Query 003869
Match_columns 790
No_of_seqs 448 out of 2428
Neff 5.0
Searched_HMMs 46136
Date Thu Mar 28 13:28:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003869.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003869hhsearch_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 99.3 7.4E-13 1.6E-17 139.0 4.2 109 267-422 127-243 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.0 1.3E-10 2.8E-15 122.4 2.8 80 345-425 128-218 (279)
3 KOG1074 Transcriptional repres 98.7 2.1E-09 4.5E-14 125.7 -0.3 44 378-421 615-660 (958)
4 KOG3576 Ovo and related transc 98.7 1.5E-08 3.3E-13 102.8 4.8 72 345-417 115-197 (267)
5 KOG3623 Homeobox transcription 98.6 4.2E-09 9E-14 121.4 -0.6 70 345-415 892-971 (1007)
6 KOG3623 Homeobox transcription 98.4 1E-07 2.2E-12 110.3 1.2 71 345-416 238-331 (1007)
7 PHA02768 hypothetical protein; 98.2 5.4E-07 1.2E-11 74.6 2.5 45 347-412 5-49 (55)
8 PHA00733 hypothetical protein 97.9 6.5E-06 1.4E-10 79.2 3.8 54 344-418 70-123 (128)
9 KOG1074 Transcriptional repres 97.6 0.00012 2.6E-09 86.9 8.1 78 345-423 603-697 (958)
10 KOG3993 Transcription factor ( 97.6 1.2E-05 2.5E-10 89.4 -0.7 102 317-421 267-383 (500)
11 PHA00732 hypothetical protein 97.6 4.9E-05 1.1E-09 67.6 3.2 48 347-418 1-48 (79)
12 KOG3576 Ovo and related transc 97.3 3.5E-05 7.6E-10 78.9 -0.8 79 339-418 137-236 (267)
13 PF13465 zf-H2C2_2: Zinc-finge 97.2 3.6E-05 7.8E-10 54.4 -1.6 23 384-406 2-26 (26)
14 COG5189 SFP1 Putative transcri 97.2 0.00018 4E-09 77.7 2.2 69 345-415 347-419 (423)
15 PHA02768 hypothetical protein; 97.0 0.0003 6.5E-09 58.6 1.5 25 394-418 5-29 (55)
16 KOG3608 Zn finger proteins [Ge 97.0 0.00012 2.6E-09 80.0 -1.1 154 260-418 197-376 (467)
17 PHA00733 hypothetical protein 97.0 0.00025 5.3E-09 68.4 0.7 59 345-418 38-97 (128)
18 KOG3608 Zn finger proteins [Ge 96.9 0.00012 2.6E-09 80.0 -1.7 71 347-418 237-316 (467)
19 PHA00616 hypothetical protein 96.9 0.00023 5E-09 56.7 -0.0 29 394-422 1-29 (44)
20 PF12756 zf-C2H2_2: C2H2 type 96.8 0.00035 7.7E-09 61.9 0.8 70 349-418 1-74 (100)
21 PF00096 zf-C2H2: Zinc finger, 96.6 0.00049 1.1E-08 46.6 -0.2 23 395-417 1-23 (23)
22 PF05605 zf-Di19: Drought indu 96.4 0.0026 5.6E-08 52.3 3.1 52 347-418 2-53 (54)
23 PLN03086 PRLI-interacting fact 96.1 0.0035 7.6E-08 73.5 2.7 71 345-417 451-537 (567)
24 PF01352 KRAB: KRAB box; Inte 95.9 0.0012 2.7E-08 51.8 -1.1 29 171-199 1-30 (41)
25 PF13912 zf-C2H2_6: C2H2-type 95.8 0.0032 6.9E-08 44.2 0.7 26 394-419 1-26 (27)
26 PF00096 zf-C2H2: Zinc finger, 95.8 0.0053 1.2E-07 41.4 1.8 21 348-368 1-21 (23)
27 PF13894 zf-C2H2_4: C2H2-type 95.6 0.0038 8.3E-08 41.6 0.3 24 395-418 1-24 (24)
28 PHA00616 hypothetical protein 95.3 0.0077 1.7E-07 48.1 1.3 22 347-368 1-22 (44)
29 PF13894 zf-C2H2_4: C2H2-type 95.1 0.017 3.6E-07 38.5 2.2 24 348-371 1-24 (24)
30 smart00355 ZnF_C2H2 zinc finge 94.6 0.013 2.8E-07 39.4 0.6 24 395-418 1-24 (26)
31 PF13912 zf-C2H2_6: C2H2-type 93.9 0.032 6.9E-07 39.1 1.5 24 347-371 1-24 (27)
32 PLN03086 PRLI-interacting fact 93.3 0.024 5.2E-07 66.8 0.1 71 349-426 435-508 (567)
33 PF13465 zf-H2C2_2: Zinc-finge 93.0 0.042 9E-07 38.9 0.8 20 340-359 7-26 (26)
34 KOG3993 Transcription factor ( 92.8 0.025 5.3E-07 63.8 -0.8 54 346-418 266-319 (500)
35 PHA00732 hypothetical protein 92.4 0.08 1.7E-06 47.3 2.1 29 394-422 1-30 (79)
36 smart00355 ZnF_C2H2 zinc finge 91.8 0.13 2.8E-06 34.3 2.2 24 348-372 1-24 (26)
37 PF09237 GAGA: GAGA factor; I 90.2 0.13 2.8E-06 42.5 1.0 27 394-420 24-50 (54)
38 PF12874 zf-met: Zinc-finger o 89.1 0.13 2.7E-06 35.4 0.1 23 395-417 1-23 (25)
39 PF09237 GAGA: GAGA factor; I 88.6 0.37 8.1E-06 39.9 2.6 31 342-372 19-49 (54)
40 PRK04860 hypothetical protein; 87.7 0.3 6.6E-06 49.1 1.9 38 346-408 118-157 (160)
41 PF12171 zf-C2H2_jaz: Zinc-fin 87.0 0.3 6.4E-06 34.6 1.0 23 395-417 2-24 (27)
42 KOG1146 Homeobox protein [Gene 86.0 0.3 6.5E-06 61.8 0.9 70 345-416 463-540 (1406)
43 PF02178 AT_hook: AT hook moti 85.1 0.31 6.7E-06 29.7 0.2 11 150-160 1-11 (13)
44 PF12874 zf-met: Zinc-finger o 82.8 0.78 1.7E-05 31.4 1.5 21 348-368 1-21 (25)
45 smart00384 AT_hook DNA binding 82.8 0.55 1.2E-05 33.7 0.7 12 150-161 1-12 (26)
46 PF13909 zf-H2C2_5: C2H2-type 82.4 0.39 8.5E-06 32.8 -0.1 23 395-418 1-23 (24)
47 KOG2893 Zn finger protein [Gen 81.6 0.64 1.4E-05 49.4 1.1 49 346-418 10-59 (341)
48 PF13909 zf-H2C2_5: C2H2-type 78.7 1.7 3.7E-05 29.6 2.1 23 348-371 1-23 (24)
49 PF09986 DUF2225: Uncharacteri 74.0 2 4.4E-05 45.0 2.1 54 346-407 4-61 (214)
50 PF13913 zf-C2HC_2: zinc-finge 73.4 1.5 3.2E-05 31.0 0.7 21 395-416 3-23 (25)
51 smart00451 ZnF_U1 U1-like zinc 72.7 2.6 5.7E-05 30.9 1.9 22 347-368 3-24 (35)
52 PF12171 zf-C2H2_jaz: Zinc-fin 71.4 1.5 3.2E-05 31.0 0.3 21 348-368 2-22 (27)
53 KOG2231 Predicted E3 ubiquitin 70.7 1.4 3E-05 53.2 -0.0 61 356-416 123-204 (669)
54 COG5048 FOG: Zn-finger [Genera 69.4 2 4.3E-05 46.5 0.9 60 346-421 288-350 (467)
55 smart00451 ZnF_U1 U1-like zinc 69.0 2.3 5.1E-05 31.2 0.9 24 393-416 2-25 (35)
56 PF13913 zf-C2HC_2: zinc-finge 65.3 4.7 0.0001 28.5 1.8 20 348-368 3-22 (25)
57 PF01429 MBD: Methyl-CpG bindi 63.6 2.5 5.4E-05 37.4 0.2 48 237-284 10-57 (77)
58 COG5048 FOG: Zn-finger [Genera 60.6 4.3 9.3E-05 43.9 1.4 79 341-420 313-444 (467)
59 KOG1146 Homeobox protein [Gene 59.5 5.7 0.00012 51.1 2.3 76 342-422 1279-1356(1406)
60 TIGR00373 conserved hypothetic 59.3 3.7 8.1E-05 41.1 0.6 31 743-779 107-137 (158)
61 PF12756 zf-C2H2_2: C2H2 type 56.3 8.6 0.00019 33.8 2.3 23 346-368 49-71 (100)
62 PF09963 DUF2197: Uncharacteri 55.5 4 8.6E-05 34.6 0.1 36 746-781 3-42 (56)
63 COG4049 Uncharacterized protei 54.6 6.5 0.00014 33.4 1.1 31 342-372 12-42 (65)
64 COG1997 RPL43A Ribosomal prote 54.1 7.2 0.00016 35.8 1.5 21 388-408 47-67 (89)
65 smart00834 CxxC_CXXC_SSSS Puta 53.8 6.1 0.00013 30.1 0.8 32 745-780 5-36 (41)
66 PRK06266 transcription initiat 53.5 5.6 0.00012 40.7 0.8 32 743-780 115-146 (178)
67 PF12773 DZR: Double zinc ribb 53.2 5.9 0.00013 31.7 0.7 32 745-784 12-43 (50)
68 COG5236 Uncharacterized conser 51.7 11 0.00023 42.4 2.5 71 347-417 151-243 (493)
