Query 040864
Match_columns 203
No_of_seqs 401 out of 2153
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 12:36:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040864.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040864hhsearch_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 99.7 1.4E-17 3E-22 138.0 0.2 111 59-184 146-264 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.5 8.8E-16 1.9E-20 127.3 -0.1 80 59-153 177-257 (279)
3 KOG3623 Homeobox transcription 99.2 3.5E-12 7.6E-17 117.2 0.8 69 52-133 903-971 (1007)
4 KOG3623 Homeobox transcription 99.1 2.1E-11 4.5E-16 112.3 1.6 90 67-169 890-984 (1007)
5 KOG1074 Transcriptional repres 99.1 3.2E-11 7E-16 112.4 2.3 72 58-138 620-694 (958)
6 KOG3576 Ovo and related transc 98.9 4.5E-10 9.8E-15 89.9 0.2 73 67-152 113-186 (267)
7 PHA02768 hypothetical protein; 98.9 1.4E-09 3E-14 69.8 2.3 44 71-129 5-48 (55)
8 KOG3576 Ovo and related transc 98.8 1.7E-10 3.6E-15 92.4 -2.9 64 59-135 133-197 (267)
9 KOG1074 Transcriptional repres 98.7 6.7E-09 1.5E-13 97.2 2.6 60 72-144 880-939 (958)
10 PHA00733 hypothetical protein 98.4 6.8E-08 1.5E-12 73.1 1.4 62 59-136 62-123 (128)
11 PF13465 zf-H2C2_2: Zinc-finge 98.4 4.1E-08 8.8E-13 53.8 -0.8 25 59-83 2-26 (26)
12 PHA00616 hypothetical protein 98.3 2.4E-07 5.2E-12 56.7 1.2 34 71-104 1-34 (44)
13 PF13465 zf-H2C2_2: Zinc-finge 98.1 1.5E-06 3.3E-11 47.5 1.5 26 86-124 1-26 (26)
14 PHA00732 hypothetical protein 97.9 6.7E-06 1.4E-10 57.1 2.4 46 71-135 1-47 (79)
15 KOG3608 Zn finger proteins [Ge 97.9 8.7E-07 1.9E-11 76.4 -2.6 85 56-152 276-364 (467)
16 KOG3608 Zn finger proteins [Ge 97.6 1.1E-06 2.4E-11 75.7 -6.0 46 59-108 195-242 (467)
17 PF00096 zf-C2H2: Zinc finger, 97.6 3.9E-05 8.5E-10 40.2 1.7 23 72-94 1-23 (23)
18 PLN03086 PRLI-interacting fact 97.6 2.6E-05 5.7E-10 72.0 1.5 67 64-148 446-512 (567)
19 PHA02768 hypothetical protein; 97.5 1.7E-05 3.7E-10 50.9 -0.6 35 104-149 6-40 (55)
20 PHA00733 hypothetical protein 97.3 4.2E-05 9.1E-10 57.9 -0.3 72 59-145 28-104 (128)
21 KOG3993 Transcription factor ( 97.1 6.1E-05 1.3E-09 66.5 -1.6 70 59-137 283-381 (500)
22 PF13912 zf-C2H2_6: C2H2-type 97.0 0.00027 5.8E-09 38.5 1.0 25 71-95 1-25 (27)
23 PLN03086 PRLI-interacting fact 97.0 0.00055 1.2E-08 63.4 3.4 73 59-149 468-550 (567)
24 PF13894 zf-C2H2_4: C2H2-type 97.0 0.00056 1.2E-08 35.5 1.8 23 72-94 1-23 (24)
25 PHA00616 hypothetical protein 96.9 6.3E-05 1.4E-09 46.1 -2.4 31 104-143 2-32 (44)
26 smart00355 ZnF_C2H2 zinc finge 96.6 0.0015 3.2E-08 34.3 1.9 24 72-95 1-24 (26)
27 COG5189 SFP1 Putative transcri 96.5 0.0029 6.2E-08 54.4 3.7 53 68-133 346-419 (423)
28 PF09237 GAGA: GAGA factor; I 96.3 0.0038 8.2E-08 39.3 2.6 34 66-99 19-52 (54)
29 PF05605 zf-Di19: Drought indu 96.3 0.0018 3.8E-08 41.4 1.1 50 71-136 2-53 (54)
30 PRK04860 hypothetical protein; 96.3 0.0032 6.9E-08 49.4 2.7 40 70-126 118-157 (160)
31 COG5048 FOG: Zn-finger [Genera 95.6 0.0082 1.8E-07 52.2 2.5 62 70-142 288-353 (467)
32 PF00096 zf-C2H2: Zinc finger, 95.5 0.0004 8.6E-09 36.3 -3.7 18 118-135 6-23 (23)
33 PF12874 zf-met: Zinc-finger o 94.9 0.012 2.6E-07 31.1 0.8 23 72-94 1-23 (25)
34 KOG3993 Transcription factor ( 94.8 0.0036 7.9E-08 55.5 -2.0 100 71-183 267-376 (500)
35 PF13909 zf-H2C2_5: C2H2-type 93.7 0.05 1.1E-06 28.5 1.7 23 72-95 1-23 (24)
36 PF13894 zf-C2H2_4: C2H2-type 93.2 0.0041 9E-08 32.1 -3.2 19 118-136 6-24 (24)
37 PF13913 zf-C2HC_2: zinc-finge 92.5 0.088 1.9E-06 28.2 1.5 21 72-93 3-23 (25)
38 PF13912 zf-C2H2_6: C2H2-type 92.4 0.01 2.2E-07 32.0 -2.3 25 104-137 2-26 (27)
39 smart00355 ZnF_C2H2 zinc finge 92.2 0.017 3.7E-07 30.0 -1.6 19 118-136 6-24 (26)
40 PF12171 zf-C2H2_jaz: Zinc-fin 91.7 0.034 7.4E-07 30.1 -0.7 22 72-93 2-23 (27)
41 KOG2893 Zn finger protein [Gen 91.2 0.089 1.9E-06 43.7 1.0 47 73-136 12-59 (341)
42 PF12756 zf-C2H2_2: C2H2 type 91.0 0.02 4.4E-07 40.1 -2.6 54 73-135 1-73 (100)
43 PRK04860 hypothetical protein; 88.4 0.12 2.6E-06 40.5 -0.3 27 58-84 130-156 (160)
44 smart00451 ZnF_U1 U1-like zinc 88.3 0.31 6.7E-06 27.6 1.4 22 71-92 3-24 (35)
45 PHA00732 hypothetical protein 85.6 0.32 6.8E-06 33.6 0.5 35 104-150 2-38 (79)
46 PF12756 zf-C2H2_2: C2H2 type 85.1 0.66 1.4E-05 32.2 2.0 24 71-94 50-73 (100)
47 KOG4167 Predicted DNA-binding 84.5 0.46 1E-05 45.3 1.2 26 70-95 791-816 (907)
48 COG5048 FOG: Zn-finger [Genera 83.5 0.91 2E-05 39.3 2.6 61 68-139 30-90 (467)
49 COG5189 SFP1 Putative transcri 79.9 2.1 4.6E-05 37.2 3.4 70 96-182 346-417 (423)
50 PF09237 GAGA: GAGA factor; I 79.2 0.15 3.3E-06 32.2 -2.7 32 96-140 21-52 (54)
51 COG4049 Uncharacterized protei 78.5 0.98 2.1E-05 29.1 0.8 30 64-93 10-39 (65)
52 PF02892 zf-BED: BED zinc fing 70.4 4 8.7E-05 24.4 2.1 25 68-92 13-41 (45)
53 smart00614 ZnF_BED BED zinc fi 69.4 4 8.7E-05 25.2 2.0 25 71-95 18-48 (50)
54 KOG1146 Homeobox protein [Gene 64.3 1.5 3.3E-05 44.5 -1.1 60 65-133 459-539 (1406)
55 KOG2636 Splicing factor 3a, su 63.4 6.3 0.00014 35.8 2.7 29 64-92 394-423 (497)
56 KOG2186 Cell growth-regulating 61.6 5.2 0.00011 33.6 1.7 48 71-134 3-50 (276)
57 PF05443 ROS_MUCR: ROS/MUCR tr 60.8 4.2 9.1E-05 30.9 1.0 28 69-99 70-97 (132)
58 PF11931 DUF3449: Domain of un 55.0 4.5 9.9E-05 32.8 0.3 28 64-91 94-122 (196)
59 PF09986 DUF2225: Uncharacteri 53.6 4.1 8.9E-05 33.3 -0.1 24 69-92 3-26 (214)
60 COG4957 Predicted transcriptio 50.9 8.4 0.00018 29.4 1.1 25 72-99 77-101 (148)
61 smart00734 ZnF_Rad18 Rad18-lik 40.3 22 0.00047 19.0 1.5 20 72-92 2-21 (26)
62 cd00350 rubredoxin_like Rubred 39.7 29 0.00063 19.4 2.0 11 72-82 2-12 (33)
63 PRK00464 nrdR transcriptional 39.2 7.5 0.00016 30.3 -0.7 16 104-128 29-44 (154)
64 PF12013 DUF3505: Protein of u 39.0 23 0.0005 25.4 1.9 25 72-96 81-109 (109)
65 COG1997 RPL43A Ribosomal prote 38.1 11 0.00023 26.5 0.0 32 70-124 34-65 (89)
66 PF09538 FYDLN_acid: Protein o 37.8 23 0.0005 25.8 1.8 30 72-125 10-39 (108)
67 PF04959 ARS2: Arsenite-resist 36.2 13 0.00028 30.6 0.2 27 67-93 73-99 (214)
68 PRK09678 DNA-binding transcrip 35.3 10 0.00022 25.7 -0.4 44 72-128 2-45 (72)
69 PF15269 zf-C2H2_7: Zinc-finge 35.0 40 0.00086 20.8 2.1 25 68-92 15-41 (54)
70 smart00154 ZnF_AN1 AN1-like Zi 34.4 22 0.00048 20.9 1.0 14 71-84 12-25 (39)
71 smart00834 CxxC_CXXC_SSSS Puta 34.3 19 0.00042 20.7 0.7 15 71-85 5-19 (41)
72 COG1592 Rubrerythrin [Energy p 34.1 29 0.00063 27.4 1.9 22 70-108 133-154 (166)
73 PF07754 DUF1610: Domain of un 32.1 25 0.00054 18.6 0.8 11 69-79 14-24 (24)
74 PRK06266 transcription initiat 32.1 26 0.00056 27.9 1.3 36 67-124 113-148 (178)
75 KOG2893 Zn finger protein [Gen 31.8 12 0.00027 31.3 -0.6 30 66-95 29-59 (341)
76 KOG2461 Transcription factor B 31.1 60 0.0013 29.2 3.6 48 59-106 319-366 (396)
77 PF09723 Zn-ribbon_8: Zinc rib 31.0 23 0.00049 21.1 0.7 15 71-85 5-19 (42)
78 PF10013 DUF2256: Uncharacteri 30.1 40 0.00086 20.4 1.6 16 73-88 10-25 (42)
79 TIGR02098 MJ0042_CXXC MJ0042 f 29.9 30 0.00064 19.7 1.0 15 72-86 3-17 (38)
80 PF10571 UPF0547: Uncharacteri 29.8 29 0.00062 18.6 0.9 10 73-82 16-25 (26)
81 TIGR00373 conserved hypothetic 29.6 34 0.00074 26.6 1.6 37 64-122 102-138 (158)
82 cd00924 Cyt_c_Oxidase_Vb Cytoc 29.3 23 0.0005 25.4 0.5 20 63-83 72-91 (97)
83 KOG2593 Transcription initiati 29.1 30 0.00065 31.4 1.3 36 66-108 123-158 (436)
84 KOG4173 Alpha-SNAP protein [In 28.4 9.2 0.0002 31.3 -1.8 53 73-136 108-171 (253)
85 COG5188 PRP9 Splicing factor 3 27.8 54 0.0012 29.1 2.6 28 64-91 367-395 (470)
86 KOG2071 mRNA cleavage and poly 27.7 37 0.0008 32.0 1.7 28 68-95 415-442 (579)
87 KOG3408 U1-like Zn-finger-cont 27.3 33 0.00072 25.7 1.1 26 68-93 54-79 (129)
88 TIGR02605 CxxC_CxxC_SSSS putat 26.7 30 0.00066 21.2 0.7 14 71-84 5-18 (52)
89 PF01428 zf-AN1: AN1-like Zinc 26.1 27 0.00059 20.8 0.4 15 70-84 12-26 (43)
90 KOG2231 Predicted E3 ubiquitin 25.8 28 0.00061 33.4 0.6 21 73-93 184-204 (669)
91 PF13717 zinc_ribbon_4: zinc-r 25.3 64 0.0014 18.5 1.9 16 72-87 3-18 (36)
92 PF01927 Mut7-C: Mut7-C RNAse 25.3 88 0.0019 23.7 3.2 22 68-89 121-142 (147)
93 PHA00626 hypothetical protein 25.1 39 0.00086 21.8 1.0 15 69-83 21-35 (59)
