeCcCCCCccceee
Confidence 678999999999877
No 116
>PLN00209 ribosomal protein S27; Provisional
Probab=29.51 E-value=36 Score=22.63 Aligned_cols=19 Identities=21% Similarity=0.403 Sum_probs=15.6
Q ss_pred ceecCCCCCCceeEEEcCc
Q 047170 48 FVICGCCKSPDTILTNGNH 66 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k~~r 66 (89)
-|.||.|.+..|.+-.-..
T Consensus 36 ~VkCp~C~n~q~VFShA~t 54 (86)
T PLN00209 36 DVKCQGCFNITTVFSHSQT 54 (86)
T ss_pred EEECCCCCCeeEEEecCce
Confidence 7999999999888876543
No 117
>PRK01343 zinc-binding protein; Provisional
Probab=29.35 E-value=27 Score=21.46 Aligned_cols=12 Identities=33% Similarity=0.589 Sum_probs=10.0
Q ss_pred ceecCCCCCCce
Q 047170 48 FVICGCCKSPDT 59 (89)
Q Consensus 48 yV~C~~C~sPdT 59 (89)
-+.||.|+.|-+
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 578999999854
No 118
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=29.30 E-value=31 Score=24.71 Aligned_cols=18 Identities=44% Similarity=0.846 Sum_probs=13.3
Q ss_pred HHHHhhcc-----ceecCCCCCC
Q 047170 40 YIEGILHK-----FVICGCCKSP 57 (89)
Q Consensus 40 ~i~~~L~~-----yV~C~~C~sP 57 (89)
+|+..|.+ |-+|-.|+.|
T Consensus 73 ~Ie~AL~Ri~~G~YG~Ce~CGe~ 95 (159)
T TIGR02890 73 EIEHALQKIENGTYGICEVCGKP 95 (159)
T ss_pred HHHHHHHHHhCCCCCeecccCCc
Confidence 45555555 9999999974
No 119
>COG3303 NrfA Formate-dependent nitrite reductase, periplasmic cytochrome c552 subunit [Inorganic ion transport and metabolism]
Probab=29.13 E-value=23 Score=29.78 Aligned_cols=25 Identities=32% Similarity=0.526 Sum_probs=17.8
Q ss_pred HHHHHhhcc-----------ceecCCCCCCcee-EEE
Q 047170 39 KYIEGILHK-----------FVICGCCKSPDTI-LTN 63 (89)
Q Consensus 39 ~~i~~~L~~-----------yV~C~~C~sPdT~-L~k 63 (89)
.++.+.|+. ---|.+|+||||- |++
T Consensus 118 tDvr~tlRt~Ap~~a~~gp~pmACwsCkspdvprLI~ 154 (501)
T COG3303 118 TDVRETLRTGAPKTAEDGPQPMACWSCKSPDVPRLIQ 154 (501)
T ss_pred eeHHHHHhccCCCCcccCCCcceeecCCCCCchHHHH
Confidence 345666665 6789999999974 444
No 120
>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=29.04 E-value=26 Score=28.02 Aligned_cols=15 Identities=20% Similarity=0.408 Sum_probs=13.3
Q ss_pred ceecCCCCCCceeEE
Q 047170 48 FVICGCCKSPDTILT 62 (89)
Q Consensus 48 yV~C~~C~sPdT~L~ 62 (89)
+-.||.|+.++|.-+
T Consensus 14 ~g~cp~c~~w~~~~e 28 (372)
T cd01121 14 LGKCPECGEWNTLVE 28 (372)
T ss_pred cEECcCCCCceeeee
Confidence 668999999999876
No 121
>TIGR01463 mtaA_cmuA methyltransferase, MtaA/CmuA family. This subfamily is closely related to, yet is distinct from, uroporphyrinogen decarboxylase (EC 4.1.1.37). It includes two isozymes from Methanosarcina barkeri of methylcobalamin--coenzyme M methyltransferase. It also includes a chloromethane utilization protein, CmuA, which transfers the methyl group of chloromethane to a corrinoid protein.
Probab=28.98 E-value=19 Score=27.46 Aligned_cols=15 Identities=20% Similarity=0.073 Sum_probs=12.1
Q ss_pred ceecCCCCC-CceeEE
Q 047170 48 FVICGCCKS-PDTILT 62 (89)
Q Consensus 48 yV~C~~C~s-PdT~L~ 62 (89)
|++.+.|+- |+|.+.
T Consensus 311 ~Il~~gcgi~~~tp~e 326 (340)
T TIGR01463 311 DIVMPGCDIDWMTPLE 326 (340)
T ss_pred eEECCCCCCCCCCCHH
Confidence 999999996 677643
No 122
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=28.75 E-value=24 Score=21.56 Aligned_cols=10 Identities=40% Similarity=0.843 Sum_probs=5.4
Q ss_pred eecCCCCCCc
Q 047170 49 VICGCCKSPD 58 (89)
Q Consensus 49 V~C~~C~sPd 58 (89)
|.||.|+.+-
T Consensus 3 v~CP~C~k~~ 12 (57)
T PF03884_consen 3 VKCPICGKPV 12 (57)
T ss_dssp EE-TTT--EE
T ss_pred ccCCCCCCee
Confidence 7899999753
No 123
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=28.65 E-value=38 Score=22.44 Aligned_cols=19 Identities=21% Similarity=0.441 Sum_probs=15.7
Q ss_pred ceecCCCCCCceeEEEcCc
Q 047170 48 FVICGCCKSPDTILTNGNH 66 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k~~r 66 (89)
-|.||.|.+.-|.+-.-..
