Query 001121
Match_columns 1150
No_of_seqs 517 out of 2085
Neff 4.6
Searched_HMMs 46136
Date Thu Mar 28 16:24:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001121.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001121hhsearch_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 99.9 2.4E-22 5.3E-27 216.9 6.9 133 984-1141 130-265 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.8 7.7E-21 1.7E-25 205.4 6.8 111 1032-1150 128-246 (279)
3 KOG3608 Zn finger proteins [Ge 99.5 8.3E-15 1.8E-19 162.1 3.3 149 989-1143 184-345 (467)
4 KOG3608 Zn finger proteins [Ge 99.4 1.1E-13 2.4E-18 153.3 2.7 152 988-1150 140-322 (467)
5 KOG1074 Transcriptional repres 99.4 1.1E-13 2.3E-18 165.9 2.8 57 1088-1148 880-936 (958)
6 KOG3623 Homeobox transcription 99.3 2E-13 4.3E-18 161.1 1.5 101 1035-1141 211-331 (1007)
7 KOG1074 Transcriptional repres 99.3 2.8E-13 6.1E-18 162.4 0.8 80 1061-1144 607-693 (958)
8 KOG3576 Ovo and related transc 99.3 8.4E-13 1.8E-17 137.9 3.6 109 1032-1146 115-239 (267)
9 KOG3623 Homeobox transcription 99.3 8.5E-13 1.8E-17 155.8 0.8 77 1060-1140 895-971 (1007)
10 KOG3576 Ovo and related transc 99.2 3.2E-12 6.9E-17 133.7 0.1 82 1059-1144 117-198 (267)
11 PLN03086 PRLI-interacting fact 98.7 3.1E-08 6.8E-13 118.7 10.7 101 1032-1143 451-564 (567)
12 PHA00733 hypothetical protein 98.5 7.6E-08 1.6E-12 96.2 5.2 87 1032-1144 38-124 (128)
13 PLN03086 PRLI-interacting fact 98.5 1.4E-07 2.9E-12 113.4 6.8 100 1036-1150 435-544 (567)
14 PHA02768 hypothetical protein; 98.0 2.6E-06 5.7E-11 73.7 2.2 42 1088-1135 6-47 (55)
15 PHA02768 hypothetical protein; 98.0 3E-06 6.4E-11 73.4 2.1 43 1060-1106 6-48 (55)
16 KOG0958 DNA damage-responsive 98.0 1.5E-06 3.3E-11 104.6 -0.1 29 3-31 278-306 (690)
17 KOG1246 DNA-binding protein ju 97.9 1.2E-05 2.6E-10 102.8 5.5 55 3-57 434-488 (904)
18 KOG3993 Transcription factor ( 97.8 9.5E-06 2.1E-10 93.3 2.8 156 981-1143 292-482 (500)
19 PF13465 zf-H2C2_2: Zinc-finge 97.7 1.4E-05 3.1E-10 59.1 1.8 26 1104-1131 1-26 (26)
20 PHA00733 hypothetical protein 97.7 5.5E-05 1.2E-09 76.0 5.6 53 1032-1113 71-123 (128)
21 KOG3993 Transcription factor ( 97.3 4.7E-05 1E-09 87.8 0.1 110 1033-1146 266-383 (500)
22 PF13465 zf-H2C2_2: Zinc-finge 97.3 0.00011 2.5E-09 54.4 1.3 26 1074-1101 1-26 (26)
23 PHA00616 hypothetical protein 97.0 0.00037 8.1E-09 58.1 1.8 34 1087-1122 1-34 (44)
24 PHA00732 hypothetical protein 97.0 0.00055 1.2E-08 63.7 3.0 46 1060-1113 2-48 (79)
25 PHA00616 hypothetical protein 96.8 0.00048 1E-08 57.5 1.5 32 1060-1091 2-33 (44)
26 COG5189 SFP1 Putative transcri 96.8 0.00042 9.1E-09 77.7 0.9 55 1085-1141 347-420 (423)
27 PHA00732 hypothetical protein 96.7 0.0014 3E-08 61.0 3.4 43 1035-1082 2-47 (79)
28 PF05605 zf-Di19: Drought indu 96.7 0.0025 5.4E-08 54.8 4.6 50 1087-1143 2-53 (54)
29 PF12756 zf-C2H2_2: C2H2 type 96.6 0.0014 3.1E-08 60.6 3.0 76 1062-1146 2-77 (100)
30 COG5189 SFP1 Putative transcri 95.9 0.0027 5.9E-08 71.4 0.7 73 1032-1110 347-419 (423)
31 PF00096 zf-C2H2: Zinc finger, 95.7 0.0063 1.4E-07 43.1 1.8 23 1118-1142 1-23 (23)
32 PF05605 zf-Di19: Drought indu 95.7 0.014 3.1E-07 50.2 4.2 49 1060-1113 3-53 (54)
33 PF13894 zf-C2H2_4: C2H2-type 95.3 0.014 3E-07 40.8 2.3 24 1118-1143 1-24 (24)
34 KOG2231 Predicted E3 ubiquitin 95.2 0.024 5.1E-07 70.2 5.4 42 1041-1082 187-235 (669)
35 PF13912 zf-C2H2_6: C2H2-type 94.4 0.02 4.2E-07 42.2 1.3 25 1117-1143 1-25 (27)
36 PF00096 zf-C2H2: Zinc finger, 94.2 0.021 4.6E-07 40.4 1.1 23 1088-1112 1-23 (23)
37 PF13894 zf-C2H2_4: C2H2-type 93.8 0.031 6.7E-07 39.0 1.2 17 1095-1111 6-22 (24)
38 COG5048 FOG: Zn-finger [Genera 93.4 0.05 1.1E-06 61.2 2.7 143 985-1147 290-446 (467)
39 PF12756 zf-C2H2_2: C2H2 type 93.2 0.049 1.1E-06 50.3 2.0 72 1036-1112 1-73 (100)
40 COG5048 FOG: Zn-finger [Genera 93.0 0.042 9.1E-07 61.8 1.3 107 1034-1142 289-411 (467)
41 smart00355 ZnF_C2H2 zinc finge 91.8 0.16 3.4E-06 35.7 2.7 23 1118-1142 1-23 (26)
42 PF13912 zf-C2H2_6: C2H2-type 91.6 0.092 2E-06 38.6 1.3 25 1087-1113 1-25 (27)
43 KOG2231 Predicted E3 ubiquitin 90.8 0.27 5.8E-06 61.3 4.9 49 1061-1113 184-236 (669)
44 PRK04860 hypothetical protein; 89.2 0.18 3.9E-06 52.9 1.4 39 1087-1133 119-157 (160)
45 PF09237 GAGA: GAGA factor; I 88.4 0.34 7.3E-06 42.1 2.3 31 1114-1146 21-51 (54)
46 smart00355 ZnF_C2H2 zinc finge 88.3 0.4 8.6E-06 33.6 2.3 24 1088-1113 1-24 (26)
47 PF09237 GAGA: GAGA factor; I 85.3 0.55 1.2E-05 40.9 1.9 40 1076-1117 12-52 (54)
48 PF13909 zf-H2C2_5: C2H2-type 85.1 0.56 1.2E-05 33.8 1.6 23 1118-1143 1-23 (24)
49 PRK04860 hypothetical protein; 83.9 0.46 1E-05 50.0 1.1 39 1059-1103 119-157 (160)
50 PF12874 zf-met: Zinc-finger o 83.0 0.38 8.2E-06 34.7 0.0 22 1118-1141 1-22 (25)
51 COG5236 Uncharacterized conser 81.6 1.5 3.3E-05 50.7 4.0 71 1035-1111 221-303 (493)
52 KOG2893 Zn finger protein [Gen 80.0 0.71 1.5E-05 51.0 0.8 48 1032-1082 9-58 (341)
53 KOG1146 Homeobox protein [Gene 79.1 1 2.2E-05 59.4 2.0 74 1060-1141 466-540 (1406)
54 KOG4377 Zn-finger protein [Gen 77.6 1.4 3E-05 52.1 2.2 28 1118-1145 402-429 (480)
55 KOG1146 Homeobox protein [Gene 77.2 0.43 9.3E-06 62.7 -2.1 93 1035-1146 1261-1355(1406)
56 PF12171 zf-C2H2_jaz: Zinc-fin 76.8 1.4 3.1E-05 32.7 1.3 19 1062-1080 4-22 (27)
57 KOG2785 C2H2-type Zn-finger pr 75.6 3.3 7E-05 48.8 4.5 156 985-1146 4-247 (390)
58 KOG4173 Alpha-SNAP protein [In 72.9 1.2 2.5E-05 48.6 0.1 82 1032-1113 77-171 (253)
59 PF12874 zf-met: Zinc-finger o 72.6 2.3 5E-05 30.6 1.6 17 1041-1057 5-21 (25)
60 KOG4173 Alpha-SNAP protein [In 72.2 1.3 2.8E-05 48.3 0.2 76 1062-1142 84-169 (253)
61 COG5236 Uncharacterized conser 70.5 3.9 8.5E-05 47.5 3.5 23 1035-1057 152-174 (493)
62 PF13909 zf-H2C2_5: C2H2-type 67.5 3 6.4E-05 30.0 1.2 22 1088-1112 1-22 (24)
63 PF12171 zf-C2H2_jaz: Zinc-fin 64.8 3.8 8.3E-05 30.4 1.3 22 1035-1058 2-23 (27)
64 smart00451 ZnF_U1 U1-like zinc 62.5 2 4.3E-05 33.2 -0.6 23 1117-1141 3-25 (35)
65 PF13913 zf-C2HC_2: zinc-finge 61.4 5.9 0.00013 29.5 1.8 8 1062-1069 5-12 (25)
66 PF13913 zf-C2HC_2: zinc-finge 50.2 14 0.0003 27.6 2.2 19 1119-1140 4-22 (25)
67 smart00451 ZnF_U1 U1-like zinc 44.3 17 0.00037 28.0 2.0 22 1034-1057 3-24 (35)
68 KOG2893 Zn finger protein [Gen 43.5 7.9 0.00017 43.2 0.1 45 1062-1112 13-58 (341)
69 PF09538 FYDLN_acid: Protein o 36.6 22 0.00048 35.5 2.0 6 1095-1100 32-37 (108)
70 COG4049 Uncharacterized protei 35.4 16 0.00036 32.6 0.7 28 1112-1141 12-39 (65)
71 KOG4377 Zn-finger protein [Gen 34.0 22 0.00047 42.7 1.6 114 987-1113 276-427 (480)
72 KOG2482 Predicted C2H2-type Zn 31.2 32 0.0007 40.4 2.4 146 985-1142 145-357 (423)
73 PF09986 DUF2225: Uncharacteri 29.0 18 0.0004 39.7 0.0 43 1086-1132 4-61 (214)
74 TIGR02098 MJ0042_CXXC MJ0042 f 27.0 28 0.0006 27.8 0.7 12 1061-1072 4-15 (38)
75 PF09986 DUF2225: Uncharacteri 24.9 22 0.00049 39.0 -0.3 23 1033-1057 4-26 (214)
76 smart00531 TFIIE Transcription 24.1 38 0.00083 35.0 1.3 11 1060-1070 100-110 (147)
77 TIGR02300 FYDLN_acid conserved 23.4 55 0.0012 33.8 2.1 8 1062-1069 12-19 (129)
78 PF12013 DUF3505: Protein of u 22.7 61 0.0013 31.7 2.3 25 1118-1144 81-109 (109)
79 KOG4124 Putative transcription 22.7 19 0.00042 42.3 -1.3 72 1032-1110 347-419 (442)
80 COG1198 PriA Primosomal protei 22.2 65 0.0014 41.7 3.0 13 1114-1128 472-484 (730)
81 PRK00464 nrdR transcriptional 22.0 27 0.0006 36.8 -0.3 18 1056-1073 25-42 (154)
82 cd04864 LigD_Pol_like_1 LigD_P 21.0 1.7E+02 0.0036 33.1 5.5 46 286-331 115-173 (228)
83 KOG4124 Putative transcription 20.1 22 0.00048 41.7 -1.5 52 1086-1139 348-418 (442)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.86 E-value=2.4e-22 Score=216.93 Aligned_cols=133 Identities=26% Similarity=0.454 Sum_probs=120.3
Q ss_pred CCccCccCccCCCchhHHHHHhhccccCccCCCCCCCCCcccccccCCCCceeccCCCCCCcccChHHHHhHhhcc---C
Q 001121 984 EGLRSRAGKDAANTSEVDIRKIAEKRATKTMRNRESVPAPCQDKKKILKGHHRCDLDGCRMSFETKRELSLHKRNR---C 1060 (1150)
Q Consensus 984 ~~~Cs~CGK~F~sks~Lk~H~r~eKpy~K~F~srssL~~~H~~r~Ht~eKpykC~~~~CGKsFssks~Lk~H~r~H---c 1060 (1150)
.+.|+.|||.+.+.++|.+|+..+.+- ...+-|.|. .|||.|.+...|+.|+++| |
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~-------------------~s~ka~~C~--~C~K~YvSmpALkMHirTH~l~c 188 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSL-------------------DSKKAFSCK--YCGKVYVSMPALKMHIRTHTLPC 188 (279)
T ss_pred ceeccccccccccccccchhhcccccc-------------------cccccccCC--CCCceeeehHHHhhHhhccCCCc
Confidence 378889999999999999998533221 114557899 9999999999999999998 8
Q ss_pred CCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHHHhhcCCCCcccCCCCCCCCcccChhHHHHHHH
Q 001121 1061 PHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRHRR 1140 (1150)
Q Consensus 1061 ~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~HmRtHtGEKPYkC~v~GCGKsFsskS~LkrH~R 1140 (1150)
.|.+|||.|.+...|+-|+|+|+|||||.|+ .|+|.|..+++|+.||++|.+.|+|+|.. |+|.|...+.|.+|..
