Query 046965
Match_columns 286
No_of_seqs 420 out of 1766
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 06:17:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046965.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046965hhsearch_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 99.4 3.1E-14 6.8E-19 131.5 1.2 65 80-145 188-252 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.3 4.8E-13 1E-17 123.7 -0.0 108 76-190 127-240 (279)
3 KOG3623 Homeobox transcription 99.2 1.3E-12 2.8E-17 133.1 0.4 81 76-164 891-976 (1007)
4 KOG3623 Homeobox transcription 98.9 1.8E-10 3.9E-15 117.8 -1.4 67 78-145 239-318 (1007)
5 KOG3576 Ovo and related transc 98.9 1.7E-10 3.7E-15 103.4 -1.8 71 74-145 112-182 (267)
6 KOG3576 Ovo and related transc 98.5 1.6E-08 3.4E-13 90.9 -0.6 67 78-145 144-221 (267)
7 KOG1074 Transcriptional repres 98.5 5.2E-08 1.1E-12 101.3 1.5 81 108-190 605-693 (958)
8 PHA02768 hypothetical protein; 98.4 1.2E-07 2.6E-12 68.6 1.1 36 108-145 5-40 (55)
9 KOG1074 Transcriptional repres 98.3 1.4E-07 3.1E-12 98.0 1.7 67 76-143 876-942 (958)
10 PF13465 zf-H2C2_2: Zinc-finge 98.0 1.3E-06 2.7E-11 53.8 -0.3 23 97-119 3-25 (26)
11 PHA02768 hypothetical protein; 97.9 1.6E-06 3.4E-11 62.8 -1.0 45 79-126 5-49 (55)
12 PF13465 zf-H2C2_2: Zinc-finge 97.8 6.8E-06 1.5E-10 50.5 1.0 23 123-145 1-23 (26)
13 PHA00733 hypothetical protein 97.8 7E-06 1.5E-10 68.8 1.0 65 78-145 39-108 (128)
14 PHA00616 hypothetical protein 97.8 4.8E-06 1E-10 57.7 -0.2 34 108-141 1-34 (44)
15 PLN03086 PRLI-interacting fact 97.7 7E-06 1.5E-10 83.7 -0.7 61 79-145 453-513 (567)
16 PLN03086 PRLI-interacting fact 97.2 0.00014 3E-09 74.4 1.7 64 78-145 477-550 (567)
17 PF00096 zf-C2H2: Zinc finger, 97.1 0.00016 3.4E-09 42.4 0.3 23 109-131 1-23 (23)
18 KOG3608 Zn finger proteins [Ge 97.0 4.4E-05 9.4E-10 73.7 -3.6 67 76-145 234-301 (467)
19 PHA00732 hypothetical protein 97.0 0.00027 5.9E-09 54.7 1.3 35 108-145 1-36 (79)
20 PHA00733 hypothetical protein 97.0 0.0002 4.3E-09 60.1 0.2 52 77-131 71-122 (128)
21 PF13912 zf-C2H2_6: C2H2-type 96.5 0.00087 1.9E-08 40.7 0.4 25 108-132 1-25 (27)
22 KOG3608 Zn finger proteins [Ge 96.3 0.00073 1.6E-08 65.5 -0.7 110 76-190 260-377 (467)
23 PF13894 zf-C2H2_4: C2H2-type 96.2 0.0018 3.9E-08 37.3 0.7 23 109-131 1-23 (24)
24 PHA00732 hypothetical protein 96.1 0.0014 2.9E-08 50.8 -0.1 45 80-131 2-47 (79)
25 PRK04860 hypothetical protein; 95.8 0.0052 1.1E-07 53.6 2.0 35 107-145 118-152 (160)
26 smart00355 ZnF_C2H2 zinc finge 95.6 0.0048 1E-07 35.8 0.7 24 109-132 1-24 (26)
27 PHA00616 hypothetical protein 95.4 0.0015 3.2E-08 45.4 -2.3 34 80-114 2-35 (44)
28 PF09237 GAGA: GAGA factor; I 94.2 0.024 5.2E-07 40.7 1.2 33 104-136 20-52 (54)
29 COG5189 SFP1 Putative transcri 93.9 0.031 6.7E-07 53.8 1.9 41 105-145 346-407 (423)
30 KOG3993 Transcription factor ( 93.9 0.014 3.1E-07 57.8 -0.4 23 109-131 357-379 (500)
31 PF12874 zf-met: Zinc-finger o 93.1 0.025 5.4E-07 33.5 -0.1 23 109-131 1-23 (25)
32 KOG3993 Transcription factor ( 92.2 0.047 1E-06 54.2 0.5 26 107-132 294-319 (500)
33 COG5048 FOG: Zn-finger [Genera 92.0 0.14 3.1E-06 47.6 3.3 62 79-141 289-356 (467)
34 PF12171 zf-C2H2_jaz: Zinc-fin 91.4 0.065 1.4E-06 32.7 0.2 22 109-130 2-23 (27)
35 PRK04860 hypothetical protein; 91.2 0.049 1.1E-06 47.5 -0.7 39 78-121 118-156 (160)
36 PF12756 zf-C2H2_2: C2H2 type 90.5 0.11 2.4E-06 39.6 0.9 24 108-131 50-73 (100)
37 PF05605 zf-Di19: Drought indu 89.8 0.07 1.5E-06 37.9 -0.8 37 108-145 2-40 (54)
38 PF05605 zf-Di19: Drought indu 89.3 0.2 4.4E-06 35.5 1.4 51 78-132 1-53 (54)
39 PF13909 zf-H2C2_5: C2H2-type 87.8 0.19 4.1E-06 29.6 0.3 23 109-132 1-23 (24)
40 KOG2893 Zn finger protein [Gen 84.0 0.28 6.1E-06 45.7 -0.4 47 81-132 12-59 (341)
41 PF13913 zf-C2HC_2: zinc-finge 83.9 0.41 8.9E-06 29.0 0.4 21 109-130 3-23 (25)
42 smart00451 ZnF_U1 U1-like zinc 83.1 0.48 1E-05 29.9 0.5 23 108-130 3-25 (35)
43 KOG2893 Zn finger protein [Gen 80.9 0.57 1.2E-05 43.8 0.4 34 107-145 10-43 (341)
44 COG5048 FOG: Zn-finger [Genera 72.5 6.6 0.00014 36.4 5.0 39 107-145 288-332 (467)
45 COG5189 SFP1 Putative transcri 64.1 2.9 6.3E-05 40.6 0.8 52 77-129 347-419 (423)
46 PHA00626 hypothetical protein 62.5 6.2 0.00013 29.0 2.0 34 81-120 2-35 (59)
47 PF09986 DUF2225: Uncharacteri 62.4 4.3 9.4E-05 36.7 1.5 25 106-130 3-27 (214)
48 KOG2186 Cell growth-regulating 61.7 2.4 5.3E-05 39.8 -0.2 51 79-133 3-53 (276)
49 PF14353 CpXC: CpXC protein 60.7 3.9 8.5E-05 33.6 0.9 20 108-127 38-57 (128)
50 TIGR02605 CxxC_CxxC_SSSS putat 59.3 5 0.00011 27.8 1.1 30 108-144 5-34 (52)
51 cd00350 rubredoxin_like Rubred 58.3 7.8 0.00017 24.8 1.8 25 109-145 2-26 (33)
52 smart00834 CxxC_CXXC_SSSS Puta 57.4 5.5 0.00012 25.9 1.0 11 109-119 6-16 (41)
53 COG4049 Uncharacterized protei 57.0 3.6 7.8E-05 30.3 0.0 30 101-130 10-39 (65)
54 COG1198 PriA Primosomal protei 56.1 8.8 0.00019 41.1 2.7 11 135-145 461-471 (730)
55 PF09538 FYDLN_acid: Protein o 54.7 7.8 0.00017 31.7 1.7 10 110-119 11-20 (108)
56 smart00659 RPOLCX RNA polymera 53.8 9.5 0.00021 26.3 1.7 26 109-145 3-28 (44)
57 smart00531 TFIIE Transcription 52.5 7.7 0.00017 33.0 1.3 38 104-145 95-132 (147)
58 KOG4167 Predicted DNA-binding 52.2 8.7 0.00019 41.1 1.9 27 107-133 791-817 (907)
59 TIGR00373 conserved hypothetic 51.9 6.6 0.00014 33.9 0.9 34 103-145 104-137 (158)
60 TIGR00595 priA primosomal prot 50.8 12 0.00026 38.1 2.6 35 110-145 215-249 (505)
61 PRK06266 transcription initiat 50.4 7 0.00015 34.6 0.8 32 105-145 114-145 (178)
62 TIGR02098 MJ0042_CXXC MJ0042 f 48.2 8.9 0.00019 24.8 0.8 11 108-118 25-35 (38)
63 PRK14873 primosome assembly pr 48.0 13 0.00028 39.3 2.5 48 80-145 384-431 (665)
64 PRK14873 primosome assembly pr 48.0 12 0.00025 39.7 2.1 35 110-145 385-419 (665)
65 KOG1146 Homeobox protein [Gene 47.9 9.3 0.0002 43.2 1.4 68 77-145 434-527 (1406)
66 COG0068 HypF Hydrogenase matur 46.2 10 0.00023 40.4 1.4 61 77-145 121-182 (750)
67 PF13719 zinc_ribbon_5: zinc-r 45.1 11 0.00024 24.7 0.9 32 81-118 4-35 (37)
68 PF09723 Zn-ribbon_8: Zinc rib 44.0 12 0.00025 25.3 0.9 29 109-144 6-34 (42)
69 PRK00464 nrdR transcriptional 42.8 14 0.0003 32.1 1.4 12 109-120 29-40 (154)
70 PRK00398 rpoP DNA-directed RNA 42.4 16 0.00034 24.9 1.4 12 108-119 3-14 (46)
71 PF02892 zf-BED: BED zinc fing 42.3 13 0.00028 24.7 1.0 24 105-128 13-40 (45)
72 PF13717 zinc_ribbon_4: zinc-r 41.6 16 0.00035 23.9 1.3 11 108-118 25-35 (36)
73 COG1996 RPC10 DNA-directed RNA 40.4 15 0.00033 26.1 1.1 29 107-145 5-33 (49)
74 TIGR00595 priA primosomal prot 39.7 23 0.00051 36.0 2.7 50 79-145 213-262 (505)
75 COG2888 Predicted Zn-ribbon RN 39.5 21 0.00046 26.5 1.7 34 107-145 26-59 (61)
76 smart00614 ZnF_BED BED zinc fi 38.0 18 0.00039 25.0 1.2 25 108-132 18-48 (50)
77 cd00729 rubredoxin_SM Rubredox 37.7 26 0.00055 22.7 1.8 26 108-145 2-27 (34)
78 PRK04023 DNA polymerase II lar 37.4 33 0.00071 38.2 3.5 17 258-274 765-781 (1121)
79 PF12760 Zn_Tnp_IS1595: Transp 35.8 21 0.00046 24.3 1.2 8 136-143 37-44 (46)
80 TIGR02300 FYDLN_acid conserved 35.7 24 0.00052 29.9 1.7 25 110-145 11-35 (129)
81 PF05443 ROS_MUCR: ROS/MUCR tr 34.7 17 0.00037 30.9 0.7 29 107-138 71-99 (132)
82 PF03604 DNA_RNApol_7kD: DNA d 34.5 36 0.00078 22.0 2.0 11 109-119 1-11 (32)
83 PF12756 zf-C2H2_2: C2H2 type 33.9 14 0.0003 27.8 0.0 21 110-130 1-21 (100)
84 PRK05580 primosome assembly pr 32.4 33 0.00071 36.3 2.5 36 109-145 382-417 (679)