T Consensus 35 ~VkCp~C~n~q~VFShA~t 53 (85)
T PTZ00083 35 DVKCPGCSQITTVFSHAQT 53 (85)
T ss_pred EEECCCCCCeeEEEecCce
Confidence 7999999999888876543
No 124
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=28.64 E-value=34 Score=24.35 Aligned_cols=19 Identities=42% Similarity=0.658 Sum_probs=14.4
Q ss_pred HHHHHhhcc-----ceecCCCCCC
Q 047170 39 KYIEGILHK-----FVICGCCKSP 57 (89)
Q Consensus 39 ~~i~~~L~~-----yV~C~~C~sP 57 (89)
..|+..|.+ |-.|-.|+-|
T Consensus 97 ~~I~~AL~Ri~~gtYG~Ce~CGe~ 120 (151)
T PRK10778 97 KKIEKTLKKVEDEDFGYCESCGVE 120 (151)
T ss_pred HHHHHHHHHHhCCCCceeccCCCc
Confidence 456666655 9999999975
No 125
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.38 E-value=42 Score=23.33 Aligned_cols=15 Identities=20% Similarity=0.581 Sum_probs=10.4
Q ss_pred ceecCCCCCC-ceeEE
Q 047170 48 FVICGCCKSP-DTILT 62 (89)
Q Consensus 48 yV~C~~C~sP-dT~L~ 62 (89)
+-.||.|++| |..++
T Consensus 49 ~t~CP~Cg~~~e~~fv 64 (115)
T COG1885 49 STSCPKCGEPFESAFV 64 (115)
T ss_pred cccCCCCCCccceeEE
Confidence 5689999986 34443
No 126
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=28.19 E-value=25 Score=17.68 Aligned_cols=9 Identities=22% Similarity=0.803 Sum_probs=7.0
Q ss_pred eecCCCCCC
Q 047170 49 VICGCCKSP 57 (89)
Q Consensus 49 V~C~~C~sP 57 (89)
+.||.|+.+
T Consensus 3 ~~Cp~Cg~~ 11 (26)
T PF13248_consen 3 MFCPNCGAE 11 (26)
T ss_pred CCCcccCCc
Confidence 579999874
No 127
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=27.74 E-value=29 Score=21.66 Aligned_cols=11 Identities=36% Similarity=0.697 Sum_probs=9.0
Q ss_pred ceecCCCCCCc
Q 047170 48 FVICGCCKSPD 58 (89)
Q Consensus 48 yV~C~~C~sPd 58 (89)
-|.||.|+.|-
T Consensus 6 ~v~CP~C~k~~ 16 (62)
T PRK00418 6 TVNCPTCGKPV 16 (62)
T ss_pred cccCCCCCCcc
Confidence 58899999873
No 128
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=27.67 E-value=34 Score=18.57 Aligned_cols=15 Identities=33% Similarity=0.868 Sum_probs=10.2
Q ss_pred eecCCCCC----CceeEEE
Q 047170 49 VICGCCKS----PDTILTN 63 (89)
Q Consensus 49 V~C~~C~s----PdT~L~k 63 (89)
+.||.|+. ||..|-.
T Consensus 3 i~CP~C~~~f~v~~~~l~~ 21 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPA 21 (37)
T ss_pred EECCCCCceEEcCHHHccc
Confidence 68999985 5555543
No 129
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=27.59 E-value=50 Score=18.77 Aligned_cols=13 Identities=23% Similarity=0.273 Sum_probs=8.8
Q ss_pred ceecCCCCCCcee
Q 047170 48 FVICGCCKSPDTI 60 (89)
Q Consensus 48 yV~C~~C~sPdT~ 60 (89)
--.||.|+.|=-+
T Consensus 17 ~~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 17 DEHCPDCGTPLMR 29 (41)
T ss_pred cCccCCCCCeeEE
Confidence 4569999766444
No 130
>PF13098 Thioredoxin_2: Thioredoxin-like domain; PDB: 1T3B_A 2L57_A 1EEJ_B 1TJD_A 1JZD_B 1JZO_A 1G0T_B 3GV1_A 1V58_A 2H0H_A ....
Probab=27.53 E-value=86 Score=19.31 Aligned_cols=33 Identities=18% Similarity=0.335 Sum_probs=19.4
Q ss_pred HHHHhhccce---ee--cCCceE--EEEeecCHHHHHHhh
Q 047170 13 FLLSEMGTSG---SL--DGQQHL--VVKGRFASKYIEGIL 45 (89)
Q Consensus 13 yl~~ELgt~g---~i--d~~~rl--ii~G~~~~~~i~~~L 45 (89)
-|..++|..| -+ |++|+. ++.|-.++++|.++|
T Consensus 73 ~l~~~~~v~gtPt~~~~d~~G~~v~~~~G~~~~~~l~~~L 112 (112)
T PF13098_consen 73 ELAQRYGVNGTPTIVFLDKDGKIVYRIPGYLSPEELLKML 112 (112)
T ss_dssp HHHHHTT--SSSEEEECTTTSCEEEEEESS--HHHHHHHH
T ss_pred HHHHHcCCCccCEEEEEcCCCCEEEEecCCCCHHHHHhhC
Confidence 3555665544 33 666664 468999999999876
No 131
>KOG3816 consensus Cell differentiation regulator of the Headcase family [Signal transduction mechanisms]
Probab=27.52 E-value=25 Score=29.69 Aligned_cols=16 Identities=31% Similarity=0.667 Sum_probs=14.8
Q ss_pred ceecCCCCCCceeEEE
Q 047170 48 FVICGCCKSPDTILTN 63 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k 63 (89)
-++||.|+.-||.++|
T Consensus 500 ~~~cP~c~~~d~hfvk 515 (526)
T KOG3816|consen 500 LRICPSCKLADRHFVK 515 (526)
T ss_pred ccccCCcCcccccccC
Confidence 7999999999999886
No 132
>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=27.46 E-value=28 Score=29.51 Aligned_cols=13 Identities=31% Similarity=0.491 Sum_probs=9.5
Q ss_pred ecCCCCCCceeEE
Q 047170 50 ICGCCKSPDTILT 62 (89)
Q Consensus 50 ~C~~C~sPdT~L~ 62 (89)
.||.|+|.|....
T Consensus 540 ~CP~Cgs~~~~~~ 552 (579)
T TIGR02487 540 KCPKCGSHDIEVI 552 (579)
T ss_pred cCcCCCCccceeh
Confidence 6999999874443
No 133
>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=26.76 E-value=39 Score=29.10 Aligned_cols=13 Identities=23% Similarity=0.439 Sum_probs=8.7
Q ss_pred ecCCCCCCceeEE
Q 047170 50 ICGCCKSPDTILT 62 (89)
Q Consensus 50 ~C~~C~sPdT~L~ 62 (89)
.||.|+|.+++..
