Query 043134
Match_columns 279
No_of_seqs 329 out of 1451
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 13:13:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043134.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043134hhsearch_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 99.0 3.7E-11 8E-16 111.1 0.7 62 66-129 187-248 (279)
2 KOG3623 Homeobox transcription 98.7 2.9E-09 6.3E-14 108.8 0.8 71 61-133 889-961 (1007)
3 KOG2462 C2H2-type Zn-finger pr 98.7 1.1E-08 2.5E-13 94.7 3.5 64 62-129 157-220 (279)
4 KOG1074 Transcriptional repres 98.6 1.8E-08 3.9E-13 104.4 1.1 67 65-133 878-944 (958)
5 KOG3576 Ovo and related transc 98.5 5E-08 1.1E-12 87.6 2.7 69 58-128 109-177 (267)
6 KOG1074 Transcriptional repres 98.4 1.9E-07 4.1E-12 97.0 3.5 56 65-122 604-659 (958)
7 KOG3623 Homeobox transcription 98.3 1.7E-07 3.7E-12 96.2 1.7 54 63-118 278-331 (1007)
8 PHA02768 hypothetical protein; 98.3 3.8E-07 8.1E-12 65.9 2.0 43 67-113 6-48 (55)
9 PF13465 zf-H2C2_2: Zinc-finge 98.2 8.4E-07 1.8E-11 54.5 1.8 25 84-108 2-26 (26)
10 KOG3576 Ovo and related transc 98.1 2.9E-07 6.4E-12 82.7 -2.3 68 62-131 141-209 (267)
11 PHA00733 hypothetical protein 97.5 2.9E-05 6.3E-10 64.9 1.0 51 64-118 71-121 (128)
12 PHA00732 hypothetical protein 97.1 0.00029 6.2E-09 54.4 2.4 44 66-117 1-45 (79)
13 PHA00616 hypothetical protein 97.0 5.5E-05 1.2E-09 52.4 -2.2 34 66-101 1-34 (44)
14 PHA02768 hypothetical protein; 97.0 0.00012 2.6E-09 53.0 -1.0 28 96-125 5-32 (55)
15 PHA00616 hypothetical protein 97.0 0.0002 4.4E-09 49.6 0.2 32 96-127 1-32 (44)
16 PF00096 zf-C2H2: Zinc finger, 96.4 0.00035 7.7E-09 40.8 -1.7 23 97-119 1-23 (23)
17 KOG3993 Transcription factor ( 96.2 0.0041 8.9E-08 61.3 3.5 52 67-120 296-380 (500)
18 PHA00733 hypothetical protein 96.2 0.001 2.2E-08 55.6 -0.7 56 61-119 35-96 (128)
19 PLN03086 PRLI-interacting fact 96.1 0.0027 5.9E-08 64.9 2.1 61 63-130 450-510 (567)
20 PF13912 zf-C2H2_6: C2H2-type 95.9 0.0013 2.7E-08 39.9 -0.9 25 96-120 1-25 (27)
21 KOG3608 Zn finger proteins [Ge 95.9 0.0022 4.8E-08 62.1 0.2 37 84-120 279-316 (467)
22 PF13894 zf-C2H2_4: C2H2-type 94.9 0.0032 6.9E-08 36.2 -1.5 23 97-119 1-23 (24)
23 KOG3608 Zn finger proteins [Ge 94.8 0.0038 8.3E-08 60.5 -2.2 66 59-128 230-296 (467)
24 PLN03086 PRLI-interacting fact 94.4 0.019 4.1E-07 58.9 1.6 59 65-128 477-545 (567)
25 PF00096 zf-C2H2: Zinc finger, 93.9 0.019 4E-07 33.3 0.2 23 67-91 1-23 (23)
26 smart00355 ZnF_C2H2 zinc finge 93.9 0.0093 2E-07 34.4 -1.1 23 97-119 1-23 (26)
27 PRK04860 hypothetical protein; 93.7 0.043 9.3E-07 47.7 2.2 39 65-109 118-156 (160)
28 PF05605 zf-Di19: Drought indu 92.3 0.061 1.3E-06 38.1 0.9 49 66-119 2-52 (54)
29 KOG2893 Zn finger protein [Gen 92.2 0.067 1.5E-06 49.7 1.4 50 64-120 9-59 (341)
30 COG5048 FOG: Zn-finger [Genera 91.9 0.12 2.6E-06 47.8 2.8 62 65-128 288-355 (467)
31 PF13912 zf-C2H2_6: C2H2-type 91.6 0.077 1.7E-06 31.9 0.7 25 66-92 1-25 (27)
32 PF12756 zf-C2H2_2: C2H2 type 91.5 0.035 7.7E-07 42.2 -1.0 24 96-119 50-73 (100)
33 PHA00732 hypothetical protein 90.5 0.082 1.8E-06 40.8 0.1 26 96-121 1-27 (79)
34 PF09237 GAGA: GAGA factor; I 90.5 0.054 1.2E-06 38.9 -0.8 34 91-124 19-52 (54)
35 PF12171 zf-C2H2_jaz: Zinc-fin 90.1 0.09 1.9E-06 32.0 0.0 22 97-118 2-23 (27)
36 PF12874 zf-met: Zinc-finger o 89.9 0.039 8.4E-07 32.6 -1.7 23 97-119 1-23 (25)
37 smart00355 ZnF_C2H2 zinc finge 88.4 0.28 6E-06 28.0 1.3 24 67-92 1-24 (26)
38 COG5189 SFP1 Putative transcri 87.8 0.38 8.3E-06 46.4 2.5 53 64-117 347-419 (423)
39 KOG3993 Transcription factor ( 87.6 0.12 2.5E-06 51.4 -1.0 55 65-121 266-320 (500)
40 PF13894 zf-C2H2_4: C2H2-type 87.1 0.23 5E-06 28.1 0.4 23 67-91 1-23 (24)
41 KOG2186 Cell growth-regulating 82.0 0.8 1.7E-05 42.8 1.7 58 66-128 3-60 (276)
42 smart00451 ZnF_U1 U1-like zinc 76.6 0.62 1.4E-05 29.3 -0.5 23 96-118 3-25 (35)
43 PF09538 FYDLN_acid: Protein o 72.8 2.1 4.6E-05 35.0 1.6 29 68-109 11-39 (108)
44 PF14353 CpXC: CpXC protein 71.5 1.5 3.3E-05 35.9 0.5 52 67-119 2-61 (128)
45 PF13717 zinc_ribbon_4: zinc-r 68.5 5 0.00011 26.3 2.3 34 67-107 3-36 (36)
46 PRK04860 hypothetical protein; 68.1 1.7 3.7E-05 37.8 0.0 33 95-131 118-150 (160)
47 PF13719 zinc_ribbon_5: zinc-r 66.2 5.4 0.00012 26.2 2.1 34 67-107 3-36 (37)
48 TIGR02098 MJ0042_CXXC MJ0042 f 64.9 5.3 0.00012 25.9 1.9 34 67-107 3-36 (38)
49 PF13913 zf-C2HC_2: zinc-finge 64.2 3.5 7.6E-05 24.9 0.9 21 66-89 2-22 (25)
50 PF13909 zf-H2C2_5: C2H2-type 59.9 1.1 2.5E-05 26.1 -1.8 21 67-90 1-21 (24)
51 TIGR02300 FYDLN_acid conserved 55.2 8.3 0.00018 32.6 1.9 33 68-113 11-43 (129)
52 PF09237 GAGA: GAGA factor; I 54.5 6.8 0.00015 28.2 1.1 33 62-96 20-52 (54)
53 smart00531 TFIIE Transcription 51.0 9.9 0.00021 32.2 1.8 39 63-107 96-134 (147)
54 COG5048 FOG: Zn-finger [Genera 48.9 13 0.00029 34.2 2.4 57 64-122 31-89 (467)
55 PRK00398 rpoP DNA-directed RNA 47.7 13 0.00028 25.2 1.6 30 66-107 3-32 (46)
56 PF09723 Zn-ribbon_8: Zinc rib 46.9 6.5 0.00014 26.5 0.0 29 67-104 6-34 (42)
57 PF05443 ROS_MUCR: ROS/MUCR tr 45.5 12 0.00026 31.7 1.4 25 65-94 71-95 (132)
58 PRK00464 nrdR transcriptional 45.1 8.3 0.00018 33.4 0.4 44 68-114 2-46 (154)
59 COG5189 SFP1 Putative transcri 41.2 22 0.00048 34.7 2.6 25 93-117 346-372 (423)
60 TIGR02605 CxxC_CxxC_SSSS putat 40.6 13 0.00028 25.5 0.8 29 67-104 6-34 (52)
61 smart00834 CxxC_CXXC_SSSS Puta 38.8 16 0.00034 23.6 0.9 30 67-105 6-35 (41)
62 COG4530 Uncharacterized protei 38.5 17 0.00036 30.2 1.2 27 68-107 11-37 (129)
63 KOG2785 C2H2-type Zn-finger pr 37.4 13 0.00028 36.7 0.5 56 61-118 161-242 (390)
64 cd00350 rubredoxin_like Rubred 36.9 22 0.00049 22.6 1.4 25 67-105 2-26 (33)
65 smart00659 RPOLCX RNA polymera 34.0 29 0.00063 23.8 1.6 26 67-105 3-28 (44)
66 COG1996 RPC10 DNA-directed RNA 28.4 31 0.00068 24.5 1.1 29 65-105 5-33 (49)
67 smart00614 ZnF_BED BED zinc fi 27.5 19 0.00042 24.8 -0.1 21 97-117 19-44 (50)
68 COG4957 Predicted transcriptio 27.2 36 0.00078 29.2 1.4 23 66-93 76-98 (148)
69 PHA00626 hypothetical protein 26.9 46 0.001 24.4 1.7 14 95-108 22-35 (59)
70 COG2888 Predicted Zn-ribbon RN 26.9 37 0.0008 25.2 1.3 31 67-104 28-58 (61)
71 COG4049 Uncharacterized protei 26.5 12 0.00027 27.5 -1.3 27 91-117 12-38 (65)
72 KOG2593 Transcription initiati 26.5 54 0.0012 33.0 2.7 41 62-107 124-164 (436)
73 KOG3408 U1-like Zn-finger-cont 26.3 17 0.00036 30.6 -0.7 37 93-133 54-90 (129)
74 PF02892 zf-BED: BED zinc fing 25.8 17 0.00038 24.0 -0.6 15 94-108 14-28 (45)
75 PRK06266 transcription initiat 24.4 31 0.00066 30.4 0.6 35 63-108 114-148 (178)
76 PF01363 FYVE: FYVE zinc finge 23.8 57 0.0012 23.5 1.8 28 67-108 10-37 (69)
77 COG1592 Rubrerythrin [Energy p 22.6 50 0.0011 29.1 1.5 24 66-104 134-157 (166)
78 PF08790 zf-LYAR: LYAR-type C2 22.4 37 0.0008 21.4 0.5 9 68-77 2-10 (28)
79 PF03604 DNA_RNApol_7kD: DNA d 22.1 51 0.0011 21.2 1.1 26 67-105 1-26 (32)
80 KOG2482 Predicted C2H2-type Zn 21.7 28 0.0006 34.3 -0.3 22 96-117 195-216 (423)
81 PRK12380 hydrogenase nickel in 21.4 47 0.001 27.0 1.1 24 67-104 71-94 (113)
