Query 001158
Match_columns 1135
No_of_seqs 366 out of 2007
Neff 4.6
Searched_HMMs 46136
Date Thu Mar 28 17:24:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001158.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001158hhsearch_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 99.8 1.9E-21 4.2E-26 209.8 6.9 133 969-1126 130-265 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.8 1E-20 2.2E-25 204.3 6.7 111 1017-1135 128-246 (279)
3 KOG3608 Zn finger proteins [Ge 99.4 5.6E-14 1.2E-18 155.5 3.7 151 973-1129 183-346 (467)
4 KOG1074 Transcriptional repres 99.4 1.2E-13 2.6E-18 165.4 3.2 57 1073-1133 880-936 (958)
5 KOG3608 Zn finger proteins [Ge 99.4 2.4E-13 5.3E-18 150.5 2.7 152 973-1135 140-322 (467)
6 KOG1074 Transcriptional repres 99.3 2.5E-13 5.5E-18 162.6 -0.2 80 1046-1129 607-693 (958)
7 KOG3623 Homeobox transcription 99.3 3.8E-13 8.2E-18 158.6 1.2 100 1020-1125 211-330 (1007)
8 KOG3576 Ovo and related transc 99.3 1.4E-12 3E-17 136.2 3.7 109 1017-1131 115-239 (267)
9 KOG3623 Homeobox transcription 99.2 1.2E-12 2.6E-17 154.4 0.7 77 1045-1125 895-971 (1007)
10 KOG3576 Ovo and related transc 99.1 1.1E-11 2.3E-16 129.6 0.3 83 1044-1130 117-200 (267)
11 PLN03086 PRLI-interacting fact 98.7 5.7E-08 1.2E-12 116.4 10.5 134 970-1127 408-563 (567)
12 PLN03086 PRLI-interacting fact 98.5 1.9E-07 4.1E-12 112.0 6.8 103 1018-1135 432-544 (567)
13 PHA00733 hypothetical protein 98.5 1.8E-07 3.8E-12 93.5 5.2 86 1017-1128 38-123 (128)
14 PHA02768 hypothetical protein; 98.0 3.1E-06 6.8E-11 73.1 2.3 42 1073-1120 6-47 (55)
15 PHA02768 hypothetical protein; 97.9 3.6E-06 7.9E-11 72.7 1.9 43 1045-1091 6-48 (55)
16 PF13465 zf-H2C2_2: Zinc-finge 97.7 1.6E-05 3.6E-10 58.7 1.9 25 1089-1115 1-25 (26)
17 KOG3993 Transcription factor ( 97.6 3.1E-05 6.6E-10 89.1 2.6 157 966-1128 292-482 (500)
18 PHA00733 hypothetical protein 97.6 0.00011 2.4E-09 73.7 5.7 46 1049-1098 78-123 (128)
19 PF13465 zf-H2C2_2: Zinc-finge 97.3 0.00011 2.4E-09 54.3 1.1 26 1059-1086 1-26 (26)
20 KOG3993 Transcription factor ( 97.2 0.00011 2.3E-09 84.8 0.3 109 1018-1131 266-383 (500)
21 PHA00616 hypothetical protein 96.8 0.0005 1.1E-08 57.3 1.4 34 1072-1107 1-34 (44)
22 PHA00732 hypothetical protein 96.8 0.00098 2.1E-08 61.9 3.4 45 1045-1097 2-47 (79)
23 COG5189 SFP1 Putative transcri 96.8 0.00048 1E-08 77.2 1.1 55 1070-1126 347-420 (423)
24 PHA00616 hypothetical protein 96.6 0.0011 2.3E-08 55.4 1.7 32 1102-1135 1-32 (44)
25 PHA00732 hypothetical protein 96.4 0.0023 5.1E-08 59.5 3.1 47 1019-1070 1-50 (79)
26 PF12756 zf-C2H2_2: C2H2 type 96.3 0.0029 6.3E-08 58.5 2.9 28 1102-1131 50-77 (100)
27 PF05605 zf-Di19: Drought indu 96.1 0.0085 1.8E-07 51.5 4.6 50 1072-1128 2-53 (54)
28 COG5189 SFP1 Putative transcri 96.0 0.0024 5.1E-08 71.9 0.8 73 1016-1095 346-419 (423)
29 PF00096 zf-C2H2: Zinc finger, 95.2 0.011 2.3E-07 41.9 1.7 23 1103-1127 1-23 (23)
30 PF13894 zf-C2H2_4: C2H2-type 94.6 0.027 5.9E-07 39.3 2.2 24 1103-1128 1-24 (24)
31 PF13912 zf-C2H2_6: C2H2-type 94.0 0.03 6.5E-07 41.1 1.5 25 1102-1128 1-25 (27)
32 PF00096 zf-C2H2: Zinc finger, 93.8 0.032 6.9E-07 39.4 1.4 23 1073-1097 1-23 (23)
33 PF05605 zf-Di19: Drought indu 93.8 0.082 1.8E-06 45.4 4.1 49 1045-1098 3-53 (54)
34 COG5048 FOG: Zn-finger [Genera 93.7 0.041 8.9E-07 61.8 2.8 142 970-1131 290-445 (467)
35 KOG2231 Predicted E3 ubiquitin 93.0 0.15 3.3E-06 63.3 6.1 46 1021-1068 184-236 (669)
36 PF12756 zf-C2H2_2: C2H2 type 92.5 0.078 1.7E-06 49.0 2.3 72 1021-1097 1-73 (100)
37 COG5048 FOG: Zn-finger [Genera 92.2 0.061 1.3E-06 60.5 1.3 61 1047-1107 292-356 (467)
38 smart00355 ZnF_C2H2 zinc finge 90.9 0.22 4.8E-06 34.8 2.6 23 1103-1127 1-23 (26)
39 PF13912 zf-C2H2_6: C2H2-type 90.6 0.13 2.9E-06 37.7 1.4 25 1072-1098 1-25 (27)
40 PF13894 zf-C2H2_4: C2H2-type 90.4 0.19 4.2E-06 34.9 1.9 23 1073-1097 1-23 (24)
41 PRK04860 hypothetical protein; 89.8 0.2 4.4E-06 52.5 2.3 39 1071-1117 118-156 (160)
42 smart00355 ZnF_C2H2 zinc finge 87.6 0.48 1E-05 33.1 2.4 24 1073-1098 1-24 (26)
43 KOG2231 Predicted E3 ubiquitin 87.0 0.63 1.4E-05 58.1 4.4 48 1047-1098 185-236 (669)
44 PF09237 GAGA: GAGA factor; I 85.6 0.53 1.2E-05 40.9 2.0 30 1099-1130 21-50 (54)
45 PF09237 GAGA: GAGA factor; I 84.2 0.78 1.7E-05 39.9 2.3 40 1061-1102 12-52 (54)
46 PRK04860 hypothetical protein; 83.8 0.56 1.2E-05 49.3 1.7 38 1044-1087 119-156 (160)
47 PF12874 zf-met: Zinc-finger o 82.3 0.47 1E-05 34.2 0.3 23 1103-1127 1-23 (25)
48 COG5236 Uncharacterized conser 80.1 1.9 4.1E-05 49.9 4.1 71 1020-1096 221-303 (493)
49 KOG4377 Zn-finger protein [Gen 77.8 1.3 2.8E-05 52.3 2.0 28 1103-1130 402-429 (480)
50 KOG4173 Alpha-SNAP protein [In 76.7 0.91 2E-05 49.3 0.4 74 1020-1093 80-165 (253)
51 PF13909 zf-H2C2_5: C2H2-type 76.6 1.7 3.7E-05 31.2 1.7 22 1103-1127 1-22 (24)
52 KOG2893 Zn finger protein [Gen 76.5 1 2.2E-05 49.7 0.8 48 1017-1067 9-58 (341)
53 PF12171 zf-C2H2_jaz: Zinc-fin 73.4 2.1 4.6E-05 31.7 1.5 20 1046-1065 3-22 (27)
54 KOG2785 C2H2-type Zn-finger pr 71.6 4.7 0.0001 47.5 4.5 156 970-1131 4-247 (390)
55 PF12171 zf-C2H2_jaz: Zinc-fin 70.5 0.98 2.1E-05 33.5 -0.8 22 1103-1126 2-23 (27)
56 KOG1146 Homeobox protein [Gene 70.5 2.4 5.2E-05 56.2 2.1 26 1099-1126 515-540 (1406)
57 PF12874 zf-met: Zinc-finger o 69.7 2.4 5.3E-05 30.4 1.1 22 1073-1096 1-22 (25)
58 KOG4173 Alpha-SNAP protein [In 69.6 1.4 3.1E-05 47.8 -0.1 73 1048-1125 85-167 (253)
59 KOG1146 Homeobox protein [Gene 65.0 1.1 2.3E-05 59.2 -2.5 36 1093-1131 1320-1355(1406)
60 smart00451 ZnF_U1 U1-like zinc 60.8 2.4 5.1E-05 32.7 -0.4 23 1102-1126 3-25 (35)
61 PF13909 zf-H2C2_5: C2H2-type 60.7 5.3 0.00012 28.6 1.4 23 1073-1098 1-23 (24)
62 COG5236 Uncharacterized conser 59.2 6.8 0.00015 45.6 2.6 75 1020-1096 152-242 (493)
63 PF13913 zf-C2HC_2: zinc-finge 51.6 10 0.00022 28.3 1.6 14 1026-1040 7-20 (25)
64 KOG2893 Zn finger protein [Gen 45.7 6.6 0.00014 43.7 -0.1 45 1047-1097 13-58 (341)
65 PF13913 zf-C2HC_2: zinc-finge 45.0 18 0.0004 26.9 2.1 19 1104-1125 4-22 (25)
66 smart00451 ZnF_U1 U1-like zinc 34.1 30 0.00065 26.6 1.9 22 1019-1042 3-24 (35)
67 KOG4377 Zn-finger protein [Gen 33.1 25 0.00055 42.0 2.0 114 972-1098 276-427 (480)
68 COG4049 Uncharacterized protei 30.8 21 0.00046 31.9 0.7 28 1097-1126 12-39 (65)
69 PF09538 FYDLN_acid: Protein o 30.2 33 0.00072 34.2 2.0 6 1026-1031 14-19 (108)
70 TIGR02098 MJ0042_CXXC MJ0042 f 29.7 27 0.00059 27.8 1.1 10 1026-1035 7-16 (38)
71 KOG4124 Putative transcription 27.0 15 0.00032 43.1 -1.2 71 1017-1094 347-418 (442)
72 PF09986 DUF2225: Uncharacteri 25.2 24 0.00052 38.7 0.0 24 1017-1042 3-26 (214)
73 cd04864 LigD_Pol_like_1 LigD_P 24.6 1.3E+02 0.0028 33.8 5.5 45 272-316 116-173 (228)
74 TIGR00622 ssl1 transcription f 24.0 1E+02 0.0022 31.2 4.1 48 1074-1127 57-104 (112)
75 KOG2482 Predicted C2H2-type Zn 23.8 52 0.0011 38.7 2.3 103 1019-1127 195-357 (423)
76 cd04861 LigD_Pol_like LigD_Pol 22.6 1.5E+02 0.0033 33.4 5.5 46 272-317 115-173 (227)
77 PRK00464 nrdR transcriptional 22.3 29 0.00062 36.6 -0.0 19 1041-1059 25-43 (154)
78 cd04865 LigD_Pol_like_2 LigD_P 21.1 1.7E+02 0.0036 33.0 5.5 45 272-316 116-173 (228)
79 cd04862 PaeLigD_Pol_like PaeLi 20.8 1.7E+02 0.0038 32.9 5.5 46 272-317 115-173 (227)
80 smart00531 TFIIE Transcription 20.8 62 0.0013 33.5 2.0 14 1019-1034 99-112 (147)
81 PF09986 DUF2225: Uncharacteri 20.4 31 0.00068 37.9 -0.3 13 1103-1117 49-61 (214)
82 cd04866 LigD_Pol_like_3 LigD_P 20.2 1.8E+02 0.0039 32.7 5.5 45 272-316 110-168 (223)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.84 E-value=1.9e-21 Score=209.77 Aligned_cols=133 Identities=26% Similarity=0.461 Sum_probs=120.2
Q ss_pred CCcCCccCcCCCCchhHHHHHhhccccCcccCCCCCCCccccccccCCCCceeccCCCCCCcccChHHHHhhhhcc---c
Q 001158 969 EGLRSRAGKDAANTSEVDIRKIAEKRATKTMRNRESVPAPCQDKKKILKGHHRCDLDGCRMSFETKRELSLHKRNR---C 1045 (1135)
Q Consensus 969 ~~lC~~CgK~Fssks~Lk~H~r~~Kp~~K~F~srssL~~~H~~k~H~~eKpykC~~~~CGKsFssks~Lq~H~r~H---c 1045 (1135)
.+.|..||+.+.+.++|.+|+..+.+ + ..++-+.|. .|||.|.+...|+.|+++| |
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~----------~---------~s~ka~~C~--~C~K~YvSmpALkMHirTH~l~c 188 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRS----------L---------DSKKAFSCK--YCGKVYVSMPALKMHIRTHTLPC 188 (279)
T ss_pred ceeccccccccccccccchhhccccc----------c---------cccccccCC--CCCceeeehHHHhhHhhccCCCc
Confidence 47899999999999999999843332 1 014558899 9999999999999999997 9
Q ss_pred cCCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHHHHHHhcCCCCcccCCCCCCCCcccChhHHHHHHH
Q 001158 1046 PHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRHRR 1125 (1135)
Q Consensus 1046 ~Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk~H~RtHTGEKPYkC~vpGCGKsF~skSsL~kH~R 1125 (1135)
.|..|||.|.....|+-|+|+|+|||||.|+ .|+|.|..+++|+.||++|.+.|+|+|.. |+|.|...+.|.+|..
