Query 027549
Match_columns 222
No_of_seqs 286 out of 1730
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 11:35:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027549.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027549hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462 C2H2-type Zn-finger pr 99.6 2E-16 4.4E-21 140.9 1.0 81 4-89 174-254 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.5 2.8E-15 6E-20 133.7 -0.4 69 1-70 197-265 (279)
3 KOG3623 Homeobox transcription 99.3 6.5E-13 1.4E-17 130.8 0.9 72 1-73 904-975 (1007)
4 KOG3623 Homeobox transcription 99.1 3.5E-11 7.6E-16 118.7 4.0 69 1-70 250-331 (1007)
5 KOG3576 Ovo and related transc 99.0 2.2E-11 4.8E-16 105.6 -3.4 81 5-86 131-220 (267)
6 KOG1074 Transcriptional repres 98.7 1.6E-08 3.5E-13 101.3 5.5 68 2-70 616-690 (958)
7 PHA02768 hypothetical protein; 98.6 1.3E-08 2.8E-13 71.2 1.9 44 19-65 5-48 (55)
8 PHA00733 hypothetical protein 98.5 1.8E-08 3.9E-13 81.3 0.8 63 6-72 61-123 (128)
9 PF13465 zf-H2C2_2: Zinc-finge 98.5 7.7E-08 1.7E-12 57.2 2.0 25 6-30 1-25 (26)
10 KOG3608 Zn finger proteins [Ge 98.4 3.7E-08 8.1E-13 91.3 -0.4 98 3-101 275-381 (467)
11 KOG1074 Transcriptional repres 98.4 2E-07 4.3E-12 93.7 4.3 71 19-90 353-433 (958)
12 KOG3576 Ovo and related transc 98.3 1.4E-07 3E-12 82.2 0.2 67 1-68 155-232 (267)
13 PF13465 zf-H2C2_2: Zinc-finge 98.3 3E-07 6.5E-12 54.7 1.4 26 34-60 1-26 (26)
14 KOG3608 Zn finger proteins [Ge 98.1 1.3E-07 2.8E-12 87.8 -3.6 67 1-68 189-257 (467)
15 PLN03086 PRLI-interacting fact 97.9 7.9E-06 1.7E-10 80.2 2.8 76 4-87 465-550 (567)
16 PHA00616 hypothetical protein 97.8 4.6E-06 9.9E-11 55.9 0.3 34 19-52 1-34 (44)
17 PHA00732 hypothetical protein 97.7 2.6E-05 5.6E-10 58.2 2.4 43 19-68 1-44 (79)
18 PHA00733 hypothetical protein 97.5 1.8E-05 3.9E-10 63.9 -0.1 68 16-88 37-109 (128)
19 COG5189 SFP1 Putative transcri 97.3 0.00016 3.4E-09 66.8 2.7 53 16-69 346-419 (423)
20 PHA02768 hypothetical protein; 97.2 0.00016 3.4E-09 50.7 1.4 35 1-37 15-49 (55)
21 PLN03086 PRLI-interacting fact 96.9 0.00061 1.3E-08 67.1 3.1 63 3-68 488-560 (567)
22 PF00096 zf-C2H2: Zinc finger, 96.8 0.00055 1.2E-08 38.6 0.9 23 20-42 1-23 (23)
23 PF13912 zf-C2H2_6: C2H2-type 96.3 0.0019 4.2E-08 37.7 1.3 25 19-43 1-25 (27)
24 PRK04860 hypothetical protein; 96.1 0.0033 7.1E-08 52.8 2.1 39 18-61 118-156 (160)
25 PF13894 zf-C2H2_4: C2H2-type 95.9 0.0039 8.5E-08 34.5 1.3 23 20-42 1-23 (24)
26 COG5189 SFP1 Putative transcri 95.8 0.0053 1.1E-07 57.0 2.3 51 44-94 346-420 (423)
27 KOG3993 Transcription factor ( 95.7 0.0014 3.1E-08 62.4 -1.8 67 6-73 282-381 (500)
28 PHA00732 hypothetical protein 95.3 0.0061 1.3E-07 45.4 0.7 38 47-89 1-38 (79)
29 PF05605 zf-Di19: Drought indu 95.2 0.0066 1.4E-07 41.6 0.5 47 19-69 2-50 (54)
30 smart00355 ZnF_C2H2 zinc finge 95.0 0.013 2.9E-07 32.5 1.3 24 20-43 1-24 (26)
31 PF09237 GAGA: GAGA factor; I 94.8 0.017 3.7E-07 40.1 1.7 40 8-47 12-52 (54)
32 PHA00616 hypothetical protein 94.3 0.0041 9E-08 41.7 -2.2 33 47-82 1-33 (44)
33 PF12756 zf-C2H2_2: C2H2 type 93.3 0.013 2.8E-07 43.0 -1.5 24 47-71 50-73 (100)
34 PF00096 zf-C2H2: Zinc finger, 92.6 0.011 2.4E-07 33.1 -2.1 21 48-69 1-21 (23)
35 PF12874 zf-met: Zinc-finger o 92.0 0.074 1.6E-06 30.3 0.9 23 20-42 1-23 (25)
36 COG5048 FOG: Zn-finger [Genera 90.9 0.16 3.4E-06 45.1 2.3 52 18-70 288-345 (467)
37 PF12171 zf-C2H2_jaz: Zinc-fin 90.2 0.14 3E-06 30.0 0.9 22 20-41 2-23 (27)
38 COG5048 FOG: Zn-finger [Genera 90.2 0.3 6.5E-06 43.3 3.5 61 1-61 299-366 (467)
39 PF13894 zf-C2H2_4: C2H2-type 90.1 0.022 4.7E-07 31.4 -2.5 22 48-70 1-22 (24)
40 KOG3993 Transcription factor ( 89.1 0.073 1.6E-06 51.1 -1.3 49 19-68 267-315 (500)
41 PF13912 zf-C2H2_6: C2H2-type 88.3 0.063 1.4E-06 31.2 -1.5 22 47-69 1-22 (27)
42 PF13909 zf-H2C2_5: C2H2-type 87.2 0.26 5.7E-06 27.9 0.7 23 20-43 1-23 (24)
43 PF05605 zf-Di19: Drought indu 86.5 0.17 3.6E-06 34.5 -0.5 38 47-86 2-39 (54)
44 KOG1146 Homeobox protein [Gene 82.8 0.47 1E-05 51.1 0.6 54 13-67 459-537 (1406)
45 smart00451 ZnF_U1 U1-like zinc 79.9 1.1 2.4E-05 27.2 1.3 22 19-40 3-24 (35)
46 PF13913 zf-C2HC_2: zinc-finge 78.1 1.2 2.6E-05 26.0 1.1 20 20-40 3-22 (25)
47 cd00350 rubredoxin_like Rubred 75.9 2 4.3E-05 26.6 1.6 24 20-56 2-25 (33)
48 PF09986 DUF2225: Uncharacteri 73.9 1.6 3.5E-05 38.0 1.1 44 17-61 3-61 (214)
49 PRK00464 nrdR transcriptional 72.2 1.6 3.5E-05 36.4 0.8 44 20-64 1-44 (154)
50 PF12756 zf-C2H2_2: C2H2 type 69.5 3 6.4E-05 30.2 1.6 24 19-42 50-73 (100)
51 PF09237 GAGA: GAGA factor; I 61.4 0.93 2E-05 31.6 -2.3 27 42-69 19-45 (54)
52 PRK09678 DNA-binding transcrip 60.2 3.2 7E-05 30.5 0.3 48 20-70 2-51 (72)
53 KOG2593 Transcription initiati 59.7 5.1 0.00011 38.7 1.5 49 118-191 239-288 (436)
54 PF09538 FYDLN_acid: Protein o 59.0 6.3 0.00014 31.1 1.7 13 47-60 26-38 (108)
55 smart00834 CxxC_CXXC_SSSS Puta 58.5 5.8 0.00013 24.8 1.2 11 20-30 6-16 (41)
56 TIGR00373 conserved hypothetic 58.1 7.9 0.00017 32.1 2.3 18 18-35 108-125 (158)
57 KOG2893 Zn finger protein [Gen 57.0 4.8 0.00011 36.5 0.9 41 22-67 13-53 (341)
58 TIGR02605 CxxC_CxxC_SSSS putat 56.9 5.5 0.00012 26.5 0.9 11 48-59 6-16 (52)
59 smart00531 TFIIE Transcription 56.9 9.8 0.00021 31.0 2.6 37 17-58 97-133 (147)
60 TIGR02098 MJ0042_CXXC MJ0042 f 52.9 11 0.00023 23.5 1.7 34 20-59 3-36 (38)
61 PRK06266 transcription initiat 52.6 10 0.00022 32.2 2.1 16 19-34 117-132 (178)
62 TIGR00373 conserved hypothetic 49.3 6.4 0.00014 32.7 0.4 36 42-89 104-139 (158)
63 PF13719 zinc_ribbon_5: zinc-r 48.9 14 0.0003 23.4 1.8 33 21-59 4-36 (37)
64 PRK12496 hypothetical protein; 48.8 12 0.00025 31.4 1.8 32 47-93 127-158 (164)
65 cd00729 rubredoxin_SM Rubredox 48.4 12 0.00027 23.3 1.5 10 20-29 3-12 (34)
66 PF09845 DUF2072: Zn-ribbon co 47.8 8.5 0.00018 31.5 0.8 34 47-93 1-35 (131)
67 PRK00398 rpoP DNA-directed RNA 47.1 11 0.00024 24.6 1.2 12 19-30 3-14 (46)
68 COG1997 RPL43A Ribosomal prote 46.8 10 0.00022 29.1 1.1 34 18-62 34-67 (89)
69 PRK06266 transcription initiat 46.3 8.3 0.00018 32.7 0.6 34 44-89 114-147 (178)
70 KOG2186 Cell growth-regulating 45.3 10 0.00023 34.4 1.1 44 20-67 4-47 (276)
71 smart00659 RPOLCX RNA polymera 44.7 17 0.00036 24.1 1.8 11 20-30 3-13 (44)
72 COG2888 Predicted Zn-ribbon RN 43.2 17 0.00037 26.0 1.7 8 20-27 28-35 (61)
73 TIGR02300 FYDLN_acid conserved 42.6 20 0.00043 29.3 2.2 30 20-61 10-39 (129)
74 PF13717 zinc_ribbon_4: zinc-r 39.5 27 0.00059 22.0 2.1 34 20-59 3-36 (36)
75 PHA00626 hypothetical protein 38.8 16 0.00035 25.9 1.0 15 46-61 22-36 (59)
76 PRK14890 putative Zn-ribbon RN 35.5 25 0.00054 25.0 1.5 9 48-57 26-34 (59)
77 KOG4173 Alpha-SNAP protein [In 33.6 4.5 9.7E-05 35.9 -3.0 52 21-72 108-170 (253)
78 COG4049 Uncharacterized protei 33.5 14 0.00031 26.3 0.1 26 15-40 13-38 (65)
79 PF05443 ROS_MUCR: ROS/MUCR tr 33.3 20 0.00043 29.3 0.8 26 19-47 72-97 (132)
80 PF05191 ADK_lid: Adenylate ki 33.3 29 0.00064 22.0 1.5 29 49-88 3-31 (36)
81 COG3357 Predicted transcriptio 33.2 21 0.00045 27.7 0.9 12 19-30 58-69 (97)
82 COG0068 HypF Hydrogenase matur 32.7 18 0.00038 37.3 0.5 57 21-87 125-182 (750)
83 COG1996 RPC10 DNA-directed RNA 30.0 30 0.00066 23.7 1.2 11 19-29 6-16 (49)