82 cd00729 rubredoxin_SM Rubredox 20.9 60 0.0013 20.9 1.3 26 66-105 2-27 (34)
83 PF09986 DUF2225: Uncharacteri 20.9 47 0.001 29.9 1.0 25 94-118 3-27 (214)
84 smart00154 ZnF_AN1 AN1-like Zi 20.3 53 0.0012 21.8 1.0 15 96-110 12-26 (39)
85 KOG4167 Predicted DNA-binding 20.3 12 0.00027 39.9 -3.1 25 96-120 792-816 (907)
86 COG2331 Uncharacterized protei 20.3 40 0.00088 26.2 0.4 31 66-106 12-43 (82)
87 TIGR00373 conserved hypothetic 20.2 35 0.00075 29.4 0.0 34 63-107 106-139 (158)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.05 E-value=3.7e-11 Score=111.07 Aligned_cols=62 Identities=16% Similarity=0.168 Sum_probs=54.8
Q ss_pred ccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCccccccccccCCCchhhhhc
Q 043134 66 LIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGGHQNAHKRERTLAKRG 129 (279)
Q Consensus 66 lf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~Hqr~HtgERpy~kr~ 129 (279)
+++|.. |||.|.... .|.-|.|+|||||||.|..|+|.|..+++|+.||++|.+.|.|+...
T Consensus 187 ~c~C~i-CGKaFSRPW-LLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~ 248 (279)
T KOG2462|consen 187 PCECGI-CGKAFSRPW-LLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPR 248 (279)
T ss_pred Cccccc-ccccccchH-HhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcc
Confidence 478999 999995444 68999999999999999999999999999999999999999888764
No 2
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.72 E-value=2.9e-09 Score=108.84 Aligned_cols=71 Identities=20% Similarity=0.336 Sum_probs=62.6
Q ss_pred CCCcCccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCccccccccccCCCchhhh--hcCCCC
Q 043134 61 KPELNLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGGHQNAHKRERTLAK--RGQRIS 133 (279)
Q Consensus 61 ~~e~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~Hqr~HtgERpy~k--r~~~~~ 133 (279)
+.+..+|.|.+ |+|.|...+ .|.+|.=-|+|.|||+|..|.|.|..+.+|..|+|.|.|||||++ .++|.+
T Consensus 889 kte~gmyaCDq-CDK~FqKqS-SLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFS 961 (1007)
T KOG3623|consen 889 KTEDGMYACDQ-CDKAFQKQS-SLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFS 961 (1007)
T ss_pred cCccccchHHH-HHHHHHhhH-HHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcc
Confidence 56677899999 999996555 599999999999999999999999999999999999999999975 445543
No 3
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=98.68 E-value=1.1e-08 Score=94.72 Aligned_cols=64 Identities=17% Similarity=0.218 Sum_probs=56.8
Q ss_pred CCcCccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCccccccccccCCCchhhhhc
Q 043134 62 PELNLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGGHQNAHKRERTLAKRG 129 (279)
Q Consensus 62 ~e~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~Hqr~HtgERpy~kr~ 129 (279)
.+.+.+.|.. |||.|.+... |..|.|+|+ -+++|.+|||.|+..--|.+|+|+|||||||....
T Consensus 157 ~s~ka~~C~~-C~K~YvSmpA-LkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~h 220 (279)
T KOG2462|consen 157 DSKKAFSCKY-CGKVYVSMPA-LKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPH 220 (279)
T ss_pred cccccccCCC-CCceeeehHH-HhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCc
Confidence 3466789999 9999987774 999999987 68999999999999999999999999999998763
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.55 E-value=1.8e-08 Score=104.35 Aligned_cols=67 Identities=21% Similarity=0.291 Sum_probs=61.0
Q ss_pred CccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCccccccccccCCCchhhhhcCCCC
Q 043134 65 NLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGGHQNAHKRERTLAKRGQRIS 133 (279)
Q Consensus 65 nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~Hqr~HtgERpy~kr~~~~~ 133 (279)
|-..|.. ||+.|.+.. .|..|+|+|+++|||.|.+|++.|.....|+.||.+|.+..+..||+.+..
T Consensus 878 n~h~C~v-Cgk~FsSSs-ALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srrG~~~~ 944 (958)
T KOG1074|consen 878 NAHVCNV-CGKQFSSSA-ALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRRGPSPF 944 (958)
T ss_pred chhhhcc-chhcccchH-HHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCccCCCCcc
Confidence 4467999 999997665 599999999999999999999999999999999999999999999976643
No 5
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.51 E-value=5e-08 Score=87.58 Aligned_cols=69 Identities=14% Similarity=0.224 Sum_probs=52.6
Q ss_pred CCCCCCcCccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCccccccccccCCCchhhhh
Q 043134 58 RGSKPELNLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGGHQNAHKRERTLAKR 128 (279)
Q Consensus 58 ~~~~~e~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~Hqr~HtgERpy~kr 128 (279)
.++..+.+.|.|.. |+|.|.-.. .|.+|++.|..-|.|-|..|||.|...-.|++|+|+|+|-|||+.-
T Consensus 109 ~gsssd~d~ftCrv-CgK~F~lQR-mlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~ 177 (267)
T KOG3576|consen 109 IGSSSDQDSFTCRV-CGKKFGLQR-MLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCS 177 (267)
T ss_pred ccCCCCCCeeeeeh-hhhhhhHHH-HHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchh
Confidence 44556678888988 888885443 5777888887777788888888888888888888888888887654
No 6
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.38 E-value=1.9e-07 Score=96.97 Aligned_cols=56 Identities=21% Similarity=0.317 Sum_probs=50.4
Q ss_pred CccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCccccccccccCCC
Q 043134 65 NLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGGHQNAHKRE 122 (279)
Q Consensus 65 nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~Hqr~HtgE 122 (279)
++-.|.. |-+..+..+ .|..|.|+|+|||||+|+.|||.|.++.+|+.|+.+|+..
T Consensus 604 dPNqCii-C~rVlSC~s-aLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~ 659 (958)
T KOG1074|consen 604 DPNQCII-CLRVLSCPS-ALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAK 659 (958)
T ss_pred Cccceee-eeecccchh-hhhhhhhcccCcCccccccccchhccccchhhcccccccC
Confidence 4567999 999997666 5999999999999999999999999999999999999754
No 7
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.33 E-value=1.7e-07 Score=96.17 Aligned_cols=54 Identities=15% Similarity=0.295 Sum_probs=48.9
Q ss_pred CcCccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCccccccccc
Q 043134 63 ELNLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGGHQNA 118 (279)
Q Consensus 63 e~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~Hqr~ 118 (279)
-..-|+|.+ |||.|.-+. .|+.|.|||.|||||.|+.|+|.|+.+..+..||..
T Consensus 278 ~lRKFKCtE-CgKAFKfKH-HLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 278 LLRKFKCTE-CGKAFKFKH-HLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hhccccccc-cchhhhhHH-HHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 345699999 999997766 599999999999999999999999999999999864
No 8
>PHA02768 hypothetical protein; Provisional
Probab=98.28 E-value=3.8e-07 Score=65.91 Aligned_cols=43 Identities=9% Similarity=0.055 Sum_probs=38.3
Q ss_pred cccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCcccc
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALG 113 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~ 113 (279)
|.|.+ ||+.|.... .|..|+++|+ ++|+|..|+|.|.+.+.|.