T Consensus 189 ~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~--hC~kAFADRSNLRAHmQTHS~~K~~qC~~--C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 189 ECGICGKAFSRPWLLQGHIRTHTGEKPFSCP--HCGKAFADRSNLRAHMQTHSDVKKHQCPR--CGKSFALKSYLNKHSE 264 (279)
T ss_pred ccccccccccchHHhhcccccccCCCCccCC--cccchhcchHHHHHHHHhhcCCccccCcc--hhhHHHHHHHHHHhhh
Confidence 9999999999999999999999999999995 59999999999999999999999999999 9999999999999976
Q ss_pred h
Q 001158 1126 K 1126 (1135)
Q Consensus 1126 ~ 1126 (1135)
.
T Consensus 265 S 265 (279)
T KOG2462|consen 265 S 265 (279)
T ss_pred h
Confidence 3
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.82 E-value=1e-20 Score=204.29 Aligned_cols=111 Identities=31% Similarity=0.614 Sum_probs=105.9
Q ss_pred CCceeccCCCCCCcccChHHHHhhhhcc--------ccCCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChh
Q 001158 1017 KGHHRCDLDGCRMSFETKRELSLHKRNR--------CPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAW 1088 (1135)
Q Consensus 1017 eKpykC~~~~CGKsFssks~Lq~H~r~H--------c~Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFssks 1088 (1135)
...|+|. .||+.+.+.++|-+|+.+| +.|+.|||.|.+...|++|+|+|+ -+++| .+|||.|.+.|
T Consensus 128 ~~r~~c~--eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C--~iCGKaFSRPW 201 (279)
T KOG2462|consen 128 HPRYKCP--ECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCEC--GICGKAFSRPW 201 (279)
T ss_pred CCceecc--ccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCccc--ccccccccchH
Confidence 3458999 9999999999999999998 679999999999999999999998 67999 67999999999
Q ss_pred HHHHHHHhcCCCCcccCCCCCCCCcccChhHHHHHHHhhCCCCCCCC
Q 001158 1089 ARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRHRRKTGHYENLSA 1135 (1135)
Q Consensus 1089 sLk~H~RtHTGEKPYkC~vpGCGKsF~skSsL~kH~R~H~h~k~~~C 1135 (1135)
.|+.|+|+|||||||.|.+ |+|.|..+++|+.||++|.+.|+|+|
T Consensus 202 LLQGHiRTHTGEKPF~C~h--C~kAFADRSNLRAHmQTHS~~K~~qC 246 (279)
T KOG2462|consen 202 LLQGHIRTHTGEKPFSCPH--CGKAFADRSNLRAHMQTHSDVKKHQC 246 (279)
T ss_pred HhhcccccccCCCCccCCc--ccchhcchHHHHHHHHhhcCCccccC
Confidence 9999999999999999999 99999999999999999999999998
No 3
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.43 E-value=5.6e-14 Score=155.47 Aligned_cols=151 Identities=21% Similarity=0.358 Sum_probs=118.0
Q ss_pred CccCcCCCCchhHHHHHh---hccc-----cCcccCCCCCCCcccccccc-CCCCceeccCCCCCCcccChHHHHhhhhc
Q 001158 973 SRAGKDAANTSEVDIRKI---AEKR-----ATKTMRNRESVPAPCQDKKK-ILKGHHRCDLDGCRMSFETKRELSLHKRN 1043 (1135)
Q Consensus 973 ~~CgK~Fssks~Lk~H~r---~~Kp-----~~K~F~srssL~~~H~~k~H-~~eKpykC~~~~CGKsFssks~Lq~H~r~ 1043 (1135)
..|.+.|.++..|+.|.+ ++|. ++.-|+++..| ..|.++.. ....+|+|. .|.|.|.+...|..|+..
T Consensus 183 ~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl-~DH~rRqt~l~~n~fqC~--~C~KrFaTeklL~~Hv~r 259 (467)
T KOG3608|consen 183 AMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKL-FDHLRRQTELNTNSFQCA--QCFKRFATEKLLKSHVVR 259 (467)
T ss_pred hhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHH-HHHHHhhhhhcCCchHHH--HHHHHHhHHHHHHHHHHH
Confidence 446677777777777776 2221 26666666666 66644433 235679998 899999999999999887
Q ss_pred c---ccCCCCCCcccChhHHHhhhhc-cCCCCcccCCCCCCCCcccChhHHHHHHHhcCCCCcccCCCCCCCCcccChhH
Q 001158 1044 R---CPHEGCGKRFSSHKYAIIHQRV-HDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSD 1119 (1135)
Q Consensus 1044 H---c~Ce~CGKsFsskssL~~Hqrt-HtGeKPfkCp~~~CGKsFsskssLk~H~RtHTGEKPYkC~vpGCGKsF~skSs 1119 (1135)
| |+|+.|..+....+.|..|++. |...|||+| +.|++.|.+.+.|.+|..+|. +.-|.|.++.|..+|++...
T Consensus 260 Hvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKC--d~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q 336 (467)
T KOG3608|consen 260 HVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKC--DECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQ 336 (467)
T ss_pred hhhcccccccccCCCChHHHHHHHHhhhccCCCccc--cchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHH
Confidence 5 8889999999999999999884 888899999 889999999999999988887 66688888888888888888
Q ss_pred HHHHHHhhCC
Q 001158 1120 ISRHRRKTGH 1129 (1135)
Q Consensus 1120 L~kH~R~H~h 1129 (1135)
+.+|++.|+.
T Consensus 337 ~~~H~~evhE 346 (467)
T KOG3608|consen 337 MRRHFLEVHE 346 (467)
T ss_pred HHHHHHHhcc
Confidence 8888887653
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.39 E-value=1.2e-13 Score=165.37 Aligned_cols=57 Identities=26% Similarity=0.498 Sum_probs=52.5
Q ss_pred ccCCCCCCCCcccChhHHHHHHHhcCCCCcccCCCCCCCCcccChhHHHHHHHhhCCCCCC
Q 001158 1073 LKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRHRRKTGHYENL 1133 (1135)
Q Consensus 1073 fkCp~~~CGKsFsskssLk~H~RtHTGEKPYkC~vpGCGKsF~skSsL~kH~R~H~h~k~~ 1133 (1135)
+.| ..||+.|...+.|..|+|+|+|+|||.|.+ |++.|..+.+|+.||.+|+-..++
T Consensus 880 h~C--~vCgk~FsSSsALqiH~rTHtg~KPF~C~f--C~~aFttrgnLKvHMgtH~w~q~~ 936 (958)
T KOG1074|consen 880 HVC--NVCGKQFSSSAALEIHMRTHTGPKPFFCHF--CEEAFTTRGNLKVHMGTHMWVQPP 936 (958)
T ss_pred hhh--ccchhcccchHHHHHhhhcCCCCCCccchh--hhhhhhhhhhhhhhhccccccCCC
Confidence 468 779999999999999999999999999999 999999999999999998766554
No 5
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.35 E-value=2.4e-13 Score=150.47 Aligned_cols=152 Identities=26% Similarity=0.372 Sum_probs=133.6
Q ss_pred CccCcCCCCchhHHHHHh----h-----------ccc--------cCcccCCCCCCCccccccccCCCCceeccCCCCCC
Q 001158 973 SRAGKDAANTSEVDIRKI----A-----------EKR--------ATKTMRNRESVPAPCQDKKKILKGHHRCDLDGCRM 1029 (1135)
Q Consensus 973 ~~CgK~Fssks~Lk~H~r----~-----------~Kp--------~~K~F~srssL~~~H~~k~H~~eKpykC~~~~CGK 1029 (1135)
..|+..|.+...|..|.- . ++| +.+.|.++..| ..| .+.|+++|...|+ .||.
T Consensus 140 edCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~L-reH-~r~Hs~eKvvACp--~Cg~ 215 (467)
T KOG3608|consen 140 EDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRL-REH-IRTHSNEKVVACP--HCGE 215 (467)
T ss_pred hhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHH-HHH-HHhcCCCeEEecc--hHHH
Confidence 679999999999999875 1 111 26778888888 888 7899999999999 9999
Q ss_pred cccChHHHHhhhhc-------cccCCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHHHHHHh-cCCCC
Q 001158 1030 SFETKRELSLHKRN-------RCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRV-HTGER 1101 (1135)
Q Consensus 1030 sFssks~Lq~H~r~-------Hc~Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk~H~Rt-HTGEK 1101 (1135)
.|.++..|..|.+. +|.|..|.|.|.+...|..|++.|-.- |+||. |+.+...++.|..|+|. |...|
T Consensus 216 ~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~--ykCpl--Cdmtc~~~ssL~~H~r~rHs~dk 291 (467)
T KOG3608|consen 216 LFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNC--YKCPL--CDMTCSSASSLTTHIRYRHSKDK 291 (467)
T ss_pred HhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhc--ccccc--cccCCCChHHHHHHHHhhhccCC
Confidence 99999999999874 599999999999999999999999754 99965 99999999999999997 99999
Q ss_pred cccCCCCCCCCcccChhHHHHHHHhhCCCCCCCC
Q 001158 1102 PYKCKFEGCGLSFRFVSDISRHRRKTGHYENLSA 1135 (1135)
Q Consensus 1102 PYkC~vpGCGKsF~skSsL~kH~R~H~h~k~~~C 1135 (1135)
||+|+. |++.|.+.+.|.+|...|. .-.|+|
T Consensus 292 pfKCd~--Cd~~c~~esdL~kH~~~HS-~~~y~C 322 (467)
T KOG3608|consen 292 PFKCDE--CDTRCVRESDLAKHVQVHS-KTVYQC 322 (467)
T ss_pred Cccccc--hhhhhccHHHHHHHHHhcc-ccceec
Confidence 999999 9999999999999999886 444444
No 6
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.31 E-value=2.5e-13 Score=162.61 Aligned_cols=80 Identities=26% Similarity=0.437 Sum_probs=67.5
Q ss_pred cCCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHHHHHHhcCCC----CcccCC---CCCCCCcccChh
Q 001158 1046 PHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGE----RPYKCK---FEGCGLSFRFVS 1118 (1135)
Q Consensus 1046 ~Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk~H~RtHTGE----KPYkC~---vpGCGKsF~skS 1118 (1135)
.|-+|-+...-++.|+.|.|+|+|+|||+| ++||+.|.++.+|+.|+-+|... -+|.|+ + |-+.|...-
T Consensus 607 qCiiC~rVlSC~saLqmHyrtHtGERPFkC--KiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~i--c~~kftn~V 682 (958)
T KOG1074|consen 607 QCIICLRVLSCPSALQMHYRTHTGERPFKC--KICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFI--CQKKFTNAV 682 (958)
T ss_pred ceeeeeecccchhhhhhhhhcccCcCcccc--ccccchhccccchhhcccccccCccccccccCCchhh--hcccccccc
Confidence 477788888888899999999999999999 77999999999999998888643 337788 8 999999999
Q ss_pred HHHHHHHhhCC
Q 001158 1119 DISRHRRKTGH 1129 (1135)
Q Consensus 1119 sL~kH~R~H~h 1129 (1135)
.|..|++.|..
T Consensus 683 ~lpQhIriH~~ 693 (958)
T KOG1074|consen 683 TLPQHIRIHLG 693 (958)
T ss_pred cccceEEeecC
Confidence 99999888763
No 7
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.31 E-value=3.8e-13 Score=158.57 Aligned_cols=100 Identities=27% Similarity=0.552 Sum_probs=92.0
Q ss_pred eeccCCCCCCcccChHHHHhhhhcc-------ccCCCCCCcccChhHHHhhhhccCC-------------CCcccCCCCC
Q 001158 1020 HRCDLDGCRMSFETKRELSLHKRNR-------CPHEGCGKRFSSHKYAIIHQRVHDD-------------ERPLKCPWKG 1079 (1135)
Q Consensus 1020 ykC~~~~CGKsFssks~Lq~H~r~H-------c~Ce~CGKsFsskssL~~HqrtHtG-------------eKPfkCp~~~ 1079 (1135)
..|+ .|.+.+.....|+.|++.. |.|..|..+|..+..|.+|+.+|.. -|.|+| .+
T Consensus 211 ltcp--ycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKC--tE 286 (1007)
T KOG3623|consen 211 LTCP--YCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKC--TE 286 (1007)
T ss_pred hcch--hHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccc--cc
Confidence 5688 8999999999999998862 8999999999999999999998852 378999 78
Q ss_pred CCCcccChhHHHHHHHhcCCCCcccCCCCCCCCcccChhHHHHHHH
Q 001158 1080 CSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRHRR 1125 (1135)
Q Consensus 1080 CGKsFsskssLk~H~RtHTGEKPYkC~vpGCGKsF~skSsL~kH~R 1125 (1135)
|||.|+.+.+|+.|+|+|.|||||.|+. |+|+|.+...+..||.
T Consensus 287 CgKAFKfKHHLKEHlRIHSGEKPfeCpn--CkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 287 CGKAFKFKHHLKEHLRIHSGEKPFECPN--CKKRFSHSGSYSSHMS 330 (1007)
T ss_pred cchhhhhHHHHHhhheeecCCCCcCCcc--cccccccCCccccccc
Confidence 9999999999999999999999999998 9999999999999985
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.29 E-value=1.4e-12 Score=136.19 Aligned_cols=109 Identities=24% Similarity=0.407 Sum_probs=97.7
Q ss_pred CCceeccCCCCCCcccChHHHHhhhhcc-----ccCCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHH
Q 001158 1017 KGHHRCDLDGCRMSFETKRELSLHKRNR-----CPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWART 1091 (1135)
Q Consensus 1017 eKpykC~~~~CGKsFssks~Lq~H~r~H-----c~Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk 1091 (1135)
...|.|. .|||.|....-|.+|++.| +-|..|||.|.....|++|+|+|+|.|||+| ..|+|+|.++-+|.