69 COG1996 RPC10 DNA-directed RNA 50.9 6.5 0.00014 32.5 0.6 30 744-780 5-34 (49)
70 COG5189 SFP1 Putative transcri 48.1 4.7 0.0001 44.7 -0.8 24 345-368 396-419 (423)
71 KOG4124 Putative transcription 47.7 5.7 0.00012 44.6 -0.3 65 344-414 346-418 (442)
72 smart00659 RPOLCX RNA polymera 47.4 9.3 0.0002 30.7 1.0 28 745-780 2-29 (44)
73 PRK00398 rpoP DNA-directed RNA 44.1 9.9 0.00021 30.3 0.7 30 744-780 2-31 (46)
74 smart00614 ZnF_BED BED zinc fi 42.6 11 0.00024 30.4 0.8 25 394-418 18-48 (50)
75 PF09538 FYDLN_acid: Protein o 41.7 14 0.00031 35.0 1.5 31 347-407 9-39 (108)
76 PF02892 zf-BED: BED zinc fing 41.6 19 0.00041 28.1 1.9 27 345-371 14-44 (45)
77 PF05443 ROS_MUCR: ROS/MUCR tr 39.4 11 0.00023 37.1 0.3 24 394-420 72-95 (132)
78 smart00531 TFIIE Transcription 38.2 15 0.00032 36.3 1.1 39 742-781 96-134 (147)
79 PF08274 PhnA_Zn_Ribbon: PhnA 38.2 7.2 0.00016 29.1 -0.9 26 747-780 4-29 (30)
80 PF05605 zf-Di19: Drought indu 37.8 18 0.0004 29.6 1.4 24 394-418 2-25 (54)
81 PHA03230 nuclear protein UL55; 35.7 18 0.0004 37.2 1.3 31 750-781 111-148 (180)
82 PF12013 DUF3505: Protein of u 34.7 58 0.0012 30.3 4.3 72 346-419 10-109 (109)
83 smart00614 ZnF_BED BED zinc fi 34.4 26 0.00057 28.3 1.7 25 347-371 18-47 (50)
84 KOG2807 RNA polymerase II tran 34.0 15 0.00033 41.0 0.4 10 770-779 276-285 (378)
85 TIGR00373 conserved hypothetic 33.4 17 0.00037 36.4 0.6 18 764-781 103-120 (158)
86 PF13821 DUF4187: Domain of un 33.0 20 0.00043 30.2 0.8 15 744-758 26-40 (55)
87 PRK04860 hypothetical protein; 32.9 18 0.0004 36.5 0.7 30 394-427 119-148 (160)
88 TIGR00622 ssl1 transcription f 32.4 62 0.0013 31.2 4.1 72 345-418 13-105 (112)
89 COG4049 Uncharacterized protei 30.7 15 0.00033 31.3 -0.2 23 394-416 17-39 (65)
90 PF14621 RFX5_DNA_bdg: RFX5 DN 30.6 21 0.00046 36.8 0.7 16 145-160 63-78 (219)
91 TIGR00280 L37a ribosomal prote 30.4 23 0.00051 32.8 0.9 19 390-408 49-67 (91)
92 PF08996 zf-DNA_Pol: DNA Polym 29.9 14 0.00029 38.1 -0.8 40 743-782 16-57 (188)
93 TIGR02300 FYDLN_acid conserved 29.9 32 0.0007 33.8 1.8 36 346-411 8-43 (129)
94 PTZ00255 60S ribosomal protein 29.7 26 0.00055 32.5 1.0 19 390-408 50-68 (90)
95 COG4896 Uncharacterized protei 29.2 17 0.00036 31.5 -0.2 17 770-786 31-56 (68)
96 TIGR00100 hypA hydrogenase nic 29.2 26 0.00055 33.4 1.0 28 743-779 68-95 (115)
97 smart00349 KRAB krueppel assoc 28.7 35 0.00076 23.6 1.5 45 175-219 5-60 (61)
98 KOG4451 Uncharacterized conser 28.4 16 0.00034 39.1 -0.7 58 698-780 216-273 (286)
99 PRK00564 hypA hydrogenase nick 28.3 26 0.00056 33.5 0.9 28 743-779 69-97 (117)
100 COG5415 Predicted integral mem 28.2 25 0.00055 37.1 0.8 32 746-780 193-224 (251)
101 PF01780 Ribosomal_L37ae: Ribo 27.2 24 0.00053 32.7 0.4 18 390-407 49-66 (90)
102 KOG4167 Predicted DNA-binding 26.9 11 0.00024 45.9 -2.2 26 393-418 791-816 (907)
103 PF13451 zf-trcl: Probable zin 26.4 13 0.00028 30.7 -1.3 37 745-781 4-44 (49)
104 PF13248 zf-ribbon_3: zinc-rib 26.3 23 0.0005 25.1 0.1 24 746-780 3-26 (26)
105 PRK03976 rpl37ae 50S ribosomal 26.2 30 0.00065 32.1 0.8 19 390-408 50-68 (90)
106 COG4957 Predicted transcriptio 25.9 27 0.00058 34.6 0.5 24 394-420 76-99 (148)
107 PRK06266 transcription initiat 25.5 29 0.00063 35.6 0.7 16 766-781 113-128 (178)
108 PF04959 ARS2: Arsenite-resist 25.4 45 0.00097 35.4 2.1 29 345-373 75-103 (214)
109 COG1592 Rubrerythrin [Energy p 24.9 40 0.00086 34.5 1.5 11 346-356 133-143 (166)
110 PRK00762 hypA hydrogenase nick 24.4 45 0.00097 32.3 1.7 30 743-777 68-99 (124)
111 smart00531 TFIIE Transcription 23.8 33 0.00072 33.8 0.7 16 766-781 95-110 (147)
112 PF09723 Zn-ribbon_8: Zinc rib 22.5 42 0.0009 26.4 0.9 30 745-778 5-34 (42)
113 KOG2186 Cell growth-regulating 21.8 47 0.001 36.2 1.4 45 348-415 4-49 (276)
114 smart00391 MBD Methyl-CpG bind 21.7 42 0.00091 30.0 0.9 46 237-282 7-52 (77)
115 PF10058 DUF2296: Predicted in 21.7 48 0.001 27.8 1.1 35 742-779 19-53 (54)
116 COG1571 Predicted DNA-binding 21.5 38 0.00083 39.3 0.7 61 711-783 320-380 (421)
117 cd00350 rubredoxin_like Rubred 21.2 59 0.0013 24.3 1.4 9 394-402 17-25 (33)
118 PRK12380 hydrogenase nickel in 21.1 47 0.001 31.6 1.1 52 711-778 43-94 (113)
119 PF07975 C1_4: TFIIH C1-like d 20.5 29 0.00063 28.9 -0.3 30 748-780 2-31 (51)
120 COG2824 PhnA Uncharacterized Z 20.4 39 0.00085 32.3 0.4 31 746-784 4-34 (112)
121 COG2888 Predicted Zn-ribbon RN 20.4 76 0.0016 27.5 2.0 12 346-357 26-37 (61)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.32 E-value=7.4e-13 Score=138.99 Aligned_cols=109 Identities=17% Similarity=0.314 Sum_probs=89.8
Q ss_pred CcccccccccccccccccCCCCCCCCCCCCCCCccccccccCCcchhhhcccccccccccccccccccccCCcccccCCc
Q 003869 267 GQHFVSCKEVSGYLQSYFGLNDTNQSINPGGDEMQQDYRVATDSLADIAQKENDQRQSNQQDKEVTLLGIDNLAEVQVRD 346 (790)
Q Consensus 267 Gqqf~TCkE~SSyf~SLlGl~e~k~t~~~~~~~vqq~~~~ss~g~a~~~~~~~~q~~s~~~~k~vt~~~~~nl~~~q~EK 346 (790)
...-+.|.+|++.+.-..||..++++.=. ....+
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~----------------------------------------------~~s~k 160 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRS----------------------------------------------LDSKK 160 (279)
T ss_pred cCCceeccccccccccccccchhhccccc----------------------------------------------ccccc
Confidence 34445888888888888888877764100 00136
Q ss_pred ccccCCCCcccCChhHHHHHHHhhhccc------CccccCCCCCCccccccCC--cccCCcCccccCCchhhhhhccccc
Q 003869 347 LFECHKCEMTFDEKDTYLQHLLSFHQRT------TRRYRLGSSVGDGVIIKDG--KFECQFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 347 PyeC~~CgKtF~~kSsLkrH~l~~H~r~------hK~F~~sssLk~H~RtHtG--PYkC~~CGKsFs~ks~L~rH~RtHt 418 (790)
.+.|++|+|.|.....|+.|++ +|.-. +|.|.+..-|+.|+|+||| ||.|.+|+|+|..+++|+.||+||.
T Consensus 161 a~~C~~C~K~YvSmpALkMHir-TH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS 239 (279)
T KOG2462|consen 161 AFSCKYCGKVYVSMPALKMHIR-THTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHS 239 (279)
T ss_pred cccCCCCCceeeehHHHhhHhh-ccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhc
Confidence 7999999999999999999999 88743 7999999999999999998 9999999999999999999999997
Q ss_pred cCcc
Q 003869 419 RNYV 422 (790)
Q Consensus 419 gE~~ 422 (790)
+.+.