85 PF07295 DUF1451: Protein of u 31.9 26 0.00055 30.2 1.4 9 137-145 113-121 (146)
86 KOG2593 Transcription initiati 31.4 26 0.00056 35.3 1.4 40 103-145 123-162 (436)
87 KOG2785 C2H2-type Zn-finger pr 31.3 12 0.00026 37.0 -0.8 54 76-130 163-242 (390)
88 PF09845 DUF2072: Zn-ribbon co 31.0 25 0.00054 29.9 1.1 13 108-120 1-13 (131)
89 PRK09678 DNA-binding transcrip 28.5 29 0.00064 26.5 1.0 14 132-145 23-38 (72)
90 COG1592 Rubrerythrin [Energy p 28.5 38 0.00082 29.9 1.9 24 108-144 134-157 (166)
91 COG1198 PriA Primosomal protei 28.4 36 0.00079 36.6 2.1 49 80-145 436-484 (730)
92 PF09332 Mcm10: Mcm10 replicat 28.1 19 0.00042 35.2 -0.0 39 107-145 251-294 (344)
93 TIGR00143 hypF [NiFe] hydrogen 28.0 30 0.00064 37.0 1.3 62 76-145 87-149 (711)
94 PRK14559 putative protein seri 27.9 54 0.0012 34.7 3.2 9 110-118 17-25 (645)
95 PRK14890 putative Zn-ribbon RN 27.7 42 0.0009 24.8 1.7 34 107-145 24-57 (59)
96 PF08790 zf-LYAR: LYAR-type C2 26.9 30 0.00065 21.8 0.7 9 110-118 2-10 (28)
97 COG3091 SprT Zn-dependent meta 23.4 44 0.00095 29.2 1.3 35 106-145 115-149 (156)
98 PRK03824 hypA hydrogenase nick 22.4 51 0.0011 27.7 1.5 18 104-121 66-83 (135)
99 TIGR01206 lysW lysine biosynth 21.4 76 0.0016 22.9 2.0 10 109-118 3-12 (54)
100 COG4957 Predicted transcriptio 21.2 38 0.00081 29.2 0.4 27 109-138 77-103 (148)
101 smart00154 ZnF_AN1 AN1-like Zi 20.8 50 0.0011 22.0 0.9 14 108-121 12-25 (39)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.42 E-value=3.1e-14 Score=131.54 Aligned_cols=65 Identities=15% Similarity=0.221 Sum_probs=39.3
Q ss_pred ccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 80 MSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 80 ~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
+.|..|||.|..-= +++.|.|+|||||||.|..|+|+|...++|..||++|.+.|.|+|..|+|+
T Consensus 188 c~C~iCGKaFSRPW-LLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~Ks 252 (279)
T KOG2462|consen 188 CECGICGKAFSRPW-LLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKS 252 (279)
T ss_pred cccccccccccchH-HhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhH
Confidence 34555555555332 234566666666666666666666666666666666666666666666666
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.28 E-value=4.8e-13 Score=123.75 Aligned_cols=108 Identities=17% Similarity=0.249 Sum_probs=67.3
Q ss_pred CccCccccCCccchhhccCCCCCcccccC---CCceeecCCCCcccCCCccchhhhhhccCCccccccccCcchhhhhhh
Q 046965 76 LFNRMSMMNNNHCHEENNGHPTSSEKKSS---EARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVDQDVGAAA 152 (286)
Q Consensus 76 e~n~~tc~~~g~S~~~~~~~~~~H~rtHt---geKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~~~~~a~~ 152 (286)
...++.|.+||+.++..+++- +|.++|- ..+.|.|.+|+|.|.+-.+|+.|+++|+ -+++|..|||.+...-..
T Consensus 127 ~~~r~~c~eCgk~ysT~snLs-rHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLL 203 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLS-RHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLL 203 (279)
T ss_pred cCCceeccccccccccccccc-hhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHh
Confidence 667788999998888777643 6777764 2456677777777777777777777766 466777777763222211
Q ss_pred ccC--CCccCcCCCccCCCCCCC-CccccCCCCCCccCCCC
Q 046965 153 FGN--QHFSFYSPYYSRFSPYYG-SFNRSLGVKMNSMIHKP 190 (286)
Q Consensus 153 f~~--~H~~~~~py~s~~~p~~g-s~~r~lgl~~Hs~iHkp 190 (286)
-|| +|++.. ||+ |+.|+ .|....+||+|..+|-.
T Consensus 204 QGHiRTHTGEK-PF~---C~hC~kAFADRSNLRAHmQTHS~ 240 (279)
T KOG2462|consen 204 QGHIRTHTGEK-PFS---CPHCGKAFADRSNLRAHMQTHSD 240 (279)
T ss_pred hcccccccCCC-Ccc---CCcccchhcchHHHHHHHHhhcC
Confidence 222 233433 554 66666 55556667777777654
No 3
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.24 E-value=1.3e-12 Score=133.11 Aligned_cols=81 Identities=16% Similarity=0.283 Sum_probs=72.2
Q ss_pred CccCccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCCccchhhhhhccCCccccccccCcchhhhhhhccC
Q 046965 76 LFNRMSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVDQDVGAAAFGN 155 (286)
Q Consensus 76 e~n~~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~~~~~a~~f~~ 155 (286)
+..+|.|.+|+|.|...+.+. +|.=-|+|.|||+|.+|.|+|..+..|..|+|.|.|||||.|..|+|. |+|
T Consensus 891 e~gmyaCDqCDK~FqKqSSLa-RHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKR-------FSH 962 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLA-RHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKR-------FSH 962 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHH-HhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhh-------ccc
Confidence 777899999999999887654 898899999999999999999999999999999999999999999999 554
Q ss_pred C-----CccCcCCC
Q 046965 156 Q-----HFSFYSPY 164 (286)
Q Consensus 156 ~-----H~~~~~py 164 (286)
. ||.+++.|
T Consensus 963 SGSYSQHMNHRYSY 976 (1007)
T KOG3623|consen 963 SGSYSQHMNHRYSY 976 (1007)
T ss_pred ccchHhhhccchhc
Confidence 3 77766444
No 4
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.89 E-value=1.8e-10 Score=117.76 Aligned_cols=67 Identities=16% Similarity=0.173 Sum_probs=58.2
Q ss_pred cCccccCCccchhhccCCCCCcccccC-------------CCceeecCCCCcccCCCccchhhhhhccCCccccccccCc
Q 046965 78 NRMSMMNNNHCHEENNGHPTSSEKKSS-------------EARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGV 144 (286)
Q Consensus 78 n~~tc~~~g~S~~~~~~~~~~H~rtHt-------------geKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk 144 (286)
--|.|+.|-.+|+.+..+. +||.+|. +-|.|+|.+|+|+|..+..|+.|.|||.|||||.|..|+|
T Consensus 239 ~nfsC~lCsytFAyRtQLE-rhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkK 317 (1007)
T KOG3623|consen 239 PNFSCMLCSYTFAYRTQLE-RHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKK 317 (1007)
T ss_pred CCCcchhhhhhhhhHHHHH-HHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCccccc
Confidence 3477999999998776554 7777763 2478999999999999999999999999999999999999
Q ss_pred c
Q 046965 145 D 145 (286)
Q Consensus 145 ~ 145 (286)
.
T Consensus 318 R 318 (1007)
T KOG3623|consen 318 R 318 (1007)
T ss_pred c
Confidence 9
No 5
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.87 E-value=1.7e-10 Score=103.36 Aligned_cols=71 Identities=14% Similarity=0.125 Sum_probs=65.2
Q ss_pred CCCccCccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 74 SGLFNRMSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 74 ~~e~n~~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
+.+.+.|+|--|||.|.-... +.+|++.|...|.|-|..|||.|.....|++|+|+|||.|||+|..|+|+
T Consensus 112 ssd~d~ftCrvCgK~F~lQRm-lnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~ka 182 (267)
T KOG3576|consen 112 SSDQDSFTCRVCGKKFGLQRM-LNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKA 182 (267)
T ss_pred CCCCCeeeeehhhhhhhHHHH-HHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHH
Confidence 346788999999999987654 45999999999999999999999999999999999999999999999998
No 6
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.51 E-value=1.6e-08 Score=90.92 Aligned_cols=67 Identities=13% Similarity=0.276 Sum_probs=56.4
Q ss_pred cCccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCCccchhhhh-hcc----------CCccccccccCcc
Q 046965 78 NRMSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTSQALGGHQN-AHK----------QERAVAKRRQGVD 145 (286)
Q Consensus 78 n~~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~sssaL~~Hqr-~Ht----------gEKpy~C~~Cgk~ 145 (286)
...-|+-||+-|...=.++ +|+|+|||.+||+|..|+|+|.+..+|..|.+ +|. ++|-|.|.+||..