T Consensus 115 ~d~ftCr--vCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc--~~c~kaftqrcsle 190 (267)
T KOG3576|consen 115 QDSFTCR--VCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKC--SLCEKAFTQRCSLE 190 (267)
T ss_pred CCeeeee--hhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccch--hhhhHHHHhhccHH
Confidence 4558999 9999999999999999987 6788999999999999999999999999999 77999999999999
Q ss_pred HHHHh-cC----------CCCcccCCCCCCCCcccChhHHHHHHHhhCCCC
Q 001158 1092 EHIRV-HT----------GERPYKCKFEGCGLSFRFVSDISRHRRKTGHYE 1131 (1135)
Q Consensus 1092 ~H~Rt-HT----------GEKPYkC~vpGCGKsF~skSsL~kH~R~H~h~k 1131 (1135)
.|.+. |. .+|.|.|.. ||..-.....+..|++.|+..-
T Consensus 191 shl~kvhgv~~~yaykerr~kl~vced--cg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 191 SHLKKVHGVQHQYAYKERRAKLYVCED--CGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred HHHHHHcCchHHHHHHHhhhheeeecc--cCCCCCChhHHHHHHHhcCCCC
Confidence 99774 53 357799998 9999999999999999887643
No 9
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.24 E-value=1.2e-12 Score=154.43 Aligned_cols=77 Identities=31% Similarity=0.619 Sum_probs=75.3
Q ss_pred ccCCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHHHHHHhcCCCCcccCCCCCCCCcccChhHHHHHH
Q 001158 1045 CPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRHR 1124 (1135)
Q Consensus 1045 c~Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk~H~RtHTGEKPYkC~vpGCGKsF~skSsL~kH~ 1124 (1135)
|.|+.|+|.|...+.|.+|..-|+|.|||+| .+|.|.|+.+.+|..|+|.|.|||||+|+. |+|+|.+...+..||
T Consensus 895 yaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC--~iCkKAFKHKHHLtEHkRLHSGEKPfQCdK--ClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 895 YACDQCDKAFQKQSSLARHKYEHSGQRPYQC--IICKKAFKHKHHLTEHKRLHSGEKPFQCDK--CLKRFSHSGSYSQHM 970 (1007)
T ss_pred chHHHHHHHHHhhHHHHHhhhhhcCCCCccc--chhhHhhhhhhhhhhhhhhccCCCcchhhh--hhhhcccccchHhhh
Confidence 8999999999999999999999999999999 889999999999999999999999999999 999999999999998
Q ss_pred H
Q 001158 1125 R 1125 (1135)
Q Consensus 1125 R 1125 (1135)
-
T Consensus 971 N 971 (1007)
T KOG3623|consen 971 N 971 (1007)
T ss_pred c
Confidence 5
No 10
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.12 E-value=1.1e-11 Score=129.62 Aligned_cols=83 Identities=30% Similarity=0.620 Sum_probs=77.8
Q ss_pred cccCCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHHHHHHhcCCCCcccCCCCCCCCcccChhHHHHH
Q 001158 1044 RCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRH 1123 (1135)
Q Consensus 1044 Hc~Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk~H~RtHTGEKPYkC~vpGCGKsF~skSsL~kH 1123 (1135)
.|.|..|||.|.....|.+|++-|...|.|-|++ |||.|.....|++|+|+|||.+||+|.. |+|.|..+-.|..|
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~--cgkgfndtfdlkrh~rthtgvrpykc~~--c~kaftqrcslesh 192 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTF--CGKGFNDTFDLKRHTRTHTGVRPYKCSL--CEKAFTQRCSLESH 192 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhh--ccCcccchhhhhhhhccccCccccchhh--hhHHHHhhccHHHH
Confidence 3789999999999999999999999999999966 9999999999999999999999999999 99999999999999
Q ss_pred HHh-hCCC
Q 001158 1124 RRK-TGHY 1130 (1135)
Q Consensus 1124 ~R~-H~h~ 1130 (1135)
.++ |+-.
T Consensus 193 l~kvhgv~ 200 (267)
T KOG3576|consen 193 LKKVHGVQ 200 (267)
T ss_pred HHHHcCch
Confidence 885 6543
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.68 E-value=5.7e-08 Score=116.39 Aligned_cols=134 Identities=18% Similarity=0.320 Sum_probs=99.9
Q ss_pred CcCCccCcCCCCchhHHHHHhhcc---------ccCcccCCCCCCCccccccccCCCCceeccCCCCCCcccChHHHHhh
Q 001158 970 GLRSRAGKDAANTSEVDIRKIAEK---------RATKTMRNRESVPAPCQDKKKILKGHHRCDLDGCRMSFETKRELSLH 1040 (1135)
Q Consensus 970 ~lC~~CgK~Fssks~Lk~H~r~~K---------p~~K~F~srssL~~~H~~k~H~~eKpykC~~~~CGKsFssks~Lq~H 1040 (1135)
..|+.|..... ..+|..|..... .|+..|. ....++++.|+ .|++.|. ...|..|
T Consensus 408 V~C~NC~~~i~-l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~------------r~el~~H~~C~--~Cgk~f~-~s~LekH 471 (567)
T PLN03086 408 VECRNCKHYIP-SRSIALHEAYCSRHNVVCPHDGCGIVLR------------VEEAKNHVHCE--KCGQAFQ-QGEMEKH 471 (567)
T ss_pred EECCCCCCccc-hhHHHHHHhhCCCcceeCCcccccceee------------ccccccCccCC--CCCCccc-hHHHHHH
Confidence 35666777655 345557776221 1333332 22224447899 9999996 6889999
Q ss_pred hhcc---ccCCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCccc----------ChhHHHHHHHhcCCCCcccCCC
Q 001158 1041 KRNR---CPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFK----------WAWARTEHIRVHTGERPYKCKF 1107 (1135)
Q Consensus 1041 ~r~H---c~Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFs----------skssLk~H~RtHTGEKPYkC~v 1107 (1135)
++.+ +.|+ ||+.| .+..|..|+.+|.+.+++.|+| |++.|. ..+.|..|+.++ |.+++.|..
T Consensus 472 ~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~f--C~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~ 546 (567)
T PLN03086 472 MKVFHEPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRF--CGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDS 546 (567)
T ss_pred HHhcCCCccCC-CCCCc-chhHHHhhhhccCCCCceeCCC--CCCccccCccccchhhhhhhHHHHHHhc-CCcceEccc
Confidence 9864 6788 99765 6789999999999999999976 999995 245899999986 999999998
Q ss_pred CCCCCcccChhHHHHHHHhh
Q 001158 1108 EGCGLSFRFVSDISRHRRKT 1127 (1135)
Q Consensus 1108 pGCGKsF~skSsL~kH~R~H 1127 (1135)
||+.|..+ .|..|+..-
T Consensus 547 --Cgk~Vrlr-dm~~H~~~~ 563 (567)
T PLN03086 547 --CGRSVMLK-EMDIHQIAV 563 (567)
T ss_pred --cCCeeeeh-hHHHHHHHh
Confidence 99998764 678888753
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.47 E-value=1.9e-07 Score=112.04 Aligned_cols=103 Identities=22% Similarity=0.414 Sum_probs=82.0
Q ss_pred CceeccCCCCCCcccChHHHHhhhhccccCCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHHHHHHhc
Q 001158 1018 GHHRCDLDGCRMSFETKRELSLHKRNRCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVH 1097 (1135)
Q Consensus 1018 KpykC~~~~CGKsFssks~Lq~H~r~Hc~Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk~H~RtH 1097 (1135)
..-.|+...||..|. +..|.. |+.|+.|++.|. ...|..|+++|+ ++|.| . ||+.| .+..|..|+++|
T Consensus 432 ~~V~Cp~~~Cg~v~~-r~el~~----H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~C--p-Cg~~~-~R~~L~~H~~th 499 (567)
T PLN03086 432 HNVVCPHDGCGIVLR-VEEAKN----HVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQC--P-CGVVL-EKEQMVQHQAST 499 (567)
T ss_pred cceeCCcccccceee-cccccc----CccCCCCCCccc-hHHHHHHHHhcC--CCccC--C-CCCCc-chhHHHhhhhcc
Confidence 345687445999983 333444 468999999996 678999999986 89999 6 99765 678999999999
Q ss_pred CCCCcccCCCCCCCCccc----------ChhHHHHHHHhhCCCCCCCC
Q 001158 1098 TGERPYKCKFEGCGLSFR----------FVSDISRHRRKTGHYENLSA 1135 (1135)
Q Consensus 1098 TGEKPYkC~vpGCGKsF~----------skSsL~kH~R~H~h~k~~~C 1135 (1135)
.+++|+.|.+ |++.|. ..+.|..|...+ +.+++.|
T Consensus 500 Cp~Kpi~C~f--C~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C 544 (567)
T PLN03086 500 CPLRLITCRF--CGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPC 544 (567)
T ss_pred CCCCceeCCC--CCCccccCccccchhhhhhhHHHHHHhc-CCcceEc
Confidence 9999999999 999995 246899999886 5565655
No 13
>PHA00733 hypothetical protein
Probab=98.45 E-value=1.8e-07 Score=93.48 Aligned_cols=86 Identities=21% Similarity=0.264 Sum_probs=67.8
Q ss_pred CCceeccCCCCCCcccChHHHHhhhhccccCCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHHHHHHh
Q 001158 1017 KGHHRCDLDGCRMSFETKRELSLHKRNRCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRV 1096 (1135)
Q Consensus 1017 eKpykC~~~~CGKsFssks~Lq~H~r~Hc~Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk~H~Rt 1096 (1135)
.+++.|. +|.+.|.....|..| ..|.+|+..| +.+||.| ..||+.|.....|..|++.
T Consensus 38 ~~~~~~~--~~~~~~~~~~~l~~~-----------------~~l~~~~~~~-~~kPy~C--~~Cgk~Fss~s~L~~H~r~ 95 (128)
T PHA00733 38 QKRLIRA--VVKTLIYNPQLLDES-----------------SYLYKLLTSK-AVSPYVC--PLCLMPFSSSVSLKQHIRY 95 (128)
T ss_pred hhhHHHH--HHhhhccChhhhcch-----------------HHHHhhcccC-CCCCccC--CCCCCcCCCHHHHHHHHhc
Confidence 4567777 777777665544443 3366665444 5889999 6799999999999999998
Q ss_pred cCCCCcccCCCCCCCCcccChhHHHHHHHhhC
Q 001158 1097 HTGERPYKCKFEGCGLSFRFVSDISRHRRKTG 1128 (1135)
Q Consensus 1097 HTGEKPYkC~vpGCGKsF~skSsL~kH~R~H~ 1128 (1135)
| +.+|.|.. |++.|.....|.+|+...|
T Consensus 96 h--~~~~~C~~--CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 96 T--EHSKVCPV--CGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred C--CcCccCCC--CCCccCCHHHHHHHHHHhc
Confidence 7 36799999 9999999999999998754
No 14
>PHA02768 hypothetical protein; Provisional
Probab=97.99 E-value=3.1e-06 Score=73.15 Aligned_cols=42 Identities=17% Similarity=0.211 Sum_probs=31.8
Q ss_pred ccCCCCCCCCcccChhHHHHHHHhcCCCCcccCCCCCCCCcccChhHH
Q 001158 1073 LKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDI 1120 (1135)
Q Consensus 1073 fkCp~~~CGKsFsskssLk~H~RtHTGEKPYkC~vpGCGKsF~skSsL 1120 (1135)
|+| ..||+.|....+|..|+++|+ +||+|.. |++.|.+.+.|
T Consensus 6 y~C--~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~--C~k~f~~~s~l 47 (55)
T PHA02768 6 YEC--PICGEIYIKRKSMITHLRKHN--TNLKLSN--CKRISLRTGEY 47 (55)
T ss_pred cCc--chhCCeeccHHHHHHHHHhcC--CcccCCc--ccceeccccee
Confidence 677 568888888888888888877 6778876 88887766655
No 15
>PHA02768 hypothetical protein; Provisional
Probab=97.95 E-value=3.6e-06 Score=72.75 Aligned_cols=43 Identities=23% Similarity=0.266 Sum_probs=38.4
Q ss_pred ccCCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHH
Q 001158 1045 CPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWART 1091 (1135)
Q Consensus 1045 c~Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk 1091 (1135)
|.|+.||+.|.....|..|+++|+ ++|+| ..|++.|.+.+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc--~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKL--SNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccC--CcccceecccceeE
Confidence 689999999999999999999999 79999 67999999887764
No 16
>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=97.72 E-value=1.6e-05 Score=58.69 Aligned_cols=25 Identities=56% Similarity=1.224 Sum_probs=19.6
Q ss_pred HHHHHHHhcCCCCcccCCCCCCCCccc
Q 001158 1089 ARTEHIRVHTGERPYKCKFEGCGLSFR 1115 (1135)
Q Consensus 1089 sLk~H~RtHTGEKPYkC~vpGCGKsF~ 1115 (1135)
+|..|+++|+|++||.|+. |++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~--C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPY--CGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESS--SSEEES
T ss_pred CHHHHhhhcCCCCCCCCCC--CcCeeC
Confidence 4677888888888888887 888775
No 17
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.59 E-value=3.1e-05 Score=89.14 Aligned_cols=157 Identities=13% Similarity=0.103 Sum_probs=100.5
Q ss_pred CCCCCcCCccCcCCCCchhHHHHHhhccccCccc--CCCC--------CCCcccc-ccccCCCCceeccCCCCCCcccCh
Q 001158 966 SPCEGLRSRAGKDAANTSEVDIRKIAEKRATKTM--RNRE--------SVPAPCQ-DKKKILKGHHRCDLDGCRMSFETK 1034 (1135)
Q Consensus 966 sPc~~lC~~CgK~Fssks~Lk~H~r~~Kp~~K~F--~srs--------sL~~~H~-~k~H~~eKpykC~~~~CGKsFssk 1034 (1135)
...++.|+.|+|.|....+|..|+|-+||....- .... .+-..-- -.......-|.|. +|+|.|++.
