Query 047542
Match_columns 270
No_of_seqs 357 out of 1451
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 12:02:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047542.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047542hhsearch_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 99.1 8.8E-12 1.9E-16 114.2 -1.8 39 97-135 187-225 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.0 9.7E-11 2.1E-15 107.4 1.1 55 86-140 204-258 (279)
3 KOG3623 Homeobox transcription 99.0 9.7E-11 2.1E-15 118.4 0.8 49 91-139 916-964 (1007)
4 KOG1074 Transcriptional repres 98.6 2.5E-08 5.4E-13 102.5 3.2 88 97-185 353-446 (958)
5 KOG1074 Transcriptional repres 98.6 2.3E-08 5.1E-13 102.7 3.0 85 96-182 604-694 (958)
6 KOG3623 Homeobox transcription 98.5 5.4E-08 1.2E-12 98.9 1.7 46 95-140 279-324 (1007)
7 PHA02768 hypothetical protein; 98.3 2E-07 4.2E-12 66.7 1.6 39 97-137 5-43 (55)
8 KOG3576 Ovo and related transc 98.1 1.9E-06 4.1E-11 76.8 3.6 78 93-179 113-197 (267)
9 PF13465 zf-H2C2_2: Zinc-finge 98.0 2.2E-06 4.7E-11 52.1 1.1 25 112-136 1-25 (26)
10 KOG3576 Ovo and related transc 98.0 1.6E-06 3.4E-11 77.3 -0.2 90 91-182 139-238 (267)
11 PHA00616 hypothetical protein 97.7 1.3E-05 2.8E-10 54.9 0.6 34 97-130 1-34 (44)
12 PHA00733 hypothetical protein 97.5 7.2E-05 1.6E-09 62.1 2.7 39 95-135 71-109 (128)
13 PHA00732 hypothetical protein 97.4 8.4E-05 1.8E-09 56.9 2.1 43 97-142 1-44 (79)
14 PF13465 zf-H2C2_2: Zinc-finge 96.9 0.00029 6.2E-09 42.7 0.2 21 89-109 6-26 (26)
15 PF00096 zf-C2H2: Zinc finger, 96.8 0.00046 9.9E-09 39.9 0.6 23 98-120 1-23 (23)
16 PHA00733 hypothetical protein 96.5 0.00034 7.4E-09 58.1 -1.8 79 94-177 37-120 (128)
17 KOG3608 Zn finger proteins [Ge 96.3 0.00069 1.5E-08 64.9 -1.1 96 86-192 281-387 (467)
18 PF13912 zf-C2H2_6: C2H2-type 96.1 0.002 4.3E-08 38.6 0.7 25 97-121 1-25 (27)
19 PRK04860 hypothetical protein; 96.0 0.0036 7.8E-08 54.0 1.8 37 96-136 118-154 (160)
20 PLN03086 PRLI-interacting fact 96.0 0.0038 8.2E-08 63.4 2.1 84 95-187 451-544 (567)
21 PF13894 zf-C2H2_4: C2H2-type 95.8 0.0042 9.1E-08 35.3 1.0 23 98-120 1-23 (24)
22 PLN03086 PRLI-interacting fact 95.4 0.0071 1.5E-07 61.5 1.7 38 96-135 477-514 (567)
23 smart00355 ZnF_C2H2 zinc finge 95.3 0.011 2.5E-07 33.7 1.6 24 98-121 1-24 (26)
24 COG5189 SFP1 Putative transcri 95.0 0.034 7.3E-07 53.0 4.8 25 94-118 346-372 (423)
25 KOG3993 Transcription factor ( 94.7 0.0024 5.2E-08 62.4 -3.9 83 97-181 267-381 (500)
26 PF09237 GAGA: GAGA factor; I 93.7 0.046 1E-06 38.7 2.0 35 91-125 18-52 (54)
27 KOG3608 Zn finger proteins [Ge 92.9 0.0082 1.8E-07 57.7 -3.7 48 90-137 200-249 (467)
28 KOG3993 Transcription factor ( 91.6 0.057 1.2E-06 53.1 0.3 25 97-121 295-319 (500)
29 PF12874 zf-met: Zinc-finger o 91.5 0.061 1.3E-06 31.4 0.2 23 98-120 1-23 (25)
30 PHA02768 hypothetical protein; 91.0 0.052 1.1E-06 38.9 -0.5 35 126-167 6-44 (55)
31 PF05605 zf-Di19: Drought indu 91.0 0.19 4E-06 35.3 2.3 39 97-136 2-42 (54)
32 PF12171 zf-C2H2_jaz: Zinc-fin 89.9 0.14 3.1E-06 30.7 0.8 22 98-119 2-23 (27)
33 PHA00732 hypothetical protein 84.3 0.45 9.7E-06 36.4 0.9 43 125-179 1-47 (79)
34 PF13913 zf-C2HC_2: zinc-finge 84.0 0.61 1.3E-05 27.9 1.2 21 98-119 3-23 (25)
35 PF13909 zf-H2C2_5: C2H2-type 83.9 0.48 1E-05 27.4 0.7 22 98-120 1-22 (24)
36 smart00451 ZnF_U1 U1-like zinc 79.9 0.98 2.1E-05 28.1 1.1 23 97-119 3-25 (35)
37 COG5048 FOG: Zn-finger [Genera 78.8 2.5 5.5E-05 38.9 4.0 43 96-138 288-336 (467)
38 PF12756 zf-C2H2_2: C2H2 type 72.4 2 4.4E-05 32.2 1.3 24 97-120 50-73 (100)
39 COG5189 SFP1 Putative transcri 70.7 2.8 6.1E-05 40.2 2.1 24 121-144 394-417 (423)
40 PRK00464 nrdR transcriptional 70.5 1.7 3.8E-05 37.3 0.6 39 98-139 1-42 (154)
41 PF09986 DUF2225: Uncharacteri 57.9 3.8 8.3E-05 36.7 0.4 25 95-119 3-27 (214)
42 cd00350 rubredoxin_like Rubred 54.8 7.5 0.00016 24.5 1.3 26 98-135 2-27 (33)
43 COG5048 FOG: Zn-finger [Genera 54.2 7.3 0.00016 35.8 1.6 40 91-130 313-356 (467)
44 PRK09678 DNA-binding transcrip 51.5 6 0.00013 29.9 0.5 40 98-139 2-43 (72)
45 KOG2893 Zn finger protein [Gen 45.6 9.1 0.0002 35.5 0.8 30 100-133 13-42 (341)
46 TIGR02605 CxxC_CxxC_SSSS putat 44.3 8.9 0.00019 26.2 0.4 29 98-133 6-34 (52)
47 PRK06266 transcription initiat 42.2 9.9 0.00021 33.2 0.4 31 95-134 115-145 (178)
48 TIGR00373 conserved hypothetic 40.8 11 0.00025 32.1 0.6 32 94-134 106-137 (158)
49 smart00659 RPOLCX RNA polymera 40.7 17 0.00036 24.7 1.3 27 97-134 2-28 (44)
50 smart00614 ZnF_BED BED zinc fi 39.2 19 0.00041 24.6 1.4 25 97-121 18-48 (50)
51 COG4049 Uncharacterized protei 39.1 11 0.00025 27.3 0.3 28 92-119 12-39 (65)
52 PRK04860 hypothetical protein; 39.1 12 0.00026 32.3 0.4 25 86-110 132-156 (160)
53 COG5188 PRP9 Splicing factor 3 39.0 23 0.00051 34.6 2.4 28 28-55 329-357 (470)
54 smart00834 CxxC_CXXC_SSSS Puta 38.1 12 0.00027 23.9 0.3 11 98-108 6-16 (41)
55 smart00531 TFIIE Transcription 37.5 17 0.00037 30.5 1.1 38 94-135 96-133 (147)
56 PF02892 zf-BED: BED zinc fing 36.8 20 0.00043 23.5 1.2 23 95-117 14-40 (45)
57 PF09538 FYDLN_acid: Protein o 36.6 21 0.00046 28.8 1.5 10 99-108 11-20 (108)
58 KOG1146 Homeobox protein [Gene 36.0 32 0.0007 38.8 3.2 48 90-137 458-530 (1406)
59 PF05443 ROS_MUCR: ROS/MUCR tr 34.2 17 0.00038 30.4 0.7 30 95-127 70-99 (132)
60 PRK00398 rpoP DNA-directed RNA 32.0 19 0.00041 24.2 0.5 29 97-135 3-31 (46)
61 PHA00626 hypothetical protein 30.2 19 0.00042 26.1 0.3 13 124-136 22-34 (59)
62 COG2888 Predicted Zn-ribbon RN 29.6 35 0.00076 25.0 1.5 32 97-133 27-58 (61)
63 KOG2186 Cell growth-regulating 29.5 25 0.00055 32.8 1.0 39 97-137 3-41 (276)
64 PF09723 Zn-ribbon_8: Zinc rib 28.2 21 0.00045 23.7 0.1 29 98-133 6-34 (42)
65 COG3091 SprT Zn-dependent meta 28.2 26 0.00056 30.3 0.8 35 94-133 114-148 (156)
66 cd00729 rubredoxin_SM Rubredox 27.5 36 0.00077 21.7 1.1 26 97-134 2-27 (34)
