Query psy1204
Match_columns 71
No_of_seqs 102 out of 281
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 17:04:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1204.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1204hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14599 zinc_ribbon_6: Zinc-r 100.0 7.5E-36 1.6E-40 172.9 2.2 60 1-60 2-61 (61)
2 KOG1940|consensus 99.8 3.7E-19 8.1E-24 127.3 5.1 65 1-65 206-270 (276)
3 TIGR00100 hypA hydrogenase nic 98.8 1.2E-08 2.5E-13 64.8 4.1 57 9-67 47-106 (115)
4 PF01155 HypA: Hydrogenase exp 98.7 1.3E-08 2.9E-13 64.2 3.6 56 9-66 47-105 (113)
5 PRK12380 hydrogenase nickel in 98.7 1E-08 2.2E-13 65.0 2.5 56 10-67 48-106 (113)
6 PRK03681 hypA hydrogenase nick 98.7 3.5E-08 7.6E-13 62.6 4.0 57 9-66 47-106 (114)
7 PRK00564 hypA hydrogenase nick 98.6 3.4E-08 7.4E-13 62.9 3.7 58 9-67 47-108 (117)
8 PRK03824 hypA hydrogenase nick 98.6 8.6E-08 1.9E-12 62.4 4.3 57 9-67 47-127 (135)
9 COG0375 HybF Zn finger protein 98.4 2.2E-07 4.8E-12 59.6 2.6 40 25-66 66-105 (115)
10 PRK00762 hypA hydrogenase nick 98.2 1.1E-06 2.4E-11 56.4 2.5 57 10-67 48-112 (124)
11 TIGR02605 CxxC_CxxC_SSSS putat 97.4 0.00035 7.6E-09 38.0 3.7 36 29-64 5-44 (52)
12 PRK00398 rpoP DNA-directed RNA 96.9 0.0011 2.3E-08 35.6 2.7 32 28-59 2-33 (46)
13 smart00834 CxxC_CXXC_SSSS Puta 96.7 0.0027 5.9E-08 32.6 3.2 34 28-61 4-40 (41)
14 TIGR00416 sms DNA repair prote 96.7 0.00097 2.1E-08 50.5 1.8 32 26-61 4-35 (454)
15 COG1066 Sms Predicted ATP-depe 96.7 0.0012 2.6E-08 50.6 2.2 34 26-63 4-37 (456)
16 PF09723 Zn-ribbon_8: Zinc rib 96.6 0.0034 7.5E-08 33.3 3.3 31 29-59 5-38 (42)
17 smart00659 RPOLCX RNA polymera 96.6 0.0017 3.7E-08 35.1 2.0 28 28-56 1-28 (44)
18 COG1996 RPC10 DNA-directed RNA 96.3 0.0031 6.8E-08 35.0 1.8 30 27-56 4-33 (49)
19 PRK11823 DNA repair protein Ra 96.2 0.0028 6E-08 47.9 1.8 31 27-61 5-35 (446)
20 cd01675 RNR_III Class III ribo 96.0 0.0073 1.6E-07 46.8 3.5 53 4-62 495-547 (555)
21 PF13597 NRDD: Anaerobic ribon 95.9 0.0073 1.6E-07 46.8 3.1 54 3-62 466-519 (546)
22 cd01121 Sms Sms (bacterial rad 95.8 0.0043 9.4E-08 46.0 1.4 27 31-61 2-28 (372)
23 PF12172 DUF35_N: Rubredoxin-l 95.7 0.012 2.5E-07 30.1 2.3 30 25-58 7-36 (37)
24 COG1545 Predicted nucleic-acid 94.8 0.062 1.3E-06 35.0 4.1 28 25-56 25-52 (140)
25 PRK00415 rps27e 30S ribosomal 94.5 0.054 1.2E-06 31.2 3.0 41 24-64 6-47 (59)
26 COG2051 RPS27A Ribosomal prote 93.9 0.075 1.6E-06 31.3 2.8 45 20-64 10-55 (67)
27 PF09538 FYDLN_acid: Protein o 93.8 0.027 5.8E-07 35.7 0.8 32 27-60 7-39 (108)
28 PF10058 DUF2296: Predicted in 93.7 0.12 2.7E-06 28.9 3.4 45 8-57 4-54 (54)
29 TIGR02098 MJ0042_CXXC MJ0042 f 93.6 0.088 1.9E-06 26.7 2.5 28 29-56 2-34 (38)
30 PF13719 zinc_ribbon_5: zinc-r 93.6 0.058 1.3E-06 27.8 1.8 27 29-55 2-33 (37)
31 PRK12286 rpmF 50S ribosomal pr 93.6 0.091 2E-06 29.7 2.7 31 26-61 24-54 (57)
32 PRK07111 anaerobic ribonucleos 93.4 0.1 2.2E-06 42.0 3.8 43 14-62 666-708 (735)
33 PRK09263 anaerobic ribonucleos 93.4 0.048 1E-06 43.7 1.9 31 27-57 639-669 (711)
34 PRK08271 anaerobic ribonucleos 93.4 0.059 1.3E-06 42.8 2.3 52 4-61 543-594 (623)
35 PRK08579 anaerobic ribonucleos 93.0 0.055 1.2E-06 42.9 1.7 43 15-62 555-597 (625)
36 COG1327 Predicted transcriptio 93.0 0.068 1.5E-06 36.0 1.8 21 48-68 1-21 (156)
37 COG3357 Predicted transcriptio 92.9 0.041 8.8E-07 34.4 0.6 32 27-58 56-87 (97)
38 TIGR02487 NrdD anaerobic ribon 92.9 0.11 2.3E-06 40.7 3.0 52 5-62 502-553 (579)
39 TIGR00244 transcriptional regu 92.7 0.085 1.9E-06 35.2 2.0 20 48-67 1-20 (147)
40 TIGR02827 RNR_anaer_Bdell anae 92.6 0.17 3.7E-06 40.0 3.8 51 6-62 511-561 (586)
41 PRK11788 tetratricopeptide rep 92.4 0.14 3.1E-06 36.0 3.0 27 30-60 355-381 (389)
42 PF13717 zinc_ribbon_4: zinc-r 92.2 0.13 2.7E-06 26.5 1.8 27 29-55 2-33 (36)
43 TIGR02159 PA_CoA_Oxy4 phenylac 92.1 0.08 1.7E-06 34.9 1.3 15 48-62 106-120 (146)
44 PRK14704 anaerobic ribonucleos 92.1 0.12 2.6E-06 41.0 2.5 38 14-57 545-582 (618)
45 TIGR01031 rpmF_bact ribosomal 92.1 0.15 3.3E-06 28.6 2.3 30 27-61 24-53 (55)
46 PF10122 Mu-like_Com: Mu-like 92.1 0.069 1.5E-06 29.9 0.8 33 29-61 4-38 (51)
47 COG1110 Reverse gyrase [DNA re 91.9 0.06 1.3E-06 45.3 0.6 27 28-58 693-719 (1187)
48 cd00729 rubredoxin_SM Rubredox 91.1 0.21 4.6E-06 25.3 1.9 27 29-57 2-28 (34)
49 KOG3507|consensus 90.9 0.13 2.8E-06 29.8 1.1 38 16-54 5-44 (62)
50 PF03604 DNA_RNApol_7kD: DNA d 90.8 0.12 2.5E-06 26.2 0.8 24 31-55 2-25 (32)
51 PRK00464 nrdR transcriptional 90.7 0.19 4.1E-06 33.6 1.9 19 48-66 1-19 (154)
52 cd00350 rubredoxin_like Rubred 90.5 0.19 4.2E-06 25.1 1.5 26 30-57 2-27 (33)
53 smart00531 TFIIE Transcription 90.4 0.15 3.2E-06 33.2 1.3 30 27-56 97-132 (147)
54 PRK06266 transcription initiat 90.2 0.2 4.3E-06 33.9 1.8 33 25-59 113-148 (178)
55 PF14369 zf-RING_3: zinc-finge 90.0 0.36 7.8E-06 24.7 2.3 32 29-60 2-34 (35)
56 PF09567 RE_MamI: MamI restric 90.0 0.14 3E-06 37.4 0.9 32 27-62 80-111 (314)
57 TIGR02300 FYDLN_acid conserved 89.6 0.18 3.8E-06 33.1 1.1 28 28-57 8-36 (129)
58 TIGR00373 conserved hypothetic 89.5 0.29 6.3E-06 32.4 2.1 31 26-58 106-139 (158)
59 PF10571 UPF0547: Uncharacteri 88.8 0.23 5E-06 24.0 1.0 21 31-55 2-22 (26)
60 PRK06260 threonine synthase; V 88.8 0.29 6.2E-06 36.2 1.9 26 29-56 3-28 (397)
61 PF02701 zf-Dof: Dof domain, z 88.8 0.22 4.8E-06 29.0 1.0 14 48-61 6-19 (63)
62 PF09082 DUF1922: Domain of un 88.8 0.24 5.3E-06 29.2 1.2 26 28-55 2-27 (68)
63 PLN00209 ribosomal protein S27 88.8 0.61 1.3E-05 28.7 3.0 41 24-64 31-72 (86)
64 PF13248 zf-ribbon_3: zinc-rib 88.5 0.15 3.3E-06 24.2 0.2 22 30-55 3-24 (26)
65 PRK14890 putative Zn-ribbon RN 88.5 0.26 5.7E-06 28.3 1.2 26 27-54 23-55 (59)
66 PRK12496 hypothetical protein; 88.3 0.33 7.2E-06 32.4 1.8 28 30-59 128-155 (164)
67 PTZ00083 40S ribosomal protein 87.8 0.78 1.7E-05 28.1 3.0 41 24-64 30-71 (85)
68 COG1198 PriA Primosomal protei 87.7 0.4 8.7E-06 38.9 2.2 29 28-61 461-489 (730)
69 KOG2703|consensus 87.7 0.23 5E-06 38.2 0.8 44 27-70 37-91 (460)
70 PRK06450 threonine synthase; V 87.6 0.34 7.4E-06 35.4 1.6 26 28-56 2-27 (338)
71 PF13240 zinc_ribbon_2: zinc-r 87.3 0.23 4.9E-06 23.2 0.4 21 31-55 1-21 (23)
72 PRK08270 anaerobic ribonucleos 87.0 0.77 1.7E-05 36.7 3.4 48 7-61 605-652 (656)
73 PF07754 DUF1610: Domain of un 87.0 0.4 8.6E-06 22.9 1.1 6 49-54 18-23 (24)
74 PF14952 zf-tcix: Putative tre 86.9 0.29 6.4E-06 26.6 0.7 11 49-59 13-23 (44)
75 PRK07591 threonine synthase; V 86.9 0.44 9.5E-06 35.7 1.9 27 28-57 17-43 (421)
76 PF01783 Ribosomal_L32p: Ribos 86.6 0.51 1.1E-05 26.3 1.6 30 27-61 24-53 (56)
77 PHA00626 hypothetical protein 86.6 0.42 9.1E-06 27.4 1.3 34 31-66 2-42 (59)
78 PF09332 Mcm10: Mcm10 replicat 86.4 0.49 1.1E-05 35.3 1.9 33 29-61 285-317 (344)
79 COG1439 Predicted nucleic acid 85.9 0.44 9.6E-06 32.7 1.3 26 27-56 137-162 (177)
80 TIGR00595 priA primosomal prot 85.8 0.56 1.2E-05 36.0 2.0 12 49-60 255-266 (505)
81 PRK12775 putative trifunctiona 85.7 0.39 8.4E-06 39.8 1.2 41 25-66 817-857 (1006)
82 COG1675 TFA1 Transcription ini 85.7 0.3 6.5E-06 33.4 0.4 49 10-58 94-143 (176)
83 PF01667 Ribosomal_S27e: Ribos 85.3 1.5 3.2E-05 24.8 3.1 39 26-64 4-43 (55)
84 COG1096 Predicted RNA-binding 85.3 1.2 2.6E-05 30.9 3.2 35 27-63 147-181 (188)
85 PRK06393 rpoE DNA-directed RNA 85.0 0.44 9.6E-06 27.8 0.9 25 28-58 4-28 (64)
86 PF09297 zf-NADH-PPase: NADH p 84.9 0.42 9E-06 23.6 0.7 26 31-56 5-30 (32)
87 PF11023 DUF2614: Protein of u 84.4 0.62 1.3E-05 30.0 1.4 32 26-59 66-97 (114)
88 COG4416 Com Mu-like prophage p 84.3 0.39 8.5E-06 27.4 0.4 35 28-62 3-39 (60)
89 TIGR00155 pqiA_fam integral me 84.1 0.73 1.6E-05 34.7 1.9 48 1-57 193-240 (403)
90 PRK14892 putative transcriptio 84.0 2 4.4E-05 26.8 3.6 36 26-62 18-57 (99)
91 PF09845 DUF2072: Zn-ribbon co 83.3 0.44 9.6E-06 31.3 0.4 32 31-62 3-34 (131)
92 PRK01110 rpmF 50S ribosomal pr 83.2 1.3 2.9E-05 25.2 2.3 30 27-62 25-54 (60)
93 PF08792 A2L_zn_ribbon: A2L zi 82.9 1.2 2.6E-05 22.5 1.9 28 29-57 3-31 (33)
94 PF07295 DUF1451: Protein of u 82.0 1.2 2.6E-05 29.5 2.1 48 5-57 87-140 (146)
95 PF06827 zf-FPG_IleRS: Zinc fi 81.8 1.2 2.7E-05 21.4 1.7 17 47-63 1-17 (30)
96 PF03367 zf-ZPR1: ZPR1 zinc-fi 81.6 2.2 4.8E-05 28.4 3.3 39 30-68 2-51 (161)
97 COG3058 FdhE Uncharacterized p 81.1 0.27 5.8E-06 36.2 -1.3 12 28-39 184-195 (308)
98 TIGR01206 lysW lysine biosynth 80.6 1.3 2.9E-05 24.8 1.7 29 30-58 3-33 (54)
99 COG1328 NrdD Oxygen-sensitive 80.4 2.3 5.1E-05 34.5 3.6 52 5-62 619-670 (700)
100 PF07282 OrfB_Zn_ribbon: Putat 80.4 1.2 2.5E-05 25.0 1.4 26 29-56 28-55 (69)
101 PF14311 DUF4379: Domain of un 80.2 1.9 4.1E-05 23.4 2.2 29 25-53 24-55 (55)
102 PF14446 Prok-RING_1: Prokaryo 80.0 1 2.3E-05 25.4 1.1 25 30-56 6-30 (54)
103 KOG2907|consensus 79.7 0.76 1.7E-05 29.6 0.6 22 46-67 73-99 (116)
104 TIGR00310 ZPR1_znf ZPR1 zinc f 79.7 2.6 5.6E-05 29.0 3.2 38 30-67 1-50 (192)
105 cd02340 ZZ_NBR1_like Zinc fing 79.5 1.1 2.4E-05 23.7 1.1 25 30-58 1-25 (43)
106 PRK05580 primosome assembly pr 79.4 1.4 3E-05 35.1 2.0 11 49-59 423-433 (679)
107 COG1933 Archaeal DNA polymeras 79.4 0.85 1.9E-05 32.9 0.8 44 14-60 148-195 (253)
108 smart00661 RPOL9 RNA polymeras 79.0 1.4 3E-05 23.3 1.4 23 31-55 2-28 (52)
109 PRK00432 30S ribosomal protein 78.9 0.94 2E-05 24.9 0.7 27 28-55 19-45 (50)
110 TIGR01384 TFS_arch transcripti 78.7 1.1 2.4E-05 27.2 1.0 22 31-54 2-23 (104)
111 PF08996 zf-DNA_Pol: DNA Polym 78.6 1.3 2.8E-05 29.9 1.4 33 23-55 11-53 (188)
112 PRK15103 paraquat-inducible me 78.5 1.2 2.6E-05 33.7 1.4 51 1-56 191-244 (419)
113 COG2956 Predicted N-acetylgluc 78.0 1.4 3.1E-05 33.4 1.6 30 26-59 351-380 (389)
114 smart00653 eIF2B_5 domain pres 77.7 1.4 3.1E-05 27.8 1.3 16 47-62 80-95 (110)
115 PF01873 eIF-5_eIF-2B: Domain 77.6 1.5 3.3E-05 28.2 1.5 17 47-63 93-109 (125)
116 PRK03988 translation initiatio 77.2 1.5 3.2E-05 28.8 1.3 16 47-62 102-117 (138)
117 PF14205 Cys_rich_KTR: Cystein 77.0 4.6 9.9E-05 22.9 3.1 31 28-58 3-39 (55)
118 PRK08197 threonine synthase; V 76.9 1.8 3.8E-05 32.0 1.8 26 28-56 6-31 (394)
119 TIGR03844 cysteate_syn cysteat 76.5 1.9 4E-05 32.3 1.9 24 29-55 2-25 (398)
120 PRK08351 DNA-directed RNA poly 76.0 1.6 3.4E-05 25.2 1.1 21 31-57 5-25 (61)
121 PF12760 Zn_Tnp_IS1595: Transp 75.9 2.1 4.5E-05 22.6 1.5 13 49-61 20-32 (46)
122 PF08271 TF_Zn_Ribbon: TFIIB z 75.9 2.3 5.1E-05 22.1 1.7 9 49-57 2-10 (43)
123 PF08274 PhnA_Zn_Ribbon: PhnA 75.8 1.1 2.4E-05 22.3 0.4 11 49-59 4-14 (30)
124 PRK11032 hypothetical protein; 75.1 2.7 5.8E-05 28.3 2.2 31 27-59 122-154 (160)
125 TIGR00354 polC DNA polymerase, 74.8 2.1 4.4E-05 36.3 1.9 44 14-60 993-1040(1095)
126 TIGR01562 FdhE formate dehydro 74.1 2.4 5.2E-05 31.1 1.9 25 29-57 210-234 (305)
127 PRK14873 primosome assembly pr 74.0 2.4 5.3E-05 33.9 2.1 11 49-59 424-434 (665)
128 PRK12722 transcriptional activ 73.9 2.2 4.7E-05 29.5 1.6 29 27-55 132-162 (187)
129 COG0333 RpmF Ribosomal protein 73.6 3.5 7.6E-05 23.4 2.1 30 27-61 25-54 (57)
130 TIGR00311 aIF-2beta translatio 73.3 2.1 4.6E-05 27.9 1.3 16 47-62 97-112 (133)
131 cd02345 ZZ_dah Zinc finger, ZZ 72.9 3.4 7.4E-05 22.3 1.9 28 30-60 1-28 (49)
132 COG1571 Predicted DNA-binding 72.8 1.5 3.2E-05 33.7 0.6 27 28-55 349-375 (421)
133 PRK04023 DNA polymerase II lar 72.5 2.1 4.5E-05 36.4 1.4 22 29-56 626-647 (1121)
134 PF04216 FdhE: Protein involve 72.5 3.3 7.1E-05 29.4 2.3 29 29-61 197-225 (290)
135 smart00709 Zpr1 Duplicated dom 72.4 6.7 0.00014 26.2 3.6 38 31-68 2-50 (160)
136 COG2888 Predicted Zn-ribbon RN 72.1 2.7 5.8E-05 24.3 1.4 12 26-37 24-35 (61)
137 cd02338 ZZ_PCMF_like Zinc fing 72.0 3.1 6.6E-05 22.4 1.6 26 30-58 1-26 (49)
138 PF14255 Cys_rich_CPXG: Cystei 71.9 3.4 7.3E-05 23.0 1.8 19 49-67 2-20 (52)
139 PF09986 DUF2225: Uncharacteri 71.8 4.1 8.8E-05 28.1 2.5 13 29-41 5-17 (214)
140 cd02339 ZZ_Mind_bomb Zinc fing 71.6 2.7 5.9E-05 22.5 1.3 26 30-58 1-26 (45)
141 COG2260 Predicted Zn-ribbon RN 71.5 3.1 6.6E-05 23.9 1.6 23 30-58 6-28 (59)
142 TIGR02443 conserved hypothetic 71.5 3.8 8.3E-05 23.5 2.0 19 44-62 6-24 (59)
143 PRK12860 transcriptional activ 71.0 2.8 6E-05 29.0 1.6 28 27-54 132-161 (189)
144 PF14319 Zn_Tnp_IS91: Transpos 70.4 3.3 7.1E-05 25.9 1.7 33 27-59 40-72 (111)
145 COG2093 DNA-directed RNA polym 70.4 2.1 4.6E-05 25.0 0.7 25 30-58 5-29 (64)
146 PRK02935 hypothetical protein; 69.9 4.3 9.4E-05 25.9 2.1 32 25-58 66-97 (110)
147 COG1867 TRM1 N2,N2-dimethylgua 69.8 3.8 8.2E-05 31.2 2.2 36 25-63 236-271 (380)
148 TIGR01562 FdhE formate dehydro 69.5 3.5 7.7E-05 30.3 1.9 13 28-40 223-235 (305)
149 PF05280 FlhC: Flagellar trans 69.2 9.6 0.00021 25.8 3.8 28 27-54 132-161 (175)
150 PF09526 DUF2387: Probable met 68.5 4.7 0.0001 23.6 2.0 19 44-62 5-23 (71)
151 COG0846 SIR2 NAD-dependent pro 68.4 3.5 7.5E-05 29.4 1.7 44 25-68 118-170 (250)
152 PF10950 DUF2775: Protein of u 68.3 4.1 8.8E-05 25.8 1.8 21 2-25 2-22 (108)
153 PF00569 ZZ: Zinc finger, ZZ t 67.2 3.4 7.4E-05 21.9 1.1 27 29-58 4-30 (46)
154 TIGR00340 zpr1_rel ZPR1-relate 66.8 7.6 0.00017 26.0 3.0 18 49-66 30-47 (163)
155 PRK04338 N(2),N(2)-dimethylgua 66.8 8.6 0.00019 28.7 3.5 30 25-55 240-269 (382)
156 PRK12336 translation initiatio 66.7 3.4 7.5E-05 28.3 1.3 16 47-62 98-113 (201)
157 smart00291 ZnF_ZZ Zinc-binding 66.6 4.2 9.1E-05 21.2 1.4 26 29-58 4-29 (44)
158 PF01907 Ribosomal_L37e: Ribos 66.5 4.5 9.7E-05 22.9 1.5 28 26-56 12-39 (55)
159 COG1326 Uncharacterized archae 66.5 7.9 0.00017 27.1 3.1 35 27-62 4-45 (201)
160 COG1601 GCD7 Translation initi 66.5 2.1 4.5E-05 28.6 0.2 18 46-63 104-121 (151)
161 cd01407 SIR2-fam SIR2 family o 65.7 2.4 5.3E-05 28.8 0.4 34 23-56 103-142 (218)
162 TIGR00375 conserved hypothetic 65.3 2.9 6.3E-05 31.5 0.8 27 29-56 240-267 (374)
163 PF05495 zf-CHY: CHY zinc fing 64.9 3.3 7.3E-05 23.9 0.8 28 29-56 41-70 (71)
164 PF14354 Lar_restr_allev: Rest 64.8 7 0.00015 21.3 2.1 15 49-63 5-19 (61)
165 PRK03564 formate dehydrogenase 64.8 5.2 0.00011 29.5 2.0 13 43-55 222-234 (309)
166 PF13695 zf-3CxxC: Zinc-bindin 64.3 14 0.00031 22.3 3.6 37 26-62 2-53 (98)
167 PF01921 tRNA-synt_1f: tRNA sy 64.3 14 0.00029 27.9 4.1 42 18-63 165-215 (360)
168 COG1198 PriA Primosomal protei 64.2 4.8 0.0001 32.8 1.9 11 29-39 435-445 (730)
169 PRK14715 DNA polymerase II lar 64.2 3.7 7.9E-05 36.1 1.2 26 27-55 1540-1565(1627)
170 PRK13130 H/ACA RNA-protein com 64.0 6.7 0.00015 22.1 1.9 25 28-58 4-28 (56)
171 PRK04136 rpl40e 50S ribosomal 63.5 3.7 8.1E-05 22.7 0.8 30 27-60 12-41 (48)
172 PF08772 NOB1_Zn_bind: Nin one 63.3 6.8 0.00015 23.2 2.0 32 28-62 8-39 (73)
173 PF01363 FYVE: FYVE zinc finge 63.1 2.4 5.2E-05 23.7 0.0 25 28-54 8-32 (69)
174 PF09862 DUF2089: Protein of u 63.1 7 0.00015 25.0 2.1 19 32-54 1-19 (113)
175 cd02344 ZZ_HERC2 Zinc finger, 63.0 4.6 9.9E-05 21.7 1.1 25 31-58 2-26 (45)
176 PF14803 Nudix_N_2: Nudix N-te 62.9 3.3 7E-05 21.1 0.5 26 31-56 2-31 (34)
177 COG2816 NPY1 NTP pyrophosphohy 62.5 4.2 9.1E-05 29.7 1.2 30 28-57 110-139 (279)
178 PRK05638 threonine synthase; V 62.4 4.8 0.0001 30.2 1.5 23 30-56 2-24 (442)
179 COG1592 Rubrerythrin [Energy p 62.4 5.5 0.00012 27.0 1.7 25 29-56 134-158 (166)
180 COG2126 RPL37A Ribosomal prote 62.3 4.6 9.9E-05 23.3 1.1 30 24-56 11-40 (61)
181 COG3364 Zn-ribbon containing p 62.3 2.5 5.4E-05 27.0 -0.0 31 31-62 4-35 (112)
182 TIGR00155 pqiA_fam integral me 61.9 5.9 0.00013 29.9 1.9 29 29-57 13-43 (403)
183 PF13451 zf-trcl: Probable zin 61.7 6.4 0.00014 21.7 1.6 13 28-40 3-15 (49)
184 COG0675 Transposase and inacti 61.6 5.3 0.00012 27.3 1.5 25 27-56 307-331 (364)
185 cd02342 ZZ_UBA_plant Zinc fing 61.6 4.7 0.0001 21.7 1.0 26 30-58 1-26 (43)
186 cd01411 SIR2H SIR2H: Uncharact 61.3 6 0.00013 27.2 1.7 29 28-56 117-145 (225)
187 TIGR03655 anti_R_Lar restricti 61.2 5.9 0.00013 21.5 1.4 13 49-61 3-15 (53)
188 PRK14714 DNA polymerase II lar 61.2 4.6 0.0001 35.1 1.3 10 29-38 667-676 (1337)
189 PRK03564 formate dehydrogenase 60.9 6.2 0.00013 29.1 1.8 34 28-61 225-266 (309)
190 PRK14894 glycyl-tRNA synthetas 60.7 8.4 0.00018 30.6 2.6 27 27-55 86-112 (539)
191 PF05191 ADK_lid: Adenylate ki 60.5 5.9 0.00013 20.2 1.2 26 30-55 2-29 (36)
192 PF14690 zf-ISL3: zinc-finger 60.2 5.9 0.00013 20.4 1.2 9 49-57 4-12 (47)
193 KOG1842|consensus 59.7 1.8 4E-05 33.8 -1.1 47 7-55 145-204 (505)
194 TIGR00354 polC DNA polymerase, 58.8 6.4 0.00014 33.5 1.7 24 28-57 624-647 (1095)
195 PF04810 zf-Sec23_Sec24: Sec23 58.5 6.1 0.00013 20.4 1.1 29 30-58 3-35 (40)
196 PF05907 DUF866: Eukaryotic pr 58.4 15 0.00033 24.4 3.3 42 21-63 23-81 (161)
197 PF14353 CpXC: CpXC protein 58.2 7.9 0.00017 24.1 1.8 17 27-43 36-52 (128)
198 PRK12495 hypothetical protein; 58.1 5 0.00011 28.6 0.9 32 26-59 39-70 (226)
199 PRK09401 reverse gyrase; Revie 57.6 5.2 0.00011 34.1 1.1 26 28-57 677-702 (1176)
200 PRK04023 DNA polymerase II lar 57.5 5.6 0.00012 33.9 1.2 41 14-56 1018-1062(1121)
201 PRK05654 acetyl-CoA carboxylas 57.3 3.9 8.4E-05 29.7 0.2 28 28-57 26-56 (292)
202 PF12387 Peptidase_C74: Pestiv 57.1 6.6 0.00014 27.3 1.3 37 24-65 157-193 (200)
203 COG3677 Transposase and inacti 57.1 6.8 0.00015 25.2 1.3 9 49-57 32-40 (129)
204 COG1656 Uncharacterized conser 56.5 5.1 0.00011 27.3 0.7 22 23-44 124-145 (165)
205 PF04606 Ogr_Delta: Ogr/Delta- 56.3 5.5 0.00012 21.2 0.7 13 49-61 1-13 (47)
206 PRK14714 DNA polymerase II lar 56.3 7.1 0.00015 34.0 1.6 20 31-55 681-700 (1337)
207 PF03107 C1_2: C1 domain; Int 56.2 11 0.00024 18.1 1.7 21 31-54 2-22 (30)
208 PRK08329 threonine synthase; V 56.2 6.1 0.00013 28.7 1.1 23 30-56 2-24 (347)
209 PF01096 TFIIS_C: Transcriptio 55.4 14 0.0003 18.9 2.1 13 49-61 2-14 (39)
210 cd01410 SIRT7 SIRT7: Eukaryoti 55.4 5 0.00011 27.3 0.5 30 27-56 93-129 (206)
211 PRK04179 rpl37e 50S ribosomal 55.3 5.6 0.00012 23.0 0.6 26 27-55 15-40 (62)
212 COG1503 eRF1 Peptide chain rel 55.2 6 0.00013 30.4 1.0 40 20-59 318-360 (411)
213 COG0777 AccD Acetyl-CoA carbox 55.2 5 0.00011 29.6 0.5 28 27-56 26-56 (294)
214 PF09779 Ima1_N: Ima1 N-termin 55.0 7.4 0.00016 25.0 1.3 32 31-64 2-37 (131)
215 cd02249 ZZ Zinc finger, ZZ typ 54.5 7.7 0.00017 20.3 1.1 24 31-58 2-25 (46)
216 COG0498 ThrC Threonine synthas 54.5 7.2 0.00016 29.7 1.3 31 27-59 3-33 (411)
217 KOG2462|consensus 54.4 6.8 0.00015 28.7 1.1 25 30-54 162-194 (279)
218 PF03811 Zn_Tnp_IS1: InsA N-te 54.3 10 0.00022 19.4 1.5 9 49-57 7-15 (36)
219 PLN02569 threonine synthase 54.3 7.5 0.00016 30.0 1.4 25 29-56 49-73 (484)
220 PF07975 C1_4: TFIIH C1-like d 53.9 5.4 0.00012 22.1 0.4 29 27-55 19-51 (51)
221 PHA02768 hypothetical protein; 53.7 6.5 0.00014 22.2 0.7 26 30-55 6-39 (55)
222 smart00440 ZnF_C2C2 C2C2 Zinc 52.4 8.2 0.00018 20.0 0.9 13 49-61 2-14 (40)
223 PRK00420 hypothetical protein; 52.3 8.4 0.00018 24.5 1.2 36 27-64 21-56 (112)
224 PF01197 Ribosomal_L31: Riboso 52.3 10 0.00022 21.9 1.4 36 20-58 6-47 (69)
225 PF12773 DZR: Double zinc ribb 52.3 6.5 0.00014 20.6 0.6 27 29-56 12-38 (50)
226 PRK00241 nudC NADH pyrophospha 52.3 9 0.0002 27.1 1.4 30 28-57 98-127 (256)
227 PF07649 C1_3: C1-like domain; 51.9 9.8 0.00021 18.1 1.1 20 31-53 2-21 (30)
228 PF09855 DUF2082: Nucleic-acid 51.7 8.6 0.00019 22.1 1.1 13 49-61 2-14 (64)
229 smart00064 FYVE Protein presen 51.7 8 0.00017 21.4 0.9 24 29-54 10-33 (68)
230 COG3041 Uncharacterized protei 51.6 15 0.00032 22.8 2.2 37 2-38 24-63 (91)
231 PF01286 XPA_N: XPA protein N- 51.5 9.2 0.0002 19.5 1.0 15 30-44 4-18 (34)
232 CHL00174 accD acetyl-CoA carbo 51.4 7.8 0.00017 28.5 1.0 27 28-56 37-66 (296)
233 cd02343 ZZ_EF Zinc finger, ZZ 51.2 8.7 0.00019 21.0 1.0 27 30-60 1-27 (48)
234 COG3478 Predicted nucleic-acid 51.0 7.6 0.00016 22.8 0.7 11 49-59 6-16 (68)
235 PRK00481 NAD-dependent deacety 50.6 10 0.00022 26.2 1.4 30 27-56 120-151 (242)
236 PTZ00073 60S ribosomal protein 50.5 7 0.00015 24.2 0.6 29 25-56 12-40 (91)
237 TIGR00686 phnA alkylphosphonat 49.5 10 0.00022 24.3 1.2 24 31-55 4-27 (109)
238 COG1552 RPL40A Ribosomal prote 49.0 3.2 6.9E-05 23.1 -1.0 32 28-63 13-44 (50)
239 cd02334 ZZ_dystrophin Zinc fin 48.8 13 0.00028 20.2 1.4 27 31-60 2-28 (49)
240 PF09788 Tmemb_55A: Transmembr 48.6 16 0.00035 26.5 2.3 28 26-54 154-184 (256)
241 COG4311 SoxD Sarcosine oxidase 48.0 11 0.00025 23.6 1.2 20 28-47 2-21 (97)
242 PF02146 SIR2: Sir2 family; I 47.5 8.8 0.00019 25.1 0.7 32 25-56 101-138 (178)
243 cd01412 SIRT5_Af1_CobB SIRT5_A 47.2 12 0.00026 25.4 1.4 29 27-55 107-138 (224)
244 PF04438 zf-HIT: HIT zinc fing 47.2 17 0.00037 17.8 1.6 19 30-55 3-21 (30)
245 PRK14715 DNA polymerase II lar 47.0 12 0.00026 33.1 1.6 23 28-56 673-695 (1627)
246 COG3877 Uncharacterized protei 46.9 11 0.00024 24.3 1.1 24 27-54 4-27 (122)
247 PRK04351 hypothetical protein; 46.7 48 0.001 21.8 4.2 54 5-58 86-143 (149)
248 PF10875 DUF2670: Protein of u 46.7 14 0.00031 24.3 1.6 15 7-21 2-16 (139)
249 KOG1280|consensus 46.6 9.9 0.00022 28.9 1.0 28 28-58 7-34 (381)
250 PF03833 PolC_DP2: DNA polymer 46.4 6.6 0.00014 32.9 0.0 24 29-58 655-678 (900)
251 PRK09710 lar restriction allev 46.2 17 0.00037 21.1 1.7 27 29-55 6-35 (64)
252 PRK06319 DNA topoisomerase I/S 46.0 34 0.00074 28.3 4.0 34 4-37 567-600 (860)
253 PF14149 YhfH: YhfH-like prote 45.8 1.7 3.6E-05 22.8 -2.4 32 21-53 6-37 (37)
254 PF06676 DUF1178: Protein of u 45.6 12 0.00025 25.0 1.1 31 29-61 5-46 (148)
255 PRK14559 putative protein seri 45.6 12 0.00026 30.1 1.3 24 28-57 14-37 (645)
256 COG1594 RPB9 DNA-directed RNA 45.0 16 0.00035 22.9 1.6 23 30-54 3-29 (113)
257 PRK00019 rpmE 50S ribosomal pr 45.0 15 0.00033 21.6 1.4 35 19-58 5-46 (72)
258 TIGR00515 accD acetyl-CoA carb 44.9 11 0.00025 27.3 1.0 27 28-56 25-54 (285)
259 PRK09678 DNA-binding transcrip 44.9 15 0.00032 21.7 1.3 10 48-57 2-11 (72)
260 PF13790 DUF4182: Domain of un 44.6 25 0.00054 18.5 2.0 26 28-54 2-32 (38)
261 smart00109 C1 Protein kinase C 44.4 12 0.00027 18.7 0.9 24 29-54 11-34 (49)
262 PF06397 Desulfoferrod_N: Desu 44.3 20 0.00042 18.5 1.6 8 49-56 8-15 (36)
263 PF00096 zf-C2H2: Zinc finger, 44.2 11 0.00023 16.4 0.5 13 31-43 2-14 (23)
264 PF12677 DUF3797: Domain of un 44.2 12 0.00026 20.7 0.8 10 48-57 14-23 (49)
265 cd00065 FYVE FYVE domain; Zinc 44.0 13 0.00028 19.7 0.9 22 31-54 4-25 (57)
266 PRK09521 exosome complex RNA-b 43.8 36 0.00079 22.7 3.3 39 27-66 147-185 (189)
267 COG4357 Zinc finger domain con 43.7 6.6 0.00014 24.8 -0.3 29 28-56 61-89 (105)
268 PF06221 zf-C2HC5: Putative zi 43.4 13 0.00028 21.0 0.9 27 29-56 18-44 (57)
269 PF09334 tRNA-synt_1g: tRNA sy 43.3 13 0.00028 27.7 1.1 32 23-56 114-145 (391)
270 cd01413 SIR2_Af2 SIR2_Af2: Arc 43.2 16 0.00034 25.1 1.5 44 24-67 108-158 (222)
271 COG1998 RPS31 Ribosomal protei 43.0 12 0.00027 20.8 0.7 29 28-56 18-46 (51)
272 PRK10220 hypothetical protein; 42.9 16 0.00034 23.4 1.3 24 31-55 5-28 (111)
273 KOG2846|consensus 42.7 21 0.00046 26.7 2.1 47 8-62 205-257 (328)
274 KOG1779|consensus 42.7 40 0.00086 20.6 3.0 39 27-65 32-71 (84)
275 PHA02942 putative transposase; 42.3 15 0.00032 27.5 1.3 27 29-57 325-352 (383)
276 cd02335 ZZ_ADA2 Zinc finger, Z 42.2 23 0.00049 18.8 1.7 26 31-59 2-27 (49)
277 PF03119 DNA_ligase_ZBD: NAD-d 42.0 16 0.00035 17.5 1.0 12 49-60 1-12 (28)
278 PF04502 DUF572: Family of unk 41.3 33 0.00071 25.1 2.9 40 27-66 38-96 (324)
279 PRK00750 lysK lysyl-tRNA synth 41.3 72 0.0016 24.8 4.9 41 18-63 166-215 (510)
280 PRK14138 NAD-dependent deacety 41.0 13 0.00028 25.9 0.8 30 27-56 117-152 (244)
281 PF10601 zf-LITAF-like: LITAF- 40.6 23 0.0005 20.1 1.7 17 24-40 2-18 (73)
282 PRK04011 peptide chain release 40.6 21 0.00046 26.9 1.9 37 20-56 319-359 (411)
283 COG1997 RPL43A Ribosomal prote 39.5 19 0.00042 22.2 1.3 10 29-38 35-44 (89)
284 cd02341 ZZ_ZZZ3 Zinc finger, Z 39.5 21 0.00046 19.2 1.3 25 31-58 2-28 (48)
285 PF10263 SprT-like: SprT-like 39.5 82 0.0018 19.7 4.3 52 5-56 86-152 (157)
286 KOG4684|consensus 39.3 6.4 0.00014 28.4 -0.9 46 10-56 152-198 (275)
287 cd04476 RPA1_DBD_C RPA1_DBD_C: 39.2 18 0.00039 23.4 1.2 29 27-57 32-61 (166)
288 smart00350 MCM minichromosome 39.0 40 0.00087 25.9 3.2 32 26-57 34-71 (509)
289 PF02150 RNA_POL_M_15KD: RNA p 38.7 23 0.00051 17.7 1.4 11 30-40 2-12 (35)
290 smart00396 ZnF_UBR1 Putative z 38.6 36 0.00078 19.5 2.3 9 28-36 12-20 (71)
291 PRK05978 hypothetical protein; 36.8 20 0.00044 23.8 1.2 32 27-58 31-63 (148)
292 PF13453 zf-TFIIB: Transcripti 36.6 17 0.00036 18.6 0.6 7 49-55 1-7 (41)
293 PF13913 zf-C2HC_2: zinc-finge 36.6 17 0.00036 16.9 0.6 12 30-41 3-14 (25)
294 cd00730 rubredoxin Rubredoxin; 36.4 22 0.00049 19.4 1.1 8 49-56 36-43 (50)
295 PF01927 Mut7-C: Mut7-C RNAse 36.3 18 0.00038 23.3 0.8 32 6-39 70-101 (147)
296 cd07973 Spt4 Transcription elo 36.2 22 0.00047 22.1 1.2 23 31-54 5-27 (98)
297 cd01409 SIRT4 SIRT4: Eukaryoti 36.0 27 0.00059 24.6 1.8 13 28-40 117-129 (260)
298 PF07635 PSCyt1: Planctomycete 35.9 17 0.00036 20.0 0.6 20 3-22 39-58 (59)
299 KOG2463|consensus 35.8 14 0.00031 28.0 0.4 28 27-57 240-267 (376)
300 PF10825 DUF2752: Protein of u 35.2 18 0.00039 19.7 0.6 12 45-56 7-18 (52)
301 PF15494 SRCR_2: Scavenger rec 34.9 30 0.00066 20.6 1.7 11 27-37 86-96 (98)
302 PF04135 Nop10p: Nucleolar RNA 34.8 73 0.0016 17.7 3.1 22 31-58 7-28 (53)
303 COG4332 Uncharacterized protei 34.6 21 0.00046 25.0 1.0 35 27-61 15-64 (203)
304 PF01780 Ribosomal_L37ae: Ribo 34.1 29 0.00064 21.3 1.5 29 26-54 32-60 (90)
305 smart00731 SprT SprT homologue 34.1 94 0.002 19.7 4.0 50 5-56 83-142 (146)
306 PF01396 zf-C4_Topoisom: Topoi 33.7 37 0.00081 17.3 1.7 6 49-54 3-8 (39)
307 PF09151 DUF1936: Domain of un 33.7 20 0.00043 18.3 0.6 9 48-56 2-10 (36)
308 PRK05333 NAD-dependent deacety 33.5 25 0.00054 25.0 1.3 16 25-40 124-139 (285)
309 PF07191 zinc-ribbons_6: zinc- 33.2 61 0.0013 19.1 2.7 9 29-37 17-25 (70)
310 cd01408 SIRT1 SIRT1: Eukaryoti 32.7 11 0.00024 26.1 -0.6 30 27-56 114-149 (235)
311 PF13912 zf-C2H2_6: C2H2-type 32.5 21 0.00045 16.0 0.5 14 30-43 2-15 (27)
312 cd00296 SIR2 SIR2 superfamily 32.4 26 0.00056 23.3 1.2 47 10-56 90-143 (222)
313 PF11781 RRN7: RNA polymerase 32.4 29 0.00062 17.6 1.1 15 49-63 10-24 (36)
314 smart00586 ZnF_DBF Zinc finger 32.4 32 0.0007 18.8 1.4 14 4-17 34-47 (49)
315 PF05876 Terminase_GpA: Phage 32.0 27 0.00059 27.3 1.4 16 45-60 198-213 (557)
316 PF10083 DUF2321: Uncharacteri 32.0 6.7 0.00014 26.6 -1.7 9 30-38 29-37 (158)
317 COG5257 GCD11 Translation init 31.9 36 0.00078 26.2 1.9 33 21-57 50-82 (415)
318 COG4530 Uncharacterized protei 31.9 21 0.00046 23.2 0.6 23 30-54 10-33 (129)
319 COG4640 Predicted membrane pro 31.7 24 0.00051 27.5 1.0 23 31-58 3-26 (465)
320 COG3813 Uncharacterized protei 31.7 11 0.00024 22.8 -0.7 11 48-58 42-52 (84)
321 COG2995 PqiA Uncharacterized p 31.7 29 0.00063 26.8 1.4 30 27-56 16-47 (418)
322 PF11672 DUF3268: Protein of u 31.6 43 0.00094 20.9 2.0 8 49-56 33-40 (102)
323 PRK03954 ribonuclease P protei 31.5 39 0.00084 21.8 1.8 37 16-57 55-103 (121)
324 COG1379 PHP family phosphoeste 31.2 12 0.00026 28.5 -0.6 25 31-55 248-273 (403)
325 PRK01678 rpmE2 50S ribosomal p 30.2 37 0.0008 20.7 1.5 21 19-41 5-25 (87)
326 COG3530 Uncharacterized protei 30.2 30 0.00066 20.3 1.0 14 13-26 8-22 (71)
327 PF13909 zf-H2C2_5: C2H2-type 30.1 27 0.00059 15.3 0.7 10 49-59 2-11 (24)
328 cd03019 DsbA_DsbA DsbA family, 30.0 19 0.00041 22.6 0.2 21 39-61 18-38 (178)
329 PF04315 DUF462: Protein of un 29.8 30 0.00065 23.6 1.1 14 54-67 8-21 (164)
330 PF06689 zf-C4_ClpX: ClpX C4-t 29.8 31 0.00066 17.8 0.9 16 49-64 3-21 (41)
331 PTZ00255 60S ribosomal protein 29.7 36 0.00077 21.0 1.4 13 49-61 38-50 (90)
332 cd00029 C1 Protein kinase C co 29.7 22 0.00048 18.0 0.4 24 30-54 12-35 (50)
333 PF00684 DnaJ_CXXCXGXG: DnaJ c 29.4 54 0.0012 18.2 2.0 11 49-59 43-53 (66)
334 PF11238 DUF3039: Protein of u 29.1 40 0.00087 19.2 1.4 26 24-54 23-51 (58)
335 TIGR00467 lysS_arch lysyl-tRNA 28.7 1.4E+02 0.0031 23.4 4.8 42 17-62 158-205 (515)
336 PLN02294 cytochrome c oxidase 28.7 53 0.0012 22.6 2.2 21 49-69 143-163 (174)
337 KOG4739|consensus 28.6 27 0.00059 24.9 0.8 13 49-62 39-51 (233)
338 PF07535 zf-DBF: DBF zinc fing 28.4 30 0.00065 18.9 0.8 14 4-17 34-47 (49)
339 PF02005 TRM: N2,N2-dimethylgu 28.2 34 0.00073 25.6 1.3 34 25-58 236-270 (377)
340 PF08790 zf-LYAR: LYAR-type C2 28.2 35 0.00076 16.7 0.9 11 31-41 2-12 (28)
341 PRK12577 succinate dehydrogena 28.1 27 0.00059 25.5 0.7 12 1-12 110-121 (329)
342 PF05180 zf-DNL: DNL zinc fing 28.1 42 0.00091 19.5 1.4 30 28-58 3-40 (66)
343 TIGR00308 TRM1 tRNA(guanine-26 27.9 58 0.0013 24.3 2.5 30 26-55 230-260 (374)
344 KOG3352|consensus 27.8 47 0.001 22.4 1.8 44 20-66 104-152 (153)
345 TIGR00280 L37a ribosomal prote 27.8 41 0.00088 20.8 1.4 12 49-60 37-48 (91)
346 PRK10954 periplasmic protein d 27.8 28 0.00061 23.2 0.7 21 36-58 37-57 (207)
347 PTZ00409 Sir2 (Silent Informat 27.4 26 0.00055 25.1 0.5 13 28-40 136-148 (271)
348 COG2191 Formylmethanofuran deh 27.0 54 0.0012 23.1 2.0 16 28-43 171-186 (206)
349 PF15389 DUF4612: Domain of un 27.0 52 0.0011 21.2 1.8 13 5-17 93-105 (115)
350 PRK03976 rpl37ae 50S ribosomal 26.6 44 0.00096 20.5 1.4 13 49-61 38-50 (90)
351 cd00674 LysRS_core_class_I cat 26.5 2E+02 0.0042 21.5 5.0 43 16-62 158-207 (353)
352 cd00974 DSRD Desulforedoxin (D 26.4 67 0.0014 15.6 1.8 12 49-60 6-17 (34)
353 PF10686 DUF2493: Protein of u 26.3 71 0.0015 18.3 2.2 17 2-18 16-32 (71)