84 cd00065 FYVE FYVE domain; Zinc 29.7 50 0.0011 21.9 2.3 28 21-61 4-31 (57)
85 KOG4173 Alpha-SNAP protein [In 29.0 9 0.00019 34.0 -1.9 70 18-91 78-157 (253)
86 PF09332 Mcm10: Mcm10 replicat 28.9 24 0.00052 33.3 0.7 42 18-60 251-297 (344)
87 PRK03824 hypA hydrogenase nick 28.8 32 0.00069 27.8 1.4 11 20-30 71-81 (135)
88 smart00614 ZnF_BED BED zinc fi 28.3 37 0.00081 22.4 1.4 24 19-42 18-47 (50)
89 PF09723 Zn-ribbon_8: Zinc rib 27.9 33 0.00072 22.1 1.1 11 20-30 6-16 (42)
90 smart00064 FYVE Protein presen 27.1 51 0.0011 22.7 2.0 29 20-61 11-39 (68)
91 PF02892 zf-BED: BED zinc fing 25.7 45 0.00097 21.2 1.4 24 16-39 13-40 (45)
92 COG4957 Predicted transcriptio 24.3 34 0.00073 28.4 0.7 25 20-47 77-101 (148)
93 smart00440 ZnF_C2C2 C2C2 Zinc 24.2 34 0.00074 22.0 0.6 11 48-59 29-39 (40)
94 COG1592 Rubrerythrin [Energy p 23.8 50 0.0011 28.0 1.7 23 47-85 134-156 (166)
95 TIGR00244 transcriptional regu 23.7 36 0.00078 28.4 0.8 14 47-61 28-41 (147)
96 KOG2593 Transcription initiati 23.6 55 0.0012 31.8 2.1 39 14-56 123-161 (436)
97 COG3677 Transposase and inacti 23.4 42 0.00091 27.0 1.1 47 9-63 22-68 (129)
98 COG1327 Predicted transcriptio 22.8 38 0.00083 28.5 0.8 14 47-61 28-41 (156)
99 COG1198 PriA Primosomal protei 22.8 45 0.00097 34.5 1.4 9 21-29 437-445 (730)
100 KOG4124 Putative transcription 22.7 42 0.00091 32.1 1.1 22 18-39 348-371 (442)
101 PF04959 ARS2: Arsenite-resist 22.0 27 0.00059 30.7 -0.3 30 16-45 74-103 (214)
102 PF08790 zf-LYAR: LYAR-type C2 21.7 46 0.00099 20.3 0.8 20 20-40 1-20 (28)
103 PF03604 DNA_RNApol_7kD: DNA d 21.4 81 0.0018 19.5 1.9 11 20-30 1-11 (32)
104 TIGR00100 hypA hydrogenase nic 21.2 53 0.0011 25.8 1.2 10 20-29 71-80 (115)
105 PF00292 PAX: 'Paired box' dom 20.7 40 0.00086 27.3 0.5 23 132-155 33-55 (125)
106 PTZ00255 60S ribosomal protein 20.7 44 0.00096 25.7 0.7 34 18-62 35-68 (90)
107 COG3091 SprT Zn-dependent meta 20.5 56 0.0012 27.5 1.3 31 19-55 117-147 (156)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.59 E-value=2e-16 Score=140.93 Aligned_cols=81 Identities=19% Similarity=0.331 Sum_probs=73.2
Q ss_pred ChhhHhhhhhhcCCCceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCCCCccccccCCCCCCCCCcccc
Q 027549 4 LPSAADGENLEKGTSAFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASIGSASTIVDPLSSNQPGNSCEV 83 (222)
Q Consensus 4 ~S~Lk~H~rtHTgEKPf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~L~sh~~~p~~~~~~~~sC~~ 83 (222)
...|+.|+|+|+ -|++|.+|||.|.+.+-|+.|.|+|||||||.|+. |+|+|+++++|..|+.+ +.+...|.|..
T Consensus 174 mpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~h-C~kAFADRSNLRAHmQT--HS~~K~~qC~~ 248 (279)
T KOG2462|consen 174 MPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPH-CGKAFADRSNLRAHMQT--HSDVKKHQCPR 248 (279)
T ss_pred hHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCc-ccchhcchHHHHHHHHh--hcCCccccCcc
Confidence 356899999998 68999999999999999999999999999999999 99999999999999987 45666899999
Q ss_pred cccccc
Q 027549 84 VGNNLA 89 (222)
Q Consensus 84 cG~~l~ 89 (222)
|++.++
T Consensus 249 C~KsFs 254 (279)
T KOG2462|consen 249 CGKSFA 254 (279)
T ss_pred hhhHHH
Confidence 997654
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.49 E-value=2.8e-15 Score=133.68 Aligned_cols=69 Identities=22% Similarity=0.294 Sum_probs=65.7
Q ss_pred CCCChhhHhhhhhhcCCCceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCCCCcccccc
Q 027549 1 MANLPSAADGENLEKGTSAFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASIGSASTIVD 70 (222)
Q Consensus 1 Fan~S~Lk~H~rtHTgEKPf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~L~sh~~~ 70 (222)
|.+..-|+.|+|+|||||||.|..|+|+|..+++|+.|+++|.+.|+|+|.. |+|.|+..+.|..|.+.
T Consensus 197 FSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~-C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 197 FSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPR-CGKSFALKSYLNKHSES 265 (279)
T ss_pred ccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcc-hhhHHHHHHHHHHhhhh
Confidence 6778889999999999999999999999999999999999999999999999 99999999999888754
No 3
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.28 E-value=6.5e-13 Score=130.75 Aligned_cols=72 Identities=21% Similarity=0.328 Sum_probs=67.3
Q ss_pred CCCChhhHhhhhhhcCCCceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCCCCccccccCCC
Q 027549 1 MANLPSAADGENLEKGTSAFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASIGSASTIVDPLS 73 (222)
Q Consensus 1 Fan~S~Lk~H~rtHTgEKPf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~L~sh~~~p~~ 73 (222)
|...++|.+|.--|+|.|||.|.+|.|+|.++.+|..|.|.|.|||||+|+. |+|+|+.+.+...||..+|.
T Consensus 904 FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdK-ClKRFSHSGSYSQHMNHRYS 975 (1007)
T KOG3623|consen 904 FQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDK-CLKRFSHSGSYSQHMNHRYS 975 (1007)
T ss_pred HHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhh-hhhhcccccchHhhhccchh
Confidence 5667899999999999999999999999999999999999999999999999 99999999999999876654
No 4
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.12 E-value=3.5e-11 Score=118.75 Aligned_cols=69 Identities=23% Similarity=0.300 Sum_probs=62.3
Q ss_pred CCCChhhHhhhhhhcC-------------CCceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCCCCccc
Q 027549 1 MANLPSAADGENLEKG-------------TSAFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASIGSAST 67 (222)
Q Consensus 1 Fan~S~Lk~H~rtHTg-------------EKPf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~L~sh 67 (222)
|+....|.+|+.+|.. .|-|+|.+|+|+|..+.+|+.|.|+|.|||||.|+. |+|+|+.+.+..+|
T Consensus 250 FAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpn-CkKRFSHSGSySSH 328 (1007)
T KOG3623|consen 250 FAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPN-CKKRFSHSGSYSSH 328 (1007)
T ss_pred hhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcc-cccccccCCccccc
Confidence 6777889999988853 356999999999999999999999999999999999 99999999999999
Q ss_pred ccc
Q 027549 68 IVD 70 (222)
Q Consensus 68 ~~~ 70 (222)
|..
T Consensus 329 mSS 331 (1007)
T KOG3623|consen 329 MSS 331 (1007)
T ss_pred ccc
Confidence 853
No 5
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.98 E-value=2.2e-11 Score=105.55 Aligned_cols=81 Identities=16% Similarity=0.203 Sum_probs=69.8
Q ss_pred hhhHhhhhhhcCCCceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCCCCccccccCCC---------CC
Q 027549 5 PSAADGENLEKGTSAFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASIGSASTIVDPLS---------SN 75 (222)
Q Consensus 5 S~Lk~H~rtHTgEKPf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~L~sh~~~p~~---------~~ 75 (222)
--|.+|++.|+..|.|-|..|||.|....+|++|.|+|+|.+||+|.. |+|+|+++.+|.+|..+.|. ..
T Consensus 131 Rmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~-c~kaftqrcsleshl~kvhgv~~~yaykerr 209 (267)
T KOG3576|consen 131 RMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSL-CEKAFTQRCSLESHLKKVHGVQHQYAYKERR 209 (267)
T ss_pred HHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhh-hhHHHHhhccHHHHHHHHcCchHHHHHHHhh
Confidence 357899999999999999999999999999999999999999999999 99999999999988754332 12
Q ss_pred CCCCccccccc
Q 027549 76 QPGNSCEVVGN 86 (222)
Q Consensus 76 ~~~~sC~~cG~ 86 (222)
...|.|+.||.