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 9999999999999986
Q ss_pred H
Q 001121 1141 K 1141 (1150)
Q Consensus 1141 k 1141 (1150)
.
T Consensus 265 S 265 (279)
T KOG2462|consen 265 S 265 (279)
T ss_pred h
Confidence 4
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.82 E-value=7.7e-21 Score=205.43 Aligned_cols=111 Identities=31% Similarity=0.614 Sum_probs=105.9
Q ss_pred CCceeccCCCCCCcccChHHHHhHhhcc--------CCCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChh
Q 001121 1032 KGHHRCDLDGCRMSFETKRELSLHKRNR--------CPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAW 1103 (1150)
Q Consensus 1032 eKpykC~~~~CGKsFssks~Lk~H~r~H--------c~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks 1103 (1150)
...|+|. .|||.+.+.++|.+|+.+| +.|+.|||.|.+...|+.|+|+|+ -+++| .+|||.|.+.|
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 3458899 9999999999999999988 689999999999999999999997 68999 66999999999
Q ss_pred HHHHHHhhcCCCCcccCCCCCCCCcccChhHHHHHHHHhCCCCCCCC
Q 001121 1104 ARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRHRRKTGHYENLSA 1150 (1150)
Q Consensus 1104 ~Lk~HmRtHtGEKPYkC~v~GCGKsFsskS~LkrH~RkHh~~kk~sC 1150 (1150)
.|+.|+|+|||||||.|++ |+|+|..+++|+.||++|.+.++|+|
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=99.49 E-value=8.3e-15 Score=162.09 Aligned_cols=149 Identities=21% Similarity=0.362 Sum_probs=108.1
Q ss_pred ccCccCCCchhHHHHHh---hccc-----cCccCCCCCCCCCcccccc-cCCCCceeccCCCCCCcccChHHHHhHhhcc
Q 001121 989 RAGKDAANTSEVDIRKI---AEKR-----ATKTMRNRESVPAPCQDKK-KILKGHHRCDLDGCRMSFETKRELSLHKRNR 1059 (1150)
Q Consensus 989 ~CGK~F~sks~Lk~H~r---~eKp-----y~K~F~srssL~~~H~~r~-Ht~eKpykC~~~~CGKsFssks~Lk~H~r~H 1059 (1150)
.|.+.|.+++.|+.|.+ ++|. ++.-|+++..| ..|.++. -....+|.|. .|.|.|.+...|+.|+..|
T Consensus 184 ~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl-~DH~rRqt~l~~n~fqC~--~C~KrFaTeklL~~Hv~rH 260 (467)
T KOG3608|consen 184 MCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKL-FDHLRRQTELNTNSFQCA--QCFKRFATEKLLKSHVVRH 260 (467)
T ss_pred hhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHH-HHHHHhhhhhcCCchHHH--HHHHHHhHHHHHHHHHHHh
Confidence 45566666666666665 2221 15555555555 4443322 2334578888 8888888888888888865
Q ss_pred ---CCCCCCCCccCChhHHHhhhhh-ccCCCCccCCCCcCCccccChhHHHHHHhhcCCCCcccCCCCCCCCcccChhHH
Q 001121 1060 ---CPHEGCGKRFSSHKYAIIHQRV-HDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDI 1135 (1150)
Q Consensus 1060 ---c~Ce~CGKsFssks~Lk~H~r~-HtgeKpfkCp~e~CgKsFssks~Lk~HmRtHtGEKPYkC~v~GCGKsFsskS~L 1135 (1150)
|+|+.|..+....+.|..|++. |...|||+| +.|++.|.+.+.|.+|..+|+ +.-|.|.++.|..+|++...+
T Consensus 261 vn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKC--d~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~ 337 (467)
T KOG3608|consen 261 VNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKC--DECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQM 337 (467)
T ss_pred hhcccccccccCCCChHHHHHHHHhhhccCCCccc--cchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHH
Confidence 7888888888888888888875 777888888 778888888888888888887 566888888888888888888
Q ss_pred HHHHHHhC
Q 001121 1136 SRHRRKTG 1143 (1150)
Q Consensus 1136 krH~RkHh 1143 (1150)
++|++.||
T Consensus 338 ~~H~~evh 345 (467)
T KOG3608|consen 338 RRHFLEVH 345 (467)
T ss_pred HHHHHHhc
Confidence 88888765
No 4
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.39 E-value=1.1e-13 Score=153.30 Aligned_cols=152 Identities=26% Similarity=0.368 Sum_probs=132.8
Q ss_pred CccCccCCCchhHHHHHh----h-----------ccc--------cCccCCCCCCCCCcccccccCCCCceeccCCCCCC
Q 001121 988 SRAGKDAANTSEVDIRKI----A-----------EKR--------ATKTMRNRESVPAPCQDKKKILKGHHRCDLDGCRM 1044 (1150)
Q Consensus 988 s~CGK~F~sks~Lk~H~r----~-----------eKp--------y~K~F~srssL~~~H~~r~Ht~eKpykC~~~~CGK 1044 (1150)
..|+..|.+...|..|.- . ++| +.+.|.++..| .+| .+.|+++|-..|+ .||.
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 679999999999999975 1 111 15667777777 777 7899999999999 9999
Q ss_pred cccChHHHHhHhhc-------cCCCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHHHhh-cCCCC
Q 001121 1045 SFETKRELSLHKRN-------RCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRV-HTGER 1116 (1150)
Q Consensus 1045 sFssks~Lk~H~r~-------Hc~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~HmRt-HtGEK 1116 (1150)
.|+++..|-.|.+. +|.|..|.|.|.+...|+.|++.|. .-|+||. |+.+....+.|..|++. |...|
T Consensus 216 ~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCpl--Cdmtc~~~ssL~~H~r~rHs~dk 291 (467)
T KOG3608|consen 216 LFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPL--CDMTCSSASSLTTHIRYRHSKDK 291 (467)
T ss_pred HhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh--hcccccc--cccCCCChHHHHHHHHhhhccCC
Confidence 99999999999874 5999999999999999999999996 4599965 99999999999999996 99999
Q ss_pred cccCCCCCCCCcccChhHHHHHHHHhCCCCCCCC
Q 001121 1117 PYKCKFEGCGLSFRFVSDISRHRRKTGHYENLSA 1150 (1150)
Q Consensus 1117 PYkC~v~GCGKsFsskS~LkrH~RkHh~~kk~sC 1150 (1150)
||+|+. |++.|.+.+.|.+|...|. ..-|+|
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 9999999999999999876 555555
No 5
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.39 E-value=1.1e-13 Score=165.93 Aligned_cols=57 Identities=26% Similarity=0.498 Sum_probs=53.2
Q ss_pred ccCCCCcCCccccChhHHHHHHhhcCCCCcccCCCCCCCCcccChhHHHHHHHHhCCCCCC
Q 001121 1088 LKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRHRRKTGHYENL 1148 (1150)
Q Consensus 1088 fkCp~e~CgKsFssks~Lk~HmRtHtGEKPYkC~v~GCGKsFsskS~LkrH~RkHh~~kk~ 1148 (1150)
+.| ..|++.|...+.|..|+|+|+|+|||.|.+ |++.|..+.+|+.||.+|+...++
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 578 779999999999999999999999999999 999999999999999999876554
No 6
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.34 E-value=2e-13 Score=161.10 Aligned_cols=101 Identities=27% Similarity=0.536 Sum_probs=93.1
Q ss_pred eeccCCCCCCcccChHHHHhHhhcc-------CCCCCCCCccCChhHHHhhhhhcc-------------CCCCccCCCCc
Q 001121 1035 HRCDLDGCRMSFETKRELSLHKRNR-------CPHEGCGKRFSSHKYAIIHQRVHD-------------DERPLKCPWKG 1094 (1150)
Q Consensus 1035 ykC~~~~CGKsFssks~Lk~H~r~H-------c~Ce~CGKsFssks~Lk~H~r~Ht-------------geKpfkCp~e~ 1094 (1150)
..|. +|.+.+.....|+.|++.. |.|..|.++|..+..|.+|+.+|. +.|.|+| .+
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 9999999999999998862 899999999999999999999884 2378999 78
Q ss_pred CCccccChhHHHHHHhhcCCCCcccCCCCCCCCcccChhHHHHHHHH
Q 001121 1095 CSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRHRRK 1141 (1150)
Q Consensus 1095 CgKsFssks~Lk~HmRtHtGEKPYkC~v~GCGKsFsskS~LkrH~Rk 1141 (1150)
|||.|+.+.+|+.|+|+|.|||||.|+. |+|+|.....+..||..
T Consensus 287 CgKAFKfKHHLKEHlRIHSGEKPfeCpn--CkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 287 CGKAFKFKHHLKEHLRIHSGEKPFECPN--CKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred cchhhhhHHHHHhhheeecCCCCcCCcc--cccccccCCcccccccc
Confidence 9999999999999999999999999998 99999999999999863
No 7
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.32 E-value=2.8e-13 Score=162.40 Aligned_cols=80 Identities=26% Similarity=0.441 Sum_probs=70.3
Q ss_pred CCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHHHhhcCCCC----cccCC---CCCCCCcccChh
Q 001121 1061 PHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGER----PYKCK---FEGCGLSFRFVS 1133 (1150)
Q Consensus 1061 ~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~HmRtHtGEK----PYkC~---v~GCGKsFsskS 1133 (1150)
.|-+|-+...-++.|+.|.|+|+|+|||+| .+||+.|.++.+|+.||-+|...- +|.|+ + |-+.|...-
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 488899999999999999999999999999 779999999999999999886543 47898 8 999999999
Q ss_pred HHHHHHHHhCC
Q 001121 1134 DISRHRRKTGH 1144 (1150)
Q Consensus 1134 ~LkrH~RkHh~ 1144 (1150)
.|..|++.|.+
T Consensus 683 ~lpQhIriH~~ 693 (958)
T KOG1074|consen 683 TLPQHIRIHLG 693 (958)
T ss_pred cccceEEeecC
Confidence 99999998864
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.31 E-value=8.4e-13 Score=137.94 Aligned_cols=109 Identities=24% Similarity=0.407 Sum_probs=98.3
Q ss_pred CCceeccCCCCCCcccChHHHHhHhhcc-----CCCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHH
Q 001121 1032 KGHHRCDLDGCRMSFETKRELSLHKRNR-----CPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWART 1106 (1150)
Q Consensus 1032 eKpykC~~~~CGKsFssks~Lk~H~r~H-----c~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk 1106 (1150)
...|.|. .|+|.|.....|.+|++.| +-|..|||.|.....|++|+|+|+|.|||+| ..|+|.|.++-.|.
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 4569999 9999999999999999986 7799999999999999999999999999999 77999999999999
Q ss_pred HHHhh-cC----------CCCcccCCCCCCCCcccChhHHHHHHHHhCCCC
Q 001121 1107 EHIRV-HT----------GERPYKCKFEGCGLSFRFVSDISRHRRKTGHYE 1146 (1150)
Q Consensus 1107 ~HmRt-Ht----------GEKPYkC~v~GCGKsFsskS~LkrH~RkHh~~k 1146 (1150)
.|.+. |. ..|-|.|.. ||..-.....+..|++.||...