T Consensus 6 y~C~~-CGK~Fs~~~-~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPI-CGEIYIKRK-SMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcch-hCCeeccHH-HHHHHHHhcC--CcccCCcccceecccceeE
Confidence 78999 999997665 5999999999 7999999999999887775
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=98.18 E-value=8.4e-07 Score=54.45 Aligned_cols=25 Identities=20% Similarity=0.517 Sum_probs=23.3
Q ss_pred HHHHhhhcCCCceeecCCCCcccCC
Q 043134 84 DIHRQGNETEPRVFSCNYCQRKFYS 108 (279)
Q Consensus 84 L~~Hqr~HtgeKPfsC~~CgKsFss 108 (279)
|..|+++|++++||.|++|++.|.+
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 7899999999999999999999963
No 10
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.09 E-value=2.9e-07 Score=82.67 Aligned_cols=68 Identities=16% Similarity=0.284 Sum_probs=55.4
Q ss_pred CCcCccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCccccccc-cccCCCchhhhhcCC
Q 043134 62 PELNLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGGHQ-NAHKRERTLAKRGQR 131 (279)
Q Consensus 62 ~e~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~Hq-r~HtgERpy~kr~~~ 131 (279)
.+++.+-|.- |||.|...- .|.+|.|+|||-+||+|..|+|.|.+.-.|..|. .+|.-...|+=+.+|
T Consensus 141 ~~vkr~lct~-cgkgfndtf-dlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr 209 (267)
T KOG3576|consen 141 SDVKRHLCTF-CGKGFNDTF-DLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERR 209 (267)
T ss_pred cHHHHHHHhh-ccCcccchh-hhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhh
Confidence 4455677999 999996554 5999999999999999999999999999999996 467665556554444
No 11
>PHA00733 hypothetical protein
Probab=97.53 E-value=2.9e-05 Score=64.91 Aligned_cols=51 Identities=12% Similarity=0.069 Sum_probs=41.6
Q ss_pred cCccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCccccccccc
Q 043134 64 LNLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGGHQNA 118 (279)
Q Consensus 64 ~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~Hqr~ 118 (279)
..+|.|.. ||+.|.... .|..|++.| +.+|.|..|++.|.....|..|++-
T Consensus 71 ~kPy~C~~-Cgk~Fss~s-~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~ 121 (128)
T PHA00733 71 VSPYVCPL-CLMPFSSSV-SLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCK 121 (128)
T ss_pred CCCccCCC-CCCcCCCHH-HHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHH
Confidence 46789999 999997665 488888876 3579999999999999999888653
No 12
>PHA00732 hypothetical protein
Probab=97.13 E-value=0.00029 Score=54.43 Aligned_cols=44 Identities=16% Similarity=0.244 Sum_probs=34.6
Q ss_pred ccccCccCCccccCCchhHHHHhhh-cCCCceeecCCCCcccCCCcccccccc
Q 043134 66 LIDCFKSTDSSQDSLENNDIHRQGN-ETEPRVFSCNYCQRKFYSSQALGGHQN 117 (279)
Q Consensus 66 lf~C~e~CGksFss~ss~L~~Hqr~-HtgeKPfsC~~CgKsFssssaL~~Hqr 117 (279)
+|.|.. ||+.|.... .|..|++. |++ +.|..|++.|. .|..|.+
T Consensus 1 py~C~~-Cgk~F~s~s-~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~ 45 (79)
T PHA00732 1 MFKCPI-CGFTTVTLF-ALKQHARRNHTL---TKCPVCNKSYR---RLNQHFY 45 (79)
T ss_pred CccCCC-CCCccCCHH-HHHHHhhcccCC---CccCCCCCEeC---Chhhhhc
Confidence 478999 999997766 59999874 653 68999999997 4666653
No 13
>PHA00616 hypothetical protein
Probab=97.02 E-value=5.5e-05 Score=52.36 Aligned_cols=34 Identities=9% Similarity=0.195 Sum_probs=23.8
Q ss_pred ccccCccCCccccCCchhHHHHhhhcCCCceeecCC
Q 043134 66 LIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNY 101 (279)
Q Consensus 66 lf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~ 101 (279)
+|.|.. ||+.|.... .+..|.+.|++++++.|++
T Consensus 1 pYqC~~-CG~~F~~~s-~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLR-CGGIFRKKK-EVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccch-hhHHHhhHH-HHHHHHHHhcCCCccceeE
Confidence 466777 777775554 4777777777777777765
No 14
>PHA02768 hypothetical protein; Provisional
Probab=96.97 E-value=0.00012 Score=53.00 Aligned_cols=28 Identities=18% Similarity=0.479 Sum_probs=25.3
Q ss_pred eeecCCCCcccCCCccccccccccCCCchh
Q 043134 96 VFSCNYCQRKFYSSQALGGHQNAHKRERTL 125 (279)
Q Consensus 96 PfsC~~CgKsFssssaL~~Hqr~HtgERpy 125 (279)
-|.|+.||+.|...++|..||++|+ ++|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~ 32 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNL 32 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--Ccc
Confidence 3899999999999999999999998 444
No 15
>PHA00616 hypothetical protein
Probab=96.97 E-value=0.0002 Score=49.55 Aligned_cols=32 Identities=16% Similarity=0.343 Sum_probs=29.5
Q ss_pred eeecCCCCcccCCCccccccccccCCCchhhh
Q 043134 96 VFSCNYCQRKFYSSQALGGHQNAHKRERTLAK 127 (279)
Q Consensus 96 PfsC~~CgKsFssssaL~~Hqr~HtgERpy~k 127 (279)
||+|..||+.|...+.|..|++.|++++++..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 68999999999999999999999999988753
No 16
>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=96.38 E-value=0.00035 Score=40.79 Aligned_cols=23 Identities=30% Similarity=0.700 Sum_probs=14.9
Q ss_pred eecCCCCcccCCCcccccccccc
Q 043134 97 FSCNYCQRKFYSSQALGGHQNAH 119 (279)
Q Consensus 97 fsC~~CgKsFssssaL~~Hqr~H 119 (279)
|.|..|++.|.....|..|++.|
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 56666777776666666666543
No 17
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=96.18 E-value=0.0041 Score=61.35 Aligned_cols=52 Identities=25% Similarity=0.388 Sum_probs=42.5
Q ss_pred cccCccCCccccCCchhHHHHhhhcC--------CCc-------------------------eeecCCCCcccCCCcccc
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNET--------EPR-------------------------VFSCNYCQRKFYSSQALG 113 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~Ht--------geK-------------------------PfsC~~CgKsFssssaL~ 113 (279)
|.|.+ |+|.|+.-. +|..|.|=|. +.. -|.|.+|+|+|....-|+
T Consensus 296 YrCPE-C~KVFsCPA-NLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLr 373 (500)
T KOG3993|consen 296 YRCPE-CDKVFSCPA-NLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLR 373 (500)
T ss_pred ecCCc-ccccccCch-hhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHH
Confidence 78999 999996655 5999987762 111 389999999999999999
Q ss_pred ccccccC
Q 043134 114 GHQNAHK 120 (279)
Q Consensus 114 ~Hqr~Ht 120 (279)
.|+-+|.
T Consensus 374 KHqlthq 380 (500)
T KOG3993|consen 374 KHQLTHQ 380 (500)
T ss_pred HhHHhhh
Confidence 9988874
No 18
>PHA00733 hypothetical protein
Probab=96.16 E-value=0.001 Score=55.61 Aligned_cols=56 Identities=16% Similarity=0.081 Sum_probs=43.6
Q ss_pred CCCcCccccCccCCccccCCchhHH------HHhhhcCCCceeecCCCCcccCCCcccccccccc
Q 043134 61 KPELNLIDCFKSTDSSQDSLENNDI------HRQGNETEPRVFSCNYCQRKFYSSQALGGHQNAH 119 (279)
Q Consensus 61 ~~e~nlf~C~e~CGksFss~ss~L~------~Hqr~HtgeKPfsC~~CgKsFssssaL~~Hqr~H 119 (279)
+++.+.+.|.. |.+.|.... .|. +|.. +.+.+||.|..|++.|.....|..|+++|
T Consensus 35 ~~~~~~~~~~~-~~~~~~~~~-~l~~~~~l~~~~~-~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h 96 (128)
T PHA00733 35 TPEQKRLIRAV-VKTLIYNPQ-LLDESSYLYKLLT-SKAVSPYVCPLCLMPFSSSVSLKQHIRYT 96 (128)
T ss_pred ChhhhhHHHHH-HhhhccChh-hhcchHHHHhhcc-cCCCCCccCCCCCCcCCCHHHHHHHHhcC
Confidence 56677889999 998886543 233 3333 34588999999999999999999999876
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.14 E-value=0.0027 Score=64.94 Aligned_cols=61 Identities=15% Similarity=0.128 Sum_probs=50.5
Q ss_pred CcCccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCccccccccccCCCchhhhhcC
Q 043134 63 ELNLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGGHQNAHKRERTLAKRGQ 130 (279)
Q Consensus 63 e~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~Hqr~HtgERpy~kr~~ 130 (279)
-.+.+.|.. |++.|. .. .+..|+.+|+ +++.|. |++.| ....|..|++.|..+|++.++-.