T Consensus 144 kr~lct~cgkgfndtfdlk-rh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t 221 (267)
T KOG3576|consen 144 KRHLCTFCGKGFNDTFDLK-RHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYT 221 (267)
T ss_pred HHHHHhhccCcccchhhhh-hhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCC
Confidence 3446788999998776554 99999999999999999999999999999965 564 3567889999986
No 7
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.46 E-value=5.2e-08 Score=101.27 Aligned_cols=81 Identities=22% Similarity=0.224 Sum_probs=40.4
Q ss_pred eeecCCCCcccCCCccchhhhhhccCCccccccccCcchhhhhhhccCCCccCc---CCCcc-CCCC---CCC-CccccC
Q 046965 108 VFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVDQDVGAAAFGNQHFSFY---SPYYS-RFSP---YYG-SFNRSL 179 (286)
Q Consensus 108 pf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~~~~~a~~f~~~H~~~~---~py~s-~~~p---~~g-s~~r~l 179 (286)
|-+|-+|.|..+...+|+-|.|+|+|||||+|++||+++ ....-...||..+ .|+.. ..|| .|- -|....
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAF--tTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V 682 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAF--TTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAV 682 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchh--ccccchhhcccccccCccccccccCCchhhhcccccccc
Confidence 445555555555555555555555555555555555551 1111111233221 12211 3344 332 455677
Q ss_pred CCCCCccCCCC
Q 046965 180 GVKMNSMIHKP 190 (286)
Q Consensus 180 gl~~Hs~iHkp 190 (286)
.++.|.+||.+
T Consensus 683 ~lpQhIriH~~ 693 (958)
T KOG1074|consen 683 TLPQHIRIHLG 693 (958)
T ss_pred cccceEEeecC
Confidence 78889999886
No 8
>PHA02768 hypothetical protein; Provisional
Probab=98.36 E-value=1.2e-07 Score=68.56 Aligned_cols=36 Identities=11% Similarity=0.221 Sum_probs=33.8
Q ss_pred eeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 108 VFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 108 pf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
-|+|++||+.|...++|..||++|+ ++|+|..|++.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~ 40 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRI 40 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccce
Confidence 4899999999999999999999999 79999999997
No 9
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.35 E-value=1.4e-07 Score=98.03 Aligned_cols=67 Identities=15% Similarity=0.243 Sum_probs=59.4
Q ss_pred CccCccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCCccchhhhhhccCCccccccccC
Q 046965 76 LFNRMSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQG 143 (286)
Q Consensus 76 e~n~~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cg 143 (286)
-.|-.-|.-||+-|.....++ .|||+|+++|||.|.+|++.|.....|+.||.+|.+..++..+.|.
T Consensus 876 vnn~h~C~vCgk~FsSSsALq-iH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srrG~~ 942 (958)
T KOG1074|consen 876 VNNAHVCNVCGKQFSSSAALE-IHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRRGPS 942 (958)
T ss_pred ccchhhhccchhcccchHHHH-HhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCccCCCC
Confidence 556678999999999887665 9999999999999999999999999999999999999998888443
No 10
>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=97.98 E-value=1.3e-06 Score=53.78 Aligned_cols=23 Identities=22% Similarity=0.691 Sum_probs=19.1
Q ss_pred CCcccccCCCceeecCCCCcccC
Q 046965 97 TSSEKKSSEARVFSCNYCKREFS 119 (286)
Q Consensus 97 ~~H~rtHtgeKpf~C~~CgK~F~ 119 (286)
..|+++|++++||.|++|++.|.
T Consensus 3 ~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 3 RRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHhhhcCCCCCCCCCCCcCeeC
Confidence 36888888888888888888885
No 11
>PHA02768 hypothetical protein; Provisional
Probab=97.90 E-value=1.6e-06 Score=62.78 Aligned_cols=45 Identities=9% Similarity=-0.025 Sum_probs=39.4
Q ss_pred CccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCCccchh
Q 046965 79 RMSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTSQALGG 126 (286)
Q Consensus 79 ~~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~sssaL~~ 126 (286)
-|.|..||+.|...+.+ +.|+++|+ ++|+|..|++.|...+.|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L-~~H~r~H~--k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 5 GYECPICGEIYIKRKSM-ITHLRKHN--TNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred ccCcchhCCeeccHHHH-HHHHHhcC--CcccCCcccceecccceeEE
Confidence 36899999999998866 59999999 79999999999998877753
No 12
>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=97.82 E-value=6.8e-06 Score=50.48 Aligned_cols=23 Identities=22% Similarity=0.224 Sum_probs=21.7
Q ss_pred cchhhhhhccCCccccccccCcc
Q 046965 123 ALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 123 aL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
+|..|+++|+++|||+|..|++.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~ 23 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKS 23 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEE
T ss_pred CHHHHhhhcCCCCCCCCCCCcCe
Confidence 47899999999999999999997
No 13
>PHA00733 hypothetical protein
Probab=97.79 E-value=7e-06 Score=68.84 Aligned_cols=65 Identities=15% Similarity=0.117 Sum_probs=50.3
Q ss_pred cCccccCCccchhhccCCCC-----CcccccCCCceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 78 NRMSMMNNNHCHEENNGHPT-----SSEKKSSEARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 78 n~~tc~~~g~S~~~~~~~~~-----~H~rtHtgeKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
....|..|.+.+.....+.. .|+.. .+++||.|+.|++.|.....|..|+++| +.+|.|..|++.
T Consensus 39 ~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~-~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~ 108 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQLLDESSYLYKLLTS-KAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKE 108 (128)
T ss_pred hhHHHHHHhhhccChhhhcchHHHHhhccc-CCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCc
Confidence 34467778877776544332 34344 4588999999999999999999999987 467999999998
No 14
>PHA00616 hypothetical protein
Probab=97.77 E-value=4.8e-06 Score=57.67 Aligned_cols=34 Identities=12% Similarity=0.280 Sum_probs=31.9
Q ss_pred eeecCCCCcccCCCccchhhhhhccCCccccccc
Q 046965 108 VFSCNYCKREFSTSQALGGHQNAHKQERAVAKRR 141 (286)
Q Consensus 108 pf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~ 141 (286)
||+|..||+.|...+.|..|++.|++++++.|..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999998863
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.69 E-value=7e-06 Score=83.70 Aligned_cols=61 Identities=13% Similarity=0.143 Sum_probs=35.3
Q ss_pred CccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 79 RMSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 79 ~~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
...|..|+++|... .+..|+++|+ ++|.|+ |++.| ....|..|++.|..+|++.|+.|++.
T Consensus 453 H~~C~~Cgk~f~~s--~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~ 513 (567)
T PLN03086 453 HVHCEKCGQAFQQG--EMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDM 513 (567)
T ss_pred CccCCCCCCccchH--HHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCc
Confidence 34566666666422 2245666553 566666 66543 44566666666666666666666665
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.20 E-value=0.00014 Score=74.43 Aligned_cols=64 Identities=11% Similarity=0.242 Sum_probs=52.4
Q ss_pred cCccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCC----------CccchhhhhhccCCccccccccCcc
Q 046965 78 NRMSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFST----------SQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 78 n~~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~s----------ssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
-.+.|. ||+.+. + ..+..|+++|..++++.|.+|++.|.. ...|..|..++ +.+++.|..||+.
T Consensus 477 kpv~Cp-Cg~~~~-R-~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~ 550 (567)
T PLN03086 477 EPLQCP-CGVVLE-K-EQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRS 550 (567)
T ss_pred CCccCC-CCCCcc-h-hHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCe
Confidence 345788 997553 3 455689999999999999999999952 24799999986 8999999999997
No 17
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.07 E-value=0.00016 Score=42.39 Aligned_cols=23 Identities=30% Similarity=0.749 Sum_probs=21.6
Q ss_pred eecCCCCcccCCCccchhhhhhc
Q 046965 109 FSCNYCKREFSTSQALGGHQNAH 131 (286)
Q Consensus 109 f~C~~CgK~F~sssaL~~Hqr~H 131 (286)
|.|+.|++.|.....|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 78999999999999999999875
No 18
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=97.04 E-value=4.4e-05 Score=73.71 Aligned_cols=67 Identities=12% Similarity=0.161 Sum_probs=53.3
Q ss_pred CccCccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCCccchhhhhh-ccCCccccccccCcc
Q 046965 76 LFNRMSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTSQALGGHQNA-HKQERAVAKRRQGVD 145 (286)
Q Consensus 76 e~n~~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~sssaL~~Hqr~-HtgEKpy~C~~Cgk~ 145 (286)
..|.|.|.+|.|-|+.+..+ ..|++.|.. .|+|+.|.......+.|..|++. |...|||+|..|.+.
T Consensus 234 ~~n~fqC~~C~KrFaTeklL-~~Hv~rHvn--~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~ 301 (467)
T KOG3608|consen 234 NTNSFQCAQCFKRFATEKLL-KSHVVRHVN--CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTR 301 (467)
T ss_pred cCCchHHHHHHHHHhHHHHH-HHHHHHhhh--cccccccccCCCChHHHHHHHHhhhccCCCccccchhhh
Confidence 77889999999999877644 377777764 58888888888888888888774 777888888888775
No 19
>PHA00732 hypothetical protein
Probab=97.01 E-value=0.00027 Score=54.71 Aligned_cols=35 Identities=23% Similarity=0.246 Sum_probs=30.6
Q ss_pred eeecCCCCcccCCCccchhhhhh-ccCCccccccccCcc
Q 046965 108 VFSCNYCKREFSTSQALGGHQNA-HKQERAVAKRRQGVD 145 (286)
Q Consensus 108 pf~C~~CgK~F~sssaL~~Hqr~-HtgEKpy~C~~Cgk~ 145 (286)
||.|..|++.|.+...|..|++. |+ ++.|..|++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKs 36 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKS 36 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCE
Confidence 68899999999999999999984 65 3689999998
No 20
>PHA00733 hypothetical protein
Probab=96.97 E-value=0.0002 Score=60.09 Aligned_cols=52 Identities=10% Similarity=0.062 Sum_probs=43.2
Q ss_pred ccCccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCCccchhhhhhc
Q 046965 77 FNRMSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTSQALGGHQNAH 131 (286)
Q Consensus 77 ~n~~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~sssaL~~Hqr~H 131 (286)
...+.|..||+.|.....+. .|++.| +.+|.|..|++.|.....|..|+...