T Consensus 548 ~CP~CGs~~~ev~ 560 (586)
T TIGR02827 548 RCPVCGSANIDYG 560 (586)
T ss_pred cCcCCCCccceEE
Confidence 6888887665443
No 134
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=26.74 E-value=41 Score=20.30 Aligned_cols=13 Identities=38% Similarity=0.961 Sum_probs=9.0
Q ss_pred hccceecCCCCCC
Q 047170 45 LHKFVICGCCKSP 57 (89)
Q Consensus 45 L~~yV~C~~C~sP 57 (89)
+.++..||.|++|
T Consensus 4 llniL~Cp~ck~p 16 (68)
T PF03966_consen 4 LLNILACPVCKGP 16 (68)
T ss_dssp GCGTBB-TTTSSB
T ss_pred HHhhhcCCCCCCc
Confidence 3447899999994
No 135
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=26.52 E-value=29 Score=24.48 Aligned_cols=14 Identities=29% Similarity=0.757 Sum_probs=10.4
Q ss_pred ceecCCCCCCceeE
Q 047170 48 FVICGCCKSPDTIL 61 (89)
Q Consensus 48 yV~C~~C~sPdT~L 61 (89)
||.|+.|+..-=.+
T Consensus 110 fv~C~~C~Gs~k~~ 123 (147)
T cd03031 110 FVPCSECNGSCKVF 123 (147)
T ss_pred eEECCCCCCcceEE
Confidence 99999998654333
No 136
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=26.31 E-value=31 Score=18.73 Aligned_cols=8 Identities=25% Similarity=0.704 Sum_probs=6.5
Q ss_pred ecCCCCCC
Q 047170 50 ICGCCKSP 57 (89)
Q Consensus 50 ~C~~C~sP 57 (89)
-||.|+|-
T Consensus 3 FCp~C~nl 10 (35)
T PF02150_consen 3 FCPECGNL 10 (35)
T ss_dssp BETTTTSB
T ss_pred eCCCCCcc
Confidence 59999983
No 137
>PHA02776 E7 protein; Provisional
Probab=26.14 E-value=78 Score=21.40 Aligned_cols=25 Identities=12% Similarity=0.263 Sum_probs=18.9
Q ss_pred EeecCHHHHHHhhcc--ceecCCCCCC
Q 047170 33 KGRFASKYIEGILHK--FVICGCCKSP 57 (89)
Q Consensus 33 ~G~~~~~~i~~~L~~--yV~C~~C~sP 57 (89)
.+...-..+|.+|-. ...||.|..+
T Consensus 74 st~~~IR~lqqLLl~~L~ivCp~Ca~~ 100 (101)
T PHA02776 74 CTEPDIQELHNLLLGSLNIVCPICAPK 100 (101)
T ss_pred cChhhHHHHHHHhcCCeEEECCCCCCC
Confidence 345556778888866 8899999865
No 138
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=25.83 E-value=43 Score=19.23 Aligned_cols=9 Identities=44% Similarity=0.962 Sum_probs=8.2
Q ss_pred ceecCCCCC
Q 047170 48 FVICGCCKS 56 (89)
Q Consensus 48 yV~C~~C~s 56 (89)
.|.||.|.+
T Consensus 31 ~v~CPiC~~ 39 (54)
T PF05605_consen 31 NVVCPICSS 39 (54)
T ss_pred CccCCCchh
Confidence 899999986
No 139
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=25.51 E-value=1.5e+02 Score=17.36 Aligned_cols=34 Identities=9% Similarity=0.198 Sum_probs=26.3
Q ss_pred HHHHHHHhhccceeecCCceEEEEeecCHHHHHHh
Q 047170 10 VVTFLLSEMGTSGSLDGQQHLVVKGRFASKYIEGI 44 (89)
Q Consensus 10 v~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~ 44 (89)
.++-|..|.|+.-+++.++.+.|.|. +++.++..
T Consensus 23 ~ik~I~~~tg~~I~i~~~g~v~I~G~-~~~~v~~A 56 (61)
T cd02393 23 TIKKIIEETGVKIDIEDDGTVYIAAS-DKEAAEKA 56 (61)
T ss_pred HHHHHHHHHCCEEEeCCCCEEEEEeC-CHHHHHHH
Confidence 46789999999999988889999993 24445443
No 140
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=25.51 E-value=35 Score=19.05 Aligned_cols=14 Identities=21% Similarity=0.347 Sum_probs=10.4
Q ss_pred eecCCCCCCceeEE
Q 047170 49 VICGCCKSPDTILT 62 (89)
Q Consensus 49 V~C~~C~sPdT~L~ 62 (89)
+-||.|++-|.-=.
T Consensus 4 ~pCP~CGG~DrFr~ 17 (37)
T smart00778 4 GPCPNCGGSDRFRF 17 (37)
T ss_pred cCCCCCCCcccccc
Confidence 46999999875443
No 141
>PF02770 Acyl-CoA_dh_M: Acyl-CoA dehydrogenase, middle domain; InterPro: IPR006091 Acyl-CoA dehydrogenases (1.3.99.3 from EC) are a family of flavoproteins that catalyse the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with the concomitant reduction of enzyme-bound FAD. Different family members share a high sequence identity, catalytic mechanisms, and structural properties, but differ in the position of their catalytic bases and in their substrate binding specificity. Butyryl-CoA dehydrogenase [] prefers short chain substrates, medium chain- and long-chain acyl-CoA dehydrogenases prefer medium and long chain substrates, respectively, and Isovaleryl-CoA dehydrogenase [] prefers branched-chain substrates. The monomeric enzyme is folded into three domains of approximately equal size, where the N-terminal domain is all-alpha, the middle domain is an open (5,8) barrel, and the C-terminal domain is a four-helical bundle. The constituent families differ in the numbers of C-terminal domains. This entry represents the middle beta-barrel domain found in medium chain acyl-CoA dehydrogenases, as well as in the related peroxisomal acyl-CoA oxidase-II enzymes. Acyl-CoA oxidase (ACO; 1.3.3.6 from EC) catalyzes the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids [].; GO: 0003995 acyl-CoA dehydrogenase activity, 0055114 oxidation-reduction process; PDB: 3MDD_B 1UDY_C 3MDE_B 2UXW_A 3B96_A 1SIQ_A 1SIR_A 2R0N_A 2R0M_A 2D29_B ....
Probab=25.37 E-value=83 Score=17.76 Aligned_cols=19 Identities=26% Similarity=0.489 Sum_probs=13.1
Q ss_pred HhhccceeecCCceEEEEee
Q 047170 16 SEMGTSGSLDGQQHLVVKGR 35 (89)
Q Consensus 16 ~ELgt~g~id~~~rlii~G~ 35 (89)
..+.|.+..+++ .++|||.