T Consensus 210 ~kl~vcedcg~ 220 (267)
T KOG3576|consen 210 AKLYVCEDCGY 220 (267)
T ss_pred hheeeecccCC
Confidence 34467888883
No 6
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.70 E-value=1.6e-08 Score=101.32 Aligned_cols=68 Identities=15% Similarity=0.314 Sum_probs=60.2
Q ss_pred CCChhhHhhhhhhcCCCceecCccCcccCCchhhhhhhhhcCCC----cccccC---CCCCccccCCCCCcccccc
Q 027549 2 ANLPSAADGENLEKGTSAFSCIYCRKSFANHRSLRGHLRSHNVQ----LKAAWR---RNCPSNSCASIGSASTIVD 70 (222)
Q Consensus 2 an~S~Lk~H~rtHTgEKPf~C~~CgKsF~~ks~Lk~H~r~Htge----KPf~C~---~~CGKsFs~s~~L~sh~~~ 70 (222)
+..+.|+.|.|+|+|||||+|.+||++|..+.+|+.|+-+|... ..|.|+ . |-+.|.....|..|+.-
T Consensus 616 SC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~i-c~~kftn~V~lpQhIri 690 (958)
T KOG1074|consen 616 SCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFI-CQKKFTNAVTLPQHIRI 690 (958)
T ss_pred cchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhh-hcccccccccccceEEe
Confidence 45678999999999999999999999999999999999988754 347899 8 99999999999887743
No 7
>PHA02768 hypothetical protein; Provisional
Probab=98.64 E-value=1.3e-08 Score=71.21 Aligned_cols=44 Identities=23% Similarity=0.434 Sum_probs=40.2
Q ss_pred ceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCCCCc
Q 027549 19 AFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASIGSA 65 (222)
Q Consensus 19 Pf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~L~ 65 (222)
-|.|+.||+.|.+.++|..|+++|+ ++|+|.. |++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~-C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSN-CKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCc-ccceecccceeE
Confidence 4899999999999999999999999 7999999 999999876654
No 8
>PHA00733 hypothetical protein
Probab=98.55 E-value=1.8e-08 Score=81.26 Aligned_cols=63 Identities=14% Similarity=0.208 Sum_probs=48.8
Q ss_pred hhHhhhhhhcCCCceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCCCCccccccCC
Q 027549 6 SAADGENLEKGTSAFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASIGSASTIVDPL 72 (222)
Q Consensus 6 ~Lk~H~rtHTgEKPf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~L~sh~~~p~ 72 (222)
.|.+|+.+| +++||.|+.|++.|.....|..|++.| +.+|.|+. |++.|.....|..|+.+.|
T Consensus 61 ~l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~-CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 61 YLYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPV-CGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred HHHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCC-CCCccCCHHHHHHHHHHhc
Confidence 355565444 478899999999999999999888876 45789988 9999988888887775543
No 9
>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=98.47 E-value=7.7e-08 Score=57.22 Aligned_cols=25 Identities=28% Similarity=0.636 Sum_probs=18.0
Q ss_pred hhHhhhhhhcCCCceecCccCcccC
Q 027549 6 SAADGENLEKGTSAFSCIYCRKSFA 30 (222)
Q Consensus 6 ~Lk~H~rtHTgEKPf~C~~CgKsF~ 30 (222)
+|.+|+++|++++||.|+.|+++|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4667777777777777777777765
No 10
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.42 E-value=3.7e-08 Score=91.30 Aligned_cols=98 Identities=13% Similarity=0.208 Sum_probs=82.1
Q ss_pred CChhhHhhhh-hhcCCCceecCccCcccCCchhhhhhhhhcCCCcccccCCC-CCccccCCCCCccccccCCC-CCCCCC
Q 027549 3 NLPSAADGEN-LEKGTSAFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRN-CPSNSCASIGSASTIVDPLS-SNQPGN 79 (222)
Q Consensus 3 n~S~Lk~H~r-tHTgEKPf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~-CGKsFs~s~~L~sh~~~p~~-~~~~~~ 79 (222)
..++|.+|++ .|+..|||+|+.|.+.|.+..+|.+|..+|+ +..|.|+.+ |..+|+....+.+|+...+. .+...|
T Consensus 275 ~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y 353 (467)
T KOG3608|consen 275 SASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILY 353 (467)
T ss_pred ChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCce
Confidence 3578999999 5999999999999999999999999999998 677999887 99999999999999988774 445678
Q ss_pred ccccc------ccccccccccCCCCCcc
Q 027549 80 SCEVV------GNNLAFHKRSSPNLTFS 101 (222)
Q Consensus 80 sC~~c------G~~l~~H~rssp~~t~s 101 (222)
+|..| |++|..|.+....+..+
T Consensus 354 ~CH~Cdr~ft~G~~L~~HL~kkH~f~~P 381 (467)
T KOG3608|consen 354 ACHCCDRFFTSGKSLSAHLMKKHGFRLP 381 (467)
T ss_pred eeecchhhhccchhHHHHHHHhhcccCC
Confidence 88877 57777787766655443
No 11
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.41 E-value=2e-07 Score=93.72 Aligned_cols=71 Identities=18% Similarity=0.268 Sum_probs=56.9
Q ss_pred ceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCCCCccccccCCCCC----------CCCCccccccccc
Q 027549 19 AFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASIGSASTIVDPLSSN----------QPGNSCEVVGNNL 88 (222)
Q Consensus 19 Pf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~L~sh~~~p~~~~----------~~~~sC~~cG~~l 88 (222)
+++|.+|.|.|...+.|+.|.|.|+||+||+|.+ ||.+|+.+.+|+-|..++.... +--..|++|...+
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnv-CG~~FSTkGNLKvH~~rH~e~~p~~~m~p~~~~e~l~~~i~st~~ 431 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNV-CGNRFSTKGNLKVHFQRHREKYPHVQMNPHPVQEHLQYVITSTGL 431 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhccCCCCCeeecc-cccccccccceeeeeeeccccCCccccCCCCchhhhcceeecccc
Confidence 4689999999999999999999999999999999 9999999999998875543322 3334566665444
Q ss_pred cc
Q 027549 89 AF 90 (222)
Q Consensus 89 ~~ 90 (222)
.+
T Consensus 432 p~ 433 (958)
T KOG1074|consen 432 PY 433 (958)
T ss_pred CC
Confidence 43
No 12
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.30 E-value=1.4e-07 Score=82.21 Aligned_cols=67 Identities=18% Similarity=0.265 Sum_probs=54.1
Q ss_pred CCCChhhHhhhhhhcCCCceecCccCcccCCchhhhhhhh-hcC----------CCcccccCCCCCccccCCCCCcccc
Q 027549 1 MANLPSAADGENLEKGTSAFSCIYCRKSFANHRSLRGHLR-SHN----------VQLKAAWRRNCPSNSCASIGSASTI 68 (222)
Q Consensus 1 Fan~S~Lk~H~rtHTgEKPf~C~~CgKsF~~ks~Lk~H~r-~Ht----------geKPf~C~~~CGKsFs~s~~L~sh~ 68 (222)
|...-+|++|.|+|||.+||+|..|+|+|++...|..|.+ +|. .+|.|.|+. ||..-.+...+..|+
T Consensus 155 fndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vced-cg~t~~~~e~~~~h~ 232 (267)
T KOG3576|consen 155 FNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCED-CGYTSERPEVYYLHL 232 (267)
T ss_pred ccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecc-cCCCCCChhHHHHHH
Confidence 4555689999999999999999999999999999999987 342 357799999 998766554444444
No 13
>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=98.29 E-value=3e-07 Score=54.65 Aligned_cols=26 Identities=23% Similarity=0.353 Sum_probs=24.0
Q ss_pred hhhhhhhhcCCCcccccCCCCCccccC
Q 027549 34 SLRGHLRSHNVQLKAAWRRNCPSNSCA 60 (222)
Q Consensus 34 ~Lk~H~r~HtgeKPf~C~~~CGKsFs~ 60 (222)
+|.+|+++|++++||.|+. |++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~-C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPY-CGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESS-SSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCC-CcCeeCc
Confidence 5789999999999999999 9999964
No 14
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.14 E-value=1.3e-07 Score=87.81 Aligned_cols=67 Identities=16% Similarity=0.168 Sum_probs=54.5
Q ss_pred CCCChhhHhhhhhhcCCCceecCccCcccCCchhhhhhhhhc--CCCcccccCCCCCccccCCCCCcccc
Q 027549 1 MANLPSAADGENLEKGTSAFSCIYCRKSFANHRSLRGHLRSH--NVQLKAAWRRNCPSNSCASIGSASTI 68 (222)
Q Consensus 1 Fan~S~Lk~H~rtHTgEKPf~C~~CgKsF~~ks~Lk~H~r~H--tgeKPf~C~~~CGKsFs~s~~L~sh~ 68 (222)
|.+++.|+.|+++|++||...|+.||..|+++..|..|.+.. ....+|.|.. |.|+|...-.|.+|+
T Consensus 189 ~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~-C~KrFaTeklL~~Hv 257 (467)
T KOG3608|consen 189 MGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQ-CFKRFATEKLLKSHV 257 (467)
T ss_pred hccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHH-HHHHHhHHHHHHHHH
Confidence 567889999999999999999999999999999999998744 3456788887 888887654444443
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.86 E-value=7.9e-06 Score=80.20 Aligned_cols=76 Identities=13% Similarity=0.150 Sum_probs=60.2
Q ss_pred ChhhHhhhhhhcCCCceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccC----------CCCCccccccCCC
Q 027549 4 LPSAADGENLEKGTSAFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCA----------SIGSASTIVDPLS 73 (222)
Q Consensus 4 ~S~Lk~H~rtHTgEKPf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~----------s~~L~sh~~~p~~ 73 (222)
.+.|..|+.+|+ +|+.|+ |++.+ .+..|..|+++|..++++.|+. |++.|.. ..+|..|...
T Consensus 465 ~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~f-C~~~v~~g~~~~d~~d~~s~Lt~HE~~--- 536 (567)
T PLN03086 465 QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRF-CGDMVQAGGSAMDVRDRLRGMSEHESI--- 536 (567)
T ss_pred hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCC-CCCccccCccccchhhhhhhHHHHHHh---
Confidence 357899999875 899999 99765 6689999999999999999999 9999953 2356666533
Q ss_pred CCCCCCcccccccc
Q 027549 74 SNQPGNSCEVVGNN 87 (222)
Q Consensus 74 ~~~~~~sC~~cG~~ 87 (222)
+....+.|..||+.
T Consensus 537 CG~rt~~C~~Cgk~ 550 (567)
T PLN03086 537 CGSRTAPCDSCGRS 550 (567)
T ss_pred cCCcceEccccCCe
Confidence 56666788888854
No 16
>PHA00616 hypothetical protein
Probab=97.82 E-value=4.6e-06 Score=55.89 Aligned_cols=34 Identities=24% Similarity=0.410 Sum_probs=32.3
Q ss_pred ceecCccCcccCCchhhhhhhhhcCCCcccccCC
Q 027549 19 AFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRR 52 (222)
Q Consensus 19 Pf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~ 52 (222)
||.|..||+.|....+|..|.+.|++++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999999875
No 17
>PHA00732 hypothetical protein
Probab=97.68 E-value=2.6e-05 Score=58.20 Aligned_cols=43 Identities=19% Similarity=0.311 Sum_probs=36.6
Q ss_pred ceecCccCcccCCchhhhhhhh-hcCCCcccccCCCCCccccCCCCCcccc
Q 027549 19 AFSCIYCRKSFANHRSLRGHLR-SHNVQLKAAWRRNCPSNSCASIGSASTI 68 (222)
Q Consensus 19 Pf~C~~CgKsF~~ks~Lk~H~r-~HtgeKPf~C~~~CGKsFs~s~~L~sh~ 68 (222)
||.|..|++.|.+...|..|++ .|. ++.|+. |++.|.+ +..|+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~-CgKsF~~---l~~H~ 44 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPV-CNKSYRR---LNQHF 44 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCC-CCCEeCC---hhhhh
Confidence 6899999999999999999998 465 368999 9999984 55555
No 18
>PHA00733 hypothetical protein
Probab=97.54 E-value=1.8e-05 Score=63.87 Aligned_cols=68 Identities=13% Similarity=0.129 Sum_probs=51.2
Q ss_pred CCCceecCccCcccCCchhhhhh--h---hhcCCCcccccCCCCCccccCCCCCccccccCCCCCCCCCccccccccc
Q 027549 16 GTSAFSCIYCRKSFANHRSLRGH--L---RSHNVQLKAAWRRNCPSNSCASIGSASTIVDPLSSNQPGNSCEVVGNNL 88 (222)
Q Consensus 16 gEKPf~C~~CgKsF~~ks~Lk~H--~---r~HtgeKPf~C~~~CGKsFs~s~~L~sh~~~p~~~~~~~~sC~~cG~~l 88 (222)
..+++.|.+|.+.|.....|..| . ..+.+++||.|+. |++.|.+...|..|+... ...+.|.+|+..+
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~-Cgk~Fss~s~L~~H~r~h----~~~~~C~~CgK~F 109 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPL-CLMPFSSSVSLKQHIRYT----EHSKVCPVCGKEF 109 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCC-CCCcCCCHHHHHHHHhcC----CcCccCCCCCCcc
Confidence 36789999999998887776665 1 1334588999999 999999999998887531 1236888887543
No 19
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.29 E-value=0.00016 Score=66.84 Aligned_cols=53 Identities=17% Similarity=0.271 Sum_probs=41.8
Q ss_pred CCCceecCc--cCcccCCchhhhhhhhh-c------------------CCCcccccCCCCCccccCCCCCccccc
Q 027549 16 GTSAFSCIY--CRKSFANHRSLRGHLRS-H------------------NVQLKAAWRRNCPSNSCASIGSASTIV 69 (222)
Q Consensus 16 gEKPf~C~~--CgKsF~~ks~Lk~H~r~-H------------------tgeKPf~C~~~CGKsFs~s~~L~sh~~ 69 (222)
++|||+|++ |.|+|.....|+.|+.. | ...|||+|++ |+|++....+|+-|..
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCev-C~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEV-CDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccc-cchhhccCccceeccc
Confidence 368999986 99999999999888752 2 1248899999 9999988888877653
No 20
>PHA02768 hypothetical protein; Provisional
Probab=97.21 E-value=0.00016 Score=50.72 Aligned_cols=35 Identities=6% Similarity=-0.011 Sum_probs=31.1
Q ss_pred CCCChhhHhhhhhhcCCCceecCccCcccCCchhhhh
Q 027549 1 MANLPSAADGENLEKGTSAFSCIYCRKSFANHRSLRG 37 (222)
Q Consensus 1 Fan~S~Lk~H~rtHTgEKPf~C~~CgKsF~~ks~Lk~ 37 (222)
|+..++|..|+++|+ +||+|..|++.|.+.+.|..