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~-~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~ 122 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLK-QHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKK 122 (128)
T ss_pred CCCccCCCCCCcCCCHHHHH-HHHhcC--CcCccCCCCCCccCCHHHHHHHHHHh
Confidence 34679999999999877654 777776 45799999999999999999998754
No 21
>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=96.46 E-value=0.00087 Score=40.73 Aligned_cols=25 Identities=36% Similarity=0.732 Sum_probs=23.3
Q ss_pred eeecCCCCcccCCCccchhhhhhcc
Q 046965 108 VFSCNYCKREFSTSQALGGHQNAHK 132 (286)
Q Consensus 108 pf~C~~CgK~F~sssaL~~Hqr~Ht 132 (286)
||+|..|++.|....+|..|++.|.
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 22
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=96.34 E-value=0.00073 Score=65.47 Aligned_cols=110 Identities=13% Similarity=0.100 Sum_probs=72.9
Q ss_pred CccCccccCCccchhhccCCCCCcccc-cCCCceeecCCCCcccCCCccchhhhhhccCCccccccc--cCcchhhh---
Q 046965 76 LFNRMSMMNNNHCHEENNGHPTSSEKK-SSEARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRR--QGVDQDVG--- 149 (286)
Q Consensus 76 e~n~~tc~~~g~S~~~~~~~~~~H~rt-HtgeKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~--Cgk~~~~~--- 149 (286)
-.|+++|+-|+-.-...+.+ .+|+|. |...|||+|+.|.+.|.....|..|..+|. +-.|.|.. |-.++..-
T Consensus 260 Hvn~ykCplCdmtc~~~ssL-~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~ 337 (467)
T KOG3608|consen 260 HVNCYKCPLCDMTCSSASSL-TTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQM 337 (467)
T ss_pred hhhcccccccccCCCChHHH-HHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHH
Confidence 67899999887544443332 366664 888999999999999999999999999998 77899987 77652111
Q ss_pred hhhccCCCccCc-CCCccCCCCCCCC-ccccCCCCCCccCCCC
Q 046965 150 AAAFGNQHFSFY-SPYYSRFSPYYGS-FNRSLGVKMNSMIHKP 190 (286)
Q Consensus 150 a~~f~~~H~~~~-~py~s~~~p~~gs-~~r~lgl~~Hs~iHkp 190 (286)
+..|.-.|-+.. .+|. |..|.. |.+-..|.+|-|-...
T Consensus 338 ~~H~~evhEg~np~~Y~---CH~Cdr~ft~G~~L~~HL~kkH~ 377 (467)
T KOG3608|consen 338 RRHFLEVHEGNNPILYA---CHCCDRFFTSGKSLSAHLMKKHG 377 (467)
T ss_pred HHHHHHhccCCCCCcee---eecchhhhccchhHHHHHHHhhc
Confidence 111211221211 2444 666664 4445557788665544
No 23
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.18 E-value=0.0018 Score=37.34 Aligned_cols=23 Identities=30% Similarity=0.766 Sum_probs=19.6
Q ss_pred eecCCCCcccCCCccchhhhhhc
Q 046965 109 FSCNYCKREFSTSQALGGHQNAH 131 (286)
Q Consensus 109 f~C~~CgK~F~sssaL~~Hqr~H 131 (286)
|.|++|++.|.+...|..|++.|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 78999999999999999999876
No 24
>PHA00732 hypothetical protein
Probab=96.13 E-value=0.0014 Score=50.80 Aligned_cols=45 Identities=9% Similarity=0.163 Sum_probs=35.2
Q ss_pred ccccCCccchhhccCCCCCcccc-cCCCceeecCCCCcccCCCccchhhhhhc
Q 046965 80 MSMMNNNHCHEENNGHPTSSEKK-SSEARVFSCNYCKREFSTSQALGGHQNAH 131 (286)
Q Consensus 80 ~tc~~~g~S~~~~~~~~~~H~rt-HtgeKpf~C~~CgK~F~sssaL~~Hqr~H 131 (286)
+.|..||+.|.....+. .|++. |++ +.|+.|++.|. .|..|.+.+
T Consensus 2 y~C~~Cgk~F~s~s~Lk-~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 2 FKCPICGFTTVTLFALK-QHARRNHTL---TKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred ccCCCCCCccCCHHHHH-HHhhcccCC---CccCCCCCEeC---Chhhhhccc
Confidence 67999999999877654 78874 653 68999999997 477787543
No 25
>PRK04860 hypothetical protein; Provisional
Probab=95.78 E-value=0.0052 Score=53.58 Aligned_cols=35 Identities=20% Similarity=0.395 Sum_probs=31.5
Q ss_pred ceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 107 RVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 107 Kpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
-+|.|. |++ ....+.+|.++|+++++|.|..|+..
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~ 152 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGET 152 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCce
Confidence 479998 998 66778999999999999999999987
No 26
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.57 E-value=0.0048 Score=35.77 Aligned_cols=24 Identities=29% Similarity=0.675 Sum_probs=22.0
Q ss_pred eecCCCCcccCCCccchhhhhhcc
Q 046965 109 FSCNYCKREFSTSQALGGHQNAHK 132 (286)
Q Consensus 109 f~C~~CgK~F~sssaL~~Hqr~Ht 132 (286)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 689999999999999999998775
No 27
>PHA00616 hypothetical protein
Probab=95.40 E-value=0.0015 Score=45.39 Aligned_cols=34 Identities=3% Similarity=-0.002 Sum_probs=30.2
Q ss_pred ccccCCccchhhccCCCCCcccccCCCceeecCCC
Q 046965 80 MSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYC 114 (286)
Q Consensus 80 ~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~C 114 (286)
+.|..||+.|..++... .|++.|+++++|.|++-
T Consensus 2 YqC~~CG~~F~~~s~l~-~H~r~~hg~~~~~~~~~ 35 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVI-EHLLSVHKQNKLTLEYF 35 (44)
T ss_pred CccchhhHHHhhHHHHH-HHHHHhcCCCccceeEE
Confidence 67999999999998655 89999999999999864
No 28
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=94.15 E-value=0.024 Score=40.69 Aligned_cols=33 Identities=15% Similarity=0.311 Sum_probs=24.0
Q ss_pred CCCceeecCCCCcccCCCccchhhhhhccCCcc
Q 046965 104 SEARVFSCNYCKREFSTSQALGGHQNAHKQERA 136 (286)
Q Consensus 104 tgeKpf~C~~CgK~F~sssaL~~Hqr~HtgEKp 136 (286)
..+.|-.|++|+..+.+..+|.+|+.++.+.||
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 357899999999999999999999988877765
No 29
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=93.94 E-value=0.031 Score=53.79 Aligned_cols=41 Identities=12% Similarity=0.379 Sum_probs=32.1
Q ss_pred CCceeecCC--CCcccCCCccchhhhhh-cc------------------CCccccccccCcc
Q 046965 105 EARVFSCNY--CKREFSTSQALGGHQNA-HK------------------QERAVAKRRQGVD 145 (286)
Q Consensus 105 geKpf~C~~--CgK~F~sssaL~~Hqr~-Ht------------------gEKpy~C~~Cgk~ 145 (286)
++|||+|++ |.|++.....|+-|+.- |. ..|||.|..|+|.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KR 407 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKR 407 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchh
Confidence 459999997 99999999999999753 31 2377777777776
No 30
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=93.90 E-value=0.014 Score=57.77 Aligned_cols=23 Identities=39% Similarity=0.767 Sum_probs=12.2
Q ss_pred eecCCCCcccCCCccchhhhhhc
Q 046965 109 FSCNYCKREFSTSQALGGHQNAH 131 (286)
Q Consensus 109 f~C~~CgK~F~sssaL~~Hqr~H 131 (286)
|.|.+|+|+|.....|+.|+.+|
T Consensus 357 ~~C~~C~KkFrRqAYLrKHqlth 379 (500)
T KOG3993|consen 357 FSCHTCGKKFRRQAYLRKHQLTH 379 (500)
T ss_pred eecHHhhhhhHHHHHHHHhHHhh
Confidence 55555555555555555555444
No 31
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.14 E-value=0.025 Score=33.52 Aligned_cols=23 Identities=30% Similarity=0.788 Sum_probs=21.0
Q ss_pred eecCCCCcccCCCccchhhhhhc
Q 046965 109 FSCNYCKREFSTSQALGGHQNAH 131 (286)
Q Consensus 109 f~C~~CgK~F~sssaL~~Hqr~H 131 (286)
|.|..|++.|.+...|..|++.+
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 78999999999999999998764
No 32
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=92.23 E-value=0.047 Score=54.19 Aligned_cols=26 Identities=31% Similarity=0.623 Sum_probs=23.7
Q ss_pred ceeecCCCCcccCCCccchhhhhhcc
Q 046965 107 RVFSCNYCKREFSTSQALGGHQNAHK 132 (286)
Q Consensus 107 Kpf~C~~CgK~F~sssaL~~Hqr~Ht 132 (286)
.-|+|++|+|.|....+|..|.|-|+
T Consensus 294 vEYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 294 VEYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred eeecCCcccccccCchhhhhhhcccC
Confidence 35999999999999999999999986
No 33
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.95 E-value=0.14 Score=47.62 Aligned_cols=62 Identities=19% Similarity=0.276 Sum_probs=43.1
Q ss_pred CccccCCccchhhccCCCCCccc--ccCCC--ceeecC--CCCcccCCCccchhhhhhccCCccccccc
Q 046965 79 RMSMMNNNHCHEENNGHPTSSEK--KSSEA--RVFSCN--YCKREFSTSQALGGHQNAHKQERAVAKRR 141 (286)
Q Consensus 79 ~~tc~~~g~S~~~~~~~~~~H~r--tHtge--Kpf~C~--~CgK~F~sssaL~~Hqr~HtgEKpy~C~~ 141 (286)
.+.|..|...+.....+. .|.+ .|+++ +++.|+ .|++.|.....+..|...|+..++++|..