67 COG1996 RPC10 DNA-directed RNA 27.2 28 0.0006 24.5 0.6 30 95-134 4-33 (49)
68 TIGR02098 MJ0042_CXXC MJ0042 f 26.0 37 0.0008 21.6 1.0 34 98-136 3-36 (38)
69 KOG3507 DNA-directed RNA polym 25.3 34 0.00074 25.0 0.8 30 95-135 18-47 (62)
70 COG1997 RPL43A Ribosomal prote 24.5 32 0.0007 27.0 0.6 31 96-136 34-64 (89)
71 KOG2593 Transcription initiati 24.1 44 0.00096 33.3 1.6 38 93-133 124-161 (436)
72 KOG2893 Zn finger protein [Gen 24.1 24 0.00051 32.9 -0.2 31 91-121 28-59 (341)
73 PF03604 DNA_RNApol_7kD: DNA d 23.8 59 0.0013 20.7 1.6 26 98-134 1-26 (32)
74 TIGR02300 FYDLN_acid conserved 23.4 51 0.0011 27.7 1.6 10 99-108 11-20 (129)
75 COG1592 Rubrerythrin [Energy p 23.4 48 0.001 28.9 1.5 24 97-133 134-157 (166)
76 PRK14890 putative Zn-ribbon RN 22.1 48 0.001 24.2 1.1 32 97-133 25-56 (59)
77 TIGR00244 transcriptional regu 22.0 36 0.00078 29.2 0.5 16 124-139 27-42 (147)
78 PRK14873 primosome assembly pr 20.2 48 0.0011 34.8 1.1 34 99-133 385-418 (665)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.08 E-value=8.8e-12 Score=114.23 Aligned_cols=39 Identities=26% Similarity=0.429 Sum_probs=23.3
Q ss_pred cccCCCCCcccCCchhhhhhhhhccCCcccccccccchh
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDM 135 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~ 135 (270)
+++|.+|||.|.+..-|++|+|+|||||||.|..|+++|
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAF 225 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAF 225 (279)
T ss_pred CcccccccccccchHHhhcccccccCCCCccCCcccchh
Confidence 555555666666555566666666666666666666555
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=98.99 E-value=9.7e-11 Score=107.43 Aligned_cols=55 Identities=18% Similarity=0.304 Sum_probs=50.4
Q ss_pred cccccccCCCCcccCCCCCcccCCchhhhhhhhhccCCcccccccccchhccccC
Q 047542 86 ESIRKKQPKQKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDMGALGH 140 (270)
Q Consensus 86 ~~~~~~HTgeKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~~~~~~ 140 (270)
.+.-|+|||||||.|..|+|+|..+++|+.|+++|.+.|.|+|.+|++.|+...-
T Consensus 204 QGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~Sy 258 (279)
T KOG2462|consen 204 QGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSY 258 (279)
T ss_pred hcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHH
Confidence 4556789999999999999999999999999999999999999999999976543
No 3
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.98 E-value=9.7e-11 Score=118.45 Aligned_cols=49 Identities=20% Similarity=0.415 Sum_probs=41.0
Q ss_pred ccCCCCcccCCCCCcccCCchhhhhhhhhccCCcccccccccchhcccc
Q 047542 91 KQPKQKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDMGALG 139 (270)
Q Consensus 91 ~HTgeKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~~~~~ 139 (270)
-|+|.|||+|.+|.|+|..+-.|+.|+|.|.|||||+|..|+++|++-|
T Consensus 916 EHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSG 964 (1007)
T KOG3623|consen 916 EHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSG 964 (1007)
T ss_pred hhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhccccc
Confidence 5788888888888888888888888888888888888888888886644
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.59 E-value=2.5e-08 Score=102.55 Aligned_cols=88 Identities=20% Similarity=0.243 Sum_probs=62.2
Q ss_pred cccCCCCCcccCCchhhhhhhhhccCCcccccccccchhccccCCCCCc------cCCCCCCCCCCCCcccccccCCCCC
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDMGALGHHHYPY------YPYSSSVAHQNPNFYGSLFNRSSPL 170 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~~~~~~~~~~~------~py~~~~~~~~p~~~G~~f~rs~~l 170 (270)
+++|.+|.|.|...++|..|.|.|||||||+|.+||.+|++.|++..|| ||+.-+++|+.+..-.. --++..+
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~e~~p~~~m~p~~~~e~l~~-~i~st~~ 431 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHREKYPHVQMNPHPVQEHLQY-VITSTGL 431 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeeccccCCccccCCCCchhhhcc-eeecccc
Confidence 4789999999999999999999999999999999999999888765554 56666666665543332 1122123
Q ss_pred CccccCCcCCCCCCC
Q 047542 171 GVSMQPMIRKPSYPW 185 (270)
Q Consensus 171 gl~~hs~iHkp~~~~ 185 (270)
+.-+--..||+..-|
T Consensus 432 p~g~~vpp~k~~~~~ 446 (958)
T KOG1074|consen 432 PYGPSVPPEKAEEEA 446 (958)
T ss_pred CCCCCCCCCCCcchh
Confidence 334444455544333
No 5
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.59 E-value=2.3e-08 Score=102.72 Aligned_cols=85 Identities=14% Similarity=0.144 Sum_probs=66.4
Q ss_pred CcccCCCCCcccCCchhhhhhhhhccCCcccccccccchhccccCCCCCccCCCCCCCC------CCCCcccccccCCCC
Q 047542 96 KGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDMGALGHHHYPYYPYSSSVAH------QNPNFYGSLFNRSSP 169 (270)
Q Consensus 96 Kpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~~~~~~~~~~~~py~~~~~~------~~p~~~G~~f~rs~~ 169 (270)
.|-+|-+|.|...-.++|+-|.|+|+|||||+|+.||++|.+.|++..||--+...++. |.-..|-+-|...
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~-- 681 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNA-- 681 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccc--
Confidence 47889999999999999999999999999999999999999988876665222221211 1112566668777
Q ss_pred CCccccCCcCCCC
Q 047542 170 LGVSMQPMIRKPS 182 (270)
Q Consensus 170 lgl~~hs~iHkp~ 182 (270)
+.+..|.+||.+.
T Consensus 682 V~lpQhIriH~~~ 694 (958)
T KOG1074|consen 682 VTLPQHIRIHLGG 694 (958)
T ss_pred ccccceEEeecCC
Confidence 9999999999854
No 6
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.46 E-value=5.4e-08 Score=98.95 Aligned_cols=46 Identities=22% Similarity=0.372 Sum_probs=43.9
Q ss_pred CCcccCCCCCcccCCchhhhhhhhhccCCcccccccccchhccccC
Q 047542 95 QKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDMGALGH 140 (270)
Q Consensus 95 eKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~~~~~~ 140 (270)
.|.|+|.+|+|+|..+-.|+.|.|+|.|||||.|..|+++|++-|.