T Consensus 15 Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 15 YIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred eccHHHHHHHHHhcC--CcccCCcccceecccceeEE
Confidence 678899999999999 79999999999998877653
No 21
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.92 E-value=0.00061 Score=67.14 Aligned_cols=63 Identities=10% Similarity=0.094 Sum_probs=51.8
Q ss_pred CChhhHhhhhhhcCCCceecCccCcccCC----------chhhhhhhhhcCCCcccccCCCCCccccCCCCCcccc
Q 027549 3 NLPSAADGENLEKGTSAFSCIYCRKSFAN----------HRSLRGHLRSHNVQLKAAWRRNCPSNSCASIGSASTI 68 (222)
Q Consensus 3 n~S~Lk~H~rtHTgEKPf~C~~CgKsF~~----------ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~L~sh~ 68 (222)
....|..|+++|..++|+.|..|++.|.. ...|..|.... |.+++.|.. |++.|..+ .+..|+
T Consensus 488 ~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~-Cgk~Vrlr-dm~~H~ 560 (567)
T PLN03086 488 EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDS-CGRSVMLK-EMDIHQ 560 (567)
T ss_pred chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccc-cCCeeeeh-hHHHHH
Confidence 34678999999999999999999999952 34799998885 999999999 99999865 344443
No 22
>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=96.77 E-value=0.00055 Score=38.62 Aligned_cols=23 Identities=39% Similarity=0.935 Sum_probs=20.5
Q ss_pred eecCccCcccCCchhhhhhhhhc
Q 027549 20 FSCIYCRKSFANHRSLRGHLRSH 42 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r~H 42 (222)
|.|+.|++.|.+...|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 68999999999999999998764
No 23
>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=96.31 E-value=0.0019 Score=37.73 Aligned_cols=25 Identities=44% Similarity=0.781 Sum_probs=22.8
Q ss_pred ceecCccCcccCCchhhhhhhhhcC
Q 027549 19 AFSCIYCRKSFANHRSLRGHLRSHN 43 (222)
Q Consensus 19 Pf~C~~CgKsF~~ks~Lk~H~r~Ht 43 (222)
||.|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 6899999999999999999998774
No 24
>PRK04860 hypothetical protein; Provisional
Probab=96.12 E-value=0.0033 Score=52.77 Aligned_cols=39 Identities=21% Similarity=0.391 Sum_probs=34.4
Q ss_pred CceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCC
Q 027549 18 SAFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCAS 61 (222)
Q Consensus 18 KPf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s 61 (222)
-+|.|. |++ ....+.+|.++|+++++|.|.. |++.|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~-C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRR-CGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCC-CCceeEEe
Confidence 379998 997 6778899999999999999999 99988654
No 25
>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=95.95 E-value=0.0039 Score=34.52 Aligned_cols=23 Identities=48% Similarity=0.983 Sum_probs=18.9
Q ss_pred eecCccCcccCCchhhhhhhhhc
Q 027549 20 FSCIYCRKSFANHRSLRGHLRSH 42 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r~H 42 (222)
|.|+.|++.|.+...|..|++.|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 68999999999999999998865
No 26
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.83 E-value=0.0053 Score=56.96 Aligned_cols=51 Identities=18% Similarity=0.255 Sum_probs=37.8
Q ss_pred CCcccccCCC-CCccccCCCCCccccccCC-----------------CCCCCCCcccccc------ccccccccc
Q 027549 44 VQLKAAWRRN-CPSNSCASIGSASTIVDPL-----------------SSNQPGNSCEVVG------NNLAFHKRS 94 (222)
Q Consensus 44 geKPf~C~~~-CGKsFs~s~~L~sh~~~p~-----------------~~~~~~~sC~~cG------~~l~~H~rs 94 (222)
++|||+|+++ |.|.+....+|+-|+..-| ....+.|.|++|+ +.|..|+..
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~H 420 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKH 420 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecccc
Confidence 3599999998 9999999999987764222 2334678999998 345566544
No 27
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=95.73 E-value=0.0014 Score=62.39 Aligned_cols=67 Identities=15% Similarity=0.106 Sum_probs=46.9
Q ss_pred hhHhhhhhhcCCCceecCccCcccCCchhhhhhhhhcC--------CC-------------------------cccccCC
Q 027549 6 SAADGENLEKGTSAFSCIYCRKSFANHRSLRGHLRSHN--------VQ-------------------------LKAAWRR 52 (222)
Q Consensus 6 ~Lk~H~rtHTgEKPf~C~~CgKsF~~ks~Lk~H~r~Ht--------ge-------------------------KPf~C~~ 52 (222)
.|.+|+-...-.--|.|++|+|.|.-..+|..|.|=|. +. .-|.|..
T Consensus 282 ~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~ 361 (500)
T KOG3993|consen 282 ALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHT 361 (500)
T ss_pred HHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHH
Confidence 35566532222234899999999999999999988663 11 1378988
Q ss_pred CCCccccCCCCCccccccCCC
Q 027549 53 NCPSNSCASIGSASTIVDPLS 73 (222)
Q Consensus 53 ~CGKsFs~s~~L~sh~~~p~~ 73 (222)
|+|.|++...|+.|...++.
T Consensus 362 -C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 362 -CGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred -hhhhhHHHHHHHHhHHhhhc
Confidence 99999998888877654433
No 28
>PHA00732 hypothetical protein
Probab=95.32 E-value=0.0061 Score=45.45 Aligned_cols=38 Identities=8% Similarity=0.053 Sum_probs=29.2
Q ss_pred ccccCCCCCccccCCCCCccccccCCCCCCCCCcccccccccc
Q 027549 47 KAAWRRNCPSNSCASIGSASTIVDPLSSNQPGNSCEVVGNNLA 89 (222)
Q Consensus 47 Pf~C~~~CGKsFs~s~~L~sh~~~p~~~~~~~~sC~~cG~~l~ 89 (222)
||.|+. |++.|.+...|..|+...+. ++.|+.||..+.
T Consensus 1 py~C~~-Cgk~F~s~s~Lk~H~r~~H~----~~~C~~CgKsF~ 38 (79)
T PHA00732 1 MFKCPI-CGFTTVTLFALKQHARRNHT----LTKCPVCNKSYR 38 (79)
T ss_pred CccCCC-CCCccCCHHHHHHHhhcccC----CCccCCCCCEeC
Confidence 689999 99999999999999753222 347888886543
No 29
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=95.20 E-value=0.0066 Score=41.57 Aligned_cols=47 Identities=23% Similarity=0.383 Sum_probs=33.3
Q ss_pred ceecCccCcccCCchhhhhhhh-hcCCC-cccccCCCCCccccCCCCCccccc
Q 027549 19 AFSCIYCRKSFANHRSLRGHLR-SHNVQ-LKAAWRRNCPSNSCASIGSASTIV 69 (222)
Q Consensus 19 Pf~C~~CgKsF~~ks~Lk~H~r-~Htge-KPf~C~~~CGKsFs~s~~L~sh~~ 69 (222)
.|.|+.|++ ......|..|.. .|..+ +.+.|+. |...+.. +|..|+.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPi-C~~~~~~--~l~~Hl~ 50 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPI-CSSRVTD--NLIRHLN 50 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCC-chhhhhh--HHHHHHH
Confidence 488999999 455678999976 45543 5789999 9876543 4555543
No 30
>smart00355 ZnF_C2H2 zinc finger.
Probab=94.99 E-value=0.013 Score=32.50 Aligned_cols=24 Identities=33% Similarity=0.825 Sum_probs=20.8
Q ss_pred eecCccCcccCCchhhhhhhhhcC
Q 027549 20 FSCIYCRKSFANHRSLRGHLRSHN 43 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r~Ht 43 (222)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999988764
No 31
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=94.84 E-value=0.017 Score=40.12 Aligned_cols=40 Identities=18% Similarity=0.341 Sum_probs=25.4
Q ss_pred Hhhhhh-hcCCCceecCccCcccCCchhhhhhhhhcCCCcc
Q 027549 8 ADGENL-EKGTSAFSCIYCRKSFANHRSLRGHLRSHNVQLK 47 (222)
Q Consensus 8 k~H~rt-HTgEKPf~C~~CgKsF~~ks~Lk~H~r~HtgeKP 47 (222)
..+.+. +..+.|..|++|+..+.+..+|.+|+..+++.||
T Consensus 12 ~~~~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 12 TKKPKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp ----CCCCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhHHHHhhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 334443 3467899999999999999999999998887776
No 32
>PHA00616 hypothetical protein
Probab=94.34 E-value=0.0041 Score=41.70 Aligned_cols=33 Identities=12% Similarity=0.005 Sum_probs=25.5
Q ss_pred ccccCCCCCccccCCCCCccccccCCCCCCCCCccc
Q 027549 47 KAAWRRNCPSNSCASIGSASTIVDPLSSNQPGNSCE 82 (222)
Q Consensus 47 Pf~C~~~CGKsFs~s~~L~sh~~~p~~~~~~~~sC~ 82 (222)
||+|+. ||+.|.+...+..|+... .++..+.|+
T Consensus 1 pYqC~~-CG~~F~~~s~l~~H~r~~--hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLR-CGGIFRKKKEVIEHLLSV--HKQNKLTLE 33 (44)
T ss_pred CCccch-hhHHHhhHHHHHHHHHHh--cCCCcccee
Confidence 689999 999999999999998653 333455554
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=93.27 E-value=0.013 Score=43.02 Aligned_cols=24 Identities=4% Similarity=-0.047 Sum_probs=16.8
Q ss_pred ccccCCCCCccccCCCCCccccccC
Q 027549 47 KAAWRRNCPSNSCASIGSASTIVDP 71 (222)
Q Consensus 47 Pf~C~~~CGKsFs~s~~L~sh~~~p 71 (222)
.+.|.. |++.|.+...|..|+...
T Consensus 50 ~~~C~~-C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPY-CNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSS-SS-EESSHHHHHHHHHHT
T ss_pred CCCCCc-cCCCCcCHHHHHHHHcCc
Confidence 477888 888888777777777543
No 34
>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=92.58 E-value=0.011 Score=33.13 Aligned_cols=21 Identities=5% Similarity=-0.020 Sum_probs=18.3
Q ss_pred cccCCCCCccccCCCCCccccc
Q 027549 48 AAWRRNCPSNSCASIGSASTIV 69 (222)
Q Consensus 48 f~C~~~CGKsFs~s~~L~sh~~ 69 (222)
|.|+. |++.|.+...|..|+.