T Consensus 240 ~~K~ 243 (279)
T KOG2462|consen 240 DVKK 243 (279)
T ss_pred CCcc
Confidence 6554
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.01 E-value=1.3e-10 Score=122.37 Aligned_cols=80 Identities=16% Similarity=0.314 Sum_probs=71.9
Q ss_pred CcccccCCCCcccCChhHHHHHHHhhhccc-----------CccccCCCCCCccccccCCcccCCcCccccCCchhhhhh
Q 003869 345 RDLFECHKCEMTFDEKDTYLQHLLSFHQRT-----------TRRYRLGSSVGDGVIIKDGKFECQFCHKVFHERRRYNGH 413 (790)
Q Consensus 345 EKPyeC~~CgKtF~~kSsLkrH~l~~H~r~-----------hK~F~~sssLk~H~RtHtGPYkC~~CGKsFs~ks~L~rH 413 (790)
...|+|+.|||.|...++|.+|+. +|... +|.|..-..|+.|+|+|+-|++|.+|||.|.+..-|+.|
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ-~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGH 206 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQ-THRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGH 206 (279)
T ss_pred CCceeccccccccccccccchhhc-ccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcc
Confidence 456999999999999999999987 77643 577777888999999999999999999999999999999
Q ss_pred ccccccCcccCc
Q 003869 414 VGIHVRNYVRGI 425 (790)
Q Consensus 414 ~RtHtgE~~~~~ 425 (790)
+|+||||+.-.+
T Consensus 207 iRTHTGEKPF~C 218 (279)
T KOG2462|consen 207 IRTHTGEKPFSC 218 (279)
T ss_pred cccccCCCCccC
Confidence 999999987444
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.71 E-value=2.1e-09 Score=125.67 Aligned_cols=44 Identities=18% Similarity=0.428 Sum_probs=39.6
Q ss_pred ccCCCCCCccccccCC--cccCCcCccccCCchhhhhhccccccCc
Q 003869 378 YRLGSSVGDGVIIKDG--KFECQFCHKVFHERRRYNGHVGIHVRNY 421 (790)
Q Consensus 378 F~~sssLk~H~RtHtG--PYkC~~CGKsFs~ks~L~rH~RtHtgE~ 421 (790)
..+++.|+.|.|+|+| ||+|++||++|+.+.+|+.|+.+|.-..
T Consensus 615 lSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p 660 (958)
T KOG1074|consen 615 LSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKP 660 (958)
T ss_pred ccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCc
Confidence 4457899999999999 9999999999999999999999996443
No 4
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.68 E-value=1.5e-08 Score=102.83 Aligned_cols=72 Identities=22% Similarity=0.516 Sum_probs=64.9
Q ss_pred CcccccCCCCcccCChhHHHHHHHhhhccc--------CccccCCCCCCccccccCC--cccCCcCccccCCchhhhhhc
Q 003869 345 RDLFECHKCEMTFDEKDTYLQHLLSFHQRT--------TRRYRLGSSVGDGVIIKDG--KFECQFCHKVFHERRRYNGHV 414 (790)
Q Consensus 345 EKPyeC~~CgKtF~~kSsLkrH~l~~H~r~--------hK~F~~sssLk~H~RtHtG--PYkC~~CGKsFs~ks~L~rH~ 414 (790)
...|.|.+|+|.|....-|.+|++ .|... +|.|.....|++|+|+|+| ||+|..|+|+|+++..|..|+
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~k-ch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLK-CHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhh-hccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 467999999999999999999986 66533 7999999999999999999 999999999999999999997
Q ss_pred c-cc
Q 003869 415 G-IH 417 (790)
Q Consensus 415 R-tH 417 (790)
+ +|
T Consensus 194 ~kvh 197 (267)
T KOG3576|consen 194 KKVH 197 (267)
T ss_pred HHHc
Confidence 5 44
No 5
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.64 E-value=4.2e-09 Score=121.40 Aligned_cols=70 Identities=19% Similarity=0.558 Sum_probs=65.8
Q ss_pred CcccccCCCCcccCChhHHHHHHHhhhccc--------CccccCCCCCCccccccCC--cccCCcCccccCCchhhhhhc
Q 003869 345 RDLFECHKCEMTFDEKDTYLQHLLSFHQRT--------TRRYRLGSSVGDGVIIKDG--KFECQFCHKVFHERRRYNGHV 414 (790)
Q Consensus 345 EKPyeC~~CgKtF~~kSsLkrH~l~~H~r~--------hK~F~~sssLk~H~RtHtG--PYkC~~CGKsFs~ks~L~rH~ 414 (790)
+..|.|+.|+|.|...++|.+|.- .|.+. .|+|+++.+|..|+|.|.| ||+|..|+|+|++.+.+..||
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKY-EHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKY-EHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhh-hhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 578999999999999999999987 78876 4899999999999999998 999999999999999999998
Q ss_pred c
Q 003869 415 G 415 (790)
Q Consensus 415 R 415 (790)
.
T Consensus 971 N 971 (1007)
T KOG3623|consen 971 N 971 (1007)
T ss_pred c
Confidence 5
No 6
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.37 E-value=1e-07 Score=110.31 Aligned_cols=71 Identities=24% Similarity=0.569 Sum_probs=63.7
Q ss_pred CcccccCCCCcccCChhHHHHHHHhhhccc---------------------CccccCCCCCCccccccCC--cccCCcCc
Q 003869 345 RDLFECHKCEMTFDEKDTYLQHLLSFHQRT---------------------TRRYRLGSSVGDGVIIKDG--KFECQFCH 401 (790)
Q Consensus 345 EKPyeC~~CgKtF~~kSsLkrH~l~~H~r~---------------------hK~F~~sssLk~H~RtHtG--PYkC~~CG 401 (790)
+..|.|..|..+|..+..|.+|+. .|... +|+|+.+.+|+.|+|+|.| ||+|+.|+
T Consensus 238 e~nfsC~lCsytFAyRtQLErhm~-~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCk 316 (1007)
T KOG3623|consen 238 EPNFSCMLCSYTFAYRTQLERHMQ-LHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCK 316 (1007)
T ss_pred CCCCcchhhhhhhhhHHHHHHHHH-hhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccc
Confidence 567999999999999999999996 55422 5889999999999999998 99999999
Q ss_pred cccCCchhhhhhccc
Q 003869 402 KVFHERRRYNGHVGI 416 (790)
Q Consensus 402 KsFs~ks~L~rH~Rt 416 (790)
|+|++.+.+..||-.
T Consensus 317 KRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 317 KRFSHSGSYSSHMSS 331 (1007)
T ss_pred cccccCCcccccccc
Confidence 999999999999854
No 7
>PHA02768 hypothetical protein; Provisional
Probab=98.25 E-value=5.4e-07 Score=74.61 Aligned_cols=45 Identities=16% Similarity=0.405 Sum_probs=40.1
Q ss_pred ccccCCCCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccCCcccCCcCccccCCchhhhh
Q 003869 347 LFECHKCEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKDGKFECQFCHKVFHERRRYNG 412 (790)
Q Consensus 347 PyeC~~CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHtGPYkC~~CGKsFs~ks~L~r 412 (790)
.|+|+.||+.|...++|..|++ +|++||+|..|+|.|.+.+.|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r---------------------~H~k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLR---------------------KHNTNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHH---------------------hcCCcccCCcccceecccceeEE
Confidence 4899999999999999999988 46679999999999999888753
No 8
>PHA00733 hypothetical protein
Probab=97.95 E-value=6.5e-06 Score=79.19 Aligned_cols=54 Identities=22% Similarity=0.370 Sum_probs=45.6
Q ss_pred CCcccccCCCCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccCCcccCCcCccccCCchhhhhhccccc
Q 003869 344 VRDLFECHKCEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKDGKFECQFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 344 ~EKPyeC~~CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHtGPYkC~~CGKsFs~ks~L~rH~RtHt 418 (790)
..+||.|+.|++.|....+|.+|++ .|+.+|.|..|+|.|.....|.+|++.++
T Consensus 70 ~~kPy~C~~Cgk~Fss~s~L~~H~r---------------------~h~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 70 AVSPYVCPLCLMPFSSSVSLKQHIR---------------------YTEHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CCCCccCCCCCCcCCCHHHHHHHHh---------------------cCCcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 3588999999999999999988876 23347999999999999999999987654
No 9
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=97.62 E-value=0.00012 Score=86.93 Aligned_cols=78 Identities=18% Similarity=0.376 Sum_probs=69.2
Q ss_pred CcccccCCCCcccCChhHHHHHHHhhhccc--------CccccCCCCCCccccccCC------cccCC---cCccccCCc
Q 003869 345 RDLFECHKCEMTFDEKDTYLQHLLSFHQRT--------TRRYRLGSSVGDGVIIKDG------KFECQ---FCHKVFHER 407 (790)
Q Consensus 345 EKPyeC~~CgKtF~~kSsLkrH~l~~H~r~--------hK~F~~sssLk~H~RtHtG------PYkC~---~CGKsFs~k 407 (790)
-.|-+|-+|-+....++.|+.|.+ .|+++ +++|..+.+|+.||-+|.- +|.|+ +|.+.|...
T Consensus 603 TdPNqCiiC~rVlSC~saLqmHyr-tHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~ 681 (958)
T KOG1074|consen 603 TDPNQCIICLRVLSCPSALQMHYR-THTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNA 681 (958)
T ss_pred CCccceeeeeecccchhhhhhhhh-cccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccc
Confidence 457899999999999999999999 89887 6889999999999998883 79999 999999999
Q ss_pred hhhhhhccccccCccc
Q 003869 408 RRYNGHVGIHVRNYVR 423 (790)
Q Consensus 408 s~L~rH~RtHtgE~~~ 423 (790)
-.|..|+|+|.+....