94 smart00531 TFIIE Transcription 24.9 86 0.0019 23.8 3.1 21 67-87 95-115 (147)
95 TIGR02300 FYDLN_acid conserved 24.7 60 0.0013 24.5 2.1 34 72-129 10-43 (129)
96 PF09845 DUF2072: Zn-ribbon co 24.4 39 0.00084 25.6 1.0 15 71-85 1-15 (131)
97 PF08790 zf-LYAR: LYAR-type C2 24.0 21 0.00046 19.6 -0.4 20 72-92 1-20 (28)
98 TIGR00622 ssl1 transcription f 23.7 87 0.0019 23.1 2.7 22 69-90 13-34 (112)
99 PF14353 CpXC: CpXC protein 23.7 92 0.002 22.8 3.0 50 73-134 3-60 (128)
100 PF13719 zinc_ribbon_5: zinc-r 23.6 53 0.0012 18.9 1.3 14 72-85 3-16 (37)
101 KOG2482 Predicted C2H2-type Zn 22.6 48 0.001 29.3 1.3 23 71-93 195-217 (423)
102 cd00729 rubredoxin_SM Rubredox 22.1 74 0.0016 18.0 1.7 11 71-81 2-12 (34)
103 PF10276 zf-CHCC: Zinc-finger 21.1 42 0.00092 20.0 0.5 12 70-81 28-39 (40)
104 PF01363 FYVE: FYVE zinc finge 20.2 41 0.00089 21.8 0.4 11 72-82 10-20 (69)
105 COG3091 SprT Zn-dependent meta 20.1 49 0.0011 25.7 0.8 32 68-108 114-145 (156)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.65 E-value=1.4e-17 Score=138.02 Aligned_cols=111 Identities=15% Similarity=0.156 Sum_probs=84.9
Q ss_pred hhcccCCCCC---CcceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCccccccc
Q 040864 59 TDRRSKPASG---NKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVD 135 (203)
Q Consensus 59 ~~~H~r~Htg---ekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H 135 (203)
+.+|+.+|-. .+.+.|.+|+|.|....+|+.|+|+|+ -| ..|.. |||+|.+.=.|+.|+|+|
T Consensus 146 LsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~----c~C~i---------CGKaFSRPWLLQGHiRTH 210 (279)
T KOG2462|consen 146 LSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LP----CECGI---------CGKAFSRPWLLQGHIRTH 210 (279)
T ss_pred cchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CC----ccccc---------ccccccchHHhhcccccc
Confidence 7788877743 566888888888888888888888887 45 67777 888888888888888888
Q ss_pred CCCCCCCCCcccc-cCCCCCCCccc---CCCccccccC-CCCCCCCCCcccCCC
Q 040864 136 RSSGALGPNLVAR-FGDATSTGFDM---IPWTPFMLED-TIDMFWPGSCHVDNS 184 (203)
Q Consensus 136 ~~~~~~~~~~~~~-f~~~~~~~~~~---~~~~p~~~~~-~~~~~~~~s~~~~~~ 184 (203)
+|||||.|.-+.| |.+.++.|-|| ++.|+|.|.. ++.|.--+.|..|.+
T Consensus 211 TGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 211 TGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred cCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 8888888877544 66666433333 4788888888 888887777777764
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.53 E-value=8.8e-16 Score=127.33 Aligned_cols=80 Identities=14% Similarity=0.191 Sum_probs=70.9
Q ss_pred hhcccCCCCCCcceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCcccccccCCC
Q 040864 59 TDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVDRSS 138 (203)
Q Consensus 59 ~~~H~r~Htgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H~~~ 138 (203)
+..|+|+|+ -+++|.+|||.|.+.+-|+.|+|+|||||| |.|.. |+|+|..+++|+.|+++|.+-
T Consensus 177 LkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKP----F~C~h---------C~kAFADRSNLRAHmQTHS~~ 241 (279)
T KOG2462|consen 177 LKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKP----FSCPH---------CGKAFADRSNLRAHMQTHSDV 241 (279)
T ss_pred HhhHhhccC--CCcccccccccccchHHhhcccccccCCCC----ccCCc---------ccchhcchHHHHHHHHhhcCC
Confidence 677889887 689999999999999999999999999999 88888 999999999999999999999
Q ss_pred CCCCCCcccc-cCCCC
Q 040864 139 GALGPNLVAR-FGDAT 153 (203)
Q Consensus 139 ~~~~~~~~~~-f~~~~ 153 (203)
|.|.|..+.+ |...+
T Consensus 242 K~~qC~~C~KsFsl~S 257 (279)
T KOG2462|consen 242 KKHQCPRCGKSFALKS 257 (279)
T ss_pred ccccCcchhhHHHHHH
Confidence 9999988666 54433
No 3
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.19 E-value=3.5e-12 Score=117.21 Aligned_cols=69 Identities=23% Similarity=0.300 Sum_probs=64.6
Q ss_pred HhhcCCchhcccCCCCCCcceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCccc
Q 040864 52 AAAAGDSTDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPH 131 (203)
Q Consensus 52 ~~~~~~~~~~H~r~Htgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H 131 (203)
++....++.+|.--|+|.|||+|.+|.|+|..+.+|..|+|.|.|||| |+|.. |+|.|+++....+|
T Consensus 903 ~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKP----fQCdK---------ClKRFSHSGSYSQH 969 (1007)
T KOG3623|consen 903 AFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKP----FQCDK---------CLKRFSHSGSYSQH 969 (1007)
T ss_pred HHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCc----chhhh---------hhhhcccccchHhh
Confidence 344677899999999999999999999999999999999999999999 99999 99999999999999
Q ss_pred cc
Q 040864 132 SL 133 (203)
Q Consensus 132 ~r 133 (203)
|-
T Consensus 970 MN 971 (1007)
T KOG3623|consen 970 MN 971 (1007)
T ss_pred hc
Confidence 84
No 4
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.11 E-value=2.1e-11 Score=112.25 Aligned_cols=90 Identities=17% Similarity=0.292 Sum_probs=76.3
Q ss_pred CCCcceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCcccccccCCCCCCCCCc-
Q 040864 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVDRSSGALGPNL- 145 (203)
Q Consensus 67 tgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H~~~~~~~~~~- 145 (203)
+.+-+|.|..|.|.|...+.|.+|.--|+|.|| |+|.. |.|+|.++.+|..|+|.|.|+|||.|.-
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRP----yqC~i---------CkKAFKHKHHLtEHkRLHSGEKPfQCdKC 956 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRP----YQCII---------CKKAFKHKHHLTEHKRLHSGEKPFQCDKC 956 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCC----cccch---------hhHhhhhhhhhhhhhhhccCCCcchhhhh
Confidence 456789999999999999999999999999999 99999 9999999999999999999999999865
Q ss_pred ccccCCCCCCCccc----CCCccccccC
Q 040864 146 VARFGDATSTGFDM----IPWTPFMLED 169 (203)
Q Consensus 146 ~~~f~~~~~~~~~~----~~~~p~~~~~ 169 (203)
++||.+.....-|| .=.|||..+-
T Consensus 957 lKRFSHSGSYSQHMNHRYSYCKpyrEer 984 (1007)
T KOG3623|consen 957 LKRFSHSGSYSQHMNHRYSYCKPYREER 984 (1007)
T ss_pred hhhcccccchHhhhccchhcccchhhcc
Confidence 88998655333343 2356666543
No 5
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.09 E-value=3.2e-11 Score=112.39 Aligned_cols=72 Identities=18% Similarity=0.318 Sum_probs=63.0
Q ss_pred chhcccCCCCCCcceecCCCCccCCCchhHHHHHHhhcCCCCCccccccc---cccccccCCcCCCCCCCCCCCcccccc
Q 040864 58 STDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNH---RMMMSSIGFLFNSVPLRSLGVQPHSLV 134 (203)
Q Consensus 58 ~~~~H~r~Htgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~---~~~~~~~g~~C~k~F~~~~~L~~H~r~ 134 (203)
.++-|.|+|+|||||+|.+||++|..+.+|+.|+.+|...-|+.-.+.|. . |-+.|.....|.+|+|+
T Consensus 620 aLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~i---------c~~kftn~V~lpQhIri 690 (958)
T KOG1074|consen 620 ALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFI---------CQKKFTNAVTLPQHIRI 690 (958)
T ss_pred hhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhh---------hcccccccccccceEEe
Confidence 47889999999999999999999999999999999998776765556777 6 99999999999999999
Q ss_pred cCCC
Q 040864 135 DRSS 138 (203)
Q Consensus 135 H~~~ 138 (203)
|.+.
T Consensus 691 H~~~ 694 (958)
T KOG1074|consen 691 HLGG 694 (958)
T ss_pred ecCC
Confidence 9843
No 6
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.85 E-value=4.5e-10 Score=89.93 Aligned_cols=73 Identities=16% Similarity=0.255 Sum_probs=61.6
Q ss_pred CCCcceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCcccccccCCCCCCCCCcc
Q 040864 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVDRSSGALGPNLV 146 (203)
Q Consensus 67 tgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H~~~~~~~~~~~ 146 (203)
.+...|.|.+|+|+|....-|.+|++.|..-|. +-|.. |||.|+....|++|+|+|+|-|||.|..+
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr----~lct~---------cgkgfndtfdlkrh~rthtgvrpykc~~c 179 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKR----HLCTF---------CGKGFNDTFDLKRHTRTHTGVRPYKCSLC 179 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHH----HHHhh---------ccCcccchhhhhhhhccccCccccchhhh
Confidence 345678999999999999999999999988777 67777 99999999999999999999999999885
Q ss_pred cc-cCCC
Q 040864 147 AR-FGDA 152 (203)
Q Consensus 147 ~~-f~~~ 152 (203)
.+ |.+.