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 99874 53 246799998 9999999999999999887653
No 9
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.26 E-value=8.5e-13 Score=155.83 Aligned_cols=77 Identities=31% Similarity=0.619 Sum_probs=75.3
Q ss_pred CCCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHHHhhcCCCCcccCCCCCCCCcccChhHHHHHH
Q 001121 1060 CPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRHR 1139 (1150)
Q Consensus 1060 c~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~HmRtHtGEKPYkC~v~GCGKsFsskS~LkrH~ 1139 (1150)
|.|+.|+|.|...+.|.+|..-|+|.|||+| .+|.|.|+.+.+|..|+|.|.|||||+|+. |+|+|.....+.+||
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 999999999999999
Q ss_pred H
Q 001121 1140 R 1140 (1150)
Q Consensus 1140 R 1140 (1150)
-
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=99.18 E-value=3.2e-12 Score=133.67 Aligned_cols=82 Identities=29% Similarity=0.606 Sum_probs=77.5
Q ss_pred cCCCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHHHhhcCCCCcccCCCCCCCCcccChhHHHHH
Q 001121 1059 RCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRH 1138 (1150)
Q Consensus 1059 Hc~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~HmRtHtGEKPYkC~v~GCGKsFsskS~LkrH 1138 (1150)
.|.|..|+|.|....-|.+|++-|...|.|-|++ |||.|.....|++|+|+|+|.+||+|.. |+|+|.++-.|..|
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 HHHhCC
Q 001121 1139 RRKTGH 1144 (1150)
Q Consensus 1139 ~RkHh~ 1144 (1150)
.++.|+
T Consensus 193 l~kvhg 198 (267)
T KOG3576|consen 193 LKKVHG 198 (267)
T ss_pred HHHHcC
Confidence 987444
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.74 E-value=3.1e-08 Score=118.72 Aligned_cols=101 Identities=23% Similarity=0.449 Sum_probs=84.9
Q ss_pred CCceeccCCCCCCcccChHHHHhHhhcc---CCCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCcccc--------
Q 001121 1032 KGHHRCDLDGCRMSFETKRELSLHKRNR---CPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFK-------- 1100 (1150)
Q Consensus 1032 eKpykC~~~~CGKsFssks~Lk~H~r~H---c~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFs-------- 1100 (1150)
++++.|+ .|++.|. ...|..|++.+ +.|+ ||+.| .+..|..|+++|...+++.|+| |++.|.
T Consensus 451 ~~H~~C~--~Cgk~f~-~s~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~f--C~~~v~~g~~~~d~ 523 (567)
T PLN03086 451 KNHVHCE--KCGQAFQ-QGEMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRF--CGDMVQAGGSAMDV 523 (567)
T ss_pred ccCccCC--CCCCccc-hHHHHHHHHhcCCCccCC-CCCCc-chhHHHhhhhccCCCCceeCCC--CCCccccCccccch
Confidence 4457899 9999996 68899999874 6798 99765 6789999999999999999976 999995
Q ss_pred --ChhHHHHHHhhcCCCCcccCCCCCCCCcccChhHHHHHHHHhC
Q 001121 1101 --WAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRHRRKTG 1143 (1150)
Q Consensus 1101 --sks~Lk~HmRtHtGEKPYkC~v~GCGKsFsskS~LkrH~RkHh 1143 (1150)
..+.|..|..++ |.+++.|.. ||+.|..+ .|..|+...|
T Consensus 524 ~d~~s~Lt~HE~~C-G~rt~~C~~--Cgk~Vrlr-dm~~H~~~~h 564 (567)
T PLN03086 524 RDRLRGMSEHESIC-GSRTAPCDS--CGRSVMLK-EMDIHQIAVH 564 (567)
T ss_pred hhhhhhHHHHHHhc-CCcceEccc--cCCeeeeh-hHHHHHHHhh
Confidence 245899999986 999999998 99998765 5788887644
No 12
>PHA00733 hypothetical protein
Probab=98.54 E-value=7.6e-08 Score=96.22 Aligned_cols=87 Identities=21% Similarity=0.266 Sum_probs=67.1
Q ss_pred CCceeccCCCCCCcccChHHHHhHhhccCCCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHHHhh
Q 001121 1032 KGHHRCDLDGCRMSFETKRELSLHKRNRCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRV 1111 (1150)
Q Consensus 1032 eKpykC~~~~CGKsFssks~Lk~H~r~Hc~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~HmRt 1111 (1150)
++++.|. .|.+.|.....|..| ..|.+|+..| +.+||.| ..|++.|.....|..|++.
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 4556666 666666655544443 2355665444 5889999 6699999999999999998
Q ss_pred cCCCCcccCCCCCCCCcccChhHHHHHHHHhCC
Q 001121 1112 HTGERPYKCKFEGCGLSFRFVSDISRHRRKTGH 1144 (1150)
Q Consensus 1112 HtGEKPYkC~v~GCGKsFsskS~LkrH~RkHh~ 1144 (1150)
| ..+|.|+. |++.|.....|.+|+.+.|+
T Consensus 96 h--~~~~~C~~--CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 96 T--EHSKVCPV--CGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred C--CcCccCCC--CCCccCCHHHHHHHHHHhcC
Confidence 7 36799999 99999999999999998654
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.50 E-value=1.4e-07 Score=113.37 Aligned_cols=100 Identities=24% Similarity=0.459 Sum_probs=80.3
Q ss_pred eccCCCCCCcccChHHHHhHhhccCCCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHHHhhcCCC
Q 001121 1036 RCDLDGCRMSFETKRELSLHKRNRCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGE 1115 (1150)
Q Consensus 1036 kC~~~~CGKsFssks~Lk~H~r~Hc~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~HmRtHtGE 1115 (1150)
.|+...||..|. +..|. .|+.|+.|++.|. ...|..|++.|+ +++.| . |++.| .+..|..|+++|.+.
T Consensus 435 ~Cp~~~Cg~v~~-r~el~----~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~C--p-Cg~~~-~R~~L~~H~~thCp~ 502 (567)
T PLN03086 435 VCPHDGCGIVLR-VEEAK----NHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQC--P-CGVVL-EKEQMVQHQASTCPL 502 (567)
T ss_pred eCCcccccceee-ccccc----cCccCCCCCCccc-hHHHHHHHHhcC--CCccC--C-CCCCc-chhHHHhhhhccCCC
Confidence 365335999993 33344 4568999999996 688999999986 89999 5 99755 678999999999999
Q ss_pred CcccCCCCCCCCcccC----------hhHHHHHHHHhCCCCCCCC
Q 001121 1116 RPYKCKFEGCGLSFRF----------VSDISRHRRKTGHYENLSA 1150 (1150)
Q Consensus 1116 KPYkC~v~GCGKsFss----------kS~LkrH~RkHh~~kk~sC 1150 (1150)
+|+.|++ |++.|.. .+.|..|...+ +.+.+.|
T Consensus 503 Kpi~C~f--C~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C 544 (567)
T PLN03086 503 RLITCRF--CGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPC 544 (567)
T ss_pred CceeCCC--CCCccccCccccchhhhhhhHHHHHHhc-CCcceEc
Confidence 9999999 9999952 45899999886 6666665
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.01 E-value=2.6e-06 Score=73.74 Aligned_cols=42 Identities=17% Similarity=0.211 Sum_probs=30.0
Q ss_pred ccCCCCcCCccccChhHHHHHHhhcCCCCcccCCCCCCCCcccChhHH
Q 001121 1088 LKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDI 1135 (1150)
Q Consensus 1088 fkCp~e~CgKsFssks~Lk~HmRtHtGEKPYkC~v~GCGKsFsskS~L 1135 (1150)
|.| +.||+.|....+|..|+++|+ +||+|.. |++.|.+.+.|
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 557777777777777777777 5777766 77777766554
No 15
>PHA02768 hypothetical protein; Provisional
Probab=97.99 E-value=3e-06 Score=73.41 Aligned_cols=43 Identities=23% Similarity=0.266 Sum_probs=38.6
Q ss_pred CCCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHH
Q 001121 1060 CPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWART 1106 (1150)
Q Consensus 1060 c~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk 1106 (1150)
|.|+.||+.|.....|..|+++|+ ++|+| ..|++.|.+.+.|.
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 789999999999999999999998 79999 67999999887764
No 16
>KOG0958 consensus DNA damage-responsive repressor GIS1/RPH1, jumonji superfamily [Replication, recombination and repair]
Probab=97.97 E-value=1.5e-06 Score=104.56 Aligned_cols=29 Identities=41% Similarity=0.888 Sum_probs=27.3
Q ss_pred CCCCCccccccccccCChhHHHHHHHHHH
Q 001121 3 PQMAIGFNCGEAANFGTPQWLMVAKEAAV 31 (1150)
Q Consensus 3 ~gf~~gfnc~e~~n~a~~~w~~~~~~a~~ 31 (1150)
-||+|||||||++|||+++|+.|||.|.+
T Consensus 278 aGFN~GfN~aES~nFat~Rwi~YgK~a~~ 306 (690)
T KOG0958|consen 278 AGFNHGFNCAESTNFATPRWIDYGKQALL 306 (690)
T ss_pred cccccchhhhhhhcccchhhhhhcccccc
Confidence 59999999999999999999999999854
No 17
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=97.87 E-value=1.2e-05 Score=102.76 Aligned_cols=55 Identities=31% Similarity=0.474 Sum_probs=51.6
Q ss_pred CCCCCccccccccccCChhHHHHHHHHHHHHHHhccCccccHHHHHHHHHHhhhc
Q 001121 3 PQMAIGFNCGEAANFGTPQWLMVAKEAAVRRAAMNYLPMLSHQQLLYLLTMSFIS 57 (1150)
Q Consensus 3 ~gf~~gfnc~e~~n~a~~~w~~~~~~a~~r~~~~~~~p~~~h~~ll~~~a~~~~~ 57 (1150)
-||++||||+|++|||+.+||++|..|+..|..+.++.+|+|+.|++..|+..+.
T Consensus 434 ~g~~~gf~~~e~vn~ap~dwl~~gr~~~~~~~~~~~~~lfs~~~l~~~~~~~~~~ 488 (904)
T KOG1246|consen 434 AGFNCGFNFAEAVNFAPSDWLPVGRGAAEAYSLLLRLSLFSHDELALLNAENPVK 488 (904)
T ss_pred ecccccccHHHhcccCCcchhHHHHHHHHHHHhhccCCccCHHHHHHhccccchh
Confidence 5999999999999999999999999999999999999999999999999875444
No 18
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.81 E-value=9.5e-06 Score=93.26 Aligned_cols=156 Identities=14% Similarity=0.130 Sum_probs=104.3
Q ss_pred CCCCCccCccCccCCCchhHHHHHhhccccCccC---CC--------CCCCCCccc-ccccCCCCceeccCCCCCCcccC
Q 001121 981 SPCEGLRSRAGKDAANTSEVDIRKIAEKRATKTM---RN--------RESVPAPCQ-DKKKILKGHHRCDLDGCRMSFET 1048 (1150)
Q Consensus 981 ~Pc~~~Cs~CGK~F~sks~Lk~H~r~eKpy~K~F---~s--------rssL~~~H~-~r~Ht~eKpykC~~~~CGKsFss 1048 (1150)
...++.|+.|+|.|....+|..|.|.+|+....- .. +... ..-. --......-|.|. +|+|.|++
T Consensus 292 V~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~-~ea~rsg~dss~gi~~C~--~C~KkFrR 368 (500)
T KOG3993|consen 292 VHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEV-QEAERSGDDSSSGIFSCH--TCGKKFRR 368 (500)
T ss_pred EEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhh-hhccccCCcccCceeecH--HhhhhhHH
Confidence 3446889999999999999999999888761111 00 0000 0000 0001223469999 99999999
Q ss_pred hHHHHhHhhcc----------------------CCCCCCCCccCChhHHHhhhhhccC-CCCccCCCCcCCccccChhHH
Q 001121 1049 KRELSLHKRNR----------------------CPHEGCGKRFSSHKYAIIHQRVHDD-ERPLKCPWKGCSMSFKWAWAR 1105 (1150)
Q Consensus 1049 ks~Lk~H~r~H----------------------c~Ce~CGKsFssks~Lk~H~r~Htg-eKpfkCp~e~CgKsFssks~L 1105 (1150)
...|+.|+..| +-|..|+-.|.....--.|...|.+ .....|++ |+-.|..+..-
T Consensus 369 qAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp~--~~~ppsss~~s 446 (500)
T KOG3993|consen 369 QAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPPY--DGSPPSSSGSS 446 (500)
T ss_pred HHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCCCC--CCCCcccCCCC
Confidence 99999997765 2244455444444333333333332 12346755 88888888777
Q ss_pred HHHHhhcCCCCcccCCCCCCCCcccChhHHHHHHHHhC
Q 001121 1106 TEHIRVHTGERPYKCKFEGCGLSFRFVSDISRHRRKTG 1143 (1150)
Q Consensus 1106 k~HmRtHtGEKPYkC~v~GCGKsFsskS~LkrH~RkHh 1143 (1150)
-.|.|.-.-+.-|.|.+ |...|.....|.+|+.+.|
T Consensus 447 gg~~rlg~~~q~f~~ky--~~atfyss~~ltrhin~~H 482 (500)
T KOG3993|consen 447 GGYGRLGIAEQGFTCKY--CPATFYSSPGLTRHINKCH 482 (500)
T ss_pred Cccccccchhhcccccc--chHhhhcCcchHhHhhhcC
Confidence 77777656677899999 9999999999999998744
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=97.74 E-value=1.4e-05 Score=59.08 Aligned_cols=26 Identities=54% Similarity=1.137 Sum_probs=19.8
Q ss_pred HHHHHHhhcCCCCcccCCCCCCCCcccC
Q 001121 1104 ARTEHIRVHTGERPYKCKFEGCGLSFRF 1131 (1150)
Q Consensus 1104 ~Lk~HmRtHtGEKPYkC~v~GCGKsFss 1131 (1150)
+|..|+++|+|++||.|+. |++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~--C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPY--CGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESS--SSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCC--CcCeeCc
Confidence 4677888888888888877 8887753
No 20
>PHA00733 hypothetical protein
Probab=97.68 E-value=5.5e-05 Score=75.96 Aligned_cols=53 Identities=23% Similarity=0.372 Sum_probs=30.9
Q ss_pred CCceeccCCCCCCcccChHHHHhHhhccCCCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHHHhh
Q 001121 1032 KGHHRCDLDGCRMSFETKRELSLHKRNRCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRV 1111 (1150)
Q Consensus 1032 eKpykC~~~~CGKsFssks~Lk~H~r~Hc~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~HmRt 1111 (1150)
.++|.|. .||+.|.+...|..|++ .| ..+|.| ..|++.|.....|..|++.