354 PF00643 zf-B_box: B-box zinc 25.9 57 0.0012 16.1 1.6 12 26-37 12-23 (42)
355 PHA02611 51 baseplate hub asse 25.6 71 0.0015 23.1 2.5 17 27-43 80-96 (249)
356 cd02337 ZZ_CBP Zinc finger, ZZ 25.6 48 0.001 17.2 1.2 22 32-58 3-24 (41)
357 PF06044 DRP: Dam-replacing fa 25.6 59 0.0013 23.6 2.1 10 29-38 31-40 (254)
358 PTZ00410 NAD-dependent SIR2; P 25.6 37 0.00081 25.4 1.1 31 25-55 143-179 (349)
359 PF04423 Rad50_zn_hook: Rad50 25.3 29 0.00063 18.6 0.4 8 49-56 22-29 (54)
360 TIGR00319 desulf_FeS4 desulfof 25.3 72 0.0016 15.4 1.8 9 49-57 9-17 (34)
361 smart00154 ZnF_AN1 AN1-like Zi 25.3 55 0.0012 16.7 1.4 10 30-39 13-22 (39)
362 PF10071 DUF2310: Zn-ribbon-co 24.9 41 0.00088 24.4 1.1 26 29-54 220-248 (258)
363 TIGR03831 YgiT_finger YgiT-typ 24.7 47 0.001 16.5 1.1 10 46-55 31-40 (46)
364 PF05265 DUF723: Protein of un 24.6 57 0.0012 18.7 1.5 30 25-54 28-60 (60)
365 KOG2593|consensus 24.5 48 0.001 25.8 1.5 46 9-56 108-162 (436)
366 PRK00528 rpmE 50S ribosomal pr 24.1 1.5E+02 0.0032 17.2 3.3 35 19-58 5-48 (71)
367 PHA00732 hypothetical protein 24.1 44 0.00095 19.7 1.0 9 32-40 4-12 (79)
368 PF13966 zf-RVT: zinc-binding 23.9 43 0.00093 19.3 0.9 25 27-52 57-81 (86)
369 PF04981 NMD3: NMD3 family ; 23.8 31 0.00067 23.9 0.3 30 30-59 14-47 (236)
370 PTZ00408 NAD-dependent deacety 23.6 44 0.00096 23.4 1.1 28 27-54 115-144 (242)
371 PF04808 CTV_P23: Citrus trist 23.5 67 0.0015 21.9 1.9 33 9-42 45-78 (209)
372 PRK13552 frdB fumarate reducta 23.5 68 0.0015 22.4 2.0 12 1-12 105-116 (239)
373 cd02663 Peptidase_C19G A subfa 23.3 1.9E+02 0.004 20.2 4.2 22 22-43 112-134 (300)
374 PF13465 zf-H2C2_2: Zinc-finge 23.2 42 0.00092 15.3 0.7 11 30-40 15-25 (26)
375 smart00355 ZnF_C2H2 zinc finge 23.2 38 0.00083 14.1 0.5 11 31-41 2-12 (26)
376 COG5270 PUA domain (predicted 23.0 53 0.0011 23.1 1.4 37 18-61 4-40 (202)
377 PF13894 zf-C2H2_4: C2H2-type 23.0 45 0.00099 13.8 0.7 11 31-41 2-12 (24)
378 PF01930 Cas_Cas4: Domain of u 23.0 98 0.0021 19.5 2.6 30 5-38 128-157 (162)
379 COG1885 Uncharacterized protei 23.0 40 0.00086 21.6 0.7 9 49-57 51-59 (115)
380 COG2401 ABC-type ATPase fused 22.9 59 0.0013 26.0 1.7 31 27-62 128-158 (593)
381 PRK00423 tfb transcription ini 22.9 39 0.00085 24.3 0.8 27 29-55 11-38 (310)
382 COG4049 Uncharacterized protei 22.9 41 0.00089 19.4 0.7 11 43-55 15-25 (65)
383 cd00021 BBOX B-Box-type zinc f 22.8 58 0.0013 15.5 1.2 12 26-37 9-20 (39)
384 CHL00136 rpl31 ribosomal prote 22.6 1.5E+02 0.0032 17.2 3.0 37 19-58 6-46 (68)
385 PF05129 Elf1: Transcription e 22.5 69 0.0015 18.9 1.7 34 27-60 20-60 (81)
386 COG4306 Uncharacterized protei 22.2 30 0.00066 23.0 0.1 14 28-41 67-80 (160)
387 KOG4582|consensus 22.1 49 0.0011 23.8 1.1 48 9-59 130-179 (278)
388 smart00336 BBOX B-Box-type zin 21.9 72 0.0016 15.4 1.5 12 26-37 12-23 (42)
389 TIGR03830 CxxCG_CxxCG_HTH puta 21.7 71 0.0015 19.2 1.7 19 36-56 22-40 (127)
390 COG1579 Zn-ribbon protein, pos 21.6 35 0.00075 24.4 0.3 25 31-57 199-231 (239)
391 smart00778 Prim_Zn_Ribbon Zinc 21.5 48 0.001 17.0 0.7 13 49-61 5-17 (37)
392 PF08273 Prim_Zn_Ribbon: Zinc- 21.4 44 0.00096 17.4 0.6 12 49-60 5-16 (40)
393 PF14634 zf-RING_5: zinc-RING 21.4 9.2 0.0002 19.7 -2.1 6 49-54 38-43 (44)
394 smart00714 LITAF Possible memb 21.3 56 0.0012 18.1 1.0 14 49-62 5-18 (67)
395 TIGR00105 L31 ribosomal protei 21.2 68 0.0015 18.4 1.4 34 19-56 5-44 (68)
396 PF08646 Rep_fac-A_C: Replicat 21.2 51 0.0011 20.8 0.9 28 27-56 16-46 (146)
397 PF06906 DUF1272: Protein of u 21.1 47 0.001 18.9 0.7 14 45-58 39-52 (57)
398 PF12322 T4_baseplate: T4 bact 21.0 87 0.0019 21.6 2.1 19 26-44 75-93 (205)
399 COG5525 Bacteriophage tail ass 20.9 67 0.0014 26.1 1.7 15 28-42 226-240 (611)
400 TIGR00622 ssl1 transcription f 20.9 58 0.0013 20.8 1.2 8 32-39 58-65 (112)
401 PRK06556 vitamin B12-dependent 20.8 66 0.0014 27.3 1.7 25 30-56 925-949 (953)
402 PF14169 YdjO: Cold-inducible 20.7 48 0.001 18.9 0.7 30 28-57 17-49 (59)
403 PF10474 DUF2451: Protein of u 20.6 99 0.0022 21.6 2.4 23 2-24 100-122 (234)
404 KOG2768|consensus 20.6 64 0.0014 23.1 1.4 32 29-60 181-215 (231)
405 TIGR03826 YvyF flagellar opero 20.5 24 0.00052 23.1 -0.7 24 29-55 3-26 (137)
406 KOG2324|consensus 20.3 71 0.0015 24.9 1.7 30 27-56 225-256 (457)
407 PF09687 PRESAN: Plasmodium RE 20.2 1.2E+02 0.0026 17.9 2.4 22 4-25 47-68 (129)
408 KOG2683|consensus 20.1 59 0.0013 24.0 1.2 26 14-39 142-167 (305)
No 1
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=100.00 E-value=7.5e-36 Score=172.87 Aligned_cols=60 Identities=55% Similarity=1.170 Sum_probs=22.2
Q ss_pred CChHHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceee
Q psy1204 1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60 (71)
Q Consensus 1 ~dm~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~i 60 (71)
+||+.+|++||++|+++|||++|++++|.|+||||+++|.++||++||||++|+||||++
T Consensus 2 ~dM~~~w~~LD~~i~~~pmP~~Y~~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT~q 61 (61)
T PF14599_consen 2 VDMSAYWRMLDAEIAATPMPEEYRNKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYNTRQ 61 (61)
T ss_dssp --------------------------EEEEEESSS--EEEEE--TT----TTTS---EEE
T ss_pred CCHHHHHHHHHHHHHhCCCCHHHhCCEEEEECCCCCCccceeeeHhhhcCCCCCCcccCC
Confidence 599999999999999999999999999999999999999999999999999999999985
No 2
>KOG1940|consensus
Probab=99.77 E-value=3.7e-19 Score=127.29 Aligned_cols=65 Identities=49% Similarity=0.921 Sum_probs=62.2
Q ss_pred CChHHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCC
Q psy1204 1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPN 65 (71)
Q Consensus 1 ~dm~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~ 65 (71)
.||+.+|+++|++|+++|||++|+++.+.|+||||+..+.+.||++++||+.|+||||++++.+.
T Consensus 206 ~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~~~l~~kc~~c~~~~~r~~~~~~ 270 (276)
T KOG1940|consen 206 GDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKYHILYHKCGKCGSYNTRMISDPS 270 (276)
T ss_pred HHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCccceehhhhhCCCcccceeeeccCCC
Confidence 48999999999999999999999999999999999999999999999999999999999998544
No 3
>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=98.75 E-value=1.2e-08 Score=64.83 Aligned_cols=57 Identities=12% Similarity=0.179 Sum_probs=44.0
Q ss_pred HHHHHHHcCCCCHh---hhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCCC
Q psy1204 9 QMDEEIASTPMPEE---YKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNGQ 67 (71)
Q Consensus 9 ~lD~~i~~~pmP~~---y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~~ 67 (71)
.+|...+.+++--. ....|+.++|++|+..+.+..+.+ .||.|||+++++++|++..
T Consensus 47 af~~~~~~t~~ega~L~I~~~p~~~~C~~Cg~~~~~~~~~~--~CP~Cgs~~~~i~~G~El~ 106 (115)
T TIGR00100 47 AFEVVREGTVAEGAKLNIEDEPVECECEDCSEEVSPEIDLY--RCPKCHGIMLQVRAGKELN 106 (115)
T ss_pred HHHHHhCCCccCCCEEEEEeeCcEEEcccCCCEEecCCcCc--cCcCCcCCCcEEecCCeEE
Confidence 34555556655222 446789999999999999877666 8999999999999999853
No 4
>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=98.72 E-value=1.3e-08 Score=64.24 Aligned_cols=56 Identities=20% Similarity=0.252 Sum_probs=38.7
Q ss_pred HHHHHHHcCCCCHh---hhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCC
Q psy1204 9 QMDEEIASTPMPEE---YKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNG 66 (71)
Q Consensus 9 ~lD~~i~~~pmP~~---y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~ 66 (71)
.++...+.++.-.. ....|+..+|++||+.|.+..+.+ .||.|||++.++++|++.
T Consensus 47 ~f~~~~~~T~~e~a~L~Ie~~p~~~~C~~Cg~~~~~~~~~~--~CP~Cgs~~~~i~~G~el 105 (113)
T PF01155_consen 47 AFEVLAEGTILEGAELEIEEVPARARCRDCGHEFEPDEFDF--SCPRCGSPDVEIISGREL 105 (113)
T ss_dssp HHHHHHCCSTTTT-EEEEEEE--EEEETTTS-EEECHHCCH--H-SSSSSS-EEEEESS-E
T ss_pred HHHHHhCCCCccCCEEEEEecCCcEECCCCCCEEecCCCCC--CCcCCcCCCcEEccCCeE
Confidence 44555556655333 346689999999999999988776 899999999999999975
No 5
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=98.70 E-value=1e-08 Score=64.99 Aligned_cols=56 Identities=14% Similarity=0.106 Sum_probs=43.1
Q ss_pred HHHHHHcCCCCHh---hhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCCC
Q psy1204 10 MDEEIASTPMPEE---YKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNGQ 67 (71)
Q Consensus 10 lD~~i~~~pmP~~---y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~~ 67 (71)
+|...+.+++--. -...|+.++|++|++.+.+..+++ .||.|||+++.+++|+|..
T Consensus 48 f~~~~~~T~~egA~L~I~~vp~~~~C~~Cg~~~~~~~~~~--~CP~Cgs~~~~i~~G~El~ 106 (113)
T PRK12380 48 FEIVCHGTVAQGCDLHIVYKPAQAWCWDCSQVVEIHQHDA--QCPHCHGERLRVDTGDSLI 106 (113)
T ss_pred HHHHhCCCccCCCEEEEEeeCcEEEcccCCCEEecCCcCc--cCcCCCCCCcEEccCCeEE
Confidence 4445555654322 335688999999999999887666 7999999999999999853
No 6
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=98.65 E-value=3.5e-08 Score=62.60 Aligned_cols=57 Identities=12% Similarity=0.166 Sum_probs=43.0
Q ss_pred HHHHHHHcCCCCHh---hhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCC
Q psy1204 9 QMDEEIASTPMPEE---YKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNG 66 (71)
Q Consensus 9 ~lD~~i~~~pmP~~---y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~ 66 (71)
.+|...+.+++--. ....|+..+|++|++.+....+.+. .||.|||+++++++|++.
T Consensus 47 ~f~~~~~~t~~egA~L~i~~~p~~~~C~~Cg~~~~~~~~~~~-~CP~Cgs~~~~i~~G~El 106 (114)
T PRK03681 47 CFDLVCRGTVAEGCKLHLEEQEAECWCETCQQYVTLLTQRVR-RCPQCHGDMLRIVADDGL 106 (114)
T ss_pred HHHHHhCCCccCCCEEEEEeeCcEEEcccCCCeeecCCccCC-cCcCcCCCCcEEccCCeE
Confidence 44555556655322 3456899999999999988765522 899999999999999985
No 7
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=98.64 E-value=3.4e-08 Score=62.89 Aligned_cols=58 Identities=19% Similarity=0.217 Sum_probs=42.8
Q ss_pred HHHHHHHcCC-CCHh---hhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCCC
Q psy1204 9 QMDEEIASTP-MPEE---YKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNGQ 67 (71)
Q Consensus 9 ~lD~~i~~~p-mP~~---y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~~ 67 (71)
.+|...+.+| +.-. ....|+.++|++||..+.+..+.+. .||.|||+++++++|++..
T Consensus 47 af~~~~~~T~~~ega~L~Ie~vp~~~~C~~Cg~~~~~~~~~~~-~CP~Cgs~~~~i~~G~El~ 108 (117)
T PRK00564 47 AFETFREESLVCKDAILDIVDEKVELECKDCSHVFKPNALDYG-VCEKCHSKNVIITQGNEMR 108 (117)
T ss_pred HHHHHhcCCcccCCCEEEEEecCCEEEhhhCCCccccCCccCC-cCcCCCCCceEEecCCEEE
Confidence 4455556663 3221 3466899999999999988754332 7999999999999998853
No 8
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=98.57 E-value=8.6e-08 Score=62.36 Aligned_cols=57 Identities=19% Similarity=0.385 Sum_probs=41.4
Q ss_pred HHHHHHHcCCCCHh---hhcceeeEEcCCCCCceeec---------------------eEeecccCCCCCCcceeeecCC
Q psy1204 9 QMDEEIASTPMPEE---YKNVILYVLCKDCHKESKVL---------------------YHIIGLKCEHCGSYNTCRIKKP 64 (71)
Q Consensus 9 ~lD~~i~~~pmP~~---y~~~~v~i~CndC~~~s~v~---------------------~h~~g~kCp~C~Synt~ii~g~ 64 (71)
.++...+.+++-.. ....++..+|++||..+.+. ..++ .||.|||+++++++|+
T Consensus 47 afe~l~~gt~~ega~L~i~~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~CP~Cgs~~~~i~~G~ 124 (135)
T PRK03824 47 ALNELLKGTILEGAEIIFEEEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFL--KCPKCGSRDFEIVKGR 124 (135)
T ss_pred HHHHHHcCCcccCCEEEEEecceEEECCCCCCEEecccccccccccccccccccccccccCc--CCcCCCCCCcEEecCc
Confidence 34444455655331 33567899999999999876 3333 8999999999999998
Q ss_pred CCC
Q psy1204 65 NGQ 67 (71)
Q Consensus 65 ~~~ 67 (71)
+..
T Consensus 125 el~ 127 (135)
T PRK03824 125 GVY 127 (135)
T ss_pred eEE
Confidence 853
No 9
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=98.39 E-value=2.2e-07 Score=59.62 Aligned_cols=40 Identities=25% Similarity=0.340 Sum_probs=36.7
Q ss_pred cceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCC
Q psy1204 25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNG 66 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~ 66 (71)
..|+.++|.+|+..++...|.+ .||.|+|.+.+|++|++.
T Consensus 66 ~~p~~~~C~~C~~~~~~e~~~~--~CP~C~s~~~~i~~G~el 105 (115)
T COG0375 66 EEPAECWCLDCGQEVELEELDY--RCPKCGSINLRIIGGDEL 105 (115)
T ss_pred EeccEEEeccCCCeecchhhee--ECCCCCCCceEEecCCee
Confidence 5689999999999999999888 699999999999999875
No 10
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=98.19 E-value=1.1e-06 Score=56.44 Aligned_cols=57 Identities=16% Similarity=0.247 Sum_probs=39.4
Q ss_pred HHHHHHcCCCCHh---hhcceeeEEcCCCCCceeec-e----EeecccCCCCCCcceeeecCCCCC
Q psy1204 10 MDEEIASTPMPEE---YKNVILYVLCKDCHKESKVL-Y----HIIGLKCEHCGSYNTCRIKKPNGQ 67 (71)
Q Consensus 10 lD~~i~~~pmP~~---y~~~~v~i~CndC~~~s~v~-~----h~~g~kCp~C~Synt~ii~g~~~~ 67 (71)
+|...+.+++--. ....++..+| +|++.|... + +.+...||.|||+++.+++|++..
T Consensus 48 f~~~~~gT~~egA~L~I~~vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~El~ 112 (124)
T PRK00762 48 LDVLAEGTIAEDADLIVEMIPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGGRECN 112 (124)
T ss_pred HHHHhCCCCcCCCEEEEEecCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecCCeEE
Confidence 3444455554322 3456899999 999997654 1 111237999999999999999864
No 11
>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=97.37 E-value=0.00035 Score=38.02 Aligned_cols=36 Identities=19% Similarity=0.358 Sum_probs=26.3
Q ss_pred eEEcCCCCCceeeceEe---ecccCCCCCCcce-eeecCC
Q psy1204 29 YVLCKDCHKESKVLYHI---IGLKCEHCGSYNT-CRIKKP 64 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~---~g~kCp~C~Synt-~ii~g~ 64 (71)
..+|.+||.+|++.... ....||.|||.++ ++++..
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~~s~~ 44 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRLLSAV 44 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEEeccc
Confidence 57899999999875421 1237999999776 677643
No 12
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=96.91 E-value=0.0011 Score=35.59 Aligned_cols=32 Identities=22% Similarity=0.392 Sum_probs=24.7
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCccee
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYNTC 59 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ 59 (71)
....|.+||..++.....-..+||.||+.-..
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 46889999999987665424499999986653
No 13
>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=96.69 E-value=0.0027 Score=32.60 Aligned_cols=34 Identities=26% Similarity=0.385 Sum_probs=23.8
Q ss_pred eeEEcCCCCCceeeceE---eecccCCCCCCcceeee
Q psy1204 28 LYVLCKDCHKESKVLYH---IIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h---~~g~kCp~C~Synt~ii 61 (71)
-..+|.+||+.|++..- .....||.||+.-.+++
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~r~~ 40 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISDDPLATCPECGGDVRRLI 40 (41)
T ss_pred EEEEcCCCCCEEEEEEecCCCCCCCCCCCCCcceecc
Confidence 36789999999986542 22348999999444443
No 14
>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=96.67 E-value=0.00097 Score=50.49 Aligned_cols=32 Identities=28% Similarity=0.577 Sum_probs=25.8
Q ss_pred ceeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204 26 VILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii 61 (71)
.+....|..||.++.. |+| +||.|++|||-+-
T Consensus 4 ~~~~y~C~~Cg~~~~~---~~g-~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 4 AKSKFVCQHCGADSPK---WQG-KCPACHAWNTITE 35 (454)
T ss_pred CCCeEECCcCCCCCcc---ccE-ECcCCCCccccch
Confidence 3567899999986543 666 9999999999875
No 15
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=96.65 E-value=0.0012 Score=50.57 Aligned_cols=34 Identities=29% Similarity=0.589 Sum_probs=27.3
Q ss_pred ceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecC
Q psy1204 26 VILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKK 63 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g 63 (71)
.+....|+.||.+| -.|+| |||.|+.|||-+-..
T Consensus 4 ~~t~f~C~~CG~~s---~KW~G-kCp~Cg~Wns~vE~~ 37 (456)
T COG1066 4 KKTAFVCQECGYVS---PKWLG-KCPACGAWNTLVEEV 37 (456)
T ss_pred cccEEEcccCCCCC---ccccc-cCCCCCCccceEEee
Confidence 34678999999855 45899 999999999977543
No 16
>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=96.62 E-value=0.0034 Score=33.25 Aligned_cols=31 Identities=29% Similarity=0.518 Sum_probs=22.8
Q ss_pred eEEcCCCCCceeeceE---eecccCCCCCCccee
Q psy1204 29 YVLCKDCHKESKVLYH---IIGLKCEHCGSYNTC 59 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h---~~g~kCp~C~Synt~ 59 (71)
...|.+||..|++... .....||.||+-+++
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 5789999999986432 234589999995543
No 17
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=96.60 E-value=0.0017 Score=35.11 Aligned_cols=28 Identities=21% Similarity=0.673 Sum_probs=22.1
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
+...|.+||.+++... ....+||.||+.
T Consensus 1 ~~Y~C~~Cg~~~~~~~-~~~irC~~CG~r 28 (44)
T smart00659 1 MIYICGECGRENEIKS-KDVVRCRECGYR 28 (44)
T ss_pred CEEECCCCCCEeecCC-CCceECCCCCce
Confidence 3578999999998874 344599999874
No 18
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=96.25 E-value=0.0031 Score=35.04 Aligned_cols=30 Identities=27% Similarity=0.663 Sum_probs=24.8
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
.....|..||++++...-.-+..||.|||-
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 568899999999986666666799999874
No 19
>PRK11823 DNA repair protein RadA; Provisional
Probab=96.18 E-value=0.0028 Score=47.86 Aligned_cols=31 Identities=32% Similarity=0.768 Sum_probs=25.3
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii 61 (71)
+....|..||.++. .|+| +||.|++|||-+-
T Consensus 5 ~~~y~C~~Cg~~~~---~~~g-~Cp~C~~w~t~~e 35 (446)
T PRK11823 5 KTAYVCQECGAESP---KWLG-RCPECGAWNTLVE 35 (446)
T ss_pred CCeEECCcCCCCCc---ccCe-eCcCCCCccceee
Confidence 56789999998554 3666 9999999999865
No 20
>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=96.02 E-value=0.0073 Score=46.85 Aligned_cols=53 Identities=23% Similarity=0.330 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204 4 TPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 4 ~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~ 62 (71)
+.+++.++......-++-. -+.++. .|++||.... ..+.+||.|||.++.++.
T Consensus 495 ~al~~lv~~a~~~~~~y~~-~~~p~~-~C~~CG~~~~----~~~~~CP~CGs~~~~~~~ 547 (555)
T cd01675 495 EALEALVKKAAKRGVIYFG-INTPID-ICNDCGYIGE----GEGFKCPKCGSEDVEVIS 547 (555)
T ss_pred HHHHHHHHHHHHcCCceEE-EecCCc-cCCCCCCCCc----CCCCCCcCCCCcCceEEE
Confidence 3455555554444344433 345667 9999998554 223499999999877664
No 21
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=95.94 E-value=0.0073 Score=46.83 Aligned_cols=54 Identities=22% Similarity=0.214 Sum_probs=26.6
Q ss_pred hHHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204 3 MTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 3 m~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~ 62 (71)
.+.+++.++.......+|-. .-.+..-.|++||..... .. +||.|||.|+.+++
T Consensus 466 ~~al~~lv~~~~~~~~i~Y~-~in~~~~~C~~CG~~~~~---~~--~CP~CGs~~~~~~~ 519 (546)
T PF13597_consen 466 PEALEKLVRYAMENTGIPYF-TINPPIDICPDCGYIGGE---GD--KCPKCGSENIEVYS 519 (546)
T ss_dssp HHHHHHHHHHHHH--H-SEE-EEE--EEEETTT---S-----EE--E-CCC----EEEEB
T ss_pred HHHHHHHHHHHHHhCCCCeE-EEecCcccccCCCcCCCC---CC--CCCCCCCcccceEE
Confidence 34566666666665666654 223567789999986543 23 89999999988875
No 22
>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=95.83 E-value=0.0043 Score=46.02 Aligned_cols=27 Identities=37% Similarity=0.853 Sum_probs=22.6
Q ss_pred EcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~Synt~ii 61 (71)
.|.+||.++. .|+| +||.|++|||-+-
T Consensus 2 ~c~~cg~~~~---~~~g-~cp~c~~w~~~~e 28 (372)
T cd01121 2 VCSECGYVSP---KWLG-KCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCCCC---CccE-ECcCCCCceeeee
Confidence 5999998554 4777 9999999999875
No 23
>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=95.65 E-value=0.012 Score=30.10 Aligned_cols=30 Identities=30% Similarity=0.538 Sum_probs=15.5
Q ss_pred cceeeEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
.+-+.-+|.+||...-.+. ..||+|+|.+.
T Consensus 7 ~~l~~~rC~~Cg~~~~pPr----~~Cp~C~s~~l 36 (37)
T PF12172_consen 7 GRLLGQRCRDCGRVQFPPR----PVCPHCGSDEL 36 (37)
T ss_dssp T-EEEEE-TTT--EEES------SEETTTT----
T ss_pred CEEEEEEcCCCCCEecCCC----cCCCCcCcccc
Confidence 3467889999998654444 28999999775
No 24
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=94.75 E-value=0.062 Score=35.04 Aligned_cols=28 Identities=29% Similarity=0.485 Sum_probs=23.2
Q ss_pred cceeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
.+-+-.+|++||+.+-.+.. .||+|+|-
T Consensus 25 ~kl~g~kC~~CG~v~~PPr~----~Cp~C~~~ 52 (140)
T COG1545 25 GKLLGTKCKKCGRVYFPPRA----YCPKCGSE 52 (140)
T ss_pred CcEEEEEcCCCCeEEcCCcc----cCCCCCCC
Confidence 45678999999988776664 89999999
No 25
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=94.54 E-value=0.054 Score=31.16 Aligned_cols=41 Identities=27% Similarity=0.455 Sum_probs=28.8
Q ss_pred hcceeeEEcCCCCCceeeceEee-cccCCCCCCcceeeecCC
Q psy1204 24 KNVILYVLCKDCHKESKVLYHII-GLKCEHCGSYNTCRIKKP 64 (71)
Q Consensus 24 ~~~~v~i~CndC~~~s~v~~h~~-g~kCp~C~Synt~ii~g~ 64 (71)
+...+.+.|+||+.+..+..|-- -.+|..||..=.+=.+|+
T Consensus 6 ~S~F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~PtGGK 47 (59)
T PRK00415 6 RSRFLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGK 47 (59)
T ss_pred CCeEEEEECCCCCCeEEEEecCCcEEECcccCCCcccCCCcc
Confidence 45588999999999998765521 228999987655444443
No 26
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=93.92 E-value=0.075 Score=31.28 Aligned_cols=45 Identities=29% Similarity=0.484 Sum_probs=31.1
Q ss_pred CHhhhcceeeEEcCCCCCceeeceEe-ecccCCCCCCcceeeecCC
Q psy1204 20 PEEYKNVILYVLCKDCHKESKVLYHI-IGLKCEHCGSYNTCRIKKP 64 (71)
Q Consensus 20 P~~y~~~~v~i~CndC~~~s~v~~h~-~g~kCp~C~Synt~ii~g~ 64 (71)
|.+-+...+.+.|.||+.+..+..|- ...+|..||..=.+=.+|+
T Consensus 10 p~~p~s~Fl~VkCpdC~N~q~vFshast~V~C~~CG~~l~~PTGGk 55 (67)
T COG2051 10 PKEPRSRFLRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEPTGGK 55 (67)
T ss_pred cCCCCceEEEEECCCCCCEEEEeccCceEEEecccccEEEecCCCe
Confidence 43446678999999999998875542 1238999987655544443
No 27
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=93.78 E-value=0.027 Score=35.65 Aligned_cols=32 Identities=19% Similarity=0.222 Sum_probs=22.8
Q ss_pred eeeEEcCCCCCceee-ceEeecccCCCCCCcceee
Q psy1204 27 ILYVLCKDCHKESKV-LYHIIGLKCEHCGSYNTCR 60 (71)
Q Consensus 27 ~v~i~CndC~~~s~v-~~h~~g~kCp~C~Synt~i 60 (71)
-..-.|..||++|.- +..-+ .||+||..-...
T Consensus 7 GtKR~Cp~CG~kFYDLnk~Pi--vCP~CG~~~~~~ 39 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDLNKDPI--VCPKCGTEFPPE 39 (108)
T ss_pred CCcccCCCCcchhccCCCCCc--cCCCCCCccCcc
Confidence 356679999999974 44444 899998754433
No 28
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=93.70 E-value=0.12 Score=28.89 Aligned_cols=45 Identities=18% Similarity=0.454 Sum_probs=30.5
Q ss_pred HHHHHHHHcCCCCHhhhcceeeEEcCCCCCcee------eceEeecccCCCCCCcc
Q psy1204 8 RQMDEEIASTPMPEEYKNVILYVLCKDCHKESK------VLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 8 ~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~------v~~h~~g~kCp~C~Syn 57 (71)
+.||.++..-|+.+.- +..+.|..|....- ..+..+ +||+|+..|
T Consensus 4 ki~d~L~G~d~~~~~~---r~aLIC~~C~~hNGla~~~~~~~i~y--~C~~Cg~~N 54 (54)
T PF10058_consen 4 KILDVLLGDDPTSPSN---RYALICSKCFSHNGLAPKEEFEEIQY--RCPYCGALN 54 (54)
T ss_pred HHHHHHhCCCCccccC---ceeEECcccchhhcccccccCCceEE--EcCCCCCcC
Confidence 5688888888844442 33455999986542 233444 999999876
No 29
>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=93.63 E-value=0.088 Score=26.72 Aligned_cols=28 Identities=21% Similarity=0.610 Sum_probs=19.4
Q ss_pred eEEcCCCCCceeece-----EeecccCCCCCCc
Q psy1204 29 YVLCKDCHKESKVLY-----HIIGLKCEHCGSY 56 (71)
Q Consensus 29 ~i~CndC~~~s~v~~-----h~~g~kCp~C~Sy 56 (71)
.+.|..|++.+.+.. .-.-..||.|++.
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 578999999887652 1111389999864
No 30
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.59 E-value=0.058 Score=27.79 Aligned_cols=27 Identities=22% Similarity=0.642 Sum_probs=19.5
Q ss_pred eEEcCCCCCceeeceE-----eecccCCCCCC
Q psy1204 29 YVLCKDCHKESKVLYH-----IIGLKCEHCGS 55 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h-----~~g~kCp~C~S 55 (71)
.|.|..|+..+.++.- -.-.+|++|+.
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGH 33 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCc
Confidence 6889999999976432 22348999975
No 31
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=93.58 E-value=0.091 Score=29.75 Aligned_cols=31 Identities=29% Similarity=0.586 Sum_probs=23.3
Q ss_pred ceeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204 26 VILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii 61 (71)
.+..+.|..||.. ...|. .|+.||.|+-+++
T Consensus 24 ~~~l~~C~~CG~~--~~~H~---vC~~CG~Y~gr~v 54 (57)
T PRK12286 24 APGLVECPNCGEP--KLPHR---VCPSCGYYKGREV 54 (57)
T ss_pred CCcceECCCCCCc--cCCeE---ECCCCCcCCCEEe
Confidence 3667899999962 23343 6999999998875
No 32
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=93.44 E-value=0.1 Score=42.04 Aligned_cols=43 Identities=26% Similarity=0.336 Sum_probs=28.4
Q ss_pred HHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204 14 IASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 14 i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~ 62 (71)
+..+.||.. .-.+-.-.|++||..... | .+||.|||.++.+++
T Consensus 666 ~~~~~i~Y~-sin~~~~~C~~CG~~~~~--~---~~CP~CG~~~~~~~~ 708 (735)
T PRK07111 666 MKNTNIGYG-SINHPVDRCPVCGYLGVI--E---DKCPKCGSTNIQRIR 708 (735)
T ss_pred HHhCCCceE-EeCCCCeecCCCCCCCCc--C---ccCcCCCCccceeee
Confidence 444556654 223557789999965542 2 399999998776664
No 33
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=93.44 E-value=0.048 Score=43.73 Aligned_cols=31 Identities=19% Similarity=0.454 Sum_probs=21.6
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
+..-.|++||.+.+....-.+..||.|||.+
T Consensus 639 ~~~~~C~~CG~~Ge~~~~~~~~~CP~CG~~~ 669 (711)
T PRK09263 639 TPIDECYECGFTGEFECTEKGFTCPKCGNHD 669 (711)
T ss_pred CCCcccCCCCCCccccCCCCCCcCcCCCCCC
Confidence 4567899999865442222234999999977
No 34
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=93.36 E-value=0.059 Score=42.76 Aligned_cols=52 Identities=23% Similarity=0.347 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204 4 TPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 4 ~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii 61 (71)
+.+++.++... .+.+|-. .-.+..-.|++||..... .+..||.|||.++.++
T Consensus 543 eal~~lv~~~~-~~~i~Yf-~in~~~~iC~~CG~~~~g----~~~~CP~CGs~~~ev~ 594 (623)
T PRK08271 543 EGYRKLLNIAA-KTGCNYF-AFNVKITICNDCHHIDKR----TGKRCPICGSENIDYY 594 (623)
T ss_pred HHHHHHHHHHH-HcCCceE-EeCCCCccCCCCCCcCCC----CCcCCcCCCCcchhHH
Confidence 34455555443 3556655 223567789999975322 2249999999886654
No 35
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=93.02 E-value=0.055 Score=42.91 Aligned_cols=43 Identities=19% Similarity=0.329 Sum_probs=28.5
Q ss_pred HcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204 15 ASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 15 ~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~ 62 (71)
..+.+|-. .-.+..-.|.+||.+.... +..||.|||.++.+++
T Consensus 555 ~~~~i~Y~-~inp~~~~C~~CG~~~~g~----~~~CP~CGs~~~~v~~ 597 (625)
T PRK08579 555 MNTKLVYW-SYTPAITVCNKCGRSTTGL----YTRCPRCGSEDVEVWS 597 (625)
T ss_pred HhcCCceE-EeCCCCccCCCCCCccCCC----CCcCcCCCCchhHHHH
Confidence 34555544 2236788999999855222 2399999998766553
No 36
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=92.97 E-value=0.068 Score=36.01 Aligned_cols=21 Identities=33% Similarity=0.645 Sum_probs=17.3
Q ss_pred ccCCCCCCcceeeecCCCCCC
Q psy1204 48 LKCEHCGSYNTCRIKKPNGQE 68 (71)
Q Consensus 48 ~kCp~C~Synt~ii~g~~~~~ 68 (71)
++||+|++.+|+|++-+...+
T Consensus 1 M~CPfC~~~~tkViDSR~~ed 21 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEE 21 (156)
T ss_pred CCCCCCCCCCCeeeecccccc
Confidence 489999999999998665443
No 37
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=92.93 E-value=0.041 Score=34.39 Aligned_cols=32 Identities=22% Similarity=0.232 Sum_probs=22.6
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
..-..|++||.+|.....-.--.||.|.|.-.
T Consensus 56 v~Pa~CkkCGfef~~~~ik~pSRCP~CKSE~I 87 (97)
T COG3357 56 VRPARCKKCGFEFRDDKIKKPSRCPKCKSEWI 87 (97)
T ss_pred ecChhhcccCccccccccCCcccCCcchhhcc
Confidence 34568999999997643332238999999643
No 38
>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=92.86 E-value=0.11 Score=40.74 Aligned_cols=52 Identities=21% Similarity=0.236 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204 5 PLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 5 ~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~ 62 (71)
.+...++..... .|+.. .-.+..-.|++||...... . .+||.|||.++.+++
T Consensus 502 al~~lv~~a~~~-~i~Y~-~~n~~~~~C~~CG~~g~~~--~--~~CP~Cgs~~~~~~~ 553 (579)
T TIGR02487 502 ALKDITKKAMKN-GIGYF-GINPPVDVCEDCGYTGEGL--N--DKCPKCGSHDIEVIS 553 (579)
T ss_pred HHHHHHHHHHhc-CCceE-EeccCCccCCCCCCCCCCC--C--CcCcCCCCccceehh
Confidence 334444443333 25544 1224567899999733321 1 399999998876664
No 39
>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=92.69 E-value=0.085 Score=35.22 Aligned_cols=20 Identities=20% Similarity=0.375 Sum_probs=16.7
Q ss_pred ccCCCCCCcceeeecCCCCC
Q psy1204 48 LKCEHCGSYNTCRIKKPNGQ 67 (71)
Q Consensus 48 ~kCp~C~Synt~ii~g~~~~ 67 (71)
++||+|++.+|+|++-+...