T Consensus 180 ~kaftqr 186 (267)
T KOG3576|consen 180 EKAFTQR 186 (267)
T ss_pred hHHHHhh
Confidence 54 5443
No 7
>PHA02768 hypothetical protein; Provisional
Probab=98.85 E-value=1.4e-09 Score=69.81 Aligned_cols=44 Identities=14% Similarity=0.314 Sum_probs=40.1
Q ss_pred ceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCc
Q 040864 71 VFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQ 129 (203)
Q Consensus 71 p~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~ 129 (203)
-|.|..||+.|...++|..|+++|+ ++ ++|.. |++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~----~kc~~---------C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TN----LKLSN---------CKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--Cc----ccCCc---------ccceecccceeE
Confidence 3899999999999999999999999 67 88888 999999888775
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.83 E-value=1.7e-10 Score=92.37 Aligned_cols=64 Identities=22% Similarity=0.305 Sum_probs=59.9
Q ss_pred hhcccCCCCCCcceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCccccc-cc
Q 040864 59 TDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSL-VD 135 (203)
Q Consensus 59 ~~~H~r~Htgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r-~H 135 (203)
+.+|++.|...|.|.|..|||.|...-.|++|.|+|+|-|| |+|.. |+|+|.++..|..|.+ +|
T Consensus 133 lnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrp----ykc~~---------c~kaftqrcsleshl~kvh 197 (267)
T KOG3576|consen 133 LNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRP----YKCSL---------CEKAFTQRCSLESHLKKVH 197 (267)
T ss_pred HHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccc----cchhh---------hhHHHHhhccHHHHHHHHc
Confidence 56799999999999999999999999999999999999999 89999 9999999999999975 45
No 9
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.70 E-value=6.7e-09 Score=97.19 Aligned_cols=60 Identities=22% Similarity=0.211 Sum_probs=56.3
Q ss_pred eecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCcccccccCCCCCCCCC
Q 040864 72 FSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVDRSSGALGPN 144 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H~~~~~~~~~ 144 (203)
+.|.+||+.|...++|..|+|+|+|+|| |+|.. |+++|..+.+|+.||.+|....|+...
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KP----F~C~f---------C~~aFttrgnLKvHMgtH~w~q~~srr 939 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKP----FFCHF---------CEEAFTTRGNLKVHMGTHMWVQPPSRR 939 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCC----ccchh---------hhhhhhhhhhhhhhhccccccCCCccC
Confidence 6899999999999999999999999999 88988 999999999999999999988866665
No 10
>PHA00733 hypothetical protein
Probab=98.44 E-value=6.8e-08 Score=73.11 Aligned_cols=62 Identities=15% Similarity=0.100 Sum_probs=52.2
Q ss_pred hhcccCCCCCCcceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCcccccccC
Q 040864 59 TDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVDR 136 (203)
Q Consensus 59 ~~~H~r~Htgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H~ 136 (203)
+.+|+..+ +.+||.|..|++.|.....|..|+++| +++ +.|.. |++.|.....|..|++..+
T Consensus 62 l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~----~~C~~---------CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 62 LYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHS----KVCPV---------CGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred HHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHhcC--CcC----ccCCC---------CCCccCCHHHHHHHHHHhc
Confidence 55665554 489999999999999999999999987 456 78888 9999999999999987544
No 11
>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=98.38 E-value=4.1e-08 Score=53.78 Aligned_cols=25 Identities=24% Similarity=0.699 Sum_probs=22.4
Q ss_pred hhcccCCCCCCcceecCCCCccCCC
Q 040864 59 TDRRSKPASGNKVFSCNFCMRKFYS 83 (203)
Q Consensus 59 ~~~H~r~Htgekp~~C~~Cgk~F~~ 83 (203)
+.+|+++|+++|||.|..|++.|.+
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEESS
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 6789999999999999999999863
No 12
>PHA00616 hypothetical protein
Probab=98.30 E-value=2.4e-07 Score=56.73 Aligned_cols=34 Identities=12% Similarity=0.275 Sum_probs=31.1
Q ss_pred ceecCCCCccCCCchhHHHHHHhhcCCCCCcccc
Q 040864 71 VFSCNFCMRKFYSSQALGGHQNAHKRERGAARRF 104 (203)
Q Consensus 71 p~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~ 104 (203)
||+|..||+.|...+.|..|++.|+|++++.|.|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999965554
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=98.09 E-value=1.5e-06 Score=47.46 Aligned_cols=26 Identities=15% Similarity=0.161 Sum_probs=23.1
Q ss_pred hHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCC
Q 040864 86 ALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLR 124 (203)
Q Consensus 86 ~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~ 124 (203)
+|..|+++|+|+|| |.|.. |++.|.+
T Consensus 1 ~l~~H~~~H~~~k~----~~C~~---------C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKP----YKCPY---------CGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSS----EEESS---------SSEEESS
T ss_pred CHHHHhhhcCCCCC----CCCCC---------CcCeeCc
Confidence 58899999999999 88888 9999864
No 14
>PHA00732 hypothetical protein
Probab=97.91 E-value=6.7e-06 Score=57.06 Aligned_cols=46 Identities=20% Similarity=0.189 Sum_probs=38.8
Q ss_pred ceecCCCCccCCCchhHHHHHHh-hcCCCCCccccccccccccccCCcCCCCCCCCCCCccccccc
Q 040864 71 VFSCNFCMRKFYSSQALGGHQNA-HKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVD 135 (203)
Q Consensus 71 p~~C~~Cgk~F~~~~~L~~H~r~-H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H 135 (203)
||.|..|++.|.....|..|++. |. + +.|.. |++.|. .|..|.+++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~----~~C~~---------CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---L----TKCPV---------CNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---C----CccCC---------CCCEeC---Chhhhhccc
Confidence 68999999999999999999984 65 4 57888 999998 478887654
No 15
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=97.90 E-value=8.7e-07 Score=76.43 Aligned_cols=85 Identities=16% Similarity=0.168 Sum_probs=63.3
Q ss_pred CCchhcccCC-CCCCcceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCcccccc
Q 040864 56 GDSTDRRSKP-ASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLV 134 (203)
Q Consensus 56 ~~~~~~H~r~-Htgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~ 134 (203)
..++..|+|. |...|||+|..|.+.|...+.|.+|..+|. +.. |+|.. ..|...|.....|++|++-
T Consensus 276 ~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~----y~C~h-------~~C~~s~r~~~q~~~H~~e 343 (467)
T KOG3608|consen 276 ASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTV----YQCEH-------PDCHYSVRTYTQMRRHFLE 343 (467)
T ss_pred hHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccc----eecCC-------CCCcHHHHHHHHHHHHHHH
Confidence 3347888875 677889999999999999999999988887 445 66655 3377788888888888875
Q ss_pred cC-CCCC--CCCCcccccCCC
Q 040864 135 DR-SSGA--LGPNLVARFGDA 152 (203)
Q Consensus 135 H~-~~~~--~~~~~~~~f~~~ 152 (203)
|+ |..| |.|-.+.||+..
T Consensus 344 vhEg~np~~Y~CH~Cdr~ft~ 364 (467)
T KOG3608|consen 344 VHEGNNPILYACHCCDRFFTS 364 (467)
T ss_pred hccCCCCCceeeecchhhhcc
Confidence 43 5443 778888887643
No 16
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=97.64 E-value=1.1e-06 Score=75.74 Aligned_cols=46 Identities=22% Similarity=0.348 Sum_probs=38.5
Q ss_pred hhcccCCCCCCcceecCCCCccCCCchhHHHHHHhhc--CCCCCcccccccc
Q 040864 59 TDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAHK--RERGAARRFQNHR 108 (203)
Q Consensus 59 ~~~H~r~Htgekp~~C~~Cgk~F~~~~~L~~H~r~H~--gekp~~c~~~C~~ 108 (203)
+.+|.|.|+++|...|+.||.-|.....|-.|.|-.+ ...+ |+|..
T Consensus 195 LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~----fqC~~ 242 (467)
T KOG3608|consen 195 LREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNS----FQCAQ 242 (467)
T ss_pred HHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCc----hHHHH
Confidence 8999999999999999999999999999999987443 3456 55554
No 17
>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=97.58 E-value=3.9e-05 Score=40.22 Aligned_cols=23 Identities=30% Similarity=0.688 Sum_probs=21.7
Q ss_pred eecCCCCccCCCchhHHHHHHhh
Q 040864 72 FSCNFCMRKFYSSQALGGHQNAH 94 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L~~H~r~H 94 (203)
|.|..|++.|.....|..|++.|
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 78999999999999999999875
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.58 E-value=2.6e-05 Score=71.95 Aligned_cols=67 Identities=9% Similarity=0.105 Sum_probs=49.2
Q ss_pred CCCCCCcceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCcccccccCCCCCCCC
Q 040864 64 KPASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVDRSSGALGP 143 (203)
Q Consensus 64 r~Htgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H~~~~~~~~ 143 (203)
+....++.+.|..|++.|. ...|..|+++|+ +|+.|+ |++.| .+..|..|+++|.+.+|+.|
T Consensus 446 ~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp--------------Cg~~~-~R~~L~~H~~thCp~Kpi~C 507 (567)
T PLN03086 446 RVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP--------------CGVVL-EKEQMVQHQASTCPLRLITC 507 (567)
T ss_pred eccccccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC--------------CCCCc-chhHHHhhhhccCCCCceeC
Confidence 3344566778999999885 577889988874 774443 66544 55788889888999998888
Q ss_pred Ccccc
Q 040864 144 NLVAR 148 (203)
Q Consensus 144 ~~~~~ 148 (203)
.-|..
T Consensus 508 ~fC~~ 512 (567)
T PLN03086 508 RFCGD 512 (567)
T ss_pred CCCCC
Confidence 87654
No 19
>PHA02768 hypothetical protein; Provisional
Probab=97.49 E-value=1.7e-05 Score=50.92 Aligned_cols=35 Identities=9% Similarity=0.077 Sum_probs=29.7
Q ss_pred cccccccccccCCcCCCCCCCCCCCcccccccCCCCCCCCCccccc
Q 040864 104 FQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVDRSSGALGPNLVARF 149 (203)
Q Consensus 104 ~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H~~~~~~~~~~~~~f 149 (203)
|.|.. ||+.|+++..|..|+++|+ +++.+..+++.
T Consensus 6 y~C~~---------CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~ 40 (55)
T PHA02768 6 YECPI---------CGEIYIKRKSMITHLRKHN--TNLKLSNCKRI 40 (55)
T ss_pred cCcch---------hCCeeccHHHHHHHHHhcC--CcccCCcccce
Confidence 67888 9999999999999999999 56667666654
No 20
>PHA00733 hypothetical protein
Probab=97.34 E-value=4.2e-05 Score=57.87 Aligned_cols=72 Identities=11% Similarity=-0.030 Sum_probs=51.9
Q ss_pred hhcccCCCCCCcceecCCCCccCCCchhHHHH--HH---hhcCCCCCccccccccccccccCCcCCCCCCCCCCCccccc
Q 040864 59 TDRRSKPASGNKVFSCNFCMRKFYSSQALGGH--QN---AHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSL 133 (203)
Q Consensus 59 ~~~H~r~Htgekp~~C~~Cgk~F~~~~~L~~H--~r---~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r 133 (203)
+.++-......+++.|.+|.+.|.....|..| ++ .+.+.+| |.|.. |++.|.....|..|++
T Consensus 28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kP----y~C~~---------Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 28 LKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSP----YVCPL---------CLMPFSSSVSLKQHIR 94 (128)
T ss_pred hhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCC----ccCCC---------CCCcCCCHHHHHHHHh
Confidence 34443333456889999999999888777766 22 2334778 88888 9999999999999998
Q ss_pred ccCCCCCCCCCc
Q 040864 134 VDRSSGALGPNL 145 (203)
Q Consensus 134 ~H~~~~~~~~~~ 145 (203)
+| ..++.|..