T Consensus 292 V~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~--~C~KkFrRq 369 (500)
T KOG3993|consen 292 VHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCH--TCGKKFRRQ 369 (500)
T ss_pred EEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecH--HhhhhhHHH
Confidence 3445899999999999999999999777651111 0000 0000000 0000223469999 999999999
Q ss_pred HHHHhhhhccc----------------------cCCCCCCcccChhHHHhhhhccCC-CCcccCCCCCCCCcccChhHHH
Q 001158 1035 RELSLHKRNRC----------------------PHEGCGKRFSSHKYAIIHQRVHDD-ERPLKCPWKGCSMSFKWAWART 1091 (1135)
Q Consensus 1035 s~Lq~H~r~Hc----------------------~Ce~CGKsFsskssL~~HqrtHtG-eKPfkCp~~~CGKsFsskssLk 1091 (1135)
..|+.|+..|. -|..|+-.|.....--.|...|.+ .....|++ |+..|..+..--
T Consensus 370 AYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp~--~~~ppsss~~sg 447 (500)
T KOG3993|consen 370 AYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPPY--DGSPPSSSGSSG 447 (500)
T ss_pred HHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCCCC--CCCCcccCCCCC
Confidence 99999977652 233333333332222222222221 12235654 888888887777
Q ss_pred HHHHhcCCCCcccCCCCCCCCcccChhHHHHHHHhhC
Q 001158 1092 EHIRVHTGERPYKCKFEGCGLSFRFVSDISRHRRKTG 1128 (1135)
Q Consensus 1092 ~H~RtHTGEKPYkC~vpGCGKsF~skSsL~kH~R~H~ 1128 (1135)
.|.|.-.-+.-|.|.+ |.-.|.....|.+|..+.|
T Consensus 448 g~~rlg~~~q~f~~ky--~~atfyss~~ltrhin~~H 482 (500)
T KOG3993|consen 448 GYGRLGIAEQGFTCKY--CPATFYSSPGLTRHINKCH 482 (500)
T ss_pred ccccccchhhcccccc--chHhhhcCcchHhHhhhcC
Confidence 7777666677899999 9999999999999987643
No 18
>PHA00733 hypothetical protein
Probab=97.55 E-value=0.00011 Score=73.66 Aligned_cols=46 Identities=24% Similarity=0.281 Sum_probs=26.8
Q ss_pred CCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHHHHHHhcC
Q 001158 1049 GCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVHT 1098 (1135)
Q Consensus 1049 ~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk~H~RtHT 1098 (1135)
.||+.|.+...|..|++.| ..+|.| ..|++.|.....|..|++.++
T Consensus 78 ~Cgk~Fss~s~L~~H~r~h--~~~~~C--~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 78 LCLMPFSSSVSLKQHIRYT--EHSKVC--PVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CCCCcCCCHHHHHHHHhcC--CcCccC--CCCCCccCCHHHHHHHHHHhc
Confidence 3444444444444444444 235777 557777777777777776543
No 19
>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=97.25 E-value=0.00011 Score=54.33 Aligned_cols=26 Identities=38% Similarity=0.623 Sum_probs=23.3
Q ss_pred HHHhhhhccCCCCcccCCCCCCCCcccC
Q 001158 1059 YAIIHQRVHDDERPLKCPWKGCSMSFKW 1086 (1135)
Q Consensus 1059 sL~~HqrtHtGeKPfkCp~~~CGKsFss 1086 (1135)
+|..|+++|+|++||+| ..|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C--~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKC--PYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEE--SSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCC--CCCcCeeCc
Confidence 48899999999999999 569999974
No 20
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.16 E-value=0.00011 Score=84.82 Aligned_cols=109 Identities=19% Similarity=0.289 Sum_probs=73.5
Q ss_pred CceeccCCCCCCcccChHHHHhhhhc-----cccCCCCCCcccChhHHHhhhhccCCCCccc-CCCCCCCC-cccChhHH
Q 001158 1018 GHHRCDLDGCRMSFETKRELSLHKRN-----RCPHEGCGKRFSSHKYAIIHQRVHDDERPLK-CPWKGCSM-SFKWAWAR 1090 (1135)
Q Consensus 1018 KpykC~~~~CGKsFssks~Lq~H~r~-----Hc~Ce~CGKsFsskssL~~HqrtHtGeKPfk-Cp~~~CGK-sFsskssL 1090 (1135)
..|.|. .|...|.....|.+|.-- -|.|+.|+|.|.-..+|..|.|.|.-...-. -. ..=.+ .-.+....
T Consensus 266 GdyiCq--LCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~-~~P~k~~~~~rae~ 342 (500)
T KOG3993|consen 266 GDYICQ--LCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAG-SPPPKQAVETRAEV 342 (500)
T ss_pred HHHHHH--HHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcC-CCChhhhhhhhhhh
Confidence 359999 999999999999999753 3999999999999999999999996321100 00 00000 11111111
Q ss_pred HHHHHh--cCCCCcccCCCCCCCCcccChhHHHHHHHhhCCCC
Q 001158 1091 TEHIRV--HTGERPYKCKFEGCGLSFRFVSDISRHRRKTGHYE 1131 (1135)
Q Consensus 1091 k~H~Rt--HTGEKPYkC~vpGCGKsF~skSsL~kH~R~H~h~k 1131 (1135)
+.-.|. -..+..|.|.+ |+|.|++...|++|+.+|+...
T Consensus 343 ~ea~rsg~dss~gi~~C~~--C~KkFrRqAYLrKHqlthq~~~ 383 (500)
T KOG3993|consen 343 QEAERSGDDSSSGIFSCHT--CGKKFRRQAYLRKHQLTHQRAP 383 (500)
T ss_pred hhccccCCcccCceeecHH--hhhhhHHHHHHHHhHHhhhccc
Confidence 111111 01234699999 9999999999999998886543
No 21
>PHA00616 hypothetical protein
Probab=96.83 E-value=0.0005 Score=57.25 Aligned_cols=34 Identities=15% Similarity=0.256 Sum_probs=25.3
Q ss_pred cccCCCCCCCCcccChhHHHHHHHhcCCCCcccCCC
Q 001158 1072 PLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKF 1107 (1135)
Q Consensus 1072 PfkCp~~~CGKsFsskssLk~H~RtHTGEKPYkC~v 1107 (1135)
||+| ..||+.|..++.|..|++.|+|+++|.|+.
T Consensus 1 pYqC--~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQC--LRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCcc--chhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 5777 557777777777777777777777777764
No 22
>PHA00732 hypothetical protein
Probab=96.81 E-value=0.00098 Score=61.93 Aligned_cols=45 Identities=22% Similarity=0.286 Sum_probs=24.9
Q ss_pred ccCCCCCCcccChhHHHhhhhc-cCCCCcccCCCCCCCCcccChhHHHHHHHhc
Q 001158 1045 CPHEGCGKRFSSHKYAIIHQRV-HDDERPLKCPWKGCSMSFKWAWARTEHIRVH 1097 (1135)
Q Consensus 1045 c~Ce~CGKsFsskssL~~Hqrt-HtGeKPfkCp~~~CGKsFsskssLk~H~RtH 1097 (1135)
|.|..||+.|.+...|..|++. |.+ +.| ..||+.|. .|..|.+++
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C--~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTL---TKC--PVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCC---Ccc--CCCCCEeC---Chhhhhccc
Confidence 4566666666666666666653 432 356 44666665 355555443
No 23
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.76 E-value=0.00048 Score=77.21 Aligned_cols=55 Identities=27% Similarity=0.744 Sum_probs=44.7
Q ss_pred CCcccCCCCCCCCcccChhHHHHHHHh-c------------------CCCCcccCCCCCCCCcccChhHHHHHHHh
Q 001158 1070 ERPLKCPWKGCSMSFKWAWARTEHIRV-H------------------TGERPYKCKFEGCGLSFRFVSDISRHRRK 1126 (1135)
Q Consensus 1070 eKPfkCp~~~CGKsFsskssLk~H~Rt-H------------------TGEKPYkC~vpGCGKsF~skSsL~kH~R~ 1126 (1135)
+|||+|++..|.|.|+....|+.|+.- | ...|||.|++ |+|+|+....|+-|+..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCev--C~KRYKNlNGLKYHr~H 420 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEV--CDKRYKNLNGLKYHRKH 420 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccc--cchhhccCccceecccc
Confidence 588888888888888888888888653 3 1249999999 99999999999999764
No 24
>PHA00616 hypothetical protein
Probab=96.58 E-value=0.0011 Score=55.36 Aligned_cols=32 Identities=25% Similarity=0.432 Sum_probs=29.5
Q ss_pred cccCCCCCCCCcccChhHHHHHHHhhCCCCCCCC
Q 001158 1102 PYKCKFEGCGLSFRFVSDISRHRRKTGHYENLSA 1135 (1135)
Q Consensus 1102 PYkC~vpGCGKsF~skSsL~kH~R~H~h~k~~~C 1135 (1135)
||+|.. ||+.|..++.|.+|+++|++.+++.|
T Consensus 1 pYqC~~--CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLR--CGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccch--hhHHHhhHHHHHHHHHHhcCCCccce
Confidence 799999 99999999999999999988888764
No 25
>PHA00732 hypothetical protein
Probab=96.43 E-value=0.0023 Score=59.45 Aligned_cols=47 Identities=21% Similarity=0.249 Sum_probs=40.9
Q ss_pred ceeccCCCCCCcccChHHHHhhhhc-c--ccCCCCCCcccChhHHHhhhhccCCC
Q 001158 1019 HHRCDLDGCRMSFETKRELSLHKRN-R--CPHEGCGKRFSSHKYAIIHQRVHDDE 1070 (1135)
Q Consensus 1019 pykC~~~~CGKsFssks~Lq~H~r~-H--c~Ce~CGKsFsskssL~~HqrtHtGe 1070 (1135)
||.|. .||+.|.+...|+.|++. | +.|+.||+.|. .|..|.+++.+.
T Consensus 1 py~C~--~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~---~l~~H~~~~~~~ 50 (79)
T PHA00732 1 MFKCP--ICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR---RLNQHFYSQYDI 50 (79)
T ss_pred CccCC--CCCCccCCHHHHHHHhhcccCCCccCCCCCEeC---ChhhhhcccCCc
Confidence 58899 999999999999999984 4 78999999998 588999877654
No 26
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.28 E-value=0.0029 Score=58.46 Aligned_cols=28 Identities=25% Similarity=0.698 Sum_probs=17.0
Q ss_pred cccCCCCCCCCcccChhHHHHHHHhhCCCC
Q 001158 1102 PYKCKFEGCGLSFRFVSDISRHRRKTGHYE 1131 (1135)
Q Consensus 1102 PYkC~vpGCGKsF~skSsL~kH~R~H~h~k 1131 (1135)
.|.|.. |++.|.....|..|++.++|..
T Consensus 50 ~~~C~~--C~~~f~s~~~l~~Hm~~~~H~~ 77 (100)
T PF12756_consen 50 SFRCPY--CNKTFRSREALQEHMRSKHHKK 77 (100)
T ss_dssp SEEBSS--SS-EESSHHHHHHHHHHTTTTC
T ss_pred CCCCCc--cCCCCcCHHHHHHHHcCccCCC
Confidence 466666 6666666666666666654443
No 27
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=96.10 E-value=0.0085 Score=51.47 Aligned_cols=50 Identities=22% Similarity=0.487 Sum_probs=36.4
Q ss_pred cccCCCCCCCCcccChhHHHHHHHh-cCCC-CcccCCCCCCCCcccChhHHHHHHHhhC
Q 001158 1072 PLKCPWKGCSMSFKWAWARTEHIRV-HTGE-RPYKCKFEGCGLSFRFVSDISRHRRKTG 1128 (1135)
Q Consensus 1072 PfkCp~~~CGKsFsskssLk~H~Rt-HTGE-KPYkC~vpGCGKsF~skSsL~kH~R~H~ 1128 (1135)
.|.||| |++. .....|..|... |..+ +.+.|++ |...+. .+|.+|+..+|
T Consensus 2 ~f~CP~--C~~~-~~~~~L~~H~~~~H~~~~~~v~CPi--C~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPY--CGKG-FSESSLVEHCEDEHRSESKNVVCPI--CSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCC--CCCc-cCHHHHHHHHHhHCcCCCCCccCCC--chhhhh--hHHHHHHHHhc
Confidence 478977 9994 445678888665 6554 5688988 988655 48889988654
No 28
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.97 E-value=0.0024 Score=71.85 Aligned_cols=73 Identities=14% Similarity=0.342 Sum_probs=51.6
Q ss_pred CCCceeccCCCCCCcccChHHHHhhhhc-cccCCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHHHHH
Q 001158 1016 LKGHHRCDLDGCRMSFETKRELSLHKRN-RCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHI 1094 (1135)
Q Consensus 1016 ~eKpykC~~~~CGKsFssks~Lq~H~r~-Hc~Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk~H~ 1094 (1135)
.+|||+|+.+.|.|.|.....|+.|+.. || .....-...-..|...-...|||.| +.|+|.|+....|+.|+
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~-----~~~~~~~p~p~~~~~F~~~~KPYrC--evC~KRYKNlNGLKYHr 418 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQ-----NQKLHENPSPEKMNIFSAKDKPYRC--EVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhcccc-----CcccCCCCCccccccccccCCceec--cccchhhccCccceecc
Confidence 3599999999999999999999999874 32 1111111111112222345699999 55999999999999985
Q ss_pred H
Q 001158 1095 R 1095 (1135)
Q Consensus 1095 R 1095 (1135)
.