T Consensus 14 ~~~~t~a~~~~~-~~~L~G~ 32 (52)
T PF02770_consen 14 AAVETTARRDGD-GYVLNGE 32 (52)
T ss_dssp GG-SSEEEEETT-EEEEEEE
T ss_pred ccCEEEeecccc-eEEEeeE
Confidence 345677777766 4999986
No 142
>cd03081 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidat
Probab=25.31 E-value=1.2e+02 Score=18.73 Aligned_cols=25 Identities=4% Similarity=0.217 Sum_probs=16.7
Q ss_pred hHHHHHHHhhccc-eeecCCceEEEE
Q 047170 9 DVVTFLLSEMGTS-GSLDGQQHLVVK 33 (89)
Q Consensus 9 ~v~kyl~~ELgt~-g~id~~~rlii~ 33 (89)
+|+++|..+||.. |....+|++.|.
T Consensus 19 ~ll~~l~~~l~~~~g~~~~dg~~~l~ 44 (80)
T cd03081 19 ALAAHIKARLGIDFHETTADGSVTLE 44 (80)
T ss_pred HHHHHHHHHhCCCCCCcCCCCeEEEE
Confidence 4899999999865 444444455544
No 143
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=25.02 E-value=1.4e+02 Score=16.80 Aligned_cols=34 Identities=12% Similarity=0.196 Sum_probs=27.3
Q ss_pred HHHHHHHhhccceeecCC---ceEEEEeecCHHHHHHhh
Q 047170 10 VVTFLLSEMGTSGSLDGQ---QHLVVKGRFASKYIEGIL 45 (89)
Q Consensus 10 v~kyl~~ELgt~g~id~~---~rlii~G~~~~~~i~~~L 45 (89)
.++-+..+.|+.-.++++ ..+.|.| +++.++...
T Consensus 21 ~i~~I~~~t~~~I~i~~~~~~~~v~I~G--~~~~v~~A~ 57 (60)
T PF00013_consen 21 NIKEIEEETGVKIQIPDDDERDIVTISG--SPEQVEKAK 57 (60)
T ss_dssp HHHHHHHHHTSEEEEESTTEEEEEEEEE--SHHHHHHHH
T ss_pred cHHHhhhhcCeEEEEcCCCCcEEEEEEe--CHHHHHHHH
Confidence 467889999999999763 5888999 888887764
No 144
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=24.88 E-value=69 Score=17.45 Aligned_cols=14 Identities=21% Similarity=0.399 Sum_probs=5.5
Q ss_pred ecCCCCCCceeEEE
Q 047170 50 ICGCCKSPDTILTN 63 (89)
Q Consensus 50 ~C~~C~sPdT~L~k 63 (89)
.||.|++|=+..+-
T Consensus 2 fC~~CG~~l~~~ip 15 (34)
T PF14803_consen 2 FCPQCGGPLERRIP 15 (34)
T ss_dssp B-TTT--B-EEE--
T ss_pred ccccccChhhhhcC
Confidence 48999998544444
No 145
>PF03471 CorC_HlyC: Transporter associated domain; InterPro: IPR005170 This small domain is found in a family of proteins with the CBS IPR002550 from INTERPRO domain and two CBS domains with this domain found at the C terminus of the proteins, the domain is also found at the C terminus of some Na+/H+ antiporters. This domain is also found in CorC that is involved in Magnesium and cobalt efflux. The function of this domain is uncertain but might be involved in modulating transport of ion substrates.; PDB: 3DED_F 2PLI_C 2R2Z_A 2P4P_A 2O3G_A 2P3H_A 3LLB_A 3LAE_A 2P13_B 2NQW_A ....
Probab=24.59 E-value=90 Score=19.04 Aligned_cols=24 Identities=21% Similarity=0.297 Sum_probs=19.9
Q ss_pred eecCCceEEEEeecCHHHHHHhhcc
Q 047170 23 SLDGQQHLVVKGRFASKYIEGILHK 47 (89)
Q Consensus 23 ~id~~~rlii~G~~~~~~i~~~L~~ 47 (89)
+++ ++.++++|+.+-++|++.+.-
T Consensus 2 ~~~-~~~~~v~G~~~l~~l~~~~~~ 25 (81)
T PF03471_consen 2 KLD-DGTYIVSGSTPLDDLNELLGL 25 (81)
T ss_dssp EET-TSEEEEETTSBHHHHHHHHTS
T ss_pred eEc-CCEEEEEecCCHHHHHHHHCc
Confidence 345 559999999999999998765
No 146
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.33 E-value=25 Score=21.36 Aligned_cols=11 Identities=36% Similarity=0.896 Sum_probs=8.4
Q ss_pred eecCCCCCCce
Q 047170 49 VICGCCKSPDT 59 (89)
Q Consensus 49 V~C~~C~sPdT 59 (89)
-+||.|+.|=+
T Consensus 13 KICpvCqRPFs 23 (54)
T COG4338 13 KICPVCQRPFS 23 (54)
T ss_pred hhhhhhcCchH
Confidence 37999998843
No 147
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=24.31 E-value=47 Score=26.70 Aligned_cols=22 Identities=27% Similarity=0.481 Sum_probs=16.4
Q ss_pred eecCCCCC-CceeEEEcC----cEEEE
Q 047170 49 VICGCCKS-PDTILTNGN----HLFFL 70 (89)
Q Consensus 49 V~C~~C~s-PdT~L~k~~----rl~~l 70 (89)
-.||.|+| |-+.++..+ ++-||
T Consensus 186 ~~CPvCGS~PvaSmV~~g~~~~GlRYL 212 (308)
T COG3058 186 QYCPVCGSMPVASMVQIGETEQGLRYL 212 (308)
T ss_pred ccCCCcCCCCcceeeeecCccccchhh
Confidence 47999999 888888643 55555
No 148
>PF04170 NlpE: NlpE N-terminal domain; InterPro: IPR007298 This family represents a bacterial outer membrane lipoprotein that is necessary for signalling by the Cpx pathway []. This pathway responds to cell envelope disturbances and increases the expression of periplasmic protein folding and degradation factors. While the molecular function of the NlpE protein is unknown, it may be involved in detecting bacterial adhesion to abiotic surfaces. NlpE from Escherichia coli and Salmonella typhi is also known to confer copper tolerance in copper-sensitive strains of E. coli, and may be involved in copper efflux and delivery of copper to copper-dependent enzymes [].; PDB: 3LHN_A 2Z4I_B 2Z4H_A.