T Consensus 682 V~lpQhIriH~~~~~s 697 (958)
T KOG1074|consen 682 VTLPQHIRIHLGGQIS 697 (958)
T ss_pred ccccceEEeecCCCCC
Confidence 9999999999866553
No 10
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.59 E-value=1.2e-05 Score=89.37 Aligned_cols=102 Identities=19% Similarity=0.272 Sum_probs=72.5
Q ss_pred ccccccccccccccccccccCCcccccCCcccccCCCCcccCChhHHHHHHHhhhccc---Cc--------cccCCCCCC
Q 003869 317 KENDQRQSNQQDKEVTLLGIDNLAEVQVRDLFECHKCEMTFDEKDTYLQHLLSFHQRT---TR--------RYRLGSSVG 385 (790)
Q Consensus 317 ~~~~q~~s~~~~k~vt~~~~~nl~~~q~EKPyeC~~CgKtF~~kSsLkrH~l~~H~r~---hK--------~F~~sssLk 385 (790)
..-.|....+|.....+..|.+.+-+.. -|+|++|+|.|+...||..|.+ .|.-. .+ .-....-.+
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~v--EYrCPEC~KVFsCPANLASHRR-WHKPR~eaa~a~~~P~k~~~~~rae~~ 343 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHV--EYRCPECDKVFSCPANLASHRR-WHKPRPEAAKAGSPPPKQAVETRAEVQ 343 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEe--eecCCcccccccCchhhhhhhc-ccCCchhhhhcCCCChhhhhhhhhhhh
Confidence 4455667778877788888888888776 4999999999999999999977 66533 11 000000011
Q ss_pred ccccc----cCCcccCCcCccccCCchhhhhhccccccCc
Q 003869 386 DGVII----KDGKFECQFCHKVFHERRRYNGHVGIHVRNY 421 (790)
Q Consensus 386 ~H~Rt----HtGPYkC~~CGKsFs~ks~L~rH~RtHtgE~ 421 (790)
.-.|. -.|-|.|.+|+|.|.+...|++|+-+|....
T Consensus 344 ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~ 383 (500)
T KOG3993|consen 344 EAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAP 383 (500)
T ss_pred hccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccc
Confidence 11111 1138999999999999999999999987443
No 11
>PHA00732 hypothetical protein
Probab=97.58 E-value=4.9e-05 Score=67.58 Aligned_cols=48 Identities=27% Similarity=0.449 Sum_probs=39.5
Q ss_pred ccccCCCCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccCCcccCCcCccccCCchhhhhhccccc
Q 003869 347 LFECHKCEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKDGKFECQFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 347 PyeC~~CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHtGPYkC~~CGKsFs~ks~L~rH~RtHt 418 (790)
||.|..|++.|.+..+|..|++..| .++.|+.|+++|. .|..|.+++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H---------------------~~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNH---------------------TLTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhccc---------------------CCCccCCCCCEeC---ChhhhhcccC
Confidence 6899999999999999999976212 2578999999998 5888887654
No 12
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=97.35 E-value=3.5e-05 Score=78.86 Aligned_cols=79 Identities=16% Similarity=0.238 Sum_probs=67.1
Q ss_pred cccccCCcccccCCCCcccCChhHHHHHHHhhhccc--------CccccCCCCCCccccccCC-------------cccC
Q 003869 339 LAEVQVRDLFECHKCEMTFDEKDTYLQHLLSFHQRT--------TRRYRLGSSVGDGVIIKDG-------------KFEC 397 (790)
Q Consensus 339 l~~~q~EKPyeC~~CgKtF~~kSsLkrH~l~~H~r~--------hK~F~~sssLk~H~RtHtG-------------PYkC 397 (790)
+.-|...|.|-|..|||.|.+...|++|++ .|++. .|.|.+..+|..|++.-+| -|.|
T Consensus 137 ~kch~~vkr~lct~cgkgfndtfdlkrh~r-thtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vc 215 (267)
T KOG3576|consen 137 LKCHSDVKRHLCTFCGKGFNDTFDLKRHTR-THTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVC 215 (267)
T ss_pred hhhccHHHHHHHhhccCcccchhhhhhhhc-cccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeee
Confidence 344555788999999999999999999999 89887 5899999999998754332 6899
Q ss_pred CcCccccCCchhhhhhccccc
Q 003869 398 QFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 398 ~~CGKsFs~ks~L~rH~RtHt 418 (790)
..||.+-.+...+..|++.|+
T Consensus 216 edcg~t~~~~e~~~~h~~~~h 236 (267)
T KOG3576|consen 216 EDCGYTSERPEVYYLHLKLHH 236 (267)
T ss_pred cccCCCCCChhHHHHHHHhcC
Confidence 999999999999999999886
No 13
>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=97.23 E-value=3.6e-05 Score=54.39 Aligned_cols=23 Identities=22% Similarity=0.681 Sum_probs=19.4
Q ss_pred CCccccccCC--cccCCcCccccCC
Q 003869 384 VGDGVIIKDG--KFECQFCHKVFHE 406 (790)
Q Consensus 384 Lk~H~RtHtG--PYkC~~CGKsFs~ 406 (790)
|.+|+++|++ ||.|+.|+|+|.+
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEESS
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 5567778887 9999999999974
No 14
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.17 E-value=0.00018 Score=77.66 Aligned_cols=69 Identities=19% Similarity=0.351 Sum_probs=48.2
Q ss_pred CcccccCC--CCcccCChhHHHHHHHhhhcccCccccCCCCCCccc--cccCCcccCCcCccccCCchhhhhhcc
Q 003869 345 RDLFECHK--CEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGV--IIKDGKFECQFCHKVFHERRRYNGHVG 415 (790)
Q Consensus 345 EKPyeC~~--CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~--RtHtGPYkC~~CGKsFs~ks~L~rH~R 415 (790)
+|||+|++ |.|+|+....|+.|++--|... +.-... .-..|. ....+||+|.+|+|+|.-...|+-|.+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~-~~~~~p-~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQ-KLHENP-SPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCc-ccCCCC-CccccccccccCCceeccccchhhccCccceeccc
Confidence 69999998 9999999999999998445322 000000 001111 123359999999999999999998864
No 15
>PHA02768 hypothetical protein; Provisional
Probab=97.01 E-value=0.0003 Score=58.57 Aligned_cols=25 Identities=24% Similarity=0.667 Sum_probs=24.1
Q ss_pred cccCCcCccccCCchhhhhhccccc
Q 003869 394 KFECQFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 394 PYkC~~CGKsFs~ks~L~rH~RtHt 418 (790)
-|+|+.|||.|++.++|.+|+|+|+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC
Confidence 4899999999999999999999999
No 16
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=97.00 E-value=0.00012 Score=80.01 Aligned_cols=154 Identities=13% Similarity=0.202 Sum_probs=95.0
Q ss_pred ccccCCCCcccccccccccccccccCCCCCCCCCCCCCCCccccccccCCcchhhhcccccccc---cccccccc-----
Q 003869 260 RRYISPGGQHFVSCKEVSGYLQSYFGLNDTNQSINPGGDEMQQDYRVATDSLADIAQKENDQRQ---SNQQDKEV----- 331 (790)
Q Consensus 260 R~~iSPkGqqf~TCkE~SSyf~SLlGl~e~k~t~~~~~~~vqq~~~~ss~g~a~~~~~~~~q~~---s~~~~k~v----- 331 (790)
++.+.+++.+...|..|+..|..--.+.++-.- .+...++...++.+.....+..+-.... ...|..+.
T Consensus 197 eH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rR---qt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc 273 (467)
T KOG3608|consen 197 EHIRTHSNEKVVACPHCGELFRTKTKLFDHLRR---QTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTC 273 (467)
T ss_pred HHHHhcCCCeEEecchHHHHhccccHHHHHHHh---hhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCC
Confidence 777788888888888888777765444443211 1112222333333332222222111111 01111111
Q ss_pred ----cccccCCcccccCCcccccCCCCcccCChhHHHHHHHhhhccc---------CccccCCCCCCccccccC-C----
Q 003869 332 ----TLLGIDNLAEVQVRDLFECHKCEMTFDEKDTYLQHLLSFHQRT---------TRRYRLGSSVGDGVIIKD-G---- 393 (790)
Q Consensus 332 ----t~~~~~nl~~~q~EKPyeC~~CgKtF~~kSsLkrH~l~~H~r~---------hK~F~~sssLk~H~RtHt-G---- 393 (790)
++..+-. ..|...|||+|+.|.+.|...+.|.+|.. .|... +-.|+....+++|++.+. |
T Consensus 274 ~~~ssL~~H~r-~rHs~dkpfKCd~Cd~~c~~esdL~kH~~-~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~ 351 (467)
T KOG3608|consen 274 SSASSLTTHIR-YRHSKDKPFKCDECDTRCVRESDLAKHVQ-VHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPI 351 (467)
T ss_pred CChHHHHHHHH-hhhccCCCccccchhhhhccHHHHHHHHH-hccccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCC
Confidence 1111111 22334799999999999999999999987 77744 345667778899987766 5
Q ss_pred cccCCcCccccCCchhhhhhccccc
Q 003869 394 KFECQFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 394 PYkC~~CGKsFs~ks~L~rH~RtHt 418 (790)
+|.|-.|.|.|++-.+|.+|++..+
T Consensus 352 ~Y~CH~Cdr~ft~G~~L~~HL~kkH 376 (467)
T KOG3608|consen 352 LYACHCCDRFFTSGKSLSAHLMKKH 376 (467)
T ss_pred ceeeecchhhhccchhHHHHHHHhh
Confidence 8999999999999999999976443
No 17
>PHA00733 hypothetical protein
Probab=96.95 E-value=0.00025 Score=68.40 Aligned_cols=59 Identities=8% Similarity=0.070 Sum_probs=48.4
Q ss_pred CcccccCCCCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccCC-cccCCcCccccCCchhhhhhccccc
Q 003869 345 RDLFECHKCEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKDG-KFECQFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 345 EKPyeC~~CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHtG-PYkC~~CGKsFs~ks~L~rH~RtHt 418 (790)
.+++.|.+|.+.|.....|..|.- |.+|+..|.. ||.|+.|++.|.....|..|+++|.