T Consensus 95 ~h--~~~~~C~~ 104 (128)
T PHA00733 95 YT--EHSKVCPV 104 (128)
T ss_pred cC--CcCccCCC
Confidence 76 23344444
No 21
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.12 E-value=6.1e-05 Score=66.49 Aligned_cols=70 Identities=19% Similarity=0.271 Sum_probs=51.3
Q ss_pred hhcccCCCCCCcceecCCCCccCCCchhHHHHHHhhc--------CCCCCccc---------------------cccccc
Q 040864 59 TDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAHK--------RERGAARR---------------------FQNHRM 109 (203)
Q Consensus 59 ~~~H~r~Htgekp~~C~~Cgk~F~~~~~L~~H~r~H~--------gekp~~c~---------------------~~C~~~ 109 (203)
+.+|.-...-..-|+|..|+|.|....+|..|.|-|. +..|-+.. |.|..
T Consensus 283 LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~- 361 (500)
T KOG3993|consen 283 LAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHT- 361 (500)
T ss_pred HhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHH-
Confidence 5666543333445999999999999999999999875 22331111 33444
Q ss_pred cccccCCcCCCCCCCCCCCcccccccCC
Q 040864 110 MMSSIGFLFNSVPLRSLGVQPHSLVDRS 137 (203)
Q Consensus 110 ~~~~~g~~C~k~F~~~~~L~~H~r~H~~ 137 (203)
|+|.|.+..-|++|+.+|+-
T Consensus 362 --------C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 362 --------CGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred --------hhhhhHHHHHHHHhHHhhhc
Confidence 99999999999999988863
No 22
>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=97.02 E-value=0.00027 Score=38.47 Aligned_cols=25 Identities=36% Similarity=0.642 Sum_probs=23.2
Q ss_pred ceecCCCCccCCCchhHHHHHHhhc
Q 040864 71 VFSCNFCMRKFYSSQALGGHQNAHK 95 (203)
Q Consensus 71 p~~C~~Cgk~F~~~~~L~~H~r~H~ 95 (203)
||.|..|++.|.....|..|++.|.
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 23
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.01 E-value=0.00055 Score=63.38 Aligned_cols=73 Identities=14% Similarity=0.118 Sum_probs=57.4
Q ss_pred hhcccCCCCCCcceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCC----------CCCC
Q 040864 59 TDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLR----------SLGV 128 (203)
Q Consensus 59 ~~~H~r~Htgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~----------~~~L 128 (203)
+..|+++|+ +++.|+ ||+.+ ....|..|+++|..+|+ +.|.. |++.|.. ...|
T Consensus 468 LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kp----i~C~f---------C~~~v~~g~~~~d~~d~~s~L 530 (567)
T PLN03086 468 MEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRL----ITCRF---------CGDMVQAGGSAMDVRDRLRGM 530 (567)
T ss_pred HHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCc----eeCCC---------CCCccccCccccchhhhhhhH
Confidence 678888874 789999 99755 56889999999999999 66666 8888842 3478
Q ss_pred cccccccCCCCCCCCCccccc
Q 040864 129 QPHSLVDRSSGALGPNLVARF 149 (203)
Q Consensus 129 ~~H~r~H~~~~~~~~~~~~~f 149 (203)
+.|..++ |.+++.|..|.+.
T Consensus 531 t~HE~~C-G~rt~~C~~Cgk~ 550 (567)
T PLN03086 531 SEHESIC-GSRTAPCDSCGRS 550 (567)
T ss_pred HHHHHhc-CCcceEccccCCe
Confidence 8998886 8888888776554
No 24
>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=96.95 E-value=0.00056 Score=35.53 Aligned_cols=23 Identities=35% Similarity=0.742 Sum_probs=19.7
Q ss_pred eecCCCCccCCCchhHHHHHHhh
Q 040864 72 FSCNFCMRKFYSSQALGGHQNAH 94 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L~~H~r~H 94 (203)
|.|.+|++.|.....|..|++.|
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 78999999999999999999876
No 25
>PHA00616 hypothetical protein
Probab=96.91 E-value=6.3e-05 Score=46.10 Aligned_cols=31 Identities=19% Similarity=0.134 Sum_probs=28.0
Q ss_pred cccccccccccCCcCCCCCCCCCCCcccccccCCCCCCCC
Q 040864 104 FQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVDRSSGALGP 143 (203)
Q Consensus 104 ~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H~~~~~~~~ 143 (203)
|+|.. ||+.|..++.|..|++.|++++++.+
T Consensus 2 YqC~~---------CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 2 YQCLR---------CGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred Cccch---------hhHHHhhHHHHHHHHHHhcCCCccce
Confidence 78999 99999999999999999999986543
No 26
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.62 E-value=0.0015 Score=34.33 Aligned_cols=24 Identities=33% Similarity=0.607 Sum_probs=22.1
Q ss_pred eecCCCCccCCCchhHHHHHHhhc
Q 040864 72 FSCNFCMRKFYSSQALGGHQNAHK 95 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L~~H~r~H~ 95 (203)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999999875
No 27
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.48 E-value=0.0029 Score=54.35 Aligned_cols=53 Identities=17% Similarity=0.339 Sum_probs=43.9
Q ss_pred CCcceecCC--CCccCCCchhHHHHHHh-h------------------cCCCCCccccccccccccccCCcCCCCCCCCC
Q 040864 68 GNKVFSCNF--CMRKFYSSQALGGHQNA-H------------------KRERGAARRFQNHRMMMSSIGFLFNSVPLRSL 126 (203)
Q Consensus 68 gekp~~C~~--Cgk~F~~~~~L~~H~r~-H------------------~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~ 126 (203)
++|||+|++ |.|++.....|+-|+.- | ...|| |+|.. |+|.+..-.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KP----YrCev---------C~KRYKNlN 412 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKP----YRCEV---------CDKRYKNLN 412 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCc----eeccc---------cchhhccCc
Confidence 369999997 99999999999988752 3 12366 89999 999999999
Q ss_pred CCccccc
Q 040864 127 GVQPHSL 133 (203)
Q Consensus 127 ~L~~H~r 133 (203)
+|+-|..
T Consensus 413 GLKYHr~ 419 (423)
T COG5189 413 GLKYHRK 419 (423)
T ss_pred cceeccc
Confidence 9999864
No 28
>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=96.31 E-value=0.0038 Score=39.33 Aligned_cols=34 Identities=15% Similarity=0.280 Sum_probs=25.0
Q ss_pred CCCCcceecCCCCccCCCchhHHHHHHhhcCCCC
Q 040864 66 ASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERG 99 (203)
Q Consensus 66 Htgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp 99 (203)
+..+.|..|++|+..+.+..+|.+|+.++.+.||
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 3567899999999999999999999998888777
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=96.28 E-value=0.0018 Score=41.42 Aligned_cols=50 Identities=20% Similarity=0.349 Sum_probs=37.3
Q ss_pred ceecCCCCccCCCchhHHHHHH-hhcCC-CCCccccccccccccccCCcCCCCCCCCCCCcccccccC
Q 040864 71 VFSCNFCMRKFYSSQALGGHQN-AHKRE-RGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVDR 136 (203)
Q Consensus 71 p~~C~~Cgk~F~~~~~L~~H~r-~H~ge-kp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H~ 136 (203)
.|.|++|++. .....|..|.. .|..+ +. +.|.. |...+.. +|..|+++++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~----v~CPi---------C~~~~~~--~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKN----VVCPI---------CSSRVTD--NLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCC----ccCCC---------chhhhhh--HHHHHHHHhc
Confidence 4899999995 55678999976 46654 34 77888 9876553 7888887765
No 30
>PRK04860 hypothetical protein; Provisional
Probab=96.28 E-value=0.0032 Score=49.42 Aligned_cols=40 Identities=13% Similarity=0.253 Sum_probs=34.3
Q ss_pred cceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCC
Q 040864 70 KVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSL 126 (203)
Q Consensus 70 kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~ 126 (203)
-+|.|. |++ ....+.+|.++|+++++ |.|.. |++.|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~----YrC~~---------C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAV----YRCRR---------CGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCcc----EECCC---------CCceeEEec
Confidence 479998 997 77789999999999999 88888 999887543
No 31
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.57 E-value=0.0082 Score=52.19 Aligned_cols=62 Identities=18% Similarity=0.185 Sum_probs=54.7
Q ss_pred cceecCCCCccCCCchhHHHHHH--hhcCC--CCCccccccccccccccCCcCCCCCCCCCCCcccccccCCCCCCC
Q 040864 70 KVFSCNFCMRKFYSSQALGGHQN--AHKRE--RGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVDRSSGALG 142 (203)
Q Consensus 70 kp~~C~~Cgk~F~~~~~L~~H~r--~H~ge--kp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H~~~~~~~ 142 (203)
.++.|..|...|.....|..|.+ .|+++ +|+.|++. . |++.|.+...+..|..+|.+-++..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~--~---------~~~~~~~~~~~~~~~~~~~~~~~~~ 353 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYS--L---------CGKLFSRNDALKRHILLHTSISPAK 353 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeecc--C---------CCccccccccccCCcccccCCCccc
Confidence 57899999999999999999999 89999 99666654 5 9999999999999999998877543
No 32
>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=95.54 E-value=0.0004 Score=36.26 Aligned_cols=18 Identities=6% Similarity=-0.104 Sum_probs=16.8
Q ss_pred CCCCCCCCCCCccccccc
Q 040864 118 FNSVPLRSLGVQPHSLVD 135 (203)
Q Consensus 118 C~k~F~~~~~L~~H~r~H 135 (203)
|++.|.++..|..|+++|
T Consensus 6 C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 6 CGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp TTEEESSHHHHHHHHHHH
T ss_pred CCCccCCHHHHHHHHhHC
Confidence 999999999999999875
No 33
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.86 E-value=0.012 Score=31.10 Aligned_cols=23 Identities=30% Similarity=0.719 Sum_probs=21.0
Q ss_pred eecCCCCccCCCchhHHHHHHhh
Q 040864 72 FSCNFCMRKFYSSQALGGHQNAH 94 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L~~H~r~H 94 (203)
|.|..|.+.|.....|..|++.+
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 68999999999999999998754
No 34
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=94.82 E-value=0.0036 Score=55.55 Aligned_cols=100 Identities=10% Similarity=0.046 Sum_probs=66.3
Q ss_pred ceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCcccccccCCCCCCCCCcccccC
Q 040864 71 VFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVDRSSGALGPNLVARFG 150 (203)
Q Consensus 71 p~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H~~~~~~~~~~~~~f~ 150 (203)
-|.|..|...|-..-.|..|.-.-.--.- |+|.. |+|.|+-..+|..|.|.|++...........-.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vE----YrCPE---------C~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k 333 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVE----YRCPE---------CDKVFSCPANLASHRRWHKPRPEAAKAGSPPPK 333 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEee----ecCCc---------ccccccCchhhhhhhcccCCchhhhhcCCCChh
Confidence 38999999999999999988632111122 89999 999999999999999999875422211111000
Q ss_pred CC--------CCCCccc-CCCccccccC-CCCCCCCCCcccCC
Q 040864 151 DA--------TSTGFDM-IPWTPFMLED-TIDMFWPGSCHVDN 183 (203)
Q Consensus 151 ~~--------~~~~~~~-~~~~p~~~~~-~~~~~~~~s~~~~~ 183 (203)
+. .+.+-+- ....-|.|-. ++.|..-..||.|+
T Consensus 334 ~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHq 376 (500)
T KOG3993|consen 334 QAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQ 376 (500)
T ss_pred hhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhH
Confidence 00 0001110 1223588988 89999989999985
No 35
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=93.70 E-value=0.05 Score=28.47 Aligned_cols=23 Identities=22% Similarity=0.481 Sum_probs=18.2
Q ss_pred eecCCCCccCCCchhHHHHHHhhc
Q 040864 72 FSCNFCMRKFYSSQALGGHQNAHK 95 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L~~H~r~H~ 95 (203)
|+|..|..... ...|..|++.|.