T Consensus 1 M~CP~C~~~dtkViDSR~~~ 20 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVE 20 (147)
T ss_pred CCCCCCCCCCCEeeeccccC
Confidence 48999999999999865543
No 40
>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=92.60 E-value=0.17 Score=39.99 Aligned_cols=51 Identities=24% Similarity=0.269 Sum_probs=31.0
Q ss_pred HHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204 6 LWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 6 ~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~ 62 (71)
.++.++.. +...+|-. .-.+..-.|++||.. ...|.. .||.|||.++.+++
T Consensus 511 ~~~lv~~~-~~~~i~Y~-tin~~~siC~~CGy~--~g~~~~--~CP~CGs~~~ev~s 561 (586)
T TIGR02827 511 YRKLLRVA-ADTGCNYF-CFNIKITICNDCHHI--DKRTLH--RCPVCGSANIDYGT 561 (586)
T ss_pred HHHHHHHH-HhcCCceE-EeCCCCeecCCCCCc--CCCcCC--cCcCCCCccceEEE
Confidence 34444443 33456655 223567789999972 222333 99999998766653
No 41
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=92.41 E-value=0.14 Score=35.98 Aligned_cols=27 Identities=19% Similarity=0.609 Sum_probs=19.3
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCcceee
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Synt~i 60 (71)
-.|..||.++. .+.+ .||.|+|++|-.
T Consensus 355 ~~c~~cg~~~~--~~~~--~c~~c~~~~~~~ 381 (389)
T PRK11788 355 YRCRNCGFTAR--TLYW--HCPSCKAWETIK 381 (389)
T ss_pred EECCCCCCCCc--ccee--ECcCCCCccCcC
Confidence 34999986443 2233 999999999854
No 42
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.20 E-value=0.13 Score=26.46 Aligned_cols=27 Identities=19% Similarity=0.621 Sum_probs=19.4
Q ss_pred eEEcCCCCCceeec-----eEeecccCCCCCC
Q psy1204 29 YVLCKDCHKESKVL-----YHIIGLKCEHCGS 55 (71)
Q Consensus 29 ~i~CndC~~~s~v~-----~h~~g~kCp~C~S 55 (71)
.|.|..|+.++.++ ....-.+|+.|+-
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred EEECCCCCCEEeCCHHHCCCCCcEEECCCCCC
Confidence 68899999999763 2233348999974
No 43
>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=92.10 E-value=0.08 Score=34.93 Aligned_cols=15 Identities=33% Similarity=0.762 Sum_probs=13.7
Q ss_pred ccCCCCCCcceeeec
Q psy1204 48 LKCEHCGSYNTCRIK 62 (71)
Q Consensus 48 ~kCp~C~Synt~ii~ 62 (71)
..||+|||.||++++
T Consensus 106 ~~cp~c~s~~t~~~s 120 (146)
T TIGR02159 106 VQCPRCGSADTTITS 120 (146)
T ss_pred CcCCCCCCCCcEeec
Confidence 499999999999986
No 44
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=92.10 E-value=0.12 Score=40.96 Aligned_cols=38 Identities=18% Similarity=0.266 Sum_probs=25.1
Q ss_pred HHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 14 IASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 14 i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
+..+.||.. .-.+..-.|++||...+. .. +||.|||.+
T Consensus 545 ~~~~~i~Y~-sin~~~~~C~~CGy~g~~---~~--~CP~CG~~d 582 (618)
T PRK14704 545 MAEHGVGYG-SINHPVDRCKCCSYHGVI---GN--ECPSCGNED 582 (618)
T ss_pred HHhcCCceE-EeCCCCeecCCCCCCCCc---Cc--cCcCCCCCC
Confidence 334556655 123567789999985442 23 999999976
No 45
>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=92.09 E-value=0.15 Score=28.55 Aligned_cols=30 Identities=30% Similarity=0.671 Sum_probs=22.6
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii 61 (71)
+..+.|..||. ....|. .|+.||.|+-+++
T Consensus 24 p~l~~C~~cG~--~~~~H~---vc~~cG~Y~gr~v 53 (55)
T TIGR01031 24 PTLVVCPNCGE--FKLPHR---VCPSCGYYKGRQV 53 (55)
T ss_pred CcceECCCCCC--cccCee---ECCccCeECCEEc
Confidence 56788999996 333343 6999999997765
No 46
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=92.06 E-value=0.069 Score=29.92 Aligned_cols=33 Identities=24% Similarity=0.479 Sum_probs=22.2
Q ss_pred eEEcCCCCCceee--ceEeecccCCCCCCcceeee
Q psy1204 29 YVLCKDCHKESKV--LYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 29 ~i~CndC~~~s~v--~~h~~g~kCp~C~Synt~ii 61 (71)
.|+|..|++.--. .+..+-.|||.|+..|.--.
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a 38 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA 38 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence 5899999964321 23334449999999986543
No 47
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=91.91 E-value=0.06 Score=45.32 Aligned_cols=27 Identities=33% Similarity=0.582 Sum_probs=22.2
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
..-+|.|||+.++-. .. +||.|||.|+
T Consensus 693 tIKrC~dcg~q~~~~--~~--~cP~Cgs~~v 719 (1187)
T COG1110 693 TIKRCRDCGEQFVDS--ED--KCPRCGSRNV 719 (1187)
T ss_pred HHHHHhhcCceeccc--cc--cCCCCCCccc
Confidence 356899999988766 33 9999999887
No 48
>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=91.05 E-value=0.21 Score=25.33 Aligned_cols=27 Identities=22% Similarity=0.327 Sum_probs=19.0
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
.-.|..||.......--- +||.||+..
T Consensus 2 ~~~C~~CG~i~~g~~~p~--~CP~Cg~~~ 28 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPE--KCPICGAPK 28 (34)
T ss_pred eEECCCCCCEeECCcCCC--cCcCCCCch
Confidence 357999998765443233 999998754
No 49
>KOG3507|consensus
Probab=90.89 E-value=0.13 Score=29.77 Aligned_cols=38 Identities=18% Similarity=0.492 Sum_probs=26.8
Q ss_pred cCCCCHhh--hcceeeEEcCCCCCceeeceEeecccCCCCC
Q psy1204 16 STPMPEEY--KNVILYVLCKDCHKESKVLYHIIGLKCEHCG 54 (71)
Q Consensus 16 ~~pmP~~y--~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~ 54 (71)
.++.|... +...+...|-||+++-++..-... .|..||
T Consensus 5 ~s~~~~aa~~r~~~miYiCgdC~~en~lk~~D~i-rCReCG 44 (62)
T KOG3507|consen 5 TSLGDPAAGPRTATMIYICGDCGQENTLKRGDVI-RCRECG 44 (62)
T ss_pred cCCCCccCCCCcccEEEEeccccccccccCCCcE-ehhhcc
Confidence 34444432 446899999999999887653332 899997
No 50
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=90.83 E-value=0.12 Score=26.21 Aligned_cols=24 Identities=25% Similarity=0.750 Sum_probs=16.9
Q ss_pred EcCCCCCceeeceEeecccCCCCCC
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
.|.+|+.++...... ..+|+.||.
T Consensus 2 ~C~~Cg~~~~~~~~~-~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELKPGD-PIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BSTSS-TSSBSSSS-
T ss_pred CCCcCCCeeEcCCCC-cEECCcCCC
Confidence 589999999866533 349999985
No 51
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=90.66 E-value=0.19 Score=33.57 Aligned_cols=19 Identities=26% Similarity=0.614 Sum_probs=15.6
Q ss_pred ccCCCCCCcceeeecCCCC
Q psy1204 48 LKCEHCGSYNTCRIKKPNG 66 (71)
Q Consensus 48 ~kCp~C~Synt~ii~g~~~ 66 (71)
++||+||+..|.+++-...
T Consensus 1 m~cp~c~~~~~~~~~s~~~ 19 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPA 19 (154)
T ss_pred CcCCCCCCCCCEeEecccc
Confidence 4899999999999976543
No 52
>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=90.53 E-value=0.19 Score=25.12 Aligned_cols=26 Identities=19% Similarity=0.294 Sum_probs=18.7
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
-.|..||.......... +||.|++..
T Consensus 2 ~~C~~CGy~y~~~~~~~--~CP~Cg~~~ 27 (33)
T cd00350 2 YVCPVCGYIYDGEEAPW--VCPVCGAPK 27 (33)
T ss_pred EECCCCCCEECCCcCCC--cCcCCCCcH
Confidence 46999998765544344 999998743
No 53
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=90.38 E-value=0.15 Score=33.16 Aligned_cols=30 Identities=27% Similarity=0.681 Sum_probs=21.1
Q ss_pred eeeEEcCCCCCceeec---eEe--ec-ccCCCCCCc
Q psy1204 27 ILYVLCKDCHKESKVL---YHI--IG-LKCEHCGSY 56 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~---~h~--~g-~kCp~C~Sy 56 (71)
.....|..|+.+++.. ... -+ ..||.||..
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 5688999999998752 222 00 399999864
No 54
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=90.19 E-value=0.2 Score=33.87 Aligned_cols=33 Identities=18% Similarity=0.541 Sum_probs=23.9
Q ss_pred cceeeEEcCCCCCceee---ceEeecccCCCCCCccee
Q psy1204 25 NVILYVLCKDCHKESKV---LYHIIGLKCEHCGSYNTC 59 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v---~~h~~g~kCp~C~Synt~ 59 (71)
....-..|..|+.+++. -.+.| .||.||+.=..
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~~~F--~Cp~Cg~~L~~ 148 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAMEYGF--RCPQCGEMLEE 148 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhhcCC--cCCCCCCCCee
Confidence 34578889999999874 23444 99999986443
No 55
>PF14369 zf-RING_3: zinc-finger
Probab=90.03 E-value=0.36 Score=24.70 Aligned_cols=32 Identities=13% Similarity=0.243 Sum_probs=20.9
Q ss_pred eEEcCCCCCceeeceEeecc-cCCCCCCcceee
Q psy1204 29 YVLCKDCHKESKVLYHIIGL-KCEHCGSYNTCR 60 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~-kCp~C~Synt~i 60 (71)
...|..|.+...+.-+.... .||.|+|--++.
T Consensus 2 ~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEe 34 (35)
T PF14369_consen 2 RYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEE 34 (35)
T ss_pred CEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEe
Confidence 35799999877653221222 499999876654
No 56
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=89.98 E-value=0.14 Score=37.40 Aligned_cols=32 Identities=28% Similarity=0.424 Sum_probs=23.2
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~ 62 (71)
...-.|++||. .|...-. .||.|+|-|....+
T Consensus 80 DQl~~C~~CGa--~V~~~e~--~Cp~C~StnI~r~D 111 (314)
T PF09567_consen 80 DQLGKCNNCGA--NVSRLEE--SCPNCGSTNIKRKD 111 (314)
T ss_pred hhhhhhccccc--eeeehhh--cCCCCCcccccccC
Confidence 34568999986 4444333 99999999987653
No 57
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=89.63 E-value=0.18 Score=33.09 Aligned_cols=28 Identities=7% Similarity=-0.096 Sum_probs=21.0
Q ss_pred eeEEcCCCCCceee-ceEeecccCCCCCCcc
Q psy1204 28 LYVLCKDCHKESKV-LYHIIGLKCEHCGSYN 57 (71)
Q Consensus 28 v~i~CndC~~~s~v-~~h~~g~kCp~C~Syn 57 (71)
..-.|..||++|.- +..-+ .||+||..-
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~--vcP~cg~~~ 36 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPA--VSPYTGEQF 36 (129)
T ss_pred ccccCCCcCccccccCCCCc--cCCCcCCcc
Confidence 45679999999974 44445 999998754
No 58
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=89.49 E-value=0.29 Score=32.40 Aligned_cols=31 Identities=13% Similarity=0.398 Sum_probs=23.1
Q ss_pred ceeeEEcCCCCCceee---ceEeecccCCCCCCcce
Q psy1204 26 VILYVLCKDCHKESKV---LYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v---~~h~~g~kCp~C~Synt 58 (71)
...-..|..|+.+++. -.+.| .||.||+.-.
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~~~F--~Cp~Cg~~L~ 139 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAMELNF--TCPRCGAMLD 139 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHHcCC--cCCCCCCEee
Confidence 3577889999998863 33445 9999998643
No 59
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=88.84 E-value=0.23 Score=23.96 Aligned_cols=21 Identities=33% Similarity=0.724 Sum_probs=13.2
Q ss_pred EcCCCCCceeeceEeecccCCCCCC
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
.|.+|+++-.+.. - .||+||-
T Consensus 2 ~CP~C~~~V~~~~--~--~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPESA--K--FCPHCGY 22 (26)
T ss_pred cCCCCcCCchhhc--C--cCCCCCC
Confidence 4788877443332 2 8888874
No 60
>PRK06260 threonine synthase; Validated
Probab=88.82 E-value=0.29 Score=36.21 Aligned_cols=26 Identities=31% Similarity=0.692 Sum_probs=21.0
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
...|..||.++......+ .||.|++.
T Consensus 3 ~~~C~~cg~~~~~~~~~~--~Cp~cg~~ 28 (397)
T PRK06260 3 WLKCIECGKEYDPDEIIY--TCPECGGL 28 (397)
T ss_pred EEEECCCCCCCCCCCccc--cCCCCCCe
Confidence 578999999987665445 89999874
No 61
>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=88.80 E-value=0.22 Score=28.99 Aligned_cols=14 Identities=43% Similarity=0.622 Sum_probs=11.8
Q ss_pred ccCCCCCCcceeee
Q psy1204 48 LKCEHCGSYNTCRI 61 (71)
Q Consensus 48 ~kCp~C~Synt~ii 61 (71)
++||.|+|.||+--
T Consensus 6 ~~CPRC~S~nTKFc 19 (63)
T PF02701_consen 6 LPCPRCDSTNTKFC 19 (63)
T ss_pred CCCCCcCCCCCEEE
Confidence 49999999999753
No 62
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=88.76 E-value=0.24 Score=29.20 Aligned_cols=26 Identities=31% Similarity=0.539 Sum_probs=18.6
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCC
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
++++| |||..+.+..-.-..+| .||.
T Consensus 2 lifrC-~Cgr~lya~e~~kTkkC-~CG~ 27 (68)
T PF09082_consen 2 LIFRC-DCGRYLYAKEGAKTKKC-VCGK 27 (68)
T ss_dssp EEEEE-TTS--EEEETT-SEEEE-TTTE
T ss_pred EEEEe-cCCCEEEecCCcceeEe-cCCC
Confidence 67899 99999888776667799 8864
No 63
>PLN00209 ribosomal protein S27; Provisional
Probab=88.75 E-value=0.61 Score=28.66 Aligned_cols=41 Identities=17% Similarity=0.344 Sum_probs=28.0
Q ss_pred hcceeeEEcCCCCCceeeceEee-cccCCCCCCcceeeecCC
Q psy1204 24 KNVILYVLCKDCHKESKVLYHII-GLKCEHCGSYNTCRIKKP 64 (71)
Q Consensus 24 ~~~~v~i~CndC~~~s~v~~h~~-g~kCp~C~Synt~ii~g~ 64 (71)
+...+.+.|.+|+....+..|-- -..|..|+..=.+=.+|.
T Consensus 31 nS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGK 72 (86)
T PLN00209 31 NSFFMDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQPTGGK 72 (86)
T ss_pred CCEEEEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCC
Confidence 34578999999999998865421 128999987654444443
No 64
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=88.53 E-value=0.15 Score=24.25 Aligned_cols=22 Identities=27% Similarity=0.781 Sum_probs=14.8
Q ss_pred EEcCCCCCceeeceEeecccCCCCCC
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
++|..||+. +....- -||+||.
T Consensus 3 ~~Cp~Cg~~--~~~~~~--fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAE--IDPDAK--FCPNCGA 24 (26)
T ss_pred CCCcccCCc--CCcccc--cChhhCC
Confidence 578999983 333333 7999985
No 65
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=88.48 E-value=0.26 Score=28.31 Aligned_cols=26 Identities=23% Similarity=0.566 Sum_probs=15.8
Q ss_pred eeeEEcCCCCCcee-------eceEeecccCCCCC
Q psy1204 27 ILYVLCKDCHKESK-------VLYHIIGLKCEHCG 54 (71)
Q Consensus 27 ~v~i~CndC~~~s~-------v~~h~~g~kCp~C~ 54 (71)
-+...|.+||+.-. ...+.| +||.||
T Consensus 23 ~~~F~CPnCG~~~I~RC~~CRk~~~~Y--~CP~CG 55 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCEKCRKQSNPY--TCPKCG 55 (59)
T ss_pred cCEeeCCCCCCeeEeechhHHhcCCce--ECCCCC
Confidence 46777888876511 123444 788886
No 66
>PRK12496 hypothetical protein; Provisional
Probab=88.35 E-value=0.33 Score=32.38 Aligned_cols=28 Identities=36% Similarity=0.551 Sum_probs=20.4
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCccee
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSYNTC 59 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Synt~ 59 (71)
..|..|++.+...+-.- -||.|||.-.+
T Consensus 128 ~~C~gC~~~~~~~~~~~--~C~~CG~~~~r 155 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDD--VCEICGSPVKR 155 (164)
T ss_pred EECCCCCccccCCCCCC--cCCCCCChhhh
Confidence 55999999887654223 79999986433
No 67
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=87.76 E-value=0.78 Score=28.14 Aligned_cols=41 Identities=20% Similarity=0.329 Sum_probs=28.0
Q ss_pred hcceeeEEcCCCCCceeeceEee-cccCCCCCCcceeeecCC
Q psy1204 24 KNVILYVLCKDCHKESKVLYHII-GLKCEHCGSYNTCRIKKP 64 (71)
Q Consensus 24 ~~~~v~i~CndC~~~s~v~~h~~-g~kCp~C~Synt~ii~g~ 64 (71)
+...+.+.|.+|+...++..|-- -..|..|+..=.+=.+|+
T Consensus 30 nS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGK 71 (85)
T PTZ00083 30 NSYFMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQPTGGK 71 (85)
T ss_pred CCeEEEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCC
Confidence 34478999999999998865421 128888876554444443
No 68
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=87.67 E-value=0.4 Score=38.90 Aligned_cols=29 Identities=21% Similarity=0.466 Sum_probs=18.6
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii 61 (71)
-...|+-||....++. .||.|||...+-.
T Consensus 461 ~~L~CH~Cg~~~~~p~-----~Cp~Cgs~~L~~~ 489 (730)
T COG1198 461 GQLRCHYCGYQEPIPQ-----SCPECGSEHLRAV 489 (730)
T ss_pred CeeEeCCCCCCCCCCC-----CCCCCCCCeeEEe
Confidence 4566666666555544 7899998854433
No 69
>KOG2703|consensus
Probab=87.65 E-value=0.23 Score=38.19 Aligned_cols=44 Identities=30% Similarity=0.582 Sum_probs=32.7
Q ss_pred eeeEEcCCCCCceee-------ce----EeecccCCCCCCcceeeecCCCCCCCC
Q psy1204 27 ILYVLCKDCHKESKV-------LY----HIIGLKCEHCGSYNTCRIKKPNGQESG 70 (71)
Q Consensus 27 ~v~i~CndC~~~s~v-------~~----h~~g~kCp~C~Synt~ii~g~~~~~~~ 70 (71)
.+...|..|+...+. +| ......|||||--|+.+-.+.+-|.+|
T Consensus 37 EvES~Cm~Cg~nG~TRlllT~IP~fREvVimSF~CpHCG~kN~eiQ~a~~iQ~~G 91 (460)
T KOG2703|consen 37 EVESLCMNCGENGTTRLLLTSIPYFREVVIMSFECPHCGHKNNEIQSAEEIQEGG 91 (460)
T ss_pred HHHHhhhhcccCCceeEEEeecchhheeeeEEeecCccCCccccccchhccccCc
Confidence 457789999988552 11 112238999999999999988888776
No 70
>PRK06450 threonine synthase; Validated
Probab=87.63 E-value=0.34 Score=35.37 Aligned_cols=26 Identities=35% Similarity=0.902 Sum_probs=19.8
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
|..+|.+||+++.... .+ .||.|++.
T Consensus 2 ~~~~C~~Cg~~~~~~~-~~--~C~~cg~~ 27 (338)
T PRK06450 2 VKEVCMKCGKERESIY-EI--RCKKCGGP 27 (338)
T ss_pred ceeEECCcCCcCCCcc-cc--cCCcCCCE
Confidence 5679999999986532 23 89999864
No 71
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=87.31 E-value=0.23 Score=23.24 Aligned_cols=21 Identities=29% Similarity=0.727 Sum_probs=13.6
Q ss_pred EcCCCCCceeeceEeecccCCCCCC
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
+|..||++-..... -||.||.
T Consensus 1 ~Cp~CG~~~~~~~~----fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAK----FCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCc----chhhhCC
Confidence 47888876554332 4888875
No 72
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=87.04 E-value=0.77 Score=36.69 Aligned_cols=48 Identities=15% Similarity=0.158 Sum_probs=27.7
Q ss_pred HHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204 7 WRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 7 ~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii 61 (71)
.+.++.....+.+|-. .-.+-.-.|++||... .. +..||.||+. +.+.
T Consensus 605 ~~lv~~~~~~~~i~Y~-~in~~~~~C~~CG~~~--g~---~~~CP~CG~~-~~v~ 652 (656)
T PRK08270 605 KKLVKKALENYRLPYI-TITPTFSICPKHGYLS--GE---HEFCPKCGEE-TEVY 652 (656)
T ss_pred HHHHHHHHHhCCCceE-EeCCCCcccCCCCCcC--CC---CCCCcCCcCc-cceE
Confidence 3333433334456655 1225567899999732 22 2499999975 5443
No 73
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=87.02 E-value=0.4 Score=22.91 Aligned_cols=6 Identities=50% Similarity=1.647 Sum_probs=4.4
Q ss_pred cCCCCC
Q psy1204 49 KCEHCG 54 (71)
Q Consensus 49 kCp~C~ 54 (71)
+||.||
T Consensus 18 ~CPnCG 23 (24)
T PF07754_consen 18 PCPNCG 23 (24)
T ss_pred eCCCCC
Confidence 777775
No 74
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=86.89 E-value=0.29 Score=26.61 Aligned_cols=11 Identities=55% Similarity=1.343 Sum_probs=9.5
Q ss_pred cCCCCCCccee
Q psy1204 49 KCEHCGSYNTC 59 (71)
Q Consensus 49 kCp~C~Synt~ 59 (71)
|||+||.||-.
T Consensus 13 kCp~CGt~NG~ 23 (44)
T PF14952_consen 13 KCPKCGTYNGT 23 (44)
T ss_pred cCCcCcCccCc
Confidence 99999999943
No 75
>PRK07591 threonine synthase; Validated
Probab=86.85 E-value=0.44 Score=35.70 Aligned_cols=27 Identities=22% Similarity=0.387 Sum_probs=21.6
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
...+|..||+++..... + .||.|++.=
T Consensus 17 ~~l~C~~Cg~~~~~~~~-~--~C~~cg~~l 43 (421)
T PRK07591 17 VALKCRECGAEYPLGPI-H--VCEECFGPL 43 (421)
T ss_pred eEEEeCCCCCcCCCCCC-c--cCCCCCCeE
Confidence 46899999999987654 4 999998743
No 76
>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=86.60 E-value=0.51 Score=26.31 Aligned_cols=30 Identities=27% Similarity=0.595 Sum_probs=21.4
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii 61 (71)
+....|..||.-.. .| +.|+.||-|+.+++
T Consensus 24 ~~l~~c~~cg~~~~--~H---~vc~~cG~y~~r~v 53 (56)
T PF01783_consen 24 PNLVKCPNCGEPKL--PH---RVCPSCGYYKGRQV 53 (56)
T ss_dssp TSEEESSSSSSEES--TT---SBCTTTBBSSSSSS
T ss_pred cceeeeccCCCEec--cc---EeeCCCCeECCEEE
Confidence 45789999995222 22 37999999987764
No 77
>PHA00626 hypothetical protein
Probab=86.59 E-value=0.42 Score=27.41 Aligned_cols=34 Identities=18% Similarity=0.328 Sum_probs=20.9
Q ss_pred EcCCCCCceeec-------eEeecccCCCCCCcceeeecCCCC
Q psy1204 31 LCKDCHKESKVL-------YHIIGLKCEHCGSYNTCRIKKPNG 66 (71)
Q Consensus 31 ~CndC~~~s~v~-------~h~~g~kCp~C~Synt~ii~g~~~ 66 (71)
.|.+||+...+. ...| +|+.||=..|.-.-|+-|
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrY--kCkdCGY~ft~~~~~~~~ 42 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDY--VCCDCGYNDSKDAFGERG 42 (59)
T ss_pred CCCCCCCceeeeeceecccCcce--EcCCCCCeechhhhhhcc
Confidence 477787754332 2344 888888777766555443
No 78
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=86.40 E-value=0.49 Score=35.32 Aligned_cols=33 Identities=30% Similarity=0.621 Sum_probs=12.0
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii 61 (71)
.+.|.+|++.+..-+.+-...|++||+.+-+.+
T Consensus 285 FFkC~~C~~Rt~sl~r~P~~~C~~Cg~~~wer~ 317 (344)
T PF09332_consen 285 FFKCKDCGNRTISLERLPKKHCSNCGSSKWERT 317 (344)
T ss_dssp EEE-T-TS-EEEESSSS--S--TTT-S---EEE
T ss_pred eEECCCCCCeeeecccCCCCCCCcCCcCceeeh
Confidence 456666666655434344456666666655444
No 79
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=85.86 E-value=0.44 Score=32.67 Aligned_cols=26 Identities=23% Similarity=0.364 Sum_probs=20.8
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
.-.+.|..|.+.|+.+. ..||.|||.
T Consensus 137 ~w~~rC~GC~~~f~~~~----~~Cp~CG~~ 162 (177)
T COG1439 137 KWRLRCHGCKRIFPEPK----DFCPICGSP 162 (177)
T ss_pred eeeEEEecCceecCCCC----CcCCCCCCc
Confidence 34788999999998333 289999998
No 80
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=85.85 E-value=0.56 Score=36.03 Aligned_cols=12 Identities=33% Similarity=0.805 Sum_probs=8.7
Q ss_pred cCCCCCCcceee
Q psy1204 49 KCEHCGSYNTCR 60 (71)
Q Consensus 49 kCp~C~Synt~i 60 (71)
.||.|+|...+-
T Consensus 255 ~Cp~C~s~~l~~ 266 (505)
T TIGR00595 255 TCPQCGSEDLVY 266 (505)
T ss_pred CCCCCCCCeeEe
Confidence 788898866443
No 81
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=85.71 E-value=0.39 Score=39.82 Aligned_cols=41 Identities=24% Similarity=0.359 Sum_probs=30.3
Q ss_pred cceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCC
Q psy1204 25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNG 66 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~ 66 (71)
...+.-+|.||++.+...-.-|+ .||.||..-.-+-.|...
T Consensus 817 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 857 (1006)
T PRK12775 817 TSELQWRCDDCGKVSEGFAFPYG-MCPACGGKLQALDRRKVE 857 (1006)
T ss_pred CcceeeehhhhccccccccCCcC-cCcccccchhhhhccCcc
Confidence 34567899999999987776666 999999875554444443
No 82
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=85.67 E-value=0.3 Score=33.36 Aligned_cols=49 Identities=18% Similarity=0.341 Sum_probs=29.8
Q ss_pred HHHHHHcCCCCHhhhcceeeEEcCCCCCceeece-EeecccCCCCCCcce
Q psy1204 10 MDEEIASTPMPEEYKNVILYVLCKDCHKESKVLY-HIIGLKCEHCGSYNT 58 (71)
Q Consensus 10 lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~-h~~g~kCp~C~Synt 58 (71)
+.+.+.....--++-....-..|+.|+.+++... .-++..||.|||-=.
T Consensus 94 ~~~~le~Lk~~le~~~~~~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~ 143 (176)
T COG1675 94 KRKILEKLKRKLEKETENNYYVCPNCHVKYSFDEAMELGFTCPKCGEDLE 143 (176)
T ss_pred HHHHHHHHHHHHHhhccCCceeCCCCCCcccHHHHHHhCCCCCCCCchhh
Confidence 3344444444444444456788999998876432 233349999998543
No 83
>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=85.32 E-value=1.5 Score=24.79 Aligned_cols=39 Identities=23% Similarity=0.389 Sum_probs=23.1
Q ss_pred ceeeEEcCCCCCceeeceEee-cccCCCCCCcceeeecCC
Q psy1204 26 VILYVLCKDCHKESKVLYHII-GLKCEHCGSYNTCRIKKP 64 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v~~h~~-g~kCp~C~Synt~ii~g~ 64 (71)
..+.+.|.+|+....+..|-- -..|..|+..=.+=.+|+
T Consensus 4 ~Fm~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~PtGGK 43 (55)
T PF01667_consen 4 YFMDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQPTGGK 43 (55)
T ss_dssp -EEEEE-TTT-SEEEEETT-SS-EE-SSSTSEEEEE-SSS
T ss_pred cEEEEECCCCCCeeEEEecCCeEEEcccCCCEecCCCCcC
Confidence 468899999999998755421 128999987655555554
No 84
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=85.30 E-value=1.2 Score=30.88 Aligned_cols=35 Identities=26% Similarity=0.665 Sum_probs=27.1
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCcceeeecC
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKK 63 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g 63 (71)
-+..+|..|+..=......+ +||.||-..+|-++-
T Consensus 147 VI~A~CsrC~~~L~~~~~~l--~Cp~Cg~tEkRKia~ 181 (188)
T COG1096 147 VIYARCSRCRAPLVKKGNML--KCPNCGNTEKRKIAK 181 (188)
T ss_pred EEEEEccCCCcceEEcCcEE--ECCCCCCEEeeeecc
Confidence 46789999997665544445 999999988887764
No 85
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=85.02 E-value=0.44 Score=27.76 Aligned_cols=25 Identities=28% Similarity=0.583 Sum_probs=17.4
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
...-|.+|+...+ ...||.|||.+|
T Consensus 4 ~~~AC~~C~~i~~------~~~Cp~Cgs~~~ 28 (64)
T PRK06393 4 QYRACKKCKRLTP------EKTCPVHGDEKT 28 (64)
T ss_pred hhhhHhhCCcccC------CCcCCCCCCCcC
Confidence 3456888986442 228999999874
No 86
>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=84.92 E-value=0.42 Score=23.58 Aligned_cols=26 Identities=23% Similarity=0.503 Sum_probs=13.4
Q ss_pred EcCCCCCceeeceEeecccCCCCCCc
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
+|.-||.......--....||.|+..
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred ccCcCCccccCCCCcCEeECCCCcCE
Confidence 68888887765443333488888753
No 87
>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=84.38 E-value=0.62 Score=29.97 Aligned_cols=32 Identities=31% Similarity=0.554 Sum_probs=25.4
Q ss_pred ceeeEEcCCCCCceeeceEeecccCCCCCCccee
Q psy1204 26 VILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTC 59 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ 59 (71)
+.+.+.|+.|++.+-.-.... .|.+|+..=|-
T Consensus 66 kav~V~CP~C~K~TKmLGr~D--~CM~C~~pLTL 97 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRVD--ACMHCKEPLTL 97 (114)
T ss_pred cceeeECCCCCChHhhhchhh--ccCcCCCcCcc
Confidence 457889999999887666666 99999877553
No 88
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=84.28 E-value=0.39 Score=27.45 Aligned_cols=35 Identities=26% Similarity=0.453 Sum_probs=23.6
Q ss_pred eeEEcCCCCCce-eeceE-eecccCCCCCCcceeeec
Q psy1204 28 LYVLCKDCHKES-KVLYH-IIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 28 v~i~CndC~~~s-~v~~h-~~g~kCp~C~Synt~ii~ 62 (71)
..|+|..|++-- .+.+- ++-.|||.|.-.|-.-+.
T Consensus 3 ~tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~~~~ 39 (60)
T COG4416 3 QTIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEFYIK 39 (60)
T ss_pred eeeehHHHhHHHHhcccceeeeecCCccceeeeeecc
Confidence 368999999643 22221 344499999988876665
No 89
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=84.12 E-value=0.73 Score=34.70 Aligned_cols=48 Identities=23% Similarity=0.443 Sum_probs=29.5
Q ss_pred CChHHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 1 ~dm~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
+|-...|+.++.+ |++. ......+.|.+|+..... .+.. .||.|++.=
T Consensus 193 ~d~~~lW~~~~~~-----~~~~-~~~~~~~~C~~Cd~~~~~-~~~a--~CpRC~~~L 240 (403)
T TIGR00155 193 LNRRWLWDDFYPE-----MPEL-RQPLKLRSCSACHTTILP-AQEP--VCPRCSTPL 240 (403)
T ss_pred cCHHHHHHhcccc-----cCCC-CCccCCCcCCCCCCccCC-CCCc--CCcCCCCcc
Confidence 4667899988733 3332 112346679999984422 2233 799998853
No 90
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=83.97 E-value=2 Score=26.77 Aligned_cols=36 Identities=22% Similarity=0.529 Sum_probs=25.0
Q ss_pred ceeeEEcCCCCCceeec--e--EeecccCCCCCCcceeeec
Q psy1204 26 VILYVLCKDCHKESKVL--Y--HIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v~--~--h~~g~kCp~C~Synt~ii~ 62 (71)
.+..+.|..|+.. .+. . ...-+.|+.||-|..+.+.
T Consensus 18 lpt~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y~~~~V~ 57 (99)
T PRK14892 18 LPKIFECPRCGKV-SISVKIKKNIAIITCGNCGLYTEFEVP 57 (99)
T ss_pred CCcEeECCCCCCe-EeeeecCCCcceEECCCCCCccCEECC
Confidence 3678999999953 332 1 1122389999999988874
No 91
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=83.33 E-value=0.44 Score=31.29 Aligned_cols=32 Identities=19% Similarity=0.317 Sum_probs=22.8
Q ss_pred EcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~ 62 (71)
.|-.||+.|....-.+-.-||.||+---.-+.
T Consensus 3 ~Ct~Cg~~f~dgs~eil~GCP~CGg~kF~yv~ 34 (131)
T PF09845_consen 3 QCTKCGRVFEDGSKEILSGCPECGGNKFQYVP 34 (131)
T ss_pred ccCcCCCCcCCCcHHHHccCcccCCcceEEcC
Confidence 59999999986552333489999986555444
No 92
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=83.19 E-value=1.3 Score=25.16 Aligned_cols=30 Identities=17% Similarity=0.058 Sum_probs=21.5
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~ 62 (71)
+..+.|..||.. ..-|. .|+ ||.|+.+.+-
T Consensus 25 ~~~~~c~~cg~~--~~pH~---vc~-cG~Y~gr~v~ 54 (60)
T PRK01110 25 PTLSVDKTTGEY--HLPHH---VSP-KGYYKGRKVL 54 (60)
T ss_pred CceeEcCCCCce--eccce---ecC-CcccCCeEee
Confidence 457889999852 22232 599 9999998774
No 93
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=82.93 E-value=1.2 Score=22.51 Aligned_cols=28 Identities=25% Similarity=0.364 Sum_probs=19.9
Q ss_pred eEEcCCCCCceee-ceEeecccCCCCCCcc
Q psy1204 29 YVLCKDCHKESKV-LYHIIGLKCEHCGSYN 57 (71)
Q Consensus 29 ~i~CndC~~~s~v-~~h~~g~kCp~C~Syn 57 (71)
.+.|..|+..-.+ ....+ ..|+.|++..
T Consensus 3 ~~~C~~C~~~~i~~~~~~~-~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDY-EVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEEecCCe-EEcccCCcEe
Confidence 4679999987776 44333 3899998753
No 94
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=81.99 E-value=1.2 Score=29.49 Aligned_cols=48 Identities=17% Similarity=0.508 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHcCCCCHhhhc----ceeeEEcCCCCCceeec--eEeecccCCCCCCcc
Q psy1204 5 PLWRQMDEEIASTPMPEEYKN----VILYVLCKDCHKESKVL--YHIIGLKCEHCGSYN 57 (71)
Q Consensus 5 ~~~~~lD~~i~~~pmP~~y~~----~~v~i~CndC~~~s~v~--~h~~g~kCp~C~Syn 57 (71)
..|+.|-+.+.... .|+- -+....|..||.+-... .+.- .||+|++..
T Consensus 87 vEw~el~~d~~h~g---~Y~sGE~~g~G~l~C~~Cg~~~~~~~~~~l~--~Cp~C~~~~ 140 (146)
T PF07295_consen 87 VEWAELAQDLEHHG---VYHSGEVVGPGTLVCENCGHEVELTHPERLP--PCPKCGHTE 140 (146)
T ss_pred HHHHHHHHHHHhcC---CeecCcEecCceEecccCCCEEEecCCCcCC--CCCCCCCCe
Confidence 35666666666655 4442 25688999999877653 3444 999998754
No 95
>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=81.81 E-value=1.2 Score=21.41 Aligned_cols=17 Identities=29% Similarity=0.403 Sum_probs=10.5
Q ss_pred cccCCCCCCcceeeecC
Q psy1204 47 GLKCEHCGSYNTCRIKK 63 (71)
Q Consensus 47 g~kCp~C~Synt~ii~g 63 (71)
|.+|+.|+.+-+.+..+
T Consensus 1 G~~C~rC~~~~~~~~~~ 17 (30)
T PF06827_consen 1 GEKCPRCWNYIEDIGIN 17 (30)
T ss_dssp TSB-TTT--BBEEEEET
T ss_pred CCcCccCCCcceEeEec
Confidence 57999999997777653
No 96
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=81.60 E-value=2.2 Score=28.40 Aligned_cols=39 Identities=28% Similarity=0.531 Sum_probs=23.0
Q ss_pred EEcCCCCCceeece-----------EeecccCCCCCCcceeeecCCCCCC
Q psy1204 30 VLCKDCHKESKVLY-----------HIIGLKCEHCGSYNTCRIKKPNGQE 68 (71)
Q Consensus 30 i~CndC~~~s~v~~-----------h~~g~kCp~C~Synt~ii~g~~~~~ 68 (71)
..|..|++...... ......|++||=-|+.|..|...+.
T Consensus 2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~~ 51 (161)
T PF03367_consen 2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNNEVKSGGQIQP 51 (161)
T ss_dssp EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEEEEEEECSS-S
T ss_pred CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEeeeEEECccCCC
Confidence 57999998875421 1122389999999999987766553
No 97
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=81.07 E-value=0.27 Score=36.22 Aligned_cols=12 Identities=17% Similarity=0.313 Sum_probs=6.2
Q ss_pred eeEEcCCCCCce
Q psy1204 28 LYVLCKDCHKES 39 (71)
Q Consensus 28 v~i~CndC~~~s 39 (71)
.+-+|.-||..-
T Consensus 184 ~~~~CPvCGS~P 195 (308)
T COG3058 184 SRQYCPVCGSMP 195 (308)
T ss_pred ccccCCCcCCCC
Confidence 445566665443
No 98
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=80.61 E-value=1.3 Score=24.77 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=19.1
Q ss_pred EEcCCCCCceeeceEe--ecccCCCCCCcce
Q psy1204 30 VLCKDCHKESKVLYHI--IGLKCEHCGSYNT 58 (71)
Q Consensus 30 i~CndC~~~s~v~~h~--~g~kCp~C~Synt 58 (71)
..|..||.+.+++.-. -...||.||+.--
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence 5789999888765411 1238999976543
No 99
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=80.37 E-value=2.3 Score=34.51 Aligned_cols=52 Identities=15% Similarity=0.164 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204 5 PLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 5 ~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~ 62 (71)
..|...+.... +.+|--- -.+-.-.|++||..-. +..- +||.|||.++.+++
T Consensus 619 al~~l~k~~~~-~ri~Y~~-~n~~i~~C~~cg~~~~--~~~~--~Cp~CG~~dve~~~ 670 (700)
T COG1328 619 ALMDLTKYIYK-TRIGYWG-YTTPISVCNRCGYSGE--GLRT--RCPKCGSEDVEVFS 670 (700)
T ss_pred HHHHHHHHHHh-cCcceEe-cCCCceeeccCCcccc--cccc--cCCCCCCccceeee
Confidence 44555554444 5555542 2345678999997432 2112 59999999987775
No 100
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=80.37 E-value=1.2 Score=25.04 Aligned_cols=26 Identities=23% Similarity=0.551 Sum_probs=19.2
Q ss_pred eEEcCCCCCceee--ceEeecccCCCCCCc
Q psy1204 29 YVLCKDCHKESKV--LYHIIGLKCEHCGSY 56 (71)
Q Consensus 29 ~i~CndC~~~s~v--~~h~~g~kCp~C~Sy 56 (71)
.-.|..||..... ..+.+ .||.||-.
T Consensus 28 Sq~C~~CG~~~~~~~~~r~~--~C~~Cg~~ 55 (69)
T PF07282_consen 28 SQTCPRCGHRNKKRRSGRVF--TCPNCGFE 55 (69)
T ss_pred ccCccCcccccccccccceE--EcCCCCCE
Confidence 4569999987765 45555 99999864
No 101
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=80.18 E-value=1.9 Score=23.45 Aligned_cols=29 Identities=28% Similarity=0.467 Sum_probs=21.6
Q ss_pred cceeeEEcCCCCCceee--ceE-eecccCCCC
Q psy1204 25 NVILYVLCKDCHKESKV--LYH-IIGLKCEHC 53 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v--~~h-~~g~kCp~C 53 (71)
+..+.=.|..||.++.. ..+ ..+..||.|
T Consensus 24 ~~~v~W~C~~Cgh~w~~~v~~R~~~~~~CP~C 55 (55)
T PF14311_consen 24 NKKVWWKCPKCGHEWKASVNDRTRRGKGCPYC 55 (55)
T ss_pred CCEEEEECCCCCCeeEccHhhhccCCCCCCCC
Confidence 45788999999988853 333 356789988
No 102
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=79.96 E-value=1 Score=25.36 Aligned_cols=25 Identities=32% Similarity=0.587 Sum_probs=16.6
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
..|.-|++++....-.+ .||.|+..