T Consensus 450 l~~H~~C~~-Cgk~f~-~s-~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC 510 (567)
T PLN03086 450 AKNHVHCEK-CGQAFQ-QG-EMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFC 510 (567)
T ss_pred cccCccCCC-CCCccc-hH-HHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCC
Confidence 356789999 999995 33 4899999874 899999 99765 66899999999999999888753
No 20
>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=95.93 E-value=0.0013 Score=39.89 Aligned_cols=25 Identities=36% Similarity=0.691 Sum_probs=19.2
Q ss_pred eeecCCCCcccCCCccccccccccC
Q 043134 96 VFSCNYCQRKFYSSQALGGHQNAHK 120 (279)
Q Consensus 96 PfsC~~CgKsFssssaL~~Hqr~Ht 120 (279)
||.|..|++.|....+|..|++.|.
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 5778888888888888888877663
No 21
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=95.91 E-value=0.0022 Score=62.07 Aligned_cols=37 Identities=16% Similarity=0.381 Sum_probs=25.9
Q ss_pred HHHHhh-hcCCCceeecCCCCcccCCCccccccccccC
Q 043134 84 DIHRQG-NETEPRVFSCNYCQRKFYSSQALGGHQNAHK 120 (279)
Q Consensus 84 L~~Hqr-~HtgeKPfsC~~CgKsFssssaL~~Hqr~Ht 120 (279)
|..|++ .|...|||+|+.|.+.|...+.|..|..+|.
T Consensus 279 L~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 279 LTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred HHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 445544 2556678888888888887777888777775
No 22
>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=94.93 E-value=0.0032 Score=36.17 Aligned_cols=23 Identities=35% Similarity=0.753 Sum_probs=15.7
Q ss_pred eecCCCCcccCCCcccccccccc
Q 043134 97 FSCNYCQRKFYSSQALGGHQNAH 119 (279)
Q Consensus 97 fsC~~CgKsFssssaL~~Hqr~H 119 (279)
|.|++|++.|.+...|..|++.|
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 57888888888888887777654
No 23
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=94.77 E-value=0.0038 Score=60.47 Aligned_cols=66 Identities=12% Similarity=0.197 Sum_probs=53.4
Q ss_pred CCCCCcCccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCccccccccc-cCCCchhhhh
Q 043134 59 GSKPELNLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGGHQNA-HKRERTLAKR 128 (279)
Q Consensus 59 ~~~~e~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~Hqr~-HtgERpy~kr 128 (279)
......|+|.|.. |-|.|.... .|..|++.|.. -|+|+.|.......+.|..|++. |...||++.-
T Consensus 230 qt~l~~n~fqC~~-C~KrFaTek-lL~~Hv~rHvn--~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd 296 (467)
T KOG3608|consen 230 QTELNTNSFQCAQ-CFKRFATEK-LLKSHVVRHVN--CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCD 296 (467)
T ss_pred hhhhcCCchHHHH-HHHHHhHHH-HHHHHHHHhhh--cccccccccCCCChHHHHHHHHhhhccCCCcccc
Confidence 3456678899999 999996654 58888888764 59999999999999999999885 7778887653
No 24
>PLN03086 PRLI-interacting factor K; Provisional
Probab=94.36 E-value=0.019 Score=58.87 Aligned_cols=59 Identities=15% Similarity=0.320 Sum_probs=46.7
Q ss_pred CccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCC----------CccccccccccCCCchhhhh
Q 043134 65 NLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYS----------SQALGGHQNAHKRERTLAKR 128 (279)
Q Consensus 65 nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFss----------ssaL~~Hqr~HtgERpy~kr 128 (279)
.++.|. ||+.+ .+. .|..|+++|..++++.|.+|++.|.. ...|..|..++ +.+++.+.
T Consensus 477 kpv~Cp--Cg~~~-~R~-~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~ 545 (567)
T PLN03086 477 EPLQCP--CGVVL-EKE-QMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCD 545 (567)
T ss_pred CCccCC--CCCCc-chh-HHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEcc
Confidence 567896 99866 443 59999999999999999999999952 23688888875 77777664
No 25
>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=93.88 E-value=0.019 Score=33.32 Aligned_cols=23 Identities=17% Similarity=0.047 Sum_probs=18.8
Q ss_pred cccCccCCccccCCchhHHHHhhhc
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNE 91 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~H 91 (279)
|.|.. |++.|.... .|..|++.|
T Consensus 1 y~C~~-C~~~f~~~~-~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPI-CGKSFSSKS-NLKRHMRRH 23 (23)
T ss_dssp EEETT-TTEEESSHH-HHHHHHHHH
T ss_pred CCCCC-CCCccCCHH-HHHHHHhHC
Confidence 57999 999997766 599998764
No 26
>smart00355 ZnF_C2H2 zinc finger.
Probab=93.87 E-value=0.0093 Score=34.42 Aligned_cols=23 Identities=35% Similarity=0.697 Sum_probs=13.7
Q ss_pred eecCCCCcccCCCcccccccccc
Q 043134 97 FSCNYCQRKFYSSQALGGHQNAH 119 (279)
Q Consensus 97 fsC~~CgKsFssssaL~~Hqr~H 119 (279)
|.|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 35666666666666666665544
No 27
>PRK04860 hypothetical protein; Provisional
Probab=93.65 E-value=0.043 Score=47.73 Aligned_cols=39 Identities=15% Similarity=0.224 Sum_probs=31.6
Q ss_pred CccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCC
Q 043134 65 NLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSS 109 (279)
Q Consensus 65 nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFsss 109 (279)
-+|.| . |++.. . .+.+|.++|+++++|.|..|++.|...
T Consensus 118 ~~Y~C-~-C~~~~---~-~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRC-K-CQEHQ---L-TVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEc-C-CCCee---C-HHHHHHHHhcCCccEECCCCCceeEEe
Confidence 36889 5 88722 2 489999999999999999999998643
No 28
>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=92.26 E-value=0.061 Score=38.08 Aligned_cols=49 Identities=12% Similarity=0.212 Sum_probs=35.4
Q ss_pred ccccCccCCccccCCchhHHHHh-hhcCCC-ceeecCCCCcccCCCcccccccccc
Q 043134 66 LIDCFKSTDSSQDSLENNDIHRQ-GNETEP-RVFSCNYCQRKFYSSQALGGHQNAH 119 (279)
Q Consensus 66 lf~C~e~CGksFss~ss~L~~Hq-r~Htge-KPfsC~~CgKsFssssaL~~Hqr~H 119 (279)
-|.|.- |++.|. .. .|..|. ..|..+ +.+.|+.|...+. ..|..|++.+
T Consensus 2 ~f~CP~-C~~~~~-~~-~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 2 SFTCPY-CGKGFS-ES-SLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred CcCCCC-CCCccC-HH-HHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 478999 999774 33 488884 446554 5799999998755 3787887654
No 29
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=92.24 E-value=0.067 Score=49.68 Aligned_cols=50 Identities=26% Similarity=0.485 Sum_probs=37.8
Q ss_pred cCccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCcccccc-ccccC
Q 043134 64 LNLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGGH-QNAHK 120 (279)
Q Consensus 64 ~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~H-qr~Ht 120 (279)
.+++ |.- |++.|.... .|.+|++ .|-|+|..|.|++.+--.|..| |++|+
T Consensus 9 ~kpw-cwy-cnrefddek-iliqhqk----akhfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 9 DKPW-CWY-CNREFDDEK-ILIQHQK----AKHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred CCce-eee-cccccchhh-hhhhhhh----hccceeeeehhhhccCCCceeehhhhhh
Confidence 4455 999 999996654 4777765 4779999999998887777777 45554
No 30
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.90 E-value=0.12 Score=47.81 Aligned_cols=62 Identities=19% Similarity=0.222 Sum_probs=53.6
Q ss_pred CccccCccCCccccCCchhHHHHhh--hcCCC--ceeecC--CCCcccCCCccccccccccCCCchhhhh
Q 043134 65 NLIDCFKSTDSSQDSLENNDIHRQG--NETEP--RVFSCN--YCQRKFYSSQALGGHQNAHKRERTLAKR 128 (279)
Q Consensus 65 nlf~C~e~CGksFss~ss~L~~Hqr--~Htge--KPfsC~--~CgKsFssssaL~~Hqr~HtgERpy~kr 128 (279)
..+.|.. |...|.... .+..|.+ .|+++ +++.|. .|++.|.....+..|...|..-++....
T Consensus 288 ~~~~~~~-~~~~~s~~~-~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 288 LPIKSKQ-CNISFSRSS-PLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred cCCCCcc-ccCCccccc-cccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 4688999 999996665 5899999 89999 999999 7999999999999999999877655444
No 31
>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=91.61 E-value=0.077 Score=31.88 Aligned_cols=25 Identities=12% Similarity=0.145 Sum_probs=20.4
Q ss_pred ccccCccCCccccCCchhHHHHhhhcC
Q 043134 66 LIDCFKSTDSSQDSLENNDIHRQGNET 92 (279)
Q Consensus 66 lf~C~e~CGksFss~ss~L~~Hqr~Ht 92 (279)
+|.|.. |++.|.... .|..|++.|.