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~---------------l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~ 97 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSY---------------LYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTE 97 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHH---------------HHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcCC
Confidence 478999999999999888877632 3345555555 9999999999999999999999774
No 18
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=96.94 E-value=0.00012 Score=79.95 Aligned_cols=71 Identities=20% Similarity=0.372 Sum_probs=36.2
Q ss_pred ccccCCCCcccCChhHHHHHHHhhhcccC------ccccCCCCCCccccccC-C--cccCCcCccccCCchhhhhhcccc
Q 003869 347 LFECHKCEMTFDEKDTYLQHLLSFHQRTT------RRYRLGSSVGDGVIIKD-G--KFECQFCHKVFHERRRYNGHVGIH 417 (790)
Q Consensus 347 PyeC~~CgKtF~~kSsLkrH~l~~H~r~h------K~F~~sssLk~H~RtHt-G--PYkC~~CGKsFs~ks~L~rH~RtH 417 (790)
+|+|..|.|.|.....|+.|+. .|...- -.....++|..|+|... + ||+|..|.+.|.+.+.|.+|..+|
T Consensus 237 ~fqC~~C~KrFaTeklL~~Hv~-rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~H 315 (467)
T KOG3608|consen 237 SFQCAQCFKRFATEKLLKSHVV-RHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVH 315 (467)
T ss_pred chHHHHHHHHHhHHHHHHHHHH-HhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhc
Confidence 4555555555555555555544 343321 12333455555554322 2 666666666666666666665555
Q ss_pred c
Q 003869 418 V 418 (790)
Q Consensus 418 t 418 (790)
.
T Consensus 316 S 316 (467)
T KOG3608|consen 316 S 316 (467)
T ss_pred c
Confidence 4
No 19
>PHA00616 hypothetical protein
Probab=96.89 E-value=0.00023 Score=56.67 Aligned_cols=29 Identities=14% Similarity=0.369 Sum_probs=27.2
Q ss_pred cccCCcCccccCCchhhhhhccccccCcc
Q 003869 394 KFECQFCHKVFHERRRYNGHVGIHVRNYV 422 (790)
Q Consensus 394 PYkC~~CGKsFs~ks~L~rH~RtHtgE~~ 422 (790)
||+|..||+.|..++.|.+|++.|+|+..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 79999999999999999999999998754
No 20
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.85 E-value=0.00035 Score=61.93 Aligned_cols=70 Identities=23% Similarity=0.410 Sum_probs=22.2
Q ss_pred ccCCCCcccCChhHHHHHHHhhhccc---CccccCCCCCCccccccCC-cccCCcCccccCCchhhhhhccccc
Q 003869 349 ECHKCEMTFDEKDTYLQHLLSFHQRT---TRRYRLGSSVGDGVIIKDG-KFECQFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 349 eC~~CgKtF~~kSsLkrH~l~~H~r~---hK~F~~sssLk~H~RtHtG-PYkC~~CGKsFs~ks~L~rH~RtHt 418 (790)
+|..|+..|.....|..|+...|.-. -+.+.....+..+.+.... .+.|..|++.|.....|..|++.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 59999999999999999997667533 1122233344444443333 6999999999999999999999763
No 21
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=96.59 E-value=0.00049 Score=46.56 Aligned_cols=23 Identities=26% Similarity=0.735 Sum_probs=21.7
Q ss_pred ccCCcCccccCCchhhhhhcccc
Q 003869 395 FECQFCHKVFHERRRYNGHVGIH 417 (790)
Q Consensus 395 YkC~~CGKsFs~ks~L~rH~RtH 417 (790)
|.|+.|++.|..+..|.+|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 78999999999999999999875
No 22
>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=96.43 E-value=0.0026 Score=52.29 Aligned_cols=52 Identities=15% Similarity=0.301 Sum_probs=40.5
Q ss_pred ccccCCCCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccCCcccCCcCccccCCchhhhhhccccc
Q 003869 347 LFECHKCEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKDGKFECQFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 347 PyeC~~CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHtGPYkC~~CGKsFs~ks~L~rH~RtHt 418 (790)
.|.|++|++ ..+...|..|....|... .+.+.|++|...+. .+|.+|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~-----------------~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSE-----------------SKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCC-----------------CCCccCCCchhhhh--hHHHHHHHHhc
Confidence 489999999 566789999987555522 12789999998766 49999998765
No 23
>PLN03086 PRLI-interacting factor K; Provisional
Probab=96.05 E-value=0.0035 Score=73.53 Aligned_cols=71 Identities=18% Similarity=0.353 Sum_probs=53.6
Q ss_pred CcccccCCCCcccCChhHHHHHHHhhhccc----CccccCCCCCCccccccCC--cccCCcCccccCC----------ch
Q 003869 345 RDLFECHKCEMTFDEKDTYLQHLLSFHQRT----TRRYRLGSSVGDGVIIKDG--KFECQFCHKVFHE----------RR 408 (790)
Q Consensus 345 EKPyeC~~CgKtF~~kSsLkrH~l~~H~r~----hK~F~~sssLk~H~RtHtG--PYkC~~CGKsFs~----------ks 408 (790)
++.+.|++|++.|. ...|..|+...|... ++ +..+..|..|+++|.. |+.|++|++.|.. ..
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~Hkpv~CpCg~-~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s 528 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFHEPLQCPCGV-VLEKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLR 528 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcCCCccCCCCC-CcchhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhh
Confidence 57789999999996 688999998434211 22 2245678889888886 9999999999952 34
Q ss_pred hhhhhcccc
Q 003869 409 RYNGHVGIH 417 (790)
Q Consensus 409 ~L~rH~RtH 417 (790)
.|..|..++
T Consensus 529 ~Lt~HE~~C 537 (567)
T PLN03086 529 GMSEHESIC 537 (567)
T ss_pred hHHHHHHhc
Confidence 788898876
No 24
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box []. The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ]. KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1V65_A.
Probab=95.94 E-value=0.0012 Score=51.80 Aligned_cols=29 Identities=24% Similarity=0.184 Sum_probs=18.4
Q ss_pred ecCCCeEEeeeccC-CCCCchHHHHhhhhc
Q 003869 171 VNKNGSVVDIVDLG-SLEDPYGEELRRRTE 199 (790)
Q Consensus 171 ~~~~gv~vd~~~~~-~~~dp~~~el~r~~~ 199 (790)
|+|++|+|+|+.++ .++||.|++|||++|
T Consensus 1 Vtf~Dvav~fs~eEW~~L~~~Qk~ly~dvm 30 (41)
T PF01352_consen 1 VTFEDVAVYFSQEEWELLDPAQKNLYRDVM 30 (41)
T ss_dssp ------TT---HHHHHTS-HHHHHHHHHHH
T ss_pred CeEEEEEEEcChhhcccccceecccchhHH
Confidence 68999999999998 999999999999998
No 25
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=95.84 E-value=0.0032 Score=44.18 Aligned_cols=26 Identities=31% Similarity=0.547 Sum_probs=24.2
Q ss_pred cccCCcCccccCCchhhhhhcccccc
Q 003869 394 KFECQFCHKVFHERRRYNGHVGIHVR 419 (790)
Q Consensus 394 PYkC~~CGKsFs~ks~L~rH~RtHtg 419 (790)
||+|..|++.|.....|..|++.|.+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 79999999999999999999999863
No 26
>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=95.83 E-value=0.0053 Score=41.43 Aligned_cols=21 Identities=24% Similarity=0.687 Sum_probs=20.2
Q ss_pred cccCCCCcccCChhHHHHHHH
Q 003869 348 FECHKCEMTFDEKDTYLQHLL 368 (790)
Q Consensus 348 yeC~~CgKtF~~kSsLkrH~l 368 (790)
|+|+.|++.|..+..|.+|++
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 789999999999999999998
No 27
>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=95.56 E-value=0.0038 Score=41.62 Aligned_cols=24 Identities=29% Similarity=0.740 Sum_probs=20.3
Q ss_pred ccCCcCccccCCchhhhhhccccc
Q 003869 395 FECQFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 395 YkC~~CGKsFs~ks~L~rH~RtHt 418 (790)
|.|++|++.|.....|..|+++|.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 789999999999999999998873
No 28
>PHA00616 hypothetical protein
Probab=95.31 E-value=0.0077 Score=48.14 Aligned_cols=22 Identities=32% Similarity=0.869 Sum_probs=21.2
Q ss_pred ccccCCCCcccCChhHHHHHHH
Q 003869 347 LFECHKCEMTFDEKDTYLQHLL 368 (790)
Q Consensus 347 PyeC~~CgKtF~~kSsLkrH~l 368 (790)
||+|..||+.|..++.|.+|++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r 22 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLL 22 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHH
Confidence 6999999999999999999998
No 29
>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=95.06 E-value=0.017 Score=38.48 Aligned_cols=24 Identities=33% Similarity=0.733 Sum_probs=19.4
Q ss_pred cccCCCCcccCChhHHHHHHHhhh
Q 003869 348 FECHKCEMTFDEKDTYLQHLLSFH 371 (790)
Q Consensus 348 yeC~~CgKtF~~kSsLkrH~l~~H 371 (790)
|.|++|++.|.....|..|++..|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 789999999999999999998433
No 30
>smart00355 ZnF_C2H2 zinc finger.