T Consensus 289 ~~~~~~~~~~~s~~~~l~-~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (467)
T COG5048 289 PIKSKQCNISFSRSSPLT-RHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356 (467)
T ss_pred CCCCccccCCcccccccc-ccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccccc
Confidence 456666766666665443 6667 67777 777777 67777777777777777777776666653
No 34
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=91.37 E-value=0.065 Score=32.66 Aligned_cols=22 Identities=32% Similarity=0.739 Sum_probs=20.3
Q ss_pred eecCCCCcccCCCccchhhhhh
Q 046965 109 FSCNYCKREFSTSQALGGHQNA 130 (286)
Q Consensus 109 f~C~~CgK~F~sssaL~~Hqr~ 130 (286)
|.|..|++.|.+...|..|++.
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 7899999999999999999875
No 35
>PRK04860 hypothetical protein; Provisional
Probab=91.15 E-value=0.049 Score=47.51 Aligned_cols=39 Identities=8% Similarity=0.106 Sum_probs=30.6
Q ss_pred cCccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCC
Q 046965 78 NRMSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTS 121 (286)
Q Consensus 78 n~~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~ss 121 (286)
-.+.|. |+.. .....+|.++|+++++|.|..|++.|...
T Consensus 118 ~~Y~C~-C~~~----~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQEH----QLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCCe----eCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 457887 8872 23345888999999999999999988654
No 36
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=90.50 E-value=0.11 Score=39.59 Aligned_cols=24 Identities=33% Similarity=0.840 Sum_probs=21.0
Q ss_pred eeecCCCCcccCCCccchhhhhhc
Q 046965 108 VFSCNYCKREFSTSQALGGHQNAH 131 (286)
Q Consensus 108 pf~C~~CgK~F~sssaL~~Hqr~H 131 (286)
.+.|..|++.|.+..+|..|++.+
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 37
>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=89.75 E-value=0.07 Score=37.88 Aligned_cols=37 Identities=27% Similarity=0.556 Sum_probs=24.9
Q ss_pred eeecCCCCcccCCCccchhhhh-hccCC-ccccccccCcc
Q 046965 108 VFSCNYCKREFSTSQALGGHQN-AHKQE-RAVAKRRQGVD 145 (286)
Q Consensus 108 pf~C~~CgK~F~sssaL~~Hqr-~HtgE-Kpy~C~~Cgk~ 145 (286)
.|.|++|++.| +...|..|.. .|..+ +.+.|..|...
T Consensus 2 ~f~CP~C~~~~-~~~~L~~H~~~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 2 SFTCPYCGKGF-SESSLVEHCEDEHRSESKNVVCPICSSR 40 (54)
T ss_pred CcCCCCCCCcc-CHHHHHHHHHhHCcCCCCCccCCCchhh
Confidence 37788888844 4567888854 46554 46788888765
No 38
>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=89.34 E-value=0.2 Score=35.47 Aligned_cols=51 Identities=12% Similarity=0.214 Sum_probs=35.1
Q ss_pred cCccccCCccchhhccCCCCCcc-cccCCC-ceeecCCCCcccCCCccchhhhhhcc
Q 046965 78 NRMSMMNNNHCHEENNGHPTSSE-KKSSEA-RVFSCNYCKREFSTSQALGGHQNAHK 132 (286)
Q Consensus 78 n~~tc~~~g~S~~~~~~~~~~H~-rtHtge-Kpf~C~~CgK~F~sssaL~~Hqr~Ht 132 (286)
+-|+|.-|++.+.... +..|. ..|..+ +.+.|++|...+. ..|..|++.+.
T Consensus 1 ~~f~CP~C~~~~~~~~--L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 1 DSFTCPYCGKGFSESS--LVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CCcCCCCCCCccCHHH--HHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 3578999999655433 33553 345543 5799999998765 38899987653
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=87.76 E-value=0.19 Score=29.56 Aligned_cols=23 Identities=26% Similarity=0.533 Sum_probs=17.7
Q ss_pred eecCCCCcccCCCccchhhhhhcc
Q 046965 109 FSCNYCKREFSTSQALGGHQNAHK 132 (286)
Q Consensus 109 f~C~~CgK~F~sssaL~~Hqr~Ht 132 (286)
|+|+.|..... ...|..|++.|.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 78999998887 889999988753
No 40
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=84.04 E-value=0.28 Score=45.73 Aligned_cols=47 Identities=19% Similarity=0.333 Sum_probs=38.8
Q ss_pred cccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCCccchhh-hhhcc
Q 046965 81 SMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTSQALGGH-QNAHK 132 (286)
Q Consensus 81 tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~sssaL~~H-qr~Ht 132 (286)
.|+-|.+-|....++.+ |...|-|+|.+|.|++.+--.|..| |.+|+
T Consensus 12 wcwycnrefddekiliq-----hqkakhfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQ-----HQKAKHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeeecccccchhhhhhh-----hhhhccceeeeehhhhccCCCceeehhhhhh
Confidence 79999999999888763 4456779999999998888888888 56775
No 41
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=83.85 E-value=0.41 Score=29.04 Aligned_cols=21 Identities=29% Similarity=0.710 Sum_probs=16.9
Q ss_pred eecCCCCcccCCCccchhhhhh
Q 046965 109 FSCNYCKREFSTSQALGGHQNA 130 (286)
Q Consensus 109 f~C~~CgK~F~sssaL~~Hqr~ 130 (286)
..|+.|++.| ....|..|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4799999999 56788888764
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=83.07 E-value=0.48 Score=29.94 Aligned_cols=23 Identities=22% Similarity=0.572 Sum_probs=20.3
Q ss_pred eeecCCCCcccCCCccchhhhhh
Q 046965 108 VFSCNYCKREFSTSQALGGHQNA 130 (286)
Q Consensus 108 pf~C~~CgK~F~sssaL~~Hqr~ 130 (286)
+|.|..|++.|....++..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999989764
No 43
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=80.91 E-value=0.57 Score=43.77 Aligned_cols=34 Identities=29% Similarity=0.439 Sum_probs=29.5
Q ss_pred ceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 107 RVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 107 Kpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
|| -|-+|.+.|.....|.+||+. |.|+|..|.|.
T Consensus 10 kp-wcwycnrefddekiliqhqka----khfkchichkk 43 (341)
T KOG2893|consen 10 KP-WCWYCNREFDDEKILIQHQKA----KHFKCHICHKK 43 (341)
T ss_pred Cc-eeeecccccchhhhhhhhhhh----ccceeeeehhh
Confidence 44 599999999999999999875 56999999886
No 44
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=72.47 E-value=6.6 Score=36.44 Aligned_cols=39 Identities=23% Similarity=0.257 Sum_probs=36.4
Q ss_pred ceeecCCCCcccCCCccchhhhh--hccCC--cccccc--ccCcc
Q 046965 107 RVFSCNYCKREFSTSQALGGHQN--AHKQE--RAVAKR--RQGVD 145 (286)
Q Consensus 107 Kpf~C~~CgK~F~sssaL~~Hqr--~HtgE--Kpy~C~--~Cgk~ 145 (286)
.++.|..|...|.....|..|.+ .|+++ +++.|. .|++.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~ 332 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKL 332 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCcc
Confidence 57899999999999999999999 89999 999999 78887
No 45
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=64.14 E-value=2.9 Score=40.60 Aligned_cols=52 Identities=13% Similarity=0.243 Sum_probs=36.2
Q ss_pred ccCcccc--CCccchhhccCCCCCccc-------cc------------CCCceeecCCCCcccCCCccchhhhh
Q 046965 77 FNRMSMM--NNNHCHEENNGHPTSSEK-------KS------------SEARVFSCNYCKREFSTSQALGGHQN 129 (286)
Q Consensus 77 ~n~~tc~--~~g~S~~~~~~~~~~H~r-------tH------------tgeKpf~C~~CgK~F~sssaL~~Hqr 129 (286)
-..|+|. -|.|.+.+.-.++ -|+. +| ...|||.|.+|+|++..-..|+-|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLK-YH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLK-YHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchh-hhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 3677885 6778777554433 3321 11 23599999999999999999998853
No 46
>PHA00626 hypothetical protein
Probab=62.52 E-value=6.2 Score=28.95 Aligned_cols=34 Identities=12% Similarity=0.071 Sum_probs=18.5
Q ss_pred cccCCccchhhccCCCCCcccccCCCceeecCCCCcccCC
Q 046965 81 SMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFST 120 (286)
Q Consensus 81 tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~s 120 (286)
.|.+||+..-.+...- +.+ ...|+|+.|+..|+.
T Consensus 2 ~CP~CGS~~Ivrcg~c----r~~--snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAKEKTM----RGW--SDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeeeecee----ccc--CcceEcCCCCCeech
Confidence 4777876432222111 111 246888888887764
No 47
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=62.45 E-value=4.3 Score=36.73 Aligned_cols=25 Identities=24% Similarity=0.595 Sum_probs=18.8
Q ss_pred CceeecCCCCcccCCCccchhhhhh
Q 046965 106 ARVFSCNYCKREFSTSQALGGHQNA 130 (286)
Q Consensus 106 eKpf~C~~CgK~F~sssaL~~Hqr~ 130 (286)
+|.+.|++|++.|....-+.+..++
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 3567899999999887766666543
No 48
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=61.69 E-value=2.4 Score=39.78 Aligned_cols=51 Identities=12% Similarity=0.206 Sum_probs=34.3
Q ss_pred CccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCCccchhhhhhccC
Q 046965 79 RMSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTSQALGGHQNAHKQ 133 (286)
Q Consensus 79 ~~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~sssaL~~Hqr~Htg 133 (286)
.|+|..||.+-..... -.|+-.-++ .-|.|-.|++.|.. -....|...-+.