T Consensus 419 ~ 419 (423)
T COG5189 419 K 419 (423)
T ss_pred c
Confidence 4
No 29
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=95.25 E-value=0.011 Score=41.87 Aligned_cols=23 Identities=48% Similarity=0.967 Sum_probs=15.3
Q ss_pred ccCCCCCCCCcccChhHHHHHHHhh
Q 001158 1103 YKCKFEGCGLSFRFVSDISRHRRKT 1127 (1135)
Q Consensus 1103 YkC~vpGCGKsF~skSsL~kH~R~H 1127 (1135)
|+|+. |++.|.+...|.+|++.|
T Consensus 1 y~C~~--C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPI--CGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETT--TTEEESSHHHHHHHHHHH
T ss_pred CCCCC--CCCccCCHHHHHHHHhHC
Confidence 56666 777777777777776653
No 30
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=94.56 E-value=0.027 Score=39.26 Aligned_cols=24 Identities=38% Similarity=0.837 Sum_probs=15.9
Q ss_pred ccCCCCCCCCcccChhHHHHHHHhhC
Q 001158 1103 YKCKFEGCGLSFRFVSDISRHRRKTG 1128 (1135)
Q Consensus 1103 YkC~vpGCGKsF~skSsL~kH~R~H~ 1128 (1135)
|.|++ |++.|.....|..|+++|+
T Consensus 1 ~~C~~--C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPI--CGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SS--TS-EESSHHHHHHHHHHHS
T ss_pred CCCcC--CCCcCCcHHHHHHHHHhhC
Confidence 56777 7777777777777777654
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=93.97 E-value=0.03 Score=41.13 Aligned_cols=25 Identities=32% Similarity=0.818 Sum_probs=18.8
Q ss_pred cccCCCCCCCCcccChhHHHHHHHhhC
Q 001158 1102 PYKCKFEGCGLSFRFVSDISRHRRKTG 1128 (1135)
Q Consensus 1102 PYkC~vpGCGKsF~skSsL~kH~R~H~ 1128 (1135)
||.|.. |++.|.....|..|++.|.
T Consensus 1 ~~~C~~--C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDE--CGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETT--TTEEESSHHHHHHHHCTTT
T ss_pred CCCCCc--cCCccCChhHHHHHhHHhc
Confidence 577777 8888888888888877664
No 32
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=93.79 E-value=0.032 Score=39.44 Aligned_cols=23 Identities=35% Similarity=0.545 Sum_probs=14.5
Q ss_pred ccCCCCCCCCcccChhHHHHHHHhc
Q 001158 1073 LKCPWKGCSMSFKWAWARTEHIRVH 1097 (1135)
Q Consensus 1073 fkCp~~~CGKsFsskssLk~H~RtH 1097 (1135)
|+| ..|++.|.+...|..|++.|
T Consensus 1 y~C--~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKC--PICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEE--TTTTEEESSHHHHHHHHHHH
T ss_pred CCC--CCCCCccCCHHHHHHHHhHC
Confidence 456 44666666666666666654
No 33
>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=93.78 E-value=0.082 Score=45.44 Aligned_cols=49 Identities=24% Similarity=0.325 Sum_probs=34.2
Q ss_pred ccCCCCCCcccChhHHHhhhhc-cCCC-CcccCCCCCCCCcccChhHHHHHHHhcC
Q 001158 1045 CPHEGCGKRFSSHKYAIIHQRV-HDDE-RPLKCPWKGCSMSFKWAWARTEHIRVHT 1098 (1135)
Q Consensus 1045 c~Ce~CGKsFsskssL~~Hqrt-HtGe-KPfkCp~~~CGKsFsskssLk~H~RtHT 1098 (1135)
|.|+.|++ ..+...|..|... |..+ +.+.|| +|...+. ..|..|+..++
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CP--iC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCP--ICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCC--Cchhhhh--hHHHHHHHHhc
Confidence 67788888 4456678888664 6543 568894 5988655 38888988754
No 34
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.70 E-value=0.041 Score=61.79 Aligned_cols=142 Identities=16% Similarity=0.165 Sum_probs=77.5
Q ss_pred CcCCccCcCCCCchhHHHHHhhccccCcccCCCCCCCccccccccCCC--CceeccCCCCCCcccChHHHHhhhhcc---
Q 001158 970 GLRSRAGKDAANTSEVDIRKIAEKRATKTMRNRESVPAPCQDKKKILK--GHHRCDLDGCRMSFETKRELSLHKRNR--- 1044 (1135)
Q Consensus 970 ~lC~~CgK~Fssks~Lk~H~r~~Kp~~K~F~srssL~~~H~~k~H~~e--KpykC~~~~CGKsFssks~Lq~H~r~H--- 1044 (1135)
..|..|...|.....|..|.+. ..|..+ +++.|.+..|++.|.....+..|...|
T Consensus 290 ~~~~~~~~~~s~~~~l~~~~~~--------------------~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~ 349 (467)
T COG5048 290 IKSKQCNISFSRSSPLTRHLRS--------------------VNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSI 349 (467)
T ss_pred CCCccccCCccccccccccccc--------------------cccccccCCceeeeccCCCccccccccccCCcccccCC
Confidence 4556677777665555444421 145556 777777555888888888777777654
Q ss_pred ----ccCCCCCCcccChhHHHhh-----hhccCCCCcccCCCCCCCCcccChhHHHHHHHhcCCCCcccCCCCCCCCccc
Q 001158 1045 ----CPHEGCGKRFSSHKYAIIH-----QRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFR 1115 (1135)
Q Consensus 1045 ----c~Ce~CGKsFsskssL~~H-----qrtHtGeKPfkCp~~~CGKsFsskssLk~H~RtHTGEKPYkC~vpGCGKsF~ 1115 (1135)
+.-..|.+.+.....-..+ .......+.+.|.+..|-..+.....+..|...|...+++.|...+|.+.|.
T Consensus 350 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 429 (467)
T COG5048 350 SPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFN 429 (467)
T ss_pred CccccccccCccccccccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhcc
Confidence 1112333333322221111 1112223445554445666666666666666666665555555455666666
Q ss_pred ChhHHHHHHHhhCCCC
Q 001158 1116 FVSDISRHRRKTGHYE 1131 (1135)
Q Consensus 1116 skSsL~kH~R~H~h~k 1131 (1135)
....+..|++.|....
T Consensus 430 ~~~~~~~~~~~~~~~~ 445 (467)
T COG5048 430 RHYNLIPHKKIHTNHA 445 (467)
T ss_pred CcccccccccccccCC
Confidence 6666666666554443
No 35
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.95 E-value=0.15 Score=63.30 Aligned_cols=46 Identities=22% Similarity=0.200 Sum_probs=27.0
Q ss_pred eccCCCCCCcccChHHHHhhhhc-cccCCCCC------CcccChhHHHhhhhccC
Q 001158 1021 RCDLDGCRMSFETKRELSLHKRN-RCPHEGCG------KRFSSHKYAIIHQRVHD 1068 (1135)
Q Consensus 1021 kC~~~~CGKsFssks~Lq~H~r~-Hc~Ce~CG------KsFsskssL~~HqrtHt 1068 (1135)
.|. .|...|.....|.+|++. |+.|..|. .-|.....|..|-+.++
T Consensus 184 ~C~--~C~~~fld~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 184 LCK--FCHERFLDDDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cch--hhhhhhccHHHHHHhhccceeheeecCcccccchhcccchHHHHHhhhcC
Confidence 355 666777777777777664 45555553 33555556666666544
No 36
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=92.55 E-value=0.078 Score=48.97 Aligned_cols=72 Identities=21% Similarity=0.327 Sum_probs=20.8
Q ss_pred eccCCCCCCcccChHHHHhhhhccccCC-CCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHHHHHHhc
Q 001158 1021 RCDLDGCRMSFETKRELSLHKRNRCPHE-GCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVH 1097 (1135)
Q Consensus 1021 kC~~~~CGKsFssks~Lq~H~r~Hc~Ce-~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk~H~RtH 1097 (1135)
+|. .|+..|.....|..|+...+.-. .....+.....+..+.+.-. ...+.| ..|++.|.+...|..|++.+
T Consensus 1 ~C~--~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~-~~~~~C--~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCL--FCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKV-KESFRC--PYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ---------------------------------------------------SSEEB--SSSS-EESSHHHHHHHHHHT
T ss_pred Ccc--cccccccccccccccccccccccccccccccccccccccccccc-CCCCCC--CccCCCCcCHHHHHHHHcCc
Confidence 477 89999999999999997542211 12222333444444443222 226999 45999999999999999974
No 37
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.21 E-value=0.061 Score=60.47 Aligned_cols=61 Identities=33% Similarity=0.520 Sum_probs=28.3
Q ss_pred CCCCCCcccChhHHHhhhh--ccCCC--CcccCCCCCCCCcccChhHHHHHHHhcCCCCcccCCC
Q 001158 1047 HEGCGKRFSSHKYAIIHQR--VHDDE--RPLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKF 1107 (1135)
Q Consensus 1047 Ce~CGKsFsskssL~~Hqr--tHtGe--KPfkCp~~~CGKsFsskssLk~H~RtHTGEKPYkC~v 1107 (1135)
|..|...|.....|..|.+ .|.++ +++.|++..|++.|.+...+..|...|++.+++.|..
T Consensus 292 ~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (467)
T COG5048 292 SKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356 (467)
T ss_pred CccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccccc
Confidence 3344444444444444444 44444 4555532235555555555555555554444444443
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=90.85 E-value=0.22 Score=34.84 Aligned_cols=23 Identities=35% Similarity=0.749 Sum_probs=13.4
Q ss_pred ccCCCCCCCCcccChhHHHHHHHhh
Q 001158 1103 YKCKFEGCGLSFRFVSDISRHRRKT 1127 (1135)
Q Consensus 1103 YkC~vpGCGKsF~skSsL~kH~R~H 1127 (1135)
|.|.. |++.|.....|..|++.|
T Consensus 1 ~~C~~--C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPE--CGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCC--CcchhCCHHHHHHHHHHh
Confidence 35555 666666666666665544
No 39
>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=90.64 E-value=0.13 Score=37.66 Aligned_cols=25 Identities=36% Similarity=0.667 Sum_probs=18.2
Q ss_pred cccCCCCCCCCcccChhHHHHHHHhcC
Q 001158 1072 PLKCPWKGCSMSFKWAWARTEHIRVHT 1098 (1135)
Q Consensus 1072 PfkCp~~~CGKsFsskssLk~H~RtHT 1098 (1135)
||.| ..|++.|.....|..|++.|.
T Consensus 1 ~~~C--~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFEC--DECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEE--TTTTEEESSHHHHHHHHCTTT
T ss_pred CCCC--CccCCccCChhHHHHHhHHhc
Confidence 5677 557777777777777777664
No 40
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=90.39 E-value=0.19 Score=34.89 Aligned_cols=23 Identities=30% Similarity=0.635 Sum_probs=12.9
Q ss_pred ccCCCCCCCCcccChhHHHHHHHhc
Q 001158 1073 LKCPWKGCSMSFKWAWARTEHIRVH 1097 (1135)
Q Consensus 1073 fkCp~~~CGKsFsskssLk~H~RtH 1097 (1135)
|.| ..|++.|.+...|..|+++|
T Consensus 1 ~~C--~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQC--PICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE---SSTS-EESSHHHHHHHHHHH
T ss_pred CCC--cCCCCcCCcHHHHHHHHHhh
Confidence 456 34666666666666666654
No 41
>PRK04860 hypothetical protein; Provisional
Probab=89.75 E-value=0.2 Score=52.50 Aligned_cols=39 Identities=36% Similarity=0.761 Sum_probs=33.3
Q ss_pred CcccCCCCCCCCcccChhHHHHHHHhcCCCCcccCCCCCCCCcccCh
Q 001158 1071 RPLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFV 1117 (1135)
Q Consensus 1071 KPfkCp~~~CGKsFsskssLk~H~RtHTGEKPYkC~vpGCGKsF~sk 1117 (1135)
-+|.| . |++ ....+.+|.++|+|+++|.|.. |++.|...
T Consensus 118 ~~Y~C--~-C~~---~~~~~rrH~ri~~g~~~YrC~~--C~~~l~~~ 156 (160)
T PRK04860 118 FPYRC--K-CQE---HQLTVRRHNRVVRGEAVYRCRR--CGETLVFK 156 (160)
T ss_pred EEEEc--C-CCC---eeCHHHHHHHHhcCCccEECCC--CCceeEEe
Confidence 36899 5 987 6778899999999999999998 99988754
No 42
>smart00355 ZnF_C2H2 zinc finger.
Probab=87.62 E-value=0.48 Score=33.08 Aligned_cols=24 Identities=38% Similarity=0.625 Sum_probs=16.2
Q ss_pred ccCCCCCCCCcccChhHHHHHHHhcC
Q 001158 1073 LKCPWKGCSMSFKWAWARTEHIRVHT 1098 (1135)
Q Consensus 1073 fkCp~~~CGKsFsskssLk~H~RtHT 1098 (1135)
|.| ..|++.|.....|..|++.|.