Probab=94.57 E-value=0.013 Score=39.37 Aligned_cols=24 Identities=29% Similarity=0.716 Sum_probs=22.4
Q ss_pred ccCCcCccccCCchhhhhhccccc
Q 003869 395 FECQFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 395 YkC~~CGKsFs~ks~L~rH~RtHt 418 (790)
|+|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 689999999999999999999875
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=93.90 E-value=0.032 Score=39.10 Aligned_cols=24 Identities=33% Similarity=0.616 Sum_probs=21.9
Q ss_pred ccccCCCCcccCChhHHHHHHHhhh
Q 003869 347 LFECHKCEMTFDEKDTYLQHLLSFH 371 (790)
Q Consensus 347 PyeC~~CgKtF~~kSsLkrH~l~~H 371 (790)
||+|..|++.|.....|..|++ .|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~-~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKR-SH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHC-TT
T ss_pred CCCCCccCCccCChhHHHHHhH-Hh
Confidence 6899999999999999999987 44
No 32
>PLN03086 PRLI-interacting factor K; Provisional
Probab=93.33 E-value=0.024 Score=66.76 Aligned_cols=71 Identities=13% Similarity=0.314 Sum_probs=49.7
Q ss_pred ccCC--CCcccCChhHHHHHHHhhhccc-CccccCCCCCCccccccCCcccCCcCccccCCchhhhhhccccccCcccCc
Q 003869 349 ECHK--CEMTFDEKDTYLQHLLSFHQRT-TRRYRLGSSVGDGVIIKDGKFECQFCHKVFHERRRYNGHVGIHVRNYVRGI 425 (790)
Q Consensus 349 eC~~--CgKtF~~kSsLkrH~l~~H~r~-hK~F~~sssLk~H~RtHtGPYkC~~CGKsFs~ks~L~rH~RtHtgE~~~~~ 425 (790)
.|+. |+..| .+..+..|. |... ++.|. ...|..|+++|+.||.|+ ||+.| .+..|..|+++|..+....+
T Consensus 435 ~Cp~~~Cg~v~-~r~el~~H~---~C~~Cgk~f~-~s~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C 507 (567)
T PLN03086 435 VCPHDGCGIVL-RVEEAKNHV---HCEKCGQAFQ-QGEMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQASTCPLRLITC 507 (567)
T ss_pred eCCccccccee-eccccccCc---cCCCCCCccc-hHHHHHHHHhcCCCccCC-CCCCc-chhHHHhhhhccCCCCceeC
Confidence 4653 77776 344455552 2222 56675 577899999988899999 99866 56899999999987665444
Q ss_pred C
Q 003869 426 E 426 (790)
Q Consensus 426 ~ 426 (790)
.
T Consensus 508 ~ 508 (567)
T PLN03086 508 R 508 (567)
T ss_pred C
Confidence 3
No 33
>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=92.96 E-value=0.042 Score=38.87 Aligned_cols=20 Identities=15% Similarity=0.441 Sum_probs=16.9
Q ss_pred ccccCCcccccCCCCcccCC
Q 003869 340 AEVQVRDLFECHKCEMTFDE 359 (790)
Q Consensus 340 ~~~q~EKPyeC~~CgKtF~~ 359 (790)
..|.++|||+|++|++.|..
T Consensus 7 ~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 7 RTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHSSSSSEEESSSSEEESS
T ss_pred hhcCCCCCCCCCCCcCeeCc
Confidence 34678899999999999963
No 34
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=92.81 E-value=0.025 Score=63.76 Aligned_cols=54 Identities=24% Similarity=0.461 Sum_probs=45.5
Q ss_pred cccccCCCCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccCCcccCCcCccccCCchhhhhhccccc
Q 003869 346 DLFECHKCEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKDGKFECQFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 346 KPyeC~~CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHtGPYkC~~CGKsFs~ks~L~rH~RtHt 418 (790)
.-|.|..|...|-+...|.+|.. .+ +-.--|+|+.|+|.|+-..+|..|.|-|.
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHrC---~R----------------IV~vEYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHRC---PR----------------IVHVEYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhccC---Ce----------------eEEeeecCCcccccccCchhhhhhhcccC
Confidence 35999999999999999999954 11 11126999999999999999999999996
No 35
>PHA00732 hypothetical protein
Probab=92.41 E-value=0.08 Score=47.29 Aligned_cols=29 Identities=17% Similarity=0.230 Sum_probs=25.0
Q ss_pred cccCCcCccccCCchhhhhhcc-ccccCcc
Q 003869 394 KFECQFCHKVFHERRRYNGHVG-IHVRNYV 422 (790)
Q Consensus 394 PYkC~~CGKsFs~ks~L~rH~R-tHtgE~~ 422 (790)
||.|..|++.|.+...|.+|++ .|++...
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C 30 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLTKC 30 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCCcc
Confidence 7999999999999999999998 4765433
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=91.85 E-value=0.13 Score=34.33 Aligned_cols=24 Identities=25% Similarity=0.672 Sum_probs=21.6
Q ss_pred cccCCCCcccCChhHHHHHHHhhhc
Q 003869 348 FECHKCEMTFDEKDTYLQHLLSFHQ 372 (790)
Q Consensus 348 yeC~~CgKtF~~kSsLkrH~l~~H~ 372 (790)
|+|..|++.|.....|..|++ .|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH-Hhc
Confidence 689999999999999999988 664
No 37
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=90.18 E-value=0.13 Score=42.52 Aligned_cols=27 Identities=22% Similarity=0.458 Sum_probs=20.7
Q ss_pred cccCCcCccccCCchhhhhhccccccC
Q 003869 394 KFECQFCHKVFHERRRYNGHVGIHVRN 420 (790)
Q Consensus 394 PYkC~~CGKsFs~ks~L~rH~RtHtgE 420 (790)
|..|++|+..+.+..+|++|+.++++.
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCcchhhccchhhHHHHHHHHhcc
Confidence 999999999999999999999877643
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=89.06 E-value=0.13 Score=35.38 Aligned_cols=23 Identities=26% Similarity=0.652 Sum_probs=21.4
Q ss_pred ccCCcCccccCCchhhhhhcccc
Q 003869 395 FECQFCHKVFHERRRYNGHVGIH 417 (790)
Q Consensus 395 YkC~~CGKsFs~ks~L~rH~RtH 417 (790)
|.|..|.+.|.....|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 68999999999999999999865
No 39
>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=88.65 E-value=0.37 Score=39.93 Aligned_cols=31 Identities=19% Similarity=0.251 Sum_probs=21.9
Q ss_pred ccCCcccccCCCCcccCChhHHHHHHHhhhc
Q 003869 342 VQVRDLFECHKCEMTFDEKDTYLQHLLSFHQ 372 (790)
Q Consensus 342 ~q~EKPyeC~~CgKtF~~kSsLkrH~l~~H~ 372 (790)
.+.+.|..|++|+..+.+..+|++|+...|.
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 3446899999999999999999999975665
No 40
>PRK04860 hypothetical protein; Provisional
Probab=87.72 E-value=0.3 Score=49.11 Aligned_cols=38 Identities=18% Similarity=0.455 Sum_probs=29.8
Q ss_pred cccccCCCCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccCC--cccCCcCccccCCch
Q 003869 346 DLFECHKCEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKDG--KFECQFCHKVFHERR 408 (790)
Q Consensus 346 KPyeC~~CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHtG--PYkC~~CGKsFs~ks 408 (790)
-+|.|. |++ ...++.+|.+ +|++ +|.|..|++.|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~r---------------------i~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNR---------------------VVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHH---------------------HhcCCccEECCCCCceeEEec
Confidence 479998 998 6667777766 4555 899999999997654
No 41
>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=87.03 E-value=0.3 Score=34.55 Aligned_cols=23 Identities=26% Similarity=0.619 Sum_probs=21.3
Q ss_pred ccCCcCccccCCchhhhhhcccc
Q 003869 395 FECQFCHKVFHERRRYNGHVGIH 417 (790)
Q Consensus 395 YkC~~CGKsFs~ks~L~rH~RtH 417 (790)
|.|..|++.|.....|..|++.+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCcccCCCCcCCHHHHHHHHccC
Confidence 78999999999999999999864
No 42
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=85.97 E-value=0.3 Score=61.85 Aligned_cols=70 Identities=17% Similarity=0.319 Sum_probs=51.8
Q ss_pred CcccccCCCCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccC-------C-cccCCcCccccCCchhhhhhccc
Q 003869 345 RDLFECHKCEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKD-------G-KFECQFCHKVFHERRRYNGHVGI 416 (790)
Q Consensus 345 EKPyeC~~CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHt-------G-PYkC~~CGKsFs~ks~L~rH~Rt 416 (790)
.|.|.|+.|+..|.....|..||+..|-...-+|. ...+.|.+... + ||.|..|..+|+.+..|.+|+..
T Consensus 463 ~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c--~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 463 FKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYC--KAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred cccccCCccchhhhhHHHhhhcccccccccchhHh--HhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 47899999999999999999999865543322221 22233333222 2 99999999999999999999864
No 43
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=85.08 E-value=0.31 Score=29.73 Aligned_cols=11 Identities=64% Similarity=0.875 Sum_probs=4.4
Q ss_pred hhhcCCCCCcc
Q 003869 150 KRKRGRKPKTK 160 (790)
Q Consensus 150 krkrgr~~~~~ 160 (790)
+|+||||+|..
T Consensus 1 ~r~RGRP~k~~ 11 (13)
T PF02178_consen 1 KRKRGRPRKNA 11 (13)
T ss_dssp S--SS--TT--
T ss_pred CCcCCCCcccc
Confidence 58999999874
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=82.84 E-value=0.78 Score=31.40 Aligned_cols=21 Identities=33% Similarity=0.754 Sum_probs=19.8
Q ss_pred cccCCCCcccCChhHHHHHHH
Q 003869 348 FECHKCEMTFDEKDTYLQHLL 368 (790)
Q Consensus 348 yeC~~CgKtF~~kSsLkrH~l 368 (790)
|.|..|++.|.....|..|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 689999999999999999986
No 45
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=82.80 E-value=0.55 Score=33.70 Aligned_cols=12 Identities=58% Similarity=0.753 Sum_probs=10.4
Q ss_pred hhhcCCCCCccc
Q 003869 150 KRKRGRKPKTKV 161 (790)
Q Consensus 150 krkrgr~~~~~~ 161 (790)
|||||||||.+.