T Consensus 3 ~FtCnvCgEsvKKp~v--ekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCITE 53 (276)
T KOG2186|consen 3 FFTCNVCGESVKKPQV--EKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCITE 53 (276)
T ss_pred EEehhhhhhhccccch--HHHHHhccC-CeeEEeeccccccc-chhhhhhhhcch
Confidence 3788888877654433 246655555 56888888888887 667777655443
No 49
>PF14353 CpXC: CpXC protein
Probab=60.72 E-value=3.9 Score=33.57 Aligned_cols=20 Identities=30% Similarity=0.572 Sum_probs=12.2
Q ss_pred eeecCCCCcccCCCccchhh
Q 046965 108 VFSCNYCKREFSTSQALGGH 127 (286)
Q Consensus 108 pf~C~~CgK~F~sssaL~~H 127 (286)
.|.|+.||..|.-...+.-|
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred EEECCCCCCceecCCCEEEE
Confidence 46677777776655554444
No 50
>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=59.31 E-value=5 Score=27.79 Aligned_cols=30 Identities=17% Similarity=0.375 Sum_probs=16.7
Q ss_pred eeecCCCCcccCCCccchhhhhhccCCccccccccCc
Q 046965 108 VFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGV 144 (286)
Q Consensus 108 pf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk 144 (286)
-|.|..|+..|...... +. +..-.|..||.
T Consensus 5 ey~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKM------SD-DPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEec------CC-CCCCCCCCCCC
Confidence 36777777777533221 11 33456777775
No 51
>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=58.26 E-value=7.8 Score=24.79 Aligned_cols=25 Identities=12% Similarity=0.282 Sum_probs=16.8
Q ss_pred eecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 109 FSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 109 f~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
|.|..||..+.... .+..|..||..
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCCc
Confidence 67888886654322 57788888764
No 52
>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=57.40 E-value=5.5 Score=25.93 Aligned_cols=11 Identities=27% Similarity=0.987 Sum_probs=6.4
Q ss_pred eecCCCCcccC
Q 046965 109 FSCNYCKREFS 119 (286)
Q Consensus 109 f~C~~CgK~F~ 119 (286)
|+|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 55666666554
No 53
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=56.95 E-value=3.6 Score=30.26 Aligned_cols=30 Identities=17% Similarity=0.341 Sum_probs=26.2
Q ss_pred cccCCCceeecCCCCcccCCCccchhhhhh
Q 046965 101 KKSSEARVFSCNYCKREFSTSQALGGHQNA 130 (286)
Q Consensus 101 rtHtgeKpf~C~~CgK~F~sssaL~~Hqr~ 130 (286)
++-.||..+.|+-|+..|.......+|.+.
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 456688899999999999999999999863
No 54
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=56.12 E-value=8.8 Score=41.09 Aligned_cols=11 Identities=9% Similarity=0.003 Sum_probs=5.8
Q ss_pred ccccccccCcc
Q 046965 135 RAVAKRRQGVD 145 (286)
Q Consensus 135 Kpy~C~~Cgk~ 145 (286)
+...|..||..
T Consensus 461 ~~L~CH~Cg~~ 471 (730)
T COG1198 461 GQLRCHYCGYQ 471 (730)
T ss_pred CeeEeCCCCCC
Confidence 44555555543
No 55
>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=54.75 E-value=7.8 Score=31.73 Aligned_cols=10 Identities=30% Similarity=0.876 Sum_probs=5.2
Q ss_pred ecCCCCcccC
Q 046965 110 SCNYCKREFS 119 (286)
Q Consensus 110 ~C~~CgK~F~ 119 (286)
.|+.||++|.
T Consensus 11 ~Cp~CG~kFY 20 (108)
T PF09538_consen 11 TCPSCGAKFY 20 (108)
T ss_pred cCCCCcchhc
Confidence 4555555554
No 56
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=53.80 E-value=9.5 Score=26.28 Aligned_cols=26 Identities=27% Similarity=0.474 Sum_probs=15.2
Q ss_pred eecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 109 FSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 109 f~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
|.|..||..|... ...+..|++||-.
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------CCCceECCCCCce
Confidence 6677777666533 1234667777654
No 57
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=52.46 E-value=7.7 Score=32.95 Aligned_cols=38 Identities=13% Similarity=0.296 Sum_probs=25.7
Q ss_pred CCCceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 104 SEARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 104 tgeKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
+...-|.|+.|++.|....++.. .+. ...|.|..||..
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~ 132 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEE 132 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCE
Confidence 34567999999999886544432 011 344999999876
No 58
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=52.24 E-value=8.7 Score=41.08 Aligned_cols=27 Identities=26% Similarity=0.635 Sum_probs=24.2
Q ss_pred ceeecCCCCcccCCCccchhhhhhccC
Q 046965 107 RVFSCNYCKREFSTSQALGGHQNAHKQ 133 (286)
Q Consensus 107 Kpf~C~~CgK~F~sssaL~~Hqr~Htg 133 (286)
--|-|.+|+|.|..-.++..||+.|.-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 359999999999999999999999964
No 59
>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=51.89 E-value=6.6 Score=33.93 Aligned_cols=34 Identities=18% Similarity=0.233 Sum_probs=26.7
Q ss_pred cCCCceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 103 SSEARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 103 HtgeKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
.+...-|.|+.|+..|+...++. .-|.|..||-.
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 34556799999999998888774 25999999875
No 60
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.79 E-value=12 Score=38.13 Aligned_cols=35 Identities=17% Similarity=0.214 Sum_probs=18.9
Q ss_pred ecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 110 SCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 110 ~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
.|..||....... -...+..|.......|..||..
T Consensus 215 ~C~~Cg~~~~C~~-C~~~l~~h~~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 215 LCRSCGYILCCPN-CDVSLTYHKKEGKLRCHYCGYQ 249 (505)
T ss_pred EhhhCcCccCCCC-CCCceEEecCCCeEEcCCCcCc
Confidence 4666665554321 1223444555566777777765
No 61
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=50.40 E-value=7 Score=34.55 Aligned_cols=32 Identities=19% Similarity=0.321 Sum_probs=25.1
Q ss_pred CCceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 105 EARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 105 geKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
...-|.|+.|++.|+...++. .-|.|..||-.
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~ 145 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEM 145 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCC
Confidence 446789999999998877753 36999999875
No 62
>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=48.19 E-value=8.9 Score=24.83 Aligned_cols=11 Identities=18% Similarity=0.628 Sum_probs=5.9
Q ss_pred eeecCCCCccc
Q 046965 108 VFSCNYCKREF 118 (286)
Q Consensus 108 pf~C~~CgK~F 118 (286)
.+.|+.|+..|
T Consensus 25 ~v~C~~C~~~~ 35 (38)
T TIGR02098 25 KVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEE
Confidence 34566665544
No 63
>PRK14873 primosome assembly protein PriA; Provisional
Probab=48.04 E-value=13 Score=39.34 Aligned_cols=48 Identities=15% Similarity=0.154 Sum_probs=27.3
Q ss_pred ccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 80 MSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 80 ~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
..|.+||..+.+.... ..+..|.......|.+||.. ..|..|..||..
T Consensus 384 l~C~~Cg~~~~C~~C~--~~L~~h~~~~~l~Ch~CG~~----------------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 384 LACARCRTPARCRHCT--GPLGLPSAGGTPRCRWCGRA----------------APDWRCPRCGSD 431 (665)
T ss_pred eEhhhCcCeeECCCCC--CceeEecCCCeeECCCCcCC----------------CcCccCCCCcCC
Confidence 3677777666555432 12344555556677777642 125677777764
No 64
>PRK14873 primosome assembly protein PriA; Provisional
Probab=48.01 E-value=12 Score=39.72 Aligned_cols=35 Identities=14% Similarity=0.192 Sum_probs=23.1
Q ss_pred ecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 110 SCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 110 ~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
.|..|+..+.... -...+..|...+...|..||..
T Consensus 385 ~C~~Cg~~~~C~~-C~~~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 385 ACARCRTPARCRH-CTGPLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred EhhhCcCeeECCC-CCCceeEecCCCeeECCCCcCC
Confidence 6888887765432 1223344566678999999975
No 65
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=47.85 E-value=9.3 Score=43.23 Aligned_cols=68 Identities=15% Similarity=0.203 Sum_probs=48.4
Q ss_pred ccCccccCCccchhhccCCCCCcc-cccCCCceeecCCCCcccCCCccchhhhhh-cc----------------------
Q 046965 77 FNRMSMMNNNHCHEENNGHPTSSE-KKSSEARVFSCNYCKREFSTSQALGGHQNA-HK---------------------- 132 (286)
Q Consensus 77 ~n~~tc~~~g~S~~~~~~~~~~H~-rtHtgeKpf~C~~CgK~F~sssaL~~Hqr~-Ht---------------------- 132 (286)
-++-.|..|+.-+.++.... .|+ ..|+-.|.|.|+.|+..|.....|..|||. |.
T Consensus 434 ~~l~e~~~~e~~~~s~r~~~-~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~ 512 (1406)
T KOG1146|consen 434 GTLVELTKAEPLLESKRSLE-GQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVY 512 (1406)
T ss_pred Cccccccchhhhhhhhcccc-cceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccc
Confidence 34445666665555555443 333 346777999999999999999999999997 21
Q ss_pred --CCccccccccCcc
Q 046965 133 --QERAVAKRRQGVD 145 (286)
Q Consensus 133 --gEKpy~C~~Cgk~ 145 (286)
+.++|.|+.|..+
T Consensus 513 ~~~~~p~~C~~C~~s 527 (1406)
T KOG1146|consen 513 RCPGKPYPCRACNYS 527 (1406)
T ss_pred cCCCCcccceeeeee
Confidence 2357899998765
No 66
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=46.21 E-value=10 Score=40.36 Aligned_cols=61 Identities=15% Similarity=0.318 Sum_probs=41.3
Q ss_pred ccCccccCCccchhhccCCCCCcccccCCCceee-cCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 77 FNRMSMMNNNHCHEENNGHPTSSEKKSSEARVFS-CNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 77 ~n~~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~-C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
.-...|++||--|+--.... =.|-+|..+.|. |+.|.+.+....+..-| . .|..|..||=.