Probab=24.23 E-value=59 Score=20.59 Aligned_cols=22 Identities=27% Similarity=0.448 Sum_probs=18.3
Q ss_pred eecCCCCCCceeEEE-cCcEEEE
Q 047170 49 VICGCCKSPDTILTN-GNHLFFL 70 (89)
Q Consensus 49 V~C~~C~sPdT~L~k-~~rl~~l 70 (89)
.=|..|...+|.|.- .++.|.+
T Consensus 5 LPCADC~GI~t~L~L~~D~ty~l 27 (87)
T PF04170_consen 5 LPCADCPGIKTTLTLNADGTYTL 27 (87)
T ss_dssp EEETTSSEEEEEEEE-TTSEEEE
T ss_pred eECCCCCCeEEEEEECCCCcEEE
Confidence 459999999999995 5777777
No 149
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=24.11 E-value=1.2e+02 Score=16.62 Aligned_cols=22 Identities=23% Similarity=0.587 Sum_probs=12.6
Q ss_pred eecCCCC---CCceeEEEcCcEEEE
Q 047170 49 VICGCCK---SPDTILTNGNHLFFL 70 (89)
Q Consensus 49 V~C~~C~---sPdT~L~k~~rl~~l 70 (89)
|.|..|+ ||=..+...++.|.-
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C 27 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWIC 27 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEE
T ss_pred cccCCCCCEECCcceEcCCCCEEEC
Confidence 5677777 466777766666655
No 150
>PF07196 Flagellin_IN: Flagellin hook IN motif; InterPro: IPR010810 The function of this region is not clear, but it is found in many flagellar hook proteins, including FliD homologues []. This motif is found in single copy or repeated in various flagellar proteins. Conserved Ile-Asn (IN) residues are seen at the centre of the motif. The diversity of these motifs makes it likely that some members of the family are not identified.; GO: 0006928 cellular component movement, 0043064 flagellum organization, 0009288 bacterial-type flagellum; PDB: 3K8V_A 2ZBI_B 3K8W_A.
Probab=23.62 E-value=1.6e+02 Score=16.88 Aligned_cols=26 Identities=27% Similarity=0.473 Sum_probs=19.7
Q ss_pred hHHHHHH---HhhccceeecCC-ceEEEEe
Q 047170 9 DVVTFLL---SEMGTSGSLDGQ-QHLVVKG 34 (89)
Q Consensus 9 ~v~kyl~---~ELgt~g~id~~-~rlii~G 34 (89)
|+..-+- .+.|..++++.+ ++|+|..
T Consensus 25 di~~aIN~~~~~tGV~As~~~~~~~L~lts 54 (56)
T PF07196_consen 25 DIADAINAASSNTGVTASIDNDGGRLVLTS 54 (56)
T ss_dssp HHHHHHHHTHHHHSEEEEEETTTTEEEEEE
T ss_pred HHHHHHhhccCCCCEEEEEEcCCCEEEEEe
Confidence 3555554 789999999885 8999864
No 151
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=23.41 E-value=32 Score=20.22 Aligned_cols=9 Identities=44% Similarity=1.254 Sum_probs=7.7
Q ss_pred ceecCCCCC
Q 047170 48 FVICGCCKS 56 (89)
Q Consensus 48 yV~C~~C~s 56 (89)
||.|..|-.
T Consensus 6 Fv~C~~C~~ 14 (46)
T PF11331_consen 6 FVVCSSCFE 14 (46)
T ss_pred EeECccHHH
Confidence 899999964
No 152
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=23.41 E-value=34 Score=29.64 Aligned_cols=11 Identities=27% Similarity=0.495 Sum_probs=8.7
Q ss_pred ecCCCCCCcee
Q 047170 50 ICGCCKSPDTI 60 (89)
Q Consensus 50 ~C~~C~sPdT~ 60 (89)
.||.|+|.+++
T Consensus 582 ~CP~CGs~~~e 592 (623)
T PRK08271 582 RCPICGSENID 592 (623)
T ss_pred CCcCCCCcchh
Confidence 69999997754
No 153
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=23.13 E-value=39 Score=20.54 Aligned_cols=9 Identities=33% Similarity=0.822 Sum_probs=7.0
Q ss_pred eecCCCCCC
Q 047170 49 VICGCCKSP 57 (89)
Q Consensus 49 V~C~~C~sP 57 (89)
-.||.|++|
T Consensus 18 ~~CP~CG~~ 26 (56)
T PRK13130 18 EICPVCGGK 26 (56)
T ss_pred ccCcCCCCC
Confidence 368999876
No 154
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=22.98 E-value=35 Score=17.76 Aligned_cols=10 Identities=40% Similarity=1.202 Sum_probs=5.0
Q ss_pred ecCCCCCCce
Q 047170 50 ICGCCKSPDT 59 (89)
Q Consensus 50 ~C~~C~sPdT 59 (89)
.|+.|++|-.
T Consensus 5 fC~~CG~~t~ 14 (32)
T PF09297_consen 5 FCGRCGAPTK 14 (32)
T ss_dssp B-TTT--BEE
T ss_pred ccCcCCcccc
Confidence 5999999744
No 155
>PF09432 THP2: Tho complex subunit THP2; InterPro: IPR018557 The THO complex plays a role in coupling transcription elongation to mRNA export. It is composed of subunits THP2, HPR1, THO2 and MFT1 [].
Probab=22.90 E-value=82 Score=22.47 Aligned_cols=52 Identities=21% Similarity=0.259 Sum_probs=39.7
Q ss_pred cHhHHHHHHHhhccceee-cC-CceEEEEeecCHHHHHHhhccceecCCCCCCceeEE
Q 047170 7 NVDVVTFLLSEMGTSGSL-DG-QQHLVVKGRFASKYIEGILHKFVICGCCKSPDTILT 62 (89)
Q Consensus 7 h~~v~kyl~~ELgt~g~i-d~-~~rlii~G~~~~~~i~~~L~~yV~C~~C~sPdT~L~ 62 (89)
|+.++.=|+-+|+-+-.+ |. ...+.++.--.+..++.+|++|.- .++||...