T Consensus 279 lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGS 324 (1007)
T KOG3623|consen 279 LRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGS 324 (1007)
T ss_pred hccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCc
Confidence 4789999999999999999999999999999999999999988776
No 7
>PHA02768 hypothetical protein; Provisional
Probab=98.34 E-value=2e-07 Score=66.72 Aligned_cols=39 Identities=18% Similarity=0.337 Sum_probs=35.8
Q ss_pred cccCCCCCcccCCchhhhhhhhhccCCcccccccccchhcc
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDMGA 137 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~~~ 137 (270)
-|+|+.||+.|...++|..|+++|+ ++|+|..|++.|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~ 43 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLR 43 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecc
Confidence 4899999999999999999999999 79999999988764
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.13 E-value=1.9e-06 Score=76.83 Aligned_cols=78 Identities=18% Similarity=0.322 Sum_probs=62.4
Q ss_pred CCCCcccCCCCCcccCCchhhhhhhhhccCCcccccccccchhcc---ccCCCCCc---cCCCCCCCCCCCCcccccccC
Q 047542 93 PKQKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDMGA---LGHHHYPY---YPYSSSVAHQNPNFYGSLFNR 166 (270)
Q Consensus 93 TgeKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~~~---~~~~~~~~---~py~~~~~~~~p~~~G~~f~r 166 (270)
.+...|.|.+|+|+|.....|.+|++.|..-|.|.|.-||+.|.. +..|.++| .||.| +.|+|+|.+
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc-------~~c~kaftq 185 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKC-------SLCEKAFTQ 185 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccch-------hhhhHHHHh
Confidence 345679999999999999999999999999999999999998842 33344444 57765 689999988
Q ss_pred CCCCCccccC-CcC
Q 047542 167 SSPLGVSMQP-MIR 179 (270)
Q Consensus 167 s~~lgl~~hs-~iH 179 (270)
. ..|..|. .||
T Consensus 186 r--csleshl~kvh 197 (267)
T KOG3576|consen 186 R--CSLESHLKKVH 197 (267)
T ss_pred h--ccHHHHHHHHc
Confidence 8 8888886 355
No 9
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.00 E-value=2.2e-06 Score=52.11 Aligned_cols=25 Identities=16% Similarity=0.147 Sum_probs=22.5
Q ss_pred hhhhhhhhccCCcccccccccchhc
Q 047542 112 ALGGHQNAHKQERALAKRRKEMDMG 136 (270)
Q Consensus 112 aL~~Hqr~HtgEKPfkCr~c~~~~~ 136 (270)
+|..|+++|+++|||+|..|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4789999999999999999998874
No 10
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=97.95 E-value=1.6e-06 Score=77.32 Aligned_cols=90 Identities=21% Similarity=0.235 Sum_probs=62.2
Q ss_pred ccCCCCcccCCCCCcccCCchhhhhhhhhccCCcccccccccchhcc-------ccCCCC--CccCCCCC-CCCCCCCcc
Q 047542 91 KQPKQKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDMGA-------LGHHHY--PYYPYSSS-VAHQNPNFY 160 (270)
Q Consensus 91 ~HTgeKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~~~-------~~~~~~--~~~py~~~-~~~~~p~~~ 160 (270)
-|...|.|.|.+|||.|..--.|.+|.|+|+|.|||+|..|+++|.. +...|- +-|-|..- .....|+.|
T Consensus 139 ch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedc 218 (267)
T KOG3576|consen 139 CHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDC 218 (267)
T ss_pred hccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeeccc
Confidence 36677889999999999999999999999999999999999999942 211110 11333221 122356789
Q ss_pred cccccCCCCCCccccCCcCCCC
Q 047542 161 GSLFNRSSPLGVSMQPMIRKPS 182 (270)
Q Consensus 161 G~~f~rs~~lgl~~hs~iHkp~ 182 (270)
|-.-. ++-..-.|...|.|.
T Consensus 219 g~t~~--~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 219 GYTSE--RPEVYYLHLKLHHPF 238 (267)
T ss_pred CCCCC--ChhHHHHHHHhcCCC
Confidence 86332 235566677777654
No 11
>PHA00616 hypothetical protein
Probab=97.67 E-value=1.3e-05 Score=54.91 Aligned_cols=34 Identities=18% Similarity=0.299 Sum_probs=32.3
Q ss_pred cccCCCCCcccCCchhhhhhhhhccCCccccccc
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAHKQERALAKRR 130 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~ 130 (270)
||.|..||+.|...+.|..|++.|++++++.|..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999999874
No 12
>PHA00733 hypothetical protein
Probab=97.48 E-value=7.2e-05 Score=62.09 Aligned_cols=39 Identities=21% Similarity=0.294 Sum_probs=22.1
Q ss_pred CCcccCCCCCcccCCchhhhhhhhhccCCcccccccccchh
Q 047542 95 QKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDM 135 (270)
Q Consensus 95 eKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~ 135 (270)
.+||.|..|++.|.....|..|++.| +++|.|..|++.|
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F 109 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEF 109 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCcc
Confidence 45556666666666666666565554 2345555555555
No 13
>PHA00732 hypothetical protein
Probab=97.40 E-value=8.4e-05 Score=56.91 Aligned_cols=43 Identities=23% Similarity=0.233 Sum_probs=36.3
Q ss_pred cccCCCCCcccCCchhhhhhhhh-ccCCcccccccccchhccccCCC
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNA-HKQERALAKRRKEMDMGALGHHH 142 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~-HtgEKPfkCr~c~~~~~~~~~~~ 142 (270)
||.|..|++.|.+...|..|++. |+ ++.|..|++.|..+..|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~l~~H~ 44 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRRLNQHF 44 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCChhhhh
Confidence 68999999999999999999984 65 468999999997665543
No 14
>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=96.85 E-value=0.00029 Score=42.70 Aligned_cols=21 Identities=29% Similarity=0.735 Sum_probs=18.4
Q ss_pred ccccCCCCcccCCCCCcccCC
Q 047542 89 RKKQPKQKGFLCNFCNKIFST 109 (270)
Q Consensus 89 ~~~HTgeKpf~C~~CgKsF~s 109 (270)
.++|++++||.|++|++.|.+
T Consensus 6 ~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 6 MRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHSSSSSEEESSSSEEESS
T ss_pred hhhcCCCCCCCCCCCcCeeCc
Confidence 357999999999999999963
No 15
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=96.77 E-value=0.00046 Score=39.95 Aligned_cols=23 Identities=35% Similarity=0.742 Sum_probs=21.5
Q ss_pred ccCCCCCcccCCchhhhhhhhhc
Q 047542 98 FLCNFCNKIFSTSQALGGHQNAH 120 (270)
Q Consensus 98 f~C~~CgKsF~sssaL~~Hqr~H 120 (270)
|.|..|++.|.....|..|++.|
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 68999999999999999999875
No 16
>PHA00733 hypothetical protein
Probab=96.48 E-value=0.00034 Score=58.06 Aligned_cols=79 Identities=11% Similarity=0.017 Sum_probs=52.9
Q ss_pred CCCcccCCCCCcccCCchhhhhh--hh---hccCCcccccccccchhccccCCCCCccCCCCCCCCCCCCcccccccCCC
Q 047542 94 KQKGFLCNFCNKIFSTSQALGGH--QN---AHKQERALAKRRKEMDMGALGHHHYPYYPYSSSVAHQNPNFYGSLFNRSS 168 (270)
Q Consensus 94 geKpf~C~~CgKsF~sssaL~~H--qr---~HtgEKPfkCr~c~~~~~~~~~~~~~~~py~~~~~~~~p~~~G~~f~rs~ 168 (270)
..+++.|.+|.+.|.....|..| .+ .+.+++||.|..|++.|........+.. +.. . ...|..||++|.+.