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 78999998887 889999998754
No 36
>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=93.16 E-value=0.0041 Score=32.09 Aligned_cols=19 Identities=5% Similarity=-0.064 Sum_probs=16.3
Q ss_pred CCCCCCCCCCCcccccccC
Q 040864 118 FNSVPLRSLGVQPHSLVDR 136 (203)
Q Consensus 118 C~k~F~~~~~L~~H~r~H~ 136 (203)
|++.|.....|..|+++|+
T Consensus 6 C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 6 CGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp TS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCcHHHHHHHHHhhC
Confidence 9999999999999998764
No 37
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.48 E-value=0.088 Score=28.18 Aligned_cols=21 Identities=33% Similarity=0.736 Sum_probs=17.6
Q ss_pred eecCCCCccCCCchhHHHHHHh
Q 040864 72 FSCNFCMRKFYSSQALGGHQNA 93 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L~~H~r~ 93 (203)
..|+.||+.| ....|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4799999999 67789999764
No 38
>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=92.38 E-value=0.01 Score=32.03 Aligned_cols=25 Identities=12% Similarity=0.052 Sum_probs=22.5
Q ss_pred cccccccccccCCcCCCCCCCCCCCcccccccCC
Q 040864 104 FQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVDRS 137 (203)
Q Consensus 104 ~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H~~ 137 (203)
|.|.. |++.|.....|..|++.|.+
T Consensus 2 ~~C~~---------C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 2 FECDE---------CGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp EEETT---------TTEEESSHHHHHHHHCTTTT
T ss_pred CCCCc---------cCCccCChhHHHHHhHHhcC
Confidence 77888 99999999999999998854
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=92.15 E-value=0.017 Score=29.99 Aligned_cols=19 Identities=11% Similarity=0.017 Sum_probs=17.4
Q ss_pred CCCCCCCCCCCcccccccC
Q 040864 118 FNSVPLRSLGVQPHSLVDR 136 (203)
Q Consensus 118 C~k~F~~~~~L~~H~r~H~ 136 (203)
|++.|.....|..|+++|.
T Consensus 6 C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 6 CGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CcchhCCHHHHHHHHHHhc
Confidence 9999999999999998775
No 40
>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=91.68 E-value=0.034 Score=30.11 Aligned_cols=22 Identities=32% Similarity=0.643 Sum_probs=19.7
Q ss_pred eecCCCCccCCCchhHHHHHHh
Q 040864 72 FSCNFCMRKFYSSQALGGHQNA 93 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L~~H~r~ 93 (203)
|.|..|++.|.....|..|++.
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 7899999999999999988764
No 41
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=91.24 E-value=0.089 Score=43.72 Aligned_cols=47 Identities=28% Similarity=0.458 Sum_probs=39.1
Q ss_pred ecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCccc-ccccC
Q 040864 73 SCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPH-SLVDR 136 (203)
Q Consensus 73 ~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H-~r~H~ 136 (203)
.|-+|.+-|-....|..|++. |- |+|.. |.|....-.+|..| +.+|+
T Consensus 12 wcwycnrefddekiliqhqka----kh----fkchi---------chkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA----KH----FKCHI---------CHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeeecccccchhhhhhhhhhh----cc----ceeee---------ehhhhccCCCceeehhhhhh
Confidence 599999999999999999874 44 89999 99987778888888 45564
No 42
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=91.04 E-value=0.02 Score=40.09 Aligned_cols=54 Identities=22% Similarity=0.246 Sum_probs=18.3
Q ss_pred ecCCCCccCCCchhHHHHHHh-hcCCCCC------------------ccccccccccccccCCcCCCCCCCCCCCccccc
Q 040864 73 SCNFCMRKFYSSQALGGHQNA-HKRERGA------------------ARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSL 133 (203)
Q Consensus 73 ~C~~Cgk~F~~~~~L~~H~r~-H~gekp~------------------~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r 133 (203)
+|..|+..|.....|..|+.. |.-..+- .-.+.|.. |++.|.....|..|++
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~---------C~~~f~s~~~l~~Hm~ 71 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPY---------CNKTFRSREALQEHMR 71 (100)
T ss_dssp ------------------------------------------------SSEEBSS---------SS-EESSHHHHHHHHH
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCc---------cCCCCcCHHHHHHHHc
Confidence 477888888888888888753 3211110 00134555 9999999999999998
Q ss_pred cc
Q 040864 134 VD 135 (203)
Q Consensus 134 ~H 135 (203)
.+
T Consensus 72 ~~ 73 (100)
T PF12756_consen 72 SK 73 (100)
T ss_dssp HT
T ss_pred Cc
Confidence 64
No 43
>PRK04860 hypothetical protein; Provisional
Probab=88.36 E-value=0.12 Score=40.51 Aligned_cols=27 Identities=19% Similarity=0.481 Sum_probs=23.9
Q ss_pred chhcccCCCCCCcceecCCCCccCCCc
Q 040864 58 STDRRSKPASGNKVFSCNFCMRKFYSS 84 (203)
Q Consensus 58 ~~~~H~r~Htgekp~~C~~Cgk~F~~~ 84 (203)
+..+|.++|+++++|.|..|++.|...
T Consensus 130 ~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 130 TVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred HHHHHHHHhcCCccEECCCCCceeEEe
Confidence 378999999999999999999988654
No 44
>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=88.31 E-value=0.31 Score=27.58 Aligned_cols=22 Identities=23% Similarity=0.534 Sum_probs=19.8
Q ss_pred ceecCCCCccCCCchhHHHHHH
Q 040864 71 VFSCNFCMRKFYSSQALGGHQN 92 (203)
Q Consensus 71 p~~C~~Cgk~F~~~~~L~~H~r 92 (203)
+|.|..|++.|.....+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5889999999999999988875
No 45
>PHA00732 hypothetical protein
Probab=85.61 E-value=0.32 Score=33.62 Aligned_cols=35 Identities=6% Similarity=0.030 Sum_probs=26.4
Q ss_pred cccccccccccCCcCCCCCCCCCCCcccccc-cCCCCCCCCCc-ccccC
Q 040864 104 FQNHRMMMSSIGFLFNSVPLRSLGVQPHSLV-DRSSGALGPNL-VARFG 150 (203)
Q Consensus 104 ~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~-H~~~~~~~~~~-~~~f~ 150 (203)
|.|.. |++.|.+...|+.|++. |.+ +.|.. ...|.
T Consensus 2 y~C~~---------Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~ 38 (79)
T PHA00732 2 FKCPI---------CGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR 38 (79)
T ss_pred ccCCC---------CCCccCCHHHHHHHhhcccCC---CccCCCCCEeC
Confidence 77888 99999999999999984 664 34555 33454
No 46
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=85.05 E-value=0.66 Score=32.18 Aligned_cols=24 Identities=33% Similarity=0.751 Sum_probs=21.4
Q ss_pred ceecCCCCccCCCchhHHHHHHhh
Q 040864 71 VFSCNFCMRKFYSSQALGGHQNAH 94 (203)
Q Consensus 71 p~~C~~Cgk~F~~~~~L~~H~r~H 94 (203)
.+.|..|++.|.....|..|++.+
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 699999999999999999999864
No 47
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=84.45 E-value=0.46 Score=45.27 Aligned_cols=26 Identities=23% Similarity=0.681 Sum_probs=23.4
Q ss_pred cceecCCCCccCCCchhHHHHHHhhc
Q 040864 70 KVFSCNFCMRKFYSSQALGGHQNAHK 95 (203)
Q Consensus 70 kp~~C~~Cgk~F~~~~~L~~H~r~H~ 95 (203)
-.|.|..|+|.|.....+..||+.|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 35899999999999999999999985
No 48
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=83.50 E-value=0.91 Score=39.30 Aligned_cols=61 Identities=21% Similarity=0.248 Sum_probs=50.0
Q ss_pred CCcceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCcccccccCCCC
Q 040864 68 GNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVDRSSG 139 (203)
Q Consensus 68 gekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H~~~~ 139 (203)
..+++.|..|...|....+...|.++|+++++ +.|.. .+ |.+.|.....+..|.+.|+...
T Consensus 30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~-----~~--~~~~~~~~~~~~~~~~~~~~~~ 90 (467)
T COG5048 30 APRPDSCPNCTDSFSRLEHLTRHIRSHTGEKP----SQCSY-----SG--CDKSFSRPLELSRHLRTHHNNP 90 (467)
T ss_pred CCchhhcccccccccccchhhhhcccccccCC----ccccc-----cc--cccccCCcchhhhhcccccccc
Confidence 35678999999999999999999999999999 55544 22 7788888888888888876544
No 49
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=79.91 E-value=2.1 Score=37.20 Aligned_cols=70 Identities=11% Similarity=0.012 Sum_probs=40.5
Q ss_pred CCCCCccccccccccccccCCcCCCCCCCCCCCcccccc-cCCCCCCCCCcccccCCCCCCCcccCCCccccccC-CCCC
Q 040864 96 RERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLV-DRSSGALGPNLVARFGDATSTGFDMIPWTPFMLED-TIDM 173 (203)
Q Consensus 96 gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~-H~~~~~~~~~~~~~f~~~~~~~~~~~~~~p~~~~~-~~~~ 173 (203)
++|| |+|.. .| |.|.+....+|+-|+.- |...+..+.+ .......|.+ -.|||.|+- ++..