T Consensus 1 ~~C--~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRC--PECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCC--CCCcchhCCHHHHHHHHHHhc
Confidence 456 447777777777777776654
No 43
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.97 E-value=0.63 Score=58.09 Aligned_cols=48 Identities=21% Similarity=0.223 Sum_probs=23.6
Q ss_pred CCCCCCcccChhHHHhhhhccCCCCcccCCC----CCCCCcccChhHHHHHHHhcC
Q 001158 1047 HEGCGKRFSSHKYAIIHQRVHDDERPLKCPW----KGCSMSFKWAWARTEHIRVHT 1098 (1135)
Q Consensus 1047 Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~----~~CGKsFsskssLk~H~RtHT 1098 (1135)
|..|...|.....|.+|++.++ |.|.+ ..++..|.....|..|-|.++
T Consensus 185 C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 185 CKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred chhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 4555666666666666655443 23322 112334555555666655433
No 44
>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=85.60 E-value=0.53 Score=40.87 Aligned_cols=30 Identities=27% Similarity=0.540 Sum_probs=14.3
Q ss_pred CCCcccCCCCCCCCcccChhHHHHHHHhhCCC
Q 001158 1099 GERPYKCKFEGCGLSFRFVSDISRHRRKTGHY 1130 (1135)
Q Consensus 1099 GEKPYkC~vpGCGKsF~skSsL~kH~R~H~h~ 1130 (1135)
.+.|-.|++ |+..+.+..+|++|+..+|..
T Consensus 21 S~~PatCP~--C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 21 SEQPATCPI--CGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp TS--EE-TT--T--EESSHHHHHHHHHHHTTT
T ss_pred cCCCCCCCc--chhhccchhhHHHHHHHHhcc
Confidence 345566666 666666666666666554433
No 45
>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=84.17 E-value=0.78 Score=39.89 Aligned_cols=40 Identities=15% Similarity=0.384 Sum_probs=23.4
Q ss_pred Hhhhhc-cCCCCcccCCCCCCCCcccChhHHHHHHHhcCCCCc
Q 001158 1061 IIHQRV-HDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGERP 1102 (1135)
Q Consensus 1061 ~~Hqrt-HtGeKPfkCp~~~CGKsFsskssLk~H~RtHTGEKP 1102 (1135)
..|.+. +..+.|..| .+|+..+.+..+|++|+..+++.||
T Consensus 12 ~~~~k~~~~S~~PatC--P~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 12 TKKPKSKSQSEQPATC--PICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp ----CCCCTTS--EE---TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhHHHHhhccCCCCCC--CcchhhccchhhHHHHHHHHhcccC
Confidence 334443 345678899 4599999999999999988777775
No 46
>PRK04860 hypothetical protein; Provisional
Probab=83.84 E-value=0.56 Score=49.30 Aligned_cols=38 Identities=18% Similarity=0.406 Sum_probs=32.2
Q ss_pred cccCCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccCh
Q 001158 1044 RCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWA 1087 (1135)
Q Consensus 1044 Hc~Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFssk 1087 (1135)
.|.|. |++ ....+++|.++|+++++|.| ..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC--~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRC--RRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEEC--CCCCceeEEe
Confidence 47786 887 66789999999999999999 6799988754
No 47
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=82.34 E-value=0.47 Score=34.17 Aligned_cols=23 Identities=26% Similarity=0.642 Sum_probs=15.1
Q ss_pred ccCCCCCCCCcccChhHHHHHHHhh
Q 001158 1103 YKCKFEGCGLSFRFVSDISRHRRKT 1127 (1135)
Q Consensus 1103 YkC~vpGCGKsF~skSsL~kH~R~H 1127 (1135)
|.|.+ |++.|.....|..|++.+
T Consensus 1 ~~C~~--C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDI--CNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETT--TTEEESSHHHHHHHHTTH
T ss_pred CCCCC--CCCCcCCHHHHHHHHCcC
Confidence 45666 777777777777776643
No 48
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=80.08 E-value=1.9 Score=49.91 Aligned_cols=71 Identities=24% Similarity=0.330 Sum_probs=53.2
Q ss_pred eeccCCCCCCcccChHHHHhhhhc-cccCCCCCCc-------ccChhHHHhhhhccCCCCcccCCCCCCC----CcccCh
Q 001158 1020 HRCDLDGCRMSFETKRELSLHKRN-RCPHEGCGKR-------FSSHKYAIIHQRVHDDERPLKCPWKGCS----MSFKWA 1087 (1135)
Q Consensus 1020 ykC~~~~CGKsFssks~Lq~H~r~-Hc~Ce~CGKs-------FsskssL~~HqrtHtGeKPfkCp~~~CG----KsFssk 1087 (1135)
-.|. .|...|..-..|.+|++. |-.|.+|++. |+....|-.|.+. --|.|++..|- ..|...
T Consensus 221 P~C~--FC~~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~----~hy~ct~qtc~~~k~~vf~~~ 294 (493)
T COG5236 221 PLCI--FCKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRN----AHYCCTFQTCRVGKCYVFPYH 294 (493)
T ss_pred chhh--hccceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhc----CceEEEEEEEecCcEEEeccH
Confidence 3488 899999999999999996 5567777653 6666777777653 23788776665 467888
Q ss_pred hHHHHHHHh
Q 001158 1088 WARTEHIRV 1096 (1135)
Q Consensus 1088 ssLk~H~Rt 1096 (1135)
..|..|+..
T Consensus 295 ~el~~h~~~ 303 (493)
T COG5236 295 TELLEHLTR 303 (493)
T ss_pred HHHHHHHHH
Confidence 888899654
No 49
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=77.84 E-value=1.3 Score=52.26 Aligned_cols=28 Identities=29% Similarity=0.608 Sum_probs=24.1
Q ss_pred ccCCCCCCCCcccChhHHHHHHHhhCCC
Q 001158 1103 YKCKFEGCGLSFRFVSDISRHRRKTGHY 1130 (1135)
Q Consensus 1103 YkC~vpGCGKsF~skSsL~kH~R~H~h~ 1130 (1135)
|.|..+||+..|...+.+..|.|+|...
T Consensus 402 fhc~r~Gc~~tl~s~sqm~shkrkheRq 429 (480)
T KOG4377|consen 402 FHCDRLGCEATLYSVSQMASHKRKHERQ 429 (480)
T ss_pred eeecccCCceEEEehhhhhhhhhhhhhh
Confidence 5688889999999999999999988543
No 50
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=76.65 E-value=0.91 Score=49.30 Aligned_cols=74 Identities=22% Similarity=0.438 Sum_probs=39.7
Q ss_pred eeccCCCCCCcccChHHHHhhhhcc--ccCCCCCCcccChhHHHhhhhc-c---------CCCCcccCCCCCCCCcccCh
Q 001158 1020 HRCDLDGCRMSFETKRELSLHKRNR--CPHEGCGKRFSSHKYAIIHQRV-H---------DDERPLKCPWKGCSMSFKWA 1087 (1135)
Q Consensus 1020 ykC~~~~CGKsFssks~Lq~H~r~H--c~Ce~CGKsFsskssL~~Hqrt-H---------tGeKPfkCp~~~CGKsFssk 1087 (1135)
|.|....|-+.|....+...|.... -.|..|.+.|.+..-|..|+.- | .|.--|.|-+++|+-.|.+.
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~ 159 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHGNSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTS 159 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhcccchhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhh
Confidence 5566556666665555554444321 2456666666666666666542 2 13334555555555555555
Q ss_pred hHHHHH
Q 001158 1088 WARTEH 1093 (1135)
Q Consensus 1088 ssLk~H 1093 (1135)
...+.|
T Consensus 160 r~RkdH 165 (253)
T KOG4173|consen 160 RDRKDH 165 (253)
T ss_pred hhhhhH
Confidence 555555
No 51
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=76.60 E-value=1.7 Score=31.20 Aligned_cols=22 Identities=36% Similarity=0.798 Sum_probs=12.2
Q ss_pred ccCCCCCCCCcccChhHHHHHHHhh
Q 001158 1103 YKCKFEGCGLSFRFVSDISRHRRKT 1127 (1135)
Q Consensus 1103 YkC~vpGCGKsF~skSsL~kH~R~H 1127 (1135)
|+|+. |+.... ...|.+|++.|
T Consensus 1 y~C~~--C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPH--CSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SS--SS-EES-HHHHHHHHHHH
T ss_pred CCCCC--CCCcCC-HHHHHHHHHhh
Confidence 45666 666665 66666666654
No 52
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=76.51 E-value=1 Score=49.71 Aligned_cols=48 Identities=25% Similarity=0.364 Sum_probs=38.6
Q ss_pred CCceeccCCCCCCcccChHHHHhhhhc-cccCCCCCCcccChhHHHhhh-hcc
Q 001158 1017 KGHHRCDLDGCRMSFETKRELSLHKRN-RCPHEGCGKRFSSHKYAIIHQ-RVH 1067 (1135)
Q Consensus 1017 eKpykC~~~~CGKsFssks~Lq~H~r~-Hc~Ce~CGKsFsskssL~~Hq-rtH 1067 (1135)
.|++ |= .|++.|....-|..|++. ||+|.+|.|.+.+--.|..|. .+|
T Consensus 9 ~kpw-cw--ycnrefddekiliqhqkakhfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 9 DKPW-CW--YCNREFDDEKILIQHQKAKHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred CCce-ee--ecccccchhhhhhhhhhhccceeeeehhhhccCCCceeehhhhh
Confidence 4555 65 799999999999999985 899999999887777777774 345
No 53
>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=73.39 E-value=2.1 Score=31.74 Aligned_cols=20 Identities=30% Similarity=0.421 Sum_probs=9.0
Q ss_pred cCCCCCCcccChhHHHhhhh
Q 001158 1046 PHEGCGKRFSSHKYAIIHQR 1065 (1135)
Q Consensus 1046 ~Ce~CGKsFsskssL~~Hqr 1065 (1135)
.|..|++.|.+...|..|++
T Consensus 3 ~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 3 YCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp BBTTTTBBBSSHHHHHCCTT
T ss_pred CcccCCCCcCCHHHHHHHHc
Confidence 34444444444444444443
No 54
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=71.56 E-value=4.7 Score=47.50 Aligned_cols=156 Identities=15% Similarity=0.235 Sum_probs=96.2
Q ss_pred CcCCccCcCCCCchhHHHHHh-hcccc-------------CcccCCCCCCCcccccc-ccCCCCceeccCCCCCCcccCh
Q 001158 970 GLRSRAGKDAANTSEVDIRKI-AEKRA-------------TKTMRNRESVPAPCQDK-KKILKGHHRCDLDGCRMSFETK 1034 (1135)
Q Consensus 970 ~lC~~CgK~Fssks~Lk~H~r-~~Kp~-------------~K~F~srssL~~~H~~k-~H~~eKpykC~~~~CGKsFssk 1034 (1135)
+.|..|...|.....-+.|++ .++.| ...|..+-.....-... ....+-++.|. .|.+.|...
T Consensus 4 ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~--~c~k~~~s~ 81 (390)
T KOG2785|consen 4 FTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCE--ACNKSFASP 81 (390)
T ss_pred ceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehH--HhhccccCh
Confidence 678889999999988889988 44444 11222211110000011 13345678999 999999998
Q ss_pred HHHHhhhhc--c--------------------ccC-------------CCCCCcccChhHHHhhhh------cc------
Q 001158 1035 RELSLHKRN--R--------------------CPH-------------EGCGKRFSSHKYAIIHQR------VH------ 1067 (1135)
Q Consensus 1035 s~Lq~H~r~--H--------------------c~C-------------e~CGKsFsskssL~~Hqr------tH------ 1067 (1135)
.....|+.. | .++ ..+-..+........+.. +-
T Consensus 82 ~a~~~hl~Sk~h~~~~~~~~r~~e~d~a~~~q~~~~~p~~l~~~~e~e~~~~E~~~~~d~~~e~~~dd~~Edi~~d~~~e 161 (390)
T KOG2785|consen 82 KAHENHLKSKKHVENLSNHQRSEEGDSAKISQLPSRRPSNLQNKGESELKWYEVDSDEDSSEEEEEDDEEEDIEEDGDDE 161 (390)
T ss_pred hhHHHHHHHhhcchhhhhhhccccccchhhhhccccCccccccCCCcccchhhcccccccchhhccCcchhhhhhccchh
Confidence 888888763 1 111 111111111111111110 00
Q ss_pred CCCCcccCCCCCCCCcccChhHHHHHHHhcCCC-----------------------CcccCCCCCCC---CcccChhHHH
Q 001158 1068 DDERPLKCPWKGCSMSFKWAWARTEHIRVHTGE-----------------------RPYKCKFEGCG---LSFRFVSDIS 1121 (1135)
Q Consensus 1068 tGeKPfkCp~~~CGKsFsskssLk~H~RtHTGE-----------------------KPYkC~vpGCG---KsF~skSsL~ 1121 (1135)
...-|-.|-| |++.|..-.....||..|+|- .-|.|-. |. +.|.+....+
T Consensus 162 ~e~~Pt~CLf--C~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~--CN~~~~~f~sleavr 237 (390)
T KOG2785|consen 162 DELIPTDCLF--CDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLF--CNELGRPFSSLEAVR 237 (390)
T ss_pred cccCCcceee--cCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEE--eccccCcccccHHHH
Confidence 0012467865 999999999999999987762 3477888 98 9999999999
Q ss_pred HHHHhhCCCC
Q 001158 1122 RHRRKTGHYE 1131 (1135)
Q Consensus 1122 kH~R~H~h~k 1131 (1135)
.||...+|.+
T Consensus 238 ~HM~~K~HCk 247 (390)
T KOG2785|consen 238 AHMRDKGHCK 247 (390)
T ss_pred HHHhhccCcc
Confidence 9999877765
No 55
>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=70.48 E-value=0.98 Score=33.51 Aligned_cols=22 Identities=18% Similarity=0.542 Sum_probs=13.7
Q ss_pred ccCCCCCCCCcccChhHHHHHHHh
Q 001158 1103 YKCKFEGCGLSFRFVSDISRHRRK 1126 (1135)
Q Consensus 1103 YkC~vpGCGKsF~skSsL~kH~R~ 1126 (1135)
|.|.. |++.|.....|..|++.