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r-~h~-~-~~~C~~CgK~F~~~- 112 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIR-YTE-H-SKVCPVCGKEFRNT- 112 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHh-cCC-c-CccCCCCCCccCCH-
Confidence 46789999999999888877766 21 2345899999999999865433211111 100 1 12456999999887
Q ss_pred CCCccccCC
Q 047542 169 PLGVSMQPM 177 (270)
Q Consensus 169 ~lgl~~hs~ 177 (270)
..++.|..
T Consensus 113 -~sL~~H~~ 120 (128)
T PHA00733 113 -DSTLDHVC 120 (128)
T ss_pred -HHHHHHHH
Confidence 66666654
No 17
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=96.30 E-value=0.00069 Score=64.91 Aligned_cols=96 Identities=17% Similarity=0.300 Sum_probs=67.4
Q ss_pred cccccccCCCCcccCCCCCcccCCchhhhhhhhhccCCccccccc--ccchhccccCCCCCc---------cCCCCCCCC
Q 047542 86 ESIRKKQPKQKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRR--KEMDMGALGHHHYPY---------YPYSSSVAH 154 (270)
Q Consensus 86 ~~~~~~HTgeKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~--c~~~~~~~~~~~~~~---------~py~~~~~~ 154 (270)
..++-.|...|||+|+.|.+.|...+.|.+|..+|. +-.|+|.. |-..|+.+.+..+|| .+|.|
T Consensus 281 ~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~C---- 355 (467)
T KOG3608|consen 281 THIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYAC---- 355 (467)
T ss_pred HHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceee----
Confidence 334446888999999999999999999999998888 67799987 888776655544443 23433
Q ss_pred CCCCcccccccCCCCCCccccCCcCCCCCCCCCCCCCC
Q 047542 155 QNPNFYGSLFNRSSPLGVSMQPMIRKPSYPWVPLWDRF 192 (270)
Q Consensus 155 ~~p~~~G~~f~rs~~lgl~~hs~iHkp~~~~~~~~~~~ 192 (270)
-.|.+-|.+- ..|.+|.|-.. -+-||+.-.||
T Consensus 356 ---H~Cdr~ft~G--~~L~~HL~kkH-~f~~PsGh~RF 387 (467)
T KOG3608|consen 356 ---HCCDRFFTSG--KSLSAHLMKKH-GFRLPSGHKRF 387 (467)
T ss_pred ---ecchhhhccc--hhHHHHHHHhh-cccCCCCCCce
Confidence 3688867655 77888876433 24466543333
No 18
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=96.14 E-value=0.002 Score=38.65 Aligned_cols=25 Identities=40% Similarity=0.699 Sum_probs=23.2
Q ss_pred cccCCCCCcccCCchhhhhhhhhcc
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAHK 121 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~Ht 121 (270)
||.|..|++.|.....|..|++.|.
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 6899999999999999999998874
No 19
>PRK04860 hypothetical protein; Provisional
Probab=95.97 E-value=0.0036 Score=54.00 Aligned_cols=37 Identities=16% Similarity=0.292 Sum_probs=32.8
Q ss_pred CcccCCCCCcccCCchhhhhhhhhccCCcccccccccchhc
Q 047542 96 KGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDMG 136 (270)
Q Consensus 96 Kpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~~ 136 (270)
-+|.|. |++ ....+.+|.++|+++++|.|+.|+..|.
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeE
Confidence 479998 987 6677899999999999999999998764
No 20
>PLN03086 PRLI-interacting factor K; Provisional
Probab=95.95 E-value=0.0038 Score=63.45 Aligned_cols=84 Identities=15% Similarity=0.198 Sum_probs=53.8
Q ss_pred CCcccCCCCCcccCCchhhhhhhhhccCCcccccccccchhc--cccCCCCCccCCCCCCCCCCCCcccccccCC-----
Q 047542 95 QKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDMG--ALGHHHYPYYPYSSSVAHQNPNFYGSLFNRS----- 167 (270)
Q Consensus 95 eKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~~--~~~~~~~~~~py~~~~~~~~p~~~G~~f~rs----- 167 (270)
++.+.|.+|++.|. ...|..|+++|+ +++.|. |++.+. .+..|...+.|.. ...|.+|+..|.+.
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~~R~~L~~H~~thCp~K----pi~C~fC~~~v~~g~~~~d 522 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVLEKEQMVQHQASTCPLR----LITCRFCGDMVQAGGSAMD 522 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCcchhHHHhhhhccCCCC----ceeCCCCCCccccCccccc
Confidence 34578999999996 577999999874 899999 986542 2333333333321 12456899877421
Q ss_pred ---CCCCccccCCcCCCCCCCCC
Q 047542 168 ---SPLGVSMQPMIRKPSYPWVP 187 (270)
Q Consensus 168 ---~~lgl~~hs~iHkp~~~~~~ 187 (270)
...+|..|..++ +..+..+
T Consensus 523 ~~d~~s~Lt~HE~~C-G~rt~~C 544 (567)
T PLN03086 523 VRDRLRGMSEHESIC-GSRTAPC 544 (567)
T ss_pred hhhhhhhHHHHHHhc-CCcceEc
Confidence 114788888876 5555443
No 21
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=95.78 E-value=0.0042 Score=35.35 Aligned_cols=23 Identities=35% Similarity=0.765 Sum_probs=19.4
Q ss_pred ccCCCCCcccCCchhhhhhhhhc
Q 047542 98 FLCNFCNKIFSTSQALGGHQNAH 120 (270)
Q Consensus 98 f~C~~CgKsF~sssaL~~Hqr~H 120 (270)
|.|++|++.|.....|..|++.|
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 68999999999999999999876
No 22
>PLN03086 PRLI-interacting factor K; Provisional
Probab=95.41 E-value=0.0071 Score=61.47 Aligned_cols=38 Identities=16% Similarity=0.238 Sum_probs=34.5
Q ss_pred CcccCCCCCcccCCchhhhhhhhhccCCcccccccccchh
Q 047542 96 KGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDM 135 (270)
Q Consensus 96 Kpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~ 135 (270)
+++.|. |++.+ .+..|..|++.|..+|++.|+.|++.+
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMV 514 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCcc
Confidence 789999 99765 668999999999999999999999887
No 23
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.25 E-value=0.011 Score=33.74 Aligned_cols=24 Identities=33% Similarity=0.728 Sum_probs=21.9
Q ss_pred ccCCCCCcccCCchhhhhhhhhcc
Q 047542 98 FLCNFCNKIFSTSQALGGHQNAHK 121 (270)
Q Consensus 98 f~C~~CgKsF~sssaL~~Hqr~Ht 121 (270)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998775
No 24
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.02 E-value=0.034 Score=52.97 Aligned_cols=25 Identities=28% Similarity=0.523 Sum_probs=21.4
Q ss_pred CCCcccCCC--CCcccCCchhhhhhhh
Q 047542 94 KQKGFLCNF--CNKIFSTSQALGGHQN 118 (270)
Q Consensus 94 geKpf~C~~--CgKsF~sssaL~~Hqr 118 (270)
++|||+|++ |.|++...-.|+-|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~l 372 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHML 372 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhh
Confidence 359999987 9999999999888854
No 25
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=94.66 E-value=0.0024 Score=62.39 Aligned_cols=83 Identities=13% Similarity=0.213 Sum_probs=54.7
Q ss_pred cccCCCCCcccCCchhhhhhhhhccCCcccccccccchhc---cccCCCCCccCCCCC----------------------
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDMG---ALGHHHYPYYPYSSS---------------------- 151 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~~---~~~~~~~~~~py~~~---------------------- 151 (270)
-|.|..|...|...-.|.+|+-...-.--|+|.+|++.|. .|..|.+-|+|-.-.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 3778888888888888888854333333588888888873 355554444442111