T Consensus 1 ~~~C~~-C~~~F~~~~-~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDE-CGKTFSSLS-ALREHKRSHC 25 (27)
T ss_dssp SEEETT-TTEEESSHH-HHHHHHCTTT
T ss_pred CCCCCc-cCCccCChh-HHHHHhHHhc
Confidence 578999 999997665 5999988764
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=91.53 E-value=0.035 Score=42.21 Aligned_cols=24 Identities=38% Similarity=0.829 Sum_probs=21.2
Q ss_pred eeecCCCCcccCCCcccccccccc
Q 043134 96 VFSCNYCQRKFYSSQALGGHQNAH 119 (279)
Q Consensus 96 PfsC~~CgKsFssssaL~~Hqr~H 119 (279)
.+.|..|++.|.+...|..|++.+
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 599999999999999999999864
No 33
>PHA00732 hypothetical protein
Probab=90.50 E-value=0.082 Score=40.78 Aligned_cols=26 Identities=27% Similarity=0.427 Sum_probs=23.2
Q ss_pred eeecCCCCcccCCCccccccccc-cCC
Q 043134 96 VFSCNYCQRKFYSSQALGGHQNA-HKR 121 (279)
Q Consensus 96 PfsC~~CgKsFssssaL~~Hqr~-Htg 121 (279)
||.|..|++.|.+...|..|++. |++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~ 27 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL 27 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC
Confidence 68999999999999999999984 654
No 34
>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=90.47 E-value=0.054 Score=38.86 Aligned_cols=34 Identities=15% Similarity=0.278 Sum_probs=22.0
Q ss_pred cCCCceeecCCCCcccCCCccccccccccCCCch
Q 043134 91 ETEPRVFSCNYCQRKFYSSQALGGHQNAHKRERT 124 (279)
Q Consensus 91 HtgeKPfsC~~CgKsFssssaL~~Hqr~HtgERp 124 (279)
+..++|..|+.|+..+.+..+|.+|+.++.+.||
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 4467889999999999999999999876655443
No 35
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=90.07 E-value=0.09 Score=31.96 Aligned_cols=22 Identities=32% Similarity=0.703 Sum_probs=18.8
Q ss_pred eecCCCCcccCCCccccccccc
Q 043134 97 FSCNYCQRKFYSSQALGGHQNA 118 (279)
Q Consensus 97 fsC~~CgKsFssssaL~~Hqr~ 118 (279)
|.|..|++.|.+...|..|++.
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 6799999999999999888864
No 36
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=89.88 E-value=0.039 Score=32.60 Aligned_cols=23 Identities=30% Similarity=0.736 Sum_probs=16.3
Q ss_pred eecCCCCcccCCCcccccccccc
Q 043134 97 FSCNYCQRKFYSSQALGGHQNAH 119 (279)
Q Consensus 97 fsC~~CgKsFssssaL~~Hqr~H 119 (279)
|.|..|++.|.+...|..|++.+
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 56777777777777777776543
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=88.42 E-value=0.28 Score=27.95 Aligned_cols=24 Identities=8% Similarity=-0.071 Sum_probs=19.1
Q ss_pred cccCccCCccccCCchhHHHHhhhcC
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNET 92 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~Ht 92 (279)
|.|.. |++.|.... .+..|++.|.
T Consensus 1 ~~C~~-C~~~f~~~~-~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPE-CGKVFKSKS-ALKEHMRTHX 24 (26)
T ss_pred CCCCC-CcchhCCHH-HHHHHHHHhc
Confidence 56999 999997665 5889988664
No 38
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=87.75 E-value=0.38 Score=46.42 Aligned_cols=53 Identities=9% Similarity=0.230 Sum_probs=40.0
Q ss_pred cCccccCc-cCCccccCCchhHHHHhhh-c------------------CCCceeecCCCCcccCCCcccccccc
Q 043134 64 LNLIDCFK-STDSSQDSLENNDIHRQGN-E------------------TEPRVFSCNYCQRKFYSSQALGGHQN 117 (279)
Q Consensus 64 ~nlf~C~e-~CGksFss~ss~L~~Hqr~-H------------------tgeKPfsC~~CgKsFssssaL~~Hqr 117 (279)
.++|+|.. .|.|.+.+.. .|+-|+.. | ...|||.|.+|+|.+..-..|+-|+.
T Consensus 347 ~KpykCpV~gC~K~Yknqn-GLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQN-GLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhcccc-chhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 48999984 2999997654 57777432 2 12489999999999999999988853
No 39
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=87.64 E-value=0.12 Score=51.39 Aligned_cols=55 Identities=15% Similarity=0.198 Sum_probs=42.0
Q ss_pred CccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCccccccccccCC
Q 043134 65 NLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGGHQNAHKR 121 (279)
Q Consensus 65 nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~Hqr~Htg 121 (279)
.-|.|.- |-..|..-- .|.+|.-.-.-.--|.|.+|+|.|+...+|..|+|-|+-
T Consensus 266 GdyiCqL-CK~kYeD~F-~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKP 320 (500)
T KOG3993|consen 266 GDYICQL-CKEKYEDAF-ALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKP 320 (500)
T ss_pred HHHHHHH-HHHhhhhHH-HHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCC
Confidence 3488999 988775443 478885332233459999999999999999999998863
No 40
>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=87.13 E-value=0.23 Score=28.09 Aligned_cols=23 Identities=13% Similarity=0.031 Sum_probs=16.7
Q ss_pred cccCccCCccccCCchhHHHHhhhc
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNE 91 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~H 91 (279)
|.|.. |++.|.... .+..|++.|
T Consensus 1 ~~C~~-C~~~~~~~~-~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPI-CGKSFRSKS-ELRQHMRTH 23 (24)
T ss_dssp EE-SS-TS-EESSHH-HHHHHHHHH
T ss_pred CCCcC-CCCcCCcHH-HHHHHHHhh
Confidence 57999 999997766 588998765
No 41
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=81.96 E-value=0.8 Score=42.81 Aligned_cols=58 Identities=16% Similarity=0.273 Sum_probs=42.7
Q ss_pred ccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCccccccccccCCCchhhhh
Q 043134 66 LIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGGHQNAHKRERTLAKR 128 (279)
Q Consensus 66 lf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~Hqr~HtgERpy~kr 128 (279)
.|+|.. ||.+-.- . .+..|+...++ .-|+|-.|++.|.. .....|...-+...-|.+.
T Consensus 3 ~FtCnv-CgEsvKK-p-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCITEaQKYg~~ 60 (276)
T KOG2186|consen 3 FFTCNV-CGESVKK-P-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCITEAQKYGKK 60 (276)
T ss_pred EEehhh-hhhhccc-c-chHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcchHHHhhhh
Confidence 478999 9998743 3 37889877766 67999999999987 6677776655544444444
No 42
>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=76.63 E-value=0.62 Score=29.33 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=19.1
Q ss_pred eeecCCCCcccCCCccccccccc
Q 043134 96 VFSCNYCQRKFYSSQALGGHQNA 118 (279)
Q Consensus 96 PfsC~~CgKsFssssaL~~Hqr~ 118 (279)
+|.|..|++.|....++..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999988888888753
No 43
>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=72.83 E-value=2.1 Score=34.95 Aligned_cols=29 Identities=17% Similarity=0.351 Sum_probs=23.6
Q ss_pred ccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCC
Q 043134 68 DCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSS 109 (279)
Q Consensus 68 ~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFsss 109 (279)
.|.. ||+.|.-. +..|-.|++||..|.-.
T Consensus 11 ~Cp~-CG~kFYDL------------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPS-CGAKFYDL------------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCC-CcchhccC------------CCCCccCCCCCCccCcc
Confidence 5999 99999533 34789999999999866
No 44
>PF14353 CpXC: CpXC protein
Probab=71.53 E-value=1.5 Score=35.91 Aligned_cols=52 Identities=17% Similarity=0.161 Sum_probs=31.2
Q ss_pred cccCccCCccccCCchh-------HHHHhhhcCCC-ceeecCCCCcccCCCcccccccccc
Q 043134 67 IDCFKSTDSSQDSLENN-------DIHRQGNETEP-RVFSCNYCQRKFYSSQALGGHQNAH 119 (279)
Q Consensus 67 f~C~e~CGksFss~ss~-------L~~Hqr~Htge-KPfsC~~CgKsFssssaL~~Hqr~H 119 (279)
++|.. |+..|...--. -..-.++..|+ ..|.|+.||+.|.-...+.-|...+
T Consensus 2 itCP~-C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~~ 61 (128)
T PF14353_consen 2 ITCPH-CGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPEK 61 (128)
T ss_pred cCCCC-CCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCCC
Confidence 46999 99988432110 00011222222 3599999999998877777665543
No 45
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=68.54 E-value=5 Score=26.32 Aligned_cols=34 Identities=18% Similarity=0.422 Sum_probs=24.8
Q ss_pred cccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccC
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFY 107 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFs 107 (279)
+.|.. |+..|.-... ++-...+..+|..|+..|.
T Consensus 3 i~Cp~-C~~~y~i~d~------~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPN-CQAKYEIDDE------KIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCC-CCCEEeCCHH------HCCCCCcEEECCCCCCEeC
Confidence 56999 9999954442 3445556799999998873
No 46
>PRK04860 hypothetical protein; Provisional
Probab=68.12 E-value=1.7 Score=37.82 Aligned_cols=33 Identities=18% Similarity=0.328 Sum_probs=27.8
Q ss_pred ceeecCCCCcccCCCccccccccccCCCchhhhhcCC
Q 043134 95 RVFSCNYCQRKFYSSQALGGHQNAHKRERTLAKRGQR 131 (279)
Q Consensus 95 KPfsC~~CgKsFssssaL~~Hqr~HtgERpy~kr~~~ 131 (279)
-+|.|. |++ ....+..|.++|+++++|..+..+
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~ 150 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCG 150 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCC
Confidence 479998 998 667789999999999999887543
No 47
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=66.23 E-value=5.4 Score=26.21 Aligned_cols=34 Identities=18% Similarity=0.320 Sum_probs=25.2
Q ss_pred cccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccC
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFY 107 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFs 107 (279)
+.|.. |+..|.-... ++..+.+...|..|+..|.