T Consensus 121 YPF~~CT~CGPRfTIi~alP--YDR~nTsM~~F~lC~~C~~EY~dP~nRRfH----A--Qp~aCp~CGP~ 182 (750)
T COG0068 121 YPFINCTNCGPRFTIIEALP--YDRENTSMADFPLCPFCDKEYKDPLNRRFH----A--QPIACPKCGPH 182 (750)
T ss_pred ccccccCCCCcceeeeccCC--CCcccCccccCcCCHHHHHHhcCccccccc----c--ccccCcccCCC
Confidence 34458999998877433221 125566667675 99999998887664444 3 47899999863
No 67
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=45.14 E-value=11 Score=24.74 Aligned_cols=32 Identities=19% Similarity=0.293 Sum_probs=16.2
Q ss_pred cccCCccchhhccCCCCCcccccCCCceeecCCCCccc
Q 046965 81 SMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREF 118 (286)
Q Consensus 81 tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F 118 (286)
+|..|+..|.-... ++-.+.+..+|..|+..|
T Consensus 4 ~CP~C~~~f~v~~~------~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD------KLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHH------HcccCCcEEECCCCCcEe
Confidence 56666655553322 112233456666666655
No 68
>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=43.95 E-value=12 Score=25.26 Aligned_cols=29 Identities=24% Similarity=0.555 Sum_probs=15.6
Q ss_pred eecCCCCcccCCCccchhhhhhccCCccccccccCc
Q 046965 109 FSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGV 144 (286)
Q Consensus 109 f~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk 144 (286)
|.|..||..|...... .. ..+-.|..||.
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 6677777666443222 12 34456666665
No 69
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=42.77 E-value=14 Score=32.13 Aligned_cols=12 Identities=33% Similarity=0.772 Sum_probs=6.6
Q ss_pred eecCCCCcccCC
Q 046965 109 FSCNYCKREFST 120 (286)
Q Consensus 109 f~C~~CgK~F~s 120 (286)
++|+.||+.|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 555555555544
No 70
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=42.45 E-value=16 Score=24.89 Aligned_cols=12 Identities=33% Similarity=0.880 Sum_probs=5.9
Q ss_pred eeecCCCCcccC
Q 046965 108 VFSCNYCKREFS 119 (286)
Q Consensus 108 pf~C~~CgK~F~ 119 (286)
.|.|..||..|.
T Consensus 3 ~y~C~~CG~~~~ 14 (46)
T PRK00398 3 EYKCARCGREVE 14 (46)
T ss_pred EEECCCCCCEEE
Confidence 355555555443
No 71
>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=42.30 E-value=13 Score=24.72 Aligned_cols=24 Identities=25% Similarity=0.556 Sum_probs=14.6
Q ss_pred CCceeecCCCCcccCCC----ccchhhh
Q 046965 105 EARVFSCNYCKREFSTS----QALGGHQ 128 (286)
Q Consensus 105 geKpf~C~~CgK~F~ss----saL~~Hq 128 (286)
+.....|.+|++.+... ..|..|+
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 44567899999988764 5677776
No 72
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=41.56 E-value=16 Score=23.91 Aligned_cols=11 Identities=27% Similarity=0.745 Sum_probs=6.3
Q ss_pred eeecCCCCccc
Q 046965 108 VFSCNYCKREF 118 (286)
Q Consensus 108 pf~C~~CgK~F 118 (286)
..+|..|+..|
T Consensus 25 ~v~C~~C~~~f 35 (36)
T PF13717_consen 25 KVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEe
Confidence 45666666554
No 73
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=40.43 E-value=15 Score=26.09 Aligned_cols=29 Identities=21% Similarity=0.431 Sum_probs=16.5
Q ss_pred ceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 107 RVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 107 Kpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
..|.|..|++.|... .......|..||..
T Consensus 5 ~~Y~C~~Cg~~~~~~----------~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVELD----------QETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeehh----------hccCceeCCCCCcE
Confidence 457777777776211 12234667777654
No 74
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.68 E-value=23 Score=36.03 Aligned_cols=50 Identities=12% Similarity=0.116 Sum_probs=32.1
Q ss_pred CccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 79 RMSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 79 ~~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
...|..||....+.... ..+..|.......|.+||.. ..-|..|..|+..
T Consensus 213 ~~~C~~Cg~~~~C~~C~--~~l~~h~~~~~l~Ch~Cg~~---------------~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 213 NLLCRSCGYILCCPNCD--VSLTYHKKEGKLRCHYCGYQ---------------EPIPKTCPQCGSE 262 (505)
T ss_pred eeEhhhCcCccCCCCCC--CceEEecCCCeEEcCCCcCc---------------CCCCCCCCCCCCC
Confidence 44677787666655543 23455666667788888753 2346788888764
No 75
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=39.51 E-value=21 Score=26.45 Aligned_cols=34 Identities=15% Similarity=0.191 Sum_probs=20.3
Q ss_pred ceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 107 RVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 107 Kpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
..|.|+.||..-.. +-++.-+...+|.|..||..
T Consensus 26 v~F~CPnCGe~~I~-----Rc~~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 26 VKFPCPNCGEVEIY-----RCAKCRKLGNPYRCPKCGFE 59 (61)
T ss_pred eEeeCCCCCceeee-----hhhhHHHcCCceECCCcCcc
Confidence 36889999864322 22233334467888888753
No 76
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=38.04 E-value=18 Score=24.96 Aligned_cols=25 Identities=32% Similarity=0.640 Sum_probs=18.0
Q ss_pred eeecCCCCcccCCC-----ccchhhhh-hcc
Q 046965 108 VFSCNYCKREFSTS-----QALGGHQN-AHK 132 (286)
Q Consensus 108 pf~C~~CgK~F~ss-----saL~~Hqr-~Ht 132 (286)
.-.|.+|++.+... +.|.+|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 45799999988765 47777776 453
No 77
>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=37.72 E-value=26 Score=22.69 Aligned_cols=26 Identities=19% Similarity=0.247 Sum_probs=16.1
Q ss_pred eeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 108 VFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 108 pf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
.|.|..||..+... +.|..|..||..
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 46788887654322 145678888764
No 78
>PRK04023 DNA polymerase II large subunit; Validated
Probab=37.43 E-value=33 Score=38.19 Aligned_cols=17 Identities=29% Similarity=0.552 Sum_probs=8.5
Q ss_pred CcccccCCCCCCCCCCC
Q 046965 258 IGVDFLQRGDPFKSDHQ 274 (286)
Q Consensus 258 ~~~~~~~~~~~~~~~~~ 274 (286)
.|..+--.|.++..+.|
T Consensus 765 LGY~~Di~G~pL~~~dQ 781 (1121)
T PRK04023 765 LGYTHDIYGNPLESEDQ 781 (1121)
T ss_pred cCCccccCCCCCCCccc
Confidence 44444444555655544
No 79
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=35.84 E-value=21 Score=24.30 Aligned_cols=8 Identities=0% Similarity=-0.263 Sum_probs=3.9
Q ss_pred cccccccC
Q 046965 136 AVAKRRQG 143 (286)
Q Consensus 136 py~C~~Cg 143 (286)
.|+|..|+
T Consensus 37 ~~~C~~C~ 44 (46)
T PF12760_consen 37 RYRCKACR 44 (46)
T ss_pred eEECCCCC
Confidence 44555544
No 80
>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=35.72 E-value=24 Score=29.94 Aligned_cols=25 Identities=16% Similarity=0.252 Sum_probs=13.7
Q ss_pred ecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 110 SCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 110 ~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
.|+.||++|..- + ..|-.|..||..
T Consensus 11 ~Cp~cg~kFYDL---n--------k~p~vcP~cg~~ 35 (129)
T TIGR02300 11 ICPNTGSKFYDL---N--------RRPAVSPYTGEQ 35 (129)
T ss_pred cCCCcCcccccc---C--------CCCccCCCcCCc
Confidence 566666666532 1 235566666665
No 81
>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=34.66 E-value=17 Score=30.88 Aligned_cols=29 Identities=24% Similarity=0.411 Sum_probs=17.7
Q ss_pred ceeecCCCCcccCCCccchhhhhhccCCcccc
Q 046965 107 RVFSCNYCKREFSTSQALGGHQNAHKQERAVA 138 (286)
Q Consensus 107 Kpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~ 138 (286)
....|-+|||.|.. |++|.+.|.|-.|-+
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp~e 99 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTPEE 99 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-HHH
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCHHH
Confidence 34689999999864 699999997766533
No 82
>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=34.49 E-value=36 Score=21.95 Aligned_cols=11 Identities=27% Similarity=0.794 Sum_probs=5.7
Q ss_pred eecCCCCcccC
Q 046965 109 FSCNYCKREFS 119 (286)
Q Consensus 109 f~C~~CgK~F~ 119 (286)
|.|..|+..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 45666665544
No 83
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=33.89 E-value=14 Score=27.82 Aligned_cols=21 Identities=29% Similarity=0.646 Sum_probs=0.0
Q ss_pred ecCCCCcccCCCccchhhhhh
Q 046965 110 SCNYCKREFSTSQALGGHQNA 130 (286)
Q Consensus 110 ~C~~CgK~F~sssaL~~Hqr~ 130 (286)
+|..|+..|.....|..|+..
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~ 21 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKK 21 (100)
T ss_dssp ---------------------
T ss_pred Ccccccccccccccccccccc
Confidence 488899999999999999854
No 84
>PRK05580 primosome assembly protein PriA; Validated
Probab=32.41 E-value=33 Score=36.31 Aligned_cols=36 Identities=14% Similarity=0.251 Sum_probs=17.5
Q ss_pred eecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 109 FSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 109 f~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
..|..|+..+.... -...+..|...+...|..||..
T Consensus 382 ~~C~~Cg~~~~C~~-C~~~l~~h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 382 LLCRDCGWVAECPH-CDASLTLHRFQRRLRCHHCGYQ 417 (679)
T ss_pred eEhhhCcCccCCCC-CCCceeEECCCCeEECCCCcCC
Confidence 34666665553321 1112233444556677777765
No 85
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=31.88 E-value=26 Score=30.21 Aligned_cols=9 Identities=11% Similarity=0.176 Sum_probs=5.7
Q ss_pred ccccccCcc
Q 046965 137 VAKRRQGVD 145 (286)
Q Consensus 137 y~C~~Cgk~ 145 (286)
|.|..||..