T Consensus 71 ~kPy~C~--~Cgk~Fss~s~L~~H~r-----------------------~h--~~~~~C--~~CgK~F~~~~sL~~H~~~ 121 (128)
T PHA00733 71 VSPYVCP--LCLMPFSSSVSLKQHIR-----------------------YT--EHSKVC--PVCGKEFRNTDSTLDHVCK 121 (128)
T ss_pred CCCccCC--CCCCcCCCHHHHHHHHh-----------------------cC--CcCccC--CCCCCccCCHHHHHHHHHH
Confidence 5666666 56666666665555554 33 124666 4466666666666666655
Q ss_pred cC
Q 001121 1112 HT 1113 (1150)
Q Consensus 1112 Ht 1113 (1150)
++
T Consensus 122 ~h 123 (128)
T PHA00733 122 KH 123 (128)
T ss_pred hc
Confidence 43
No 21
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.34 E-value=4.7e-05 Score=87.77 Aligned_cols=110 Identities=19% Similarity=0.275 Sum_probs=74.8
Q ss_pred CceeccCCCCCCcccChHHHHhHhhc---c--CCCCCCCCccCChhHHHhhhhhccCCCCcc-CCCCcCCccccChhHHH
Q 001121 1033 GHHRCDLDGCRMSFETKRELSLHKRN---R--CPHEGCGKRFSSHKYAIIHQRVHDDERPLK-CPWKGCSMSFKWAWART 1106 (1150)
Q Consensus 1033 KpykC~~~~CGKsFssks~Lk~H~r~---H--c~Ce~CGKsFssks~Lk~H~r~HtgeKpfk-Cp~e~CgKsFssks~Lk 1106 (1150)
..|.|. .|...|.....|.+|..- | |.|+.|+|.|+-..+|-.|.|+|.-..--. -...-=.+.-.+....+
T Consensus 266 GdyiCq--LCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ 343 (500)
T KOG3993|consen 266 GDYICQ--LCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQ 343 (500)
T ss_pred HHHHHH--HHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhh
Confidence 459999 999999999999999753 2 999999999999999999999995321100 00000000111111111
Q ss_pred HHHhh--cCCCCcccCCCCCCCCcccChhHHHHHHHHhCCCC
Q 001121 1107 EHIRV--HTGERPYKCKFEGCGLSFRFVSDISRHRRKTGHYE 1146 (1150)
Q Consensus 1107 ~HmRt--HtGEKPYkC~v~GCGKsFsskS~LkrH~RkHh~~k 1146 (1150)
.-.|. -....-|.|.+ |+|.|++...|++|+.+|+...
T Consensus 344 ea~rsg~dss~gi~~C~~--C~KkFrRqAYLrKHqlthq~~~ 383 (500)
T KOG3993|consen 344 EAERSGDDSSSGIFSCHT--CGKKFRRQAYLRKHQLTHQRAP 383 (500)
T ss_pred hccccCCcccCceeecHH--hhhhhHHHHHHHHhHHhhhccc
Confidence 11111 11234699999 9999999999999999887543
No 22
>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=97.26 E-value=0.00011 Score=54.36 Aligned_cols=26 Identities=38% Similarity=0.623 Sum_probs=23.4
Q ss_pred HHHhhhhhccCCCCccCCCCcCCccccC
Q 001121 1074 YAIIHQRVHDDERPLKCPWKGCSMSFKW 1101 (1150)
Q Consensus 1074 ~Lk~H~r~HtgeKpfkCp~e~CgKsFss 1101 (1150)
+|.+|+++|++++||.| ..|++.|.+
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 58999999999999999 569999974
No 23
>PHA00616 hypothetical protein
Probab=96.97 E-value=0.00037 Score=58.08 Aligned_cols=34 Identities=15% Similarity=0.256 Sum_probs=27.4
Q ss_pred CccCCCCcCCccccChhHHHHHHhhcCCCCcccCCC
Q 001121 1087 PLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKF 1122 (1150)
Q Consensus 1087 pfkCp~e~CgKsFssks~Lk~HmRtHtGEKPYkC~v 1122 (1150)
||+| ..||+.|..++.|..|++.|+|+++|.|+.
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 5788 558888888888888888888888888765
No 24
>PHA00732 hypothetical protein
Probab=96.96 E-value=0.00055 Score=63.66 Aligned_cols=46 Identities=22% Similarity=0.278 Sum_probs=29.9
Q ss_pred CCCCCCCCccCChhHHHhhhhh-ccCCCCccCCCCcCCccccChhHHHHHHhhcC
Q 001121 1060 CPHEGCGKRFSSHKYAIIHQRV-HDDERPLKCPWKGCSMSFKWAWARTEHIRVHT 1113 (1150)
Q Consensus 1060 c~Ce~CGKsFssks~Lk~H~r~-HtgeKpfkCp~e~CgKsFssks~Lk~HmRtHt 1113 (1150)
|.|..|++.|.+...|+.|++. |. ++.| ..|++.|. .|..|++++.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C--~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT---LTKC--PVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC---CCcc--CCCCCEeC---ChhhhhcccC
Confidence 5677777777777777777764 44 2467 45777776 3666765544
No 25
>PHA00616 hypothetical protein
Probab=96.85 E-value=0.00048 Score=57.46 Aligned_cols=32 Identities=22% Similarity=0.229 Sum_probs=20.7
Q ss_pred CCCCCCCCccCChhHHHhhhhhccCCCCccCC
Q 001121 1060 CPHEGCGKRFSSHKYAIIHQRVHDDERPLKCP 1091 (1150)
Q Consensus 1060 c~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp 1091 (1150)
|+|..||+.|..++.|..|++.|+|++++.|.
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 55666666666666666666666666666663
No 26
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.78 E-value=0.00042 Score=77.72 Aligned_cols=55 Identities=27% Similarity=0.744 Sum_probs=39.5
Q ss_pred CCCccCCCCcCCccccChhHHHHHHhh-c------------------CCCCcccCCCCCCCCcccChhHHHHHHHH
Q 001121 1085 ERPLKCPWKGCSMSFKWAWARTEHIRV-H------------------TGERPYKCKFEGCGLSFRFVSDISRHRRK 1141 (1150)
Q Consensus 1085 eKpfkCp~e~CgKsFssks~Lk~HmRt-H------------------tGEKPYkC~v~GCGKsFsskS~LkrH~Rk 1141 (1150)
+|||+||+..|.|.|+....|+.|+.- | ...|||+|++ |+|+|+.-..|+-|+..
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 366666666666666666666666542 2 1358999999 99999999999999753
No 27
>PHA00732 hypothetical protein
Probab=96.69 E-value=0.0014 Score=61.05 Aligned_cols=43 Identities=21% Similarity=0.288 Sum_probs=22.6
Q ss_pred eeccCCCCCCcccChHHHHhHhhc-c--CCCCCCCCccCChhHHHhhhhhc
Q 001121 1035 HRCDLDGCRMSFETKRELSLHKRN-R--CPHEGCGKRFSSHKYAIIHQRVH 1082 (1150)
Q Consensus 1035 ykC~~~~CGKsFssks~Lk~H~r~-H--c~Ce~CGKsFssks~Lk~H~r~H 1082 (1150)
|.|. .||+.|.+...|+.|++. | +.|+.||+.|. .|..|.+++
T Consensus 2 y~C~--~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 2 FKCP--ICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred ccCC--CCCCccCCHHHHHHHhhcccCCCccCCCCCEeC---Chhhhhccc
Confidence 4555 555555555555555542 2 45555555554 355555444
No 28
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=96.67 E-value=0.0025 Score=54.81 Aligned_cols=50 Identities=22% Similarity=0.487 Sum_probs=36.1
Q ss_pred CccCCCCcCCccccChhHHHHHHhh-cCCC-CcccCCCCCCCCcccChhHHHHHHHHhC
Q 001121 1087 PLKCPWKGCSMSFKWAWARTEHIRV-HTGE-RPYKCKFEGCGLSFRFVSDISRHRRKTG 1143 (1150)
Q Consensus 1087 pfkCp~e~CgKsFssks~Lk~HmRt-HtGE-KPYkC~v~GCGKsFsskS~LkrH~RkHh 1143 (1150)
.|.||| |++. .....|..|... |..+ +.+.|++ |...+. .+|.+|++.+|
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 478877 8884 445678888665 6554 4688888 888655 48888888755
No 29
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.62 E-value=0.0014 Score=60.57 Aligned_cols=76 Identities=17% Similarity=0.242 Sum_probs=19.2
Q ss_pred CCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHHHhhcCCCCcccCCCCCCCCcccChhHHHHHHHH
Q 001121 1062 HEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRHRRK 1141 (1150)
Q Consensus 1062 Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~HmRtHtGEKPYkC~v~GCGKsFsskS~LkrH~Rk 1141 (1150)
|..|+..|.+...|..|+...++...- ....+.....+..+.+.-. ...|.|.. |++.|.....|..|++.
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~------~~~~l~~~~~~~~~~~~~~-~~~~~C~~--C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIP------DQKYLVDPNRLLNYLRKKV-KESFRCPY--CNKTFRSREALQEHMRS 72 (100)
T ss_dssp ------------------------------------------------------SSEEBSS--SS-EESSHHHHHHHHHH
T ss_pred ccccccccccccccccccccccccccc------ccccccccccccccccccc-CCCCCCCc--cCCCCcCHHHHHHHHcC
Confidence 666777777777777776543322110 1111223333333333211 12577777 77777777777777776
Q ss_pred hCCCC
Q 001121 1142 TGHYE 1146 (1150)
Q Consensus 1142 Hh~~k 1146 (1150)
++|..