T Consensus 6 ~~C~~Cg~~~~~~dDiV--vCp~Cgap 30 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIV--VCPECGAP 30 (54)
T ss_pred ccChhhCCcccCCCCEE--ECCCCCCc
Confidence 45777777776555455 77777654
No 103
>KOG2907|consensus
Probab=79.68 E-value=0.76 Score=29.63 Aligned_cols=22 Identities=45% Similarity=0.902 Sum_probs=16.2
Q ss_pred ecccCCCCC----Ccceeee-cCCCCC
Q psy1204 46 IGLKCEHCG----SYNTCRI-KKPNGQ 67 (71)
Q Consensus 46 ~g~kCp~C~----Synt~ii-~g~~~~ 67 (71)
+-++||+|| +|+|.++ +..|||
T Consensus 73 I~~kCpkCghe~m~Y~T~QlRSADEGQ 99 (116)
T KOG2907|consen 73 IKHKCPKCGHEEMSYHTLQLRSADEGQ 99 (116)
T ss_pred hhccCcccCCchhhhhhhhcccccCCc
Confidence 346899997 7888887 466665
No 104
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=79.65 E-value=2.6 Score=29.01 Aligned_cols=38 Identities=21% Similarity=0.410 Sum_probs=24.7
Q ss_pred EEcCCCCCceeeceE------------eecccCCCCCCcceeeecCCCCC
Q psy1204 30 VLCKDCHKESKVLYH------------IIGLKCEHCGSYNTCRIKKPNGQ 67 (71)
Q Consensus 30 i~CndC~~~s~v~~h------------~~g~kCp~C~Synt~ii~g~~~~ 67 (71)
|.|..|++....... .....|++||=.|+.|..|..-+
T Consensus 1 ~~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev~~~g~~~ 50 (192)
T TIGR00310 1 IDCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSNDVKTLGAKE 50 (192)
T ss_pred CcCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccceeEECCCCC
Confidence 358889876543221 11237999999998887765543
No 105
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=79.49 E-value=1.1 Score=23.67 Aligned_cols=25 Identities=28% Similarity=0.721 Sum_probs=16.8
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
+.|+.|+. .+....+ +|..|.+|+.
T Consensus 1 v~Cd~C~~--~i~G~ry--~C~~C~d~dL 25 (43)
T cd02340 1 VICDGCQG--PIVGVRY--KCLVCPDYDL 25 (43)
T ss_pred CCCCCCCC--cCcCCeE--ECCCCCCccc
Confidence 35888887 4444455 8888877764
No 106
>PRK05580 primosome assembly protein PriA; Validated
Probab=79.42 E-value=1.4 Score=35.10 Aligned_cols=11 Identities=36% Similarity=0.918 Sum_probs=7.6
Q ss_pred cCCCCCCccee
Q psy1204 49 KCEHCGSYNTC 59 (71)
Q Consensus 49 kCp~C~Synt~ 59 (71)
.||.|||...+
T Consensus 423 ~Cp~Cg~~~l~ 433 (679)
T PRK05580 423 ACPECGSTDLV 433 (679)
T ss_pred CCCCCcCCeeE
Confidence 68888886433
No 107
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=79.40 E-value=0.85 Score=32.87 Aligned_cols=44 Identities=20% Similarity=0.288 Sum_probs=30.1
Q ss_pred HHcCCCCHhhhc----ceeeEEcCCCCCceeeceEeecccCCCCCCcceee
Q psy1204 14 IASTPMPEEYKN----VILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60 (71)
Q Consensus 14 i~~~pmP~~y~~----~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~i 60 (71)
|..-++|--+-+ ......|-.|++++...-..- +|++||+ +..+
T Consensus 148 ~~~hfLpd~~gn~r~f~rq~~rc~~c~~k~rr~pl~g--~c~kcg~-~~~l 195 (253)
T COG1933 148 LNSHFIPDLRGNLRSFTRQEFRCVKCNTKFRRPPLDG--KCPICGG-KIVL 195 (253)
T ss_pred hccCCCcchhhhhhhhhhheeehHhhhhhhcCCCccc--cccccCC-eEEE
Confidence 444566655432 245789999999997666444 9999999 4443
No 108
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=79.00 E-value=1.4 Score=23.31 Aligned_cols=23 Identities=22% Similarity=0.547 Sum_probs=12.1
Q ss_pred EcCCCCCceeece----EeecccCCCCCC
Q psy1204 31 LCKDCHKESKVLY----HIIGLKCEHCGS 55 (71)
Q Consensus 31 ~CndC~~~s~v~~----h~~g~kCp~C~S 55 (71)
+|.+||.--.... ..+ .||.|+.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~--vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRF--VCRKCGY 28 (52)
T ss_pred CCCCCCCccccccCCCCCEE--ECCcCCC
Confidence 5777775433321 123 6777763
No 109
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=78.95 E-value=0.94 Score=24.85 Aligned_cols=27 Identities=22% Similarity=0.527 Sum_probs=17.5
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCC
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
..-+|..||.. -...|.-.+.|+.|+-
T Consensus 19 ~~~fCP~Cg~~-~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSG-FMAEHLDRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcc-hheccCCcEECCCcCC
Confidence 34589999876 3333444558888863
No 110
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=78.74 E-value=1.1 Score=27.16 Aligned_cols=22 Identities=23% Similarity=0.643 Sum_probs=10.7
Q ss_pred EcCCCCCceeeceEeecccCCCCC
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCG 54 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~ 54 (71)
+|.+||.-.......+ +|+.|+
T Consensus 2 fC~~Cg~~l~~~~~~~--~C~~C~ 23 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVY--VCPSCG 23 (104)
T ss_pred CCcccCcccccCCCeE--ECcCCC
Confidence 4555555443333333 566555
No 111
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 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 DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=78.63 E-value=1.3 Score=29.92 Aligned_cols=33 Identities=27% Similarity=0.596 Sum_probs=18.6
Q ss_pred hhcc-eeeEEcCCCCCceeeceE---------eecccCCCCCC
Q psy1204 23 YKNV-ILYVLCKDCHKESKVLYH---------IIGLKCEHCGS 55 (71)
Q Consensus 23 y~~~-~v~i~CndC~~~s~v~~h---------~~g~kCp~C~S 55 (71)
|++- +..+.|..|+.++..+.- ..+..||+|+.
T Consensus 11 f~~c~~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~ 53 (188)
T PF08996_consen 11 FKDCEPLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCST 53 (188)
T ss_dssp TTT---EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--
T ss_pred hcCCCceEeECCCCCCCccccccccCCccccccCcCcCCCCCC
Confidence 5544 789999999998865322 33679999987
No 112
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=78.47 E-value=1.2 Score=33.71 Aligned_cols=51 Identities=18% Similarity=0.238 Sum_probs=29.2
Q ss_pred CChHHHHHHHHHHHHcCCCCHh---hhcceeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 1 MDMTPLWRQMDEEIASTPMPEE---YKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 1 ~dm~~~~~~lD~~i~~~pmP~~---y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
+|-..+|+.++..- ..+.|.. =....-.+.|.+|+.... .... .||.|++.
T Consensus 191 ~d~~~lW~~~~~~~-~~~~~~~~~~~~~~~~l~~C~~Cd~l~~--~~~a--~CpRC~~~ 244 (419)
T PRK15103 191 VDRRWLWDDIAPMP-ALPQPLKPGVTGLRQGLRSCSCCTAILP--ADQP--VCPRCHTK 244 (419)
T ss_pred cCHHHHHHhhcccc-ccCccccccCCccccCCCcCCCCCCCCC--CCCC--CCCCCCCc
Confidence 46778999886421 1222210 011123667999998532 2222 79999885
No 113
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=77.97 E-value=1.4 Score=33.40 Aligned_cols=30 Identities=23% Similarity=0.573 Sum_probs=21.8
Q ss_pred ceeeEEcCCCCCceeeceEeecccCCCCCCccee
Q psy1204 26 VILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTC 59 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ 59 (71)
+....+|..||.+.-+-+ . .||.|.-+.|-
T Consensus 351 ~~~~YRC~~CGF~a~~l~--W--~CPsC~~W~Ti 380 (389)
T COG2956 351 RKPRYRCQNCGFTAHTLY--W--HCPSCRAWETI 380 (389)
T ss_pred hcCCceecccCCcceeee--e--eCCCccccccc
Confidence 356789999997554332 2 89999988763
No 114
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=77.68 E-value=1.4 Score=27.79 Aligned_cols=16 Identities=44% Similarity=0.646 Sum_probs=14.0
Q ss_pred cccCCCCCCcceeeec
Q psy1204 47 GLKCEHCGSYNTCRIK 62 (71)
Q Consensus 47 g~kCp~C~Synt~ii~ 62 (71)
+..|+.|+|.+|.++.
T Consensus 80 yVlC~~C~spdT~l~k 95 (110)
T smart00653 80 YVLCPECGSPDTELIK 95 (110)
T ss_pred cEECCCCCCCCcEEEE
Confidence 3489999999999985
No 115
>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=77.57 E-value=1.5 Score=28.23 Aligned_cols=17 Identities=41% Similarity=0.632 Sum_probs=14.4
Q ss_pred cccCCCCCCcceeeecC
Q psy1204 47 GLKCEHCGSYNTCRIKK 63 (71)
Q Consensus 47 g~kCp~C~Synt~ii~g 63 (71)
+..|+.|+|++|.++.-
T Consensus 93 yVlC~~C~spdT~l~k~ 109 (125)
T PF01873_consen 93 YVLCPECGSPDTELIKE 109 (125)
T ss_dssp HSSCTSTSSSSEEEEEE
T ss_pred EEEcCCCCCCccEEEEc
Confidence 45899999999999853
No 116
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=77.20 E-value=1.5 Score=28.79 Aligned_cols=16 Identities=44% Similarity=0.650 Sum_probs=14.0
Q ss_pred cccCCCCCCcceeeec
Q psy1204 47 GLKCEHCGSYNTCRIK 62 (71)
Q Consensus 47 g~kCp~C~Synt~ii~ 62 (71)
+..|+.|+|.+|.++.
T Consensus 102 yVlC~~C~spdT~l~k 117 (138)
T PRK03988 102 YVICPECGSPDTKLIK 117 (138)
T ss_pred cEECCCCCCCCcEEEE
Confidence 3489999999999985
No 117
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=77.00 E-value=4.6 Score=22.91 Aligned_cols=31 Identities=19% Similarity=0.573 Sum_probs=21.3
Q ss_pred eeEEcCCCCCceee------ceEeecccCCCCCCcce
Q psy1204 28 LYVLCKDCHKESKV------LYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 28 v~i~CndC~~~s~v------~~h~~g~kCp~C~Synt 58 (71)
-+++|.-||.+..+ .-..|-+-||+|.-...
T Consensus 3 ~Wi~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~Etl 39 (55)
T PF14205_consen 3 EWILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETL 39 (55)
T ss_pred eEEECCCCCCccceeeecCceeccccccCCCCCceEE
Confidence 58999999977743 22344458999975443
No 118
>PRK08197 threonine synthase; Validated
Probab=76.91 E-value=1.8 Score=32.04 Aligned_cols=26 Identities=19% Similarity=0.374 Sum_probs=20.9
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
....|.+||+++......+ .| .|++.
T Consensus 6 ~~~~C~~Cg~~~~~~~~~~--~C-~cg~~ 31 (394)
T PRK08197 6 SHLECSKCGETYDADQVHN--LC-KCGKP 31 (394)
T ss_pred eEEEECCCCCCCCCCCcce--ec-CCCCe
Confidence 3589999999998777666 89 79764
No 119
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=76.53 E-value=1.9 Score=32.33 Aligned_cols=24 Identities=13% Similarity=0.191 Sum_probs=17.7
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCC
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
.+.|..||+++. ....+ .||.|++
T Consensus 2 ~l~C~~Cg~~~~-~~~~~--~C~~c~g 25 (398)
T TIGR03844 2 TLRCPGCGEVLP-DHYTL--SCPLDCG 25 (398)
T ss_pred EEEeCCCCCccC-Ccccc--CCCCCCC
Confidence 468999999987 33334 9998764
No 120
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=76.03 E-value=1.6 Score=25.18 Aligned_cols=21 Identities=33% Similarity=0.860 Sum_probs=15.2
Q ss_pred EcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
-|..|+..-+. ..||.|||..
T Consensus 5 AC~~C~~i~~~------~~CP~Cgs~~ 25 (61)
T PRK08351 5 ACRHCHYITTE------DRCPVCGSRD 25 (61)
T ss_pred hhhhCCcccCC------CcCCCCcCCc
Confidence 68888764422 2799999987
No 121
>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=75.95 E-value=2.1 Score=22.61 Aligned_cols=13 Identities=46% Similarity=1.055 Sum_probs=7.0
Q ss_pred cCCCCCCcceeee
Q psy1204 49 KCEHCGSYNTCRI 61 (71)
Q Consensus 49 kCp~C~Synt~ii 61 (71)
.||+|||.....+
T Consensus 20 ~CP~Cg~~~~~~~ 32 (46)
T PF12760_consen 20 VCPHCGSTKHYRL 32 (46)
T ss_pred CCCCCCCeeeEEe
Confidence 5666666544333
No 122
>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=75.92 E-value=2.3 Score=22.06 Aligned_cols=9 Identities=56% Similarity=1.276 Sum_probs=4.8
Q ss_pred cCCCCCCcc
Q psy1204 49 KCEHCGSYN 57 (71)
Q Consensus 49 kCp~C~Syn 57 (71)
+||.|+|.+
T Consensus 2 ~Cp~Cg~~~ 10 (43)
T PF08271_consen 2 KCPNCGSKE 10 (43)
T ss_dssp SBTTTSSSE
T ss_pred CCcCCcCCc
Confidence 455555544
No 123
>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=75.81 E-value=1.1 Score=22.34 Aligned_cols=11 Identities=55% Similarity=0.924 Sum_probs=3.6
Q ss_pred cCCCCCCccee
Q psy1204 49 KCEHCGSYNTC 59 (71)
Q Consensus 49 kCp~C~Synt~ 59 (71)
+||.|+|.+|-
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 89999998876
No 124
>PRK11032 hypothetical protein; Provisional
Probab=75.10 E-value=2.7 Score=28.33 Aligned_cols=31 Identities=19% Similarity=0.496 Sum_probs=23.0
Q ss_pred eeeEEcCCCCCceeec--eEeecccCCCCCCccee
Q psy1204 27 ILYVLCKDCHKESKVL--YHIIGLKCEHCGSYNTC 59 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~--~h~~g~kCp~C~Synt~ 59 (71)
+....|..||.+-... .+.- -||+|++..-+
T Consensus 122 ~G~LvC~~Cg~~~~~~~p~~i~--pCp~C~~~~F~ 154 (160)
T PRK11032 122 LGNLVCEKCHHHLAFYTPEVLP--LCPKCGHDQFQ 154 (160)
T ss_pred cceEEecCCCCEEEecCCCcCC--CCCCCCCCeee
Confidence 4578999999877653 4555 99999876543
No 125
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=74.85 E-value=2.1 Score=36.30 Aligned_cols=44 Identities=27% Similarity=0.458 Sum_probs=27.4
Q ss_pred HHcCCCCHhhhc----ceeeEEcCCCCCceeeceEeecccCCCCCCcceee
Q psy1204 14 IASTPMPEEYKN----VILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60 (71)
Q Consensus 14 i~~~pmP~~y~~----~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~i 60 (71)
|..-=+|.-+-+ .....+|.+|+.++.-.-..- +||.||+ |+.+
T Consensus 993 i~sHFlPDl~GNLRaFsrQ~fRC~kC~~kYRR~PL~G--~C~kCGg-~lil 1040 (1095)
T TIGR00354 993 INSHFLPDIIGNLRAFSRQEVRCTKCNTKYRRIPLVG--KCLKCGN-NLTL 1040 (1095)
T ss_pred HHhccchHhhhhHhhhhccceeecccCCccccCCCCC--cccccCC-eEEE
Confidence 344445554322 245789999999885433222 9999998 4433
No 126
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=74.10 E-value=2.4 Score=31.13 Aligned_cols=25 Identities=32% Similarity=0.894 Sum_probs=15.8
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
...|.-|+. ..|+...+||+||+-.
T Consensus 210 yL~CslC~t----eW~~~R~~C~~Cg~~~ 234 (305)
T TIGR01562 210 YLSCSLCAT----EWHYVRVKCSHCEESK 234 (305)
T ss_pred EEEcCCCCC----cccccCccCCCCCCCC
Confidence 556666653 3455556899998743
No 127
>PRK14873 primosome assembly protein PriA; Provisional
Probab=73.95 E-value=2.4 Score=33.93 Aligned_cols=11 Identities=36% Similarity=0.866 Sum_probs=6.3
Q ss_pred cCCCCCCccee
Q psy1204 49 KCEHCGSYNTC 59 (71)
Q Consensus 49 kCp~C~Synt~ 59 (71)
.||+|||...+
T Consensus 424 ~Cp~Cgs~~l~ 434 (665)
T PRK14873 424 RCPRCGSDRLR 434 (665)
T ss_pred cCCCCcCCcce
Confidence 56666665444
No 128
>PRK12722 transcriptional activator FlhC; Provisional
Probab=73.95 E-value=2.2 Score=29.48 Aligned_cols=29 Identities=17% Similarity=0.323 Sum_probs=22.4
Q ss_pred eeeEEcCCCCCceeeceEee--cccCCCCCC
Q psy1204 27 ILYVLCKDCHKESKVLYHII--GLKCEHCGS 55 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~--g~kCp~C~S 55 (71)
-....|..|+..|.+..|.. ..+||.|.-
T Consensus 132 L~l~~C~~Cgg~fv~~~~e~~~~f~CplC~~ 162 (187)
T PRK12722 132 LQLSSCNCCGGHFVTHAHDPVGSFVCGLCQP 162 (187)
T ss_pred EeeccCCCCCCCeeccccccCCCCcCCCCCC
Confidence 34667999999998766554 559999975
No 129
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=73.58 E-value=3.5 Score=23.43 Aligned_cols=30 Identities=23% Similarity=0.667 Sum_probs=21.4
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii 61 (71)
+....|..||. ++.-.+.|+.||.|+-+.+
T Consensus 25 ~~~~~c~~cG~-----~~l~Hrvc~~cg~Y~g~~v 54 (57)
T COG0333 25 PTLSVCPNCGE-----YKLPHRVCLKCGYYKGRQV 54 (57)
T ss_pred ccceeccCCCC-----cccCceEcCCCCCccCeEe
Confidence 45788999985 2233348999999987654
No 130
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=73.28 E-value=2.1 Score=27.87 Aligned_cols=16 Identities=31% Similarity=0.499 Sum_probs=13.9
Q ss_pred cccCCCCCCcceeeec
Q psy1204 47 GLKCEHCGSYNTCRIK 62 (71)
Q Consensus 47 g~kCp~C~Synt~ii~ 62 (71)
+..|+.|+|.+|.++.
T Consensus 97 yVlC~~C~sPdT~l~k 112 (133)
T TIGR00311 97 YVICRECNRPDTRIIK 112 (133)
T ss_pred eEECCCCCCCCcEEEE
Confidence 3489999999999986
No 131
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=72.91 E-value=3.4 Score=22.28 Aligned_cols=28 Identities=25% Similarity=0.668 Sum_probs=18.1
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCcceee
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Synt~i 60 (71)
|.|+.|.+.-.+ ...+ +|-.|..|+.-+
T Consensus 1 ~~C~~C~~~~i~-g~R~--~C~~C~dydLC~ 28 (49)
T cd02345 1 LSCSACRKQDIS-GIRF--PCQVCRDYSLCL 28 (49)
T ss_pred CcCCCCCCCCce-EeeE--ECCCCCCcCchH
Confidence 468888874322 3344 888888777643
No 132
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=72.79 E-value=1.5 Score=33.72 Aligned_cols=27 Identities=26% Similarity=0.716 Sum_probs=20.1
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCC
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
+.-.|+.||.+-...... |.+|++||-
T Consensus 349 ~~p~Cp~Cg~~m~S~G~~-g~rC~kCg~ 375 (421)
T COG1571 349 VNPVCPRCGGRMKSAGRN-GFRCKKCGT 375 (421)
T ss_pred cCCCCCccCCchhhcCCC-Ccccccccc
Confidence 345799999877665554 559999974
No 133
>PRK04023 DNA polymerase II large subunit; Validated
Probab=72.54 E-value=2.1 Score=36.43 Aligned_cols=22 Identities=32% Similarity=0.783 Sum_probs=15.7
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
.-+|+.||..+ ..+ .||+||+.
T Consensus 626 ~RfCpsCG~~t----~~f--rCP~CG~~ 647 (1121)
T PRK04023 626 RRKCPSCGKET----FYR--RCPFCGTH 647 (1121)
T ss_pred CccCCCCCCcC----Ccc--cCCCCCCC
Confidence 44899999874 223 88888876
No 134
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=72.49 E-value=3.3 Score=29.45 Aligned_cols=29 Identities=24% Similarity=0.768 Sum_probs=11.1
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii 61 (71)
...|.-|+. ..|+...+||+||+-+-.-+
T Consensus 197 ~L~Cs~C~t----~W~~~R~~Cp~Cg~~~~~~l 225 (290)
T PF04216_consen 197 YLHCSLCGT----EWRFVRIKCPYCGNTDHEKL 225 (290)
T ss_dssp EEEETTT------EEE--TTS-TTT---SS-EE
T ss_pred EEEcCCCCC----eeeecCCCCcCCCCCCCcce
Confidence 444555542 33444557888877665544
No 135
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=72.38 E-value=6.7 Score=26.16 Aligned_cols=38 Identities=26% Similarity=0.507 Sum_probs=24.8
Q ss_pred EcCCCCCceee-------ce----EeecccCCCCCCcceeeecCCCCCC
Q psy1204 31 LCKDCHKESKV-------LY----HIIGLKCEHCGSYNTCRIKKPNGQE 68 (71)
Q Consensus 31 ~CndC~~~s~v-------~~----h~~g~kCp~C~Synt~ii~g~~~~~ 68 (71)
.|..|++.... +| ......|++||=-|+.|..|..-+.
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~p 50 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRNNEVKSGGAIEP 50 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCccceEEECcccCC
Confidence 58888866652 21 1113389999999999876665443
No 136
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=72.12 E-value=2.7 Score=24.30 Aligned_cols=12 Identities=17% Similarity=0.587 Sum_probs=7.5
Q ss_pred ceeeEEcCCCCC
Q psy1204 26 VILYVLCKDCHK 37 (71)
Q Consensus 26 ~~v~i~CndC~~ 37 (71)
.-+...|.+||.
T Consensus 24 ~~v~F~CPnCGe 35 (61)
T COG2888 24 TAVKFPCPNCGE 35 (61)
T ss_pred ceeEeeCCCCCc
Confidence 346667777773
No 137
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=71.96 E-value=3.1 Score=22.44 Aligned_cols=26 Identities=31% Similarity=0.570 Sum_probs=15.6
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
|.|+.|+..... ...+ +|-.|..|+.
T Consensus 1 i~C~~C~~~~i~-g~R~--~C~~C~d~dl 26 (49)
T cd02338 1 VSCDGCGKSNFT-GRRY--KCLICYDYDL 26 (49)
T ss_pred CCCCCCcCCCcE-EeeE--EeCCCCCCcc
Confidence 468888854333 3344 7777766654
No 138
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=71.86 E-value=3.4 Score=22.95 Aligned_cols=19 Identities=26% Similarity=0.541 Sum_probs=15.9
Q ss_pred cCCCCCCcceeeecCCCCC
Q psy1204 49 KCEHCGSYNTCRIKKPNGQ 67 (71)
Q Consensus 49 kCp~C~Synt~ii~g~~~~ 67 (71)
.||.||..+...++-..+.
T Consensus 2 ~CPyCge~~~~~iD~s~~~ 20 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGD 20 (52)
T ss_pred CCCCCCCeeEEEEecCCCC
Confidence 6999999999999866653
No 139
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=71.84 E-value=4.1 Score=28.08 Aligned_cols=13 Identities=38% Similarity=0.641 Sum_probs=10.0
Q ss_pred eEEcCCCCCceee
Q psy1204 29 YVLCKDCHKESKV 41 (71)
Q Consensus 29 ~i~CndC~~~s~v 41 (71)
.+.|.-|+++|.+
T Consensus 5 ~~~CPvC~~~F~~ 17 (214)
T PF09986_consen 5 KITCPVCGKEFKT 17 (214)
T ss_pred ceECCCCCCeeee
Confidence 5778888888864
No 140
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=71.59 E-value=2.7 Score=22.50 Aligned_cols=26 Identities=27% Similarity=0.838 Sum_probs=15.8
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
|.|..|++.. +....+ ||..|..|+.
T Consensus 1 i~Cd~C~~~~-i~G~Ry--kC~~C~dyDL 26 (45)
T cd02339 1 IICDTCRKQG-IIGIRW--KCAECPNYDL 26 (45)
T ss_pred CCCCCCCCCC-cccCeE--ECCCCCCccc
Confidence 4688888543 333344 7777776654
No 141
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=71.53 E-value=3.1 Score=23.93 Aligned_cols=23 Identities=26% Similarity=0.641 Sum_probs=14.0
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
-+|.+|+.- .+--+||.||+.-.
T Consensus 6 rkC~~cg~Y------TLke~Cp~CG~~t~ 28 (59)
T COG2260 6 RKCPKCGRY------TLKEKCPVCGGDTK 28 (59)
T ss_pred hcCcCCCce------eecccCCCCCCccc
Confidence 357777731 22238999987543
No 142
>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=71.50 E-value=3.8 Score=23.49 Aligned_cols=19 Identities=26% Similarity=0.525 Sum_probs=12.6
Q ss_pred EeecccCCCCCCcceeeec
Q psy1204 44 HIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 44 h~~g~kCp~C~Synt~ii~ 62 (71)
++.|-+||.|++-++-++-
T Consensus 6 FIAGA~CP~C~~~Dtl~~~ 24 (59)
T TIGR02443 6 FIAGAVCPACSAQDTLAMW 24 (59)
T ss_pred EeccccCCCCcCccEEEEE
Confidence 4556677777777766653
No 143
>PRK12860 transcriptional activator FlhC; Provisional
Probab=71.02 E-value=2.8 Score=29.01 Aligned_cols=28 Identities=18% Similarity=0.407 Sum_probs=22.1
Q ss_pred eeeEEcCCCCCceeeceEee--cccCCCCC
Q psy1204 27 ILYVLCKDCHKESKVLYHII--GLKCEHCG 54 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~--g~kCp~C~ 54 (71)
-....|..|+..|.+..|.. ..+||.|.
T Consensus 132 L~l~~C~~Cgg~fv~~~~e~~~~f~CplC~ 161 (189)
T PRK12860 132 LQLARCCRCGGKFVTHAHDLRHNFVCGLCQ 161 (189)
T ss_pred eeeccCCCCCCCeeccccccCCCCcCCCCC
Confidence 45778999999998765544 55999997
No 144
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=70.39 E-value=3.3 Score=25.91 Aligned_cols=33 Identities=24% Similarity=0.411 Sum_probs=21.8
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCccee
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTC 59 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ 59 (71)
.....|.+||....+.+--=.--||.||...+.
T Consensus 40 ~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~~~~ 72 (111)
T PF14319_consen 40 FHRYRCEDCGHEKIVYNSCKNRHCPSCQAKATE 72 (111)
T ss_pred cceeecCCCCceEEecCcccCcCCCCCCChHHH
Confidence 467899999987765441111157999876654
No 145
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=70.38 E-value=2.1 Score=24.96 Aligned_cols=25 Identities=28% Similarity=0.610 Sum_probs=15.5
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
.-|.+|..-.+...- .||.|||..+
T Consensus 5 kAC~~Ck~l~~~d~e----~CP~Cgs~~~ 29 (64)
T COG2093 5 KACKNCKRLTPEDTE----ICPVCGSTDL 29 (64)
T ss_pred HHHhhccccCCCCCc----cCCCCCCccc
Confidence 347788654333221 6999999844
No 146
>PRK02935 hypothetical protein; Provisional
Probab=69.86 E-value=4.3 Score=25.94 Aligned_cols=32 Identities=31% Similarity=0.626 Sum_probs=25.7
Q ss_pred cceeeEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
.+.+.+.|+.|++....-.... .|.+|+-.=|
T Consensus 66 tkavqV~CP~C~K~TKmLGrvD--~CM~C~~PLT 97 (110)
T PRK02935 66 TKAVQVICPSCEKPTKMLGRVD--ACMHCNQPLT 97 (110)
T ss_pred ccceeeECCCCCchhhhcccee--ecCcCCCcCC
Confidence 3467899999999988877777 8999975543
No 147
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=69.76 E-value=3.8 Score=31.17 Aligned_cols=36 Identities=22% Similarity=0.490 Sum_probs=22.0
Q ss_pred cceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecC
Q psy1204 25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKK 63 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g 63 (71)
+..-..+|..|+..-.... ..--+||+||+ ...+.|
T Consensus 236 ~~g~~~~c~~cg~~~~~~~-~~~~~c~~Cg~--~~~~~G 271 (380)
T COG1867 236 NLGYIYHCSRCGEIVGSFR-EVDEKCPHCGG--KVHLAG 271 (380)
T ss_pred hcCcEEEcccccceecccc-cccccCCcccc--cceecc
Confidence 3345789999993332222 33349999999 444444
No 148
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=69.50 E-value=3.5 Score=30.25 Aligned_cols=13 Identities=23% Similarity=0.700 Sum_probs=6.6
Q ss_pred eeEEcCCCCCcee
Q psy1204 28 LYVLCKDCHKESK 40 (71)
Q Consensus 28 v~i~CndC~~~s~ 40 (71)
+.+.|..||.+..
T Consensus 223 ~R~~C~~Cg~~~~ 235 (305)
T TIGR01562 223 VRVKCSHCEESKH 235 (305)
T ss_pred cCccCCCCCCCCc
Confidence 3555555554443
No 149
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=69.17 E-value=9.6 Score=25.83 Aligned_cols=28 Identities=18% Similarity=0.422 Sum_probs=13.6
Q ss_pred eeeEEcCCCCCceeeceEee--cccCCCCC
Q psy1204 27 ILYVLCKDCHKESKVLYHII--GLKCEHCG 54 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~--g~kCp~C~ 54 (71)
-....|..|+..|.+..|.. ...||.|+
T Consensus 132 l~l~~C~~C~~~fv~~~~~~~~~~~Cp~C~ 161 (175)
T PF05280_consen 132 LQLAPCRRCGGHFVTHAHDPRHSFVCPFCQ 161 (175)
T ss_dssp EEEEE-TTT--EEEEESS--SS----TT--
T ss_pred ccccCCCCCCCCeECcCCCCCcCcCCCCCC
Confidence 56789999999998754441 22999997
No 150
>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=68.53 E-value=4.7 Score=23.65 Aligned_cols=19 Identities=26% Similarity=0.539 Sum_probs=13.1
Q ss_pred EeecccCCCCCCcceeeec
Q psy1204 44 HIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 44 h~~g~kCp~C~Synt~ii~ 62 (71)
++.|-.||.|++-++-.+-
T Consensus 5 FIAGa~CP~C~~~D~i~~~ 23 (71)
T PF09526_consen 5 FIAGAVCPKCQAMDTIMMW 23 (71)
T ss_pred EecCccCCCCcCccEEEEE
Confidence 4566778888877776653
No 151
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=68.44 E-value=3.5 Score=29.42 Aligned_cols=44 Identities=14% Similarity=0.107 Sum_probs=26.7
Q ss_pred cceeeEEcCCCCCceeece----Eee--cccCCCCCCc--ceeee-cCCCCCC
Q psy1204 25 NVILYVLCKDCHKESKVLY----HII--GLKCEHCGSY--NTCRI-KKPNGQE 68 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v~~----h~~--g~kCp~C~Sy--nt~ii-~g~~~~~ 68 (71)
......+|..|+.+..... .-- --+||.||++ +..|+ =||..|+
T Consensus 118 Gsl~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~~lrP~VV~fGE~lp~ 170 (250)
T COG0846 118 GSLKRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGPVLRPDVVWFGEPLPA 170 (250)
T ss_pred cceeeeEeCCCcCccchhhhhhhcccCCCCcCccCCCccccCCEEEeCCCCCH
Confidence 3455678999998776322 111 1259999994 33333 4777665
No 152
>PF10950 DUF2775: Protein of unknown function (DUF2775); InterPro: IPR024489 This eukaryotic family includes a number of plant organ-specific proteins. While their function is unknown, their predicted amino acid sequence suggests that these proteins could be exported and glycosylated [].
Probab=68.28 E-value=4.1 Score=25.80 Aligned_cols=21 Identities=29% Similarity=0.767 Sum_probs=17.5
Q ss_pred ChHHHHHHHHHHHHcCCCCHhhhc
Q psy1204 2 DMTPLWRQMDEEIASTPMPEEYKN 25 (71)
Q Consensus 2 dm~~~~~~lD~~i~~~pmP~~y~~ 25 (71)
|+..||+.+=. .+|||++-|.
T Consensus 2 D~geYWK~vMK---DqpMPeaIqg 22 (108)
T PF10950_consen 2 DLGEYWKDVMK---DQPMPEAIQG 22 (108)
T ss_pred cHHHHHHHhhc---CCCChHHHHH
Confidence 78899988655 9999998774
No 153
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=67.17 E-value=3.4 Score=21.85 Aligned_cols=27 Identities=19% Similarity=0.461 Sum_probs=15.0
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
.+.|+.|+....+ ...+ +|..|..|+.
T Consensus 4 ~~~C~~C~~~~i~-g~Ry--~C~~C~d~dL 30 (46)
T PF00569_consen 4 GYTCDGCGTDPII-GVRY--HCLVCPDYDL 30 (46)
T ss_dssp SCE-SSS-SSSEE-SSEE--EESSSSS-EE
T ss_pred CeECcCCCCCcCc-CCeE--ECCCCCCCch
Confidence 4679999974322 2334 7877877764
No 154
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=66.80 E-value=7.6 Score=26.05 Aligned_cols=18 Identities=28% Similarity=0.449 Sum_probs=13.4
Q ss_pred cCCCCCCcceeeecCCCC
Q psy1204 49 KCEHCGSYNTCRIKKPNG 66 (71)
Q Consensus 49 kCp~C~Synt~ii~g~~~ 66 (71)
.|++||=.|+.|..|.+-
T Consensus 30 ~C~~CGyr~~ev~~~~~~ 47 (163)
T TIGR00340 30 ICEKCGYRSTDVYQLEEK 47 (163)
T ss_pred ECCCCCCchhheeEcCCc
Confidence 788998888887665543
No 155
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=66.77 E-value=8.6 Score=28.70 Aligned_cols=30 Identities=23% Similarity=0.453 Sum_probs=21.8
Q ss_pred cceeeEEcCCCCCceeeceEeecccCCCCCC
Q psy1204 25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
+.-.+.+|..|+....+.. ....+||.|++
T Consensus 240 ~~g~~~~C~~c~~~~~~~~-~~~~~C~~c~~ 269 (382)
T PRK04338 240 NLGYVYYCPKCLYREEVEG-LPPEECPVCGG 269 (382)
T ss_pred hceeEEECCCCCcEEEecC-CCCCCCCCCCC
Confidence 3356889999998776554 33348999987
No 156
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=66.71 E-value=3.4 Score=28.33 Aligned_cols=16 Identities=31% Similarity=0.569 Sum_probs=13.5
Q ss_pred cccCCCCCCcceeeec
Q psy1204 47 GLKCEHCGSYNTCRIK 62 (71)
Q Consensus 47 g~kCp~C~Synt~ii~ 62 (71)
+..|+.|+|.+|.++.
T Consensus 98 yV~C~~C~~pdT~l~k 113 (201)
T PRK12336 98 YVICSECGLPDTRLVK 113 (201)
T ss_pred eEECCCCCCCCcEEEE
Confidence 3489999999999985
No 157
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=66.61 E-value=4.2 Score=21.24 Aligned_cols=26 Identities=23% Similarity=0.536 Sum_probs=16.7
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
.+.|+.|+. ......+ +|..|..|++
T Consensus 4 ~~~C~~C~~--~i~g~ry--~C~~C~d~dl 29 (44)
T smart00291 4 SYSCDTCGK--PIVGVRY--HCLVCPDYDL 29 (44)
T ss_pred CcCCCCCCC--CCcCCEE--ECCCCCCccc
Confidence 467999997 3333344 7877776664
No 158
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 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 consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=66.54 E-value=4.5 Score=22.92 Aligned_cols=28 Identities=32% Similarity=0.667 Sum_probs=20.5
Q ss_pred ceeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 26 VILYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
.+.-++|.-||. ..||.--..|..||=.
T Consensus 12 ~ktH~~CrRCG~---~syH~qK~~CasCGyp 39 (55)
T PF01907_consen 12 NKTHTLCRRCGR---RSYHIQKKTCASCGYP 39 (55)
T ss_dssp S-SEEE-TTTSS---EEEETTTTEETTTBTT
T ss_pred CccEeeecccCC---eeeecCCCcccccCCC
Confidence 468899999997 5677777789999733
No 159
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=66.53 E-value=7.9 Score=27.13 Aligned_cols=35 Identities=31% Similarity=0.712 Sum_probs=23.1
Q ss_pred eeeEEcCCCCCcee---e----ceEeecccCCCCCCcceeeec
Q psy1204 27 ILYVLCKDCHKESK---V----LYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 27 ~v~i~CndC~~~s~---v----~~h~~g~kCp~C~Synt~ii~ 62 (71)
...+.|..|+.... + -.+.+ ..|..||..++.++.
T Consensus 4 ~iy~~Cp~Cg~eev~hEVik~~g~~~l-vrC~eCG~V~~~~i~ 45 (201)
T COG1326 4 EIYIECPSCGSEEVSHEVIKERGREPL-VRCEECGTVHPAIIK 45 (201)
T ss_pred eEEEECCCCCcchhhHHHHHhcCCceE-EEccCCCcEeeceee
Confidence 46789999994333 1 12333 399999999865553
No 160
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=66.51 E-value=2.1 Score=28.64 Aligned_cols=18 Identities=44% Similarity=0.676 Sum_probs=15.2
Q ss_pred ecccCCCCCCcceeeecC
Q psy1204 46 IGLKCEHCGSYNTCRIKK 63 (71)
Q Consensus 46 ~g~kCp~C~Synt~ii~g 63 (71)
.+.+|+.|+|++|.++.+
T Consensus 104 ~yv~C~~c~s~dt~l~~~ 121 (151)
T COG1601 104 EYVKCKECGSPDTELIKE 121 (151)
T ss_pred heeEeccCCCCchhhhhh
Confidence 344999999999999876
No 161
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=65.71 E-value=2.4 Score=28.81 Aligned_cols=34 Identities=24% Similarity=0.436 Sum_probs=22.1
Q ss_pred hhcceeeEEcCCCCCceeece------EeecccCCCCCCc
Q psy1204 23 YKNVILYVLCKDCHKESKVLY------HIIGLKCEHCGSY 56 (71)
Q Consensus 23 y~~~~v~i~CndC~~~s~v~~------h~~g~kCp~C~Sy 56 (71)
....--...|..|++...... ....-+||.|++.
T Consensus 103 lHG~~~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 142 (218)
T cd01407 103 LHGSLFRVRCTKCGKEYPRDELQADIDREEVPRCPKCGGL 142 (218)
T ss_pred CcCCcCcceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCc
Confidence 334455678999998775321 2233489999874
No 162
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=65.28 E-value=2.9 Score=31.49 Aligned_cols=27 Identities=19% Similarity=0.463 Sum_probs=18.0
Q ss_pred eEEcCCCCCceeece-EeecccCCCCCCc
Q psy1204 29 YVLCKDCHKESKVLY-HIIGLKCEHCGSY 56 (71)
Q Consensus 29 ~i~CndC~~~s~v~~-h~~g~kCp~C~Sy 56 (71)
.-.|..|+....... .-++.+|| ||+.
T Consensus 240 ~~~c~~C~~~~~~~~~~~~~~~Cp-CG~~ 267 (374)
T TIGR00375 240 QTACEACGEPAVSEDAETACANCP-CGGR 267 (374)
T ss_pred hhhhcccCCcCCchhhhhcCCCCC-CCCc
Confidence 346888987776433 11234999 9998
No 163
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=64.86 E-value=3.3 Score=23.90 Aligned_cols=28 Identities=32% Similarity=0.689 Sum_probs=18.4
Q ss_pred eEEcCCCCCceeeceEeec--ccCCCCCCc
Q psy1204 29 YVLCKDCHKESKVLYHIIG--LKCEHCGSY 56 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g--~kCp~C~Sy 56 (71)
.+.|..|+.+.++....-+ ..||.|+++
T Consensus 41 ~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~~ 70 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEYSCGADYFCPICGLY 70 (71)
T ss_dssp EEEETTT--EEES-SBTT--SEEETTTTEE
T ss_pred CeECCCCCCccChhhhhcCCCccCcCcCCC
Confidence 8999999999887653111 289999876
No 164
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=64.79 E-value=7 Score=21.26 Aligned_cols=15 Identities=27% Similarity=0.585 Sum_probs=10.8
Q ss_pred cCCCCCCcceeeecC
Q psy1204 49 KCEHCGSYNTCRIKK 63 (71)
Q Consensus 49 kCp~C~Synt~ii~g 63 (71)
-||+||+-.+.+...