Q ss_pred -------CCCCCCCcccccccCCCCCCccccCCcCCC
Q 047542 152 -------VAHQNPNFYGSLFNRSSPLGVSMQPMIRKP 181 (270)
Q Consensus 152 -------~~~~~p~~~G~~f~rs~~lgl~~hs~iHkp 181 (270)
.....|-+|||.|.|. .=||.|+..|.-
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRq--AYLrKHqlthq~ 381 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQ--AYLRKHQLTHQR 381 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHH--HHHHHhHHhhhc
Confidence 1123456999999998 779999888743
No 26
>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=93.70 E-value=0.046 Score=38.75 Aligned_cols=35 Identities=17% Similarity=0.392 Sum_probs=25.1
Q ss_pred ccCCCCcccCCCCCcccCCchhhhhhhhhccCCcc
Q 047542 91 KQPKQKGFLCNFCNKIFSTSQALGGHQNAHKQERA 125 (270)
Q Consensus 91 ~HTgeKpf~C~~CgKsF~sssaL~~Hqr~HtgEKP 125 (270)
.+..+.|..|++|+..+.+..+|.+|+.++.+.||
T Consensus 18 ~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 34567899999999999999999999988877765
No 27
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=92.93 E-value=0.0082 Score=57.74 Aligned_cols=48 Identities=15% Similarity=0.290 Sum_probs=36.5
Q ss_pred cccCCCCcccCCCCCcccCCchhhhhhhhhcc--CCcccccccccchhcc
Q 047542 90 KKQPKQKGFLCNFCNKIFSTSQALGGHQNAHK--QERALAKRRKEMDMGA 137 (270)
Q Consensus 90 ~~HTgeKpf~C~~CgKsF~sssaL~~Hqr~Ht--gEKPfkCr~c~~~~~~ 137 (270)
+.|+++|...|..|++-|.+...|-.|.+..+ ...+|+|..|-++|++
T Consensus 200 r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaT 249 (467)
T KOG3608|consen 200 RTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFAT 249 (467)
T ss_pred HhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhH
Confidence 46888888888888888888888888866544 3457888888887743
No 28
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=91.63 E-value=0.057 Score=53.06 Aligned_cols=25 Identities=36% Similarity=0.743 Sum_probs=23.4
Q ss_pred cccCCCCCcccCCchhhhhhhhhcc
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAHK 121 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~Ht 121 (270)
-|+|.+|+|.|.-..+|..|+|-|+
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred eecCCcccccccCchhhhhhhcccC
Confidence 4899999999999999999999885
No 29
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=91.50 E-value=0.061 Score=31.43 Aligned_cols=23 Identities=39% Similarity=0.862 Sum_probs=20.8
Q ss_pred ccCCCCCcccCCchhhhhhhhhc
Q 047542 98 FLCNFCNKIFSTSQALGGHQNAH 120 (270)
Q Consensus 98 f~C~~CgKsF~sssaL~~Hqr~H 120 (270)
|.|..|.+.|.....|..|.+.+
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 67999999999999999998764
No 30
>PHA02768 hypothetical protein; Provisional
Probab=91.05 E-value=0.052 Score=38.94 Aligned_cols=35 Identities=6% Similarity=-0.251 Sum_probs=18.8
Q ss_pred cccccccchhc---cccCCCCCcc-CCCCCCCCCCCCcccccccCC
Q 047542 126 LAKRRKEMDMG---ALGHHHYPYY-PYSSSVAHQNPNFYGSLFNRS 167 (270)
Q Consensus 126 fkCr~c~~~~~---~~~~~~~~~~-py~~~~~~~~p~~~G~~f~rs 167 (270)
|+|.+||+.|. ++..|++.|. ||.+ ..||++|.+.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc-------~~C~k~f~~~ 44 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHNTNLKL-------SNCKRISLRT 44 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcCCcccC-------Ccccceeccc
Confidence 67777777763 3444444332 4432 3666666554
No 31
>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=91.01 E-value=0.19 Score=35.27 Aligned_cols=39 Identities=21% Similarity=0.377 Sum_probs=29.7
Q ss_pred cccCCCCCcccCCchhhhhhhh-hccCC-cccccccccchhc
Q 047542 97 GFLCNFCNKIFSTSQALGGHQN-AHKQE-RALAKRRKEMDMG 136 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr-~HtgE-KPfkCr~c~~~~~ 136 (270)
.|.|++|++. .....|..|.. .|..+ +.+.|..|...+.
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~ 42 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT 42 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh
Confidence 4899999995 55688999955 46654 5799999986543
No 32
>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=89.88 E-value=0.14 Score=30.75 Aligned_cols=22 Identities=36% Similarity=0.830 Sum_probs=20.2
Q ss_pred ccCCCCCcccCCchhhhhhhhh
Q 047542 98 FLCNFCNKIFSTSQALGGHQNA 119 (270)
Q Consensus 98 f~C~~CgKsF~sssaL~~Hqr~ 119 (270)
|.|..|++.|.....+..|++.
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 7899999999999999999865
No 33
>PHA00732 hypothetical protein
Probab=84.35 E-value=0.45 Score=36.38 Aligned_cols=43 Identities=7% Similarity=-0.065 Sum_probs=29.0
Q ss_pred ccccccccchhcc---ccCCCC-CccCCCCCCCCCCCCcccccccCCCCCCccccCCcC
Q 047542 125 ALAKRRKEMDMGA---LGHHHY-PYYPYSSSVAHQNPNFYGSLFNRSSPLGVSMQPMIR 179 (270)
Q Consensus 125 PfkCr~c~~~~~~---~~~~~~-~~~py~~~~~~~~p~~~G~~f~rs~~lgl~~hs~iH 179 (270)
||+|..|++.|.. +..|.. ++.++ .|..||+.|.+ +.+|.+.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~-------~C~~CgKsF~~-----l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLT-------KCPVCNKSYRR-----LNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCC-------ccCCCCCEeCC-----hhhhhccc
Confidence 6899999999854 333333 33444 35699998863 67788665
No 34
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=84.02 E-value=0.61 Score=27.94 Aligned_cols=21 Identities=24% Similarity=0.634 Sum_probs=17.3
Q ss_pred ccCCCCCcccCCchhhhhhhhh
Q 047542 98 FLCNFCNKIFSTSQALGGHQNA 119 (270)
Q Consensus 98 f~C~~CgKsF~sssaL~~Hqr~ 119 (270)
..|..|++.| ....|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4699999999 56778999764
No 35
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=83.92 E-value=0.48 Score=27.43 Aligned_cols=22 Identities=27% Similarity=0.523 Sum_probs=17.2
Q ss_pred ccCCCCCcccCCchhhhhhhhhc
Q 047542 98 FLCNFCNKIFSTSQALGGHQNAH 120 (270)
Q Consensus 98 f~C~~CgKsF~sssaL~~Hqr~H 120 (270)
|.|..|..... ...|..|++.|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 68999998887 88999998875
No 36
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=79.91 E-value=0.98 Score=28.15 Aligned_cols=23 Identities=30% Similarity=0.811 Sum_probs=19.9
Q ss_pred cccCCCCCcccCCchhhhhhhhh
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNA 119 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~ 119 (270)
+|.|.+|.+.|.....+..|.+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999998888888754
No 37
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=78.82 E-value=2.5 Score=38.87 Aligned_cols=43 Identities=21% Similarity=0.166 Sum_probs=37.6
Q ss_pred CcccCCCCCcccCCchhhhhhhh--hccCC--cccccc--cccchhccc
Q 047542 96 KGFLCNFCNKIFSTSQALGGHQN--AHKQE--RALAKR--RKEMDMGAL 138 (270)
Q Consensus 96 Kpf~C~~CgKsF~sssaL~~Hqr--~HtgE--KPfkCr--~c~~~~~~~ 138 (270)
.++.|..|...|.....|..|.+ .|.++ +++.|. .|++.|...