T Consensus 346 d~Kp----ykCpV-----~g--C~K~YknqnGLKYH~lhGH~~~~~~~~p-----~p~~~~~F~~-~~KPYrCevC~KRY 408 (423)
T COG5189 346 DGKP----YKCPV-----EG--CNKKYKNQNGLKYHMLHGHQNQKLHENP-----SPEKMNIFSA-KDKPYRCEVCDKRY 408 (423)
T ss_pred cCce----ecCCC-----CC--chhhhccccchhhhhhccccCcccCCCC-----Cccccccccc-cCCceeccccchhh
Confidence 4689 66655 44 99999999999999753 3222211111 0001133332 568999887 6655
Q ss_pred CCCCCcccC
Q 040864 174 FWPGSCHVD 182 (203)
Q Consensus 174 ~~~~s~~~~ 182 (203)
.--..|..|
T Consensus 409 KNlNGLKYH 417 (423)
T COG5189 409 KNLNGLKYH 417 (423)
T ss_pred ccCccceec
Confidence 544445544
No 50
>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=79.21 E-value=0.15 Score=32.18 Aligned_cols=32 Identities=13% Similarity=0.006 Sum_probs=22.9
Q ss_pred CCCCCccccccccccccccCCcCCCCCCCCCCCcccccccCCCCC
Q 040864 96 RERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLVDRSSGA 140 (203)
Q Consensus 96 gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~H~~~~~ 140 (203)
.+.| -.|.. |+..+.++-+|++|+.++++.+|
T Consensus 21 S~~P----atCP~---------C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQP----ATCPI---------CGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS------EE-TT---------T--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCC----CCCCc---------chhhccchhhHHHHHHHHhcccC
Confidence 4566 67888 99999999999999999988885
No 51
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=78.53 E-value=0.98 Score=29.06 Aligned_cols=30 Identities=20% Similarity=0.367 Sum_probs=25.7
Q ss_pred CCCCCCcceecCCCCccCCCchhHHHHHHh
Q 040864 64 KPASGNKVFSCNFCMRKFYSSQALGGHQNA 93 (203)
Q Consensus 64 r~Htgekp~~C~~Cgk~F~~~~~L~~H~r~ 93 (203)
+...||..+.|+.|+..|.......+|.+.
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 345688899999999999999999999863
No 52
>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=70.41 E-value=4 Score=24.36 Aligned_cols=25 Identities=20% Similarity=0.429 Sum_probs=16.6
Q ss_pred CCcceecCCCCccCCC----chhHHHHHH
Q 040864 68 GNKVFSCNFCMRKFYS----SQALGGHQN 92 (203)
Q Consensus 68 gekp~~C~~Cgk~F~~----~~~L~~H~r 92 (203)
+..-..|.+|++.+.. .++|..|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 3456789999998876 478888883
No 53
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=69.42 E-value=4 Score=25.23 Aligned_cols=25 Identities=28% Similarity=0.545 Sum_probs=19.3
Q ss_pred ceecCCCCccCCCc-----hhHHHHHH-hhc
Q 040864 71 VFSCNFCMRKFYSS-----QALGGHQN-AHK 95 (203)
Q Consensus 71 p~~C~~Cgk~F~~~-----~~L~~H~r-~H~ 95 (203)
.-.|..|++.+... ++|.+|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 35799999988665 68999987 553
No 54
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=64.32 E-value=1.5 Score=44.52 Aligned_cols=60 Identities=18% Similarity=0.155 Sum_probs=44.5
Q ss_pred CCCCCcceecCCCCccCCCchhHHHHHHh-hc----------------CC-CCCcc---ccccccccccccCCcCCCCCC
Q 040864 65 PASGNKVFSCNFCMRKFYSSQALGGHQNA-HK----------------RE-RGAAR---RFQNHRMMMSSIGFLFNSVPL 123 (203)
Q Consensus 65 ~Htgekp~~C~~Cgk~F~~~~~L~~H~r~-H~----------------ge-kp~~c---~~~C~~~~~~~~g~~C~k~F~ 123 (203)
.|+-.|-|+|+.|+..|.....|..|+|. |. ++ -.|.| +|.|.. |..++.
T Consensus 459 L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~---------C~~stt 529 (1406)
T KOG1146|consen 459 LHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRA---------CNYSTT 529 (1406)
T ss_pred eecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCccccee---------eeeeee
Confidence 34556889999999999999999999997 21 11 12222 256777 999999
Q ss_pred CCCCCccccc
Q 040864 124 RSLGVQPHSL 133 (203)
Q Consensus 124 ~~~~L~~H~r 133 (203)
....|.+|+.
T Consensus 530 tng~Lsihlq 539 (1406)
T KOG1146|consen 530 TNGNLSIHLQ 539 (1406)
T ss_pred cchHHHHHHH
Confidence 8888888864
No 55
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=63.43 E-value=6.3 Score=35.75 Aligned_cols=29 Identities=21% Similarity=0.387 Sum_probs=24.2
Q ss_pred CCCCCCcceecCCCC-ccCCCchhHHHHHH
Q 040864 64 KPASGNKVFSCNFCM-RKFYSSQALGGHQN 92 (203)
Q Consensus 64 r~Htgekp~~C~~Cg-k~F~~~~~L~~H~r 92 (203)
+.|.-.+-|.|.+|| +++.-..++.+|-.
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 456667889999999 88888888988864
No 56
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=61.58 E-value=5.2 Score=33.63 Aligned_cols=48 Identities=17% Similarity=0.286 Sum_probs=33.8
Q ss_pred ceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCcccccc
Q 040864 71 VFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLV 134 (203)
Q Consensus 71 p~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~ 134 (203)
.|.|+.||....-. .+-+|+...++ .- |.|.. |++.|.+ .....|...
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCrn-~~----fSCID---------C~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCRN-AY----FSCID---------CGKTFER-VSYKNHTKC 50 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhccC-Ce----eEEee---------ccccccc-chhhhhhhh
Confidence 47899999876544 46668765554 33 67877 9999988 667777653
No 57
>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=60.75 E-value=4.2 Score=30.87 Aligned_cols=28 Identities=25% Similarity=0.368 Sum_probs=17.9
Q ss_pred CcceecCCCCccCCCchhHHHHHHhhcCCCC
Q 040864 69 NKVFSCNFCMRKFYSSQALGGHQNAHKRERG 99 (203)
Q Consensus 69 ekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp 99 (203)
+.-..|-+|||.|.. |++|++.|.|-.|
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCH
Confidence 445689999999875 6999999977666
No 58
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=54.95 E-value=4.5 Score=32.76 Aligned_cols=28 Identities=18% Similarity=0.381 Sum_probs=0.0
Q ss_pred CCCCCCcceecCCCCcc-CCCchhHHHHH
Q 040864 64 KPASGNKVFSCNFCMRK-FYSSQALGGHQ 91 (203)
Q Consensus 64 r~Htgekp~~C~~Cgk~-F~~~~~L~~H~ 91 (203)
+.|--.+-|.|.+||-. |.-..++.+|-
T Consensus 94 KLhGL~~ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 94 KLHGLGVEYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp -----------------------------
T ss_pred HHhCCCCeeeeEeCCCcceecHHHHHHhc
Confidence 44555788999999953 44555565554
No 59
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=53.61 E-value=4.1 Score=33.33 Aligned_cols=24 Identities=21% Similarity=0.566 Sum_probs=18.1
Q ss_pred CcceecCCCCccCCCchhHHHHHH
Q 040864 69 NKVFSCNFCMRKFYSSQALGGHQN 92 (203)
Q Consensus 69 ekp~~C~~Cgk~F~~~~~L~~H~r 92 (203)
.|.+.|++|++.|....-.....+
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r 26 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIR 26 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCce
Confidence 466899999999988765555544
No 60
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=50.86 E-value=8.4 Score=29.36 Aligned_cols=25 Identities=28% Similarity=0.212 Sum_probs=21.8
Q ss_pred eecCCCCccCCCchhHHHHHHhhcCCCC
Q 040864 72 FSCNFCMRKFYSSQALGGHQNAHKRERG 99 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp 99 (203)
..|-+|||.|.+ |++|+++|.|.-|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 569999999974 9999999988777
No 61
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=40.29 E-value=22 Score=18.97 Aligned_cols=20 Identities=20% Similarity=0.674 Sum_probs=15.0
Q ss_pred eecCCCCccCCCchhHHHHHH
Q 040864 72 FSCNFCMRKFYSSQALGGHQN 92 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L~~H~r 92 (203)
..|+.|++.+ ....+..|..
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999998 5566777765
No 62
>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=39.70 E-value=29 Score=19.43 Aligned_cols=11 Identities=18% Similarity=0.642 Sum_probs=7.9
Q ss_pred eecCCCCccCC
Q 040864 72 FSCNFCMRKFY 82 (203)
Q Consensus 72 ~~C~~Cgk~F~ 82 (203)
|.|..||..+.
T Consensus 2 ~~C~~CGy~y~ 12 (33)
T cd00350 2 YVCPVCGYIYD 12 (33)
T ss_pred EECCCCCCEEC
Confidence 67888886543
No 63
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=39.16 E-value=7.5 Score=30.29 Aligned_cols=16 Identities=6% Similarity=-0.342 Sum_probs=11.8
Q ss_pred cccccccccccCCcCCCCCCCCCCC
Q 040864 104 FQNHRMMMSSIGFLFNSVPLRSLGV 128 (203)
Q Consensus 104 ~~C~~~~~~~~g~~C~k~F~~~~~L 128 (203)
++|.. ||+.|..--.+
T Consensus 29 ~~c~~---------c~~~f~~~e~~ 44 (154)
T PRK00464 29 RECLA---------CGKRFTTFERV 44 (154)
T ss_pred eeccc---------cCCcceEeEec
Confidence 67888 99998875443
No 64
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=38.96 E-value=23 Score=25.40 Aligned_cols=25 Identities=16% Similarity=0.319 Sum_probs=22.0
Q ss_pred eec----CCCCccCCCchhHHHHHHhhcC
Q 040864 72 FSC----NFCMRKFYSSQALGGHQNAHKR 96 (203)
Q Consensus 72 ~~C----~~Cgk~F~~~~~L~~H~r~H~g 96 (203)
|.| ..|+..+.+...+..|.+.+.|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999987543
No 65
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=38.11 E-value=11 Score=26.53 Aligned_cols=32 Identities=13% Similarity=0.195 Sum_probs=20.8
Q ss_pred cceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCC
Q 040864 70 KVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLR 124 (203)
Q Consensus 70 kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~ 124 (203)
..|.|+.|++. .+.|+-+| - +.|.. ||..|.-
T Consensus 34 ~~~~Cp~C~~~--------~VkR~a~G--I----W~C~k---------Cg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRIATG--I----WKCRK---------CGAKFAG 65 (89)
T ss_pred cCCcCCCCCCc--------ceeeeccC--e----EEcCC---------CCCeecc
Confidence 46889999874 22333333 2 67888 8888764
No 66
>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=37.81 E-value=23 Score=25.85 Aligned_cols=30 Identities=17% Similarity=0.242 Sum_probs=22.5
Q ss_pred eecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCC
Q 040864 72 FSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRS 125 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~ 125 (203)
..|+.||++|.-.. ..| ..|.. ||..|.-.
T Consensus 10 R~Cp~CG~kFYDLn-----------k~P----ivCP~---------CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLN-----------KDP----IVCPK---------CGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCC-----------CCC----ccCCC---------CCCccCcc
Confidence 47999999997632 267 55666 99998876
No 67
>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=36.21 E-value=13 Score=30.60 Aligned_cols=27 Identities=15% Similarity=0.373 Sum_probs=21.2
Q ss_pred CCCcceecCCCCccCCCchhHHHHHHh
Q 040864 67 SGNKVFSCNFCMRKFYSSQALGGHQNA 93 (203)
Q Consensus 67 tgekp~~C~~Cgk~F~~~~~L~~H~r~ 93 (203)
..+.-|.|..|+|.|.-......|+..