T Consensus 5 PCPFCG~~~~~~~~~ 19 (61)
T PF14354_consen 5 PCPFCGSADVLIRQD 19 (61)
T ss_pred CCCCCCCcceEeecc
Confidence 699997777766653
No 165
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=64.78 E-value=5.2 Score=29.51 Aligned_cols=13 Identities=31% Similarity=1.129 Sum_probs=8.4
Q ss_pred eEeecccCCCCCC
Q psy1204 43 YHIIGLKCEHCGS 55 (71)
Q Consensus 43 ~h~~g~kCp~C~S 55 (71)
.|+...+||+||+
T Consensus 222 W~~~R~~C~~Cg~ 234 (309)
T PRK03564 222 WHVVRVKCSNCEQ 234 (309)
T ss_pred ccccCccCCCCCC
Confidence 3444557888876
No 166
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=64.28 E-value=14 Score=22.34 Aligned_cols=37 Identities=16% Similarity=0.517 Sum_probs=24.0
Q ss_pred ceeeEEcCCCCCcee-----ec----------eEeecccCCCCCCcceeeec
Q psy1204 26 VILYVLCKDCHKESK-----VL----------YHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 26 ~~v~i~CndC~~~s~-----v~----------~h~~g~kCp~C~Synt~ii~ 62 (71)
..+...|..|+...+ +. ..+++++|..|+.+..-.++
T Consensus 2 ~~grF~C~~C~~~W~S~~v~i~f~~~~~g~v~~rv~~Q~C~~C~~~~~P~~~ 53 (98)
T PF13695_consen 2 AFGRFQCSKCSRGWTSAKVWILFHMYRGGQVNMRVFGQRCKKCNPLERPYFS 53 (98)
T ss_pred cEEEEECCCCCCCCccCEEEEEEEEcCCCeEEEEEECCCCCCCCCCCCccCc
Confidence 356778888865443 22 33588999999766554443
No 167
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 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. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=64.26 E-value=14 Score=27.93 Aligned_cols=42 Identities=26% Similarity=0.591 Sum_probs=21.5
Q ss_pred CCCHhhhcceeeEEcCCCCCce--eec-------eEeecccCCCCCCcceeeecC
Q psy1204 18 PMPEEYKNVILYVLCKDCHKES--KVL-------YHIIGLKCEHCGSYNTCRIKK 63 (71)
Q Consensus 18 pmP~~y~~~~v~i~CndC~~~s--~v~-------~h~~g~kCp~C~Synt~ii~g 63 (71)
+.|+.| .|....|..||+.- ++. ...| +|+.||-..+.-+.+
T Consensus 165 ~~~~~y--~Pf~piC~~cGri~tt~v~~~d~~~~~v~Y--~c~~cG~~g~~~i~~ 215 (360)
T PF01921_consen 165 ERPETY--SPFLPICEKCGRIDTTEVTEYDPEGGTVTY--RCEECGHEGEVDITG 215 (360)
T ss_dssp T--TT----SEEEEETTTEE--EEEEEEE--SSSEEEE--E--TTS---EEETTT
T ss_pred CCCCCe--eeeeeeccccCCcccceeeEeecCCCEEEE--EecCCCCEEEEecCC
Confidence 477777 48999999999932 221 1233 999999877766543
No 168
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=64.17 E-value=4.8 Score=32.84 Aligned_cols=11 Identities=36% Similarity=0.942 Sum_probs=8.4
Q ss_pred eEEcCCCCCce
Q psy1204 29 YVLCKDCHKES 39 (71)
Q Consensus 29 ~i~CndC~~~s 39 (71)
.+.|.+||..+
T Consensus 435 ~l~C~~Cg~v~ 445 (730)
T COG1198 435 LLLCRDCGYIA 445 (730)
T ss_pred eeecccCCCcc
Confidence 67899998644
No 169
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=64.15 E-value=3.7 Score=36.08 Aligned_cols=26 Identities=27% Similarity=0.490 Sum_probs=19.4
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCC
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
....+| +|+.++.-.-..- +||+|||
T Consensus 1540 rQ~~RC-kC~~kyRR~PL~G--~C~kCGg 1565 (1627)
T PRK14715 1540 RQEFRC-KCGAKYRRVPLKG--KCPKCGS 1565 (1627)
T ss_pred ccceee-cCCCccccCCCCC--cCcccCC
Confidence 457899 9998875433222 9999998
No 170
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=64.00 E-value=6.7 Score=22.13 Aligned_cols=25 Identities=20% Similarity=0.396 Sum_probs=16.6
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
..-.|.+||..+- ...||.||+...
T Consensus 4 ~mr~C~~CgvYTL------k~~CP~CG~~t~ 28 (56)
T PRK13130 4 KIRKCPKCGVYTL------KEICPVCGGKTK 28 (56)
T ss_pred cceECCCCCCEEc------cccCcCCCCCCC
Confidence 3567888985333 238999987643
No 171
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=63.49 E-value=3.7 Score=22.67 Aligned_cols=30 Identities=23% Similarity=0.453 Sum_probs=21.4
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCcceee
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~i 60 (71)
.-...|..|+..-.+.- .+|..|||-+.+.
T Consensus 12 ~~k~ICrkC~ARnp~~A----~~CRKCg~~~LRp 41 (48)
T PRK04136 12 FNKKICMRCNARNPWRA----TKCRKCGYKNLRP 41 (48)
T ss_pred hcccchhcccCCCCccc----cccccCCCCCcCc
Confidence 34667999987655543 3999999866654
No 172
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=63.28 E-value=6.8 Score=23.17 Aligned_cols=32 Identities=25% Similarity=0.545 Sum_probs=14.5
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~ 62 (71)
-+.+|..|-+........ -||+||.-...-++
T Consensus 8 ~vlrC~aCf~~t~~~~k~---FCp~CGn~TL~rvs 39 (73)
T PF08772_consen 8 WVLRCHACFKITKDMTKQ---FCPKCGNATLKRVS 39 (73)
T ss_dssp EEEE-SSS--EES-SS-----S-SSS--S--EEEE
T ss_pred eeEEccccccCcCCCCce---eCcccCCCcceEEE
Confidence 467899998765533322 59999988766554
No 173
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=63.15 E-value=2.4 Score=23.66 Aligned_cols=25 Identities=24% Similarity=0.519 Sum_probs=10.1
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCC
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCG 54 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~ 54 (71)
-.-.|..|+++|..-..-. .|..||
T Consensus 8 ~~~~C~~C~~~F~~~~rrh--hCr~CG 32 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRH--HCRNCG 32 (69)
T ss_dssp G-SB-TTT--B-BSSS-EE--E-TTT-
T ss_pred CCCcCcCcCCcCCCceeeE--ccCCCC
Confidence 3557888999986533222 666654
No 174
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=63.05 E-value=7 Score=24.95 Aligned_cols=19 Identities=42% Similarity=0.912 Sum_probs=11.9
Q ss_pred cCCCCCceeeceEeecccCCCCC
Q psy1204 32 CKDCHKESKVLYHIIGLKCEHCG 54 (71)
Q Consensus 32 CndC~~~s~v~~h~~g~kCp~C~ 54 (71)
|..||..-.|.. + +|++|+
T Consensus 1 CPvCg~~l~vt~--l--~C~~C~ 19 (113)
T PF09862_consen 1 CPVCGGELVVTR--L--KCPSCG 19 (113)
T ss_pred CCCCCCceEEEE--E--EcCCCC
Confidence 667776555543 2 777774
No 175
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=62.97 E-value=4.6 Score=21.75 Aligned_cols=25 Identities=20% Similarity=0.610 Sum_probs=15.7
Q ss_pred EcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
.|+.|+..- +....+ ||..|..|+.
T Consensus 2 ~Cd~C~~~p-I~G~Ry--kC~~C~dyDL 26 (45)
T cd02344 2 TCDGCQMFP-INGPRF--KCRNCDDFDF 26 (45)
T ss_pred CCCCCCCCC-CccCeE--ECCCCCCccc
Confidence 578887533 333344 8888877764
No 176
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=62.86 E-value=3.3 Score=21.08 Aligned_cols=26 Identities=23% Similarity=0.459 Sum_probs=11.0
Q ss_pred EcCCCCCceee--c--eEeecccCCCCCCc
Q psy1204 31 LCKDCHKESKV--L--YHIIGLKCEHCGSY 56 (71)
Q Consensus 31 ~CndC~~~s~v--~--~h~~g~kCp~C~Sy 56 (71)
+|..||..-+. + .+...+.|+.||..
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCE
Confidence 57777765431 2 23334477777653
No 177
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=62.51 E-value=4.2 Score=29.71 Aligned_cols=30 Identities=17% Similarity=0.299 Sum_probs=25.1
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
..-+|..||.+.....+-....||+|+-.-
T Consensus 110 ~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 110 SHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred hCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 466899999999988888878999998654
No 178
>PRK05638 threonine synthase; Validated
Probab=62.44 E-value=4.8 Score=30.23 Aligned_cols=23 Identities=26% Similarity=0.654 Sum_probs=17.4
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
..|..||++...... + .| .|++.
T Consensus 2 l~C~~Cg~~~~~~~~-~--~C-~c~~~ 24 (442)
T PRK05638 2 MKCPKCGREYNSYIP-P--FC-ICGEL 24 (442)
T ss_pred eEeCCCCCCCCCCCc-e--ec-CCCCc
Confidence 589999999875443 4 89 89864
No 179
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=62.40 E-value=5.5 Score=26.98 Aligned_cols=25 Identities=20% Similarity=0.349 Sum_probs=18.8
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
+-.|.-||..... .-.- +||.||..
T Consensus 134 ~~vC~vCGy~~~g-e~P~--~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEG-EAPE--VCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccC-CCCC--cCCCCCCh
Confidence 6779999988765 3233 99999854
No 180
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=62.29 E-value=4.6 Score=23.30 Aligned_cols=30 Identities=27% Similarity=0.599 Sum_probs=22.9
Q ss_pred hcceeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 24 KNVILYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 24 ~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
++.+..|.|.-||. ..||.--..|..||=.
T Consensus 11 rnk~tH~~CRRCGr---~syhv~k~~CaaCGfg 40 (61)
T COG2126 11 RNKKTHIRCRRCGR---RSYHVRKKYCAACGFG 40 (61)
T ss_pred cCCcceehhhhccc---hheeeccceecccCCC
Confidence 34578999999997 4567766689999754
No 181
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=62.26 E-value=2.5 Score=27.00 Aligned_cols=31 Identities=19% Similarity=0.424 Sum_probs=21.7
Q ss_pred EcCCCCCceee-ceEeecccCCCCCCcceeeec
Q psy1204 31 LCKDCHKESKV-LYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 31 ~CndC~~~s~v-~~h~~g~kCp~C~Synt~ii~ 62 (71)
.|-.||..|.. ....+ .-||.||+---.-+.
T Consensus 4 ~CtrCG~vf~~g~~~il-~GCp~CG~nkF~yv~ 35 (112)
T COG3364 4 QCTRCGEVFDDGSEEIL-SGCPKCGCNKFLYVP 35 (112)
T ss_pred eecccccccccccHHHH-ccCccccchheEecc
Confidence 58899999975 44444 389999986544443
No 182
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=61.94 E-value=5.9 Score=29.88 Aligned_cols=29 Identities=24% Similarity=0.525 Sum_probs=19.4
Q ss_pred eEEcCCCCCceeeceEeecc--cCCCCCCcc
Q psy1204 29 YVLCKDCHKESKVLYHIIGL--KCEHCGSYN 57 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~--kCp~C~Syn 57 (71)
.+.|.+|+....++..--|. .||.||+.=
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 56799999777554322221 699998754
No 183
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=61.65 E-value=6.4 Score=21.69 Aligned_cols=13 Identities=38% Similarity=0.634 Sum_probs=11.1
Q ss_pred eeEEcCCCCCcee
Q psy1204 28 LYVLCKDCHKESK 40 (71)
Q Consensus 28 v~i~CndC~~~s~ 40 (71)
..+.|.|||+.|.
T Consensus 3 k~l~C~dCg~~Fv 15 (49)
T PF13451_consen 3 KTLTCKDCGAEFV 15 (49)
T ss_pred eeEEcccCCCeEE
Confidence 4688999999886
No 184
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=61.63 E-value=5.3 Score=27.34 Aligned_cols=25 Identities=24% Similarity=0.542 Sum_probs=17.7
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
.....|..||. .....+ .||.||-.
T Consensus 307 ~tS~~C~~cg~---~~~r~~--~C~~cg~~ 331 (364)
T COG0675 307 YTSKTCPCCGH---LSGRLF--KCPRCGFV 331 (364)
T ss_pred CCcccccccCC---ccceeE--ECCCCCCe
Confidence 34578999998 333444 99999864
No 185
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=61.58 E-value=4.7 Score=21.74 Aligned_cols=26 Identities=15% Similarity=0.208 Sum_probs=16.9
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
|.|..|+.... ....+ ||..|..|+.
T Consensus 1 I~CDgCg~~PI-~G~Ry--kC~~C~dyDL 26 (43)
T cd02342 1 IQCDGCGVLPI-TGPRY--KSKVKEDYDL 26 (43)
T ss_pred CCCCCCCCCcc-cccce--EeCCCCCCcc
Confidence 46888885433 33345 8888877764
No 186
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=61.28 E-value=6 Score=27.25 Aligned_cols=29 Identities=17% Similarity=0.298 Sum_probs=18.9
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
-...|..|+...........-+||.|++.
T Consensus 117 ~~~~C~~C~~~~~~~~~~~~p~C~~Cgg~ 145 (225)
T cd01411 117 YRIYCTVCGKTVDWEEYLKSPYHAKCGGV 145 (225)
T ss_pred CeeEeCCCCCccchhhcCCCCCCCCCCCE
Confidence 45789999876643332222489999875
No 187
>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=61.23 E-value=5.9 Score=21.46 Aligned_cols=13 Identities=23% Similarity=0.608 Sum_probs=10.6
Q ss_pred cCCCCCCcceeee
Q psy1204 49 KCEHCGSYNTCRI 61 (71)
Q Consensus 49 kCp~C~Synt~ii 61 (71)
-||+||+-...+.
T Consensus 3 PCPfCGg~~~~~~ 15 (53)
T TIGR03655 3 PCPFCGGADVYLR 15 (53)
T ss_pred CCCCCCCcceeeE
Confidence 6999999777665
No 188
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=61.21 E-value=4.6 Score=35.06 Aligned_cols=10 Identities=30% Similarity=0.640 Sum_probs=6.2
Q ss_pred eEEcCCCCCc
Q psy1204 29 YVLCKDCHKE 38 (71)
Q Consensus 29 ~i~CndC~~~ 38 (71)
..+|..||..
T Consensus 667 ~rkCPkCG~~ 676 (1337)
T PRK14714 667 RRRCPSCGTE 676 (1337)
T ss_pred EEECCCCCCc
Confidence 4567777653
No 189
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=60.95 E-value=6.2 Score=29.11 Aligned_cols=34 Identities=26% Similarity=0.683 Sum_probs=20.9
Q ss_pred eeEEcCCCCCceeeceEee--------cccCCCCCCcceeee
Q psy1204 28 LYVLCKDCHKESKVLYHII--------GLKCEHCGSYNTCRI 61 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~--------g~kCp~C~Synt~ii 61 (71)
+.+.|..||......|+.+ -..|..|+||=-.+.
T Consensus 225 ~R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~~ 266 (309)
T PRK03564 225 VRVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKILY 266 (309)
T ss_pred cCccCCCCCCCCceeeeeecCCCcceEeeecccccccceecc
Confidence 4667777776544444322 137888888876653
No 190
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=60.68 E-value=8.4 Score=30.58 Aligned_cols=27 Identities=30% Similarity=0.480 Sum_probs=21.6
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCC
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
...+.|..|++.+.+.-..+ +||.||+
T Consensus 86 DpmV~CkkCk~ryRaD~Lii--kCP~CGs 112 (539)
T PRK14894 86 DPLVDCRDCKMRWRADHIQG--VCPNCGS 112 (539)
T ss_pred CceeECCCCCccccCcccee--eCCCCCC
Confidence 35788999999887765444 9999998
No 191
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=60.50 E-value=5.9 Score=20.24 Aligned_cols=26 Identities=19% Similarity=0.706 Sum_probs=17.9
Q ss_pred EEcCCCCCceeeceEe--ecccCCCCCC
Q psy1204 30 VLCKDCHKESKVLYHI--IGLKCEHCGS 55 (71)
Q Consensus 30 i~CndC~~~s~v~~h~--~g~kCp~C~S 55 (71)
..|..||+.+.+.|.- ...+|..||+
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCC
Confidence 4689999877665432 2238999998
No 192
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=60.16 E-value=5.9 Score=20.38 Aligned_cols=9 Identities=56% Similarity=1.398 Sum_probs=7.4
Q ss_pred cCCCCCCcc
Q psy1204 49 KCEHCGSYN 57 (71)
Q Consensus 49 kCp~C~Syn 57 (71)
.||.||+.+
T Consensus 4 ~Cp~Cg~~~ 12 (47)
T PF14690_consen 4 RCPHCGSPS 12 (47)
T ss_pred cCCCcCCCc
Confidence 688888877
No 193
>KOG1842|consensus
Probab=59.66 E-value=1.8 Score=33.77 Aligned_cols=47 Identities=13% Similarity=0.277 Sum_probs=31.6
Q ss_pred HHHHHHHHHcCC---CCH----------hhhcceeeEEcCCCCCceeeceEeecccCCCCCC
Q psy1204 7 WRQMDEEIASTP---MPE----------EYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 7 ~~~lD~~i~~~p---mP~----------~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
.-+|+++++..| ++. +|.+-..+.+|++|+.+|....+- |.|.-||+
T Consensus 145 iiRl~rL~~~~~t~~d~~k~k~~EqsvVpW~DDs~V~~CP~Ca~~F~l~rRr--HHCRLCG~ 204 (505)
T KOG1842|consen 145 IIRLKRLEEGLPTEKDSVKRKRLEQSVVPWLDDSSVQFCPECANSFGLTRRR--HHCRLCGR 204 (505)
T ss_pred HHHHHHHHccCccccchHHHHHHHhccccccCCCcccccccccchhhhHHHh--hhhhhcch
Confidence 345666666655 222 355666789999999999875432 28888875
No 194
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=58.80 E-value=6.4 Score=33.51 Aligned_cols=24 Identities=38% Similarity=0.735 Sum_probs=17.7
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
..-+|.+||.. .+...||.||+..
T Consensus 624 ~~RKCPkCG~y------Tlk~rCP~CG~~T 647 (1095)
T TIGR00354 624 AIRKCPQCGKE------SFWLKCPVCGELT 647 (1095)
T ss_pred EEEECCCCCcc------cccccCCCCCCcc
Confidence 35689999974 2233999999984
No 195
>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=58.51 E-value=6.1 Score=20.36 Aligned_cols=29 Identities=24% Similarity=0.583 Sum_probs=11.5
Q ss_pred EEcCCCCCceeeceEee----cccCCCCCCcce
Q psy1204 30 VLCKDCHKESKVLYHII----GLKCEHCGSYNT 58 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~----g~kCp~C~Synt 58 (71)
++|..|+.--....++. .-+|+.|++.|.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~ 35 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNP 35 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--EEE
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCCcCC
Confidence 57888875443211111 128899988664
No 196
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=58.42 E-value=15 Score=24.37 Aligned_cols=42 Identities=19% Similarity=0.385 Sum_probs=21.2
Q ss_pred HhhhcceeeEEcCCCCCcee--e--c------------eEeecccCCCCCCccee-eecC
Q psy1204 21 EEYKNVILYVLCKDCHKESK--V--L------------YHIIGLKCEHCGSYNTC-RIKK 63 (71)
Q Consensus 21 ~~y~~~~v~i~CndC~~~s~--v--~------------~h~~g~kCp~C~Synt~-ii~g 63 (71)
++| .+...+.|..|+.... + . ...+-.||..|+..++. |+.+
T Consensus 23 ~~~-~~~fkvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re~si~i~~~ 81 (161)
T PF05907_consen 23 PDF-EWFFKVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRESSIDIIPG 81 (161)
T ss_dssp TT---EEEEEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--EEEEEE--
T ss_pred CCC-EEEEEEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCccEEEEEec
Confidence 344 3689999999997653 1 0 12233599999988887 4444
No 197
>PF14353 CpXC: CpXC protein
Probab=58.21 E-value=7.9 Score=24.12 Aligned_cols=17 Identities=18% Similarity=0.622 Sum_probs=9.5
Q ss_pred eeeEEcCCCCCceeece
Q psy1204 27 ILYVLCKDCHKESKVLY 43 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~ 43 (71)
--.+.|..||+++.+.+
T Consensus 36 l~~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 36 LFSFTCPSCGHKFRLEY 52 (128)
T ss_pred cCEEECCCCCCceecCC
Confidence 34556666666665543
No 198
>PRK12495 hypothetical protein; Provisional
Probab=58.06 E-value=5 Score=28.59 Aligned_cols=32 Identities=16% Similarity=0.182 Sum_probs=20.6
Q ss_pred ceeeEEcCCCCCceeeceEeecccCCCCCCccee
Q psy1204 26 VILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTC 59 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ 59 (71)
.+...+|.+||.-=...-... .|+.|+...++
T Consensus 39 tmsa~hC~~CG~PIpa~pG~~--~Cp~CQ~~~~~ 70 (226)
T PRK12495 39 TMTNAHCDECGDPIFRHDGQE--FCPTCQQPVTE 70 (226)
T ss_pred ccchhhcccccCcccCCCCee--ECCCCCCcccc
Confidence 367889999996322111222 69999987664
No 199
>PRK09401 reverse gyrase; Reviewed
Probab=57.64 E-value=5.2 Score=34.11 Aligned_cols=26 Identities=35% Similarity=0.639 Sum_probs=20.7
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
..-.|.+||..|+.... +||.|+|.+
T Consensus 677 ~~k~c~~~g~~f~~~~~----~~~~c~~~~ 702 (1176)
T PRK09401 677 TIKRCRDCGYQFTDESD----KCPRCGSTN 702 (1176)
T ss_pred eeccccccccccccccc----ccccccccc
Confidence 56689999998887532 999999865
No 200
>PRK04023 DNA polymerase II large subunit; Validated
Probab=57.54 E-value=5.6 Score=33.93 Aligned_cols=41 Identities=24% Similarity=0.374 Sum_probs=26.1
Q ss_pred HHcCCCCHhhhc----ceeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 14 IASTPMPEEYKN----VILYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 14 i~~~pmP~~y~~----~~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
|..-=||.-+-+ .....+|.+|+.++.-.=..- +||+||+-
T Consensus 1018 i~sHFlPDl~GNLRaFsrQ~fRC~kC~~kYRR~PL~G--~C~kCGg~ 1062 (1121)
T PRK04023 1018 ISSHFLPDLIGNLRAFSRQEFRCTKCGAKYRRPPLSG--KCPKCGGN 1062 (1121)
T ss_pred HHhccchhhhhhhhhhcccceeecccCcccccCCCCC--cCccCCCe
Confidence 444445654322 245789999998875433222 99999763
No 201
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=57.31 E-value=3.9 Score=29.75 Aligned_cols=28 Identities=21% Similarity=0.491 Sum_probs=20.3
Q ss_pred eeEEcCCCCCceeec---eEeecccCCCCCCcc
Q psy1204 28 LYVLCKDCHKESKVL---YHIIGLKCEHCGSYN 57 (71)
Q Consensus 28 v~i~CndC~~~s~v~---~h~~g~kCp~C~Syn 57 (71)
+++.|..|+...... .+.. .||+|+.+-
T Consensus 26 ~~~~c~~c~~~~~~~~l~~~~~--vc~~c~~h~ 56 (292)
T PRK05654 26 LWTKCPSCGQVLYRKELEANLN--VCPKCGHHM 56 (292)
T ss_pred CeeECCCccchhhHHHHHhcCC--CCCCCCCCe
Confidence 699999999766432 2333 999998765
No 202
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=57.13 E-value=6.6 Score=27.31 Aligned_cols=37 Identities=19% Similarity=0.340 Sum_probs=27.2
Q ss_pred hcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCC
Q psy1204 24 KNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPN 65 (71)
Q Consensus 24 ~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~ 65 (71)
.+.+-.|.|.-|..+- |-|-.||+||++..-|.=|.-
T Consensus 157 sk~~hcilCtvCe~r~-----w~g~~CPKCGr~G~pi~CGmt 193 (200)
T PF12387_consen 157 SKSKHCILCTVCEGRE-----WKGGNCPKCGRHGKPITCGMT 193 (200)
T ss_pred cCCCceEEEeeeecCc-----cCCCCCCcccCCCCCeecccC
Confidence 3456789999996543 345589999999988876643
No 203
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=57.12 E-value=6.8 Score=25.20 Aligned_cols=9 Identities=44% Similarity=0.995 Sum_probs=5.0
Q ss_pred cCCCCCCcc
Q psy1204 49 KCEHCGSYN 57 (71)
Q Consensus 49 kCp~C~Syn 57 (71)
.||.|+|++
T Consensus 32 ~cP~C~s~~ 40 (129)
T COG3677 32 NCPRCKSSN 40 (129)
T ss_pred cCCCCCccc
Confidence 455555555
No 204
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=56.55 E-value=5.1 Score=27.27 Aligned_cols=22 Identities=27% Similarity=0.366 Sum_probs=9.1
Q ss_pred hhcceeeEEcCCCCCceeeceE
Q psy1204 23 YKNVILYVLCKDCHKESKVLYH 44 (71)
Q Consensus 23 y~~~~v~i~CndC~~~s~v~~h 44 (71)
|........|..||+....-.|
T Consensus 124 ~~~~~~f~~C~~CgkiYW~GsH 145 (165)
T COG1656 124 YRNYEEFYRCPKCGKIYWKGSH 145 (165)
T ss_pred hhcccceeECCCCcccccCchH
Confidence 3333334444444444443333
No 205
>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=56.29 E-value=5.5 Score=21.17 Aligned_cols=13 Identities=46% Similarity=1.035 Sum_probs=9.4
Q ss_pred cCCCCCCcceeee
Q psy1204 49 KCEHCGSYNTCRI 61 (71)
Q Consensus 49 kCp~C~Synt~ii 61 (71)
+||+||+.-....
T Consensus 1 ~CP~Cg~~a~ir~ 13 (47)
T PF04606_consen 1 RCPHCGSKARIRT 13 (47)
T ss_pred CcCCCCCeeEEEE
Confidence 5999998765443
No 206
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=56.25 E-value=7.1 Score=33.99 Aligned_cols=20 Identities=35% Similarity=1.055 Sum_probs=11.2
Q ss_pred EcCCCCCceeeceEeecccCCCCCC
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
+|..||......+ .||.||+
T Consensus 681 fCP~CGs~te~vy-----~CPsCGa 700 (1337)
T PRK14714 681 RCPDCGTHTEPVY-----VCPDCGA 700 (1337)
T ss_pred cCcccCCcCCCce-----eCccCCC
Confidence 6777776654322 5555555
No 207
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=56.20 E-value=11 Score=18.12 Aligned_cols=21 Identities=24% Similarity=0.827 Sum_probs=16.1
Q ss_pred EcCCCCCceeeceEeecccCCCCC
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCG 54 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~ 54 (71)
.|.-|+++....+ +| .|..|.
T Consensus 2 ~C~~C~~~~~~~~-~Y--~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY-FY--HCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE-eE--EeCCCC
Confidence 4778888877776 66 888876
No 208
>PRK08329 threonine synthase; Validated
Probab=56.18 E-value=6.1 Score=28.73 Aligned_cols=23 Identities=22% Similarity=0.860 Sum_probs=17.0
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
.+|..||.++....+ + .| .|++.
T Consensus 2 l~C~~Cg~~~~~~~~-~--~C-~c~~~ 24 (347)
T PRK08329 2 LRCTKCGRTYEEKFK-L--RC-DCGGT 24 (347)
T ss_pred cCcCCCCCCcCCCCc-e--ec-CCCCc
Confidence 579999999875544 4 89 68764
No 209
>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=55.43 E-value=14 Score=18.95 Aligned_cols=13 Identities=31% Similarity=0.784 Sum_probs=7.4
Q ss_pred cCCCCCCcceeee
Q psy1204 49 KCEHCGSYNTCRI 61 (71)
Q Consensus 49 kCp~C~Synt~ii 61 (71)
+||.||+-++...
T Consensus 2 ~Cp~Cg~~~a~~~ 14 (39)
T PF01096_consen 2 KCPKCGHNEAVFF 14 (39)
T ss_dssp --SSS-SSEEEEE
T ss_pred CCcCCCCCeEEEE
Confidence 7888888776655
No 210
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=55.39 E-value=5 Score=27.34 Aligned_cols=30 Identities=27% Similarity=0.588 Sum_probs=19.7
Q ss_pred eeeEEcCCCCCceeece-------EeecccCCCCCCc
Q psy1204 27 ILYVLCKDCHKESKVLY-------HIIGLKCEHCGSY 56 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~-------h~~g~kCp~C~Sy 56 (71)
.-...|.+|+....... +...-+||.|++.
T Consensus 93 ~~~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~ 129 (206)
T cd01410 93 MFIEVCKSCGPEYVRDDVVETRGDKETGRRCHACGGI 129 (206)
T ss_pred cCcccCCCCCCccchHHHHHHhhcCCCCCcCCCCcCc
Confidence 44667999998765432 1123479999864
No 211
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=55.31 E-value=5.6 Score=23.04 Aligned_cols=26 Identities=23% Similarity=0.650 Sum_probs=20.9
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCC
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
+..++|.-||.. .||.--..|..||=
T Consensus 15 ~tHt~CrRCG~~---syh~qK~~CasCGy 40 (62)
T PRK04179 15 KTHIRCRRCGRH---SYNVRKKYCAACGF 40 (62)
T ss_pred cccchhcccCcc---cccccccchhhcCC
Confidence 488999999984 67777678999974
No 212
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=55.22 E-value=6 Score=30.37 Aligned_cols=40 Identities=20% Similarity=0.358 Sum_probs=27.4
Q ss_pred CHhhhcceeeEEcCCCCCceeeceEee---cccCCCCCCccee
Q psy1204 20 PEEYKNVILYVLCKDCHKESKVLYHII---GLKCEHCGSYNTC 59 (71)
Q Consensus 20 P~~y~~~~v~i~CndC~~~s~v~~h~~---g~kCp~C~Synt~ 59 (71)
++.+....+...|+.|+.++.....+. .+.||.||+....
T Consensus 318 ~Edl~~~r~~~~c~~~~~e~~~t~~~~~~~~~~~~~~~~e~~~ 360 (411)
T COG1503 318 SEDLEKERVTYKCPTCGYENLKSKREFEQKRFRCPECGSEMEE 360 (411)
T ss_pred eccccccceeecCCCcchhhhhcccccccccccCccccccccc
Confidence 667777789999999998885421111 1179999994433
No 213
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=55.15 E-value=5 Score=29.59 Aligned_cols=28 Identities=21% Similarity=0.508 Sum_probs=20.1
Q ss_pred eeeEEcCCCCCcee---eceEeecccCCCCCCc
Q psy1204 27 ILYVLCKDCHKESK---VLYHIIGLKCEHCGSY 56 (71)
Q Consensus 27 ~v~i~CndC~~~s~---v~~h~~g~kCp~C~Sy 56 (71)
-++++|..|++.-. +..+.. .||+|+.+
T Consensus 26 ~lw~KCp~c~~~~y~~eL~~n~~--vcp~c~~h 56 (294)
T COG0777 26 GLWTKCPSCGEMLYRKELESNLK--VCPKCGHH 56 (294)
T ss_pred CceeECCCccceeeHHHHHhhhh--cccccCcc
Confidence 47999999997553 334455 89999654
No 214
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=55.02 E-value=7.4 Score=24.96 Aligned_cols=32 Identities=34% Similarity=0.589 Sum_probs=23.8
Q ss_pred EcCCCCCceeeceE----eecccCCCCCCcceeeecCC
Q psy1204 31 LCKDCHKESKVLYH----IIGLKCEHCGSYNTCRIKKP 64 (71)
Q Consensus 31 ~CndC~~~s~v~~h----~~g~kCp~C~Synt~ii~g~ 64 (71)
.|--||+.+.+++. .+ .||+|+.||----+|.
T Consensus 2 ~C~fC~~~s~~~~~~~~~~w--~C~~C~q~N~f~e~Gd 37 (131)
T PF09779_consen 2 NCWFCGQNSKVPYDNRNSNW--TCPHCEQYNGFDEDGD 37 (131)
T ss_pred eeccCCCCCCCCCCCCCCee--ECCCCCCccCccccCC
Confidence 57789988877642 24 8999999997666555
No 215
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=54.52 E-value=7.7 Score=20.32 Aligned_cols=24 Identities=21% Similarity=0.591 Sum_probs=12.6
Q ss_pred EcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
.|+.|++ .+....+ +|..|..|+.
T Consensus 2 ~C~~C~~--~i~g~r~--~C~~C~d~dL 25 (46)
T cd02249 2 SCDGCLK--PIVGVRY--HCLVCEDFDL 25 (46)
T ss_pred CCcCCCC--CCcCCEE--ECCCCCCCcC
Confidence 4677776 2222333 6666655553
No 216
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=54.46 E-value=7.2 Score=29.74 Aligned_cols=31 Identities=19% Similarity=0.425 Sum_probs=22.5
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCccee
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTC 59 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ 59 (71)
.+..+|..|+.++....... .||.||.+-..
T Consensus 3 ~~~~rc~~cg~~f~~a~~~~--~c~~cGl~lp~ 33 (411)
T COG0498 3 YVSLRCLKCGREFSQALLQG--LCPDCGLFLPA 33 (411)
T ss_pred eeEeecCCCCcchhhHHhhC--cCCcCCccccc
Confidence 46789999998776443333 89999987554
No 217
>KOG2462|consensus
Probab=54.39 E-value=6.8 Score=28.72 Aligned_cols=25 Identities=32% Similarity=0.662 Sum_probs=13.7
Q ss_pred EEcCCCCCcee--------eceEeecccCCCCC
Q psy1204 30 VLCKDCHKESK--------VLYHIIGLKCEHCG 54 (71)
Q Consensus 30 i~CndC~~~s~--------v~~h~~g~kCp~C~ 54 (71)
..|..|++... +.-|.+.++|+.||
T Consensus 162 ~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCG 194 (279)
T KOG2462|consen 162 FSCKYCGKVYVSMPALKMHIRTHTLPCECGICG 194 (279)
T ss_pred ccCCCCCceeeehHHHhhHhhccCCCccccccc
Confidence 34666665543 23455666666665
No 218
>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=54.35 E-value=10 Score=19.45 Aligned_cols=9 Identities=33% Similarity=0.885 Sum_probs=6.3
Q ss_pred cCCCCCCcc
Q psy1204 49 KCEHCGSYN 57 (71)
Q Consensus 49 kCp~C~Syn 57 (71)
+||.|+|..
T Consensus 7 ~CP~C~s~~ 15 (36)
T PF03811_consen 7 HCPRCQSTE 15 (36)
T ss_pred eCCCCCCCC
Confidence 677777766
No 219
>PLN02569 threonine synthase
Probab=54.33 E-value=7.5 Score=30.02 Aligned_cols=25 Identities=8% Similarity=0.211 Sum_probs=20.4
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
...|..||++..+....+ .| .||+.
T Consensus 49 ~l~C~~Cg~~y~~~~~~~--~C-~cgg~ 73 (484)
T PLN02569 49 FLECPLTGEKYSLDEVVY--RS-KSGGL 73 (484)
T ss_pred ccEeCCCCCcCCCccccc--cC-CCCCe
Confidence 589999999998887666 89 69654
No 220
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=53.95 E-value=5.4 Score=22.10 Aligned_cols=29 Identities=21% Similarity=0.394 Sum_probs=14.8
Q ss_pred eeeEEcCCCCCceee----ceEeecccCCCCCC
Q psy1204 27 ILYVLCKDCHKESKV----LYHIIGLKCEHCGS 55 (71)
Q Consensus 27 ~v~i~CndC~~~s~v----~~h~~g~kCp~C~S 55 (71)
..+..|..|++.|=. .-|.--|-||.|.|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~s 51 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHNCPGCES 51 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-SSSTT--
T ss_pred CCeEECCCCCCccccCcChhhhccccCCcCCCC
Confidence 467889999888743 33666678888875
No 221
>PHA02768 hypothetical protein; Provisional
Probab=53.70 E-value=6.5 Score=22.15 Aligned_cols=26 Identities=23% Similarity=0.285 Sum_probs=18.0
Q ss_pred EEcCCCCCceee--------ceEeecccCCCCCC
Q psy1204 30 VLCKDCHKESKV--------LYHIIGLKCEHCGS 55 (71)
Q Consensus 30 i~CndC~~~s~v--------~~h~~g~kCp~C~S 55 (71)
..|..||+.|.. .-|.-+.+|..|+-
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k 39 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHNTNLKLSNCKR 39 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcCCcccCCcccc
Confidence 479999999974 34554457877753
No 222
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=52.41 E-value=8.2 Score=19.96 Aligned_cols=13 Identities=23% Similarity=0.692 Sum_probs=10.1
Q ss_pred cCCCCCCcceeee
Q psy1204 49 KCEHCGSYNTCRI 61 (71)
Q Consensus 49 kCp~C~Synt~ii 61 (71)
+||+|++-+..-.
T Consensus 2 ~Cp~C~~~~a~~~ 14 (40)
T smart00440 2 PCPKCGNREATFF 14 (40)
T ss_pred cCCCCCCCeEEEE
Confidence 8999998776643
No 223
>PRK00420 hypothetical protein; Validated
Probab=52.33 E-value=8.4 Score=24.54 Aligned_cols=36 Identities=17% Similarity=0.101 Sum_probs=21.5
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCC
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKP 64 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~ 64 (71)
+....|..||....-..+.- ..||.||.. ..+.+++
T Consensus 21 ml~~~CP~Cg~pLf~lk~g~-~~Cp~Cg~~-~~v~~~e 56 (112)
T PRK00420 21 MLSKHCPVCGLPLFELKDGE-VVCPVHGKV-YIVKSDE 56 (112)
T ss_pred HccCCCCCCCCcceecCCCc-eECCCCCCe-eeeccHH
Confidence 35678999996554312221 279999983 3344444
No 224
>PF01197 Ribosomal_L31: Ribosomal protein L31; InterPro: IPR002150 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 L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3D5D_4 3PYO_1 3D5B_4 3PYV_1 3PYT_1 3MRZ_1 3MS1_1 3PYR_1 3F1F_4 3F1H_4 ....
Probab=52.32 E-value=10 Score=21.93 Aligned_cols=36 Identities=25% Similarity=0.558 Sum_probs=22.5
Q ss_pred CHhhhcceeeEEcCCCCCceee----ce--EeecccCCCCCCcce
Q psy1204 20 PEEYKNVILYVLCKDCHKESKV----LY--HIIGLKCEHCGSYNT 58 (71)
Q Consensus 20 P~~y~~~~v~i~CndC~~~s~v----~~--h~~g~kCp~C~Synt 58 (71)
.++|+ .+.+.|+.|+.++.+ .+ ..+ -.|+.|.-+=|
T Consensus 6 HP~y~--~v~v~c~s~g~~~~~~St~~~~~~~v-di~s~~HPfyt 47 (69)
T PF01197_consen 6 HPEYR--EVKVTCSSCGNTFETRSTKEYPVIKV-DICSNCHPFYT 47 (69)
T ss_dssp SSSHC--EEEEEES-SSSCECECSSSSES-EEE-CSCSSSSCTTC
T ss_pred CCCCE--EEEEEEcCCCCEEEEEECCcceEEEE-eecCCCCEEEc
Confidence 34475 589999999998864 22 222 37887754433
No 225
>PF12773 DZR: Double zinc ribbon
Probab=52.29 E-value=6.5 Score=20.56 Aligned_cols=27 Identities=19% Similarity=0.400 Sum_probs=14.7
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
..+|..||..-...... ...||.|++.
T Consensus 12 ~~fC~~CG~~l~~~~~~-~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQS-KKICPNCGAE 38 (50)
T ss_pred ccCChhhcCChhhccCC-CCCCcCCcCC
Confidence 45677777655511211 1267777765
No 226
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=52.25 E-value=9 Score=27.06 Aligned_cols=30 Identities=17% Similarity=0.308 Sum_probs=20.8
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
..-+|..||.......-.....|+.|+...
T Consensus 98 ~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 98 SHRFCGYCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred cCccccccCCCCeecCCceeEECCCCCCEE
Confidence 467999999987654323334899998554
No 227
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=51.92 E-value=9.8 Score=18.15 Aligned_cols=20 Identities=25% Similarity=0.659 Sum_probs=8.3
Q ss_pred EcCCCCCceeeceEeecccCCCC
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHC 53 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C 53 (71)
.|+-|++.... ..+| .|+.|
T Consensus 2 ~C~~C~~~~~~-~~~Y--~C~~C 21 (30)
T PF07649_consen 2 RCDACGKPIDG-GWFY--RCSEC 21 (30)
T ss_dssp --TTTS----S---EE--E-TTT
T ss_pred cCCcCCCcCCC-CceE--ECccC
Confidence 58888876655 3455 78888
No 228
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=51.75 E-value=8.6 Score=22.15 Aligned_cols=13 Identities=31% Similarity=0.575 Sum_probs=10.2
Q ss_pred cCCCCCCcceeee
Q psy1204 49 KCEHCGSYNTCRI 61 (71)
Q Consensus 49 kCp~C~Synt~ii 61 (71)
+||+||+-..++.
T Consensus 2 ~C~KCg~~~~e~~ 14 (64)
T PF09855_consen 2 KCPKCGNEEYESG 14 (64)
T ss_pred CCCCCCCcceecc
Confidence 8999998776654
No 229
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the COG3041 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.61 E-value=15 Score=22.77 Aligned_cols=37 Identities=30% Similarity=0.515 Sum_probs=29.3
Q ss_pred ChHHHHHHHHHHHHcCCCCHhhhccee---eEEcCCCCCc
Q psy1204 2 DMTPLWRQMDEEIASTPMPEEYKNVIL---YVLCKDCHKE 38 (71)
Q Consensus 2 dm~~~~~~lD~~i~~~pmP~~y~~~~v---~i~CndC~~~ 38 (71)
||+.+-.-|..++...|+|+.|++-+. +.=+.||+-+
T Consensus 24 d~~~l~~vi~~L~~~~Pl~~~~kDH~LtG~wkg~RdCHi~ 63 (91)
T COG3041 24 DMDKLKKVITLLANDLPLPPRYKDHPLTGDWKGYRDCHIK 63 (91)
T ss_pred hHHHHHHHHHHHHhCCCCCccccCCccccCccchhhcccC
Confidence 788888899999999999999997655 3446677644
No 231
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=51.54 E-value=9.2 Score=19.54 Aligned_cols=15 Identities=27% Similarity=0.452 Sum_probs=8.4
Q ss_pred EEcCCCCCceeeceE
Q psy1204 30 VLCKDCHKESKVLYH 44 (71)
Q Consensus 30 i~CndC~~~s~v~~h 44 (71)
-.|-+|++.|...|.
T Consensus 4 ~~C~eC~~~f~dSyL 18 (34)
T PF01286_consen 4 PKCDECGKPFMDSYL 18 (34)
T ss_dssp EE-TTT--EES-SSC
T ss_pred chHhHhCCHHHHHHH
Confidence 479999999987663
No 232
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=51.43 E-value=7.8 Score=28.46 Aligned_cols=27 Identities=30% Similarity=0.640 Sum_probs=19.8
Q ss_pred eeEEcCCCCCceeec---eEeecccCCCCCCc
Q psy1204 28 LYVLCKDCHKESKVL---YHIIGLKCEHCGSY 56 (71)
Q Consensus 28 v~i~CndC~~~s~v~---~h~~g~kCp~C~Sy 56 (71)
++.+|..|++..... .+.. .||+|+.+
T Consensus 37 lw~kc~~C~~~~~~~~l~~~~~--vcp~c~~h 66 (296)
T CHL00174 37 LWVQCENCYGLNYKKFLKSKMN--ICEQCGYH 66 (296)
T ss_pred CeeECCCccchhhHHHHHHcCC--CCCCCCCC
Confidence 599999999866533 3344 99999754
No 233
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=51.22 E-value=8.7 Score=21.02 Aligned_cols=27 Identities=22% Similarity=0.835 Sum_probs=17.5
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCcceee
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Synt~i 60 (71)
|.|.-|++.. ....+ +|-.|..|+.-+
T Consensus 1 i~CdgC~~~~--~~~Ry--kCl~C~d~DlC~ 27 (48)
T cd02343 1 ISCDGCDEIA--PWHRY--RCLQCTDMDLCK 27 (48)
T ss_pred CCCCCCCCcC--CCceE--ECCCCCCchhHH
Confidence 4588898753 33344 888887776543
No 234
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=51.05 E-value=7.6 Score=22.85 Aligned_cols=11 Identities=45% Similarity=0.933 Sum_probs=8.9
Q ss_pred cCCCCCCccee
Q psy1204 49 KCEHCGSYNTC 59 (71)
Q Consensus 49 kCp~C~Synt~ 59 (71)
+||+||+.|-.