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~ 336 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRN 336 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCcccccc
Confidence 47899999999999999999999 89999 999998 687776543
No 38
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=72.40 E-value=2 Score=32.17 Aligned_cols=24 Identities=38% Similarity=0.836 Sum_probs=21.3
Q ss_pred cccCCCCCcccCCchhhhhhhhhc
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAH 120 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~H 120 (270)
.+.|.+|++.|.+...|..|++.+
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 689999999999999999999864
No 39
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=70.70 E-value=2.8 Score=40.25 Aligned_cols=24 Identities=8% Similarity=0.097 Sum_probs=12.6
Q ss_pred cCCcccccccccchhccccCCCCC
Q 047542 121 KQERALAKRRKEMDMGALGHHHYP 144 (270)
Q Consensus 121 tgEKPfkCr~c~~~~~~~~~~~~~ 144 (270)
...|||+|.+|++++..+.-+.||
T Consensus 394 ~~~KPYrCevC~KRYKNlNGLKYH 417 (423)
T COG5189 394 AKDKPYRCEVCDKRYKNLNGLKYH 417 (423)
T ss_pred ccCCceeccccchhhccCccceec
Confidence 344666666666665544433333
No 40
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=70.50 E-value=1.7 Score=37.28 Aligned_cols=39 Identities=13% Similarity=0.145 Sum_probs=21.5
Q ss_pred ccCCCCCcccCC---chhhhhhhhhccCCcccccccccchhcccc
Q 047542 98 FLCNFCNKIFST---SQALGGHQNAHKQERALAKRRKEMDMGALG 139 (270)
Q Consensus 98 f~C~~CgKsF~s---ssaL~~Hqr~HtgEKPfkCr~c~~~~~~~~ 139 (270)
++|++|+-.+.. +..+.. .-+- .+.++|+.||..|.++-
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~--~~~~-~~~~~c~~c~~~f~~~e 42 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAED--GNAI-RRRRECLACGKRFTTFE 42 (154)
T ss_pred CcCCCCCCCCCEeEeccccCC--CCce-eeeeeccccCCcceEeE
Confidence 369999965521 111111 0011 23388999998886643
No 41
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=57.89 E-value=3.8 Score=36.68 Aligned_cols=25 Identities=28% Similarity=0.547 Sum_probs=18.3
Q ss_pred CCcccCCCCCcccCCchhhhhhhhh
Q 047542 95 QKGFLCNFCNKIFSTSQALGGHQNA 119 (270)
Q Consensus 95 eKpf~C~~CgKsF~sssaL~~Hqr~ 119 (270)
.+.+.|++|++.|....-..+..++
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 3567899999999887666555543
No 42
>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=54.79 E-value=7.5 Score=24.54 Aligned_cols=26 Identities=12% Similarity=0.319 Sum_probs=17.8
Q ss_pred ccCCCCCcccCCchhhhhhhhhccCCcccccccccchh
Q 047542 98 FLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDM 135 (270)
Q Consensus 98 f~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~ 135 (270)
|.|..||..+.... .++.|..|+...
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~~~ 27 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGAPK 27 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCCcH
Confidence 67888886654322 678888887643
No 43
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=54.17 E-value=7.3 Score=35.79 Aligned_cols=40 Identities=28% Similarity=0.491 Sum_probs=37.0
Q ss_pred ccCCC--CcccCC--CCCcccCCchhhhhhhhhccCCccccccc
Q 047542 91 KQPKQ--KGFLCN--FCNKIFSTSQALGGHQNAHKQERALAKRR 130 (270)
Q Consensus 91 ~HTge--Kpf~C~--~CgKsF~sssaL~~Hqr~HtgEKPfkCr~ 130 (270)
.|+++ +++.|. .|++.|.+...+..|...|..-+++.|..
T Consensus 313 ~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (467)
T COG5048 313 NHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356 (467)
T ss_pred ccccccCCceeeeccCCCccccccccccCCcccccCCCcccccc
Confidence 79999 999999 79999999999999999999988888865
No 44
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=51.53 E-value=6 Score=29.86 Aligned_cols=40 Identities=13% Similarity=0.130 Sum_probs=24.6
Q ss_pred ccCCCCCcccCCchhhhhhhhhccCCcccccc--cccchhcccc
Q 047542 98 FLCNFCNKIFSTSQALGGHQNAHKQERALAKR--RKEMDMGALG 139 (270)
Q Consensus 98 f~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr--~c~~~~~~~~ 139 (270)
+.|+.|+....-...-..+ ....++-++|. +||..|.+.-
T Consensus 2 m~CP~Cg~~a~irtSr~~s--~~~~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYIT--DTTKERYHQCQNVNCSATFITYE 43 (72)
T ss_pred ccCCCCCCccEEEEChhcC--hhhheeeeecCCCCCCCEEEEEE
Confidence 5799998765322221111 12567889998 8998886543
No 45
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=45.59 E-value=9.1 Score=35.55 Aligned_cols=30 Identities=27% Similarity=0.470 Sum_probs=19.1
Q ss_pred CCCCCcccCCchhhhhhhhhccCCcccccccccc
Q 047542 100 CNFCNKIFSTSQALGGHQNAHKQERALAKRRKEM 133 (270)
Q Consensus 100 C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~ 133 (270)
|=+|.+.|....-|++||++ |-|+|..|-+
T Consensus 13 cwycnrefddekiliqhqka----khfkchichk 42 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKCHICHK 42 (341)
T ss_pred eeecccccchhhhhhhhhhh----ccceeeeehh
Confidence 66677777777667776653 4466666644
No 46
>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=44.27 E-value=8.9 Score=26.17 Aligned_cols=29 Identities=14% Similarity=0.264 Sum_probs=16.0
Q ss_pred ccCCCCCcccCCchhhhhhhhhccCCcccccccccc
Q 047542 98 FLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEM 133 (270)
Q Consensus 98 f~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~ 133 (270)
|.|..|+..|...... +. +..-.|..|+.
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKM------SD-DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEec------CC-CCCCCCCCCCC
Confidence 6677777766533221 11 34456777764
No 47
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=42.15 E-value=9.9 Score=33.23 Aligned_cols=31 Identities=16% Similarity=0.227 Sum_probs=21.2
Q ss_pred CCcccCCCCCcccCCchhhhhhhhhccCCcccccccccch
Q 047542 95 QKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMD 134 (270)
Q Consensus 95 eKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~ 134 (270)
..-|.|+.|++.|+.-.++. .-|.|..||-.
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~ 145 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEM 145 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCC
Confidence 34577888888877666652 25888888743
No 48
>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=40.81 E-value=11 Score=32.12 Aligned_cols=32 Identities=16% Similarity=0.132 Sum_probs=23.2
Q ss_pred CCCcccCCCCCcccCCchhhhhhhhhccCCcccccccccch
Q 047542 94 KQKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMD 134 (270)
Q Consensus 94 geKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~ 134 (270)
...-|.|+.|+..|+.-.++. .-|.|..||-.
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 345678888888888777764 25888888754
No 49
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=40.70 E-value=17 Score=24.74 Aligned_cols=27 Identities=11% Similarity=0.255 Sum_probs=19.1
Q ss_pred cccCCCCCcccCCchhhhhhhhhccCCcccccccccch
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMD 134 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~ 134 (270)
.|.|..||..|... ..-+.+|+.||.+
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC-----------CCCceECCCCCce
Confidence 37899999877643 2346889888854
No 50
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=39.20 E-value=19 Score=24.57 Aligned_cols=25 Identities=32% Similarity=0.571 Sum_probs=18.6
Q ss_pred cccCCCCCcccCCc-----hhhhhhhh-hcc
Q 047542 97 GFLCNFCNKIFSTS-----QALGGHQN-AHK 121 (270)
Q Consensus 97 pf~C~~CgKsF~ss-----saL~~Hqr-~Ht 121 (270)
.-.|.+|++.+... ++|.+|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 34699999998765 57888876 453
No 51
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=39.10 E-value=11 Score=27.32 Aligned_cols=28 Identities=18% Similarity=0.337 Sum_probs=23.5
Q ss_pred cCCCCcccCCCCCcccCCchhhhhhhhh
Q 047542 92 QPKQKGFLCNFCNKIFSTSQALGGHQNA 119 (270)
Q Consensus 92 HTgeKpf~C~~CgKsF~sssaL~~Hqr~ 119 (270)
..|+.-+.|+-|+..|...-...+|.+.