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhh
Confidence 345569999999999999999999875
No 68
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=35.33 E-value=10 Score=25.66 Aligned_cols=44 Identities=16% Similarity=0.175 Sum_probs=22.7
Q ss_pred eecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCC
Q 040864 72 FSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGV 128 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L 128 (203)
+.|+.||..-.-...-..+. -+.++- ++|.. ..||..|.....+
T Consensus 2 m~CP~Cg~~a~irtSr~~s~--~~~~~Y----~qC~N-------~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITD--TTKERY----HQCQN-------VNCSATFITYESV 45 (72)
T ss_pred ccCCCCCCccEEEEChhcCh--hhheee----eecCC-------CCCCCEEEEEEEE
Confidence 57999986542222111111 122333 67872 1299998865443
No 69
>PF15269 zf-C2H2_7: Zinc-finger
Probab=35.02 E-value=40 Score=20.76 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=19.4
Q ss_pred CCcc--eecCCCCccCCCchhHHHHHH
Q 040864 68 GNKV--FSCNFCMRKFYSSQALGGHQN 92 (203)
Q Consensus 68 gekp--~~C~~Cgk~F~~~~~L~~H~r 92 (203)
..|| |+|-.|..+..-+++|-.|++
T Consensus 15 ~gkp~~ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 15 PGKPFKYKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred CCCCccceeecCCcccchHHHHHHHHH
Confidence 3445 678899888888888888886
No 70
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=34.41 E-value=22 Score=20.87 Aligned_cols=14 Identities=29% Similarity=0.686 Sum_probs=12.1
Q ss_pred ceecCCCCccCCCc
Q 040864 71 VFSCNFCMRKFYSS 84 (203)
Q Consensus 71 p~~C~~Cgk~F~~~ 84 (203)
||.|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999998754
No 71
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=34.30 E-value=19 Score=20.68 Aligned_cols=15 Identities=27% Similarity=0.523 Sum_probs=11.7
Q ss_pred ceecCCCCccCCCch
Q 040864 71 VFSCNFCMRKFYSSQ 85 (203)
Q Consensus 71 p~~C~~Cgk~F~~~~ 85 (203)
.|+|..||+.|....
T Consensus 5 ~y~C~~Cg~~fe~~~ 19 (41)
T smart00834 5 EYRCEDCGHTFEVLQ 19 (41)
T ss_pred EEEcCCCCCEEEEEE
Confidence 489999999886543
No 72
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=34.14 E-value=29 Score=27.37 Aligned_cols=22 Identities=27% Similarity=0.351 Sum_probs=17.4
Q ss_pred cceecCCCCccCCCchhHHHHHHhhcCCCCCcccccccc
Q 040864 70 KVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHR 108 (203)
Q Consensus 70 kp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~ 108 (203)
+.|.|++||.. |.|+-| ..|..
T Consensus 133 ~~~vC~vCGy~-------------~~ge~P----~~CPi 154 (166)
T COG1592 133 KVWVCPVCGYT-------------HEGEAP----EVCPI 154 (166)
T ss_pred CEEEcCCCCCc-------------ccCCCC----CcCCC
Confidence 37999999863 567788 78888
No 73
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=32.13 E-value=25 Score=18.60 Aligned_cols=11 Identities=27% Similarity=0.483 Sum_probs=8.7
Q ss_pred CcceecCCCCc
Q 040864 69 NKVFSCNFCMR 79 (203)
Q Consensus 69 ekp~~C~~Cgk 79 (203)
-.+|.|+.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 35799999985
No 74
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=32.08 E-value=26 Score=27.87 Aligned_cols=36 Identities=22% Similarity=0.397 Sum_probs=26.6
Q ss_pred CCCcceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCC
Q 040864 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLR 124 (203)
Q Consensus 67 tgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~ 124 (203)
....-|.|+.|++.|+...++. -- |.|.. ||.....
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~---------~~----F~Cp~---------Cg~~L~~ 148 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAME---------YG----FRCPQ---------CGEMLEE 148 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhh---------cC----CcCCC---------CCCCCee
Confidence 4456799999999998877663 24 78888 9876543
No 75
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=31.75 E-value=12 Score=31.32 Aligned_cols=30 Identities=33% Similarity=0.678 Sum_probs=22.2
Q ss_pred CCCCcceecCCCCccCCCchhHHHH-HHhhc
Q 040864 66 ASGNKVFSCNFCMRKFYSSQALGGH-QNAHK 95 (203)
Q Consensus 66 Htgekp~~C~~Cgk~F~~~~~L~~H-~r~H~ 95 (203)
|..-|.|+|.+|.|...+--.|..| +.+|.
T Consensus 29 hqkakhfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 29 HQKAKHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred hhhhccceeeeehhhhccCCCceeehhhhhh
Confidence 3446789999999988777777776 45553
No 76
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=31.12 E-value=60 Score=29.25 Aligned_cols=48 Identities=13% Similarity=-0.044 Sum_probs=33.2
Q ss_pred hhcccCCCCCCcceecCCCCccCCCchhHHHHHHhhcCCCCCcccccc
Q 040864 59 TDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQN 106 (203)
Q Consensus 59 ~~~H~r~Htgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C 106 (203)
...+...+++..+..+..+.+.+.....+..|...+.++.++.+++.+
T Consensus 319 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 366 (396)
T KOG2461|consen 319 LDQSEVPATVSVWTGETIPVRTPAGQLIYTQSHSMEVAEPTDMAPNQI 366 (396)
T ss_pred cccccccccccccCcCcccccccccccchhhhhhcccCCCCccccccc
Confidence 445566677777777777777777777777787888887775544443
No 77
>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=30.99 E-value=23 Score=21.06 Aligned_cols=15 Identities=27% Similarity=0.561 Sum_probs=11.9
Q ss_pred ceecCCCCccCCCch
Q 040864 71 VFSCNFCMRKFYSSQ 85 (203)
Q Consensus 71 p~~C~~Cgk~F~~~~ 85 (203)
-|.|..||..|....
T Consensus 5 ey~C~~Cg~~fe~~~ 19 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQ 19 (42)
T ss_pred EEEeCCCCCEEEEEE
Confidence 389999999887554
No 78
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=30.10 E-value=40 Score=20.36 Aligned_cols=16 Identities=25% Similarity=0.490 Sum_probs=12.6
Q ss_pred ecCCCCccCCCchhHH
Q 040864 73 SCNFCMRKFYSSQALG 88 (203)
Q Consensus 73 ~C~~Cgk~F~~~~~L~ 88 (203)
.|.+|++.|.......
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 5999999998765544
No 79
>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=29.90 E-value=30 Score=19.74 Aligned_cols=15 Identities=20% Similarity=0.532 Sum_probs=10.8
Q ss_pred eecCCCCccCCCchh
Q 040864 72 FSCNFCMRKFYSSQA 86 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~ 86 (203)
+.|+.|+..|.-...
T Consensus 3 ~~CP~C~~~~~v~~~ 17 (38)
T TIGR02098 3 IQCPNCKTSFRVVDS 17 (38)
T ss_pred EECCCCCCEEEeCHH
Confidence 578888888765543
No 80
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=29.80 E-value=29 Score=18.59 Aligned_cols=10 Identities=30% Similarity=0.623 Sum_probs=8.3
Q ss_pred ecCCCCccCC
Q 040864 73 SCNFCMRKFY 82 (203)
Q Consensus 73 ~C~~Cgk~F~ 82 (203)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 6999998884
No 81
>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=29.57 E-value=34 Score=26.56 Aligned_cols=37 Identities=19% Similarity=0.269 Sum_probs=28.0
Q ss_pred CCCCCCcceecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCC
Q 040864 64 KPASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVP 122 (203)
Q Consensus 64 r~Htgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F 122 (203)
...+...-|.|+.|+..|+...++. -- |.|.. ||...
T Consensus 102 ~~e~~~~~Y~Cp~c~~r~tf~eA~~---------~~----F~Cp~---------Cg~~L 138 (158)
T TIGR00373 102 EFETNNMFFICPNMCVRFTFNEAME---------LN----FTCPR---------CGAML 138 (158)
T ss_pred hhccCCCeEECCCCCcEeeHHHHHH---------cC----CcCCC---------CCCEe
Confidence 3345567799999999999888775 14 78888 88764
No 82
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=29.27 E-value=23 Score=25.40 Aligned_cols=20 Identities=25% Similarity=0.232 Sum_probs=15.4
Q ss_pred cCCCCCCcceecCCCCccCCC
Q 040864 63 SKPASGNKVFSCNFCMRKFYS 83 (203)
Q Consensus 63 ~r~Htgekp~~C~~Cgk~F~~ 83 (203)
+..+.+ +|++|..||..|.-
T Consensus 72 ~~l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 72 MWLEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EEEeCC-CceeCCCCCcEEEE
Confidence 455666 79999999988753
No 83
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=29.10 E-value=30 Score=31.38 Aligned_cols=36 Identities=19% Similarity=0.341 Sum_probs=24.1
Q ss_pred CCCCcceecCCCCccCCCchhHHHHHHhhcCCCCCcccccccc
Q 040864 66 ASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHR 108 (203)
Q Consensus 66 Htgekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~ 108 (203)
-+...-|.|+.|.+.|.....+. .+-...-. |.|..
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~----F~C~~ 158 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQ---LLDNETGE----FHCEN 158 (436)
T ss_pred ccccccccCCccccchhhhHHHH---hhcccCce----EEEec
Confidence 35566799999999998877664 22222223 67777
No 84
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.39 E-value=9.2 Score=31.31 Aligned_cols=53 Identities=25% Similarity=0.380 Sum_probs=39.2
Q ss_pred ecCCCCccCCCchhHHHHHHh-h---------cCCCCCccccccccccccccCCcCCCCCCCCCCCcccc-cccC
Q 040864 73 SCNFCMRKFYSSQALGGHQNA-H---------KRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHS-LVDR 136 (203)
Q Consensus 73 ~C~~Cgk~F~~~~~L~~H~r~-H---------~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~-r~H~ 136 (203)
.|.+|.+.|....-|..|+.- | .| ++. |+|.. -| |+..|...-.-+.|+ ++|+
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG-~dM---y~Clv-----Eg--Ct~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERG-QDM---YQCLV-----EG--CTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcC-ccH---HHHHH-----Hh--hhhhhhhhhhhhhHHHHhcc
Confidence 799999999999999988752 2 23 332 67755 44 999999888888886 4554
No 85
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=27.83 E-value=54 Score=29.14 Aligned_cols=28 Identities=21% Similarity=0.445 Sum_probs=21.5
Q ss_pred CCCCCCcceecCCCC-ccCCCchhHHHHH
Q 040864 64 KPASGNKVFSCNFCM-RKFYSSQALGGHQ 91 (203)
Q Consensus 64 r~Htgekp~~C~~Cg-k~F~~~~~L~~H~ 91 (203)
+.|.-.+-|.|.+|| +.+.....+-+|-
T Consensus 367 klhgLd~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 367 KLHGLDIEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred HhcCCCcceeeeecccccccchHHHHhhh
Confidence 456678899999999 6666667777664
No 86
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=27.73 E-value=37 Score=31.97 Aligned_cols=28 Identities=21% Similarity=0.395 Sum_probs=23.4
Q ss_pred CCcceecCCCCccCCCchhHHHHHHhhc
Q 040864 68 GNKVFSCNFCMRKFYSSQALGGHQNAHK 95 (203)
Q Consensus 68 gekp~~C~~Cgk~F~~~~~L~~H~r~H~ 95 (203)
..+|-.|..||..|........||.+|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 3567899999999999988888887774
No 87
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=27.35 E-value=33 Score=25.67 Aligned_cols=26 Identities=35% Similarity=0.591 Sum_probs=22.4
Q ss_pred CCcceecCCCCccCCCchhHHHHHHh
Q 040864 68 GNKVFSCNFCMRKFYSSQALGGHQNA 93 (203)
Q Consensus 68 gekp~~C~~Cgk~F~~~~~L~~H~r~ 93 (203)
|.-.|-|-.|.+-|.....|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 44568999999999999999998763
No 88
>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=26.70 E-value=30 Score=21.15 Aligned_cols=14 Identities=21% Similarity=0.600 Sum_probs=11.4
Q ss_pred ceecCCCCccCCCc
Q 040864 71 VFSCNFCMRKFYSS 84 (203)
Q Consensus 71 p~~C~~Cgk~F~~~ 84 (203)
-|+|..||..|...