T Consensus 2 ~~C~~--C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDA--CDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTT--TTBBBSSHHHHHCCTTS
T ss_pred CCccc--CCCCcCCHHHHHHHHcc
Confidence 45666 66666666666666653
No 56
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=70.47 E-value=2.4 Score=56.18 Aligned_cols=26 Identities=27% Similarity=0.576 Sum_probs=23.1
Q ss_pred CCCcccCCCCCCCCcccChhHHHHHHHh
Q 001158 1099 GERPYKCKFEGCGLSFRFVSDISRHRRK 1126 (1135)
Q Consensus 1099 GEKPYkC~vpGCGKsF~skSsL~kH~R~ 1126 (1135)
+.+||.|.. |...|..+.+|..|+..
T Consensus 515 ~~~p~~C~~--C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 515 PGKPYPCRA--CNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CCCccccee--eeeeeecchHHHHHHHH
Confidence 357899999 99999999999999874
No 57
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=69.68 E-value=2.4 Score=30.45 Aligned_cols=22 Identities=27% Similarity=0.511 Sum_probs=14.3
Q ss_pred ccCCCCCCCCcccChhHHHHHHHh
Q 001158 1073 LKCPWKGCSMSFKWAWARTEHIRV 1096 (1135)
Q Consensus 1073 fkCp~~~CGKsFsskssLk~H~Rt 1096 (1135)
|.| ..|++.|.....|..|++.
T Consensus 1 ~~C--~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYC--DICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEE--TTTTEEESSHHHHHHHHTT
T ss_pred CCC--CCCCCCcCCHHHHHHHHCc
Confidence 456 4577777777777777654
No 58
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=69.62 E-value=1.4 Score=47.80 Aligned_cols=73 Identities=26% Similarity=0.450 Sum_probs=36.3
Q ss_pred CCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHHHHHHh-c---------CCCCcccCCCCCCCCcccCh
Q 001158 1048 EGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRV-H---------TGERPYKCKFEGCGLSFRFV 1117 (1135)
Q Consensus 1048 e~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk~H~Rt-H---------TGEKPYkC~vpGCGKsF~sk 1117 (1135)
-.|...|.....+..|..+-++. .| ..|.+.|.+...|..|+.- | .|.--|+|-+.||+..|.+.
T Consensus 85 agc~~~~d~lD~~E~hY~~~h~~---sC--s~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~ 159 (253)
T KOG4173|consen 85 AGCCQVFDALDDYEHHYHTLHGN---SC--SFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTS 159 (253)
T ss_pred cchHHHHhhhhhHHHhhhhcccc---hh--HHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhh
Confidence 34555555555455554332221 35 3355666655555555432 2 23334556555566666555
Q ss_pred hHHHHHHH
Q 001158 1118 SDISRHRR 1125 (1135)
Q Consensus 1118 SsL~kH~R 1125 (1135)
..-..|+-
T Consensus 160 r~RkdH~I 167 (253)
T KOG4173|consen 160 RDRKDHMI 167 (253)
T ss_pred hhhhhHHH
Confidence 55555544
No 59
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=64.95 E-value=1.1 Score=59.20 Aligned_cols=36 Identities=14% Similarity=0.096 Sum_probs=26.4
Q ss_pred HHHhcCCCCcccCCCCCCCCcccChhHHHHHHHhhCCCC
Q 001158 1093 HIRVHTGERPYKCKFEGCGLSFRFVSDISRHRRKTGHYE 1131 (1135)
Q Consensus 1093 H~RtHTGEKPYkC~vpGCGKsF~skSsL~kH~R~H~h~k 1131 (1135)
|.-.|..-++| |.. |...|.....|+.||+..+|+.
T Consensus 1320 ~~l~~~d~~~~-c~~--c~~~~~~~~alqihm~~~~~~~ 1355 (1406)
T KOG1146|consen 1320 PPLRVPDCTYH-CLA--CEVLLSGREALQIHMRSSAHRR 1355 (1406)
T ss_pred CcccCcccccc-chH--HHhhcchhHHHHHHHHHhhhcc
Confidence 33334444566 999 9999999999999999754543
No 60
>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=60.76 E-value=2.4 Score=32.74 Aligned_cols=23 Identities=22% Similarity=0.587 Sum_probs=16.1
Q ss_pred cccCCCCCCCCcccChhHHHHHHHh
Q 001158 1102 PYKCKFEGCGLSFRFVSDISRHRRK 1126 (1135)
Q Consensus 1102 PYkC~vpGCGKsF~skSsL~kH~R~ 1126 (1135)
+|.|.. |++.|.....+..|++.
T Consensus 3 ~~~C~~--C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKL--CNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccc--cCCccCCHHHHHHHHCh
Confidence 466777 77777777777777664
No 61
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=60.74 E-value=5.3 Score=28.63 Aligned_cols=23 Identities=30% Similarity=0.519 Sum_probs=14.0
Q ss_pred ccCCCCCCCCcccChhHHHHHHHhcC
Q 001158 1073 LKCPWKGCSMSFKWAWARTEHIRVHT 1098 (1135)
Q Consensus 1073 fkCp~~~CGKsFsskssLk~H~RtHT 1098 (1135)
|+| ..|+.... ...|..|++.|.
T Consensus 1 y~C--~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKC--PHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE---SSSS-EES-HHHHHHHHHHHH
T ss_pred CCC--CCCCCcCC-HHHHHHHHHhhC
Confidence 567 44777776 777777777643
No 62
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=59.23 E-value=6.8 Score=45.61 Aligned_cols=75 Identities=19% Similarity=0.272 Sum_probs=39.2
Q ss_pred eeccCCCCCCcccChHHHHhhhhc-c--ccCCCCCC---cc------cChhHHHhhhhccCCC---C-cccCCCCCCCCc
Q 001158 1020 HRCDLDGCRMSFETKRELSLHKRN-R--CPHEGCGK---RF------SSHKYAIIHQRVHDDE---R-PLKCPWKGCSMS 1083 (1135)
Q Consensus 1020 ykC~~~~CGKsFssks~Lq~H~r~-H--c~Ce~CGK---sF------sskssL~~HqrtHtGe---K-PfkCp~~~CGKs 1083 (1135)
|.|+...|.........|+.|.+. | +.|..|-+ .| .++..|+.|...-..+ | --.|-| |...
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~F--C~~~ 229 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIF--CKIY 229 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCcEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhh--ccce
Confidence 667666666666666677777664 1 33444421 12 2334455555432211 1 124633 6666
Q ss_pred ccChhHHHHHHHh
Q 001158 1084 FKWAWARTEHIRV 1096 (1135)
Q Consensus 1084 FsskssLk~H~Rt 1096 (1135)
|..-..|..|+|.
T Consensus 230 FYdDDEL~~HcR~ 242 (493)
T COG5236 230 FYDDDELRRHCRL 242 (493)
T ss_pred ecChHHHHHHHHh
Confidence 6666666666664
No 63
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=51.63 E-value=10 Score=28.26 Aligned_cols=14 Identities=29% Similarity=0.465 Sum_probs=5.7
Q ss_pred CCCCcccChHHHHhh
Q 001158 1026 GCRMSFETKRELSLH 1040 (1135)
Q Consensus 1026 ~CGKsFssks~Lq~H 1040 (1135)
.||+.| ....|..|
T Consensus 7 ~CgR~F-~~~~l~~H 20 (25)
T PF13913_consen 7 ICGRKF-NPDRLEKH 20 (25)
T ss_pred CCCCEE-CHHHHHHH
Confidence 444444 33334444
No 64
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=45.67 E-value=6.6 Score=43.68 Aligned_cols=45 Identities=27% Similarity=0.434 Sum_probs=28.2
Q ss_pred CCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHHHH-HHhc
Q 001158 1047 HEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEH-IRVH 1097 (1135)
Q Consensus 1047 Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk~H-~RtH 1097 (1135)
|=.|++.|....-|.+|++.. -|+| .+|-|.+.+--.|.-| |++|
T Consensus 13 cwycnrefddekiliqhqkak----hfkc--hichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAK----HFKC--HICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeecccccchhhhhhhhhhhc----ccee--eeehhhhccCCCceeehhhhh
Confidence 456777777777777776642 3777 6677665555555555 4444
No 65
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=44.98 E-value=18 Score=26.89 Aligned_cols=19 Identities=26% Similarity=0.779 Sum_probs=11.2
Q ss_pred cCCCCCCCCcccChhHHHHHHH
Q 001158 1104 KCKFEGCGLSFRFVSDISRHRR 1125 (1135)
Q Consensus 1104 kC~vpGCGKsF~skSsL~kH~R 1125 (1135)
.|+. ||+.| ....|.+|+.
T Consensus 4 ~C~~--CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPI--CGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCC--CCCEE-CHHHHHHHHH
Confidence 4655 66666 4555666654
No 66
>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=34.09 E-value=30 Score=26.57 Aligned_cols=22 Identities=18% Similarity=0.493 Sum_probs=15.2
Q ss_pred ceeccCCCCCCcccChHHHHhhhh
Q 001158 1019 HHRCDLDGCRMSFETKRELSLHKR 1042 (1135)
Q Consensus 1019 pykC~~~~CGKsFssks~Lq~H~r 1042 (1135)
+|.|. .|++.|.....+..|+.
T Consensus 3 ~~~C~--~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCK--LCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEcc--ccCCccCCHHHHHHHHC
Confidence 46677 77777777777777754
No 67
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=33.08 E-value=25 Score=42.04 Aligned_cols=114 Identities=16% Similarity=0.198 Sum_probs=63.4
Q ss_pred CCccCcCCCCchhHHHHHhhccccCcccCCCCCCCccccccccCCCCceeccCCCCCCcccChHHHHhhhh---------
Q 001158 972 RSRAGKDAANTSEVDIRKIAEKRATKTMRNRESVPAPCQDKKKILKGHHRCDLDGCRMSFETKRELSLHKR--------- 1042 (1135)
Q Consensus 972 C~~CgK~Fssks~Lk~H~r~~Kp~~K~F~srssL~~~H~~k~H~~eKpykC~~~~CGKsFssks~Lq~H~r--------- 1042 (1135)
.+.|+..+-.+..+.+|...++.... .| .+ -.|.-...|-|....|.+ +-++...|..
T Consensus 276 ~e~C~ykr~~k~DvirH~~~hkkrdn------sL--~d--gf~rfs~syhC~~~~C~k---sTsdV~~h~nFht~~~n~G 342 (480)
T KOG4377|consen 276 NEYCFYKRGQKNDVIRHVEIHKKRDN------SL--ID--GFHRFSNSYHCTGQICEK---STSDVLLHDNFHTDKRNNG 342 (480)
T ss_pred CccccccccchhhhHHHHHHHhhccc------cc--cc--chhhcCccchhhhcccCc---ccccccccCccccccccCc
Confidence 46688887778888888763332110 11 00 001111226777778877 3344455533
Q ss_pred ---ccccCCCCC--CcccChhHHHhhhhccCCC------------------------CcccCCCCCCCCcccChhHHHHH
Q 001158 1043 ---NRCPHEGCG--KRFSSHKYAIIHQRVHDDE------------------------RPLKCPWKGCSMSFKWAWARTEH 1093 (1135)
Q Consensus 1043 ---~Hc~Ce~CG--KsFsskssL~~HqrtHtGe------------------------KPfkCp~~~CGKsFsskssLk~H 1093 (1135)
.||.|-.|| -.|.....-..|.+-+.++ .-|-|.+.+|+.+|..-+.+..|
T Consensus 343 frrthfhC~r~gCTdtfK~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~~cnhfhc~r~Gc~~tl~s~sqm~sh 422 (480)
T KOG4377|consen 343 FRRTHFHCQRIGCTDTFKDSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSGICNHFHCDRLGCEATLYSVSQMASH 422 (480)
T ss_pred eecceeEEeccCCccccccccccccccCcchhhhhhhhhhhccccCCccCcccccceeeeeecccCCceEEEehhhhhhh
Confidence 356665555 4454333333333333222 11446667899999999999999
Q ss_pred HHhcC
Q 001158 1094 IRVHT 1098 (1135)
Q Consensus 1094 ~RtHT 1098 (1135)
.|.|.
T Consensus 423 krkhe 427 (480)
T KOG4377|consen 423 KRKHE 427 (480)
T ss_pred hhhhh
Confidence 98885
No 68
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=30.77 E-value=21 Score=31.86 Aligned_cols=28 Identities=39% Similarity=0.699 Sum_probs=19.8
Q ss_pred cCCCCcccCCCCCCCCcccChhHHHHHHHh
Q 001158 1097 HTGERPYKCKFEGCGLSFRFVSDISRHRRK 1126 (1135)
Q Consensus 1097 HTGEKPYkC~vpGCGKsF~skSsL~kH~R~ 1126 (1135)
-.||.-+.|+. ||..|+...++.+|..+
T Consensus 12 RDGE~~lrCPR--C~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPR--CGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCc--hhHHHHHhHHHHHHhhH
Confidence 34666677776 77777777777777654
No 69
>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=30.20 E-value=33 Score=34.22 Aligned_cols=6 Identities=33% Similarity=0.960 Sum_probs=2.5
Q ss_pred CCCCcc
Q 001158 1026 GCRMSF 1031 (1135)
Q Consensus 1026 ~CGKsF 1031 (1135)
.||+.|
T Consensus 14 ~CG~kF 19 (108)
T PF09538_consen 14 SCGAKF 19 (108)
T ss_pred CCcchh
Confidence 344443
No 70
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=29.72 E-value=27 Score=27.78 Aligned_cols=10 Identities=30% Similarity=0.720 Sum_probs=4.6
Q ss_pred CCCCcccChH
Q 001158 1026 GCRMSFETKR 1035 (1135)
Q Consensus 1026 ~CGKsFssks 1035 (1135)
.|+..|.-..