T Consensus 113 l~C~~Cg~~ 121 (146)
T PF07295_consen 113 LVCENCGHE 121 (146)
T ss_pred EecccCCCE
Confidence 666666654
No 86
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=31.42 E-value=26 Score=35.34 Aligned_cols=40 Identities=13% Similarity=0.341 Sum_probs=27.6
Q ss_pred cCCCceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 103 SSEARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 103 HtgeKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
-+...-|.|+.|.++|..--++. .+-...-.|.|..|+-.
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGGE 162 (436)
T ss_pred ccccccccCCccccchhhhHHHH---hhcccCceEEEecCCCc
Confidence 45566799999999997655543 33333456999999854
No 87
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=31.26 E-value=12 Score=37.02 Aligned_cols=54 Identities=17% Similarity=0.228 Sum_probs=38.5
Q ss_pred CccCccccCCccchhhccCCCCCcccccCC-----------------------CceeecCCCC---cccCCCccchhhhh
Q 046965 76 LFNRMSMMNNNHCHEENNGHPTSSEKKSSE-----------------------ARVFSCNYCK---REFSTSQALGGHQN 129 (286)
Q Consensus 76 e~n~~tc~~~g~S~~~~~~~~~~H~rtHtg-----------------------eKpf~C~~Cg---K~F~sssaL~~Hqr 129 (286)
++..-.|.-|++.+...... ..||..++| ..-|.|-+|. +.|.+-.+...||+
T Consensus 163 e~~Pt~CLfC~~~~k~~e~~-~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 163 ELIPTDCLFCDKKSKSLEEN-LKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred ccCCcceeecCCCcccHHHH-HHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 44445788888776654432 267777665 2457899998 99999999999986
Q ss_pred h
Q 046965 130 A 130 (286)
Q Consensus 130 ~ 130 (286)
.
T Consensus 242 ~ 242 (390)
T KOG2785|consen 242 D 242 (390)
T ss_pred h
Confidence 4
No 88
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=31.04 E-value=25 Score=29.94 Aligned_cols=13 Identities=31% Similarity=0.733 Sum_probs=6.9
Q ss_pred eeecCCCCcccCC
Q 046965 108 VFSCNYCKREFST 120 (286)
Q Consensus 108 pf~C~~CgK~F~s 120 (286)
|++|..||+.|..
T Consensus 1 PH~Ct~Cg~~f~d 13 (131)
T PF09845_consen 1 PHQCTKCGRVFED 13 (131)
T ss_pred CcccCcCCCCcCC
Confidence 3455555555553
No 89
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=28.54 E-value=29 Score=26.46 Aligned_cols=14 Identities=14% Similarity=0.064 Sum_probs=8.6
Q ss_pred cCCcccccc--ccCcc
Q 046965 132 KQERAVAKR--RQGVD 145 (286)
Q Consensus 132 tgEKpy~C~--~Cgk~ 145 (286)
..++-+.|+ +||..
T Consensus 23 ~~~~Y~qC~N~eCg~t 38 (72)
T PRK09678 23 TKERYHQCQNVNCSAT 38 (72)
T ss_pred hheeeeecCCCCCCCE
Confidence 445556676 67666
No 90
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=28.52 E-value=38 Score=29.90 Aligned_cols=24 Identities=25% Similarity=0.416 Sum_probs=17.2
Q ss_pred eeecCCCCcccCCCccchhhhhhccCCccccccccCc
Q 046965 108 VFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGV 144 (286)
Q Consensus 108 pf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk 144 (286)
.|.|.+||.. |.++-|-.|..||-
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCCC
Confidence 6888888653 44567788888874
No 91
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=28.41 E-value=36 Score=36.56 Aligned_cols=49 Identities=12% Similarity=0.168 Sum_probs=29.5
Q ss_pred ccccCCccchhhccCCCCCcccccCCCceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 80 MSMMNNNHCHEENNGHPTSSEKKSSEARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 80 ~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
.-|.+||..+.+..... -+..|...+...|.+||. ....|..|..||..
T Consensus 436 l~C~~Cg~v~~Cp~Cd~--~lt~H~~~~~L~CH~Cg~---------------~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 436 LLCRDCGYIAECPNCDS--PLTLHKATGQLRCHYCGY---------------QEPIPQSCPECGSE 484 (730)
T ss_pred eecccCCCcccCCCCCc--ceEEecCCCeeEeCCCCC---------------CCCCCCCCCCCCCC
Confidence 46777776655544321 123344445566777764 34568999999976
No 92
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=28.14 E-value=19 Score=35.20 Aligned_cols=39 Identities=21% Similarity=0.348 Sum_probs=18.4
Q ss_pred ceeecCCCCcccCCCccc---hhhh-hhccC-CccccccccCcc
Q 046965 107 RVFSCNYCKREFSTSQAL---GGHQ-NAHKQ-ERAVAKRRQGVD 145 (286)
Q Consensus 107 Kpf~C~~CgK~F~sssaL---~~Hq-r~Htg-EKpy~C~~Cgk~ 145 (286)
+.|.|..|.+........ ..|. ..|.. .|-|+|..|++.
T Consensus 251 kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~R 294 (344)
T PF09332_consen 251 KAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNR 294 (344)
T ss_dssp EEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-E
T ss_pred EEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCe
Confidence 568899998765543332 2342 23444 355899999987
No 93
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=28.00 E-value=30 Score=37.01 Aligned_cols=62 Identities=18% Similarity=0.293 Sum_probs=38.8
Q ss_pred CccCccccCCccchhhccCCCCCcccccCCCceee-cCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 76 LFNRMSMMNNNHCHEENNGHPTSSEKKSSEARVFS-CNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 76 e~n~~tc~~~g~S~~~~~~~~~~H~rtHtgeKpf~-C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
.+-..+|++||--|+-...+. =.|.+|..+.|. |+.|.+.+.......- |. .+-.|..||=.
T Consensus 87 ~YpF~nCt~CGPr~~i~~~lp--ydr~~t~m~~f~~C~~C~~ey~~p~~rr~----h~--~~~~C~~Cgp~ 149 (711)
T TIGR00143 87 LYPFISCTHCGPRFTIIEALP--YDRENTSMADFPLCPDCAKEYKDPLDRRF----HA--QPIACPRCGPQ 149 (711)
T ss_pred cCCcccccCCCCCeEEeecCC--CCCCCcCCCCCcCCHHHHHHhcCCccccC----CC--CCccCCCCCcE
Confidence 555669999998776443311 113455555554 9999988876654333 32 35688888865
No 94
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=27.91 E-value=54 Score=34.74 Aligned_cols=9 Identities=22% Similarity=0.730 Sum_probs=6.4
Q ss_pred ecCCCCccc
Q 046965 110 SCNYCKREF 118 (286)
Q Consensus 110 ~C~~CgK~F 118 (286)
-|..||..+
T Consensus 17 FC~~CG~~l 25 (645)
T PRK14559 17 FCQKCGTSL 25 (645)
T ss_pred cccccCCCC
Confidence 477887765
No 95
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=27.73 E-value=42 Score=24.81 Aligned_cols=34 Identities=18% Similarity=0.276 Sum_probs=18.9
Q ss_pred ceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 107 RVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 107 Kpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
-.|.|+.||..-. .+-.+.-....+|.|..||..
T Consensus 24 ~~F~CPnCG~~~I-----~RC~~CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 24 VKFLCPNCGEVII-----YRCEKCRKQSNPYTCPKCGFE 57 (59)
T ss_pred CEeeCCCCCCeeE-----eechhHHhcCCceECCCCCCc
Confidence 3588888887521 112222233456777777753
No 96
>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=26.90 E-value=30 Score=21.85 Aligned_cols=9 Identities=44% Similarity=1.187 Sum_probs=4.4
Q ss_pred ecCCCCccc
Q 046965 110 SCNYCKREF 118 (286)
Q Consensus 110 ~C~~CgK~F 118 (286)
.|-.|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 444455554
No 97
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=23.38 E-value=44 Score=29.23 Aligned_cols=35 Identities=14% Similarity=0.381 Sum_probs=24.7
Q ss_pred CceeecCCCCcccCCCccchhhhhhccCCccccccccCcc
Q 046965 106 ARVFSCNYCKREFSTSQALGGHQNAHKQERAVAKRRQGVD 145 (286)
Q Consensus 106 eKpf~C~~CgK~F~sssaL~~Hqr~HtgEKpy~C~~Cgk~ 145 (286)
.-+|.|. |+..|.+. .+|-.+-.|+ .|.|..|+-.
T Consensus 115 ~~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 115 TYPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred ceeEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 3589999 99876543 4455555666 8999999754
No 98
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.36 E-value=51 Score=27.74 Aligned_cols=18 Identities=33% Similarity=0.704 Sum_probs=12.5
Q ss_pred CCCceeecCCCCcccCCC
Q 046965 104 SEARVFSCNYCKREFSTS 121 (286)
Q Consensus 104 tgeKpf~C~~CgK~F~ss 121 (286)
.....+.|..||..|...
T Consensus 66 ~~p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLK 83 (135)
T ss_pred ecceEEECCCCCCEEecc
Confidence 334568899998877654
No 99
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=21.35 E-value=76 Score=22.87 Aligned_cols=10 Identities=40% Similarity=0.979 Sum_probs=5.2
Q ss_pred eecCCCCccc
Q 046965 109 FSCNYCKREF 118 (286)
Q Consensus 109 f~C~~CgK~F 118 (286)
|+|+.|+..+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 4555555544
No 100
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=21.19 E-value=38 Score=29.19 Aligned_cols=27 Identities=19% Similarity=0.218 Sum_probs=21.1
Q ss_pred eecCCCCcccCCCccchhhhhhccCCcccc
Q 046965 109 FSCNYCKREFSTSQALGGHQNAHKQERAVA 138 (286)
Q Consensus 109 f~C~~CgK~F~sssaL~~Hqr~HtgEKpy~ 138 (286)
..|-+|||.|. +|++|..+|.+--|-.
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTPd~ 103 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTPDE 103 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCHHH
Confidence 46999999986 5899999987765533
No 101
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=20.84 E-value=50 Score=21.98 Aligned_cols=14 Identities=29% Similarity=0.655 Sum_probs=12.0
Q ss_pred eeecCCCCcccCCC
Q 046965 108 VFSCNYCKREFSTS 121 (286)
Q Consensus 108 pf~C~~CgK~F~ss 121 (286)
||+|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999998754
Done!