T Consensus 1 kRkRGRPrK~~~ 12 (26)
T smart00384 1 KRKRGRPRKAPK 12 (26)
T ss_pred CCCCCCCCCCCC
Confidence 699999999864
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=82.44 E-value=0.39 Score=32.83 Aligned_cols=23 Identities=17% Similarity=0.496 Sum_probs=18.7
Q ss_pred ccCCcCccccCCchhhhhhccccc
Q 003869 395 FECQFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 395 YkC~~CGKsFs~ks~L~rH~RtHt 418 (790)
|+|+.|.-... +..|.+|++.|.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 78999998888 889999999865
No 47
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=81.60 E-value=0.64 Score=49.36 Aligned_cols=49 Identities=27% Similarity=0.596 Sum_probs=38.6
Q ss_pred cccccCCCCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccCCcccCCcCccccCCchhhhhh-ccccc
Q 003869 346 DLFECHKCEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKDGKFECQFCHKVFHERRRYNGH-VGIHV 418 (790)
Q Consensus 346 KPyeC~~CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHtGPYkC~~CGKsFs~ks~L~rH-~RtHt 418 (790)
|| .|=+|++.|.+..-|.+|++. +.|+|.+|+|..-.-..|..| |.+|.
T Consensus 10 kp-wcwycnrefddekiliqhqka-----------------------khfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 10 KP-WCWYCNREFDDEKILIQHQKA-----------------------KHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred Cc-eeeecccccchhhhhhhhhhh-----------------------ccceeeeehhhhccCCCceeehhhhhh
Confidence 45 577999999999999999762 247899999887777777777 56664
No 48
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=78.71 E-value=1.7 Score=29.64 Aligned_cols=23 Identities=26% Similarity=0.664 Sum_probs=17.9
Q ss_pred cccCCCCcccCChhHHHHHHHhhh
Q 003869 348 FECHKCEMTFDEKDTYLQHLLSFH 371 (790)
Q Consensus 348 yeC~~CgKtF~~kSsLkrH~l~~H 371 (790)
|+|+.|..... ...|.+|++..|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 78999999888 999999988444
No 49
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=73.96 E-value=2 Score=45.01 Aligned_cols=54 Identities=19% Similarity=0.255 Sum_probs=32.2
Q ss_pred cccccCCCCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccCC----cccCCcCccccCCc
Q 003869 346 DLFECHKCEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKDG----KFECQFCHKVFHER 407 (790)
Q Consensus 346 KPyeC~~CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHtG----PYkC~~CGKsFs~k 407 (790)
|.+.|++|++.|..+.-. .+..+....-+.|..|-..-.- ...|+.||-+|...
T Consensus 4 k~~~CPvC~~~F~~~~vr--------s~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVR--------SGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEE--------cCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 678999999999976533 2222222333334333221111 46899999998865
No 50
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=73.43 E-value=1.5 Score=30.99 Aligned_cols=21 Identities=29% Similarity=0.654 Sum_probs=17.6
Q ss_pred ccCCcCccccCCchhhhhhccc
Q 003869 395 FECQFCHKVFHERRRYNGHVGI 416 (790)
Q Consensus 395 YkC~~CGKsFs~ks~L~rH~Rt 416 (790)
..|+.||+.| ....|.+|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4799999999 67788999764
No 51
>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=72.67 E-value=2.6 Score=30.92 Aligned_cols=22 Identities=32% Similarity=0.588 Sum_probs=20.3
Q ss_pred ccccCCCCcccCChhHHHHHHH
Q 003869 347 LFECHKCEMTFDEKDTYLQHLL 368 (790)
Q Consensus 347 PyeC~~CgKtF~~kSsLkrH~l 368 (790)
+|.|..|++.|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 6899999999999999999975
No 52
>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=71.39 E-value=1.5 Score=31.00 Aligned_cols=21 Identities=29% Similarity=0.716 Sum_probs=19.4
Q ss_pred cccCCCCcccCChhHHHHHHH
Q 003869 348 FECHKCEMTFDEKDTYLQHLL 368 (790)
Q Consensus 348 yeC~~CgKtF~~kSsLkrH~l 368 (790)
|.|..|++.|.....|..|+.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 789999999999999999875
No 53
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.68 E-value=1.4 Score=53.19 Aligned_cols=61 Identities=16% Similarity=0.344 Sum_probs=32.5
Q ss_pred ccCChhHHHHHHHhhhccc--------CccccC------CCCCCcccc-------ccCCcccCCcCccccCCchhhhhhc
Q 003869 356 TFDEKDTYLQHLLSFHQRT--------TRRYRL------GSSVGDGVI-------IKDGKFECQFCHKVFHERRRYNGHV 414 (790)
Q Consensus 356 tF~~kSsLkrH~l~~H~r~--------hK~F~~------sssLk~H~R-------tHtGPYkC~~CGKsFs~ks~L~rH~ 414 (790)
.|.....|+.|+...|... -|-|.. ...|..|+. .|.|.-.|..|...|-....|.+|+
T Consensus 123 ~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~ 202 (669)
T KOG2231|consen 123 EFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHL 202 (669)
T ss_pred chhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhh
Confidence 3347789999997666543 122221 222333332 1222235666666666666666666
Q ss_pred cc
Q 003869 415 GI 416 (790)
Q Consensus 415 Rt 416 (790)
+.
T Consensus 203 ~~ 204 (669)
T KOG2231|consen 203 RF 204 (669)
T ss_pred cc
Confidence 64
No 54
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=69.44 E-value=2 Score=46.45 Aligned_cols=60 Identities=22% Similarity=0.455 Sum_probs=48.1
Q ss_pred cccccCCCCcccCChhHHHHHHHh-hhcccCccccCCCCCCccccccCCcccCC--cCccccCCchhhhhhccccccCc
Q 003869 346 DLFECHKCEMTFDEKDTYLQHLLS-FHQRTTRRYRLGSSVGDGVIIKDGKFECQ--FCHKVFHERRRYNGHVGIHVRNY 421 (790)
Q Consensus 346 KPyeC~~CgKtF~~kSsLkrH~l~-~H~r~hK~F~~sssLk~H~RtHtGPYkC~--~CGKsFs~ks~L~rH~RtHtgE~ 421 (790)
.++.|..|...|.....|.+|.+. .|.... ..|+.|+ .|++.|.+...+.+|..+|++-.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~----------------~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~ 350 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGES----------------LKPFSCPYSLCGKLFSRNDALKRHILLHTSIS 350 (467)
T ss_pred cCCCCccccCCcccccccccccccccccccc----------------CCceeeeccCCCccccccccccCCcccccCCC
Confidence 579999999999999999888763 333211 2478888 79999999999999999998554
No 55
>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=69.05 E-value=2.3 Score=31.18 Aligned_cols=24 Identities=25% Similarity=0.632 Sum_probs=21.5
Q ss_pred CcccCCcCccccCCchhhhhhccc
Q 003869 393 GKFECQFCHKVFHERRRYNGHVGI 416 (790)
Q Consensus 393 GPYkC~~CGKsFs~ks~L~rH~Rt 416 (790)
++|.|..|++.|.....+..|++.
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHCh
Confidence 378999999999999999999865
No 56
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=65.33 E-value=4.7 Score=28.47 Aligned_cols=20 Identities=25% Similarity=0.478 Sum_probs=17.0
Q ss_pred cccCCCCcccCChhHHHHHHH
Q 003869 348 FECHKCEMTFDEKDTYLQHLL 368 (790)
Q Consensus 348 yeC~~CgKtF~~kSsLkrH~l 368 (790)
..|+.||+.| ....|.+|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4799999999 6788999865
No 57
>PF01429 MBD: Methyl-CpG binding domain; InterPro: IPR001739 Methylation at CpG dinucleotide, the most common DNA modification in eukaryotes, has been correlated with gene silencing associated with various phenomena such as genomic imprinting, transposon and chromosome X inactivation, differentiation, and cancer. Effects of DNA methylation are mediated through proteins which bind to symmetrically methylated CpGs. Such proteins contain a specific domain of ~70 residues, the methyl-CpG-binding domain (MBD), which is linked to additional domains associated with chromatin, such as the bromodomain, the AT hook motif,the SET domain, or the PHD finger. MBD-containing proteins appear to act as structural proteins, which recruit a variety of histone deacetylase (HDAC) complexes and chromatin remodelling factors, leading to chromatin compaction and, consequently, to transcriptional repression. The MBD of MeCP2, MBD1, MBD2, MBD4 and BAZ2 mediates binding to DNA, in case of MeCP2, MBD1 and MBD2 preferentially to methylated CpG. In case of human MBD3 and SETDB1 the MBD has been shown to mediate protein-protein interactions [, ]. The MBD folds into an alpha/beta sandwich structure comprising a layer of twisted beta sheet, backed by another layer formed by the alpha1 helix and a hairpin loop at the C terminus. These layers are both amphipathic, with the alpha1 helix and the beta sheet lying parallel and the hydrophobic faces tightly packed against each other. The beta sheet is composed of two long inner strands (beta2 and beta3) sandwiched by two shorter outer strands (beta1 and beta4) [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 2KY8_A 1UB1_A 1D9N_A 1IG4_A 1QK9_A 3C2I_A.