T Consensus 6 kCpKCgn~~~~ 16 (68)
T COG3478 6 KCPKCGNTNYE 16 (68)
T ss_pred cCCCcCCcchh
Confidence 79999987754
No 235
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=50.64 E-value=10 Score=26.24 Aligned_cols=30 Identities=20% Similarity=0.515 Sum_probs=18.8
Q ss_pred eeeEEcCCCCCceeeceEe--ecccCCCCCCc
Q psy1204 27 ILYVLCKDCHKESKVLYHI--IGLKCEHCGSY 56 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~--~g~kCp~C~Sy 56 (71)
--...|.+|++.....+.. -..+||.|++.
T Consensus 120 ~~~~~C~~C~~~~~~~~~~~~~~p~C~~Cgg~ 151 (242)
T PRK00481 120 LLRARCTKCGQTYDLDEYLKPEPPRCPKCGGI 151 (242)
T ss_pred cCceeeCCCCCCcChhhhccCCCCCCCCCCCc
Confidence 4467899998876533211 11359999863
No 236
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=50.55 E-value=7 Score=24.25 Aligned_cols=29 Identities=28% Similarity=0.639 Sum_probs=22.0
Q ss_pred cceeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
..+..++|.-||. ..||.--..|..||=.
T Consensus 12 ~~ktHtlCrRCG~---~syH~qK~~CasCGyp 40 (91)
T PTZ00073 12 HGKTHTLCRRCGK---RSFHVQKKRCASCGYP 40 (91)
T ss_pred cCcCcchhcccCc---cccccccccchhcCCc
Confidence 4478899999997 4566666689999743
No 237
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=49.50 E-value=10 Score=24.27 Aligned_cols=24 Identities=25% Similarity=0.444 Sum_probs=15.0
Q ss_pred EcCCCCCceeeceEeecccCCCCCC
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
.|..|+.+.+-.--.+ +.||.|+-
T Consensus 4 ~CP~C~seytY~dg~~-~iCpeC~~ 27 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQ-LICPSCLY 27 (109)
T ss_pred cCCcCCCcceEecCCe-eECccccc
Confidence 4778887776543222 27888854
No 238
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=49.04 E-value=3.2 Score=23.11 Aligned_cols=32 Identities=28% Similarity=0.475 Sum_probs=22.8
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCcceeeecC
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKK 63 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g 63 (71)
....|..|+......- .+|..|+|-|.+.-..
T Consensus 13 ~kkIC~rC~Arnp~~A----~kCRkC~~k~LR~K~k 44 (50)
T COG1552 13 NKKICRRCYARNPPRA----TKCRKCGYKNLRPKKK 44 (50)
T ss_pred hHHHHHHhcCCCCcch----hHHhhccCCCcccccc
Confidence 3456888887766543 3999999988876543
No 239
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=48.76 E-value=13 Score=20.21 Aligned_cols=27 Identities=22% Similarity=0.638 Sum_probs=16.8
Q ss_pred EcCCCCCceeeceEeecccCCCCCCcceee
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~Synt~i 60 (71)
.|+.|++.- +....+ +|-.|..|+.-.
T Consensus 2 ~Cd~C~~~p-i~g~Ry--kC~~C~d~DLC~ 28 (49)
T cd02334 2 KCNICKEFP-ITGFRY--RCLKCFNYDLCQ 28 (49)
T ss_pred CCCCCCCCC-ceeeeE--ECCCCCCcCchH
Confidence 588888532 233345 888887776543
No 240
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=48.64 E-value=16 Score=26.46 Aligned_cols=28 Identities=21% Similarity=0.516 Sum_probs=21.2
Q ss_pred ceeeEEcCCCCCceeece---EeecccCCCCC
Q psy1204 26 VILYVLCKDCHKESKVLY---HIIGLKCEHCG 54 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v~~---h~~g~kCp~C~ 54 (71)
....+.|..|+..|.-.. ..+ .+||+|.
T Consensus 154 ~~~rv~CghC~~~Fl~~~~~~~tl-ARCPHCr 184 (256)
T PF09788_consen 154 GSCRVICGHCSNTFLFNTLTSNTL-ARCPHCR 184 (256)
T ss_pred CceeEECCCCCCcEeccCCCCCcc-ccCCCCc
Confidence 467899999999996543 233 3999996
No 241
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=47.99 E-value=11 Score=23.56 Aligned_cols=20 Identities=20% Similarity=0.524 Sum_probs=16.6
Q ss_pred eeEEcCCCCCceeeceEeec
Q psy1204 28 LYVLCKDCHKESKVLYHIIG 47 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g 47 (71)
..|.|.-||...+..|++.|
T Consensus 2 lLI~CP~Cg~R~e~EFt~~G 21 (97)
T COG4311 2 LLIPCPYCGERPEEEFTYAG 21 (97)
T ss_pred ceecCCCCCCCchhheeecc
Confidence 57899999998888888775
No 242
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=47.47 E-value=8.8 Score=25.11 Aligned_cols=32 Identities=22% Similarity=0.452 Sum_probs=20.8
Q ss_pred cceeeEEcCCCCCceeeceE------eecccCCCCCCc
Q psy1204 25 NVILYVLCKDCHKESKVLYH------IIGLKCEHCGSY 56 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v~~h------~~g~kCp~C~Sy 56 (71)
...-...|..|+++...... ....+||.|++.
T Consensus 101 G~l~~~~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~ 138 (178)
T PF02146_consen 101 GSLFRLRCSKCGKEYDREDIVDSIDEEEPPRCPKCGGL 138 (178)
T ss_dssp EEEEEEEETTTSBEEEGHHHHHHHHTTSSCBCTTTSCB
T ss_pred hhhceeeecCCCccccchhhcccccccccccccccCcc
Confidence 33456899999998764321 111279999873
No 243
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=47.22 E-value=12 Score=25.38 Aligned_cols=29 Identities=21% Similarity=0.424 Sum_probs=19.7
Q ss_pred eeeEEcCCCCCceeec---eEeecccCCCCCC
Q psy1204 27 ILYVLCKDCHKESKVL---YHIIGLKCEHCGS 55 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~---~h~~g~kCp~C~S 55 (71)
--...|..|+.+.... .....-+||.|++
T Consensus 107 ~~~~~C~~C~~~~~~~~~~~~~~~p~C~~Cgg 138 (224)
T cd01412 107 LFRVRCSSCGYVGENNEEIPEEELPRCPKCGG 138 (224)
T ss_pred cCccccCCCCCCCCcchhhhccCCCCCCCCCC
Confidence 3456799999877542 1233458999987
No 244
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=47.19 E-value=17 Score=17.77 Aligned_cols=19 Identities=37% Similarity=1.062 Sum_probs=10.7
Q ss_pred EEcCCCCCceeeceEeecccCCCCCC
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
.+|.-|+. ...| +||.|+.
T Consensus 3 ~~C~vC~~--~~kY-----~Cp~C~~ 21 (30)
T PF04438_consen 3 KLCSVCGN--PAKY-----RCPRCGA 21 (30)
T ss_dssp EEETSSSS--EESE-----E-TTT--
T ss_pred CCCccCcC--CCEE-----ECCCcCC
Confidence 46777876 3333 8998875
No 245
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=47.04 E-value=12 Score=33.15 Aligned_cols=23 Identities=26% Similarity=0.710 Sum_probs=17.2
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
..-.|++||..+ +.+.||.||+.
T Consensus 673 ~~~~Cp~Cg~~~------~~~~Cp~CG~~ 695 (1627)
T PRK14715 673 AFFKCPKCGKVG------LYHVCPFCGTR 695 (1627)
T ss_pred EeeeCCCCCCcc------ccccCcccCCc
Confidence 356899999742 33499999987
No 246
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.87 E-value=11 Score=24.30 Aligned_cols=24 Identities=25% Similarity=0.510 Sum_probs=18.3
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCC
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCG 54 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~ 54 (71)
++.-.|.+|+++-.|... +|+.|+
T Consensus 4 ~~~~~cPvcg~~~iVTeL----~c~~~e 27 (122)
T COG3877 4 KVINRCPVCGRKLIVTEL----KCSNCE 27 (122)
T ss_pred CCCCCCCcccccceeEEE----ecCCCC
Confidence 567789999987766553 888885
No 247
>PRK04351 hypothetical protein; Provisional
Probab=46.75 E-value=48 Score=21.77 Aligned_cols=54 Identities=9% Similarity=0.215 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHcCCC-C-HhhhcceeeEEcCCCCCcee-eceEee-cccCCCCCCcce
Q psy1204 5 PLWRQMDEEIASTPM-P-EEYKNVILYVLCKDCHKESK-VLYHII-GLKCEHCGSYNT 58 (71)
Q Consensus 5 ~~~~~lD~~i~~~pm-P-~~y~~~~v~i~CndC~~~s~-v~~h~~-g~kCp~C~Synt 58 (71)
..|+.+=+.+.+.+- | ..-.+.+-...|.+|+...- ...|.. -..|..|++.=.
T Consensus 86 ~~fk~~~~~v~~~r~~~~~~~~~~~y~Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L~ 143 (149)
T PRK04351 86 RDFKELLKQVGGPRYCPPLPSQKKNYLYECQSCGQQYLRKRRINTKRYRCGKCRGKLK 143 (149)
T ss_pred HHHHHHHHHhCCCcccCCCCCCCceEEEECCCCCCEeeeeeecCCCcEEeCCCCcEee
Confidence 568887777764322 1 11134567899999997553 222221 127899986543
No 248
>PF10875 DUF2670: Protein of unknown function (DUF2670); InterPro: IPR022714 This bacterial family of proteins has no known function and appears to be restricted to Rickettsiaceae.
Probab=46.69 E-value=14 Score=24.27 Aligned_cols=15 Identities=33% Similarity=0.667 Sum_probs=13.5
Q ss_pred HHHHHHHHHcCCCCH
Q psy1204 7 WRQMDEEIASTPMPE 21 (71)
Q Consensus 7 ~~~lD~~i~~~pmP~ 21 (71)
|+.|-++|++.||--
T Consensus 2 wqalrrlIaaNPMg~ 16 (139)
T PF10875_consen 2 WQALRRLIAANPMGF 16 (139)
T ss_pred hHHHHHHHhhCCchh
Confidence 999999999999954
No 249
>KOG1280|consensus
Probab=46.56 E-value=9.9 Score=28.91 Aligned_cols=28 Identities=29% Similarity=0.641 Sum_probs=21.0
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
-.|.|..|++..-. ++.| ||-.|..|+.
T Consensus 7 e~v~CdgC~k~~~t-~rrY--kCL~C~DyDl 34 (381)
T KOG1280|consen 7 EGVSCDGCGKTAFT-FRRY--KCLRCSDYDL 34 (381)
T ss_pred CCceecccccccee-eeee--EeeeecchhH
Confidence 45889999976543 4466 9999988874
No 250
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=46.42 E-value=6.6 Score=32.88 Aligned_cols=24 Identities=33% Similarity=0.733 Sum_probs=0.0
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
.-+|++||..+ ++. +||.||+..+
T Consensus 655 ~r~Cp~Cg~~t----~~~--~Cp~CG~~T~ 678 (900)
T PF03833_consen 655 RRRCPKCGKET----FYN--RCPECGSHTE 678 (900)
T ss_dssp ------------------------------
T ss_pred cccCcccCCcc----hhh--cCcccCCccc
Confidence 45688887542 122 6777777643
No 251
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=46.19 E-value=17 Score=21.12 Aligned_cols=27 Identities=26% Similarity=0.379 Sum_probs=17.6
Q ss_pred eEEcCCCCCceeec---eEeecccCCCCCC
Q psy1204 29 YVLCKDCHKESKVL---YHIIGLKCEHCGS 55 (71)
Q Consensus 29 ~i~CndC~~~s~v~---~h~~g~kCp~C~S 55 (71)
+.-|.-||...... ..++..+|..|++
T Consensus 6 lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA 35 (64)
T PRK09710 6 VKPCPFCGCPSVTVKAISGYYRAKCNGCES 35 (64)
T ss_pred ccCCCCCCCceeEEEecCceEEEEcCCCCc
Confidence 44588888777532 2233349999987
No 252
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=46.00 E-value=34 Score=28.28 Aligned_cols=34 Identities=15% Similarity=0.404 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCC
Q psy1204 4 TPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHK 37 (71)
Q Consensus 4 ~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~ 37 (71)
...|..+-..+....-............|..||.
T Consensus 567 ~~f~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cg~ 600 (860)
T PRK06319 567 QEFWELFLPVVVTAEKEAFIPRIVTEIDCPKCHK 600 (860)
T ss_pred HHHHHHHHHHHHHHhhhhcccccccCcccCCCCC
Confidence 3456655555543111111111223467888864
No 253
>PF14149 YhfH: YhfH-like protein
Probab=45.79 E-value=1.7 Score=22.83 Aligned_cols=32 Identities=28% Similarity=0.607 Sum_probs=19.3
Q ss_pred HhhhcceeeEEcCCCCCceeeceEeecccCCCC
Q psy1204 21 EEYKNVILYVLCKDCHKESKVLYHIIGLKCEHC 53 (71)
Q Consensus 21 ~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C 53 (71)
+.||+.| ...|..||+.-.-..-.|+..|..|
T Consensus 6 eFfrnLp-~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 6 EFFRNLP-PKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred HHHHhCC-CcccHHHHHHHHHHHHHHhCcCCCC
Confidence 4466654 5569999976543333445567665
No 254
>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=45.62 E-value=12 Score=24.98 Aligned_cols=31 Identities=19% Similarity=0.443 Sum_probs=20.8
Q ss_pred eEEcCCCCCceeeceE-----------eecccCCCCCCcceeee
Q psy1204 29 YVLCKDCHKESKVLYH-----------IIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h-----------~~g~kCp~C~Synt~ii 61 (71)
.+.|. ++.+|+.=|. -+ +.||.|||.++.-.
T Consensus 5 ~L~C~-~gH~FEgWF~ss~~fd~Q~~~gl-v~CP~Cgs~~V~K~ 46 (148)
T PF06676_consen 5 DLRCE-NGHEFEGWFRSSAAFDRQQARGL-VSCPVCGSTEVSKA 46 (148)
T ss_pred EEecC-CCCccceecCCHHHHHHHHHcCC-ccCCCCCCCeEeee
Confidence 45565 8888875321 22 38999999988654
No 255
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=45.57 E-value=12 Score=30.14 Aligned_cols=24 Identities=21% Similarity=0.552 Sum_probs=13.8
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
.-.+|..||.+... .+||+||..+
T Consensus 14 ~akFC~~CG~~l~~------~~Cp~CG~~~ 37 (645)
T PRK14559 14 NNRFCQKCGTSLTH------KPCPQCGTEV 37 (645)
T ss_pred CCccccccCCCCCC------CcCCCCCCCC
Confidence 34567777765431 2566666553
No 256
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=45.04 E-value=16 Score=22.94 Aligned_cols=23 Identities=22% Similarity=0.496 Sum_probs=12.1
Q ss_pred EEcCCCCCceee----ceEeecccCCCCC
Q psy1204 30 VLCKDCHKESKV----LYHIIGLKCEHCG 54 (71)
Q Consensus 30 i~CndC~~~s~v----~~h~~g~kCp~C~ 54 (71)
.+|.+||.-=.+ ....+ +|+.||
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l--~C~kCg 29 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKL--VCRKCG 29 (113)
T ss_pred cccCCccCeeEEeEcCCCcEE--ECCCCC
Confidence 567777643332 12233 777775
No 257
>PRK00019 rpmE 50S ribosomal protein L31; Reviewed
Probab=44.98 E-value=15 Score=21.58 Aligned_cols=35 Identities=20% Similarity=0.518 Sum_probs=22.7
Q ss_pred CCHhhhcceeeEEcCCCCCceeec-------eEeecccCCCCCCcce
Q psy1204 19 MPEEYKNVILYVLCKDCHKESKVL-------YHIIGLKCEHCGSYNT 58 (71)
Q Consensus 19 mP~~y~~~~v~i~CndC~~~s~v~-------~h~~g~kCp~C~Synt 58 (71)
+.++|+ ++.+.|. ||.++.+. .+.- .|+.|.-+=|
T Consensus 5 IHP~y~--~v~~~c~-~g~~f~~~ST~~~~~i~vd--i~s~~HPFyT 46 (72)
T PRK00019 5 IHPKYE--EVTVTCS-CGNVFETRSTLGKDEINVD--VCSKCHPFYT 46 (72)
T ss_pred CCCCCE--EEEEEEC-CCCEEEEeecCCCCcEEEE--eCCCCCCcCc
Confidence 345674 6888999 99988742 2333 7888754433
No 258
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=44.94 E-value=11 Score=27.25 Aligned_cols=27 Identities=15% Similarity=0.460 Sum_probs=19.8
Q ss_pred eeEEcCCCCCceeec---eEeecccCCCCCCc
Q psy1204 28 LYVLCKDCHKESKVL---YHIIGLKCEHCGSY 56 (71)
Q Consensus 28 v~i~CndC~~~s~v~---~h~~g~kCp~C~Sy 56 (71)
++..|..|++.-... .++. .||+|+-+
T Consensus 25 ~~~~c~~c~~~~~~~~l~~~~~--vc~~c~~h 54 (285)
T TIGR00515 25 VWTKCPKCGQVLYTKELERNLE--VCPKCDHH 54 (285)
T ss_pred CeeECCCCcchhhHHHHHhhCC--CCCCCCCc
Confidence 589999999766433 3333 99999765
No 259
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=44.88 E-value=15 Score=21.66 Aligned_cols=10 Identities=20% Similarity=0.650 Sum_probs=8.4
Q ss_pred ccCCCCCCcc
Q psy1204 48 LKCEHCGSYN 57 (71)
Q Consensus 48 ~kCp~C~Syn 57 (71)
++||+||+..
T Consensus 2 m~CP~Cg~~a 11 (72)
T PRK09678 2 FHCPLCQHAA 11 (72)
T ss_pred ccCCCCCCcc
Confidence 3899999888
No 260
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=44.62 E-value=25 Score=18.46 Aligned_cols=26 Identities=23% Similarity=0.718 Sum_probs=15.8
Q ss_pred eeEEcCCCCCceee-----ceEeecccCCCCC
Q psy1204 28 LYVLCKDCHKESKV-----LYHIIGLKCEHCG 54 (71)
Q Consensus 28 v~i~CndC~~~s~v-----~~h~~g~kCp~C~ 54 (71)
..|.|..|+..-.. .--+|| +|..|.
T Consensus 2 GtIvCq~C~~~Id~~e~ekV~~lYg-~C~~~e 32 (38)
T PF13790_consen 2 GTIVCQHCNETIDHFETEKVTTLYG-KCGKCE 32 (38)
T ss_pred CEEEeccccceeeeecCCcEEEEEE-ECCCCc
Confidence 46899999964321 123444 887653
No 261
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=44.39 E-value=12 Score=18.70 Aligned_cols=24 Identities=29% Similarity=0.601 Sum_probs=16.0
Q ss_pred eEEcCCCCCceeeceEeecccCCCCC
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCG 54 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~ 54 (71)
..+|.-|++...... -+++|+.|+
T Consensus 11 ~~~C~~C~~~i~~~~--~~~~C~~C~ 34 (49)
T smart00109 11 PTKCCVCRKSIWGSF--QGLRCSWCK 34 (49)
T ss_pred CCCccccccccCcCC--CCcCCCCCC
Confidence 346999987654322 366999884
No 262
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=44.30 E-value=20 Score=18.51 Aligned_cols=8 Identities=75% Similarity=1.771 Sum_probs=2.9
Q ss_pred cCCCCCCc
Q psy1204 49 KCEHCGSY 56 (71)
Q Consensus 49 kCp~C~Sy 56 (71)
+|..||..
T Consensus 8 kC~~CGni 15 (36)
T PF06397_consen 8 KCEHCGNI 15 (36)
T ss_dssp E-TTT--E
T ss_pred EccCCCCE
Confidence 56666555
No 263
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=44.25 E-value=11 Score=16.40 Aligned_cols=13 Identities=23% Similarity=0.278 Sum_probs=9.6
Q ss_pred EcCCCCCceeece
Q psy1204 31 LCKDCHKESKVLY 43 (71)
Q Consensus 31 ~CndC~~~s~v~~ 43 (71)
.|..|++.|....
T Consensus 2 ~C~~C~~~f~~~~ 14 (23)
T PF00096_consen 2 KCPICGKSFSSKS 14 (23)
T ss_dssp EETTTTEEESSHH
T ss_pred CCCCCCCccCCHH
Confidence 5889998886543
No 264
>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=44.21 E-value=12 Score=20.74 Aligned_cols=10 Identities=40% Similarity=1.009 Sum_probs=7.6
Q ss_pred ccCCCCCCcc
Q psy1204 48 LKCEHCGSYN 57 (71)
Q Consensus 48 ~kCp~C~Syn 57 (71)
-+||.||+-.
T Consensus 14 ~~Cp~CGN~~ 23 (49)
T PF12677_consen 14 CKCPKCGNDK 23 (49)
T ss_pred ccCcccCCcE
Confidence 3999998654
No 265
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=44.01 E-value=13 Score=19.71 Aligned_cols=22 Identities=27% Similarity=0.682 Sum_probs=13.0
Q ss_pred EcCCCCCceeeceEeecccCCCCC
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCG 54 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~ 54 (71)
.|..|+++|.....- +.|..||
T Consensus 4 ~C~~C~~~F~~~~rk--~~Cr~Cg 25 (57)
T cd00065 4 SCMGCGKPFTLTRRR--HHCRNCG 25 (57)
T ss_pred cCcccCccccCCccc--cccCcCc
Confidence 577888877763321 2555554
No 266
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=43.76 E-value=36 Score=22.67 Aligned_cols=39 Identities=26% Similarity=0.607 Sum_probs=26.9
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCC
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNG 66 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~ 66 (71)
.+..+|..|+..=.. .-|-.++||.|+....|-++-+-|
T Consensus 147 vv~a~~~~~g~~~~~-~~~~~~~c~~~~~~e~rkva~~~~ 185 (189)
T PRK09521 147 VIYAMCSRCRTPLVK-KGENELKCPNCGNIETRKLSSYYG 185 (189)
T ss_pred EEEEEccccCCceEE-CCCCEEECCCCCCEEeeccchhhc
Confidence 467789999975533 323445999999888887764433
No 267
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=43.72 E-value=6.6 Score=24.85 Aligned_cols=29 Identities=21% Similarity=0.250 Sum_probs=21.7
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
-.|.|--|.+.-+..+......||.|+|.
T Consensus 61 ~~iiCGvC~~~LT~~EY~~~~~Cp~C~sp 89 (105)
T COG4357 61 KAIICGVCRKLLTRAEYGMCGSCPYCQSP 89 (105)
T ss_pred ccEEhhhhhhhhhHHHHhhcCCCCCcCCC
Confidence 35789999888776654434489999985
No 268
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=43.43 E-value=13 Score=21.04 Aligned_cols=27 Identities=26% Similarity=0.453 Sum_probs=18.4
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
.--|..||+.-=..+-.++ .|++|++.
T Consensus 18 ~~NCl~CGkIiC~~Eg~~~-pC~fCg~~ 44 (57)
T PF06221_consen 18 APNCLNCGKIICEQEGPLG-PCPFCGTP 44 (57)
T ss_pred cccccccChhhcccccCcC-cCCCCCCc
Confidence 5568999986544443244 99999853
No 269
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=43.30 E-value=13 Score=27.74 Aligned_cols=32 Identities=28% Similarity=0.492 Sum_probs=18.3
Q ss_pred hhcceeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 23 YKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 23 y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
|++.-...+|..|+. |-.....-| .||.|++.
T Consensus 114 ~~~~~~~~Yc~~~e~-fl~e~~v~g-~CP~C~~~ 145 (391)
T PF09334_consen 114 YKREYEGWYCPSCER-FLPESFVEG-TCPYCGSD 145 (391)
T ss_dssp EEEEEEEEEETTTTE-EE-GGGETC-EETTT--S
T ss_pred eecccceeEecCcCc-ccccceeec-cccCcCcc
Confidence 555667788999975 433332334 78777643
No 270
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=43.17 E-value=16 Score=25.06 Aligned_cols=44 Identities=11% Similarity=0.192 Sum_probs=25.2
Q ss_pred hcceeeEEcCCCCCceeece-----EeecccCCCCCCcce-e-eecCCCCC
Q psy1204 24 KNVILYVLCKDCHKESKVLY-----HIIGLKCEHCGSYNT-C-RIKKPNGQ 67 (71)
Q Consensus 24 ~~~~v~i~CndC~~~s~v~~-----h~~g~kCp~C~Synt-~-ii~g~~~~ 67 (71)
...--...|..|++...... ....-+||.|++.-- . +.-|+..|
T Consensus 108 HG~l~~~~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~lrP~Vv~fgE~lp 158 (222)
T cd01413 108 HGTLQTAYCVNCGSKYDLEEVKYAKKHEVPRCPKCGGIIRPDVVLFGEPLP 158 (222)
T ss_pred cCCcCcceECCCCCCcchhHHHHhccCCCCcCCCCCCccCCCEEECCCCCC
Confidence 34445678999998775431 112238999987421 1 22465554
No 271
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=42.96 E-value=12 Score=20.83 Aligned_cols=29 Identities=21% Similarity=0.377 Sum_probs=19.6
Q ss_pred eeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 28 LYVLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 28 v~i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
..-+|..||.-+-...|--...|-.||.-
T Consensus 18 k~~~CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 18 KNRFCPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred ccccCCCCCCcchhhhcCceeEeccccce
Confidence 35579999975555555555588888753
No 272
>PRK10220 hypothetical protein; Provisional
Probab=42.94 E-value=16 Score=23.43 Aligned_cols=24 Identities=21% Similarity=0.524 Sum_probs=14.7
Q ss_pred EcCCCCCceeeceEeecccCCCCCC
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
.|..|+.+.+-.--.+ +.||.|+-
T Consensus 5 ~CP~C~seytY~d~~~-~vCpeC~h 28 (111)
T PRK10220 5 HCPKCNSEYTYEDNGM-YICPECAH 28 (111)
T ss_pred cCCCCCCcceEcCCCe-EECCcccC
Confidence 4777877776443222 27888854
No 273
>KOG2846|consensus
Probab=42.70 E-value=21 Score=26.74 Aligned_cols=47 Identities=26% Similarity=0.678 Sum_probs=31.7
Q ss_pred HHHHHHHHcCCCCHhhhcceeeEEcCCCCCce------eeceEeecccCCCCCCcceeeec
Q psy1204 8 RQMDEEIASTPMPEEYKNVILYVLCKDCHKES------KVLYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 8 ~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s------~v~~h~~g~kCp~C~Synt~ii~ 62 (71)
+-+|-++...| +. .--+.|..|+... +.++..| .|++|+-.|.....
T Consensus 205 RI~d~lvGdsP-----~~-ryALIC~~C~~HNGla~~ee~~yi~F--~C~~Cn~LN~~~k~ 257 (328)
T KOG2846|consen 205 RILDYLVGDSP-----NN-RYALICSQCHHHNGLARKEEYEYITF--RCPHCNALNPAKKS 257 (328)
T ss_pred HHHHHHhcCCC-----cc-hhhhcchhhccccCcCChhhcCceEE--ECccccccCCCcCC
Confidence 44555556654 22 3345698898654 3356667 99999999998876
No 274
>KOG1779|consensus
Probab=42.66 E-value=40 Score=20.56 Aligned_cols=39 Identities=23% Similarity=0.416 Sum_probs=29.9
Q ss_pred eeeEEcCCCCCceeeceEeec-ccCCCCCCcceeeecCCC
Q psy1204 27 ILYVLCKDCHKESKVLYHIIG-LKCEHCGSYNTCRIKKPN 65 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g-~kCp~C~Synt~ii~g~~ 65 (71)
.+.++|..|-+..++..|--. ..|+.|+..-...++|+.
T Consensus 32 Fm~VkC~gc~~iT~vfSHaqtvVvc~~c~~il~~~tggra 71 (84)
T KOG1779|consen 32 FMDVKCPGCFKITTVFSHAQTVVVCEGCSTILCQPTGGKA 71 (84)
T ss_pred EEEEEcCCceEEEEEeecCceEEEcCCCceEEEEecCCcE
Confidence 689999999999888776421 278999887777777764
No 275
>PHA02942 putative transposase; Provisional
Probab=42.29 E-value=15 Score=27.52 Aligned_cols=27 Identities=26% Similarity=0.543 Sum_probs=18.1
Q ss_pred eEEcCCCCCceee-ceEeecccCCCCCCcc
Q psy1204 29 YVLCKDCHKESKV-LYHIIGLKCEHCGSYN 57 (71)
Q Consensus 29 ~i~CndC~~~s~v-~~h~~g~kCp~C~Syn 57 (71)
.-.|..||..... ....+ +|+.||-..
T Consensus 325 Sq~Cs~CG~~~~~l~~r~f--~C~~CG~~~ 352 (383)
T PHA02942 325 SVSCPKCGHKMVEIAHRYF--HCPSCGYEN 352 (383)
T ss_pred CccCCCCCCccCcCCCCEE--ECCCCCCEe
Confidence 3569999976532 23455 999998644
No 276
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=42.15 E-value=23 Score=18.82 Aligned_cols=26 Identities=31% Similarity=0.777 Sum_probs=14.5
Q ss_pred EcCCCCCceeeceEeecccCCCCCCccee
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGSYNTC 59 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~Synt~ 59 (71)
.|+.|++.-... ..+ +|..|..|+.-
T Consensus 2 ~Cd~C~~~~~~g-~r~--~C~~C~d~dLC 27 (49)
T cd02335 2 HCDYCSKDITGT-IRI--KCAECPDFDLC 27 (49)
T ss_pred CCCCcCCCCCCC-cEE--ECCCCCCcchh
Confidence 377777644322 233 77777666543
No 277
>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=42.00 E-value=16 Score=17.53 Aligned_cols=12 Identities=33% Similarity=0.625 Sum_probs=5.5
Q ss_pred cCCCCCCcceee
Q psy1204 49 KCEHCGSYNTCR 60 (71)
Q Consensus 49 kCp~C~Synt~i 60 (71)
.||.|+|.=.+.
T Consensus 1 ~CP~C~s~l~~~ 12 (28)
T PF03119_consen 1 TCPVCGSKLVRE 12 (28)
T ss_dssp B-TTT--BEEE-
T ss_pred CcCCCCCEeEcC
Confidence 488898876543
No 278
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=41.32 E-value=33 Score=25.07 Aligned_cols=40 Identities=15% Similarity=0.334 Sum_probs=26.3
Q ss_pred eeeEEcCCCCC------cee-------------eceEeecccCCCCCCcceeeecCCCC
Q psy1204 27 ILYVLCKDCHK------ESK-------------VLYHIIGLKCEHCGSYNTCRIKKPNG 66 (71)
Q Consensus 27 ~v~i~CndC~~------~s~-------------v~~h~~g~kCp~C~Synt~ii~g~~~ 66 (71)
|..|.|+.|+. +|. ++-+.|+.+|+.|+++=+-.++-+++
T Consensus 38 Pf~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~~kTDPkn~ 96 (324)
T PF04502_consen 38 PFNIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEIEFKTDPKNT 96 (324)
T ss_pred CccCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEEeeecCCCCC
Confidence 55688999973 221 22344556999999987777665543
No 279
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=41.29 E-value=72 Score=24.76 Aligned_cols=41 Identities=20% Similarity=0.417 Sum_probs=28.0
Q ss_pred CCCHhhhcceeeEEcCCCCCceeece---------EeecccCCCCCCcceeeecC
Q psy1204 18 PMPEEYKNVILYVLCKDCHKESKVLY---------HIIGLKCEHCGSYNTCRIKK 63 (71)
Q Consensus 18 pmP~~y~~~~v~i~CndC~~~s~v~~---------h~~g~kCp~C~Synt~ii~g 63 (71)
+.|+.| .|....|..||+..++.- -.| .|. ||...+.-+.|
T Consensus 166 ~~~~~~--~P~~pic~~cg~~~~~~~~~~d~~~~~v~y--~~~-cG~~~~~~~~~ 215 (510)
T PRK00750 166 ERQATY--SPFLPICPKCGKVLTTPVISYDAEAGTVTY--DCE-CGHEGEVPVTG 215 (510)
T ss_pred ccCCCe--eeeeeeCCCCCccceEEEEEEeCCCCEEEE--EcC-CCCEEEEecCC
Confidence 567777 489999999999876431 122 564 88777765543
No 280
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=41.04 E-value=13 Score=25.94 Aligned_cols=30 Identities=20% Similarity=0.358 Sum_probs=19.1
Q ss_pred eeeEEcCCCCCceeeceE------eecccCCCCCCc
Q psy1204 27 ILYVLCKDCHKESKVLYH------IIGLKCEHCGSY 56 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h------~~g~kCp~C~Sy 56 (71)
.-...|..|++....... .-.-+||.|++.
T Consensus 117 ~~~~~C~~C~~~~~~~~~~~~~~~~~~p~Cp~Cgg~ 152 (244)
T PRK14138 117 VEEYYCVRCGKRYTVEDVIEKLEKSDVPRCDDCSGL 152 (244)
T ss_pred cCeeEECCCCCcccHHHHHHHHhcCCCCCCCCCCCe
Confidence 445679999987764321 112379999864
No 281
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=40.64 E-value=23 Score=20.05 Aligned_cols=17 Identities=12% Similarity=0.415 Sum_probs=11.3
Q ss_pred hcceeeEEcCCCCCcee
Q psy1204 24 KNVILYVLCKDCHKESK 40 (71)
Q Consensus 24 ~~~~v~i~CndC~~~s~ 40 (71)
.+.++.+.|..|++...
T Consensus 2 ~~~p~~~~CP~C~~~~~ 18 (73)
T PF10601_consen 2 GPEPVRIYCPYCQQQVQ 18 (73)
T ss_pred CCCceeeECCCCCCEEE
Confidence 34567777777776653
No 282
>PRK04011 peptide chain release factor 1; Provisional
Probab=40.58 E-value=21 Score=26.94 Aligned_cols=37 Identities=22% Similarity=0.442 Sum_probs=24.2
Q ss_pred CHhhhcceeeEEcCCCCCceeec----eEeecccCCCCCCc
Q psy1204 20 PEEYKNVILYVLCKDCHKESKVL----YHIIGLKCEHCGSY 56 (71)
Q Consensus 20 P~~y~~~~v~i~CndC~~~s~v~----~h~~g~kCp~C~Sy 56 (71)
.+.+....+.+.|.+|+...... .-.....||.|++.
T Consensus 319 ~d~l~~~r~~~~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~ 359 (411)
T PRK04011 319 SEDLRKDRVTYKCPNCGYEEEKTVKRREELPEKTCPKCGSE 359 (411)
T ss_pred eccccceeEEEEcCCCCcceeeecccccccccccCcccCcc
Confidence 55555556788999999766431 11223489999875
No 283
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=39.55 E-value=19 Score=22.20 Aligned_cols=10 Identities=20% Similarity=0.560 Sum_probs=4.8
Q ss_pred eEEcCCCCCc
Q psy1204 29 YVLCKDCHKE 38 (71)
Q Consensus 29 ~i~CndC~~~ 38 (71)
.-.|..|+++
T Consensus 35 ~~~Cp~C~~~ 44 (89)
T COG1997 35 KHVCPFCGRT 44 (89)
T ss_pred CCcCCCCCCc
Confidence 3445555544
No 284
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=39.52 E-value=21 Score=19.25 Aligned_cols=25 Identities=20% Similarity=0.559 Sum_probs=14.3
Q ss_pred EcCCCCCceeeceEeecccCCCCC--Ccce
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCG--SYNT 58 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~--Synt 58 (71)
.|+.|+..-.+ ...+ +|..|. +|+.
T Consensus 2 ~Cd~C~~~pI~-G~R~--~C~~C~~~d~Dl 28 (48)
T cd02341 2 KCDSCGIEPIP-GTRY--HCSECDDGDFDL 28 (48)
T ss_pred CCCCCCCCccc-cceE--ECCCCCCCCCcc
Confidence 47788764333 2233 677776 6654
No 285
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=39.48 E-value=82 Score=19.72 Aligned_cols=52 Identities=23% Similarity=0.454 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHcCCC-----CHh---hhc-----ceeeEEcCCCCCceeeceE--eecccCCCCCCc
Q psy1204 5 PLWRQMDEEIASTPM-----PEE---YKN-----VILYVLCKDCHKESKVLYH--IIGLKCEHCGSY 56 (71)
Q Consensus 5 ~~~~~lD~~i~~~pm-----P~~---y~~-----~~v~i~CndC~~~s~v~~h--~~g~kCp~C~Sy 56 (71)
..|+.+-+.|...+- |.. |.. ......|..|+........ ..-..|+.|++.
T Consensus 86 ~~fk~~~~~ig~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~ 152 (157)
T PF10263_consen 86 KEFKQWARRIGASPPRGRPNPTTCHSYEIEGKEYKKYVYRCPSCGREYKRHRRSKRKRYRCGRCGGP 152 (157)
T ss_pred HHHHHHHHHHCCcccccccccccccccccccccccceEEEcCCCCCEeeeecccchhhEECCCCCCE
Confidence 478888888888541 111 211 2468899999977653322 111279999864
No 286
>KOG4684|consensus
Probab=39.31 E-value=6.4 Score=28.36 Aligned_cols=46 Identities=20% Similarity=0.303 Sum_probs=29.9
Q ss_pred HHHHHHcCCCCHhhhcceeeEEcCCCCCceee-ceEeecccCCCCCCc
Q psy1204 10 MDEEIASTPMPEEYKNVILYVLCKDCHKESKV-LYHIIGLKCEHCGSY 56 (71)
Q Consensus 10 lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v-~~h~~g~kCp~C~Sy 56 (71)
||-.+...+.|.. +-..+.+.|+.|..+|-- .+|..--.||+|.-+
T Consensus 152 L~p~~~~p~~P~~-~P~gcRV~CgHC~~tFLfnt~tnaLArCPHCrKv 198 (275)
T KOG4684|consen 152 LDPLIEKPRDPGT-APTGCRVKCGHCNETFLFNTLTNALARCPHCRKV 198 (275)
T ss_pred cCCCCCCCCCCCC-CCcceEEEecCccceeehhhHHHHHhcCCcccch
Confidence 4444444455555 444689999999999853 344433489999644
No 287
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=39.24 E-value=18 Score=23.37 Aligned_cols=29 Identities=24% Similarity=0.490 Sum_probs=18.8
Q ss_pred eeeEEcCCCCCceeece-EeecccCCCCCCcc
Q psy1204 27 ILYVLCKDCHKESKVLY-HIIGLKCEHCGSYN 57 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~-h~~g~kCp~C~Syn 57 (71)
.....|..|+++-.... -.+ .|+.|+...
T Consensus 32 ~~Y~aC~~C~kkv~~~~~~~~--~C~~C~~~~ 61 (166)
T cd04476 32 WWYPACPGCNKKVVEEGNGTY--RCEKCNKSV 61 (166)
T ss_pred eEEccccccCcccEeCCCCcE--ECCCCCCcC
Confidence 45667888988754332 244 899887653
No 288
>smart00350 MCM minichromosome maintenance proteins.
Probab=39.03 E-value=40 Score=25.88 Aligned_cols=32 Identities=16% Similarity=0.189 Sum_probs=22.2
Q ss_pred ceeeEEcCCCCCceeeceEe----ecccCCC--CCCcc
Q psy1204 26 VILYVLCKDCHKESKVLYHI----IGLKCEH--CGSYN 57 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v~~h~----~g~kCp~--C~Syn 57 (71)
+.....|..|+.++.+.+.. .-..||. |++.+
T Consensus 34 ~~~~f~C~~C~~~~~~~~~~~~~~~p~~C~~~~C~~~~ 71 (509)
T smart00350 34 KRASFTCEKCGATLGPEIQSGRETEPTVCPPRECQSPT 71 (509)
T ss_pred EEEEEEecCCCCEEeEEecCCcccCCCcCCCCcCCCCC
Confidence 45788999999887654321 1237987 99865
No 289
>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=38.74 E-value=23 Score=17.75 Aligned_cols=11 Identities=18% Similarity=0.531 Sum_probs=5.6
Q ss_pred EEcCCCCCcee
Q psy1204 30 VLCKDCHKESK 40 (71)
Q Consensus 30 i~CndC~~~s~ 40 (71)
.+|.+|+.-=.
T Consensus 2 ~FCp~C~nlL~ 12 (35)
T PF02150_consen 2 RFCPECGNLLY 12 (35)
T ss_dssp -BETTTTSBEE
T ss_pred eeCCCCCccce
Confidence 45666665433
No 290
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=38.56 E-value=36 Score=19.53 Aligned_cols=9 Identities=33% Similarity=0.836 Sum_probs=4.9
Q ss_pred eeEEcCCCC
Q psy1204 28 LYVLCKDCH 36 (71)
Q Consensus 28 v~i~CndC~ 36 (71)
....|.+|+
T Consensus 12 ~~y~C~tC~ 20 (71)
T smart00396 12 VIYRCKTCG 20 (71)
T ss_pred EEEECcCCC
Confidence 345566665
No 291
>PRK05978 hypothetical protein; Provisional
Probab=36.80 E-value=20 Score=23.81 Aligned_cols=32 Identities=19% Similarity=0.246 Sum_probs=21.4
Q ss_pred eeeEEcCCCCCcee-eceEeecccCCCCCCcce
Q psy1204 27 ILYVLCKDCHKESK-VLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 27 ~v~i~CndC~~~s~-v~~h~~g~kCp~C~Synt 58 (71)
-...+|..||+--- ..|.-....|++||-.-.