T Consensus 73 ~~H~~ 77 (100)
T PF12756_consen 73 KHHKK 77 (100)
T ss_dssp TTTTC
T ss_pred ccCCC
Confidence 55543
No 30
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.86 E-value=0.0027 Score=71.45 Aligned_cols=73 Identities=14% Similarity=0.347 Sum_probs=52.0
Q ss_pred CCceeccCCCCCCcccChHHHHhHhhccCCCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHHHh
Q 001121 1032 KGHHRCDLDGCRMSFETKRELSLHKRNRCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIR 1110 (1150)
Q Consensus 1032 eKpykC~~~~CGKsFssks~Lk~H~r~Hc~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~HmR 1110 (1150)
+|||+|+.+.|.|.|.....|+.|+..-+ |.....-...-..|.-.-...|||.| +.|+|+|+....|+.|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH----~~~~~~~~p~p~~~~~F~~~~KPYrC--evC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGH----QNQKLHENPSPEKMNIFSAKDKPYRC--EVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccc----cCcccCCCCCccccccccccCCceec--cccchhhccCccceeccc
Confidence 59999999999999999999999987421 22111111111222222345699999 669999999999999864
No 31
>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=95.71 E-value=0.0063 Score=43.14 Aligned_cols=23 Identities=48% Similarity=0.967 Sum_probs=16.3
Q ss_pred ccCCCCCCCCcccChhHHHHHHHHh
Q 001121 1118 YKCKFEGCGLSFRFVSDISRHRRKT 1142 (1150)
Q Consensus 1118 YkC~v~GCGKsFsskS~LkrH~RkH 1142 (1150)
|+|+. |++.|.++..|.+|++.|
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 56776 777777777777777664
No 32
>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=95.68 E-value=0.014 Score=50.18 Aligned_cols=49 Identities=24% Similarity=0.344 Sum_probs=36.6
Q ss_pred CCCCCCCCccCChhHHHhhhhh-ccCC-CCccCCCCcCCccccChhHHHHHHhhcC
Q 001121 1060 CPHEGCGKRFSSHKYAIIHQRV-HDDE-RPLKCPWKGCSMSFKWAWARTEHIRVHT 1113 (1150)
Q Consensus 1060 c~Ce~CGKsFssks~Lk~H~r~-Htge-KpfkCp~e~CgKsFssks~Lk~HmRtHt 1113 (1150)
|.|+.|++ ..+...|..|... |..+ +.+.||+ |...+. .+|..|+..++
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPi--C~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPI--CSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCC--chhhhh--hHHHHHHHHhc
Confidence 68889999 4556789999665 6553 5699954 998655 48999988755
No 33
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=95.27 E-value=0.014 Score=40.82 Aligned_cols=24 Identities=38% Similarity=0.837 Sum_probs=16.7
Q ss_pred ccCCCCCCCCcccChhHHHHHHHHhC
Q 001121 1118 YKCKFEGCGLSFRFVSDISRHRRKTG 1143 (1150)
Q Consensus 1118 YkC~v~GCGKsFsskS~LkrH~RkHh 1143 (1150)
|.|++ |++.|.+...|.+|+++||
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 8888888888888877764
No 34
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.17 E-value=0.024 Score=70.23 Aligned_cols=42 Identities=21% Similarity=0.139 Sum_probs=21.3
Q ss_pred CCCCcccChHHHHhHhhc-cCCCCCCC------CccCChhHHHhhhhhc
Q 001121 1041 GCRMSFETKRELSLHKRN-RCPHEGCG------KRFSSHKYAIIHQRVH 1082 (1150)
Q Consensus 1041 ~CGKsFssks~Lk~H~r~-Hc~Ce~CG------KsFssks~Lk~H~r~H 1082 (1150)
.|...|.....|.+|++. |+.|..|. .-|.....|..|-+.+
T Consensus 187 ~C~~~fld~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR~~ 235 (669)
T KOG2231|consen 187 FCHERFLDDDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFRKG 235 (669)
T ss_pred hhhhhhccHHHHHHhhccceeheeecCcccccchhcccchHHHHHhhhc
Confidence 555555555555555554 34444442 2344445555555543
No 35
>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=94.43 E-value=0.02 Score=42.17 Aligned_cols=25 Identities=32% Similarity=0.818 Sum_probs=18.6
Q ss_pred cccCCCCCCCCcccChhHHHHHHHHhC
Q 001121 1117 PYKCKFEGCGLSFRFVSDISRHRRKTG 1143 (1150)
Q Consensus 1117 PYkC~v~GCGKsFsskS~LkrH~RkHh 1143 (1150)
||.|.. |++.|.....|..|++.|+
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 7777777777777777664
No 36
>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=94.23 E-value=0.021 Score=40.42 Aligned_cols=23 Identities=35% Similarity=0.545 Sum_probs=12.7
Q ss_pred ccCCCCcCCccccChhHHHHHHhhc
Q 001121 1088 LKCPWKGCSMSFKWAWARTEHIRVH 1112 (1150)
Q Consensus 1088 fkCp~e~CgKsFssks~Lk~HmRtH 1112 (1150)
|.| ..|++.|.++..|..|++.|
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 445 33666666666666665543
No 37
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=93.77 E-value=0.031 Score=39.03 Aligned_cols=17 Identities=29% Similarity=0.547 Sum_probs=7.3
Q ss_pred CCccccChhHHHHHHhh
Q 001121 1095 CSMSFKWAWARTEHIRV 1111 (1150)
Q Consensus 1095 CgKsFssks~Lk~HmRt 1111 (1150)
|++.|.+...|..|+++
T Consensus 6 C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 6 CGKSFRSKSELRQHMRT 22 (24)
T ss_dssp TS-EESSHHHHHHHHHH
T ss_pred CCCcCCcHHHHHHHHHh
Confidence 44444444444444443
No 38
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.35 E-value=0.05 Score=61.19 Aligned_cols=143 Identities=17% Similarity=0.173 Sum_probs=83.0
Q ss_pred CccCccCccCCCchhHHHHHhhccccCccCCCCCCCCCcccccccCCC--CceeccCCCCCCcccChHHHHhHhhcc---
Q 001121 985 GLRSRAGKDAANTSEVDIRKIAEKRATKTMRNRESVPAPCQDKKKILK--GHHRCDLDGCRMSFETKRELSLHKRNR--- 1059 (1150)
Q Consensus 985 ~~Cs~CGK~F~sks~Lk~H~r~eKpy~K~F~srssL~~~H~~r~Ht~e--KpykC~~~~CGKsFssks~Lk~H~r~H--- 1059 (1150)
..|..|...|.....|..|.+. ..|..+ +++.|.+..|++.|.....+..|...|
T Consensus 290 ~~~~~~~~~~s~~~~l~~~~~~--------------------~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~ 349 (467)
T COG5048 290 IKSKQCNISFSRSSPLTRHLRS--------------------VNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSI 349 (467)
T ss_pred CCCccccCCccccccccccccc--------------------cccccccCCceeeeccCCCccccccccccCCcccccCC
Confidence 4556777777766666555431 145556 778887556888888888888887764
Q ss_pred --CC--CCCCCCccCChhHHHhhhh-----hccCCCCccCCCCcCCccccChhHHHHHHhhcCCCCcccCCCCCCCCccc
Q 001121 1060 --CP--HEGCGKRFSSHKYAIIHQR-----VHDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFR 1130 (1150)
Q Consensus 1060 --c~--Ce~CGKsFssks~Lk~H~r-----~HtgeKpfkCp~e~CgKsFssks~Lk~HmRtHtGEKPYkC~v~GCGKsFs 1130 (1150)
+. -..|.+.+.....-..+.. .....+.+.|.+..|-..+.....+..|...|...+++.|...+|.+.|.
T Consensus 350 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 429 (467)
T COG5048 350 SPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFN 429 (467)
T ss_pred CccccccccCccccccccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhcc
Confidence 11 1334444333322111111 11223445555455666666666777776666666655555555777777
Q ss_pred ChhHHHHHHHHhCCCCC
Q 001121 1131 FVSDISRHRRKTGHYEN 1147 (1150)
Q Consensus 1131 skS~LkrH~RkHh~~kk 1147 (1150)
....+..|++.|.....
T Consensus 430 ~~~~~~~~~~~~~~~~~ 446 (467)
T COG5048 430 RHYNLIPHKKIHTNHAP 446 (467)
T ss_pred CcccccccccccccCCc
Confidence 77777777666554443
No 39
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=93.25 E-value=0.049 Score=50.35 Aligned_cols=72 Identities=22% Similarity=0.342 Sum_probs=20.7
Q ss_pred eccCCCCCCcccChHHHHhHhhccCC-CCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHHHhhc
Q 001121 1036 RCDLDGCRMSFETKRELSLHKRNRCP-HEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVH 1112 (1150)
Q Consensus 1036 kC~~~~CGKsFssks~Lk~H~r~Hc~-Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~HmRtH 1112 (1150)
+|. .|+..|.+...|..|+...+. .-.....+.....+..+.+.-. ...+.|+ .|++.|.+...|..||+.+
T Consensus 1 ~C~--~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~-~~~~~C~--~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCL--FCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKV-KESFRCP--YCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ---------------------------------------------------SSEEBS--SSS-EESSHHHHHHHHHHT
T ss_pred Ccc--cccccccccccccccccccccccccccccccccccccccccccc-CCCCCCC--ccCCCCcCHHHHHHHHcCc
Confidence 377 899999999999999976432 1112223334444444444322 2368995 5999999999999999964
No 40
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.97 E-value=0.042 Score=61.80 Aligned_cols=107 Identities=21% Similarity=0.234 Sum_probs=54.2
Q ss_pred ceeccCCCCCCcccChHHHHhHhh---------ccCCCC--CCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccCh
Q 001121 1034 HHRCDLDGCRMSFETKRELSLHKR---------NRCPHE--GCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWA 1102 (1150)
Q Consensus 1034 pykC~~~~CGKsFssks~Lk~H~r---------~Hc~Ce--~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssk 1102 (1150)
++.|. .|...|.....|..|.+ ..+.|+ .|++.|.....+..|...|.+.+++.|.+..|.+.+...
T Consensus 289 ~~~~~--~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 366 (467)
T COG5048 289 PIKSK--QCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPL 366 (467)
T ss_pred CCCCc--cccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCccccccc
Confidence 45555 66666666666666655 224454 466666666666666666665555555544455444443
Q ss_pred hHHHHH-----HhhcCCCCcccCCCCCCCCcccChhHHHHHHHHh
Q 001121 1103 WARTEH-----IRVHTGERPYKCKFEGCGLSFRFVSDISRHRRKT 1142 (1150)
Q Consensus 1103 s~Lk~H-----mRtHtGEKPYkC~v~GCGKsFsskS~LkrH~RkH 1142 (1150)
..-..+ .......+.+.|...+|-..+.....+..|...|
T Consensus 367 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 411 (467)
T COG5048 367 LNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITH 411 (467)
T ss_pred cCCCCccchhhccCccCCccccccccchhhhhccccccccccccc
Confidence 331111 1112223445555445555555555555554444
No 41
>smart00355 ZnF_C2H2 zinc finger.
Probab=91.83 E-value=0.16 Score=35.65 Aligned_cols=23 Identities=35% Similarity=0.749 Sum_probs=14.4
Q ss_pred ccCCCCCCCCcccChhHHHHHHHHh
Q 001121 1118 YKCKFEGCGLSFRFVSDISRHRRKT 1142 (1150)
Q Consensus 1118 YkC~v~GCGKsFsskS~LkrH~RkH 1142 (1150)
|.|.. |++.|.....|..|++.|
T Consensus 1 ~~C~~--C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPE--CGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCC--CcchhCCHHHHHHHHHHh
Confidence 45666 666666666666666654
No 42
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=91.59 E-value=0.092 Score=38.59 Aligned_cols=25 Identities=36% Similarity=0.667 Sum_probs=17.4
Q ss_pred CccCCCCcCCccccChhHHHHHHhhcC
Q 001121 1087 PLKCPWKGCSMSFKWAWARTEHIRVHT 1113 (1150)
Q Consensus 1087 pfkCp~e~CgKsFssks~Lk~HmRtHt 1113 (1150)
||.| ..|++.|.+...|..|++.|.
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 4667 557777777777777776664
No 43
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.78 E-value=0.27 Score=61.30 Aligned_cols=49 Identities=20% Similarity=0.203 Sum_probs=24.2
Q ss_pred CCCCCCCccCChhHHHhhhhhccCCCCccCCC----CcCCccccChhHHHHHHhhcC
Q 001121 1061 PHEGCGKRFSSHKYAIIHQRVHDDERPLKCPW----KGCSMSFKWAWARTEHIRVHT 1113 (1150)
Q Consensus 1061 ~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~----e~CgKsFssks~Lk~HmRtHt 1113 (1150)
.|..|...|.....|.+|++.++ |.|.+ ..++-.|..-..|..|.|.++
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 35556666666666666665543 23311 112233455555666655544
No 44
>PRK04860 hypothetical protein; Provisional
Probab=89.16 E-value=0.18 Score=52.95 Aligned_cols=39 Identities=36% Similarity=0.792 Sum_probs=33.1
Q ss_pred CccCCCCcCCccccChhHHHHHHhhcCCCCcccCCCCCCCCcccChh
Q 001121 1087 PLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVS 1133 (1150)
Q Consensus 1087 pfkCp~e~CgKsFssks~Lk~HmRtHtGEKPYkC~v~GCGKsFsskS 1133 (1150)
+|.| . |++ ....+.+|.++|+++++|.|.. |+..|....