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 3467778999999999999999999764
No 52
>PRK04860 hypothetical protein; Provisional
Probab=39.07 E-value=12 Score=32.32 Aligned_cols=25 Identities=8% Similarity=0.224 Sum_probs=20.6
Q ss_pred cccccccCCCCcccCCCCCcccCCc
Q 047542 86 ESIRKKQPKQKGFLCNFCNKIFSTS 110 (270)
Q Consensus 86 ~~~~~~HTgeKpf~C~~CgKsF~ss 110 (270)
....++|+++++|.|..|++.|...
T Consensus 132 rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 132 RRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred HHHHHHhcCCccEECCCCCceeEEe
Confidence 4455689999999999999988654
No 53
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=39.02 E-value=23 Score=34.61 Aligned_cols=28 Identities=21% Similarity=0.163 Sum_probs=17.8
Q ss_pred chhhhcccCccc-ccCccccccccccccC
Q 047542 28 NKQVAEVTEPIQ-TKSKFNILFNQNIAID 55 (270)
Q Consensus 28 ~~~~~~~~e~~~-~~~~~~~~ld~~ls~~ 55 (270)
.++.++.++.+| .+...-..+|+.|..|
T Consensus 329 e~EGaeq~d~eQ~DE~~~~k~fdmPLG~D 357 (470)
T COG5188 329 EKEGAEQVDGEQRDEHVSGKSFDMPLGPD 357 (470)
T ss_pred hhcccccccccccchhhccCcccCCCCCC
Confidence 356666666666 4444556777777776
No 54
>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=38.06 E-value=12 Score=23.92 Aligned_cols=11 Identities=27% Similarity=0.905 Sum_probs=6.7
Q ss_pred ccCCCCCcccC
Q 047542 98 FLCNFCNKIFS 108 (270)
Q Consensus 98 f~C~~CgKsF~ 108 (270)
|.|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 56666666554
No 55
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=37.47 E-value=17 Score=30.48 Aligned_cols=38 Identities=11% Similarity=0.172 Sum_probs=24.0
Q ss_pred CCCcccCCCCCcccCCchhhhhhhhhccCCcccccccccchh
Q 047542 94 KQKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDM 135 (270)
Q Consensus 94 geKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~ 135 (270)
...-|.|+.|+..|....++.. .+. ..-|.|..|+...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEE
Confidence 3456889999988885444332 111 3349999998643
No 56
>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=36.85 E-value=20 Score=23.50 Aligned_cols=23 Identities=30% Similarity=0.615 Sum_probs=14.5
Q ss_pred CCcccCCCCCcccCCc----hhhhhhh
Q 047542 95 QKGFLCNFCNKIFSTS----QALGGHQ 117 (270)
Q Consensus 95 eKpf~C~~CgKsF~ss----saL~~Hq 117 (270)
.....|.+|++.+... ..|..|+
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 4456899999988764 6688887
No 57
>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=36.63 E-value=21 Score=28.83 Aligned_cols=10 Identities=30% Similarity=0.700 Sum_probs=5.4
Q ss_pred cCCCCCcccC
Q 047542 99 LCNFCNKIFS 108 (270)
Q Consensus 99 ~C~~CgKsF~ 108 (270)
.|..||+.|.
T Consensus 11 ~Cp~CG~kFY 20 (108)
T PF09538_consen 11 TCPSCGAKFY 20 (108)
T ss_pred cCCCCcchhc
Confidence 4555555554
No 58
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=36.04 E-value=32 Score=38.77 Aligned_cols=48 Identities=21% Similarity=0.258 Sum_probs=38.3
Q ss_pred cccCCCCcccCCCCCcccCCchhhhhhhhh-c------------------------cCCcccccccccchhcc
Q 047542 90 KKQPKQKGFLCNFCNKIFSTSQALGGHQNA-H------------------------KQERALAKRRKEMDMGA 137 (270)
Q Consensus 90 ~~HTgeKpf~C~~CgKsF~sssaL~~Hqr~-H------------------------tgEKPfkCr~c~~~~~~ 137 (270)
..|.-.|.|.|+.|+..|.....|..|+|. | -+-++|.|+.|-..+..
T Consensus 458 ~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~sttt 530 (1406)
T KOG1146|consen 458 VLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTT 530 (1406)
T ss_pred eeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeec
Confidence 356667899999999999999999999997 1 12378999999876643
No 59
>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=34.21 E-value=17 Score=30.44 Aligned_cols=30 Identities=27% Similarity=0.386 Sum_probs=18.4
Q ss_pred CCcccCCCCCcccCCchhhhhhhhhccCCcccc
Q 047542 95 QKGFLCNFCNKIFSTSQALGGHQNAHKQERALA 127 (270)
Q Consensus 95 eKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfk 127 (270)
+.-..|-+||+.|.. |.+|.+.|.|--|-.
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp~e 99 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTPEE 99 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-HHH
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCHHH
Confidence 334679999999975 799999997765533
No 60
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=31.97 E-value=19 Score=24.15 Aligned_cols=29 Identities=7% Similarity=0.130 Sum_probs=17.2
Q ss_pred cccCCCCCcccCCchhhhhhhhhccCCcccccccccchh
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDM 135 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~ 135 (270)
.|.|..||..|...... ..+.|..||..+
T Consensus 3 ~y~C~~CG~~~~~~~~~----------~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEYG----------TGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCCC----------CceECCCCCCeE
Confidence 47788887766542211 146777777543
No 61
>PHA00626 hypothetical protein
Probab=30.19 E-value=19 Score=26.07 Aligned_cols=13 Identities=0% Similarity=-0.253 Sum_probs=9.4
Q ss_pred cccccccccchhc
Q 047542 124 RALAKRRKEMDMG 136 (270)
Q Consensus 124 KPfkCr~c~~~~~ 136 (270)
..|+|..|+..|.
T Consensus 22 nrYkCkdCGY~ft 34 (59)
T PHA00626 22 DDYVCCDCGYNDS 34 (59)
T ss_pred cceEcCCCCCeec
Confidence 4688888887763
No 62
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=29.55 E-value=35 Score=24.99 Aligned_cols=32 Identities=13% Similarity=0.175 Sum_probs=20.1
Q ss_pred cccCCCCCcccCCchhhhhhhhhccCCcccccccccc
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEM 133 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~ 133 (270)
.|.|+.||+.--... ++-.+-..+|+|..||.
T Consensus 27 ~F~CPnCGe~~I~Rc-----~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRC-----AKCRKLGNPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehh-----hhHHHcCCceECCCcCc
Confidence 588999996543332 22223346888888874
No 63
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=29.47 E-value=25 Score=32.80 Aligned_cols=39 Identities=13% Similarity=0.210 Sum_probs=31.0
Q ss_pred cccCCCCCcccCCchhhhhhhhhccCCcccccccccchhcc
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDMGA 137 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~~~ 137 (270)
.|.|..||..... ..+-+|+...++ .-|.|-.|+..|..
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER 41 (276)
T ss_pred EEehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc
Confidence 4789999988764 457779877766 67999999998854
No 64
>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=28.25 E-value=21 Score=23.74 Aligned_cols=29 Identities=14% Similarity=0.351 Sum_probs=15.0
Q ss_pred ccCCCCCcccCCchhhhhhhhhccCCcccccccccc
Q 047542 98 FLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEM 133 (270)
Q Consensus 98 f~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~ 133 (270)
|.|..||..|...... .. ..+-.|..|+.
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSI------SE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEc------CC-CCCCcCCCCCC
Confidence 5666776666433221 12 34555666654
No 65
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=28.24 E-value=26 Score=30.27 Aligned_cols=35 Identities=11% Similarity=0.298 Sum_probs=25.3
Q ss_pred CCCcccCCCCCcccCCchhhhhhhhhccCCcccccccccc
Q 047542 94 KQKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEM 133 (270)
Q Consensus 94 geKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~ 133 (270)
..-+|.|. |+..|.+ ..+|-.+-.|+ .|.|..|+-
T Consensus 114 ~~~~Y~C~-C~q~~l~---~RRhn~~~~g~-~YrC~~C~g 148 (156)
T COG3091 114 TTYPYRCQ-CQQHYLR---IRRHNTVRRGE-VYRCGKCGG 148 (156)
T ss_pred cceeEEee-cCCccch---hhhcccccccc-eEEeccCCc
Confidence 34579999 9987654 44555555677 899999974
No 66
>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=27.50 E-value=36 Score=21.72 Aligned_cols=26 Identities=15% Similarity=0.192 Sum_probs=16.3
Q ss_pred cccCCCCCcccCCchhhhhhhhhccCCcccccccccch
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMD 134 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~ 134 (270)
.|.|..||..+... +.|..|..|+..