T Consensus 31 Gl~grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 31 GFRGRCPACGEGKLFRAFLKPVDHCAACGEDFT 63 (148)
T ss_pred HHcCcCCCCCCCcccccccccCCCccccCCccc
Confidence 36789999996443 234455568999975443
No 292
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=36.62 E-value=17 Score=18.57 Aligned_cols=7 Identities=57% Similarity=1.635 Sum_probs=5.8
Q ss_pred cCCCCCC
Q psy1204 49 KCEHCGS 55 (71)
Q Consensus 49 kCp~C~S 55 (71)
+||.|+.
T Consensus 1 ~CP~C~~ 7 (41)
T PF13453_consen 1 KCPRCGT 7 (41)
T ss_pred CcCCCCc
Confidence 6899987
No 293
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=36.59 E-value=17 Score=16.90 Aligned_cols=12 Identities=25% Similarity=0.512 Sum_probs=9.3
Q ss_pred EEcCCCCCceee
Q psy1204 30 VLCKDCHKESKV 41 (71)
Q Consensus 30 i~CndC~~~s~v 41 (71)
+.|..||.+|..
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 568889988854
No 294
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=36.40 E-value=22 Score=19.37 Aligned_cols=8 Identities=38% Similarity=0.937 Sum_probs=5.9
Q ss_pred cCCCCCCc
Q psy1204 49 KCEHCGSY 56 (71)
Q Consensus 49 kCp~C~Sy 56 (71)
+||.|++-
T Consensus 36 ~CP~C~a~ 43 (50)
T cd00730 36 VCPVCGAG 43 (50)
T ss_pred CCCCCCCc
Confidence 78888764
No 295
>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=36.28 E-value=18 Score=23.32 Aligned_cols=32 Identities=13% Similarity=0.168 Sum_probs=21.7
Q ss_pred HHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCce
Q psy1204 6 LWRQMDEEIASTPMPEEYKNVILYVLCKDCHKES 39 (71)
Q Consensus 6 ~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s 39 (71)
..+.|.+.++...+... ..+...+|..|+..-
T Consensus 70 ~~~QL~ev~~~~~l~~~--~~~~~sRC~~CN~~L 101 (147)
T PF01927_consen 70 PEEQLREVLERFGLKLR--LDPIFSRCPKCNGPL 101 (147)
T ss_pred HHHHHHHHHHHcCCccc--cCCCCCccCCCCcEe
Confidence 45677777777776543 335678899998644
No 296
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=36.22 E-value=22 Score=22.09 Aligned_cols=23 Identities=17% Similarity=0.268 Sum_probs=15.0
Q ss_pred EcCCCCCceeeceEeecccCCCCC
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCG 54 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~ 54 (71)
-|..|+..-+... |....||.|+
T Consensus 5 AC~~C~~I~~~~q-f~~~gCpnC~ 27 (98)
T cd07973 5 ACLLCSLIKTEDQ-FERDGCPNCE 27 (98)
T ss_pred hhccCCccccccc-ccCCCCCCCc
Confidence 5888886554433 2234899996
No 297
>cd01409 SIRT4 SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=36.02 E-value=27 Score=24.63 Aligned_cols=13 Identities=23% Similarity=0.501 Sum_probs=10.0
Q ss_pred eeEEcCCCCCcee
Q psy1204 28 LYVLCKDCHKESK 40 (71)
Q Consensus 28 v~i~CndC~~~s~ 40 (71)
-...|..|++++.
T Consensus 117 ~~~~C~~C~~~~~ 129 (260)
T cd01409 117 HRVVCLSCGFRTP 129 (260)
T ss_pred CEEEeCCCcCccC
Confidence 4678999998764
No 298
>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=35.94 E-value=17 Score=20.00 Aligned_cols=20 Identities=20% Similarity=0.498 Sum_probs=15.2
Q ss_pred hHHHHHHHHHHHHcCCCCHh
Q psy1204 3 MTPLWRQMDEEIASTPMPEE 22 (71)
Q Consensus 3 m~~~~~~lD~~i~~~pmP~~ 22 (71)
-|..|++|-.......||++
T Consensus 39 ~S~L~~~i~~~~~~~~MPP~ 58 (59)
T PF07635_consen 39 ESLLWQRITSQDDDGRMPPK 58 (59)
T ss_pred HhHHHHHHHccCCCCCCCcC
Confidence 36788888766778889874
No 299
>KOG2463|consensus
Probab=35.80 E-value=14 Score=27.99 Aligned_cols=28 Identities=18% Similarity=0.454 Sum_probs=20.5
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
.-+++|..|-+.+...... -||+||.--
T Consensus 240 ~~iLRCh~Cfsit~~m~k~---FCp~CG~~T 267 (376)
T KOG2463|consen 240 SYILRCHGCFSITSEMPKD---FCPSCGHKT 267 (376)
T ss_pred hheeEeeeeeEecCccchh---cccccCCCe
Confidence 4588999998877554433 599999873
No 300
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=35.24 E-value=18 Score=19.66 Aligned_cols=12 Identities=33% Similarity=0.982 Sum_probs=9.0
Q ss_pred eecccCCCCCCc
Q psy1204 45 IIGLKCEHCGSY 56 (71)
Q Consensus 45 ~~g~kCp~C~Sy 56 (71)
..|..||.||.-
T Consensus 7 ltG~~CPgCG~t 18 (52)
T PF10825_consen 7 LTGIPCPGCGMT 18 (52)
T ss_pred hhCCCCCCCcHH
Confidence 457799999853
No 301
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=34.86 E-value=30 Score=20.55 Aligned_cols=11 Identities=36% Similarity=0.993 Sum_probs=5.8
Q ss_pred eeeEEcCCCCC
Q psy1204 27 ILYVLCKDCHK 37 (71)
Q Consensus 27 ~v~i~CndC~~ 37 (71)
.|.+.|.+||+
T Consensus 86 vVsL~C~~CG~ 96 (98)
T PF15494_consen 86 VVSLQCSDCGK 96 (98)
T ss_pred EEEEECcccCC
Confidence 45555555554
No 302
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=34.79 E-value=73 Score=17.69 Aligned_cols=22 Identities=27% Similarity=0.658 Sum_probs=13.8
Q ss_pred EcCCCCCceeeceEeecccCCCCCCcce
Q psy1204 31 LCKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 31 ~CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
.|+.|+. - .|--+||.||+.-.
T Consensus 7 ~c~~~~~-Y-----TLk~~cp~cG~~T~ 28 (53)
T PF04135_consen 7 KCPGCRV-Y-----TLKDKCPPCGGPTE 28 (53)
T ss_dssp ECTTTCE-E-----ESSSBBTTTSSBSE
T ss_pred cCCCCCc-E-----eCCCccCCCCCCCc
Confidence 7888872 1 22237999987543
No 303
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.56 E-value=21 Score=24.98 Aligned_cols=35 Identities=23% Similarity=0.413 Sum_probs=21.1
Q ss_pred eeeEEcCCCCCcee--------ec------eEeecccCCCCC-Ccceeee
Q psy1204 27 ILYVLCKDCHKESK--------VL------YHIIGLKCEHCG-SYNTCRI 61 (71)
Q Consensus 27 ~v~i~CndC~~~s~--------v~------~h~~g~kCp~C~-Synt~ii 61 (71)
.+.+.||.||.+-. ++ --|+.-||.+|. |+|..|-
T Consensus 15 q~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~Cd~tWN~~If 64 (203)
T COG4332 15 QPAKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTHCDYTWNISIF 64 (203)
T ss_pred hhhhhCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeeccCCccchhhh
Confidence 46788999996532 21 112323999994 5665543
No 304
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=34.14 E-value=29 Score=21.35 Aligned_cols=29 Identities=28% Similarity=0.337 Sum_probs=18.3
Q ss_pred ceeeEEcCCCCCceeeceEeecccCCCCC
Q psy1204 26 VILYVLCKDCHKESKVLYHIIGLKCEHCG 54 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~ 54 (71)
+.....|..|++...-..-.-.-+|.+|+
T Consensus 32 q~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~ 60 (90)
T PF01780_consen 32 QHAKYTCPFCGKTSVKRVATGIWKCKKCG 60 (90)
T ss_dssp HHS-BEESSSSSSEEEEEETTEEEETTTT
T ss_pred HhCCCcCCCCCCceeEEeeeEEeecCCCC
Confidence 35678899999988543322112888885
No 305
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=34.07 E-value=94 Score=19.75 Aligned_cols=50 Identities=20% Similarity=0.373 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHcCCCCH-------hhhcceeeEEcCCCCCcee-eceEe--ecccCCCCCCc
Q psy1204 5 PLWRQMDEEIASTPMPE-------EYKNVILYVLCKDCHKESK-VLYHI--IGLKCEHCGSY 56 (71)
Q Consensus 5 ~~~~~lD~~i~~~pmP~-------~y~~~~v~i~CndC~~~s~-v~~h~--~g~kCp~C~Sy 56 (71)
..|+.+=+.+...+ |+ ++. ......|..|+...- ...|. .-..|..|++.
T Consensus 83 ~~f~~~~~~~~~~~-~~~~h~~~~~~~-~~~~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~ 142 (146)
T smart00731 83 DEWKRWMRQVNGLF-PERCHTFLIESV-KKYPYRCTGCGQRYLRVRRSNNVSRYRCGKCGGK 142 (146)
T ss_pred HHHHHHHHHHcCCC-cceEcCCccccc-ceEEEECCCCCCCCceEccccCcceEEcCCCCCE
Confidence 45666666665553 22 221 256888999997664 22221 11288889874
No 306
>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=33.70 E-value=37 Score=17.29 Aligned_cols=6 Identities=67% Similarity=1.824 Sum_probs=4.0
Q ss_pred cCCCCC
Q psy1204 49 KCEHCG 54 (71)
Q Consensus 49 kCp~C~ 54 (71)
+||.|+
T Consensus 3 ~CP~Cg 8 (39)
T PF01396_consen 3 KCPKCG 8 (39)
T ss_pred CCCCCC
Confidence 566666
No 307
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=33.69 E-value=20 Score=18.33 Aligned_cols=9 Identities=33% Similarity=0.767 Sum_probs=5.2
Q ss_pred ccCCCCCCc
Q psy1204 48 LKCEHCGSY 56 (71)
Q Consensus 48 ~kCp~C~Sy 56 (71)
|.||+||--
T Consensus 2 hlcpkcgvg 10 (36)
T PF09151_consen 2 HLCPKCGVG 10 (36)
T ss_dssp -B-TTTSSS
T ss_pred ccCCccCce
Confidence 579999753
No 308
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=33.48 E-value=25 Score=25.03 Aligned_cols=16 Identities=19% Similarity=0.291 Sum_probs=10.7
Q ss_pred cceeeEEcCCCCCcee
Q psy1204 25 NVILYVLCKDCHKESK 40 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~ 40 (71)
..-....|..|++...
T Consensus 124 G~~~~~~C~~C~~~~~ 139 (285)
T PRK05333 124 GRLDGVRCMGCGARHP 139 (285)
T ss_pred CCcCEEEECCCCCcCC
Confidence 3345678999996543
No 309
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=33.24 E-value=61 Score=19.08 Aligned_cols=9 Identities=33% Similarity=0.855 Sum_probs=3.3
Q ss_pred eEEcCCCCC
Q psy1204 29 YVLCKDCHK 37 (71)
Q Consensus 29 ~i~CndC~~ 37 (71)
...|..|++
T Consensus 17 ~~~C~~C~~ 25 (70)
T PF07191_consen 17 HYHCEACQK 25 (70)
T ss_dssp EEEETTT--
T ss_pred EEECccccc
Confidence 444545544
No 310
>cd01408 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
Probab=32.70 E-value=11 Score=26.08 Aligned_cols=30 Identities=20% Similarity=0.429 Sum_probs=18.0
Q ss_pred eeeEEcCCCCCceeece------EeecccCCCCCCc
Q psy1204 27 ILYVLCKDCHKESKVLY------HIIGLKCEHCGSY 56 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~------h~~g~kCp~C~Sy 56 (71)
--...|..|+......+ ..-.-+||.|++.
T Consensus 114 l~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~ 149 (235)
T cd01408 114 FATAHCIKCKHKYPGDWMREDIFNQEVPKCPRCGGL 149 (235)
T ss_pred CCccccccCCCcCCHHHHHHHHhCCCCccCCCCCCC
Confidence 44567999998654221 0001379999864
No 311
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=32.50 E-value=21 Score=16.04 Aligned_cols=14 Identities=29% Similarity=0.563 Sum_probs=10.5
Q ss_pred EEcCCCCCceeece
Q psy1204 30 VLCKDCHKESKVLY 43 (71)
Q Consensus 30 i~CndC~~~s~v~~ 43 (71)
..|..|++.|....
T Consensus 2 ~~C~~C~~~F~~~~ 15 (27)
T PF13912_consen 2 FECDECGKTFSSLS 15 (27)
T ss_dssp EEETTTTEEESSHH
T ss_pred CCCCccCCccCChh
Confidence 47999999886543
No 312
>cd00296 SIR2 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic
Probab=32.44 E-value=26 Score=23.34 Aligned_cols=47 Identities=19% Similarity=0.260 Sum_probs=25.6
Q ss_pred HHHHHHcCCCCHh----hhcceeeEEcCCCCCceeeceE---eecccCCCCCCc
Q psy1204 10 MDEEIASTPMPEE----YKNVILYVLCKDCHKESKVLYH---IIGLKCEHCGSY 56 (71)
Q Consensus 10 lD~~i~~~pmP~~----y~~~~v~i~CndC~~~s~v~~h---~~g~kCp~C~Sy 56 (71)
+|-+.+..-.+.+ ....--...|..|++....... ...-+||.|++.
T Consensus 90 iD~L~~~ag~~~~~v~~lHG~~~~~~C~~C~~~~~~~~~~~~~~~p~C~~C~~~ 143 (222)
T cd00296 90 VDGLHERAGSRRNRVIELHGSLDRVRCTSCGKEYPRDEVLEREKPPRCPKCGGL 143 (222)
T ss_pred hHHHHHHhCCCcCcEEEecCCCCccEECCCCCCcchhhhhhccCCCCCCCCCCc
Confidence 4555544444421 2233345679999876543221 123489999873
No 313
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=32.42 E-value=29 Score=17.62 Aligned_cols=15 Identities=27% Similarity=0.357 Sum_probs=9.5
Q ss_pred cCCCCCCcceeeecC
Q psy1204 49 KCEHCGSYNTCRIKK 63 (71)
Q Consensus 49 kCp~C~Synt~ii~g 63 (71)
.|+.|+|......+|
T Consensus 10 ~C~~C~~~~~~~~dG 24 (36)
T PF11781_consen 10 PCPVCGSRWFYSDDG 24 (36)
T ss_pred cCCCCCCeEeEccCC
Confidence 488888875554444
No 314
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=32.40 E-value=32 Score=18.84 Aligned_cols=14 Identities=14% Similarity=0.313 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHcC
Q psy1204 4 TPLWRQMDEEIAST 17 (71)
Q Consensus 4 ~~~~~~lD~~i~~~ 17 (71)
+..|..||.+|+..
T Consensus 34 ~~Nf~~lD~Li~~l 47 (49)
T smart00586 34 NDNFQALDDLISQL 47 (49)
T ss_pred chhHHHHHHHHHHh
Confidence 35899999999864
No 315
>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=32.04 E-value=27 Score=27.34 Aligned_cols=16 Identities=25% Similarity=0.548 Sum_probs=11.9
Q ss_pred eecccCCCCCCcceee
Q psy1204 45 IIGLKCEHCGSYNTCR 60 (71)
Q Consensus 45 ~~g~kCp~C~Synt~i 60 (71)
.+...||+||.+.+-.
T Consensus 198 ~~~vpCPhCg~~~~l~ 213 (557)
T PF05876_consen 198 RYYVPCPHCGEEQVLE 213 (557)
T ss_pred EEEccCCCCCCCcccc
Confidence 4445999999988744
No 316
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=32.00 E-value=6.7 Score=26.55 Aligned_cols=9 Identities=22% Similarity=0.862 Sum_probs=5.0
Q ss_pred EEcCCCCCc
Q psy1204 30 VLCKDCHKE 38 (71)
Q Consensus 30 i~CndC~~~ 38 (71)
-+|..||++
T Consensus 29 ~fC~kCG~~ 37 (158)
T PF10083_consen 29 KFCSKCGAK 37 (158)
T ss_pred HHHHHhhHH
Confidence 456666653
No 317
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=31.90 E-value=36 Score=26.15 Aligned_cols=33 Identities=21% Similarity=0.484 Sum_probs=21.7
Q ss_pred HhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204 21 EEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYN 57 (71)
Q Consensus 21 ~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Syn 57 (71)
--|.+. ....|.+|... ..+....+||.|++..
T Consensus 50 LGYAd~-~i~kC~~c~~~---~~y~~~~~C~~cg~~~ 82 (415)
T COG5257 50 LGYADA-KIYKCPECYRP---ECYTTEPKCPNCGAET 82 (415)
T ss_pred eccccC-ceEeCCCCCCC---cccccCCCCCCCCCCc
Confidence 346663 46789999864 2223334999998764
No 318
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.86 E-value=21 Score=23.19 Aligned_cols=23 Identities=13% Similarity=-0.028 Sum_probs=16.8
Q ss_pred EEcCCCCCcee-eceEeecccCCCCC
Q psy1204 30 VLCKDCHKESK-VLYHIIGLKCEHCG 54 (71)
Q Consensus 30 i~CndC~~~s~-v~~h~~g~kCp~C~ 54 (71)
-.|.+||++|. .+..-+ .||.||
T Consensus 10 ridPetg~KFYDLNrdPi--VsPytG 33 (129)
T COG4530 10 RIDPETGKKFYDLNRDPI--VSPYTG 33 (129)
T ss_pred ccCccccchhhccCCCcc--ccCccc
Confidence 35889999996 445555 888886
No 319
>COG4640 Predicted membrane protein [Function unknown]
Probab=31.74 E-value=24 Score=27.51 Aligned_cols=23 Identities=26% Similarity=0.709 Sum_probs=15.1
Q ss_pred EcCCCCCc-eeeceEeecccCCCCCCcce
Q psy1204 31 LCKDCHKE-SKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 31 ~CndC~~~-s~v~~h~~g~kCp~C~Synt 58 (71)
+|..||+. -+-.. .|+.||+.-|
T Consensus 3 fC~kcG~qk~Ed~~-----qC~qCG~~~t 26 (465)
T COG4640 3 FCPKCGSQKAEDDV-----QCTQCGHKFT 26 (465)
T ss_pred cccccccccccccc-----cccccCCcCC
Confidence 69999942 23322 6999987644
No 320
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.67 E-value=11 Score=22.78 Aligned_cols=11 Identities=27% Similarity=0.561 Sum_probs=8.1
Q ss_pred ccCCCCCCcce
Q psy1204 48 LKCEHCGSYNT 58 (71)
Q Consensus 48 ~kCp~C~Synt 58 (71)
-.||.||+.-+
T Consensus 42 g~CPnCGGelv 52 (84)
T COG3813 42 GLCPNCGGELV 52 (84)
T ss_pred CcCCCCCchhh
Confidence 37999987544
No 321
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=31.66 E-value=29 Score=26.81 Aligned_cols=30 Identities=23% Similarity=0.465 Sum_probs=21.0
Q ss_pred eeeEEcCCCCCceeeceEeecc--cCCCCCCc
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGL--KCEHCGSY 56 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~--kCp~C~Sy 56 (71)
.-.+.|.+|+-...++....++ .||.||.-
T Consensus 16 ~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~~ 47 (418)
T COG2995 16 GHLILCPECDMLVSLPRLDSGQSAYCPRCGHT 47 (418)
T ss_pred cceecCCCCCceeccccCCCCCcccCCCCCCc
Confidence 4578999999988775422222 79999754
No 322
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=31.57 E-value=43 Score=20.93 Aligned_cols=8 Identities=38% Similarity=1.211 Sum_probs=6.5
Q ss_pred cCCCCCCc
Q psy1204 49 KCEHCGSY 56 (71)
Q Consensus 49 kCp~C~Sy 56 (71)
.|+.|++|
T Consensus 33 ~C~~C~Ay 40 (102)
T PF11672_consen 33 VCTPCDAY 40 (102)
T ss_pred ECCCCCce
Confidence 78888877
No 323
>PRK03954 ribonuclease P protein component 4; Validated
Probab=31.47 E-value=39 Score=21.76 Aligned_cols=37 Identities=30% Similarity=0.712 Sum_probs=20.0
Q ss_pred cCCCCHhhhcceeeEEcCCCCCc------eee--c----eEeecccCCCCCCcc
Q psy1204 16 STPMPEEYKNVILYVLCKDCHKE------SKV--L----YHIIGLKCEHCGSYN 57 (71)
Q Consensus 16 ~~pmP~~y~~~~v~i~CndC~~~------s~v--~----~h~~g~kCp~C~Syn 57 (71)
...||++++. -+|..|..- ..+ . -|... .|-.||...
T Consensus 55 rirlp~~~KR----~~CK~C~t~LiPG~n~~vRi~~~~~~~vvi-tCl~CG~~k 103 (121)
T PRK03954 55 KVKLPRKWKR----RYCKRCHSFLVPGVNARVRLRQKRMPHVVI-TCLECGHIM 103 (121)
T ss_pred ccCCCHHHHH----HHhhcCCCeeecCCceEEEEecCCcceEEE-ECccCCCEE
Confidence 3566777764 357777532 111 1 14543 788887643
No 324
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=31.17 E-value=12 Score=28.49 Aligned_cols=25 Identities=20% Similarity=0.628 Sum_probs=17.2
Q ss_pred EcCCCCCceeece-EeecccCCCCCC
Q psy1204 31 LCKDCHKESKVLY-HIIGLKCEHCGS 55 (71)
Q Consensus 31 ~CndC~~~s~v~~-h~~g~kCp~C~S 55 (71)
-|.-|..++.... -.+.-+||.||+
T Consensus 248 AC~rC~t~y~le~A~~~~wrCpkCGg 273 (403)
T COG1379 248 ACSRCYTRYSLEEAKSLRWRCPKCGG 273 (403)
T ss_pred HHHHhhhccCcchhhhhcccCccccc
Confidence 4888887776533 233339999998
No 325
>PRK01678 rpmE2 50S ribosomal protein L31 type B; Reviewed
Probab=30.23 E-value=37 Score=20.69 Aligned_cols=21 Identities=10% Similarity=-0.001 Sum_probs=16.1
Q ss_pred CCHhhhcceeeEEcCCCCCceee
Q psy1204 19 MPEEYKNVILYVLCKDCHKESKV 41 (71)
Q Consensus 19 mP~~y~~~~v~i~CndC~~~s~v 41 (71)
+.++|+ ++.+.|-.||.+|.+
T Consensus 5 IHP~y~--~v~~~~~t~g~~f~~ 25 (87)
T PRK01678 5 IHPEYR--PVVFHDTSTGFKFLT 25 (87)
T ss_pred CCCCCE--EEEEEECCCCCEEEE
Confidence 345674 689999999998863
No 326
>COG3530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.17 E-value=30 Score=20.32 Aligned_cols=14 Identities=57% Similarity=0.854 Sum_probs=11.5
Q ss_pred HHHcCCCCHh-hhcc
Q psy1204 13 EIASTPMPEE-YKNV 26 (71)
Q Consensus 13 ~i~~~pmP~~-y~~~ 26 (71)
+|+.+|||.- |+.+
T Consensus 8 ~ia~t~MPFGKYqGR 22 (71)
T COG3530 8 EIANTPMPFGKYQGR 22 (71)
T ss_pred HHHcCCCCcccccce
Confidence 5899999988 8764
No 327
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=30.12 E-value=27 Score=15.33 Aligned_cols=10 Identities=60% Similarity=1.444 Sum_probs=4.9
Q ss_pred cCCCCCCccee
Q psy1204 49 KCEHCGSYNTC 59 (71)
Q Consensus 49 kCp~C~Synt~ 59 (71)
+|+.|. |.+.
T Consensus 2 ~C~~C~-y~t~ 11 (24)
T PF13909_consen 2 KCPHCS-YSTS 11 (24)
T ss_dssp E-SSSS--EES
T ss_pred CCCCCC-CcCC
Confidence 677774 6553
No 328
>cd03019 DsbA_DsbA DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins secreted into the bacterial periplasm. This rapid and unidirectional process helps to catalyze the folding of newly-synthesized polypeptides. To regain catalytic activity, reduced DsbA is then reoxidized by the membrane protein DsbB, which generates its disulfides from oxidized quinones, which in turn are reoxidized by the electron transport chain.
Probab=30.01 E-value=19 Score=22.56 Aligned_cols=21 Identities=14% Similarity=0.409 Sum_probs=15.0
Q ss_pred eeeceEeecccCCCCCCcceeee
Q psy1204 39 SKVLYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 39 s~v~~h~~g~kCp~C~Synt~ii 61 (71)
..+.|..+ .||+|......+.
T Consensus 18 ~i~~f~D~--~Cp~C~~~~~~~~ 38 (178)
T cd03019 18 EVIEFFSY--GCPHCYNFEPILE 38 (178)
T ss_pred EEEEEECC--CCcchhhhhHHHH
Confidence 34556566 9999988877653
No 329
>PF04315 DUF462: Protein of unknown function, DUF462; InterPro: IPR007411 This family consists of bacterial proteins of uncharacterised function.
Probab=29.84 E-value=30 Score=23.56 Aligned_cols=14 Identities=36% Similarity=0.401 Sum_probs=12.5
Q ss_pred CCcceeeecCCCCC
Q psy1204 54 GSYNTCRIKKPNGQ 67 (71)
Q Consensus 54 ~Synt~ii~g~~~~ 67 (71)
.+|||+++.|.+.|
T Consensus 8 ~~~nT~Lv~G~dEP 21 (164)
T PF04315_consen 8 ESYNTRLVKGDDEP 21 (164)
T ss_pred hccCcEEecCCCCc
Confidence 48999999999887
No 330
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=29.75 E-value=31 Score=17.83 Aligned_cols=16 Identities=31% Similarity=0.785 Sum_probs=6.7
Q ss_pred cCCCCCCcce---eeecCC
Q psy1204 49 KCEHCGSYNT---CRIKKP 64 (71)
Q Consensus 49 kCp~C~Synt---~ii~g~ 64 (71)
.|.+||...+ ++++|+
T Consensus 3 ~CSFCgr~~~~v~~li~g~ 21 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGP 21 (41)
T ss_dssp B-TTT--BTTTSSSEEEES
T ss_pred CccCCCCCHHHHhceecCC
Confidence 5666665543 444444
No 331
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=29.73 E-value=36 Score=20.97 Aligned_cols=13 Identities=31% Similarity=0.598 Sum_probs=7.2
Q ss_pred cCCCCCCcceeee
Q psy1204 49 KCEHCGSYNTCRI 61 (71)
Q Consensus 49 kCp~C~Synt~ii 61 (71)
.||+|+...++-.
T Consensus 38 ~CpfCgk~~vkR~ 50 (90)
T PTZ00255 38 FCPFCGKHAVKRQ 50 (90)
T ss_pred cCCCCCCCceeee
Confidence 6666665554433
No 332
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=29.72 E-value=22 Score=17.95 Aligned_cols=24 Identities=33% Similarity=0.729 Sum_probs=14.6
Q ss_pred EEcCCCCCceeeceEeecccCCCCC
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCG 54 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~ 54 (71)
.+|..|++..... ...+++|+.|+
T Consensus 12 ~~C~~C~~~i~~~-~~~~~~C~~C~ 35 (50)
T cd00029 12 TFCDVCRKSIWGL-FKQGLRCSWCK 35 (50)
T ss_pred CChhhcchhhhcc-ccceeEcCCCC
Confidence 4588887765432 23445888774
No 333
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=29.37 E-value=54 Score=18.23 Aligned_cols=11 Identities=27% Similarity=0.839 Sum_probs=4.4
Q ss_pred cCCCCCCccee
Q psy1204 49 KCEHCGSYNTC 59 (71)
Q Consensus 49 kCp~C~Synt~ 59 (71)
.|+.|+..-..
T Consensus 43 ~C~~C~G~G~~ 53 (66)
T PF00684_consen 43 TCPKCGGTGKI 53 (66)
T ss_dssp E-TTTSSSSEE
T ss_pred ECCCCcceeeE
Confidence 44555444333
No 334
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=29.06 E-value=40 Score=19.24 Aligned_cols=26 Identities=19% Similarity=0.255 Sum_probs=18.2
Q ss_pred hcceeeEEcCCCCCceeec---eEeecccCCCCC
Q psy1204 24 KNVILYVLCKDCHKESKVL---YHIIGLKCEHCG 54 (71)
Q Consensus 24 ~~~~v~i~CndC~~~s~v~---~h~~g~kCp~C~ 54 (71)
..++|+.+| |+.|.+. .-+- .||.|.
T Consensus 23 ~G~pVvALC---Gk~wvp~rdp~~~P--VCP~Ck 51 (58)
T PF11238_consen 23 MGTPVVALC---GKVWVPTRDPKPFP--VCPECK 51 (58)
T ss_pred cCceeEeee---CceeCCCCCCCCCC--CCcCHH
Confidence 466889887 9888652 2333 899885
No 335
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=28.75 E-value=1.4e+02 Score=23.38 Aligned_cols=42 Identities=26% Similarity=0.656 Sum_probs=28.1
Q ss_pred CCCCHhhhcceeeEEcCCCCCcee--ece----EeecccCCCCCCcceeeec
Q psy1204 17 TPMPEEYKNVILYVLCKDCHKESK--VLY----HIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 17 ~pmP~~y~~~~v~i~CndC~~~s~--v~~----h~~g~kCp~C~Synt~ii~ 62 (71)
.+.|+.| .|....|..||+..+ +.+ ..-| .|. ||...+.-+.
T Consensus 158 ~~~~~~~--~P~~pic~~cGrv~~~~~~~~~~~~v~Y-~c~-cG~~g~~~~~ 205 (515)
T TIGR00467 158 SKLEENW--YPISVFCENCGRDTTTVNNYDNEYSIEY-SCE-CGNQESVDIY 205 (515)
T ss_pred CccCCCc--eeeeeecCCcCccCceEEEecCCceEEE-EcC-CCCEEEEeec
Confidence 3667776 489999999998753 211 1223 784 8888877553
No 336
>PLN02294 cytochrome c oxidase subunit Vb
Probab=28.72 E-value=53 Score=22.57 Aligned_cols=21 Identities=24% Similarity=0.619 Sum_probs=16.7
Q ss_pred cCCCCCCcceeeecCCCCCCC
Q psy1204 49 KCEHCGSYNTCRIKKPNGQES 69 (71)
Q Consensus 49 kCp~C~Synt~ii~g~~~~~~ 69 (71)
.||.||+|-.-..-|++++.-
T Consensus 143 RCpeCG~~fkL~~vG~~~~~~ 163 (174)
T PLN02294 143 ECPVCTQYFELEVVGPGGPPD 163 (174)
T ss_pred eCCCCCCEEEEEEeCCCCCCC
Confidence 699999998888777777643
No 337
>KOG4739|consensus
Probab=28.57 E-value=27 Score=24.94 Aligned_cols=13 Identities=23% Similarity=0.419 Sum_probs=9.0
Q ss_pred cCCCCCCcceeeec
Q psy1204 49 KCEHCGSYNTCRIK 62 (71)
Q Consensus 49 kCp~C~Synt~ii~ 62 (71)
.|+.|+.+ ++++.
T Consensus 39 ~C~lCkk~-ir~i~ 51 (233)
T KOG4739|consen 39 VCPLCKKS-IRIIQ 51 (233)
T ss_pred ccccccce-eeeee
Confidence 56778777 77664
No 338
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=28.36 E-value=30 Score=18.88 Aligned_cols=14 Identities=14% Similarity=0.342 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHcC
Q psy1204 4 TPLWRQMDEEIAST 17 (71)
Q Consensus 4 ~~~~~~lD~~i~~~ 17 (71)
+..|..||.+|+..
T Consensus 34 ~~Nf~~lD~li~~l 47 (49)
T PF07535_consen 34 DSNFKELDSLISQL 47 (49)
T ss_pred cccHHHHHHHHHHh
Confidence 46799999999864
No 339
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=28.25 E-value=34 Score=25.63 Aligned_cols=34 Identities=24% Similarity=0.419 Sum_probs=18.6
Q ss_pred cceeeEEcCCCCCceeece-EeecccCCCCCCcce
Q psy1204 25 NVILYVLCKDCHKESKVLY-HIIGLKCEHCGSYNT 58 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v~~-h~~g~kCp~C~Synt 58 (71)
+.--+.+|..|+....... ..+..+|+.|++.-+
T Consensus 236 ~~G~v~~C~~C~~~~~~~~~~~~~~~c~~cg~~~~ 270 (377)
T PF02005_consen 236 KLGYVYYCPSCGYREEVKGLQKLKSKCPECGSKLH 270 (377)
T ss_dssp TEEEEEEETTT--EECCT-GCC--CEETTT-SCCC
T ss_pred heeEEEECCCccccccccCccccCCcCCCCCCccc
Confidence 3456899999986544332 221248999988543
No 340
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=28.23 E-value=35 Score=16.69 Aligned_cols=11 Identities=36% Similarity=0.715 Sum_probs=9.1
Q ss_pred EcCCCCCceee
Q psy1204 31 LCKDCHKESKV 41 (71)
Q Consensus 31 ~CndC~~~s~v 41 (71)
-|-||++.|..
T Consensus 2 sCiDC~~~F~~ 12 (28)
T PF08790_consen 2 SCIDCSKDFDG 12 (28)
T ss_dssp EETTTTEEEEG
T ss_pred eeecCCCCcCc
Confidence 58999999964
No 341
>PRK12577 succinate dehydrogenase iron-sulfur subunit; Provisional
Probab=28.08 E-value=27 Score=25.46 Aligned_cols=12 Identities=25% Similarity=1.010 Sum_probs=10.7
Q ss_pred CChHHHHHHHHH
Q psy1204 1 MDMTPLWRQMDE 12 (71)
Q Consensus 1 ~dm~~~~~~lD~ 12 (71)
+||+..|++|.+
T Consensus 110 VD~~~~~~k~~~ 121 (329)
T PRK12577 110 VDMSSFWQNLEA 121 (329)
T ss_pred eccHHHHHHHHh
Confidence 699999999977
No 342
>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=28.06 E-value=42 Score=19.48 Aligned_cols=30 Identities=23% Similarity=0.508 Sum_probs=15.2
Q ss_pred eeEEcCCCCCceee--------ceEeecccCCCCCCcce
Q psy1204 28 LYVLCKDCHKESKV--------LYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 28 v~i~CndC~~~s~v--------~~h~~g~kCp~C~Synt 58 (71)
+...|+.|+.++.- ..-.+ .+||.|++...
T Consensus 3 l~FTC~~C~~Rs~~~~sk~aY~~GvVi-v~C~gC~~~Hl 40 (66)
T PF05180_consen 3 LTFTCNKCGTRSAKMFSKQAYHKGVVI-VQCPGCKNRHL 40 (66)
T ss_dssp EEEEETTTTEEEEEEEEHHHHHTSEEE-EE-TTS--EEE
T ss_pred EEEEcCCCCCccceeeCHHHHhCCeEE-EECCCCcceee
Confidence 45678888866642 11122 27888876543
No 343
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=27.87 E-value=58 Score=24.34 Aligned_cols=30 Identities=20% Similarity=0.370 Sum_probs=19.5
Q ss_pred ceeeEEcCCCCCceeece-EeecccCCCCCC
Q psy1204 26 VILYVLCKDCHKESKVLY-HIIGLKCEHCGS 55 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v~~-h~~g~kCp~C~S 55 (71)
.-.+.+|..|+....+.. -.....|+.|++
T Consensus 230 ~g~v~~C~~c~~~~~~~~~~~~~~~C~~c~~ 260 (374)
T TIGR00308 230 TGYTYHCSRCLHNKPVNGISQRKGRCKECGG 260 (374)
T ss_pred ceeEEECCCcccccccccccCCCCCCCCCCC
Confidence 345788999987655431 111237999987
No 344
>KOG3352|consensus
Probab=27.79 E-value=47 Score=22.39 Aligned_cols=44 Identities=27% Similarity=0.583 Sum_probs=28.7
Q ss_pred CHhhhcceeeEEcCCCCCce-eeceEeec----ccCCCCCCcceeeecCCCC
Q psy1204 20 PEEYKNVILYVLCKDCHKES-KVLYHIIG----LKCEHCGSYNTCRIKKPNG 66 (71)
Q Consensus 20 P~~y~~~~v~i~CndC~~~s-~v~~h~~g----~kCp~C~Synt~ii~g~~~ 66 (71)
|..|. +-++=| -|..-+ .|.+.|+. .+||.||+|---+..|..+
T Consensus 104 ~S~~d--~RiVGC-~c~eD~~~V~Wmwl~Kge~~rc~eCG~~fkL~~v~~~~ 152 (153)
T KOG3352|consen 104 PSYYD--KRIVGC-GCEEDSHAVVWMWLEKGETQRCPECGHYFKLVPVGPVN 152 (153)
T ss_pred cccCC--ceEEee-cccCCCcceEEEEEEcCCcccCCcccceEEeeecCCCC
Confidence 44443 346667 777655 35665653 3699999998877766654
No 345
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=27.76 E-value=41 Score=20.77 Aligned_cols=12 Identities=33% Similarity=0.769 Sum_probs=6.6
Q ss_pred cCCCCCCcceee
Q psy1204 49 KCEHCGSYNTCR 60 (71)
Q Consensus 49 kCp~C~Synt~i 60 (71)
.||+|+...++.
T Consensus 37 ~CpfCgk~~vkR 48 (91)
T TIGR00280 37 VCPFCGKKTVKR 48 (91)
T ss_pred cCCCCCCCceEE
Confidence 666665554443
No 346
>PRK10954 periplasmic protein disulfide isomerase I; Provisional
Probab=27.76 E-value=28 Score=23.25 Aligned_cols=21 Identities=14% Similarity=0.469 Sum_probs=15.4
Q ss_pred CCceeeceEeecccCCCCCCcce
Q psy1204 36 HKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 36 ~~~s~v~~h~~g~kCp~C~Synt 58 (71)
++...+.|..| .||+|..++.
T Consensus 37 ~~~~VvEffdy--~CphC~~~~~ 57 (207)
T PRK10954 37 GEPQVLEFFSF--YCPHCYQFEE 57 (207)
T ss_pred CCCeEEEEeCC--CCccHHHhcc
Confidence 34445667777 9999998876
No 347
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=27.44 E-value=26 Score=25.08 Aligned_cols=13 Identities=23% Similarity=0.534 Sum_probs=9.5
Q ss_pred eeEEcCCCCCcee
Q psy1204 28 LYVLCKDCHKESK 40 (71)
Q Consensus 28 v~i~CndC~~~s~ 40 (71)
-...|.+|+.++.
T Consensus 136 ~~~~C~~C~~~~~ 148 (271)
T PTZ00409 136 FEARCCTCRKTIQ 148 (271)
T ss_pred CcceeCCCCCCcc
Confidence 3567999987665
No 348
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=26.98 E-value=54 Score=23.08 Aligned_cols=16 Identities=19% Similarity=0.112 Sum_probs=11.3
Q ss_pred eeEEcCCCCCceeece
Q psy1204 28 LYVLCKDCHKESKVLY 43 (71)
Q Consensus 28 v~i~CndC~~~s~v~~ 43 (71)
..+.|+.||.-+.-..
T Consensus 171 ~~v~C~kCGE~~~e~~ 186 (206)
T COG2191 171 GSVRCSKCGELFMEPR 186 (206)
T ss_pred ceeeccccCcccccch
Confidence 3478999998775443
No 349
>PF15389 DUF4612: Domain of unknown function (DUF4612)
Probab=26.96 E-value=52 Score=21.15 Aligned_cols=13 Identities=31% Similarity=0.613 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHcC
Q psy1204 5 PLWRQMDEEIAST 17 (71)
Q Consensus 5 ~~~~~lD~~i~~~ 17 (71)
..||+||+-|+.=
T Consensus 93 dFFRMLDeKIekG 105 (115)
T PF15389_consen 93 DFFRMLDEKIEKG 105 (115)
T ss_pred HHHHHHHHHHHcC
Confidence 4899999998763
No 350
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=26.58 E-value=44 Score=20.55 Aligned_cols=13 Identities=31% Similarity=0.715 Sum_probs=7.3
Q ss_pred cCCCCCCcceeee
Q psy1204 49 KCEHCGSYNTCRI 61 (71)
Q Consensus 49 kCp~C~Synt~ii 61 (71)
.||+|+...++..
T Consensus 38 ~CpfCgk~~vkR~ 50 (90)
T PRK03976 38 VCPVCGRPKVKRV 50 (90)
T ss_pred cCCCCCCCceEEE
Confidence 6666665555443
No 351
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=26.46 E-value=2e+02 Score=21.50 Aligned_cols=43 Identities=30% Similarity=0.692 Sum_probs=27.2
Q ss_pred cCCCCHhhhcceeeEEcCCCCCcee-e-ceE-----eecccCCCCCCcceeeec
Q psy1204 16 STPMPEEYKNVILYVLCKDCHKESK-V-LYH-----IIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 16 ~~pmP~~y~~~~v~i~CndC~~~s~-v-~~h-----~~g~kCp~C~Synt~ii~ 62 (71)
..+.|+.| .|....|..||.-.+ + .+. .-| .|. ||...+.-+.
T Consensus 158 ~~~~~~~~--~P~~p~c~~cg~~~~~v~~~d~~~~~v~y-~c~-cG~~g~~~~~ 207 (353)
T cd00674 158 GRELQETW--YPFMPYCEKCGKDTTTVEAYDAKAGTVTY-KCE-CGHEETVDIR 207 (353)
T ss_pred CCccCCCc--eeeeeecCCcCcceeEEEEEeCCCCeEEE-EcC-CCCEEEEeec
Confidence 34667776 489999999995432 2 111 222 784 8887777553
No 352
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=26.40 E-value=67 Score=15.59 Aligned_cols=12 Identities=42% Similarity=0.830 Sum_probs=5.8
Q ss_pred cCCCCCCcceee
Q psy1204 49 KCEHCGSYNTCR 60 (71)
Q Consensus 49 kCp~C~Synt~i 60 (71)
+|..||..=..+
T Consensus 6 kC~~CGniv~v~ 17 (34)
T cd00974 6 KCEICGNIVEVL 17 (34)
T ss_pred EcCCCCcEEEEE
Confidence 555555444333
No 353
>PF10686 DUF2493: Protein of unknown function (DUF2493); InterPro: IPR019627 This entry is represented by Mycobacteriophage D29, Gp61. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family are mainly Proteobacteria. The function is not known.