T Consensus 1 y~C~~-C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPI-CGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETT-TTEEESSHHHHHHHHH
T ss_pred CCCCC-CCCccCCHHHHHHHHh
Confidence 68999 9999999988888764
No 35
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=91.98 E-value=0.074 Score=30.28 Aligned_cols=23 Identities=57% Similarity=0.961 Sum_probs=19.8
Q ss_pred eecCccCcccCCchhhhhhhhhc
Q 027549 20 FSCIYCRKSFANHRSLRGHLRSH 42 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r~H 42 (222)
|.|..|.+.|.....+..|.+.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 67999999999999999998754
No 36
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.94 E-value=0.16 Score=45.14 Aligned_cols=52 Identities=19% Similarity=0.205 Sum_probs=44.1
Q ss_pred CceecCccCcccCCchhhhhhhh--hcCCC--cccccC--CCCCccccCCCCCcccccc
Q 027549 18 SAFSCIYCRKSFANHRSLRGHLR--SHNVQ--LKAAWR--RNCPSNSCASIGSASTIVD 70 (222)
Q Consensus 18 KPf~C~~CgKsF~~ks~Lk~H~r--~Htge--KPf~C~--~~CGKsFs~s~~L~sh~~~ 70 (222)
.++.|..|...|.....+..|.+ .|+++ +|+.|+ . |++.|.+...+..|+..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~-~~~~~~~~~~~~~~~~~ 345 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSL-CGKLFSRNDALKRHILL 345 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccC-CCccccccccccCCccc
Confidence 46888889999999999999998 79998 899998 7 99999888887777654
No 37
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=90.23 E-value=0.14 Score=30.02 Aligned_cols=22 Identities=36% Similarity=0.794 Sum_probs=18.2
Q ss_pred eecCccCcccCCchhhhhhhhh
Q 027549 20 FSCIYCRKSFANHRSLRGHLRS 41 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r~ 41 (222)
|.|..|++.|.....+..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6788888888888888888764
No 38
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.19 E-value=0.3 Score=43.31 Aligned_cols=61 Identities=20% Similarity=0.257 Sum_probs=49.1
Q ss_pred CCCChhhHhhhh--hhcCC--CceecC--ccCcccCCchhhhhhhhhcCCCcccccCCC-CCccccCC
Q 027549 1 MANLPSAADGEN--LEKGT--SAFSCI--YCRKSFANHRSLRGHLRSHNVQLKAAWRRN-CPSNSCAS 61 (222)
Q Consensus 1 Fan~S~Lk~H~r--tHTgE--KPf~C~--~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~-CGKsFs~s 61 (222)
|.....|..|.+ .|+++ +|+.|+ .|++.|.+...+..|...|++.+++.|... |.+.+...
T Consensus 299 ~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 366 (467)
T COG5048 299 FSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPL 366 (467)
T ss_pred ccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCccccccc
Confidence 455677888999 79999 999999 799999999999999999999888877653 44444443
No 39
>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=90.11 E-value=0.022 Score=31.38 Aligned_cols=22 Identities=5% Similarity=-0.067 Sum_probs=16.5
Q ss_pred cccCCCCCccccCCCCCcccccc
Q 027549 48 AAWRRNCPSNSCASIGSASTIVD 70 (222)
Q Consensus 48 f~C~~~CGKsFs~s~~L~sh~~~ 70 (222)
|.|+. |++.|.+...|..|+..
T Consensus 1 ~~C~~-C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPI-CGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SS-TS-EESSHHHHHHHHHH
T ss_pred CCCcC-CCCcCCcHHHHHHHHHh
Confidence 68999 99999998888777643
No 40
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=89.15 E-value=0.073 Score=51.08 Aligned_cols=49 Identities=16% Similarity=0.303 Sum_probs=42.0
Q ss_pred ceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCCCCcccc
Q 027549 19 AFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASIGSASTI 68 (222)
Q Consensus 19 Pf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~L~sh~ 68 (222)
-|.|..|-..|...-.|.+|.-..--..-|+|++ |+|.|+-..+|.+|.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPE-C~KVFsCPANLASHR 315 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPE-CDKVFSCPANLASHR 315 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCc-ccccccCchhhhhhh
Confidence 3899999999999999999986443345699999 999999999999886
No 41
>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=88.34 E-value=0.063 Score=31.16 Aligned_cols=22 Identities=5% Similarity=-0.076 Sum_probs=18.6
Q ss_pred ccccCCCCCccccCCCCCccccc
Q 027549 47 KAAWRRNCPSNSCASIGSASTIV 69 (222)
Q Consensus 47 Pf~C~~~CGKsFs~s~~L~sh~~ 69 (222)
||.|.. |++.|.....|..|+.
T Consensus 1 ~~~C~~-C~~~F~~~~~l~~H~~ 22 (27)
T PF13912_consen 1 PFECDE-CGKTFSSLSALREHKR 22 (27)
T ss_dssp SEEETT-TTEEESSHHHHHHHHC
T ss_pred CCCCCc-cCCccCChhHHHHHhH
Confidence 689999 9999999877777764
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=87.20 E-value=0.26 Score=27.86 Aligned_cols=23 Identities=30% Similarity=0.709 Sum_probs=17.4
Q ss_pred eecCccCcccCCchhhhhhhhhcC
Q 027549 20 FSCIYCRKSFANHRSLRGHLRSHN 43 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r~Ht 43 (222)
|.|+.|..... ...|..|.+.|.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 68999998887 889999988753
No 43
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=86.53 E-value=0.17 Score=34.54 Aligned_cols=38 Identities=11% Similarity=0.121 Sum_probs=30.2
Q ss_pred ccccCCCCCccccCCCCCccccccCCCCCCCCCccccccc
Q 027549 47 KAAWRRNCPSNSCASIGSASTIVDPLSSNQPGNSCEVVGN 86 (222)
Q Consensus 47 Pf~C~~~CGKsFs~s~~L~sh~~~p~~~~~~~~sC~~cG~ 86 (222)
.|.|+. |++.|. ...|..|+.+.|......+.|++|..
T Consensus 2 ~f~CP~-C~~~~~-~~~L~~H~~~~H~~~~~~v~CPiC~~ 39 (54)
T PF05605_consen 2 SFTCPY-CGKGFS-ESSLVEHCEDEHRSESKNVVCPICSS 39 (54)
T ss_pred CcCCCC-CCCccC-HHHHHHHHHhHCcCCCCCccCCCchh
Confidence 489999 999554 56799998887776666789999974
No 44
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=82.82 E-value=0.47 Score=51.09 Aligned_cols=54 Identities=19% Similarity=0.242 Sum_probs=42.6
Q ss_pred hhcCCCceecCccCcccCCchhhhhhhhh-c------------------------CCCcccccCCCCCccccCCCCCccc
Q 027549 13 LEKGTSAFSCIYCRKSFANHRSLRGHLRS-H------------------------NVQLKAAWRRNCPSNSCASIGSAST 67 (222)
Q Consensus 13 tHTgEKPf~C~~CgKsF~~ks~Lk~H~r~-H------------------------tgeKPf~C~~~CGKsFs~s~~L~sh 67 (222)
.|+-.+.|.|+.|+..|.....|-.|+|. | .+.+||.|.. |...++....|..|
T Consensus 459 L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~-C~~stttng~Lsih 537 (1406)
T KOG1146|consen 459 LHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRA-CNYSTTTNGNLSIH 537 (1406)
T ss_pred eecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCccccee-eeeeeecchHHHHH
Confidence 46667889999999999999999999986 1 1246789999 99998886665433
No 45
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=79.91 E-value=1.1 Score=27.16 Aligned_cols=22 Identities=32% Similarity=0.788 Sum_probs=18.5
Q ss_pred ceecCccCcccCCchhhhhhhh
Q 027549 19 AFSCIYCRKSFANHRSLRGHLR 40 (222)
Q Consensus 19 Pf~C~~CgKsF~~ks~Lk~H~r 40 (222)
+|.|+.|++.|.....+..|..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5789999999998888888875
No 46
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=78.10 E-value=1.2 Score=25.98 Aligned_cols=20 Identities=30% Similarity=0.674 Sum_probs=15.8
Q ss_pred eecCccCcccCCchhhhhhhh
Q 027549 20 FSCIYCRKSFANHRSLRGHLR 40 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r 40 (222)
..|+.|++.| ..+.|..|..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4688999999 6777888865
No 47
>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=75.92 E-value=2 Score=26.58 Aligned_cols=24 Identities=13% Similarity=0.366 Sum_probs=16.0
Q ss_pred eecCccCcccCCchhhhhhhhhcCCCcccccCCCCCc
Q 027549 20 FSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPS 56 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGK 56 (222)
|.|..||..+.-.. .++.|+. |+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~-Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPV-CGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcC-CCC
Confidence 67888886653321 5778888 874
No 48
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=73.87 E-value=1.6 Score=37.97 Aligned_cols=44 Identities=16% Similarity=0.291 Sum_probs=30.1
Q ss_pred CCceecCccCcccCCchhhhhhhhh----------cCCCcc-----cccCCCCCccccCC
Q 027549 17 TSAFSCIYCRKSFANHRSLRGHLRS----------HNVQLK-----AAWRRNCPSNSCAS 61 (222)
Q Consensus 17 EKPf~C~~CgKsF~~ks~Lk~H~r~----------HtgeKP-----f~C~~~CGKsFs~s 61 (222)
++...|++|++.|..+.-.....+. ..+..| ..|+. ||.+|...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~-CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPH-CGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCC-CCCccccc
Confidence 3567999999999887666555542 122233 47999 99887764
No 49
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=72.21 E-value=1.6 Score=36.45 Aligned_cols=44 Identities=9% Similarity=0.143 Sum_probs=23.4
Q ss_pred eecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCCCC
Q 027549 20 FSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASIGS 64 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~L 64 (222)
++|+.|+..++.--.-..-..-..-.+.++|+. ||++|...-..
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~-c~~~f~~~e~~ 44 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLA-CGKRFTTFERV 44 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccc-cCCcceEeEec
Confidence 369999976522111000000011123389998 99999876443
No 50
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=69.48 E-value=3 Score=30.20 Aligned_cols=24 Identities=42% Similarity=0.992 Sum_probs=21.2
Q ss_pred ceecCccCcccCCchhhhhhhhhc
Q 027549 19 AFSCIYCRKSFANHRSLRGHLRSH 42 (222)
Q Consensus 19 Pf~C~~CgKsF~~ks~Lk~H~r~H 42 (222)
.+.|..|++.|.....|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 589999999999999999999864
No 51
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=61.38 E-value=0.93 Score=31.57 Aligned_cols=27 Identities=11% Similarity=0.005 Sum_probs=17.8
Q ss_pred cCCCcccccCCCCCccccCCCCCccccc
Q 027549 42 HNVQLKAAWRRNCPSNSCASIGSASTIV 69 (222)
Q Consensus 42 HtgeKPf~C~~~CGKsFs~s~~L~sh~~ 69 (222)
+..+.|-.|+. |+..++++.+|..|+.
T Consensus 19 ~~S~~PatCP~-C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 19 SQSEQPATCPI-CGAVIRQSRNLRRHLE 45 (54)
T ss_dssp CTTS--EE-TT-T--EESSHHHHHHHHH
T ss_pred hccCCCCCCCc-chhhccchhhHHHHHH
Confidence 45678999999 9999999988887764
No 52
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=60.22 E-value=3.2 Score=30.52 Aligned_cols=48 Identities=15% Similarity=0.162 Sum_probs=28.7
Q ss_pred eecCccCcccCCchhhhhhhhhcCCCcccccC--CCCCccccCCCCCcccccc
Q 027549 20 FSCIYCRKSFANHRSLRGHLRSHNVQLKAAWR--RNCPSNSCASIGSASTIVD 70 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~--~~CGKsFs~s~~L~sh~~~ 70 (222)
+.|+.|+..-....+-..+. ...+.-++|. . ||.+|.........+..
T Consensus 2 m~CP~Cg~~a~irtSr~~s~--~~~~~Y~qC~N~e-Cg~tF~t~es~s~tis~ 51 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITD--TTKERYHQCQNVN-CSATFITYESVQRYIVK 51 (72)
T ss_pred ccCCCCCCccEEEEChhcCh--hhheeeeecCCCC-CCCEEEEEEEEEEEEcC
Confidence 46899987553322222221 1445678898 6 99999877555554443
No 53
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=59.68 E-value=5.1 Score=38.74 Aligned_cols=49 Identities=33% Similarity=0.534 Sum_probs=28.5
Q ss_pred Ccccceeeccccccccchh-hhhhhccccchhhhhhhhcceecCCcceeeeCccccccceeecccccccccCCcc
Q 027549 118 PLDVSLSLGLNGVQKLRND-EIQTCQDGLAEGCVSKMVGFLNFGQGERIYPIDSLANIDVMKISKRAKIVPRWPV 191 (222)
Q Consensus 118 pl~~~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 (222)
|.+.+-+-|+.|...+..+ +.+. - .++|.+ |-|-..-+|++||+|-|-.