T Consensus 119 ~Y~C--~-C~~---~~~~~rrH~ri~~g~~~YrC~~--C~~~l~~~~ 157 (160)
T PRK04860 119 PYRC--K-CQE---HQLTVRRHNRVVRGEAVYRCRR--CGETLVFKG 157 (160)
T ss_pred EEEc--C-CCC---eeCHHHHHHHHhcCCccEECCC--CCceeEEec
Confidence 6899 5 987 6777899999999999999998 999887543
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=88.45 E-value=0.34 Score=42.13 Aligned_cols=31 Identities=26% Similarity=0.535 Sum_probs=16.8
Q ss_pred CCCcccCCCCCCCCcccChhHHHHHHHHhCCCC
Q 001121 1114 GERPYKCKFEGCGLSFRFVSDISRHRRKTGHYE 1146 (1150)
Q Consensus 1114 GEKPYkC~v~GCGKsFsskS~LkrH~RkHh~~k 1146 (1150)
.+.|-.|++ |+..+.+..+|++|+..+|..+
T Consensus 21 S~~PatCP~--C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 21 SEQPATCPI--CGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp TS--EE-TT--T--EESSHHHHHHHHHHHTTTS
T ss_pred cCCCCCCCc--chhhccchhhHHHHHHHHhccc
Confidence 455666776 7777777777777776655543
No 46
>smart00355 ZnF_C2H2 zinc finger.
Probab=88.31 E-value=0.4 Score=33.57 Aligned_cols=24 Identities=38% Similarity=0.625 Sum_probs=14.3
Q ss_pred ccCCCCcCCccccChhHHHHHHhhcC
Q 001121 1088 LKCPWKGCSMSFKWAWARTEHIRVHT 1113 (1150)
Q Consensus 1088 fkCp~e~CgKsFssks~Lk~HmRtHt 1113 (1150)
|.| ..|++.|.....|..|++.|.
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 346666666666666666553
No 47
>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=85.27 E-value=0.55 Score=40.86 Aligned_cols=40 Identities=18% Similarity=0.459 Sum_probs=23.0
Q ss_pred Hhhhhhc-cCCCCccCCCCcCCccccChhHHHHHHhhcCCCCc
Q 001121 1076 IIHQRVH-DDERPLKCPWKGCSMSFKWAWARTEHIRVHTGERP 1117 (1150)
Q Consensus 1076 k~H~r~H-tgeKpfkCp~e~CgKsFssks~Lk~HmRtHtGEKP 1117 (1150)
..|.+.| ..+.|..|| +|+..+.+..+|++|+.++++.||
T Consensus 12 ~~~~k~~~~S~~PatCP--~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 12 TKKPKSKSQSEQPATCP--ICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp ----CCCCTTS--EE-T--TT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhHHHHhhccCCCCCCC--cchhhccchhhHHHHHHHHhcccC
Confidence 4444443 456788894 599999999999999988777765
No 48
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=85.11 E-value=0.56 Score=33.76 Aligned_cols=23 Identities=35% Similarity=0.743 Sum_probs=14.3
Q ss_pred ccCCCCCCCCcccChhHHHHHHHHhC
Q 001121 1118 YKCKFEGCGLSFRFVSDISRHRRKTG 1143 (1150)
Q Consensus 1118 YkC~v~GCGKsFsskS~LkrH~RkHh 1143 (1150)
|+|+. |+.... ...|.+|++.||
T Consensus 1 y~C~~--C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPH--CSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SS--SS-EES-HHHHHHHHHHHH
T ss_pred CCCCC--CCCcCC-HHHHHHHHHhhC
Confidence 56776 777666 667777777654
No 49
>PRK04860 hypothetical protein; Provisional
Probab=83.92 E-value=0.46 Score=49.98 Aligned_cols=39 Identities=18% Similarity=0.362 Sum_probs=32.7
Q ss_pred cCCCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChh
Q 001121 1059 RCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAW 1103 (1150)
Q Consensus 1059 Hc~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks 1103 (1150)
.|.|. |++ ....+++|.++|+++++|.| ..|+..|....
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC--~~C~~~l~~~~ 157 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRC--RRCGETLVFKG 157 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEEC--CCCCceeEEec
Confidence 47786 887 66789999999999999999 77999987643
No 50
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=83.01 E-value=0.38 Score=34.70 Aligned_cols=22 Identities=27% Similarity=0.670 Sum_probs=14.4
Q ss_pred ccCCCCCCCCcccChhHHHHHHHH
Q 001121 1118 YKCKFEGCGLSFRFVSDISRHRRK 1141 (1150)
Q Consensus 1118 YkC~v~GCGKsFsskS~LkrH~Rk 1141 (1150)
|.|.+ |++.|.....|..|++.
T Consensus 1 ~~C~~--C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDI--CNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETT--TTEEESSHHHHHHHHTT
T ss_pred CCCCC--CCCCcCCHHHHHHHHCc
Confidence 45666 66666666666666654
No 51
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=81.61 E-value=1.5 Score=50.73 Aligned_cols=71 Identities=24% Similarity=0.330 Sum_probs=52.2
Q ss_pred eeccCCCCCCcccChHHHHhHhhc-cCCCCCCCCc-------cCChhHHHhhhhhccCCCCccCCCCcCC----ccccCh
Q 001121 1035 HRCDLDGCRMSFETKRELSLHKRN-RCPHEGCGKR-------FSSHKYAIIHQRVHDDERPLKCPWKGCS----MSFKWA 1102 (1150)
Q Consensus 1035 ykC~~~~CGKsFssks~Lk~H~r~-Hc~Ce~CGKs-------Fssks~Lk~H~r~HtgeKpfkCp~e~Cg----KsFssk 1102 (1150)
-.|. .|...|..-..|..|+|. |-.|.+|++. |.....|-.|.+. --|.|++..|- ..|...
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 3588 899999999999999986 5567777654 6666777777653 23777776664 457778
Q ss_pred hHHHHHHhh
Q 001121 1103 WARTEHIRV 1111 (1150)
Q Consensus 1103 s~Lk~HmRt 1111 (1150)
..|..|+..
T Consensus 295 ~el~~h~~~ 303 (493)
T COG5236 295 TELLEHLTR 303 (493)
T ss_pred HHHHHHHHH
Confidence 888888764
No 52
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=80.01 E-value=0.71 Score=50.98 Aligned_cols=48 Identities=25% Similarity=0.381 Sum_probs=39.7
Q ss_pred CCceeccCCCCCCcccChHHHHhHhh-ccCCCCCCCCccCChhHHHhh-hhhc
Q 001121 1032 KGHHRCDLDGCRMSFETKRELSLHKR-NRCPHEGCGKRFSSHKYAIIH-QRVH 1082 (1150)
Q Consensus 1032 eKpykC~~~~CGKsFssks~Lk~H~r-~Hc~Ce~CGKsFssks~Lk~H-~r~H 1082 (1150)
.+++ |= .|++.|....-|.+|++ .||+|.+|-|.+.+--.|..| |.+|
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 4454 66 79999999999999998 489999999988888888888 4455
No 53
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=79.13 E-value=1 Score=59.45 Aligned_cols=74 Identities=16% Similarity=0.244 Sum_probs=41.6
Q ss_pred CCCCCCCCccCChhHHHhhhhh-ccCCCCccCCCCcCCccccChhHHHHHHhhcCCCCcccCCCCCCCCcccChhHHHHH
Q 001121 1060 CPHEGCGKRFSSHKYAIIHQRV-HDDERPLKCPWKGCSMSFKWAWARTEHIRVHTGERPYKCKFEGCGLSFRFVSDISRH 1138 (1150)
Q Consensus 1060 c~Ce~CGKsFssks~Lk~H~r~-HtgeKpfkCp~e~CgKsFssks~Lk~HmRtHtGEKPYkC~v~GCGKsFsskS~LkrH 1138 (1150)
++|+.|+..|+....|-.|||. |...+--.|. .+...-.+.+-.-.-.+.+||.|.. |...|..+.+|.+|
T Consensus 466 ~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~------~gq~~~~~arg~~~~~~~~p~~C~~--C~~stttng~Lsih 537 (1406)
T KOG1146|consen 466 LKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCK------AGQNHPRLARGEVYRCPGKPYPCRA--CNYSTTTNGNLSIH 537 (1406)
T ss_pred ccCCccchhhhhHHHhhhcccccccccchhHhH------hccccccccccccccCCCCccccee--eeeeeecchHHHHH
Confidence 5566666666666666666664 3322222221 0111100000000112457899999 99999999999999
Q ss_pred HHH
Q 001121 1139 RRK 1141 (1150)
Q Consensus 1139 ~Rk 1141 (1150)
+..
T Consensus 538 lqS 540 (1406)
T KOG1146|consen 538 LQS 540 (1406)
T ss_pred HHH
Confidence 985
No 54
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=77.55 E-value=1.4 Score=52.11 Aligned_cols=28 Identities=29% Similarity=0.608 Sum_probs=24.2
Q ss_pred ccCCCCCCCCcccChhHHHHHHHHhCCC
Q 001121 1118 YKCKFEGCGLSFRFVSDISRHRRKTGHY 1145 (1150)
Q Consensus 1118 YkC~v~GCGKsFsskS~LkrH~RkHh~~ 1145 (1150)
|.|..+||+..|...+.+..|.|+|...
T Consensus 402 fhc~r~Gc~~tl~s~sqm~shkrkheRq 429 (480)
T KOG4377|consen 402 FHCDRLGCEATLYSVSQMASHKRKHERQ 429 (480)
T ss_pred eeecccCCceEEEehhhhhhhhhhhhhh
Confidence 5688889999999999999999988643
No 55
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=77.23 E-value=0.43 Score=62.75 Aligned_cols=93 Identities=15% Similarity=0.136 Sum_probs=59.0
Q ss_pred eeccCCCCCCcccChHHHHhHhh--ccCCCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHHHhhc
Q 001121 1035 HRCDLDGCRMSFETKRELSLHKR--NRCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRVH 1112 (1150)
Q Consensus 1035 ykC~~~~CGKsFssks~Lk~H~r--~Hc~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~HmRtH 1112 (1150)
+.|. .|.+.|.....+. |+- .||.|..|...|.....|..|.+ + |.+.|.....+.-|+..|
T Consensus 1261 ~~c~--~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~~~~l~~~~~--------k-----~~~~~~~~~~~~~~~l~~ 1324 (1406)
T KOG1146|consen 1261 GECG--AVDELLTPSFGIS-TLDVTHRYLCRQCKMAFDGEAPLTAHQR--------K-----FCFAGRGSGGSMPPPLRV 1324 (1406)
T ss_pred chhh--hccccccCcccee-ecccchhHHHHHHHhhhcchhHHHHHHH--------H-----HHhccCccccCCCCcccC
Confidence 5566 6666666666555 543 24566666666666666666651 1 223344444444555556
Q ss_pred CCCCcccCCCCCCCCcccChhHHHHHHHHhCCCC
Q 001121 1113 TGERPYKCKFEGCGLSFRFVSDISRHRRKTGHYE 1146 (1150)
Q Consensus 1113 tGEKPYkC~v~GCGKsFsskS~LkrH~RkHh~~k 1146 (1150)
...++| |.. |...|.....|..||+..+|+.
T Consensus 1325 ~d~~~~-c~~--c~~~~~~~~alqihm~~~~~~~ 1355 (1406)
T KOG1146|consen 1325 PDCTYH-CLA--CEVLLSGREALQIHMRSSAHRR 1355 (1406)
T ss_pred cccccc-chH--HHhhcchhHHHHHHHHHhhhcc
Confidence 566777 999 9999999999999999754443
No 56
>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=76.83 E-value=1.4 Score=32.74 Aligned_cols=19 Identities=32% Similarity=0.497 Sum_probs=8.2
Q ss_pred CCCCCCccCChhHHHhhhh
Q 001121 1062 HEGCGKRFSSHKYAIIHQR 1080 (1150)
Q Consensus 1062 Ce~CGKsFssks~Lk~H~r 1080 (1150)
|..|++.|.+...|..|++
T Consensus 4 C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 4 CDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp BTTTTBBBSSHHHHHCCTT
T ss_pred cccCCCCcCCHHHHHHHHc
Confidence 4444444444444444433
No 57
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=75.65 E-value=3.3 Score=48.83 Aligned_cols=156 Identities=15% Similarity=0.223 Sum_probs=96.5
Q ss_pred CccCccCccCCCchhHHHHHh-hcccc-------------CccCCCCCCCCCcc-cccccCCCCceeccCCCCCCcccCh
Q 001121 985 GLRSRAGKDAANTSEVDIRKI-AEKRA-------------TKTMRNRESVPAPC-QDKKKILKGHHRCDLDGCRMSFETK 1049 (1150)
Q Consensus 985 ~~Cs~CGK~F~sks~Lk~H~r-~eKpy-------------~K~F~srssL~~~H-~~r~Ht~eKpykC~~~~CGKsFssk 1049 (1150)
+.|..|...|.....-+.|++ .++.| .-.|..+-.....- ....-...-++.|. .|.+.|.+.