Probab=26.34 E-value=71 Score=18.31 Aligned_cols=17 Identities=29% Similarity=0.614 Sum_probs=14.2
Q ss_pred ChHHHHHHHHHHHHcCC
Q psy1204 2 DMTPLWRQMDEEIASTP 18 (71)
Q Consensus 2 dm~~~~~~lD~~i~~~p 18 (71)
|-..+|..||+..+..|
T Consensus 16 D~~~i~~~Ld~~~~~~~ 32 (71)
T PF10686_consen 16 DHELIWAALDKVHARHP 32 (71)
T ss_pred cHHHHHHHHHHHHHhCC
Confidence 55779999999988875
No 354
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=25.86 E-value=57 Score=16.09 Aligned_cols=12 Identities=33% Similarity=0.908 Sum_probs=9.6
Q ss_pred ceeeEEcCCCCC
Q psy1204 26 VILYVLCKDCHK 37 (71)
Q Consensus 26 ~~v~i~CndC~~ 37 (71)
.++.++|.+|+.
T Consensus 12 ~~~~~~C~~C~~ 23 (42)
T PF00643_consen 12 EPLSLFCEDCNE 23 (42)
T ss_dssp SBEEEEETTTTE
T ss_pred cceEEEecCCCC
Confidence 458999999974
No 355
>PHA02611 51 baseplate hub assembly protein; Provisional
Probab=25.61 E-value=71 Score=23.10 Aligned_cols=17 Identities=35% Similarity=0.767 Sum_probs=10.4
Q ss_pred eeeEEcCCCCCceeece
Q psy1204 27 ILYVLCKDCHKESKVLY 43 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~ 43 (71)
++.+.|.+||++..+.+
T Consensus 80 ~~~~tCp~Cg~e~~v~~ 96 (249)
T PHA02611 80 PVTFTCPKCKKEKTVLF 96 (249)
T ss_pred eEEEECCCCCCceeEEE
Confidence 45566777776655543
No 356
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=25.60 E-value=48 Score=17.18 Aligned_cols=22 Identities=23% Similarity=0.754 Sum_probs=12.9
Q ss_pred cCCCCCceeeceEeecccCCCCCCcce
Q psy1204 32 CKDCHKESKVLYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 32 CndC~~~s~v~~h~~g~kCp~C~Synt 58 (71)
|+.|.... ...+ +|..|..|+.
T Consensus 3 C~~C~~~~---~~r~--~C~~C~dfDL 24 (41)
T cd02337 3 CNECKHHV---ETRW--HCTVCEDYDL 24 (41)
T ss_pred CCCCCCcC---CCce--ECCCCcchhh
Confidence 77786622 2233 7777766654
No 357
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=25.58 E-value=59 Score=23.61 Aligned_cols=10 Identities=20% Similarity=0.823 Sum_probs=2.9
Q ss_pred eEEcCCCCCc
Q psy1204 29 YVLCKDCHKE 38 (71)
Q Consensus 29 ~i~CndC~~~ 38 (71)
.++|..||..
T Consensus 31 n~yCP~Cg~~ 40 (254)
T PF06044_consen 31 NMYCPNCGSK 40 (254)
T ss_dssp H---TTT--S
T ss_pred CCcCCCCCCh
Confidence 4566666654
No 358
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=25.57 E-value=37 Score=25.44 Aligned_cols=31 Identities=19% Similarity=0.450 Sum_probs=19.3
Q ss_pred cceeeEEcCCCCCceeeceEe------ecccCCCCCC
Q psy1204 25 NVILYVLCKDCHKESKVLYHI------IGLKCEHCGS 55 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v~~h~------~g~kCp~C~S 55 (71)
...-...|..|+........+ -.-+||.|++
T Consensus 143 Gsl~~~~C~~C~~~~~~~~~~~~~~~~~vP~C~~CgG 179 (349)
T PTZ00410 143 GSFSAASCIECHTPYDIEQAYLEARSGKVPHCSTCGG 179 (349)
T ss_pred cCCCeeEeCCCCCCcchhHHHHHhhcCCCCCCCCCCC
Confidence 344567899999766533211 0127999987
No 359
>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=25.34 E-value=29 Score=18.57 Aligned_cols=8 Identities=38% Similarity=0.879 Sum_probs=3.6
Q ss_pred cCCCCCCc
Q psy1204 49 KCEHCGSY 56 (71)
Q Consensus 49 kCp~C~Sy 56 (71)
+||-|++.
T Consensus 22 ~CPlC~r~ 29 (54)
T PF04423_consen 22 CCPLCGRP 29 (54)
T ss_dssp E-TTT--E
T ss_pred cCCCCCCC
Confidence 78888764
No 360
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=25.32 E-value=72 Score=15.44 Aligned_cols=9 Identities=56% Similarity=1.198 Sum_probs=4.4
Q ss_pred cCCCCCCcc
Q psy1204 49 KCEHCGSYN 57 (71)
Q Consensus 49 kCp~C~Syn 57 (71)
+|..||..=
T Consensus 9 kC~~Cgniv 17 (34)
T TIGR00319 9 KCEVCGNIV 17 (34)
T ss_pred EcCCCCcEE
Confidence 555554443
No 361
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=25.26 E-value=55 Score=16.72 Aligned_cols=10 Identities=20% Similarity=0.597 Sum_probs=5.3
Q ss_pred EEcCCCCCce
Q psy1204 30 VLCKDCHKES 39 (71)
Q Consensus 30 i~CndC~~~s 39 (71)
+.|..|+..|
T Consensus 13 f~C~~C~~~F 22 (39)
T smart00154 13 FKCRHCGNLF 22 (39)
T ss_pred eECCccCCcc
Confidence 4455555544
No 362
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=24.93 E-value=41 Score=24.37 Aligned_cols=26 Identities=23% Similarity=0.616 Sum_probs=18.3
Q ss_pred eEEcCCCCCceeec---eEeecccCCCCC
Q psy1204 29 YVLCKDCHKESKVL---YHIIGLKCEHCG 54 (71)
Q Consensus 29 ~i~CndC~~~s~v~---~h~~g~kCp~C~ 54 (71)
.-.|..||+...+. .+.|..||..|.
T Consensus 220 ~r~CP~Cg~~W~L~~plh~iFdFKCD~CR 248 (258)
T PF10071_consen 220 ARKCPSCGGDWRLKEPLHDIFDFKCDPCR 248 (258)
T ss_pred CCCCCCCCCccccCCchhhceeccCCcce
Confidence 45799999988643 244455999994
No 363
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=24.67 E-value=47 Score=16.47 Aligned_cols=10 Identities=40% Similarity=1.022 Sum_probs=5.5
Q ss_pred ecccCCCCCC
Q psy1204 46 IGLKCEHCGS 55 (71)
Q Consensus 46 ~g~kCp~C~S 55 (71)
-+..|+.||.
T Consensus 31 p~~~C~~CGE 40 (46)
T TIGR03831 31 PALVCPQCGE 40 (46)
T ss_pred CccccccCCC
Confidence 3346666653
No 364
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=24.56 E-value=57 Score=18.70 Aligned_cols=30 Identities=13% Similarity=0.306 Sum_probs=19.4
Q ss_pred cceeeEEcCCCCCceeeceEeec---ccCCCCC
Q psy1204 25 NVILYVLCKDCHKESKVLYHIIG---LKCEHCG 54 (71)
Q Consensus 25 ~~~v~i~CndC~~~s~v~~h~~g---~kCp~C~ 54 (71)
..|+.|.|.-=|..+...++.+- +-||.|+
T Consensus 28 ~~PvtI~CP~HG~~~~s~~~~~~~sk~GCP~Cg 60 (60)
T PF05265_consen 28 ATPVTIRCPKHGNFTCSTFNSFIKSKHGCPECG 60 (60)
T ss_pred CCceEEECCCCCcEEeccHHhhhhhccCCCCCC
Confidence 34899999888776665543331 1378775
No 365
>KOG2593|consensus
Probab=24.46 E-value=48 Score=25.79 Aligned_cols=46 Identities=15% Similarity=0.288 Sum_probs=28.4
Q ss_pred HHHHHHHcCCCCHhhhcceeeEEcCCCCCceee-------ce--EeecccCCCCCCc
Q psy1204 9 QMDEEIASTPMPEEYKNVILYVLCKDCHKESKV-------LY--HIIGLKCEHCGSY 56 (71)
Q Consensus 9 ~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v-------~~--h~~g~kCp~C~Sy 56 (71)
+||+..+...==..-.....-..|..|+++++. .. -.| .|..|++.
T Consensus 108 Klh~m~krled~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F--~C~~C~ge 162 (436)
T KOG2593|consen 108 KLHQMRKRLEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLDNETGEF--HCENCGGE 162 (436)
T ss_pred HHHHHHHHHHHHhhhccccccccCCccccchhhhHHHHhhcccCceE--EEecCCCc
Confidence 566666554422222233567889999999752 11 244 89999764
No 366
>PRK00528 rpmE 50S ribosomal protein L31; Reviewed
Probab=24.15 E-value=1.5e+02 Score=17.17 Aligned_cols=35 Identities=11% Similarity=-0.003 Sum_probs=22.1
Q ss_pred CCHhhhcceeeEEcCCCCCceeec---------eEeecccCCCCCCcce
Q psy1204 19 MPEEYKNVILYVLCKDCHKESKVL---------YHIIGLKCEHCGSYNT 58 (71)
Q Consensus 19 mP~~y~~~~v~i~CndC~~~s~v~---------~h~~g~kCp~C~Synt 58 (71)
+.++|+. +.+.|. ||.++.+. .+.- .|+.|..+=|
T Consensus 5 IHP~y~~--v~~~~~-~g~~f~~~ST~g~~~~~i~vd--v~s~~HPfyT 48 (71)
T PRK00528 5 IHPDYHP--IKVVMT-DGTEYETRSTWGKTGPELRLD--IDSGNHPAWT 48 (71)
T ss_pred CCCCCEE--EEEEEe-CCCEEEEEEcCCCCCCeEEEE--ECCCCCccEe
Confidence 3456754 555665 89888644 2233 8888877666
No 367
>PHA00732 hypothetical protein
Probab=24.12 E-value=44 Score=19.69 Aligned_cols=9 Identities=22% Similarity=0.504 Sum_probs=4.6
Q ss_pred cCCCCCcee
Q psy1204 32 CKDCHKESK 40 (71)
Q Consensus 32 CndC~~~s~ 40 (71)
|..|++.|.
T Consensus 4 C~~Cgk~F~ 12 (79)
T PHA00732 4 CPICGFTTV 12 (79)
T ss_pred CCCCCCccC
Confidence 555555543
No 368
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=23.85 E-value=43 Score=19.25 Aligned_cols=25 Identities=20% Similarity=0.495 Sum_probs=19.5
Q ss_pred eeeEEcCCCCCceeeceEeecccCCC
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEH 52 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~ 52 (71)
.+...|.-|+..-+...|.+. .||.
T Consensus 57 ~~~~~C~~C~~~~Et~~Hlf~-~C~~ 81 (86)
T PF13966_consen 57 QVDPICPLCGNEEETIEHLFF-HCPF 81 (86)
T ss_pred ccCCccccCCCccccccceec-cCcC
Confidence 455689999988888888885 8875
No 369
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=23.77 E-value=31 Score=23.88 Aligned_cols=30 Identities=30% Similarity=0.599 Sum_probs=17.6
Q ss_pred EEcCCCCCce----eeceEeecccCCCCCCccee
Q psy1204 30 VLCKDCHKES----KVLYHIIGLKCEHCGSYNTC 59 (71)
Q Consensus 30 i~CndC~~~s----~v~~h~~g~kCp~C~Synt~ 59 (71)
-.|.+|-.+. +++.+.--..||.||+|-..
T Consensus 14 ~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 14 GLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIG 47 (236)
T ss_pred ccChHHhcccCCeeecCCccCceECCCCCCEECC
Confidence 4677776433 23332222389999988664
No 370
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=23.57 E-value=44 Score=23.41 Aligned_cols=28 Identities=21% Similarity=0.413 Sum_probs=17.4
Q ss_pred eeeEEcCCCCCceeeceEe--ecccCCCCC
Q psy1204 27 ILYVLCKDCHKESKVLYHI--IGLKCEHCG 54 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~--~g~kCp~C~ 54 (71)
.-...|..|+..+...... ..-+||.|+
T Consensus 115 ~~~~~C~~C~~~~~~~~~~~~~~p~C~~Cg 144 (242)
T PTZ00408 115 LLKVRCTATGHVFDWTEDVVHGSSRCKCCG 144 (242)
T ss_pred cceEEECCCCcccCchhhhhcCCCccccCC
Confidence 3457899999876543211 113799996
No 371
>PF04808 CTV_P23: Citrus tristeza virus (CTV) P23 protein ; InterPro: IPR006893 This family of proteins contains p23 from the citrus tristeza virus, which is a member of the Closteroviridae. CTV produces more positive than negative RNA strands, and p23 controls this asymmetrical RNA accumulation. Amino acids 42-180 are essential for function and are thought to contain RNA-binding and zinc finger domains [].
Probab=23.48 E-value=67 Score=21.85 Aligned_cols=33 Identities=18% Similarity=0.402 Sum_probs=20.9
Q ss_pred HHHHHHHcCCCCHh-hhcceeeEEcCCCCCceeec
Q psy1204 9 QMDEEIASTPMPEE-YKNVILYVLCKDCHKESKVL 42 (71)
Q Consensus 9 ~lD~~i~~~pmP~~-y~~~~v~i~CndC~~~s~v~ 42 (71)
.+|++|..+.-.-. |+ ...+..|-|||.+-.-.
T Consensus 45 iidalirktsyqgarfr-ariigvcvdcgrkhdka 78 (209)
T PF04808_consen 45 IIDALIRKTSYQGARFR-ARIIGVCVDCGRKHDKA 78 (209)
T ss_pred HHHHHHHhcccccceee-eeeEEEeeccccccccc
Confidence 36777766553332 33 35678899999876543
No 372
>PRK13552 frdB fumarate reductase iron-sulfur subunit; Provisional
Probab=23.48 E-value=68 Score=22.42 Aligned_cols=12 Identities=25% Similarity=0.534 Sum_probs=10.0
Q ss_pred CChHHHHHHHHH
Q psy1204 1 MDMTPLWRQMDE 12 (71)
Q Consensus 1 ~dm~~~~~~lD~ 12 (71)
+||+.+|++|.+
T Consensus 105 VD~~~~~~~~~~ 116 (239)
T PRK13552 105 VNTGKWFREMSE 116 (239)
T ss_pred cccHHHHHHHHH
Confidence 699999999943
No 373
>cd02663 Peptidase_C19G A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=23.27 E-value=1.9e+02 Score=20.15 Aligned_cols=22 Identities=14% Similarity=0.184 Sum_probs=14.8
Q ss_pred hhhcc-eeeEEcCCCCCceeece
Q psy1204 22 EYKNV-ILYVLCKDCHKESKVLY 43 (71)
Q Consensus 22 ~y~~~-~v~i~CndC~~~s~v~~ 43 (71)
.|..+ ...+.|..|+..+...+
T Consensus 112 ~F~G~~~~~~~C~~C~~~s~~~e 134 (300)
T cd02663 112 IFQGILTNETRCLTCETVSSRDE 134 (300)
T ss_pred hCceEEEeeEEeCCCCCCccccc
Confidence 34443 45789999998775543
No 374
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=23.20 E-value=42 Score=15.34 Aligned_cols=11 Identities=27% Similarity=0.477 Sum_probs=8.2
Q ss_pred EEcCCCCCcee
Q psy1204 30 VLCKDCHKESK 40 (71)
Q Consensus 30 i~CndC~~~s~ 40 (71)
..|..|++.|.
T Consensus 15 ~~C~~C~k~F~ 25 (26)
T PF13465_consen 15 YKCPYCGKSFS 25 (26)
T ss_dssp EEESSSSEEES
T ss_pred CCCCCCcCeeC
Confidence 67888887663
No 375
>smart00355 ZnF_C2H2 zinc finger.
Probab=23.16 E-value=38 Score=14.05 Aligned_cols=11 Identities=36% Similarity=0.673 Sum_probs=8.0
Q ss_pred EcCCCCCceee
Q psy1204 31 LCKDCHKESKV 41 (71)
Q Consensus 31 ~CndC~~~s~v 41 (71)
.|..|++.|..
T Consensus 2 ~C~~C~~~f~~ 12 (26)
T smart00355 2 RCPECGKVFKS 12 (26)
T ss_pred CCCCCcchhCC
Confidence 48888887754
No 376
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=23.04 E-value=53 Score=23.06 Aligned_cols=37 Identities=24% Similarity=0.511 Sum_probs=26.0
Q ss_pred CCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204 18 PMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI 61 (71)
Q Consensus 18 pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii 61 (71)
.||..|.+ .-...|.+|+ ++- ++-.|+.|||--+.+.
T Consensus 4 k~~~~~gk-~~iyWCe~cN----lPl--~~~~c~~cg~~~~~l~ 40 (202)
T COG5270 4 KMPVVLGK-FPIYWCEKCN----LPL--LGRRCSVCGSKVEELR 40 (202)
T ss_pred ccceeecc-cceeehhhCC----Ccc--ccccccccCCcceEEE
Confidence 37777754 5678899997 443 3449999997766654
No 377
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=23.01 E-value=45 Score=13.75 Aligned_cols=11 Identities=27% Similarity=0.543 Sum_probs=5.7
Q ss_pred EcCCCCCceee
Q psy1204 31 LCKDCHKESKV 41 (71)
Q Consensus 31 ~CndC~~~s~v 41 (71)
.|.-|++++..
T Consensus 2 ~C~~C~~~~~~ 12 (24)
T PF13894_consen 2 QCPICGKSFRS 12 (24)
T ss_dssp E-SSTS-EESS
T ss_pred CCcCCCCcCCc
Confidence 47777776653
No 378
>PF01930 Cas_Cas4: Domain of unknown function DUF83; InterPro: IPR022765 This entry represents an uncharacterised domain found in several proteins, including DNA replication helicase Dna2, clustered regularly interspaced short palindromic repeats (CRISPR)-associated exonuclease Cas4 and putative RecB family exonuclease proteins.
Probab=22.98 E-value=98 Score=19.52 Aligned_cols=30 Identities=17% Similarity=0.351 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCc
Q psy1204 5 PLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKE 38 (71)
Q Consensus 5 ~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~ 38 (71)
...+.+-+.++...+|+.- +.+ +|..|...
T Consensus 128 ~~i~~i~~~~~~~~~P~~~-~~~---~C~~C~y~ 157 (162)
T PF01930_consen 128 KLIEEIRKILEGESPPPPE-NSK---KCRRCSYR 157 (162)
T ss_pred HHHHHHHHHHhCCCcCCCC-CCC---CCCCCCCc
Confidence 4556677777777667653 222 89999753
No 379
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.97 E-value=40 Score=21.63 Aligned_cols=9 Identities=33% Similarity=0.881 Sum_probs=7.6
Q ss_pred cCCCCCCcc
Q psy1204 49 KCEHCGSYN 57 (71)
Q Consensus 49 kCp~C~Syn 57 (71)
+||+||+.-
T Consensus 51 ~CP~Cg~~~ 59 (115)
T COG1885 51 SCPKCGEPF 59 (115)
T ss_pred cCCCCCCcc
Confidence 899999864
No 380
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=22.91 E-value=59 Score=26.02 Aligned_cols=31 Identities=19% Similarity=0.493 Sum_probs=21.2
Q ss_pred eeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204 27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK 62 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~ 62 (71)
-..-.|++||..-+.+-. -.| .||| ++.+..
T Consensus 128 va~w~c~~cg~~iean~k---p~c-~cg~-~~~~~e 158 (593)
T COG2401 128 VALWRCEKCGTIIEANTK---PEC-KCGS-HVHILE 158 (593)
T ss_pred EEEEecchhchhhhhcCC---ccc-CCCC-ceEEEE
Confidence 346689999975444332 278 9999 777764
No 381
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=22.86 E-value=39 Score=24.34 Aligned_cols=27 Identities=22% Similarity=0.674 Sum_probs=15.9
Q ss_pred eEEcCCCCCceee-ceEeecccCCCCCC
Q psy1204 29 YVLCKDCHKESKV-LYHIIGLKCEHCGS 55 (71)
Q Consensus 29 ~i~CndC~~~s~v-~~h~~g~kCp~C~S 55 (71)
...|.+||....+ .+-.--..|..||-
T Consensus 11 ~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~ 38 (310)
T PRK00423 11 KLVCPECGSDKLIYDYERGEIVCADCGL 38 (310)
T ss_pred CCcCcCCCCCCeeEECCCCeEeecccCC
Confidence 3569999874332 22122238889987
No 382
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=22.85 E-value=41 Score=19.39 Aligned_cols=11 Identities=27% Similarity=0.984 Sum_probs=8.0
Q ss_pred eEeecccCCCCCC
Q psy1204 43 YHIIGLKCEHCGS 55 (71)
Q Consensus 43 ~h~~g~kCp~C~S 55 (71)
+.++ +||.|+-
T Consensus 15 E~~l--rCPRC~~ 25 (65)
T COG4049 15 EEFL--RCPRCGM 25 (65)
T ss_pred ceee--eCCchhH
Confidence 3456 9999974
No 383
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=22.83 E-value=58 Score=15.50 Aligned_cols=12 Identities=17% Similarity=0.310 Sum_probs=9.4
Q ss_pred ceeeEEcCCCCC
Q psy1204 26 VILYVLCKDCHK 37 (71)
Q Consensus 26 ~~v~i~CndC~~ 37 (71)
.++.++|.+|+.
T Consensus 9 ~~~~~fC~~~~~ 20 (39)
T cd00021 9 EPLSLFCETDRA 20 (39)
T ss_pred cceEEEeCccCh
Confidence 377889999874
No 384
>CHL00136 rpl31 ribosomal protein L31; Validated
Probab=22.62 E-value=1.5e+02 Score=17.16 Aligned_cols=37 Identities=14% Similarity=0.019 Sum_probs=22.7
Q ss_pred CCHhhhcceeeEEcCCCCCceee----ceEeecccCCCCCCcce
Q psy1204 19 MPEEYKNVILYVLCKDCHKESKV----LYHIIGLKCEHCGSYNT 58 (71)
Q Consensus 19 mP~~y~~~~v~i~CndC~~~s~v----~~h~~g~kCp~C~Synt 58 (71)
+.++|.. .+.+.| +|+..+++ +...+ -.|+.|.-+=|
T Consensus 6 IHP~y~~-~~~v~c-~~~~~~~~~ST~~~i~v-dv~s~~HPfyT 46 (68)
T CHL00136 6 IHPQWFP-ETKVYC-DGQLVMTVGSTKPELNV-DIWSGNHPFYT 46 (68)
T ss_pred CCCCcee-eEEEEE-cCCCEEEEeecCCCEEE-EeCCCCCccCc
Confidence 3456643 467789 59986653 33333 28888865544
No 385
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=22.54 E-value=69 Score=18.94 Aligned_cols=34 Identities=26% Similarity=0.349 Sum_probs=13.2
Q ss_pred eeeEEcCCCC-Cceee-----ceEeecccCCCCCC-cceee
Q psy1204 27 ILYVLCKDCH-KESKV-----LYHIIGLKCEHCGS-YNTCR 60 (71)
Q Consensus 27 ~v~i~CndC~-~~s~v-----~~h~~g~kCp~C~S-ynt~i 60 (71)
+-...|.-|+ ..+.. ..-...+.|..||- |.+.|
T Consensus 20 ~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i 60 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKI 60 (81)
T ss_dssp SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE-
T ss_pred CceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEcc
Confidence 4567788898 43321 11233448888864 44443
No 386
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.17 E-value=30 Score=23.05 Aligned_cols=14 Identities=14% Similarity=0.346 Sum_probs=10.8
Q ss_pred eeEEcCCCCCceee
Q psy1204 28 LYVLCKDCHKESKV 41 (71)
Q Consensus 28 v~i~CndC~~~s~v 41 (71)
.-.+|++||+.|.-
T Consensus 67 ~psfchncgs~fpw 80 (160)
T COG4306 67 PPSFCHNCGSRFPW 80 (160)
T ss_pred CcchhhcCCCCCCc
Confidence 34689999998863
No 387
>KOG4582|consensus
Probab=22.10 E-value=49 Score=23.78 Aligned_cols=48 Identities=27% Similarity=0.501 Sum_probs=27.7
Q ss_pred HHHHHHHcCCCCHhhh--cceeeEEcCCCCCceeeceEeecccCCCCCCccee
Q psy1204 9 QMDEEIASTPMPEEYK--NVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTC 59 (71)
Q Consensus 9 ~lD~~i~~~pmP~~y~--~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ 59 (71)
..+..+...|+=..+. .++..+-|..|+..- +..|.| ||..|-.|+.-
T Consensus 130 ~~~~~~~~~~~~~~~H~~~~~~~v~CD~C~~~~-IvG~Ry--KC~~C~dYDLC 179 (278)
T KOG4582|consen 130 LASLVITLNPVVGEMHPNISKLSVPCDNCGKPG-IVGARY--KCTVCPDYDLC 179 (278)
T ss_pred hhhhhhhcCCCccccCCCcccccccCCCccCCc-ccccee--eecCCCccchh
Confidence 3445555555422221 112258999998633 344566 89888888753
No 388
>smart00336 BBOX B-Box-type zinc finger.
Probab=21.85 E-value=72 Score=15.36 Aligned_cols=12 Identities=17% Similarity=0.523 Sum_probs=9.4
Q ss_pred ceeeEEcCCCCC
Q psy1204 26 VILYVLCKDCHK 37 (71)
Q Consensus 26 ~~v~i~CndC~~ 37 (71)
.++.++|.+|+.
T Consensus 12 ~~~~~~C~~c~~ 23 (42)
T smart00336 12 EPAEFFCEECGA 23 (42)
T ss_pred CceEEECCCCCc
Confidence 567889988874
No 389
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=21.70 E-value=71 Score=19.23 Aligned_cols=19 Identities=16% Similarity=0.216 Sum_probs=10.1
Q ss_pred CCceeeceEeecccCCCCCCc
Q psy1204 36 HKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 36 ~~~s~v~~h~~g~kCp~C~Sy 56 (71)
|....+....+ .|+.||..
T Consensus 22 G~~~~v~~~~~--~C~~CGe~ 40 (127)
T TIGR03830 22 GESITIGVPGW--YCPACGEE 40 (127)
T ss_pred CEEEEEeeeee--ECCCCCCE
Confidence 33344433333 78888764
No 390
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=21.61 E-value=35 Score=24.39 Aligned_cols=25 Identities=28% Similarity=0.643 Sum_probs=16.0
Q ss_pred EcCCCCCceee--------ceEeecccCCCCCCcc
Q psy1204 31 LCKDCHKESKV--------LYHIIGLKCEHCGSYN 57 (71)
Q Consensus 31 ~CndC~~~s~v--------~~h~~g~kCp~C~Syn 57 (71)
.|..|+-+=+. ..... .||+||.+=
T Consensus 199 ~C~GC~m~l~~~~~~~V~~~d~iv--~CP~CgRIL 231 (239)
T COG1579 199 VCGGCHMKLPSQTLSKVRKKDEIV--FCPYCGRIL 231 (239)
T ss_pred cccCCeeeecHHHHHHHhcCCCCc--cCCccchHH
Confidence 57778743321 33455 899999864
No 391
>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=21.53 E-value=48 Score=17.03 Aligned_cols=13 Identities=31% Similarity=0.899 Sum_probs=9.1
Q ss_pred cCCCCCCcceeee
Q psy1204 49 KCEHCGSYNTCRI 61 (71)
Q Consensus 49 kCp~C~Synt~ii 61 (71)
-||.|++-+--..
T Consensus 5 pCP~CGG~DrFr~ 17 (37)
T smart00778 5 PCPNCGGSDRFRF 17 (37)
T ss_pred CCCCCCCcccccc
Confidence 7999988654433
No 392
>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=21.41 E-value=44 Score=17.44 Aligned_cols=12 Identities=33% Similarity=0.847 Sum_probs=6.9
Q ss_pred cCCCCCCcceee
Q psy1204 49 KCEHCGSYNTCR 60 (71)
Q Consensus 49 kCp~C~Synt~i 60 (71)
.||.|++-+--.
T Consensus 5 pCP~CGG~DrFr 16 (40)
T PF08273_consen 5 PCPICGGKDRFR 16 (40)
T ss_dssp --TTTT-TTTEE
T ss_pred CCCCCcCccccc
Confidence 799999876555
No 393
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=21.38 E-value=9.2 Score=19.66 Aligned_cols=6 Identities=50% Similarity=1.248 Sum_probs=4.1
Q ss_pred cCCCCC
Q psy1204 49 KCEHCG 54 (71)
Q Consensus 49 kCp~C~ 54 (71)
+||.|+
T Consensus 38 ~CP~C~ 43 (44)
T PF14634_consen 38 KCPICR 43 (44)
T ss_pred CCcCCC
Confidence 677765
No 394
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=21.32 E-value=56 Score=18.15 Aligned_cols=14 Identities=29% Similarity=0.645 Sum_probs=6.9
Q ss_pred cCCCCCCcceeeec
Q psy1204 49 KCEHCGSYNTCRIK 62 (71)
Q Consensus 49 kCp~C~Synt~ii~ 62 (71)
.||.|+..-++.+.
T Consensus 5 ~Cp~C~~~~~T~v~ 18 (67)
T smart00714 5 FCPRCQNNVTTRVE 18 (67)
T ss_pred ECCCCCCEEEEEEE
Confidence 45555554444443
No 395
>TIGR00105 L31 ribosomal protein L31. This family consists exclusively of bacterial (and organellar) 50S ribosomal protein L31. In some species, such as Bacillus subtilis, this protein exists in two forms (RpmE and YtiA), one of which (RpmE) contains a pair of motifs, CXC and CXXC, for binding zinc.
Probab=21.21 E-value=68 Score=18.42 Aligned_cols=34 Identities=18% Similarity=0.452 Sum_probs=19.9
Q ss_pred CCHhhhcceeeEEcCCCCCceeece------EeecccCCCCCCc
Q psy1204 19 MPEEYKNVILYVLCKDCHKESKVLY------HIIGLKCEHCGSY 56 (71)
Q Consensus 19 mP~~y~~~~v~i~CndC~~~s~v~~------h~~g~kCp~C~Sy 56 (71)
+.++|+ ++.+.|. ||.++.+.. ..+ -.|+.|.-+
T Consensus 5 IHP~y~--~v~~~~s-~g~~f~~~ST~~~~~i~v-di~s~~HPf 44 (68)
T TIGR00105 5 IHPDYH--EITVTCT-CGNVFTTRSTWGKETLNL-DICSKCHPF 44 (68)
T ss_pred CCCCCE--EEEEEEC-CCCEEEEeeecCCceEEE-EECCCCccc
Confidence 344575 4677785 999887422 122 158777443
No 396
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=21.19 E-value=51 Score=20.79 Aligned_cols=28 Identities=25% Similarity=0.552 Sum_probs=15.3
Q ss_pred eeeEEcC--CCCCceeece-EeecccCCCCCCc
Q psy1204 27 ILYVLCK--DCHKESKVLY-HIIGLKCEHCGSY 56 (71)
Q Consensus 27 ~v~i~Cn--dC~~~s~v~~-h~~g~kCp~C~Sy 56 (71)
..-.-|. .|+++-.... -.+ .|+.|+..
T Consensus 16 ~~Y~aC~~~~C~kKv~~~~~~~y--~C~~C~~~ 46 (146)
T PF08646_consen 16 WYYPACPNEKCNKKVTENGDGSY--RCEKCNKT 46 (146)
T ss_dssp TEEEE-TSTTTS-B-EEETTTEE--EETTTTEE
T ss_pred cEECCCCCccCCCEeecCCCcEE--ECCCCCCc
Confidence 3456788 8888754331 133 78888755
No 397
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=21.10 E-value=47 Score=18.90 Aligned_cols=14 Identities=21% Similarity=0.586 Sum_probs=9.7
Q ss_pred eecccCCCCCCcce
Q psy1204 45 IIGLKCEHCGSYNT 58 (71)
Q Consensus 45 ~~g~kCp~C~Synt 58 (71)
.+...||+||+.-+
T Consensus 39 ~l~~~CPNCgGelv 52 (57)
T PF06906_consen 39 MLNGVCPNCGGELV 52 (57)
T ss_pred HhcCcCcCCCCccc
Confidence 33459999987544
No 398
>PF12322 T4_baseplate: T4 bacteriophage base plate protein; InterPro: IPR024364 Proteins in this family are found in T4-like viruses. They have a single completely conserved residue S that may be functionally important. The family includes the two base plate proteins from bacteriophage T4: Gp51 and Gp26, encoded by late genes []. Gp26 is a structural component of central hub of the baseplate. It associates with Gp25 (tail lysozyme) in the assembly process. Gp51 is essential for the formation of the central hub of the phage baseplate, playing a catalytic role for the central hub formation. It may be also a structural component of the hub.
Probab=20.99 E-value=87 Score=21.61 Aligned_cols=19 Identities=37% Similarity=0.581 Sum_probs=13.1
Q ss_pred ceeeEEcCCCCCceeeceE
Q psy1204 26 VILYVLCKDCHKESKVLYH 44 (71)
Q Consensus 26 ~~v~i~CndC~~~s~v~~h 44 (71)
.++.+.|.+||++..+...
T Consensus 75 v~~~~~C~~cg~~~~~~i~ 93 (205)
T PF12322_consen 75 VPVNYTCPDCGEEVKVPIN 93 (205)
T ss_pred ceEEEECCCCCcEEEEEec
Confidence 5677888888876655543
No 399
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=20.94 E-value=67 Score=26.08 Aligned_cols=15 Identities=33% Similarity=0.855 Sum_probs=7.4
Q ss_pred eeEEcCCCCCceeec
Q psy1204 28 LYVLCKDCHKESKVL 42 (71)
Q Consensus 28 v~i~CndC~~~s~v~ 42 (71)
-.+.|..||..+...
T Consensus 226 ~yvpCPHCGe~q~l~ 240 (611)
T COG5525 226 FYVPCPHCGEEQQLK 240 (611)
T ss_pred EEeeCCCCCchhhcc
Confidence 344555555555443
No 400
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.92 E-value=58 Score=20.77 Aligned_cols=8 Identities=25% Similarity=0.692 Sum_probs=3.9
Q ss_pred cCCCCCce
Q psy1204 32 CKDCHKES 39 (71)
Q Consensus 32 CndC~~~s 39 (71)
|..|++.|
T Consensus 58 C~~C~~~f 65 (112)
T TIGR00622 58 CFGCQGPF 65 (112)
T ss_pred ccCcCCCC
Confidence 55555444
No 401
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=20.76 E-value=66 Score=27.31 Aligned_cols=25 Identities=32% Similarity=0.545 Sum_probs=18.5
Q ss_pred EEcCCCCCceeeceEeecccCCCCCCc
Q psy1204 30 VLCKDCHKESKVLYHIIGLKCEHCGSY 56 (71)
Q Consensus 30 i~CndC~~~s~v~~h~~g~kCp~C~Sy 56 (71)
-.|..||.+-.-..--+ +|..|||-
T Consensus 925 ~~c~~c~~~~~~~g~c~--~c~~cg~t 949 (953)
T PRK06556 925 PLCPTCGTKMVRNGSCY--VCEGCGST 949 (953)
T ss_pred CcCCCccCeeeECCceE--eccCCCCC
Confidence 35999987665555566 99999984
No 402
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=20.67 E-value=48 Score=18.89 Aligned_cols=30 Identities=17% Similarity=0.235 Sum_probs=15.7
Q ss_pred eeEEcCC--CCCceeeceEe-ecccCCCCCCcc
Q psy1204 28 LYVLCKD--CHKESKVLYHI-IGLKCEHCGSYN 57 (71)
Q Consensus 28 v~i~Cnd--C~~~s~v~~h~-~g~kCp~C~Syn 57 (71)
.+-.|.+ |..=-..+|-+ -.-+||.|+|.=
T Consensus 17 ~VW~Ct~e~C~gWmR~nFs~~~~p~CPlC~s~M 49 (59)
T PF14169_consen 17 KVWECTSEDCNGWMRDNFSFEEEPVCPLCKSPM 49 (59)
T ss_pred eeEEeCCCCCCcccccccccCCCccCCCcCCcc
Confidence 4556765 65322222211 113899999864
No 403
>PF10474 DUF2451: Protein of unknown function C-terminus (DUF2451); InterPro: IPR019514 This protein is found in eukaryotes but its function is not known. The N-terminal domain of some members is PF10475 from PFAM (DUF2450).
Probab=20.65 E-value=99 Score=21.59 Aligned_cols=23 Identities=22% Similarity=0.453 Sum_probs=19.4
Q ss_pred ChHHHHHHHHHHHHcCCCCHhhh
Q psy1204 2 DMTPLWRQMDEEIASTPMPEEYK 24 (71)
Q Consensus 2 dm~~~~~~lD~~i~~~pmP~~y~ 24 (71)
++..++.+||+..+..++|.+-+
T Consensus 100 ~~~~f~~rL~~i~~~~~i~~~~~ 122 (234)
T PF10474_consen 100 EFQQFSERLDEISKQGPIPPEVQ 122 (234)
T ss_pred HHHHHHHHHHHHHhcCCCCHHHH
Confidence 35678999999999999999844
No 404
>KOG2768|consensus
Probab=20.60 E-value=64 Score=23.09 Aligned_cols=32 Identities=34% Similarity=0.781 Sum_probs=20.8
Q ss_pred eEEcCCCCCceee---ceEeecccCCCCCCcceee
Q psy1204 29 YVLCKDCHKESKV---LYHIIGLKCEHCGSYNTCR 60 (71)
Q Consensus 29 ~i~CndC~~~s~v---~~h~~g~kCp~C~Synt~i 60 (71)
-+.|.-|.+.-+. ..+.|.++|..|||++...
T Consensus 181 yV~C~~CkSpdt~L~kenRLfFL~C~~cgs~~sv~ 215 (231)
T KOG2768|consen 181 YVTCKTCKSPDTILQKENRLFFLRCEKCGSRCSVA 215 (231)
T ss_pred heEeeecCChhHHhhhhcceEEEEecCCCCeeeee
Confidence 4678889754432 2334445999999996443
No 405
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=20.49 E-value=24 Score=23.09 Aligned_cols=24 Identities=17% Similarity=0.285 Sum_probs=16.7
Q ss_pred eEEcCCCCCceeeceEeecccCCCCCC
Q psy1204 29 YVLCKDCHKESKVLYHIIGLKCEHCGS 55 (71)
Q Consensus 29 ~i~CndC~~~s~v~~h~~g~kCp~C~S 55 (71)
..-|..||+-|..... -.||.|.-
T Consensus 3 l~nC~~CgklF~~~~~---~iCp~C~~ 26 (137)
T TIGR03826 3 LANCPKCGRLFVKTGR---DVCPSCYE 26 (137)
T ss_pred CccccccchhhhhcCC---ccCHHHhH
Confidence 3469999998876422 27999853
No 406
>KOG2324|consensus
Probab=20.31 E-value=71 Score=24.87 Aligned_cols=30 Identities=13% Similarity=0.273 Sum_probs=17.9
Q ss_pred eeeEEcCCCCCceeeceEeec--ccCCCCCCc
Q psy1204 27 ILYVLCKDCHKESKVLYHIIG--LKCEHCGSY 56 (71)
Q Consensus 27 ~v~i~CndC~~~s~v~~h~~g--~kCp~C~Sy 56 (71)
.....|..|+..-...-.-+- .+||+|.+-
T Consensus 225 D~l~~C~~C~~s~n~e~~~~sk~~~Cp~C~~~ 256 (457)
T KOG2324|consen 225 DTLMSCPSCGYSKNSEDLDLSKIASCPKCNEG 256 (457)
T ss_pred cceeecCcCCccCchhhhcCCccccCCcccCC
Confidence 457789999754432211111 389999874
No 407
>PF09687 PRESAN: Plasmodium RESA N-terminal; InterPro: IPR019111 The short, four-helical domain first identified in the Plasmodium export proteins PHISTa and PHISTc [] has been extended to become this six-helical PRESAC domain identified in the P. falciparum-specific RESA-type (Ring-infected erythrocyte surface antigen) proteins in association with the DnaJ domain. Overall, at least 67 proteins have been detected in P. falciparum with complete copies of the PRESAC domain. No versions of this domain were detected in other apicomplexan genera, suggesting that the domain was 'invented' after the divergence of the lineage leading to the genus Plasmodium undergoing a dramatic proliferation only in P. falciparum. A secondary structure-prediction derived from the multiple alignment of the PRESAC family reveals that it is composed of an all-helical fold with six conserved helical segments. There is some evidence it might localise to membranes [].
Probab=20.25 E-value=1.2e+02 Score=17.92 Aligned_cols=22 Identities=36% Similarity=0.748 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHcCCCCHhhhc
Q psy1204 4 TPLWRQMDEEIASTPMPEEYKN 25 (71)
Q Consensus 4 ~~~~~~lD~~i~~~pmP~~y~~ 25 (71)
...|..++.+.....||.+|+.
T Consensus 47 ~~L~~~~~~la~~~~ip~~~~~ 68 (129)
T PF09687_consen 47 NKLWKYFEELAKKYNIPEEYKK 68 (129)
T ss_pred HHHHHHHHHHHHHcCCChHHHH
Confidence 4678889999999999999875
No 408
>KOG2683|consensus
Probab=20.10 E-value=59 Score=23.96 Aligned_cols=26 Identities=23% Similarity=0.277 Sum_probs=22.3
Q ss_pred HHcCCCCHhhhcceeeEEcCCCCCce
Q psy1204 14 IASTPMPEEYKNVILYVLCKDCHKES 39 (71)
Q Consensus 14 i~~~pmP~~y~~~~v~i~CndC~~~s 39 (71)
-|.+.|+.|.......+.|.+|+...
T Consensus 142 kAGS~~~tElHG~~~~VkCl~C~y~~ 167 (305)
T KOG2683|consen 142 KAGSRMVTELHGSAYQVKCLSCGYIE 167 (305)
T ss_pred hccccceeeeccceEEEEecccCccc
Confidence 46788999988888999999999754
Done!