T Consensus 4 yiNLl~rLSvdL~~qve~sd~~~~~~~vd~~~pP~el~~iLe~y~~----~~~d~~~l 57 (132)
T PF09432_consen 4 YINLLERLSVDLAKQVEISDPEVSEFVVDDWNPPKELQSILEKYNT----PSTDTEEL 57 (132)
T ss_pred HHHHHHHHHHHHHHHhcccCCCcceeeecCCCCCHHHHHHHHHHcC----CCccHHHH
Confidence 455677777788777777 32 669999999999999999999876 55666543
No 156
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.80 E-value=37 Score=22.38 Aligned_cols=22 Identities=9% Similarity=0.312 Sum_probs=15.2
Q ss_pred HHHHHhhcc-ceecCCCCCCcee
Q 047170 39 KYIEGILHK-FVICGCCKSPDTI 60 (89)
Q Consensus 39 ~~i~~~L~~-yV~C~~C~sPdT~ 60 (89)
+-+|.+=+. ++.|++|+.+=-+
T Consensus 23 dvvq~~~ddplt~ce~c~a~~kk 45 (82)
T COG2331 23 DVVQAMTDDPLTTCEECGARLKK 45 (82)
T ss_pred HHHHhcccCccccChhhChHHHH
Confidence 345555555 9999999985433
No 157
>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=22.77 E-value=41 Score=19.93 Aligned_cols=10 Identities=40% Similarity=0.986 Sum_probs=8.4
Q ss_pred ceecCCCCCC
Q 047170 48 FVICGCCKSP 57 (89)
Q Consensus 48 yV~C~~C~sP 57 (89)
.+.||.|+.+
T Consensus 26 l~~c~~cg~~ 35 (56)
T PF01783_consen 26 LVKCPNCGEP 35 (56)
T ss_dssp EEESSSSSSE
T ss_pred eeeeccCCCE
Confidence 7899999963
No 158
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=22.54 E-value=33 Score=22.54 Aligned_cols=10 Identities=50% Similarity=1.085 Sum_probs=3.7
Q ss_pred ceecCCCCCC
Q 047170 48 FVICGCCKSP 57 (89)
Q Consensus 48 yV~C~~C~sP 57 (89)
||.|.+|..|
T Consensus 28 FVAC~eC~fP 37 (80)
T PF14569_consen 28 FVACHECAFP 37 (80)
T ss_dssp --S-SSS---
T ss_pred EEEEcccCCc
Confidence 9999999877
No 159
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.44 E-value=54 Score=28.69 Aligned_cols=9 Identities=33% Similarity=0.792 Sum_probs=7.5
Q ss_pred ecCCCCCCc
Q 047170 50 ICGCCKSPD 58 (89)
Q Consensus 50 ~C~~C~sPd 58 (89)
.||.|+|.|
T Consensus 661 ~CP~CG~~~ 669 (711)
T PRK09263 661 TCPKCGNHD 669 (711)
T ss_pred cCcCCCCCC
Confidence 699999876
No 160
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=22.43 E-value=62 Score=18.65 Aligned_cols=13 Identities=31% Similarity=0.652 Sum_probs=9.9
Q ss_pred ecCCCCCCceeEE
Q 047170 50 ICGCCKSPDTILT 62 (89)
Q Consensus 50 ~C~~C~sPdT~L~ 62 (89)
-||.|++.+-.+.
T Consensus 3 PCPfCGg~~~~~~ 15 (53)
T TIGR03655 3 PCPFCGGADVYLR 15 (53)
T ss_pred CCCCCCCcceeeE
Confidence 4999999776554
No 161
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=22.33 E-value=38 Score=18.92 Aligned_cols=9 Identities=22% Similarity=0.575 Sum_probs=7.5
Q ss_pred ceecCCCCC
Q 047170 48 FVICGCCKS 56 (89)
Q Consensus 48 yV~C~~C~s 56 (89)
.+.|+.|+-
T Consensus 13 ~~~C~~CgM 21 (41)
T PF13878_consen 13 ATTCPTCGM 21 (41)
T ss_pred CcCCCCCCC
Confidence 589999984
No 162
>cd00862 ProRS_anticodon_zinc ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only, and an additional C-terminal zinc-binding domain specific to this subfamily of aaRSs.
Probab=22.12 E-value=42 Score=24.33 Aligned_cols=26 Identities=12% Similarity=0.189 Sum_probs=21.6
Q ss_pred CHHHHHHhhcc--ceecCCCCCCceeEE
Q 047170 37 ASKYIEGILHK--FVICGCCKSPDTILT 62 (89)
Q Consensus 37 ~~~~i~~~L~~--yV~C~~C~sPdT~L~ 62 (89)
+-+.+...|++ ||++|-|+++++...
T Consensus 133 ~~~e~~~~~~~~~~v~~~wcg~~~~e~~ 160 (202)
T cd00862 133 TWEEFKEALNEKGIVLAPWCGEEECEEE 160 (202)
T ss_pred CHHHHHHHHhcCCEEEEEecCCHHHHHH
Confidence 66888888975 999999999987654
No 163
>PF14577 SEO_C: Sieve element occlusion C-terminus
Probab=22.08 E-value=46 Score=25.66 Aligned_cols=10 Identities=30% Similarity=0.956 Sum_probs=8.9
Q ss_pred ceecCCCCCC
Q 047170 48 FVICGCCKSP 57 (89)
Q Consensus 48 yV~C~~C~sP 57 (89)
-|.||+|+.|
T Consensus 214 ~i~CpeC~R~ 223 (235)
T PF14577_consen 214 TIVCPECGRP 223 (235)
T ss_pred eeECCCCCCc
Confidence 7999999986
No 164
>KOG3239 consensus Density-regulated protein related to translation initiation factor 1 (eIF-1/SUI1) [General function prediction only]
Probab=22.07 E-value=1.4e+02 Score=22.59 Aligned_cols=37 Identities=16% Similarity=0.348 Sum_probs=30.1
Q ss_pred hHHHHHHHhhccceeecC----CceEEEEeecCHHHHHHhh
Q 047170 9 DVVTFLLSEMGTSGSLDG----QQHLVVKGRFASKYIEGIL 45 (89)
Q Consensus 9 ~v~kyl~~ELgt~g~id~----~~rlii~G~~~~~~i~~~L 45 (89)
+..|||..-++|.+|+-+ .+.++|+|.+..+-+.=+.