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 568899999999999999998 44444 11111111100000 00012345578999 999999999
Q ss_pred HHHHhHhhc--c--------------------CC-------------CCCCCCccCChhHHHhhhhh--c----------
Q 001121 1050 RELSLHKRN--R--------------------CP-------------HEGCGKRFSSHKYAIIHQRV--H---------- 1082 (1150)
Q Consensus 1050 s~Lk~H~r~--H--------------------c~-------------Ce~CGKsFssks~Lk~H~r~--H---------- 1082 (1150)
.....|+.. | .+ +..+-..+........+... +
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 998888763 1 11 11111111111111111110 0
Q ss_pred cCCCCccCCCCcCCccccChhHHHHHHhhcCCC-----------------------CcccCCCCCCC---CcccChhHHH
Q 001121 1083 DDERPLKCPWKGCSMSFKWAWARTEHIRVHTGE-----------------------RPYKCKFEGCG---LSFRFVSDIS 1136 (1150)
Q Consensus 1083 tgeKpfkCp~e~CgKsFssks~Lk~HmRtHtGE-----------------------KPYkC~v~GCG---KsFsskS~Lk 1136 (1150)
...-|-.|-| |++.|.....-..||..|+|- .-|.|-. |. +.|.+-...+
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 0012467855 999999999999999987762 3477888 98 9999999999
Q ss_pred HHHHHhCCCC
Q 001121 1137 RHRRKTGHYE 1146 (1150)
Q Consensus 1137 rH~RkHh~~k 1146 (1150)
.||...+|.+
T Consensus 238 ~HM~~K~HCk 247 (390)
T KOG2785|consen 238 AHMRDKGHCK 247 (390)
T ss_pred HHHhhccCcc
Confidence 9999766654
No 58
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=72.91 E-value=1.2 Score=48.56 Aligned_cols=82 Identities=21% Similarity=0.411 Sum_probs=64.1
Q ss_pred CCceeccCCCCCCcccChHHHHhHhhcc--CCCCCCCCccCChhHHHhhhhh-c---------cCCCCccCCCCcCCccc
Q 001121 1032 KGHHRCDLDGCRMSFETKRELSLHKRNR--CPHEGCGKRFSSHKYAIIHQRV-H---------DDERPLKCPWKGCSMSF 1099 (1150)
Q Consensus 1032 eKpykC~~~~CGKsFssks~Lk~H~r~H--c~Ce~CGKsFssks~Lk~H~r~-H---------tgeKpfkCp~e~CgKsF 1099 (1150)
...|.|....|.+.|........|.... -.|..|.+.|.+...|..|+.- | .|.--|.|-++.|+-.|
T Consensus 77 ~~~~~cqvagc~~~~d~lD~~E~hY~~~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 77 VPAFACQVAGCCQVFDALDDYEHHYHTLHGNSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred cccccccccchHHHHhhhhhHHHhhhhcccchhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 3458899888999998888888776543 4799999999999999999763 4 24445888878888888
Q ss_pred cChhHHHHHHh-hcC
Q 001121 1100 KWAWARTEHIR-VHT 1113 (1150)
Q Consensus 1100 ssks~Lk~HmR-tHt 1113 (1150)
.+....+.|+- +|.
T Consensus 157 kT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 157 KTSRDRKDHMIRMHK 171 (253)
T ss_pred hhhhhhhhHHHHhcc
Confidence 88888888854 464
No 59
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=72.65 E-value=2.3 Score=30.61 Aligned_cols=17 Identities=35% Similarity=0.575 Sum_probs=8.7
Q ss_pred CCCCcccChHHHHhHhh
Q 001121 1041 GCRMSFETKRELSLHKR 1057 (1150)
Q Consensus 1041 ~CGKsFssks~Lk~H~r 1057 (1150)
.|++.|.+...|..|++
T Consensus 5 ~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 5 ICNKSFSSENSLRQHLR 21 (25)
T ss_dssp TTTEEESSHHHHHHHHT
T ss_pred CCCCCcCCHHHHHHHHC
Confidence 45555555555555543
No 60
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=72.22 E-value=1.3 Score=48.28 Aligned_cols=76 Identities=25% Similarity=0.433 Sum_probs=61.0
Q ss_pred CCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHHHhh-c---------CCCCcccCCCCCCCCcccC
Q 001121 1062 HEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIRV-H---------TGERPYKCKFEGCGLSFRF 1131 (1150)
Q Consensus 1062 Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~HmRt-H---------tGEKPYkC~v~GCGKsFss 1131 (1150)
--.|...|........|-..-++. .| ..|.+.|.+...|..|+.- | .|.--|.|-+.||+..|.+
T Consensus 84 vagc~~~~d~lD~~E~hY~~~h~~---sC--s~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT 158 (253)
T KOG4173|consen 84 VAGCCQVFDALDDYEHHYHTLHGN---SC--SFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKT 158 (253)
T ss_pred ccchHHHHhhhhhHHHhhhhcccc---hh--HHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhh
Confidence 356889999888888886553332 69 5699999999999999863 3 3555699999999999999
Q ss_pred hhHHHHHHHHh
Q 001121 1132 VSDISRHRRKT 1142 (1150)
Q Consensus 1132 kS~LkrH~RkH 1142 (1150)
...-+.|+-..
T Consensus 159 ~r~RkdH~I~~ 169 (253)
T KOG4173|consen 159 SRDRKDHMIRM 169 (253)
T ss_pred hhhhhhHHHHh
Confidence 99999998653
No 61
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=70.45 E-value=3.9 Score=47.49 Aligned_cols=23 Identities=22% Similarity=0.488 Sum_probs=12.4
Q ss_pred eeccCCCCCCcccChHHHHhHhh
Q 001121 1035 HRCDLDGCRMSFETKRELSLHKR 1057 (1150)
Q Consensus 1035 ykC~~~~CGKsFssks~Lk~H~r 1057 (1150)
|.|+...|..+......|+.|.+
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K 174 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYK 174 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHH
Confidence 55554455555555555555554
No 62
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=67.53 E-value=3 Score=30.00 Aligned_cols=22 Identities=32% Similarity=0.547 Sum_probs=11.4
Q ss_pred ccCCCCcCCccccChhHHHHHHhhc
Q 001121 1088 LKCPWKGCSMSFKWAWARTEHIRVH 1112 (1150)
Q Consensus 1088 fkCp~e~CgKsFssks~Lk~HmRtH 1112 (1150)
|+| ..|+.... ...|..|++.|
T Consensus 1 y~C--~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKC--PHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE---SSSS-EES-HHHHHHHHHHH
T ss_pred CCC--CCCCCcCC-HHHHHHHHHhh
Confidence 456 33666555 55666666654
No 63
>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=64.77 E-value=3.8 Score=30.43 Aligned_cols=22 Identities=27% Similarity=0.686 Sum_probs=20.3
Q ss_pred eeccCCCCCCcccChHHHHhHhhc
Q 001121 1035 HRCDLDGCRMSFETKRELSLHKRN 1058 (1150)
Q Consensus 1035 ykC~~~~CGKsFssks~Lk~H~r~ 1058 (1150)
|.|. .|++.|.+...|..|++.
T Consensus 2 ~~C~--~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCD--ACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBT--TTTBBBSSHHHHHCCTTS
T ss_pred CCcc--cCCCCcCCHHHHHHHHcc
Confidence 7799 999999999999999874
No 64
>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=62.52 E-value=2 Score=33.21 Aligned_cols=23 Identities=22% Similarity=0.587 Sum_probs=15.8
Q ss_pred cccCCCCCCCCcccChhHHHHHHHH
Q 001121 1117 PYKCKFEGCGLSFRFVSDISRHRRK 1141 (1150)
Q Consensus 1117 PYkC~v~GCGKsFsskS~LkrH~Rk 1141 (1150)
+|.|.. |++.|.....+..|++.
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 65
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=61.44 E-value=5.9 Score=29.53 Aligned_cols=8 Identities=38% Similarity=1.007 Sum_probs=3.4
Q ss_pred CCCCCCcc
Q 001121 1062 HEGCGKRF 1069 (1150)
Q Consensus 1062 Ce~CGKsF 1069 (1150)
|+.||+.|
T Consensus 5 C~~CgR~F 12 (25)
T PF13913_consen 5 CPICGRKF 12 (25)
T ss_pred CCCCCCEE
Confidence 44444444
No 66
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=50.16 E-value=14 Score=27.58 Aligned_cols=19 Identities=26% Similarity=0.779 Sum_probs=11.4
Q ss_pred cCCCCCCCCcccChhHHHHHHH
Q 001121 1119 KCKFEGCGLSFRFVSDISRHRR 1140 (1150)
Q Consensus 1119 kC~v~GCGKsFsskS~LkrH~R 1140 (1150)
.|+. ||+.| ....|.+|+.
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 4666 66666 5556666654
No 67
>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=44.34 E-value=17 Score=28.01 Aligned_cols=22 Identities=18% Similarity=0.493 Sum_probs=15.6
Q ss_pred ceeccCCCCCCcccChHHHHhHhh
Q 001121 1034 HHRCDLDGCRMSFETKRELSLHKR 1057 (1150)
Q Consensus 1034 pykC~~~~CGKsFssks~Lk~H~r 1057 (1150)
+|.|+ .|++.|.....+..|+.
T Consensus 3 ~~~C~--~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCK--LCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEcc--ccCCccCCHHHHHHHHC
Confidence 46677 77777777777777765
No 68
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=43.51 E-value=7.9 Score=43.15 Aligned_cols=45 Identities=27% Similarity=0.449 Sum_probs=27.2
Q ss_pred CCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHH-Hhhc
Q 001121 1062 HEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEH-IRVH 1112 (1150)
Q Consensus 1062 Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~H-mRtH 1112 (1150)
|=.|++.|....-|.+|++. |-|+| .+|-|.+.+--.|..| |++|
T Consensus 13 cwycnrefddekiliqhqka----khfkc--hichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKC--HICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeecccccchhhhhhhhhhh----cccee--eeehhhhccCCCceeehhhhh
Confidence 55677777777777776654 23677 5577665555555555 4444
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=36.62 E-value=22 Score=35.46 Aligned_cols=6 Identities=33% Similarity=0.993 Sum_probs=2.4
Q ss_pred CCcccc
Q 001121 1095 CSMSFK 1100 (1150)
Q Consensus 1095 CgKsFs 1100 (1150)
||..|.
T Consensus 32 CG~~~~ 37 (108)
T PF09538_consen 32 CGTEFP 37 (108)
T ss_pred CCCccC
Confidence 444333
No 70
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=35.41 E-value=16 Score=32.59 Aligned_cols=28 Identities=39% Similarity=0.699 Sum_probs=19.8
Q ss_pred cCCCCcccCCCCCCCCcccChhHHHHHHHH
Q 001121 1112 HTGERPYKCKFEGCGLSFRFVSDISRHRRK 1141 (1150)
Q Consensus 1112 HtGEKPYkC~v~GCGKsFsskS~LkrH~Rk 1141 (1150)
--||--+.|+. ||..|..+..+.+|..+
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 34566677777 77777777777777665
No 71
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=34.02 E-value=22 Score=42.66 Aligned_cols=114 Identities=17% Similarity=0.228 Sum_probs=64.0
Q ss_pred cCccCccCCCchhHHHHHhhccccCccCCCCCCCCCcccccccCCCCceeccCCCCCCcccChHHHHhHhh---------
Q 001121 987 RSRAGKDAANTSEVDIRKIAEKRATKTMRNRESVPAPCQDKKKILKGHHRCDLDGCRMSFETKRELSLHKR--------- 1057 (1150)
Q Consensus 987 Cs~CGK~F~sks~Lk~H~r~eKpy~K~F~srssL~~~H~~r~Ht~eKpykC~~~~CGKsFssks~Lk~H~r--------- 1057 (1150)
.+.|+..+-.+..+.+|...++.... .| . .-.|.-...|.|....|.+ +-+....|..
T Consensus 276 ~e~C~ykr~~k~DvirH~~~hkkrdn------sL--~--dgf~rfs~syhC~~~~C~k---sTsdV~~h~nFht~~~n~G 342 (480)
T KOG4377|consen 276 NEYCFYKRGQKNDVIRHVEIHKKRDN------SL--I--DGFHRFSNSYHCTGQICEK---STSDVLLHDNFHTDKRNNG 342 (480)
T ss_pred CccccccccchhhhHHHHHHHhhccc------cc--c--cchhhcCccchhhhcccCc---ccccccccCccccccccCc
Confidence 46788888778899988873332211 11 0 0001112227788778877 3344444532
Q ss_pred ---ccCCCCCCC--CccCChhHHHhhhhhccCC----C--------------------CccCCCCcCCccccChhHHHHH
Q 001121 1058 ---NRCPHEGCG--KRFSSHKYAIIHQRVHDDE----R--------------------PLKCPWKGCSMSFKWAWARTEH 1108 (1150)
Q Consensus 1058 ---~Hc~Ce~CG--KsFssks~Lk~H~r~Htge----K--------------------pfkCp~e~CgKsFssks~Lk~H 1108 (1150)
.||.|-.|| -.|.-...-..|.+-+.++ + -|-|.+..|+.+|...+.+..|
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 457776666 4444222222233222221 1 1446667789999999999999
Q ss_pred HhhcC
Q 001121 1109 IRVHT 1113 (1150)
Q Consensus 1109 mRtHt 1113 (1150)
.|.|.