T Consensus 239 ~~d~~rs~G~~~s~~~~~~~~t~~-~--------------v~~~d~----------neD~~~e~k~~~~~P~W~~ 288 (436)
T KOG2593|consen 239 PDDASRSQGGYGSTPMVEEFETDN-E--------------VNLGDD----------NEDAVEEKKSQKILPEWLA 288 (436)
T ss_pred CCchhhcCCCCCCCcceeeeeccc-c--------------eecccc----------ccchhhhhhhhhcCChHHH
Confidence 6677777777776666654 3322 1 233322 3343344677999999964
No 54
>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=59.04 E-value=6.3 Score=31.07 Aligned_cols=13 Identities=8% Similarity=0.161 Sum_probs=6.4
Q ss_pred ccccCCCCCccccC
Q 027549 47 KAAWRRNCPSNSCA 60 (222)
Q Consensus 47 Pf~C~~~CGKsFs~ 60 (222)
|..|+. ||..|.-
T Consensus 26 PivCP~-CG~~~~~ 38 (108)
T PF09538_consen 26 PIVCPK-CGTEFPP 38 (108)
T ss_pred CccCCC-CCCccCc
Confidence 444555 5555443
No 55
>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=58.54 E-value=5.8 Score=24.78 Aligned_cols=11 Identities=27% Similarity=0.923 Sum_probs=6.0
Q ss_pred eecCccCcccC
Q 027549 20 FSCIYCRKSFA 30 (222)
Q Consensus 20 f~C~~CgKsF~ 30 (222)
|.|..||+.|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 45555555554
No 56
>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=58.07 E-value=7.9 Score=32.14 Aligned_cols=18 Identities=17% Similarity=0.261 Sum_probs=9.3
Q ss_pred CceecCccCcccCCchhh
Q 027549 18 SAFSCIYCRKSFANHRSL 35 (222)
Q Consensus 18 KPf~C~~CgKsF~~ks~L 35 (222)
.=|.|+.|+..|+....+
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAM 125 (158)
T ss_pred CeEECCCCCcEeeHHHHH
Confidence 345555555555554444
No 57
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=56.97 E-value=4.8 Score=36.48 Aligned_cols=41 Identities=20% Similarity=0.438 Sum_probs=32.8
Q ss_pred cCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCCCCccc
Q 027549 22 CIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASIGSAST 67 (222)
Q Consensus 22 C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~L~sh 67 (222)
|=.|++.|-...-|.+|++ .|.|+|.. |-|..-+--+|.-|
T Consensus 13 cwycnrefddekiliqhqk----akhfkchi-chkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK----AKHFKCHI-CHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhh----hccceeee-ehhhhccCCCceee
Confidence 6679999999999999887 36799999 98876666667655
No 58
>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=56.91 E-value=5.5 Score=26.49 Aligned_cols=11 Identities=9% Similarity=-0.010 Sum_probs=5.1
Q ss_pred cccCCCCCcccc
Q 027549 48 AAWRRNCPSNSC 59 (222)
Q Consensus 48 f~C~~~CGKsFs 59 (222)
|.|.. ||..|.
T Consensus 6 y~C~~-Cg~~fe 16 (52)
T TIGR02605 6 YRCTA-CGHRFE 16 (52)
T ss_pred EEeCC-CCCEeE
Confidence 44444 554443
No 59
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=56.86 E-value=9.8 Score=31.00 Aligned_cols=37 Identities=11% Similarity=0.223 Sum_probs=18.4
Q ss_pred CCceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccc
Q 027549 17 TSAFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNS 58 (222)
Q Consensus 17 EKPf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsF 58 (222)
..-|.|+.|+..|.....+..- +. +.-|.|+. ||...
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~---d~-~~~f~Cp~-Cg~~l 133 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLL---DM-DGTFTCPR-CGEEL 133 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhc---CC-CCcEECCC-CCCEE
Confidence 3456677777666644333220 11 22266766 66543
No 60
>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=52.93 E-value=11 Score=23.51 Aligned_cols=34 Identities=24% Similarity=0.308 Sum_probs=20.9
Q ss_pred eecCccCcccCCchhhhhhhhhcCCCcccccCCCCCcccc
Q 027549 20 FSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSC 59 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs 59 (222)
+.|+.|+..|.-...... .......|+. |+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~-----~~~~~v~C~~-C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG-----ANGGKVRCGK-CGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC-----CCCCEEECCC-CCCEEE
Confidence 568888887766544321 1122467888 887764
No 61
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=52.55 E-value=10 Score=32.23 Aligned_cols=16 Identities=25% Similarity=0.534 Sum_probs=7.9
Q ss_pred ceecCccCcccCCchh
Q 027549 19 AFSCIYCRKSFANHRS 34 (222)
Q Consensus 19 Pf~C~~CgKsF~~ks~ 34 (222)
-|.|+.|+..|+....
T Consensus 117 ~Y~Cp~C~~rytf~eA 132 (178)
T PRK06266 117 FFFCPNCHIRFTFDEA 132 (178)
T ss_pred EEECCCCCcEEeHHHH
Confidence 3455555555544443
No 62
>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=49.28 E-value=6.4 Score=32.66 Aligned_cols=36 Identities=8% Similarity=-0.048 Sum_probs=25.4
Q ss_pred cCCCcccccCCCCCccccCCCCCccccccCCCCCCCCCcccccccccc
Q 027549 42 HNVQLKAAWRRNCPSNSCASIGSASTIVDPLSSNQPGNSCEVVGNNLA 89 (222)
Q Consensus 42 HtgeKPf~C~~~CGKsFs~s~~L~sh~~~p~~~~~~~~sC~~cG~~l~ 89 (222)
.....-|.|+. |+..|+.-..+. -+|.|+.||..|.
T Consensus 104 e~~~~~Y~Cp~-c~~r~tf~eA~~-----------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 104 ETNNMFFICPN-MCVRFTFNEAME-----------LNFTCPRCGAMLD 139 (158)
T ss_pred ccCCCeEECCC-CCcEeeHHHHHH-----------cCCcCCCCCCEee
Confidence 34456699999 999887653331 3789999996554
No 63
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=48.89 E-value=14 Score=23.39 Aligned_cols=33 Identities=15% Similarity=0.195 Sum_probs=22.1
Q ss_pred ecCccCcccCCchhhhhhhhhcCCCcccccCCCCCcccc
Q 027549 21 SCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSC 59 (222)
Q Consensus 21 ~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs 59 (222)
.|+.|+..|.-..+- +..+....+|+. |+..|.
T Consensus 4 ~CP~C~~~f~v~~~~-----l~~~~~~vrC~~-C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDK-----LPAGGRKVRCPK-CGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHH-----cccCCcEEECCC-CCcEee
Confidence 688888888765542 123344678988 888774
No 64
>PRK12496 hypothetical protein; Provisional
Probab=48.82 E-value=12 Score=31.39 Aligned_cols=32 Identities=16% Similarity=0.395 Sum_probs=22.1
Q ss_pred ccccCCCCCccccCCCCCccccccCCCCCCCCCcccccccccccccc
Q 027549 47 KAAWRRNCPSNSCASIGSASTIVDPLSSNQPGNSCEVVGNNLAFHKR 93 (222)
Q Consensus 47 Pf~C~~~CGKsFs~s~~L~sh~~~p~~~~~~~~sC~~cG~~l~~H~r 93 (222)
-|.|.. |++.|... ....-|++||..+.....
T Consensus 127 ~~~C~g-C~~~~~~~--------------~~~~~C~~CG~~~~r~~~ 158 (164)
T PRK12496 127 RKVCKG-CKKKYPED--------------YPDDVCEICGSPVKRKMV 158 (164)
T ss_pred eEECCC-CCccccCC--------------CCCCcCCCCCChhhhcch
Confidence 378999 99988542 123469999987765443
No 65
>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=48.38 E-value=12 Score=23.28 Aligned_cols=10 Identities=20% Similarity=0.564 Sum_probs=6.4
Q ss_pred eecCccCccc
Q 027549 20 FSCIYCRKSF 29 (222)
Q Consensus 20 f~C~~CgKsF 29 (222)
|.|..||..+
T Consensus 3 ~~C~~CG~i~ 12 (34)
T cd00729 3 WVCPVCGYIH 12 (34)
T ss_pred EECCCCCCEe
Confidence 6677777543
No 66
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=47.76 E-value=8.5 Score=31.53 Aligned_cols=34 Identities=12% Similarity=0.211 Sum_probs=20.8
Q ss_pred ccccCCCCCccccCCCCCccccccCCCCCCCCCcccccccc-cccccc
Q 027549 47 KAAWRRNCPSNSCASIGSASTIVDPLSSNQPGNSCEVVGNN-LAFHKR 93 (222)
Q Consensus 47 Pf~C~~~CGKsFs~s~~L~sh~~~p~~~~~~~~sC~~cG~~-l~~H~r 93 (222)
|++|.. ||+.|...+ ..-...|..||.+ |.++..
T Consensus 1 PH~Ct~-Cg~~f~dgs------------~eil~GCP~CGg~kF~yv~~ 35 (131)
T PF09845_consen 1 PHQCTK-CGRVFEDGS------------KEILSGCPECGGNKFQYVPE 35 (131)
T ss_pred CcccCc-CCCCcCCCc------------HHHHccCcccCCcceEEcCC
Confidence 578888 999987652 1123457788744 344433
No 67
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=47.12 E-value=11 Score=24.64 Aligned_cols=12 Identities=17% Similarity=0.767 Sum_probs=7.1
Q ss_pred ceecCccCcccC
Q 027549 19 AFSCIYCRKSFA 30 (222)
Q Consensus 19 Pf~C~~CgKsF~ 30 (222)
.|.|..||..|.
T Consensus 3 ~y~C~~CG~~~~ 14 (46)
T PRK00398 3 EYKCARCGREVE 14 (46)
T ss_pred EEECCCCCCEEE
Confidence 466666666554
No 68
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=46.81 E-value=10 Score=29.11 Aligned_cols=34 Identities=15% Similarity=0.307 Sum_probs=23.8
Q ss_pred CceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCC
Q 027549 18 SAFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASI 62 (222)
Q Consensus 18 KPf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~ 62 (222)
.+|.|+.|++. .+.|.-+ .-+.|.. ||..|.--.
T Consensus 34 ~~~~Cp~C~~~--------~VkR~a~--GIW~C~k-Cg~~fAGga 67 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRIAT--GIWKCRK-CGAKFAGGA 67 (89)
T ss_pred cCCcCCCCCCc--------ceeeecc--CeEEcCC-CCCeecccc
Confidence 46899999975 2333333 3589999 999997653
No 69
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=46.29 E-value=8.3 Score=32.72 Aligned_cols=34 Identities=15% Similarity=0.127 Sum_probs=24.4
Q ss_pred CCcccccCCCCCccccCCCCCccccccCCCCCCCCCcccccccccc
Q 027549 44 VQLKAAWRRNCPSNSCASIGSASTIVDPLSSNQPGNSCEVVGNNLA 89 (222)
Q Consensus 44 geKPf~C~~~CGKsFs~s~~L~sh~~~p~~~~~~~~sC~~cG~~l~ 89 (222)
...-|.|+. |++.|+.-..+ .-+|.|+.||..|.