T Consensus 131 ~aaK~fa~KFAtGaSVtk~a~kkdEIvIQGDv~dDi~d~I~ 171 (193)
T KOG3239|consen 131 KAAKFFAQKFATGASVTKNAEKKDEIVIQGDVKDDIFDFIP 171 (193)
T ss_pred HHHHHHHHhhccCccccCCCCccceEEEeccchHHHHHHHH
Confidence 378999999999999966 7899999999876554443
No 165
>PRK11827 hypothetical protein; Provisional
Probab=21.98 E-value=70 Score=19.69 Aligned_cols=30 Identities=23% Similarity=0.602 Sum_probs=16.4
Q ss_pred ceecCCCCCCceeEEEc-CcEEE----EEeecccce
Q 047170 48 FVICGCCKSPDTILTNG-NHLFF----LIFPIKAGF 78 (89)
Q Consensus 48 yV~C~~C~sPdT~L~k~-~rl~~----lv~~ik~g~ 78 (89)
...||.|+.|=. +..+ +.+.- +..||+.|-
T Consensus 8 ILaCP~ckg~L~-~~~~~~~Lic~~~~laYPI~dgI 42 (60)
T PRK11827 8 IIACPVCNGKLW-YNQEKQELICKLDNLAFPLRDGI 42 (60)
T ss_pred heECCCCCCcCe-EcCCCCeEECCccCeeccccCCc
Confidence 568999998632 2221 11111 167777764
No 166
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=21.86 E-value=44 Score=18.91 Aligned_cols=15 Identities=20% Similarity=0.284 Sum_probs=8.8
Q ss_pred eecCCCCCCceeEEE
Q 047170 49 VICGCCKSPDTILTN 63 (89)
Q Consensus 49 V~C~~C~sPdT~L~k 63 (89)
+-||.|++-|---+-
T Consensus 4 ~pCP~CGG~DrFri~ 18 (40)
T PF08273_consen 4 GPCPICGGKDRFRIF 18 (40)
T ss_dssp E--TTTT-TTTEEEE
T ss_pred CCCCCCcCccccccC
Confidence 469999998866643
No 167
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.76 E-value=51 Score=28.98 Aligned_cols=13 Identities=23% Similarity=0.376 Sum_probs=8.8
Q ss_pred ecCCCCCCceeEE
Q 047170 50 ICGCCKSPDTILT 62 (89)
Q Consensus 50 ~C~~C~sPdT~L~ 62 (89)
.||.|+|.++...
T Consensus 695 ~CP~CG~~~~~~~ 707 (735)
T PRK07111 695 KCPKCGSTNIQRI 707 (735)
T ss_pred cCcCCCCccceee
Confidence 5888888664444
No 168
>PF09180 ProRS-C_1: Prolyl-tRNA synthetase, C-terminal; InterPro: IPR016061 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Prolyl tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa. This domain is found at the C-terminal in archaeal and eukaryotic enzymes, as well as in certain bacterial ones.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1NJ6_A 1NJ2_A 1NJ5_A 1NJ1_A 1H4T_C 1H4S_A 1HC7_C 1H4Q_B 3IAL_B.
Probab=21.73 E-value=32 Score=21.10 Aligned_cols=23 Identities=17% Similarity=0.322 Sum_probs=13.9
Q ss_pred HHHHhhcc--ceecCCCCCCceeEE
Q 047170 40 YIEGILHK--FVICGCCKSPDTILT 62 (89)
Q Consensus 40 ~i~~~L~~--yV~C~~C~sPdT~L~ 62 (89)
++...|++ ||+.|-|++++-...
T Consensus 3 E~k~~i~~gg~v~~pwcg~~ece~~ 27 (68)
T PF09180_consen 3 EFKEAIEKGGFVLVPWCGDEECEEK 27 (68)
T ss_dssp HHHHHHHTSSEEEEEES-SHHHHHH
T ss_pred HHHHHHhCCCEEEEEccCCHHHHHH
Confidence 45555644 888888887665443
No 169
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=21.71 E-value=40 Score=16.90 Aligned_cols=8 Identities=38% Similarity=0.825 Sum_probs=6.6
Q ss_pred eecCCCCC
Q 047170 49 VICGCCKS 56 (89)
Q Consensus 49 V~C~~C~s 56 (89)
+.|+.|+.
T Consensus 3 ~~C~~CgR 10 (25)
T PF13913_consen 3 VPCPICGR 10 (25)
T ss_pred CcCCCCCC
Confidence 68999985
No 170
>TIGR01464 hemE uroporphyrinogen decarboxylase. This model represents uroporphyrinogen decarboxylase (HemE), which converts uroporphyrinogen III to coproporphyrinogen III. This step takes the pathway toward protoporphyrin IX, a common precursor of both heme and chlorophyll, rather than toward precorrin 2 and its products.
Probab=21.69 E-value=50 Score=25.26 Aligned_cols=43 Identities=21% Similarity=0.209 Sum_probs=24.9
Q ss_pred HHhhccceeecCCceEEEEeecCHHHHHHhhcc----------ceecCCCCC-CceeEE
Q 047170 15 LSEMGTSGSLDGQQHLVVKGRFASKYIEGILHK----------FVICGCCKS-PDTILT 62 (89)
Q Consensus 15 ~~ELgt~g~id~~~rlii~G~~~~~~i~~~L~~----------yV~C~~C~s-PdT~L~ 62 (89)
......+|++|.. .+ .| ++++|++..++ |++.+.|+- |+|.++
T Consensus 274 ~~~~~i~Gni~p~-~l--~g--t~e~i~~~v~~~l~~~~~~~g~Il~~Gc~i~~~tp~e 327 (338)
T TIGR01464 274 GPGVAIQGNLDPA-VL--YA--PEEALEEKVEKILEAFGGKSRYIFNLGHGILPDTPPE 327 (338)
T ss_pred CCCeeEEeCCChH-Hh--cC--CHHHHHHHHHHHHHHhccCCCceecCCCcCCCCcCHH
Confidence 3334556666542 22 44 45555544322 999999995 577653
No 171
>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=21.64 E-value=44 Score=28.14 Aligned_cols=20 Identities=25% Similarity=0.581 Sum_probs=14.7
Q ss_pred HHHHHhhcc------ceecCCCCCCc
Q 047170 39 KYIEGILHK------FVICGCCKSPD 58 (89)
Q Consensus 39 ~~i~~~L~~------yV~C~~C~sPd 58 (89)
..|+..... ||-||.|+-.-
T Consensus 185 ~~I~~~~~~sdqr~~~vpCPhCg~~~ 210 (557)
T PF05876_consen 185 SRIERLYEESDQRRYYVPCPHCGEEQ 210 (557)
T ss_pred CHHHHHHHhCCceEEEccCCCCCCCc
Confidence 456666655 99999999643
No 172
>PF07635 PSCyt1: Planctomycete cytochrome C; InterPro: IPR011429 These proteins share a region of homology at their N terminus that contains the C-{CPWHF}-{CPWR}-C-H-{CFYW} motif typical of cytochrome c.