T Consensus 423 krkhe 427 (480)
T KOG4377|consen 423 KRKHE 427 (480)
T ss_pred hhhhh
Confidence 88875
No 72
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=31.22 E-value=32 Score=40.42 Aligned_cols=146 Identities=19% Similarity=0.212 Sum_probs=81.3
Q ss_pred CccCccCccCC-CchhHHHHHhhcccc------CccCCCCCCCCCcccccccCCCCceeccCCCCCCcccChHHHHhHhh
Q 001121 985 GLRSRAGKDAA-NTSEVDIRKIAEKRA------TKTMRNRESVPAPCQDKKKILKGHHRCDLDGCRMSFETKRELSLHKR 1057 (1150)
Q Consensus 985 ~~Cs~CGK~F~-sks~Lk~H~r~eKpy------~K~F~srssL~~~H~~r~Ht~eKpykC~~~~CGKsFssks~Lk~H~r 1057 (1150)
..|=.|...+. +++....|+-..+.. .-.|.+ .+ ..|.. ..-..+.|- .|.+.|+.+..|+.||+
T Consensus 145 lqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvn--el-LehLk---ekL~r~~CL--yCekifrdkntLkeHMr 216 (423)
T KOG2482|consen 145 LQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVN--EL-LEHLK---EKLERLRCL--YCEKIFRDKNTLKEHMR 216 (423)
T ss_pred eEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHH--HH-HHHHH---HHHhhheee--eeccccCCcHHHHHHHH
Confidence 45556766554 556666776533222 111111 11 22211 112348899 89999999999999998
Q ss_pred c--cCCC---------------CCCCCccC-ChhHHHhhhh-hc------------cCCCC--ccCCCCcCCccccChhH
Q 001121 1058 N--RCPH---------------EGCGKRFS-SHKYAIIHQR-VH------------DDERP--LKCPWKGCSMSFKWAWA 1104 (1150)
Q Consensus 1058 ~--Hc~C---------------e~CGKsFs-sks~Lk~H~r-~H------------tgeKp--fkCp~e~CgKsFssks~ 1104 (1150)
. |+.- ..=|++.. ....+.+-.. -+ .+..+ .+|-+ |...+-+...
T Consensus 217 kK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLf--C~~~~en~~~ 294 (423)
T KOG2482|consen 217 KKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLF--CTNFYENPVF 294 (423)
T ss_pred hccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEe--eccchhhHHH
Confidence 5 3211 11122211 1111110000 01 01122 48955 9998888999
Q ss_pred HHHHHhh-cCC--------------------------CCcccCCCCCCCCcccChhHHHHHHHHh
Q 001121 1105 RTEHIRV-HTG--------------------------ERPYKCKFEGCGLSFRFVSDISRHRRKT 1142 (1150)
Q Consensus 1105 Lk~HmRt-HtG--------------------------EKPYkC~v~GCGKsFsskS~LkrH~RkH 1142 (1150)
|..||++ |.= .+.-.|-. |.-.|-....|..||--|
T Consensus 295 l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~--cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 295 LFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAE--CDLSFWKEPGLLIHMVED 357 (423)
T ss_pred HHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhcccccc--ccccccCcchhhhhcccc
Confidence 9999985 420 01123555 999999999999999753
No 73
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=28.99 E-value=18 Score=39.68 Aligned_cols=43 Identities=33% Similarity=0.658 Sum_probs=25.0
Q ss_pred CCccCCCCcCCccccChhHHHHHHhh----------cCCCCc-----ccCCCCCCCCcccCh
Q 001121 1086 RPLKCPWKGCSMSFKWAWARTEHIRV----------HTGERP-----YKCKFEGCGLSFRFV 1132 (1150)
Q Consensus 1086 KpfkCp~e~CgKsFssks~Lk~HmRt----------HtGEKP-----YkC~v~GCGKsFssk 1132 (1150)
+.+.||+ |++.|.++.-+....+. ..+..| ..|+. ||.+|...
T Consensus 4 k~~~CPv--C~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~--CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPV--CGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPH--CGYAAFEE 61 (214)
T ss_pred CceECCC--CCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCC--CCCccccc
Confidence 4456644 77766665544444432 123444 36998 99887644
No 74
>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=26.96 E-value=28 Score=27.80 Aligned_cols=12 Identities=17% Similarity=0.349 Sum_probs=5.5
Q ss_pred CCCCCCCccCCh
Q 001121 1061 PHEGCGKRFSSH 1072 (1150)
Q Consensus 1061 ~Ce~CGKsFssk 1072 (1150)
.|+.|+..|.-.
T Consensus 4 ~CP~C~~~~~v~ 15 (38)
T TIGR02098 4 QCPNCKTSFRVV 15 (38)
T ss_pred ECCCCCCEEEeC
Confidence 344555544433
No 75
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=24.88 E-value=22 Score=39.04 Aligned_cols=23 Identities=30% Similarity=0.398 Sum_probs=15.2
Q ss_pred CceeccCCCCCCcccChHHHHhHhh
Q 001121 1033 GHHRCDLDGCRMSFETKRELSLHKR 1057 (1150)
Q Consensus 1033 KpykC~~~~CGKsFssks~Lk~H~r 1057 (1150)
+.+.|+ .|++.|.++.-+....+
T Consensus 4 k~~~CP--vC~~~F~~~~vrs~~~r 26 (214)
T PF09986_consen 4 KKITCP--VCGKEFKTKKVRSGKIR 26 (214)
T ss_pred CceECC--CCCCeeeeeEEEcCCce
Confidence 456777 88888877665555444
No 76
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=24.14 E-value=38 Score=35.05 Aligned_cols=11 Identities=9% Similarity=0.528 Sum_probs=5.1
Q ss_pred CCCCCCCCccC
Q 001121 1060 CPHEGCGKRFS 1070 (1150)
Q Consensus 1060 c~Ce~CGKsFs 1070 (1150)
|.|+.|+..|.
T Consensus 100 Y~Cp~C~~~y~ 110 (147)
T smart00531 100 YKCPNCQSKYT 110 (147)
T ss_pred EECcCCCCEee
Confidence 44444444444
No 77
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=23.40 E-value=55 Score=33.79 Aligned_cols=8 Identities=25% Similarity=0.605 Sum_probs=3.4
Q ss_pred CCCCCCcc
Q 001121 1062 HEGCGKRF 1069 (1150)
Q Consensus 1062 Ce~CGKsF 1069 (1150)
|+.||++|
T Consensus 12 Cp~cg~kF 19 (129)
T TIGR02300 12 CPNTGSKF 19 (129)
T ss_pred CCCcCccc
Confidence 44444444
No 78
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=22.68 E-value=61 Score=31.68 Aligned_cols=25 Identities=32% Similarity=0.668 Sum_probs=21.8
Q ss_pred ccC----CCCCCCCcccChhHHHHHHHHhCC
Q 001121 1118 YKC----KFEGCGLSFRFVSDISRHRRKTGH 1144 (1150)
Q Consensus 1118 YkC----~v~GCGKsFsskS~LkrH~RkHh~ 1144 (1150)
|.| .. |+..+.+...+++|.+.+|+
T Consensus 81 ~~C~~~~~~--C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPH--CGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCC--CCcEeccHHHHHHHHHHhcC
Confidence 889 66 99999999999999998764
No 79
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=22.66 E-value=19 Score=42.26 Aligned_cols=72 Identities=21% Similarity=0.419 Sum_probs=46.8
Q ss_pred CCceeccCCCCCCcccChHHHHhHhhc-cCCCCCCCCccCChhHHHhhhhhccCCCCccCCCCcCCccccChhHHHHHHh
Q 001121 1032 KGHHRCDLDGCRMSFETKRELSLHKRN-RCPHEGCGKRFSSHKYAIIHQRVHDDERPLKCPWKGCSMSFKWAWARTEHIR 1110 (1150)
Q Consensus 1032 eKpykC~~~~CGKsFssks~Lk~H~r~-Hc~Ce~CGKsFssks~Lk~H~r~HtgeKpfkCp~e~CgKsFssks~Lk~HmR 1110 (1150)
.++|+|..+.|.+.+.....|+.|... ||.- - ...++ .-+-|+-.....|+|.| .+|.++++..-.|+-|..
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~--i--~~~s~-~~~ph~~~~~~nk~~r~--~i~~~~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSP--I--TTPTP-APIPHQGFVVENKPYRC--EVCSKRYKNLNGLKYHRT 419 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCC--C--CCCCC-CCCCcceeeeccCcccC--hhhhhhhccCCCCCceee
Confidence 578999999999999999999999764 3211 0 11111 12223333344688888 558888887777666643
No 80
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=22.15 E-value=65 Score=41.72 Aligned_cols=13 Identities=31% Similarity=0.654 Sum_probs=8.3
Q ss_pred CCCcccCCCCCCCCc
Q 001121 1114 GERPYKCKFEGCGLS 1128 (1150)
Q Consensus 1114 GEKPYkC~v~GCGKs 1128 (1150)
...|+.|+. ||..
T Consensus 472 ~~~p~~Cp~--Cgs~ 484 (730)
T COG1198 472 EPIPQSCPE--CGSE 484 (730)
T ss_pred CCCCCCCCC--CCCC
Confidence 345677777 7754
No 81
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=21.98 E-value=27 Score=36.84 Aligned_cols=18 Identities=39% Similarity=0.711 Sum_probs=10.2
Q ss_pred hhccCCCCCCCCccCChh
Q 001121 1056 KRNRCPHEGCGKRFSSHK 1073 (1150)
Q Consensus 1056 ~r~Hc~Ce~CGKsFssks 1073 (1150)
.+.++.|+.||++|.+..
T Consensus 25 ~~~~~~c~~c~~~f~~~e 42 (154)
T PRK00464 25 IRRRRECLACGKRFTTFE 42 (154)
T ss_pred eeeeeeccccCCcceEeE
Confidence 333356667777666543
No 82
>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=21.02 E-value=1.7e+02 Score=33.06 Aligned_cols=46 Identities=24% Similarity=0.398 Sum_probs=40.4
Q ss_pred hhhhhhHHHHHHHHHhcC-----------CceEEEEecc--chHhHHHHHHHHHHHhCC
Q 001121 286 IFCLEHAAQIEEILQSKG-----------GAEILVICHS--DYQKIKAHAAAVAEEIGS 331 (1150)
Q Consensus 286 ifCleHa~e~e~~L~~~G-----------G~~~ll~ch~--dY~kiea~A~~vAee~~~ 331 (1150)
--|.|=|+.|-++|...| |.||++=.-| +|..+++-|+.||++|.-
T Consensus 115 ~~v~~~A~~~r~~L~~~gL~~f~KTSG~kGlHv~vPl~~~~~~~~~r~fa~~lA~~l~~ 173 (228)
T cd04864 115 EAVRTAALAVRELLDELGLPSFVKTTGSRGFHVVVPLDGRGDFDDVRAFAAEAADALAK 173 (228)
T ss_pred HHHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHH
Confidence 369999999999999987 8999998887 578999999999999853
No 83
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=20.14 E-value=22 Score=41.74 Aligned_cols=52 Identities=27% Similarity=0.682 Sum_probs=36.8
Q ss_pred CCccCCCCcCCccccChhHHHHHHhh-c--------------C----CCCcccCCCCCCCCcccChhHHHHHH
Q 001121 1086 RPLKCPWKGCSMSFKWAWARTEHIRV-H--------------T----GERPYKCKFEGCGLSFRFVSDISRHR 1139 (1150)
Q Consensus 1086 KpfkCp~e~CgKsFssks~Lk~HmRt-H--------------t----GEKPYkC~v~GCGKsFsskS~LkrH~ 1139 (1150)
++|+|++..|.+.++....|+.|... | + ..|||+|++ |.++++.-..|+-|+
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i--~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEV--CSKRYKNLNGLKYHR 418 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChh--hhhhhccCCCCCcee
Confidence 66777777777777776666666432 2 2 258999999 999998776666654
Done!