T Consensus 114 ~~~~Y~Cp~-C~~rytf~eA~-----------~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 114 NNMFFFCPN-CHIRFTFDEAM-----------EYGFRCPQCGEMLE 147 (178)
T ss_pred CCCEEECCC-CCcEEeHHHHh-----------hcCCcCCCCCCCCe
Confidence 345689999 99998765322 23789999996654
No 70
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=45.33 E-value=10 Score=34.40 Aligned_cols=44 Identities=14% Similarity=0.256 Sum_probs=30.4
Q ss_pred eecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCCCCccc
Q 027549 20 FSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASIGSAST 67 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~L~sh 67 (222)
|.|..||.... +..+.+|+..-++ .-|.|-. |++.|.+ .....|
T Consensus 4 FtCnvCgEsvK-Kp~vekH~srCrn-~~fSCID-C~k~F~~-~sYknH 47 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSRCRN-AYFSCID-CGKTFER-VSYKNH 47 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHhccC-CeeEEee-ccccccc-chhhhh
Confidence 77888887754 4456667765555 5688888 9999987 334444
No 71
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=44.71 E-value=17 Score=24.10 Aligned_cols=11 Identities=18% Similarity=0.543 Sum_probs=6.5
Q ss_pred eecCccCcccC
Q 027549 20 FSCIYCRKSFA 30 (222)
Q Consensus 20 f~C~~CgKsF~ 30 (222)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 56666666554
No 72
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=43.17 E-value=17 Score=26.01 Aligned_cols=8 Identities=38% Similarity=1.107 Sum_probs=4.0
Q ss_pred eecCccCc
Q 027549 20 FSCIYCRK 27 (222)
Q Consensus 20 f~C~~CgK 27 (222)
|.|+.||.
T Consensus 28 F~CPnCGe 35 (61)
T COG2888 28 FPCPNCGE 35 (61)
T ss_pred eeCCCCCc
Confidence 44555553
No 73
>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=42.58 E-value=20 Score=29.30 Aligned_cols=30 Identities=13% Similarity=-0.013 Sum_probs=18.8
Q ss_pred eecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCC
Q 027549 20 FSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCAS 61 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s 61 (222)
..|+.||+.|-- | ...|..|+. ||..|...
T Consensus 10 r~Cp~cg~kFYD---L--------nk~p~vcP~-cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYD---L--------NRRPAVSPY-TGEQFPPE 39 (129)
T ss_pred ccCCCcCccccc---c--------CCCCccCCC-cCCccCcc
Confidence 467777777632 2 124677777 87776554
No 74
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=39.50 E-value=27 Score=21.95 Aligned_cols=34 Identities=12% Similarity=0.217 Sum_probs=22.1
Q ss_pred eecCccCcccCCchhhhhhhhhcCCCcccccCCCCCcccc
Q 027549 20 FSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSC 59 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs 59 (222)
..|+.|+..|.-..... -......+|+. |+..|.
T Consensus 3 i~Cp~C~~~y~i~d~~i-----p~~g~~v~C~~-C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKI-----PPKGRKVRCSK-CGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHHHC-----CCCCcEEECCC-CCCEeC
Confidence 46888888887665532 22234578888 887763
No 75
>PHA00626 hypothetical protein
Probab=38.76 E-value=16 Score=25.90 Aligned_cols=15 Identities=13% Similarity=0.078 Sum_probs=12.0
Q ss_pred cccccCCCCCccccCC
Q 027549 46 LKAAWRRNCPSNSCAS 61 (222)
Q Consensus 46 KPf~C~~~CGKsFs~s 61 (222)
..|.|+. ||..|+..
T Consensus 22 nrYkCkd-CGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCD-CGYNDSKD 36 (59)
T ss_pred cceEcCC-CCCeechh
Confidence 4699999 99988753
No 76
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=35.46 E-value=25 Score=25.04 Aligned_cols=9 Identities=11% Similarity=0.106 Sum_probs=4.7
Q ss_pred cccCCCCCcc
Q 027549 48 AAWRRNCPSN 57 (222)
Q Consensus 48 f~C~~~CGKs 57 (222)
|.|+. ||..
T Consensus 26 F~CPn-CG~~ 34 (59)
T PRK14890 26 FLCPN-CGEV 34 (59)
T ss_pred eeCCC-CCCe
Confidence 55555 5544
No 77
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.61 E-value=4.5 Score=35.85 Aligned_cols=52 Identities=17% Similarity=0.303 Sum_probs=31.3
Q ss_pred ecCccCcccCCchhhhhhhhh----------cCCCcccccCCC-CCccccCCCCCccccccCC
Q 027549 21 SCIYCRKSFANHRSLRGHLRS----------HNVQLKAAWRRN-CPSNSCASIGSASTIVDPL 72 (222)
Q Consensus 21 ~C~~CgKsF~~ks~Lk~H~r~----------HtgeKPf~C~~~-CGKsFs~s~~L~sh~~~p~ 72 (222)
.|.+|.+.|.+..-|..|..- ..|.--|+|-++ |+..|.+.-.-+.|+.+.|
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 577777777766666655431 223344677555 7777776666666666544
No 78
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=33.47 E-value=14 Score=26.26 Aligned_cols=26 Identities=19% Similarity=0.476 Sum_probs=15.6
Q ss_pred cCCCceecCccCcccCCchhhhhhhh
Q 027549 15 KGTSAFSCIYCRKSFANHRSLRGHLR 40 (222)
Q Consensus 15 TgEKPf~C~~CgKsF~~ks~Lk~H~r 40 (222)
.||.-+.|+-|+..|....+..+|..
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhh
Confidence 35555666666666666666666654
No 79
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=33.30 E-value=20 Score=29.32 Aligned_cols=26 Identities=35% Similarity=0.664 Sum_probs=16.6
Q ss_pred ceecCccCcccCCchhhhhhhhhcCCCcc
Q 027549 19 AFSCIYCRKSFANHRSLRGHLRSHNVQLK 47 (222)
Q Consensus 19 Pf~C~~CgKsF~~ks~Lk~H~r~HtgeKP 47 (222)
--.|-+||+.|.. |++|.+.|.|-.|
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eeEEccCCcccch---HHHHHHHccCCCH
Confidence 3589999999875 6999999977655
No 80
>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=33.26 E-value=29 Score=21.97 Aligned_cols=29 Identities=14% Similarity=0.308 Sum_probs=14.7
Q ss_pred ccCCCCCccccCCCCCccccccCCCCCCCCCccccccccc
Q 027549 49 AWRRNCPSNSCASIGSASTIVDPLSSNQPGNSCEVVGNNL 88 (222)
Q Consensus 49 ~C~~~CGKsFs~s~~L~sh~~~p~~~~~~~~sC~~cG~~l 88 (222)
.|+. ||+.|.-.. ........|+.||..|
T Consensus 3 ~C~~-Cg~~Yh~~~----------~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 3 ICPK-CGRIYHIEF----------NPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EETT-TTEEEETTT----------B--SSTTBCTTTTEBE
T ss_pred CcCC-CCCcccccc----------CCCCCCCccCCCCCee
Confidence 4666 776664321 1223345677777543
No 81
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=33.23 E-value=21 Score=27.73 Aligned_cols=12 Identities=25% Similarity=0.526 Sum_probs=6.2
Q ss_pred ceecCccCcccC
Q 027549 19 AFSCIYCRKSFA 30 (222)
Q Consensus 19 Pf~C~~CgKsF~ 30 (222)
|-.|..||..|.
T Consensus 58 Pa~CkkCGfef~ 69 (97)
T COG3357 58 PARCKKCGFEFR 69 (97)
T ss_pred ChhhcccCcccc
Confidence 445555555554
No 82
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=32.66 E-value=18 Score=37.33 Aligned_cols=57 Identities=14% Similarity=0.220 Sum_probs=36.9
Q ss_pred ecCccCcccCCchhhhhhhhhcCCCccc-ccCCCCCccccCCCCCccccccCCCCCCCCCcccccccc
Q 027549 21 SCIYCRKSFANHRSLRGHLRSHNVQLKA-AWRRNCPSNSCASIGSASTIVDPLSSNQPGNSCEVVGNN 87 (222)
Q Consensus 21 ~C~~CgKsF~~ks~Lk~H~r~HtgeKPf-~C~~~CGKsFs~s~~L~sh~~~p~~~~~~~~sC~~cG~~ 87 (222)
.|..||-.|+--..|-.- |-+|..+.| .|+. |.+.+.+..+-.-|. ...+|..||-.
T Consensus 125 ~CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~-C~~EY~dP~nRRfHA--------Qp~aCp~CGP~ 182 (750)
T COG0068 125 NCTNCGPRFTIIEALPYD-RENTSMADFPLCPF-CDKEYKDPLNRRFHA--------QPIACPKCGPH 182 (750)
T ss_pred ccCCCCcceeeeccCCCC-cccCccccCcCCHH-HHHHhcCcccccccc--------ccccCcccCCC
Confidence 488888888877766543 445556665 4888 888877765433333 23567778743
No 83
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=30.00 E-value=30 Score=23.68 Aligned_cols=11 Identities=18% Similarity=0.836 Sum_probs=6.0
Q ss_pred ceecCccCccc
Q 027549 19 AFSCIYCRKSF 29 (222)
Q Consensus 19 Pf~C~~CgKsF 29 (222)
-|.|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 35555555555
No 84
>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=29.71 E-value=50 Score=21.86 Aligned_cols=28 Identities=29% Similarity=0.617 Sum_probs=18.1
Q ss_pred ecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCC
Q 027549 21 SCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCAS 61 (222)
Q Consensus 21 ~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s 61 (222)
.|..|++.|... .+.+.|.. ||+.|-..
T Consensus 4 ~C~~C~~~F~~~------------~rk~~Cr~-Cg~~~C~~ 31 (57)
T cd00065 4 SCMGCGKPFTLT------------RRRHHCRN-CGRIFCSK 31 (57)
T ss_pred cCcccCccccCC------------ccccccCc-CcCCcChH
Confidence 577788877651 23356777 88877654
No 85
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.02 E-value=9 Score=34.00 Aligned_cols=70 Identities=19% Similarity=0.239 Sum_probs=49.3
Q ss_pred CceecCc--cCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCCCCccccccCC--------CCCCCCCcccccccc
Q 027549 18 SAFSCIY--CRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASIGSASTIVDPL--------SSNQPGNSCEVVGNN 87 (222)
Q Consensus 18 KPf~C~~--CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~L~sh~~~p~--------~~~~~~~sC~~cG~~ 87 (222)
..|.|++ |...|....+...|..+-++ -.|.. |.+.|.+.--|..||..-| ..+++-|.|-+-|+.
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~-C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt 153 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSF-CKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCT 153 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhccc---chhHH-HHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhh
Confidence 3477886 77888888877777654333 26988 9999999888888885443 334666788776665
Q ss_pred cccc
Q 027549 88 LAFH 91 (222)
Q Consensus 88 l~~H 91 (222)
+.+|
T Consensus 154 ~KFk 157 (253)
T KOG4173|consen 154 EKFK 157 (253)
T ss_pred hhhh
Confidence 5553
No 86
>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=28.86 E-value=24 Score=33.26 Aligned_cols=42 Identities=17% Similarity=0.270 Sum_probs=19.9
Q ss_pred CceecCccCcccCCchhhh---hhhh-hcCCC-cccccCCCCCccccC
Q 027549 18 SAFSCIYCRKSFANHRSLR---GHLR-SHNVQ-LKAAWRRNCPSNSCA 60 (222)
Q Consensus 18 KPf~C~~CgKsF~~ks~Lk---~H~r-~Htge-KPf~C~~~CGKsFs~ 60 (222)
+.+.|..|.+.+......- .|.. .|... +-|+|.. |+++...
T Consensus 251 kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~-C~~Rt~s 297 (344)
T PF09332_consen 251 KAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKD-CGNRTIS 297 (344)
T ss_dssp EEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T--TS-EEEE
T ss_pred EEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCC-CCCeeee
Confidence 4689999987655544332 2321 23333 3489999 9987553
No 87
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.81 E-value=32 Score=27.84 Aligned_cols=11 Identities=18% Similarity=0.788 Sum_probs=5.3
Q ss_pred eecCccCcccC
Q 027549 20 FSCIYCRKSFA 30 (222)
Q Consensus 20 f~C~~CgKsF~ 30 (222)
+.|..||..|.