T Consensus 7 ~C~~~~~v~~ 16 (38)
T TIGR02098 7 NCKTSFRVVD 16 (38)
T ss_pred CCCCEEEeCH
Confidence 4555544433
No 71
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=26.96 E-value=15 Score=43.10 Aligned_cols=71 Identities=21% Similarity=0.418 Sum_probs=46.7
Q ss_pred CCceeccCCCCCCcccChHHHHhhhhc-cccCCCCCCcccChhHHHhhhhccCCCCcccCCCCCCCCcccChhHHHHHH
Q 001158 1017 KGHHRCDLDGCRMSFETKRELSLHKRN-RCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHI 1094 (1135)
Q Consensus 1017 eKpykC~~~~CGKsFssks~Lq~H~r~-Hc~Ce~CGKsFsskssL~~HqrtHtGeKPfkCp~~~CGKsFsskssLk~H~ 1094 (1135)
.++|.|+.+.|.+.+....+|+.|... ||.-- ...++ .-+-|+-.....|+|.| .+|.++++....|+.|.
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i----~~~s~-~~~ph~~~~~~nk~~r~--~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPI----TTPTP-APIPHQGFVVENKPYRC--EVCSKRYKNLNGLKYHR 418 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCC----CCCCC-CCCCcceeeeccCcccC--hhhhhhhccCCCCCcee
Confidence 578999999999999999999999764 33210 11111 12223333445688889 56888888777666653
No 72
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=25.20 E-value=24 Score=38.74 Aligned_cols=24 Identities=29% Similarity=0.389 Sum_probs=16.1
Q ss_pred CCceeccCCCCCCcccChHHHHhhhh
Q 001158 1017 KGHHRCDLDGCRMSFETKRELSLHKR 1042 (1135)
Q Consensus 1017 eKpykC~~~~CGKsFssks~Lq~H~r 1042 (1135)
.+.+.|+ .|++.|.++.-+....+
T Consensus 3 ~k~~~CP--vC~~~F~~~~vrs~~~r 26 (214)
T PF09986_consen 3 DKKITCP--VCGKEFKTKKVRSGKIR 26 (214)
T ss_pred CCceECC--CCCCeeeeeEEEcCCce
Confidence 3557788 88888887765544443
No 73
>cd04864 LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=24.57 E-value=1.3e+02 Score=33.84 Aligned_cols=45 Identities=24% Similarity=0.427 Sum_probs=40.2
Q ss_pred hhhhhHHHHHHHHHhcC-----------CceEEEEecc--chHhHHHHHHHHHHHhCC
Q 001158 272 FCLEHAAQIEEILQSKG-----------GAEILVICHS--DYQKIKAHAAAVAEEIGS 316 (1135)
Q Consensus 272 fCleHa~e~e~~l~~~G-----------G~~~l~~ch~--dY~ki~a~A~~vAee~~~ 316 (1135)
-|.|=|+.|-++|...| |.||+|=.-| +|..+++-|+.||++|.-
T Consensus 116 ~v~~~A~~~r~~L~~~gL~~f~KTSG~kGlHv~vPl~~~~~~~~~r~fa~~lA~~l~~ 173 (228)
T cd04864 116 AVRTAALAVRELLDELGLPSFVKTTGSRGFHVVVPLDGRGDFDDVRAFAAEAADALAK 173 (228)
T ss_pred HHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHH
Confidence 59999999999999987 8999998887 678999999999999863
No 74
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.95 E-value=1e+02 Score=31.17 Aligned_cols=48 Identities=21% Similarity=0.305 Sum_probs=26.7
Q ss_pred cCCCCCCCCcccChhHHHHHHHhcCCCCcccCCCCCCCCcccChhHHHHHHHhh
Q 001158 1074 KCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRHRRKT 1127 (1135)
Q Consensus 1074 kCp~~~CGKsFsskssLk~H~RtHTGEKPYkC~vpGCGKsF~skSsL~kH~R~H 1127 (1135)
.| -.|.+.|........- .-.....|+|+. |...|-..-+.-.|...|
T Consensus 57 ~C--~~C~~~f~~~~~~~~~--~~~~~~~y~C~~--C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 57 FC--FGCQGPFPKPPVSPFD--ELKDSHRYVCAV--CKNVFCVDCDVFVHESLH 104 (112)
T ss_pred cc--cCcCCCCCCccccccc--ccccccceeCCC--CCCccccccchhhhhhcc
Confidence 37 5677777654311100 011234577777 777777666666666555
No 75
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=23.81 E-value=52 Score=38.74 Aligned_cols=103 Identities=22% Similarity=0.336 Sum_probs=63.8
Q ss_pred ceeccCCCCCCcccChHHHHhhhhc--ccc---------------CCCCCCcccCh-hHHHhhhh-cc------------
Q 001158 1019 HHRCDLDGCRMSFETKRELSLHKRN--RCP---------------HEGCGKRFSSH-KYAIIHQR-VH------------ 1067 (1135)
Q Consensus 1019 pykC~~~~CGKsFssks~Lq~H~r~--Hc~---------------Ce~CGKsFssk-ssL~~Hqr-tH------------ 1067 (1135)
.+.|- .|.+.|+.+..|+.||+. |.. +..-|++..-. ..+.+-.. -+
T Consensus 195 r~~CL--yCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~e 272 (423)
T KOG2482|consen 195 RLRCL--YCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNE 272 (423)
T ss_pred hheee--eeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhc
Confidence 48898 899999999999999984 311 11123322111 11110000 00
Q ss_pred CCCCc--ccCCCCCCCCcccChhHHHHHHHh-cCC-------C-------------------CcccCCCCCCCCcccChh
Q 001158 1068 DDERP--LKCPWKGCSMSFKWAWARTEHIRV-HTG-------E-------------------RPYKCKFEGCGLSFRFVS 1118 (1135)
Q Consensus 1068 tGeKP--fkCp~~~CGKsFsskssLk~H~Rt-HTG-------E-------------------KPYkC~vpGCGKsF~skS 1118 (1135)
.+..+ .+|-+ |....-+...|..||++ |.= . +.-.|-. |.-.|-...
T Consensus 273 d~a~a~~v~CLf--C~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~--cd~~F~~e~ 348 (423)
T KOG2482|consen 273 DDAEALSVVCLF--CTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAE--CDLSFWKEP 348 (423)
T ss_pred CCCCccceEEEe--eccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhcccccc--ccccccCcc
Confidence 01122 48955 99988889999999985 520 0 1123555 999999999
Q ss_pred HHHHHHHhh
Q 001158 1119 DISRHRRKT 1127 (1135)
Q Consensus 1119 sL~kH~R~H 1127 (1135)
.|..||--|
T Consensus 349 ~l~~hm~e~ 357 (423)
T KOG2482|consen 349 GLLIHMVED 357 (423)
T ss_pred hhhhhcccc
Confidence 999998743
No 76
>cd04861 LigD_Pol_like LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase do
Probab=22.61 E-value=1.5e+02 Score=33.35 Aligned_cols=46 Identities=26% Similarity=0.406 Sum_probs=41.0
Q ss_pred hhhhhHHHHHHHHHhcC-----------CceEEEEecc--chHhHHHHHHHHHHHhCCC
Q 001158 272 FCLEHAAQIEEILQSKG-----------GAEILVICHS--DYQKIKAHAAAVAEEIGSP 317 (1135)
Q Consensus 272 fCleHa~e~e~~l~~~G-----------G~~~l~~ch~--dY~ki~a~A~~vAee~~~~ 317 (1135)
-|.|=|+.|-+.|...| |.||.+=..| +|..+++-|+.||++|.-.
T Consensus 115 ~v~~~A~~vr~~L~~lgL~~f~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~iA~~l~~~ 173 (227)
T cd04861 115 DVVEAALLLRELLDELGLESFPKTSGGKGLHVYVPLAPRYTWDEVRAFAKALARELARR 173 (227)
T ss_pred HHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHH
Confidence 59999999999999987 8999999887 6789999999999998643
No 77
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=22.30 E-value=29 Score=36.63 Aligned_cols=19 Identities=37% Similarity=0.642 Sum_probs=10.6
Q ss_pred hhccccCCCCCCcccChhH
Q 001158 1041 KRNRCPHEGCGKRFSSHKY 1059 (1135)
Q Consensus 1041 ~r~Hc~Ce~CGKsFsskss 1059 (1135)
.+.++.|+.||++|.+...
T Consensus 25 ~~~~~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 25 IRRRRECLACGKRFTTFER 43 (154)
T ss_pred eeeeeeccccCCcceEeEe
Confidence 3333566667776665433
No 78
>cd04865 LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=21.09 E-value=1.7e+02 Score=33.00 Aligned_cols=45 Identities=24% Similarity=0.386 Sum_probs=40.4
Q ss_pred hhhhhHHHHHHHHHhcC-----------CceEEEEecc--chHhHHHHHHHHHHHhCC
Q 001158 272 FCLEHAAQIEEILQSKG-----------GAEILVICHS--DYQKIKAHAAAVAEEIGS 316 (1135)
Q Consensus 272 fCleHa~e~e~~l~~~G-----------G~~~l~~ch~--dY~ki~a~A~~vAee~~~ 316 (1135)
-|.|=|+.|-++|...| |.||++=.-| +|..+++-|+.||++|.-
T Consensus 116 ~v~~~A~~vr~~L~~lgL~sf~KTSG~kGlHv~vPl~~~~~~~~~r~fa~~iA~~l~~ 173 (228)
T cd04865 116 DVVEVALLVREVLDELGLRGYPKTSGARGLHIYVPIAPRYTFEEVRRFAELLAREVER 173 (228)
T ss_pred HHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHH
Confidence 59999999999999987 8999998887 678999999999999864
No 79
>cd04862 PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nu
Probab=20.81 E-value=1.7e+02 Score=32.88 Aligned_cols=46 Identities=26% Similarity=0.434 Sum_probs=40.6
Q ss_pred hhhhhHHHHHHHHHhcC-----------CceEEEEecc--chHhHHHHHHHHHHHhCCC
Q 001158 272 FCLEHAAQIEEILQSKG-----------GAEILVICHS--DYQKIKAHAAAVAEEIGSP 317 (1135)
Q Consensus 272 fCleHa~e~e~~l~~~G-----------G~~~l~~ch~--dY~ki~a~A~~vAee~~~~ 317 (1135)
-|.|=|+.|-+.|...| |.||.+=..| +|..+++-|+.||++|.-.
T Consensus 115 ~v~~~A~~~r~~L~~lgL~~~~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~lA~~l~~~ 173 (227)
T cd04862 115 AVVEAALLVRELLDELGLESFVKTSGGKGLHVVVPLAPRAGWDEVKAFAKALAQHLART 173 (227)
T ss_pred HHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHH
Confidence 59999999999999887 8999998887 6789999999999998643
No 80
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=20.77 E-value=62 Score=33.46 Aligned_cols=14 Identities=14% Similarity=0.522 Sum_probs=7.4
Q ss_pred ceeccCCCCCCcccCh
Q 001158 1019 HHRCDLDGCRMSFETK 1034 (1135)
Q Consensus 1019 pykC~~~~CGKsFssk 1034 (1135)
-|.|+ .|+..|...
T Consensus 99 ~Y~Cp--~C~~~y~~~ 112 (147)
T smart00531 99 YYKCP--NCQSKYTFL 112 (147)
T ss_pred EEECc--CCCCEeeHH
Confidence 35565 555555543
No 81
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=20.39 E-value=31 Score=37.88 Aligned_cols=13 Identities=23% Similarity=0.541 Sum_probs=9.7
Q ss_pred ccCCCCCCCCcccCh
Q 001158 1103 YKCKFEGCGLSFRFV 1117 (1135)
Q Consensus 1103 YkC~vpGCGKsF~sk 1117 (1135)
..|+. ||.+|...
T Consensus 49 ~vCP~--CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPH--CGYAAFEE 61 (214)
T ss_pred EECCC--CCCccccc
Confidence 46988 99887644
No 82
>cd04866 LigD_Pol_like_3 LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated repair DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=20.17 E-value=1.8e+02 Score=32.65 Aligned_cols=45 Identities=22% Similarity=0.409 Sum_probs=40.2
Q ss_pred hhhhhHHHHHHHHHhcC-----------CceEEEEec-c--chHhHHHHHHHHHHHhCC
Q 001158 272 FCLEHAAQIEEILQSKG-----------GAEILVICH-S--DYQKIKAHAAAVAEEIGS 316 (1135)
Q Consensus 272 fCleHa~e~e~~l~~~G-----------G~~~l~~ch-~--dY~ki~a~A~~vAee~~~ 316 (1135)
-|.|=|+.|-+.|...| |.||.+=.. | +|..+++-|+.||++|.-
T Consensus 110 ~v~~~A~~vr~~L~~lgL~~f~KTSG~kGlHV~vPl~~~~~~~~~~r~fa~~iA~~l~~ 168 (223)
T cd04866 110 LAVEAANLLKEILDALGLTSFVKTSGNKGLQVYIPLPDNKFTYDETRLFTEFIAEYLCQ 168 (223)
T ss_pred HHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 58999999999999987 899999888 5 688999999999999864
Done!