T Consensus 3 i~CP~-C~~~f~v~~~------~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPN-CQTRFRVPDD------KLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCC-CCceEEcCHH------HcccCCcEEECCCCCcEee
Confidence 46999 9999954432 3445667899999998884
No 48
>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=64.94 E-value=5.3 Score=25.85 Aligned_cols=34 Identities=18% Similarity=0.408 Sum_probs=23.1
Q ss_pred cccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccC
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFY 107 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFs 107 (279)
+.|.. |+..|.-... ..........|..|+..|.
T Consensus 3 ~~CP~-C~~~~~v~~~------~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPN-CKTSFRVVDS------QLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCC-CCCEEEeCHH------HcCCCCCEEECCCCCCEEE
Confidence 56999 9999854432 2222334688999998874
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=64.23 E-value=3.5 Score=24.87 Aligned_cols=21 Identities=10% Similarity=0.112 Sum_probs=11.6
Q ss_pred ccccCccCCccccCCchhHHHHhh
Q 043134 66 LIDCFKSTDSSQDSLENNDIHRQG 89 (279)
Q Consensus 66 lf~C~e~CGksFss~ss~L~~Hqr 89 (279)
+..|.. ||+.|. .. .|..|+.
T Consensus 2 l~~C~~-CgR~F~-~~-~l~~H~~ 22 (25)
T PF13913_consen 2 LVPCPI-CGRKFN-PD-RLEKHEK 22 (25)
T ss_pred CCcCCC-CCCEEC-HH-HHHHHHH
Confidence 345666 777773 22 2566643
No 50
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=59.88 E-value=1.1 Score=26.07 Aligned_cols=21 Identities=14% Similarity=0.121 Sum_probs=9.6
Q ss_pred cccCccCCccccCCchhHHHHhhh
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGN 90 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~ 90 (279)
|.|.. |..... ...|..|++.
T Consensus 1 y~C~~-C~y~t~--~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPH-CSYSTS--KSNLKRHLKR 21 (24)
T ss_dssp EE-SS-SS-EES--HHHHHHHHHH
T ss_pred CCCCC-CCCcCC--HHHHHHHHHh
Confidence 34666 665442 3345555544
No 51
>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=55.21 E-value=8.3 Score=32.59 Aligned_cols=33 Identities=27% Similarity=0.276 Sum_probs=24.9
Q ss_pred ccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCCCcccc
Q 043134 68 DCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYSSQALG 113 (279)
Q Consensus 68 ~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~ 113 (279)
.|.. ||+.|.-. +..|-.|++||..|.-...+.
T Consensus 11 ~Cp~-cg~kFYDL------------nk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 11 ICPN-TGSKFYDL------------NRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred cCCC-cCcccccc------------CCCCccCCCcCCccCcchhhc
Confidence 5999 99999432 347899999999987654433
No 52
>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=54.46 E-value=6.8 Score=28.24 Aligned_cols=33 Identities=6% Similarity=-0.135 Sum_probs=21.0
Q ss_pred CCcCccccCccCCccccCCchhHHHHhhhcCCCce
Q 043134 62 PELNLIDCFKSTDSSQDSLENNDIHRQGNETEPRV 96 (279)
Q Consensus 62 ~e~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKP 96 (279)
....+-+|.. |+..+.... +|.+|+.++.+.||
T Consensus 20 ~S~~PatCP~-C~a~~~~sr-nLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPI-CGAVIRQSR-NLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TT-T--EESSHH-HHHHHHHHHTTTS-
T ss_pred ccCCCCCCCc-chhhccchh-hHHHHHHHHhcccC
Confidence 3456788999 999996555 59999988877765
No 53
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=51.02 E-value=9.9 Score=32.17 Aligned_cols=39 Identities=21% Similarity=0.310 Sum_probs=25.4
Q ss_pred CcCccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccC
Q 043134 63 ELNLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFY 107 (279)
Q Consensus 63 e~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFs 107 (279)
+...|.|.. |+..|..... -..... ..-|.|+.||....
T Consensus 96 ~~~~Y~Cp~-C~~~y~~~ea----~~~~d~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 96 NNAYYKCPN-CQSKYTFLEA----NQLLDM-DGTFTCPRCGEELE 134 (147)
T ss_pred CCcEEECcC-CCCEeeHHHH----HHhcCC-CCcEECCCCCCEEE
Confidence 445799999 9999954322 111122 34499999998753
No 54
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=48.85 E-value=13 Score=34.23 Aligned_cols=57 Identities=21% Similarity=0.350 Sum_probs=46.0
Q ss_pred cCccccCccCCccccCCchhHHHHhhhcCCCceeecCC--CCcccCCCccccccccccCCC
Q 043134 64 LNLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNY--CQRKFYSSQALGGHQNAHKRE 122 (279)
Q Consensus 64 ~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~--CgKsFssssaL~~Hqr~HtgE 122 (279)
...+.|.. |...|.... ....|.+.|++++++.|.. |...|.....+..|++.|...
T Consensus 31 ~~~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (467)
T COG5048 31 PRPDSCPN-CTDSFSRLE-HLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNN 89 (467)
T ss_pred Cchhhccc-ccccccccc-hhhhhcccccccCCccccccccccccCCcchhhhhccccccc
Confidence 34577999 999996665 4889999999999999988 667788888888888776543
No 55
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=47.72 E-value=13 Score=25.23 Aligned_cols=30 Identities=17% Similarity=0.336 Sum_probs=20.8
Q ss_pred ccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccC
Q 043134 66 LIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFY 107 (279)
Q Consensus 66 lf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFs 107 (279)
.|.|.. ||..|.... ....+.|++||..+.
T Consensus 3 ~y~C~~-CG~~~~~~~-----------~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCAR-CGREVELDE-----------YGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCC-CCCEEEECC-----------CCCceECCCCCCeEE
Confidence 478999 999884322 112689999987654
No 56
>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=46.93 E-value=6.5 Score=26.47 Aligned_cols=29 Identities=17% Similarity=0.310 Sum_probs=20.1
Q ss_pred cccCccCCccccCCchhHHHHhhhcCCCceeecCCCCc
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQR 104 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgK 104 (279)
|.|.. ||..|... +.+.. ..+-.|..|+.
T Consensus 6 y~C~~-Cg~~fe~~-------~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEE-CGHEFEVL-------QSISE-DDPVPCPECGS 34 (42)
T ss_pred EEeCC-CCCEEEEE-------EEcCC-CCCCcCCCCCC
Confidence 67999 99988322 22333 56788999987
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=45.46 E-value=12 Score=31.73 Aligned_cols=25 Identities=8% Similarity=0.073 Sum_probs=14.1
Q ss_pred CccccCccCCccccCCchhHHHHhhhcCCC
Q 043134 65 NLIDCFKSTDSSQDSLENNDIHRQGNETEP 94 (279)
Q Consensus 65 nlf~C~e~CGksFss~ss~L~~Hqr~Htge 94 (279)
+-+.|.+ ||+.|. .|.+|.+.|.|-
T Consensus 71 d~i~cle-cGk~~k----~LkrHL~~~~gl 95 (132)
T PF05443_consen 71 DYIICLE-CGKKFK----TLKRHLRTHHGL 95 (132)
T ss_dssp S-EE-TB-T--EES----BHHHHHHHTT-S
T ss_pred CeeEEcc-CCcccc----hHHHHHHHccCC
Confidence 4567999 999884 267787777553
No 58
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=45.11 E-value=8.3 Score=33.40 Aligned_cols=44 Identities=16% Similarity=0.314 Sum_probs=24.5
Q ss_pred ccCccCCccccC-CchhHHHHhhhcCCCceeecCCCCcccCCCccccc
Q 043134 68 DCFKSTDSSQDS-LENNDIHRQGNETEPRVFSCNYCQRKFYSSQALGG 114 (279)
Q Consensus 68 ~C~e~CGksFss-~ss~L~~Hqr~HtgeKPfsC~~CgKsFssssaL~~ 114 (279)
.|.. ||.-++. ..+.... ...+ -.+-++|+.||+.|.....+..
T Consensus 2 ~cp~-c~~~~~~~~~s~~~~-~~~~-~~~~~~c~~c~~~f~~~e~~~~ 46 (154)
T PRK00464 2 RCPF-CGHPDTRVIDSRPAE-DGNA-IRRRRECLACGKRFTTFERVEL 46 (154)
T ss_pred cCCC-CCCCCCEeEeccccC-CCCc-eeeeeeccccCCcceEeEeccC
Confidence 5889 9976622 1110000 0111 1234999999999987665543
No 59
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=41.25 E-value=22 Score=34.68 Aligned_cols=25 Identities=20% Similarity=0.547 Sum_probs=21.5
Q ss_pred CCceeecCC--CCcccCCCcccccccc
Q 043134 93 EPRVFSCNY--CQRKFYSSQALGGHQN 117 (279)
Q Consensus 93 geKPfsC~~--CgKsFssssaL~~Hqr 117 (279)
++|||+|++ |.|.+.....|+-|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~l 372 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHML 372 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhh
Confidence 359999997 9999999988888864
No 60
>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=40.60 E-value=13 Score=25.55 Aligned_cols=29 Identities=14% Similarity=0.296 Sum_probs=18.5
Q ss_pred cccCccCCccccCCchhHHHHhhhcCCCceeecCCCCc
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQR 104 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgK 104 (279)
|.|.+ ||..|.... .... +.+-.|+.|+.