T Consensus 5 ey~C~~Cg~~fe~~ 18 (52)
T TIGR02605 5 EYRCTACGHRFEVL 18 (52)
T ss_pred EEEeCCCCCEeEEE
Confidence 38999999988754
No 89
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=26.12 E-value=27 Score=20.76 Aligned_cols=15 Identities=27% Similarity=0.682 Sum_probs=10.0
Q ss_pred cceecCCCCccCCCc
Q 040864 70 KVFSCNFCMRKFYSS 84 (203)
Q Consensus 70 kp~~C~~Cgk~F~~~ 84 (203)
-||.|..|++.|-..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 589999999998754
No 90
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.80 E-value=28 Score=33.40 Aligned_cols=21 Identities=29% Similarity=0.648 Sum_probs=12.9
Q ss_pred ecCCCCccCCCchhHHHHHHh
Q 040864 73 SCNFCMRKFYSSQALGGHQNA 93 (203)
Q Consensus 73 ~C~~Cgk~F~~~~~L~~H~r~ 93 (203)
.|.+|...|.....|.+|++.
T Consensus 184 ~C~~C~~~fld~~el~rH~~~ 204 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRF 204 (669)
T ss_pred cchhhhhhhccHHHHHHhhcc
Confidence 466666666666666666653
No 91
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=25.31 E-value=64 Score=18.48 Aligned_cols=16 Identities=19% Similarity=0.480 Sum_probs=11.0
Q ss_pred eecCCCCccCCCchhH
Q 040864 72 FSCNFCMRKFYSSQAL 87 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L 87 (203)
..|+.|+..|.-....
T Consensus 3 i~Cp~C~~~y~i~d~~ 18 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK 18 (36)
T ss_pred EECCCCCCEEeCCHHH
Confidence 4688888887765543
No 92
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=25.28 E-value=88 Score=23.75 Aligned_cols=22 Identities=9% Similarity=0.356 Sum_probs=17.2
Q ss_pred CCcceecCCCCccCCCchhHHH
Q 040864 68 GNKVFSCNFCMRKFYSSQALGG 89 (203)
Q Consensus 68 gekp~~C~~Cgk~F~~~~~L~~ 89 (203)
...-+.|+.|||.|..-+++.+
T Consensus 121 ~~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 121 YDEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CCeEEECCCCCCEecccccHHH
Confidence 3457889999999988776654
No 93
>PHA00626 hypothetical protein
Probab=25.13 E-value=39 Score=21.75 Aligned_cols=15 Identities=13% Similarity=0.191 Sum_probs=12.4
Q ss_pred CcceecCCCCccCCC
Q 040864 69 NKVFSCNFCMRKFYS 83 (203)
Q Consensus 69 ekp~~C~~Cgk~F~~ 83 (203)
...|+|..||..|+.
T Consensus 21 snrYkCkdCGY~ft~ 35 (59)
T PHA00626 21 SDDYVCCDCGYNDSK 35 (59)
T ss_pred CcceEcCCCCCeech
Confidence 457999999998864
No 94
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=24.93 E-value=86 Score=23.85 Aligned_cols=21 Identities=24% Similarity=0.474 Sum_probs=15.8
Q ss_pred CCCcceecCCCCccCCCchhH
Q 040864 67 SGNKVFSCNFCMRKFYSSQAL 87 (203)
Q Consensus 67 tgekp~~C~~Cgk~F~~~~~L 87 (203)
....-|.|+.|+..|.....+
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~ 115 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEAN 115 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHH
Confidence 455679999999999864443
No 95
>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=24.71 E-value=60 Score=24.49 Aligned_cols=34 Identities=15% Similarity=0.040 Sum_probs=23.5
Q ss_pred eecCCCCccCCCchhHHHHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCc
Q 040864 72 FSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQ 129 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~ 129 (203)
..|+.||++|.-. +..| ..|.. ||..|.....++
T Consensus 10 r~Cp~cg~kFYDL-----------nk~p----~vcP~---------cg~~~~~~~~~~ 43 (129)
T TIGR02300 10 RICPNTGSKFYDL-----------NRRP----AVSPY---------TGEQFPPEEALK 43 (129)
T ss_pred ccCCCcCcccccc-----------CCCC----ccCCC---------cCCccCcchhhc
Confidence 4799999999753 2357 56666 998886664443
No 96
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=24.38 E-value=39 Score=25.60 Aligned_cols=15 Identities=27% Similarity=0.521 Sum_probs=12.9
Q ss_pred ceecCCCCccCCCch
Q 040864 71 VFSCNFCMRKFYSSQ 85 (203)
Q Consensus 71 p~~C~~Cgk~F~~~~ 85 (203)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 689999999998655
No 97
>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=23.96 E-value=21 Score=19.62 Aligned_cols=20 Identities=30% Similarity=0.713 Sum_probs=12.3
Q ss_pred eecCCCCccCCCchhHHHHHH
Q 040864 72 FSCNFCMRKFYSSQALGGHQN 92 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~~L~~H~r 92 (203)
|.|-.|++.| .....+.|..
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 5799999999 4444555543
No 98
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.74 E-value=87 Score=23.08 Aligned_cols=22 Identities=18% Similarity=0.285 Sum_probs=15.9
Q ss_pred CcceecCCCCccCCCchhHHHH
Q 040864 69 NKVFSCNFCMRKFYSSQALGGH 90 (203)
Q Consensus 69 ekp~~C~~Cgk~F~~~~~L~~H 90 (203)
+-|..|+.||-....+.+|.+.
T Consensus 13 ~LP~~CpiCgLtLVss~HLARS 34 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARS 34 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHh
Confidence 3567788888877777777654
No 99
>PF14353 CpXC: CpXC protein
Probab=23.68 E-value=92 Score=22.85 Aligned_cols=50 Identities=10% Similarity=-0.009 Sum_probs=28.3
Q ss_pred ecCCCCccCCCchhHH--------HHHHhhcCCCCCccccccccccccccCCcCCCCCCCCCCCcccccc
Q 040864 73 SCNFCMRKFYSSQALG--------GHQNAHKRERGAARRFQNHRMMMSSIGFLFNSVPLRSLGVQPHSLV 134 (203)
Q Consensus 73 ~C~~Cgk~F~~~~~L~--------~H~r~H~gekp~~c~~~C~~~~~~~~g~~C~k~F~~~~~L~~H~r~ 134 (203)
.|+.|+..|...-... .-.++-.|.--. +.|.. ||..|.-...+.-|-.-
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~---~~CP~---------Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFS---FTCPS---------CGHKFRLEYPLLYHDPE 60 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCE---EECCC---------CCCceecCCCEEEEcCC
Confidence 6999998875322111 112333343221 56877 99998776666655443
No 100
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=23.60 E-value=53 Score=18.88 Aligned_cols=14 Identities=21% Similarity=0.679 Sum_probs=10.1
Q ss_pred eecCCCCccCCCch
Q 040864 72 FSCNFCMRKFYSSQ 85 (203)
Q Consensus 72 ~~C~~Cgk~F~~~~ 85 (203)
..|+.|+..|.-..
T Consensus 3 i~CP~C~~~f~v~~ 16 (37)
T PF13719_consen 3 ITCPNCQTRFRVPD 16 (37)
T ss_pred EECCCCCceEEcCH
Confidence 36888888876654
No 101
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=22.56 E-value=48 Score=29.33 Aligned_cols=23 Identities=22% Similarity=0.545 Sum_probs=21.1
Q ss_pred ceecCCCCccCCCchhHHHHHHh
Q 040864 71 VFSCNFCMRKFYSSQALGGHQNA 93 (203)
Q Consensus 71 p~~C~~Cgk~F~~~~~L~~H~r~ 93 (203)
.+.|-+|.|.|..+..|+.|||.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 47899999999999999999984
No 102
>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=22.07 E-value=74 Score=17.98 Aligned_cols=11 Identities=27% Similarity=0.627 Sum_probs=8.1
Q ss_pred ceecCCCCccC
Q 040864 71 VFSCNFCMRKF 81 (203)
Q Consensus 71 p~~C~~Cgk~F 81 (203)
.|.|..||..+
T Consensus 2 ~~~C~~CG~i~ 12 (34)
T cd00729 2 VWVCPVCGYIH 12 (34)
T ss_pred eEECCCCCCEe
Confidence 47899998653
No 103
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=21.10 E-value=42 Score=19.96 Aligned_cols=12 Identities=17% Similarity=0.764 Sum_probs=10.2
Q ss_pred cceecCCCCccC
Q 040864 70 KVFSCNFCMRKF 81 (203)
Q Consensus 70 kp~~C~~Cgk~F 81 (203)
++-.|++|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 578999999877
No 104
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=20.19 E-value=41 Score=21.77 Aligned_cols=11 Identities=36% Similarity=0.830 Sum_probs=5.2
Q ss_pred eecCCCCccCC
Q 040864 72 FSCNFCMRKFY 82 (203)
Q Consensus 72 ~~C~~Cgk~F~ 82 (203)
-.|..|++.|.
T Consensus 10 ~~C~~C~~~F~ 20 (69)
T PF01363_consen 10 SNCMICGKKFS 20 (69)
T ss_dssp SB-TTT--B-B
T ss_pred CcCcCcCCcCC
Confidence 36888999885
No 105
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=20.10 E-value=49 Score=25.75 Aligned_cols=32 Identities=13% Similarity=0.442 Sum_probs=21.9
Q ss_pred CCcceecCCCCccCCCchhHHHHHHhhcCCCCCcccccccc
Q 040864 68 GNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAARRFQNHR 108 (203)
Q Consensus 68 gekp~~C~~Cgk~F~~~~~L~~H~r~H~gekp~~c~~~C~~ 108 (203)
..-+|.|. |+..|.+. .+|-.+-.|+ . |.|..
T Consensus 114 ~~~~Y~C~-C~q~~l~~---RRhn~~~~g~-~----YrC~~ 145 (156)
T COG3091 114 TTYPYRCQ-CQQHYLRI---RRHNTVRRGE-V----YRCGK 145 (156)
T ss_pred cceeEEee-cCCccchh---hhcccccccc-e----EEecc
Confidence 34579999 99876543 3454555566 6 88888
Done!