Probab=21.56 E-value=47 Score=19.57 Aligned_cols=10 Identities=40% Similarity=0.979 Sum_probs=9.0
Q ss_pred cCCCCCCcee
Q 047170 51 CGCCKSPDTI 60 (89)
Q Consensus 51 C~~C~sPdT~ 60 (89)
|-.|++++..
T Consensus 1 C~~CHg~~~~ 10 (59)
T PF07635_consen 1 CFSCHGPDKQ 10 (59)
T ss_pred CcCCCCCCCc
Confidence 8999999986
No 173
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=21.43 E-value=43 Score=20.69 Aligned_cols=11 Identities=45% Similarity=0.827 Sum_probs=8.8
Q ss_pred ceecCCCCCCc
Q 047170 48 FVICGCCKSPD 58 (89)
Q Consensus 48 yV~C~~C~sPd 58 (89)
.-.||-|+||=
T Consensus 39 ~p~CPlC~s~M 49 (59)
T PF14169_consen 39 EPVCPLCKSPM 49 (59)
T ss_pred CccCCCcCCcc
Confidence 46799999973
No 174
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=21.41 E-value=42 Score=26.72 Aligned_cols=9 Identities=44% Similarity=1.110 Sum_probs=8.6
Q ss_pred ceecCCCCC
Q 047170 48 FVICGCCKS 56 (89)
Q Consensus 48 yV~C~~C~s 56 (89)
||.|.+|++
T Consensus 283 fv~C~ecgn 291 (296)
T KOG1105|consen 283 FVTCNECGN 291 (296)
T ss_pred eeeecccCC
Confidence 999999997
No 175
>COG4654 Cytochrome c551/c552 [Energy production and conversion]
Probab=21.37 E-value=34 Score=23.67 Aligned_cols=13 Identities=31% Similarity=0.652 Sum_probs=11.7
Q ss_pred ecCCCCCCceeEE
Q 047170 50 ICGCCKSPDTILT 62 (89)
Q Consensus 50 ~C~~C~sPdT~L~ 62 (89)
-|..|+-||++++
T Consensus 34 gC~~CHq~~vktV 46 (110)
T COG4654 34 GCVACHQPDVKTV 46 (110)
T ss_pred cchhhcccccccc
Confidence 5999999999886
No 176
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.70 E-value=47 Score=19.31 Aligned_cols=11 Identities=45% Similarity=0.848 Sum_probs=8.5
Q ss_pred eecCCCCCCce
Q 047170 49 VICGCCKSPDT 59 (89)
Q Consensus 49 V~C~~C~sPdT 59 (89)
-+|+.|+.|=|
T Consensus 9 K~C~~C~rpf~ 19 (42)
T PF10013_consen 9 KICPVCGRPFT 19 (42)
T ss_pred CcCcccCCcch
Confidence 37999998854
No 177
>PF05042 Caleosin: Caleosin related protein; InterPro: IPR007736 This family contains plant proteins related to caleosin. Caleosins contain calcium-binding domains and have an oleosin-like association with lipid bodies. Caleosins are present at relatively low levels and are mainly bound to microsomal membrane fractions at the early stages of seed development. As the seeds mature, overall levels of caleosins increased dramatically and they were associated almost exclusively with storage lipid bodies []. The calcium binding domain is probably related to the calcium-binding EF-hands motif IPR002048 from INTERPRO.
Probab=20.65 E-value=53 Score=24.32 Aligned_cols=16 Identities=38% Similarity=0.777 Sum_probs=14.4
Q ss_pred EeecCHHHHHHhhccc
Q 047170 33 KGRFASKYIEGILHKF 48 (89)
Q Consensus 33 ~G~~~~~~i~~~L~~y 48 (89)
.|+|.++++|++..+|
T Consensus 90 eGrFvp~kFe~iF~ky 105 (174)
T PF05042_consen 90 EGRFVPQKFEEIFSKY 105 (174)
T ss_pred CCcCCHHHHHHHHHHh
Confidence 5999999999998886
No 178
>cd03308 CmuA_CmuC_like CmuA_CmuC_like: uncharacterized protein family similar to uroporphyrinogen decarboxylase (URO-D) and the methyltransferases CmuA and CmuC.
Probab=20.46 E-value=32 Score=27.18 Aligned_cols=13 Identities=8% Similarity=-0.102 Sum_probs=10.7
Q ss_pred ceecCCCCC-Ccee
Q 047170 48 FVICGCCKS-PDTI 60 (89)
Q Consensus 48 yV~C~~C~s-PdT~ 60 (89)
|++++.|+- |+|.
T Consensus 350 fIl~~gcgi~p~tp 363 (378)
T cd03308 350 FIFGTDKPIISADD 363 (378)
T ss_pred EEEeCCCcCCCCCC
Confidence 999999985 6665
No 179
>PHA00626 hypothetical protein
Probab=20.45 E-value=45 Score=20.72 Aligned_cols=11 Identities=27% Similarity=0.519 Sum_probs=8.2
Q ss_pred ecCCCCCCcee
Q 047170 50 ICGCCKSPDTI 60 (89)
Q Consensus 50 ~C~~C~sPdT~ 60 (89)
.||.|+|-+-.
T Consensus 2 ~CP~CGS~~Iv 12 (59)
T PHA00626 2 SCPKCGSGNIA 12 (59)
T ss_pred CCCCCCCceee
Confidence 59999996533
Done!