T Consensus 6 y~C~~-Cg~~fe~~~-------~~~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTA-CGHRFEVLQ-------KMSD-DPLATCPECGG 34 (52)
T ss_pred EEeCC-CCCEeEEEE-------ecCC-CCCCCCCCCCC
Confidence 67999 999884221 1122 44567999986
No 61
>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=38.77 E-value=16 Score=23.64 Aligned_cols=30 Identities=13% Similarity=0.295 Sum_probs=19.3
Q ss_pred cccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcc
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRK 105 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKs 105 (279)
|.|.+ ||..|.... .... ...-.|..||..
T Consensus 6 y~C~~-Cg~~fe~~~-------~~~~-~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCED-CGHTFEVLQ-------KISD-DPLATCPECGGD 35 (41)
T ss_pred EEcCC-CCCEEEEEE-------ecCC-CCCCCCCCCCCc
Confidence 67999 999884221 1111 456679999874
No 62
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.53 E-value=17 Score=30.25 Aligned_cols=27 Identities=11% Similarity=0.009 Sum_probs=21.7
Q ss_pred ccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccC
Q 043134 68 DCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFY 107 (279)
Q Consensus 68 ~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFs 107 (279)
.|.+ ||+.|... ...|..|++||++|.
T Consensus 11 idPe-tg~KFYDL------------NrdPiVsPytG~s~P 37 (129)
T COG4530 11 IDPE-TGKKFYDL------------NRDPIVSPYTGKSYP 37 (129)
T ss_pred cCcc-ccchhhcc------------CCCccccCcccccch
Confidence 4899 99999432 357899999999994
No 63
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=37.42 E-value=13 Score=36.73 Aligned_cols=56 Identities=30% Similarity=0.476 Sum_probs=41.2
Q ss_pred CCCcCccccCccCCccccCCchhHHHHhhhcCC-----------------------CceeecCCCC---cccCCCccccc
Q 043134 61 KPELNLIDCFKSTDSSQDSLENNDIHRQGNETE-----------------------PRVFSCNYCQ---RKFYSSQALGG 114 (279)
Q Consensus 61 ~~e~nlf~C~e~CGksFss~ss~L~~Hqr~Htg-----------------------eKPfsC~~Cg---KsFssssaL~~ 114 (279)
+.+..|-.|.- |++.|..... ...||..+.| ..-|.|-+|. +.|.+-.+...
T Consensus 161 e~e~~Pt~CLf-C~~~~k~~e~-~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~ 238 (390)
T KOG2785|consen 161 EDELIPTDCLF-CDKKSKSLEE-NLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRA 238 (390)
T ss_pred hcccCCcceee-cCCCcccHHH-HHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHH
Confidence 44556677999 9999877765 4455555444 1348888998 99999999999
Q ss_pred cccc
Q 043134 115 HQNA 118 (279)
Q Consensus 115 Hqr~ 118 (279)
||+.
T Consensus 239 HM~~ 242 (390)
T KOG2785|consen 239 HMRD 242 (390)
T ss_pred HHhh
Confidence 9874
No 64
>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=36.88 E-value=22 Score=22.57 Aligned_cols=25 Identities=20% Similarity=0.319 Sum_probs=18.0
Q ss_pred cccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcc
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRK 105 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKs 105 (279)
+.|.. ||..+.. .+.++.|+.|+..
T Consensus 2 ~~C~~-CGy~y~~-------------~~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPV-CGYIYDG-------------EEAPWVCPVCGAP 26 (33)
T ss_pred EECCC-CCCEECC-------------CcCCCcCcCCCCc
Confidence 57888 9987632 1267899999764
No 65
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=33.97 E-value=29 Score=23.81 Aligned_cols=26 Identities=15% Similarity=0.324 Sum_probs=18.6
Q ss_pred cccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcc
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRK 105 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKs 105 (279)
|.|.+ ||..|... ...+..|++||-.
T Consensus 3 Y~C~~-Cg~~~~~~------------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGE-CGRENEIK------------SKDVVRCRECGYR 28 (44)
T ss_pred EECCC-CCCEeecC------------CCCceECCCCCce
Confidence 77999 99987322 2356889999764
No 66
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=28.43 E-value=31 Score=24.47 Aligned_cols=29 Identities=21% Similarity=0.523 Sum_probs=19.6
Q ss_pred CccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcc
Q 043134 65 NLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRK 105 (279)
Q Consensus 65 nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKs 105 (279)
-.|.|.. ||+.|.. -.......|++||-.
T Consensus 5 ~~Y~C~~-Cg~~~~~-----------~~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCAR-CGREVEL-----------DQETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhh-cCCeeeh-----------hhccCceeCCCCCcE
Confidence 3578999 9998821 113456789999754
No 67
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=27.47 E-value=19 Score=24.78 Aligned_cols=21 Identities=33% Similarity=0.683 Sum_probs=11.0
Q ss_pred eecCCCCcccCCC-----cccccccc
Q 043134 97 FSCNYCQRKFYSS-----QALGGHQN 117 (279)
Q Consensus 97 fsC~~CgKsFsss-----saL~~Hqr 117 (279)
-.|.+|++.+... +.|..|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 4466666665433 34555544
No 68
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=27.20 E-value=36 Score=29.25 Aligned_cols=23 Identities=9% Similarity=0.069 Sum_probs=15.2
Q ss_pred ccccCccCCccccCCchhHHHHhhhcCC
Q 043134 66 LIDCFKSTDSSQDSLENNDIHRQGNETE 93 (279)
Q Consensus 66 lf~C~e~CGksFss~ss~L~~Hqr~Htg 93 (279)
.+.|.+ ||+.|. .|++|.++|-+
T Consensus 76 ~IicLE-DGkkfK----SLKRHL~t~~g 98 (148)
T COG4957 76 YIICLE-DGKKFK----SLKRHLTTHYG 98 (148)
T ss_pred eEEEec-cCcchH----HHHHHHhcccC
Confidence 456777 888773 36777666654
No 69
>PHA00626 hypothetical protein
Probab=26.93 E-value=46 Score=24.43 Aligned_cols=14 Identities=14% Similarity=0.263 Sum_probs=11.2
Q ss_pred ceeecCCCCcccCC
Q 043134 95 RVFSCNYCQRKFYS 108 (279)
Q Consensus 95 KPfsC~~CgKsFss 108 (279)
..|.|..|+-.|+.
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 56899999888864
No 70
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=26.90 E-value=37 Score=25.16 Aligned_cols=31 Identities=10% Similarity=0.115 Sum_probs=18.1
Q ss_pred cccCccCCccccCCchhHHHHhhhcCCCceeecCCCCc
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQR 104 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgK 104 (279)
|.|.+ ||+.--.+-. +--.-..+|.|+.||-
T Consensus 28 F~CPn-CGe~~I~Rc~------~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 28 FPCPN-CGEVEIYRCA------KCRKLGNPYRCPKCGF 58 (61)
T ss_pred eeCCC-CCceeeehhh------hHHHcCCceECCCcCc
Confidence 77888 8865433321 1112245788888863
No 71
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=26.50 E-value=12 Score=27.47 Aligned_cols=27 Identities=19% Similarity=0.324 Sum_probs=22.2
Q ss_pred cCCCceeecCCCCcccCCCcccccccc
Q 043134 91 ETEPRVFSCNYCQRKFYSSQALGGHQN 117 (279)
Q Consensus 91 HtgeKPfsC~~CgKsFssssaL~~Hqr 117 (279)
-.||--+.|+-|+..|.......+|.+
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 446778889999999988888888876
No 72
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=26.46 E-value=54 Score=33.00 Aligned_cols=41 Identities=22% Similarity=0.306 Sum_probs=28.3
Q ss_pred CCcCccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccC
Q 043134 62 PELNLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFY 107 (279)
Q Consensus 62 ~e~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFs 107 (279)
...+-|.|.. |.+.|+... .-+-+-...-.|.|..|+-...
T Consensus 124 t~~~~Y~Cp~-C~kkyt~Le----a~~L~~~~~~~F~C~~C~gelv 164 (436)
T KOG2593|consen 124 TNVAGYVCPN-CQKKYTSLE----ALQLLDNETGEFHCENCGGELV 164 (436)
T ss_pred cccccccCCc-cccchhhhH----HHHhhcccCceEEEecCCCchh
Confidence 3456799999 999996543 3333343345799999987653
No 73
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=26.31 E-value=17 Score=30.65 Aligned_cols=37 Identities=24% Similarity=0.423 Sum_probs=27.8
Q ss_pred CCceeecCCCCcccCCCccccccccccCCCchhhhhcCCCC
Q 043134 93 EPRVFSCNYCQRKFYSSQALGGHQNAHKRERTLAKRGQRIS 133 (279)
Q Consensus 93 geKPfsC~~CgKsFssssaL~~Hqr~HtgERpy~kr~~~~~ 133 (279)
|--.|-|-.|.+-|....+|..|.+ -|.++||-+.+.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~k----tK~HKrRvK~l~ 90 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFK----TKVHKRRVKELR 90 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHh----ccHHHHHHHhcc
Confidence 4456889999999999999987765 356777765544
No 74
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=25.78 E-value=17 Score=24.02 Aligned_cols=15 Identities=20% Similarity=0.596 Sum_probs=6.8
Q ss_pred CceeecCCCCcccCC
Q 043134 94 PRVFSCNYCQRKFYS 108 (279)
Q Consensus 94 eKPfsC~~CgKsFss 108 (279)
..-..|.+|++.+..