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCCc
Confidence 36788888654321 246678888764
No 67
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=27.18 E-value=28 Score=24.46 Aligned_cols=30 Identities=10% Similarity=0.212 Sum_probs=19.7
Q ss_pred CCcccCCCCCcccCCchhhhhhhhhccCCcccccccccch
Q 047542 95 QKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMD 134 (270)
Q Consensus 95 eKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~ 134 (270)
...|.|-.|++.|..- .......|..||.+
T Consensus 4 ~~~Y~C~~Cg~~~~~~----------~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELD----------QETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehh----------hccCceeCCCCCcE
Confidence 3468899999888211 12346788888754
No 68
>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=25.98 E-value=37 Score=21.58 Aligned_cols=34 Identities=12% Similarity=0.113 Sum_probs=20.8
Q ss_pred ccCCCCCcccCCchhhhhhhhhccCCcccccccccchhc
Q 047542 98 FLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDMG 136 (270)
Q Consensus 98 f~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~~ 136 (270)
+.|+.|+..|.-...... .......|..|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~-----~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG-----ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC-----CCCCEEECCCCCCEEE
Confidence 468888888765544321 1122577888886653
No 69
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=25.26 E-value=34 Score=25.01 Aligned_cols=30 Identities=13% Similarity=0.249 Sum_probs=20.2
Q ss_pred CCcccCCCCCcccCCchhhhhhhhhccCCcccccccccchh
Q 047542 95 QKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDM 135 (270)
Q Consensus 95 eKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~ 135 (270)
.--|.|-.|+..- .-...-.++|++||.+.
T Consensus 18 ~miYiCgdC~~en-----------~lk~~D~irCReCG~RI 47 (62)
T KOG3507|consen 18 TMIYICGDCGQEN-----------TLKRGDVIRCRECGYRI 47 (62)
T ss_pred cEEEEeccccccc-----------cccCCCcEehhhcchHH
Confidence 3458999997532 22334579999999764
No 70
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=24.54 E-value=32 Score=27.01 Aligned_cols=31 Identities=13% Similarity=0.313 Sum_probs=22.1
Q ss_pred CcccCCCCCcccCCchhhhhhhhhccCCcccccccccchhc
Q 047542 96 KGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMDMG 136 (270)
Q Consensus 96 Kpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~~~ 136 (270)
..|.|+.|++. .+.|+-++ -+.|+.|+..|.
T Consensus 34 ~~~~Cp~C~~~--------~VkR~a~G--IW~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRIATG--IWKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCc--------ceeeeccC--eEEcCCCCCeec
Confidence 46899999975 23444333 588999998874
No 71
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.11 E-value=44 Score=33.34 Aligned_cols=38 Identities=16% Similarity=0.317 Sum_probs=25.2
Q ss_pred CCCCcccCCCCCcccCCchhhhhhhhhccCCcccccccccc
Q 047542 93 PKQKGFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEM 133 (270)
Q Consensus 93 TgeKpf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~ 133 (270)
+...-|.|+.|.++|..-.++. -+-...-.|.|..|+-
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGG 161 (436)
T ss_pred cccccccCCccccchhhhHHHH---hhcccCceEEEecCCC
Confidence 3455799999999987755543 2222234688988873
No 72
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=24.08 E-value=24 Score=32.90 Aligned_cols=31 Identities=32% Similarity=0.603 Sum_probs=24.9
Q ss_pred ccCCCCcccCCCCCcccCCchhhhhh-hhhcc
Q 047542 91 KQPKQKGFLCNFCNKIFSTSQALGGH-QNAHK 121 (270)
Q Consensus 91 ~HTgeKpf~C~~CgKsF~sssaL~~H-qr~Ht 121 (270)
.|...|-|+|.+|-|++.+...|..| +.+|+
T Consensus 28 qhqkakhfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 28 QHQKAKHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred hhhhhccceeeeehhhhccCCCceeehhhhhh
Confidence 46677889999999998888888887 55663
No 73
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=23.81 E-value=59 Score=20.67 Aligned_cols=26 Identities=8% Similarity=0.213 Sum_probs=14.4
Q ss_pred ccCCCCCcccCCchhhhhhhhhccCCcccccccccch
Q 047542 98 FLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEMD 134 (270)
Q Consensus 98 f~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~~ 134 (270)
|.|..|+..+.-. ..-+.+|+.||.+
T Consensus 1 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVELK-----------PGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-BS-----------TSSTSSBSSSS-S
T ss_pred CCCCcCCCeeEcC-----------CCCcEECCcCCCe
Confidence 5677777766511 1235678888754
No 74
>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=23.42 E-value=51 Score=27.67 Aligned_cols=10 Identities=20% Similarity=0.444 Sum_probs=5.0
Q ss_pred cCCCCCcccC
Q 047542 99 LCNFCNKIFS 108 (270)
Q Consensus 99 ~C~~CgKsF~ 108 (270)
.|..|+++|.
T Consensus 11 ~Cp~cg~kFY 20 (129)
T TIGR02300 11 ICPNTGSKFY 20 (129)
T ss_pred cCCCcCcccc
Confidence 3555555543
No 75
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=23.40 E-value=48 Score=28.93 Aligned_cols=24 Identities=17% Similarity=0.257 Sum_probs=17.6
Q ss_pred cccCCCCCcccCCchhhhhhhhhccCCcccccccccc
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEM 133 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~ 133 (270)
.|.|.+||.. |.++-|-+|..|+.
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCCC
Confidence 6888888653 45677888888874
No 76
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=22.08 E-value=48 Score=24.18 Aligned_cols=32 Identities=19% Similarity=0.378 Sum_probs=18.6
Q ss_pred cccCCCCCcccCCchhhhhhhhhccCCcccccccccc
Q 047542 97 GFLCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEM 133 (270)
Q Consensus 97 pf~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~ 133 (270)
.|.|+.||+..-... .+-.....+|.|..||.
T Consensus 25 ~F~CPnCG~~~I~RC-----~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEVIIYRC-----EKCRKQSNPYTCPKCGF 56 (59)
T ss_pred EeeCCCCCCeeEeec-----hhHHhcCCceECCCCCC
Confidence 588888987622221 12222345788888874
No 77
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=21.97 E-value=36 Score=29.16 Aligned_cols=16 Identities=6% Similarity=-0.103 Sum_probs=11.0
Q ss_pred cccccccccchhcccc
Q 047542 124 RALAKRRKEMDMGALG 139 (270)
Q Consensus 124 KPfkCr~c~~~~~~~~ 139 (270)
+.-+|..|+++|.++-
T Consensus 27 RRReC~~C~~RFTTyE 42 (147)
T TIGR00244 27 RRRECLECHERFTTFE 42 (147)
T ss_pred ecccCCccCCccceee
Confidence 4467888888876543
No 78
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.22 E-value=48 Score=34.78 Aligned_cols=34 Identities=12% Similarity=0.042 Sum_probs=21.3
Q ss_pred cCCCCCcccCCchhhhhhhhhccCCcccccccccc
Q 047542 99 LCNFCNKIFSTSQALGGHQNAHKQERALAKRRKEM 133 (270)
Q Consensus 99 ~C~~CgKsF~sssaL~~Hqr~HtgEKPfkCr~c~~ 133 (270)
.|..|+..+.- ......+..|...+...|..||.
T Consensus 385 ~C~~Cg~~~~C-~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 385 ACARCRTPARC-RHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred EhhhCcCeeEC-CCCCCceeEecCCCeeECCCCcC
Confidence 58888776542 22344455566666788888874
Done!