T Consensus 71 ~~C~~CG~~~~ 81 (135)
T PRK03824 71 LKCRNCGNEWS 81 (135)
T ss_pred EECCCCCCEEe
Confidence 44555554443
No 88
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=28.27 E-value=37 Score=22.45 Aligned_cols=24 Identities=42% Similarity=0.841 Sum_probs=17.8
Q ss_pred ceecCccCcccCCc-----hhhhhhhh-hc
Q 027549 19 AFSCIYCRKSFANH-----RSLRGHLR-SH 42 (222)
Q Consensus 19 Pf~C~~CgKsF~~k-----s~Lk~H~r-~H 42 (222)
--.|..|++.+... ++|.+|++ .|
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 35799999988665 47888877 44
No 89
>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=27.93 E-value=33 Score=22.12 Aligned_cols=11 Identities=27% Similarity=0.887 Sum_probs=5.6
Q ss_pred eecCccCcccC
Q 027549 20 FSCIYCRKSFA 30 (222)
Q Consensus 20 f~C~~CgKsF~ 30 (222)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 45555555443
No 90
>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 PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=25.66 E-value=45 Score=21.16 Aligned_cols=24 Identities=29% Similarity=0.598 Sum_probs=13.6
Q ss_pred CCCceecCccCcccCCc----hhhhhhh
Q 027549 16 GTSAFSCIYCRKSFANH----RSLRGHL 39 (222)
Q Consensus 16 gEKPf~C~~CgKsF~~k----s~Lk~H~ 39 (222)
+..-..|..|++.+... ..|.+|+
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 34556788888877654 5677776
No 92
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=24.33 E-value=34 Score=28.43 Aligned_cols=25 Identities=32% Similarity=0.448 Sum_probs=20.9
Q ss_pred eecCccCcccCCchhhhhhhhhcCCCcc
Q 027549 20 FSCIYCRKSFANHRSLRGHLRSHNVQLK 47 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r~HtgeKP 47 (222)
-.|-+|||.|. +|++|..+|.+--|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 36889999986 59999999988765
No 93
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=24.18 E-value=34 Score=21.98 Aligned_cols=11 Identities=9% Similarity=0.120 Sum_probs=8.0
Q ss_pred cccCCCCCcccc
Q 027549 48 AAWRRNCPSNSC 59 (222)
Q Consensus 48 f~C~~~CGKsFs 59 (222)
|.|.. |+..|.
T Consensus 29 y~C~~-C~~~w~ 39 (40)
T smart00440 29 YVCTK-CGHRWR 39 (40)
T ss_pred EEeCC-CCCEeC
Confidence 77887 887664
No 94
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=23.79 E-value=50 Score=28.05 Aligned_cols=23 Identities=13% Similarity=0.258 Sum_probs=17.4
Q ss_pred ccccCCCCCccccCCCCCccccccCCCCCCCCCcccccc
Q 027549 47 KAAWRRNCPSNSCASIGSASTIVDPLSSNQPGNSCEVVG 85 (222)
Q Consensus 47 Pf~C~~~CGKsFs~s~~L~sh~~~p~~~~~~~~sC~~cG 85 (222)
-|.|++ ||..+.. .++..|++||
T Consensus 134 ~~vC~v-CGy~~~g---------------e~P~~CPiCg 156 (166)
T COG1592 134 VWVCPV-CGYTHEG---------------EAPEVCPICG 156 (166)
T ss_pred EEEcCC-CCCcccC---------------CCCCcCCCCC
Confidence 599999 9876532 4567888998
No 95
>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=23.73 E-value=36 Score=28.40 Aligned_cols=14 Identities=7% Similarity=0.114 Sum_probs=11.4
Q ss_pred ccccCCCCCccccCC
Q 027549 47 KAAWRRNCPSNSCAS 61 (222)
Q Consensus 47 Pf~C~~~CGKsFs~s 61 (222)
.-.|.. |+++|++-
T Consensus 28 RReC~~-C~~RFTTy 41 (147)
T TIGR00244 28 RRECLE-CHERFTTF 41 (147)
T ss_pred cccCCc-cCCcccee
Confidence 357998 99999875
No 96
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=23.57 E-value=55 Score=31.82 Aligned_cols=39 Identities=15% Similarity=0.395 Sum_probs=27.1
Q ss_pred hcCCCceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCc
Q 027549 14 EKGTSAFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPS 56 (222)
Q Consensus 14 HTgEKPf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGK 56 (222)
-+...-|.|+.|.+.|.....+. ..-..+--|.|.. |+-
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~-C~g 161 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCEN-CGG 161 (436)
T ss_pred ccccccccCCccccchhhhHHHH---hhcccCceEEEec-CCC
Confidence 34556799999999998766553 2333344689998 873
No 97
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.44 E-value=42 Score=27.04 Aligned_cols=47 Identities=13% Similarity=0.157 Sum_probs=26.9
Q ss_pred hhhhhhcCCCceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCCC
Q 027549 9 DGENLEKGTSAFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASIG 63 (222)
Q Consensus 9 ~H~rtHTgEKPf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~~ 63 (222)
.+++.+... -.|+.|+... ...+-..-.+...|.|+. |++.|....+
T Consensus 22 ~~~~~~~~~--~~cP~C~s~~-----~~k~g~~~~~~qRyrC~~-C~~tf~~~~~ 68 (129)
T COG3677 22 YAIRMQITK--VNCPRCKSSN-----VVKIGGIRRGHQRYKCKS-CGSTFTVETG 68 (129)
T ss_pred HHHhhhccc--CcCCCCCccc-----eeeECCccccccccccCC-cCcceeeecc
Confidence 444544432 3688887543 112222223355699999 9999987643
No 98
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=22.81 E-value=38 Score=28.51 Aligned_cols=14 Identities=7% Similarity=0.102 Sum_probs=11.2
Q ss_pred ccccCCCCCccccCC
Q 027549 47 KAAWRRNCPSNSCAS 61 (222)
Q Consensus 47 Pf~C~~~CGKsFs~s 61 (222)
.-.|+. |+++|++-
T Consensus 28 RReC~~-C~~RFTTf 41 (156)
T COG1327 28 RRECLE-CGERFTTF 41 (156)
T ss_pred hhcccc-cccccchh
Confidence 357998 99999874
No 99
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=22.79 E-value=45 Score=34.49 Aligned_cols=9 Identities=22% Similarity=0.316 Sum_probs=5.2
Q ss_pred ecCccCccc
Q 027549 21 SCIYCRKSF 29 (222)
Q Consensus 21 ~C~~CgKsF 29 (222)
.|..||..+
T Consensus 437 ~C~~Cg~v~ 445 (730)
T COG1198 437 LCRDCGYIA 445 (730)
T ss_pred ecccCCCcc
Confidence 466666544
No 100
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=22.69 E-value=42 Score=32.07 Aligned_cols=22 Identities=27% Similarity=0.696 Sum_probs=12.6
Q ss_pred CceecCc--cCcccCCchhhhhhh
Q 027549 18 SAFSCIY--CRKSFANHRSLRGHL 39 (222)
Q Consensus 18 KPf~C~~--CgKsF~~ks~Lk~H~ 39 (222)
+||+|.+ |.+.+.....|+.|.
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~ 371 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHK 371 (442)
T ss_pred CCCCCCCCcchhhcccCcceeecc
Confidence 5666654 666666555555543
No 101
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=22.05 E-value=27 Score=30.74 Aligned_cols=30 Identities=20% Similarity=0.458 Sum_probs=20.9
Q ss_pred CCCceecCccCcccCCchhhhhhhhhcCCC
Q 027549 16 GTSAFSCIYCRKSFANHRSLRGHLRSHNVQ 45 (222)
Q Consensus 16 gEKPf~C~~CgKsF~~ks~Lk~H~r~Htge 45 (222)
.+.-|.|..|+|.|.-...+.+|...-+.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 345688999999999999999988754444
No 102
>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=21.65 E-value=46 Score=20.26 Aligned_cols=20 Identities=45% Similarity=0.903 Sum_probs=9.6
Q ss_pred eecCccCcccCCchhhhhhhh
Q 027549 20 FSCIYCRKSFANHRSLRGHLR 40 (222)
Q Consensus 20 f~C~~CgKsF~~ks~Lk~H~r 40 (222)
|.|-.|++.| .....+.|..
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 4566666666 3444454543
No 103
>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=21.38 E-value=81 Score=19.53 Aligned_cols=11 Identities=18% Similarity=0.546 Sum_probs=5.5
Q ss_pred eecCccCcccC
Q 027549 20 FSCIYCRKSFA 30 (222)
Q Consensus 20 f~C~~CgKsF~ 30 (222)
|.|..|+..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 45566665543
No 104
>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=21.19 E-value=53 Score=25.79 Aligned_cols=10 Identities=20% Similarity=0.607 Sum_probs=4.5
Q ss_pred eecCccCccc
Q 027549 20 FSCIYCRKSF 29 (222)
Q Consensus 20 f~C~~CgKsF 29 (222)
+.|..|++.|
T Consensus 71 ~~C~~Cg~~~ 80 (115)
T TIGR00100 71 CECEDCSEEV 80 (115)
T ss_pred EEcccCCCEE
Confidence 3444444433
No 105
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=20.72 E-value=40 Score=27.34 Aligned_cols=23 Identities=35% Similarity=0.589 Sum_probs=15.7
Q ss_pred ccchhhhhhhccccchhhhhhhhc
Q 027549 132 KLRNDEIQTCQDGLAEGCVSKMVG 155 (222)
Q Consensus 132 ~~~~~~~~~~~~~~~~~~~~~~~~ 155 (222)
-++.-||-. +..+..|||||+++
T Consensus 33 G~rp~~Isr-~l~Vs~gcVsKIl~ 55 (125)
T PF00292_consen 33 GVRPCDISR-QLRVSHGCVSKILS 55 (125)
T ss_dssp T--HHHHHH-HHT--HHHHHHHHH
T ss_pred cCCHHHHHH-HHccchhHHHHHHH
Confidence 456668855 89999999999986
No 106
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=20.68 E-value=44 Score=25.66 Aligned_cols=34 Identities=12% Similarity=0.297 Sum_probs=22.8
Q ss_pred CceecCccCcccCCchhhhhhhhhcCCCcccccCCCCCccccCCC
Q 027549 18 SAFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCPSNSCASI 62 (222)
Q Consensus 18 KPf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CGKsFs~s~ 62 (222)
..|.|+.|++.-.. ....-.+.|.. |++.|+-..
T Consensus 35 a~y~CpfCgk~~vk----------R~a~GIW~C~~-C~~~~AGGA 68 (90)
T PTZ00255 35 AKYFCPFCGKHAVK----------RQAVGIWRCKG-CKKTVAGGA 68 (90)
T ss_pred CCccCCCCCCCcee----------eeeeEEEEcCC-CCCEEeCCc
Confidence 47899999864211 11224689999 999997653
No 107
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=20.47 E-value=56 Score=27.53 Aligned_cols=31 Identities=16% Similarity=0.506 Sum_probs=17.0
Q ss_pred ceecCccCcccCCchhhhhhhhhcCCCcccccCCCCC
Q 027549 19 AFSCIYCRKSFANHRSLRGHLRSHNVQLKAAWRRNCP 55 (222)
Q Consensus 19 Pf~C~~CgKsF~~ks~Lk~H~r~HtgeKPf~C~~~CG 55 (222)
+|.|. |+..|.+ ..+|-..-.|+ .|.|.. |+
T Consensus 117 ~Y~C~-C~q~~l~---~RRhn~~~~g~-~YrC~~-C~ 147 (156)
T COG3091 117 PYRCQ-CQQHYLR---IRRHNTVRRGE-VYRCGK-CG 147 (156)
T ss_pred eEEee-cCCccch---hhhcccccccc-eEEecc-CC
Confidence 56666 6665443 23444444455 566666 65
Done!