T Consensus 14 ~~~a~C~~C~~~~~~ 28 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKY 28 (45)
T ss_dssp SS-EEETTTTEE---
T ss_pred cCeEEeCCCCeEEee
Confidence 344566666666654
No 75
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=24.45 E-value=31 Score=30.40 Aligned_cols=35 Identities=14% Similarity=0.115 Sum_probs=24.6
Q ss_pred CcCccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCC
Q 043134 63 ELNLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYS 108 (279)
Q Consensus 63 e~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFss 108 (279)
+...|.|.. |+..|+.-.. . +.-|.|+.||.....
T Consensus 114 ~~~~Y~Cp~-C~~rytf~eA----~------~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPN-CHIRFTFDEA----M------EYGFRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCC-CCcEEeHHHH----h------hcCCcCCCCCCCCee
Confidence 345789999 9999854332 1 235999999987653
No 76
>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=23.80 E-value=57 Score=23.48 Aligned_cols=28 Identities=21% Similarity=0.362 Sum_probs=13.6
Q ss_pred cccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccCC
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFYS 108 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFss 108 (279)
-.|.. |++.|.. -.+.+.|..||+.|-.
T Consensus 10 ~~C~~-C~~~F~~-------------~~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 10 SNCMI-CGKKFSL-------------FRRRHHCRNCGRVVCS 37 (69)
T ss_dssp SB-TT-T--B-BS-------------SS-EEE-TTT--EEEC
T ss_pred CcCcC-cCCcCCC-------------ceeeEccCCCCCEECC
Confidence 35999 9999932 1356789999998864
No 77
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=22.58 E-value=50 Score=29.08 Aligned_cols=24 Identities=13% Similarity=0.205 Sum_probs=19.4
Q ss_pred ccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCc
Q 043134 66 LIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQR 104 (279)
Q Consensus 66 lf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgK 104 (279)
.+.|.. ||..+ .++-|-.|+.||-
T Consensus 134 ~~vC~v-CGy~~--------------~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPV-CGYTH--------------EGEAPEVCPICGA 157 (166)
T ss_pred EEEcCC-CCCcc--------------cCCCCCcCCCCCC
Confidence 689999 98764 3577899999984
No 78
>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=22.36 E-value=37 Score=21.40 Aligned_cols=9 Identities=11% Similarity=0.427 Sum_probs=5.1
Q ss_pred ccCccCCccc
Q 043134 68 DCFKSTDSSQ 77 (279)
Q Consensus 68 ~C~e~CGksF 77 (279)
.|.+ |++.|
T Consensus 2 sCiD-C~~~F 10 (28)
T PF08790_consen 2 SCID-CSKDF 10 (28)
T ss_dssp EETT-TTEEE
T ss_pred eeec-CCCCc
Confidence 4555 55555
No 79
>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=22.07 E-value=51 Score=21.21 Aligned_cols=26 Identities=12% Similarity=0.248 Sum_probs=15.2
Q ss_pred cccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcc
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRK 105 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKs 105 (279)
|.|.+ ||..+... ...+..|.+||-.
T Consensus 1 Y~C~~-Cg~~~~~~------------~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGE-CGAEVELK------------PGDPIRCPECGHR 26 (32)
T ss_dssp EBESS-SSSSE-BS------------TSSTSSBSSSS-S
T ss_pred CCCCc-CCCeeEcC------------CCCcEECCcCCCe
Confidence 46888 88876311 1235688888754
No 80
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=21.71 E-value=28 Score=34.26 Aligned_cols=22 Identities=27% Similarity=0.673 Sum_probs=20.5
Q ss_pred eeecCCCCcccCCCcccccccc
Q 043134 96 VFSCNYCQRKFYSSQALGGHQN 117 (279)
Q Consensus 96 PfsC~~CgKsFssssaL~~Hqr 117 (279)
.+.|-+|.|.|..+..|..|||
T Consensus 195 r~~CLyCekifrdkntLkeHMr 216 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMR 216 (423)
T ss_pred hheeeeeccccCCcHHHHHHHH
Confidence 4889999999999999999997
No 81
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=21.43 E-value=47 Score=27.00 Aligned_cols=24 Identities=13% Similarity=0.304 Sum_probs=16.8
Q ss_pred cccCccCCccccCCchhHHHHhhhcCCCceeecCCCCc
Q 043134 67 IDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQR 104 (279)
Q Consensus 67 f~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgK 104 (279)
+.|.. ||..|... +..+.|+.||.
T Consensus 71 ~~C~~-Cg~~~~~~-------------~~~~~CP~Cgs 94 (113)
T PRK12380 71 AWCWD-CSQVVEIH-------------QHDAQCPHCHG 94 (113)
T ss_pred EEccc-CCCEEecC-------------CcCccCcCCCC
Confidence 67999 99887321 23466999984
No 82
>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=20.87 E-value=60 Score=20.88 Aligned_cols=26 Identities=15% Similarity=0.250 Sum_probs=17.5
Q ss_pred ccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcc
Q 043134 66 LIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRK 105 (279)
Q Consensus 66 lf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKs 105 (279)
.+.|.. ||..+.. .+.|..|+.|+..
T Consensus 2 ~~~C~~-CG~i~~g-------------~~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPV-CGYIHEG-------------EEAPEKCPICGAP 27 (34)
T ss_pred eEECCC-CCCEeEC-------------CcCCCcCcCCCCc
Confidence 367888 9976521 1256789999863
No 83
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=20.86 E-value=47 Score=29.95 Aligned_cols=25 Identities=16% Similarity=0.517 Sum_probs=19.3
Q ss_pred CceeecCCCCcccCCCccccccccc
Q 043134 94 PRVFSCNYCQRKFYSSQALGGHQNA 118 (279)
Q Consensus 94 eKPfsC~~CgKsFssssaL~~Hqr~ 118 (279)
++.+.|++|++.|....-+.+..++
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 3568999999999887776666654
No 84
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=20.31 E-value=53 Score=21.80 Aligned_cols=15 Identities=27% Similarity=0.676 Sum_probs=12.7
Q ss_pred eeecCCCCcccCCCc
Q 043134 96 VFSCNYCQRKFYSSQ 110 (279)
Q Consensus 96 PfsC~~CgKsFssss 110 (279)
||.|..|++.|-...
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 899999999997544
No 85
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=20.31 E-value=12 Score=39.88 Aligned_cols=25 Identities=24% Similarity=0.772 Sum_probs=23.0
Q ss_pred eeecCCCCcccCCCccccccccccC
Q 043134 96 VFSCNYCQRKFYSSQALGGHQNAHK 120 (279)
Q Consensus 96 PfsC~~CgKsFssssaL~~Hqr~Ht 120 (279)
-|-|.+|+|.|..-..+..||..|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4999999999999999999999984
No 86
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.27 E-value=40 Score=26.22 Aligned_cols=31 Identities=10% Similarity=0.322 Sum_probs=20.9
Q ss_pred ccccCccCCccccCCchhHHHHhhhcCCCce-eecCCCCccc
Q 043134 66 LIDCFKSTDSSQDSLENNDIHRQGNETEPRV-FSCNYCQRKF 106 (279)
Q Consensus 66 lf~C~e~CGksFss~ss~L~~Hqr~HtgeKP-fsC~~CgKsF 106 (279)
.|.|.+ ||..| .+.+|++ +-| -.|..|+-.|
T Consensus 12 ~Y~c~~-cg~~~-----dvvq~~~----ddplt~ce~c~a~~ 43 (82)
T COG2331 12 SYECTE-CGNRF-----DVVQAMT----DDPLTTCEECGARL 43 (82)
T ss_pred EEeecc-cchHH-----HHHHhcc----cCccccChhhChHH
Confidence 478999 99988 3555543 334 4588887755
No 87
>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=20.19 E-value=35 Score=29.39 Aligned_cols=34 Identities=15% Similarity=0.117 Sum_probs=23.5
Q ss_pred CcCccccCccCCccccCCchhHHHHhhhcCCCceeecCCCCcccC
Q 043134 63 ELNLIDCFKSTDSSQDSLENNDIHRQGNETEPRVFSCNYCQRKFY 107 (279)
Q Consensus 63 e~nlf~C~e~CGksFss~ss~L~~Hqr~HtgeKPfsC~~CgKsFs 107 (279)
+...|.|.. |+..|+.-.. . +.-|.|+.||....
T Consensus 106 ~~~~Y~Cp~-c~~r~tf~eA----~------~~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 106 NNMFFICPN-MCVRFTFNEA----M------ELNFTCPRCGAMLD 139 (158)
T ss_pred CCCeEECCC-CCcEeeHHHH----H------HcCCcCCCCCCEee
Confidence 345688999 9998854332 1 12599999998753
Done!