Probab=63.65 E-value=2.5 Score=37.39 Aligned_cols=48 Identities=35% Similarity=0.481 Sum_probs=38.9
Q ss_pred cccccceeecccccccCccCcccccccCCCCccccccccccccccccc
Q 003869 237 TLPVGWKLLLGLKRREGRASVYCRRYISPGGQHFVSCKEVSGYLQSYF 284 (790)
Q Consensus 237 ~l~~~~kl~~glKr~e~r~~~~CR~~iSPkGqqf~TCkE~SSyf~SLl 284 (790)
.|+.||+..+-+++....+...+..|.+|.|++|.+..++..|+..-.
T Consensus 10 ~Lp~GW~re~~~R~~g~~~~~~dv~Y~sP~Gk~~RS~~eV~~yL~~~~ 57 (77)
T PF01429_consen 10 PLPDGWKREVVVRKSGSSAGKKDVYYYSPCGKRFRSKKEVVRYLKENP 57 (77)
T ss_dssp TSTTT-EEEEEESSSSTTTTSEEEEEEETTSEEESSHHHHHHHHTTSS
T ss_pred CCCCCCEEEEEEecCCCcCCceEEEEECCCCCEEeCHHHHHHHHHhCC
Confidence 477899999999876666665568899999999999999999987744
No 58
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=60.56 E-value=4.3 Score=43.91 Aligned_cols=79 Identities=22% Similarity=0.388 Sum_probs=57.0
Q ss_pred cccCC--cccccC--CCCcccCChhHHHHHHHhhhccc------------------------------------------
Q 003869 341 EVQVR--DLFECH--KCEMTFDEKDTYLQHLLSFHQRT------------------------------------------ 374 (790)
Q Consensus 341 ~~q~E--KPyeC~--~CgKtF~~kSsLkrH~l~~H~r~------------------------------------------ 374 (790)
.+..+ +++.|+ .|++.|.+...+.+|.+ .|...
T Consensus 313 ~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 391 (467)
T COG5048 313 NHSGESLKPFSCPYSLCGKLFSRNDALKRHIL-LHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLS 391 (467)
T ss_pred ccccccCCceeeeccCCCccccccccccCCcc-cccCCCccccccccCccccccccCCCCccchhhccCccCCccccccc
Confidence 56667 899999 79999999999999986 55433
Q ss_pred ---CccccCCCCCCccccccCC----cccCCcCccccCCchhhhhhccccccC
Q 003869 375 ---TRRYRLGSSVGDGVIIKDG----KFECQFCHKVFHERRRYNGHVGIHVRN 420 (790)
Q Consensus 375 ---hK~F~~sssLk~H~RtHtG----PYkC~~CGKsFs~ks~L~rH~RtHtgE 420 (790)
-+.+.....+..|...|.. .+.|..|.+.|.....+..|++.|...
T Consensus 392 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 (467)
T COG5048 392 NSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNH 444 (467)
T ss_pred cchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccC
Confidence 0123334555555555553 566778888999888888888888643
No 59
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=59.48 E-value=5.7 Score=51.06 Aligned_cols=76 Identities=16% Similarity=0.236 Sum_probs=57.6
Q ss_pred ccCCcccccCCCCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccCC--cccCCcCccccCCchhhhhhcccccc
Q 003869 342 VQVRDLFECHKCEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKDG--KFECQFCHKVFHERRRYNGHVGIHVR 419 (790)
Q Consensus 342 ~q~EKPyeC~~CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHtG--PYkC~~CGKsFs~ks~L~rH~RtHtg 419 (790)
+....+|.|..|...|.....|..|++ . ..+.|+....+.-|...|.- +| |..|...|.....|..|+|+-.+
T Consensus 1279 l~~~~~~~~~~~~~~~~~~~~l~~~~~---k-~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~~ 1353 (1406)
T KOG1146|consen 1279 LDVTHRYLCRQCKMAFDGEAPLTAHQR---K-FCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSAH 1353 (1406)
T ss_pred cccchhHHHHHHHhhhcchhHHHHHHH---H-HHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhhh
Confidence 445689999999999999999999964 1 12344445555666655554 67 99999999999999999997554
Q ss_pred Ccc
Q 003869 420 NYV 422 (790)
Q Consensus 420 E~~ 422 (790)
+..
T Consensus 1354 ~~k 1356 (1406)
T KOG1146|consen 1354 RRK 1356 (1406)
T ss_pred ccc
Confidence 443
No 60
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=59.27 E-value=3.7 Score=41.12 Aligned_cols=31 Identities=19% Similarity=0.531 Sum_probs=24.7
Q ss_pred ceeeEEeeeCCccchhhhccccCCCcccccccccccc
Q 003869 743 HLTTLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAK 779 (790)
Q Consensus 743 ~~~~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k 779 (790)
..-.+|.-|+..|+.+-.-+ .||.||.|++-
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME------LNFTCPRCGAM 137 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH------cCCcCCCCCCE
Confidence 34789999999998865433 59999999864
No 61
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=56.27 E-value=8.6 Score=33.81 Aligned_cols=23 Identities=26% Similarity=0.716 Sum_probs=20.7
Q ss_pred cccccCCCCcccCChhHHHHHHH
Q 003869 346 DLFECHKCEMTFDEKDTYLQHLL 368 (790)
Q Consensus 346 KPyeC~~CgKtF~~kSsLkrH~l 368 (790)
..+.|..|++.|.....|..|+.
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~ 71 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMR 71 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHH
T ss_pred CCCCCCccCCCCcCHHHHHHHHc
Confidence 46999999999999999999998
No 62
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=55.53 E-value=4 Score=34.57 Aligned_cols=36 Identities=25% Similarity=0.533 Sum_probs=22.1
Q ss_pred eEEeeeCCccchhhhcccc---C-CCcccccccccccccc
Q 003869 746 TLCVWCGMEFSHEVVDSEM---Q-PDSVGYMCPTCKAKIS 781 (790)
Q Consensus 746 ~~cvwc~~ef~~~~~~~e~---q-~~s~g~~c~~ck~k~s 781 (790)
..|+-|+..+.=+.-.-++ . ----.|||..|+.+|.
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~RI~ 42 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKERIR 42 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHHHh
Confidence 4688998876433211111 1 1234799999999983
No 63
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=54.55 E-value=6.5 Score=33.40 Aligned_cols=31 Identities=23% Similarity=0.658 Sum_probs=26.1
Q ss_pred ccCCcccccCCCCcccCChhHHHHHHHhhhc
Q 003869 342 VQVRDLFECHKCEMTFDEKDTYLQHLLSFHQ 372 (790)
Q Consensus 342 ~q~EKPyeC~~CgKtF~~kSsLkrH~l~~H~ 372 (790)
-.+|.-+.|+-|++.|.....+.+|....|.
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 3467789999999999999999999875554
No 64
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=54.14 E-value=7.2 Score=35.81 Aligned_cols=21 Identities=24% Similarity=0.482 Sum_probs=16.5
Q ss_pred ccccCCcccCCcCccccCCch
Q 003869 388 VIIKDGKFECQFCHKVFHERR 408 (790)
Q Consensus 388 ~RtHtGPYkC~~CGKsFs~ks 408 (790)
.|..+|-+.|..||..|.--.
T Consensus 47 kR~a~GIW~C~kCg~~fAGga 67 (89)
T COG1997 47 KRIATGIWKCRKCGAKFAGGA 67 (89)
T ss_pred eeeccCeEEcCCCCCeecccc
Confidence 346677899999999997543
No 65
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=53.78 E-value=6.1 Score=30.09 Aligned_cols=32 Identities=25% Similarity=0.441 Sum_probs=23.0
Q ss_pred eeEEeeeCCccchhhhccccCCCccccccccccccc
Q 003869 745 TTLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAKI 780 (790)
Q Consensus 745 ~~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k~ 780 (790)
...|..||.+|.-..-.++ ..--.||.|.+.+
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~----~~~~~CP~Cg~~~ 36 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISD----DPLATCPECGGDV 36 (41)
T ss_pred EEEcCCCCCEEEEEEecCC----CCCCCCCCCCCcc
Confidence 5689999999976544333 3445799999854
No 66
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=53.51 E-value=5.6 Score=40.71 Aligned_cols=32 Identities=22% Similarity=0.698 Sum_probs=25.1
Q ss_pred ceeeEEeeeCCccchhhhccccCCCccccccccccccc
Q 003869 743 HLTTLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAKI 780 (790)
Q Consensus 743 ~~~~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k~ 780 (790)
..-.+|.-|+..|..+-.- +.||.||.|..-+
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~------~~~F~Cp~Cg~~L 146 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAM------EYGFRCPQCGEML 146 (178)
T ss_pred CCEEECCCCCcEEeHHHHh------hcCCcCCCCCCCC
Confidence 3578999999999887432 3699999998643
No 67
>PF12773 DZR: Double zinc ribbon
Probab=53.23 E-value=5.9 Score=31.70 Aligned_cols=32 Identities=28% Similarity=0.736 Sum_probs=25.2
Q ss_pred eeEEeeeCCccchhhhccccCCCccccccccccccccccc
Q 003869 745 TTLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAKISGQL 784 (790)
Q Consensus 745 ~~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k~sg~~ 784 (790)
..+|.|||..+. ........||.|++.++...
T Consensus 12 ~~fC~~CG~~l~--------~~~~~~~~C~~Cg~~~~~~~ 43 (50)
T PF12773_consen 12 AKFCPHCGTPLP--------PPDQSKKICPNCGAENPPNA 43 (50)
T ss_pred ccCChhhcCChh--------hccCCCCCCcCCcCCCcCCc
Confidence 568999999988 44555689999999877553
No 68
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=51.70 E-value=11 Score=42.45 Aligned_cols=71 Identities=20% Similarity=0.327 Sum_probs=51.4
Q ss_pred ccccCC--CCcccCChhHHHHHHHhhhccc--------CccccC------CCCCCccccccC---C---cccCCcCcccc
Q 003869 347 LFECHK--CEMTFDEKDTYLQHLLSFHQRT--------TRRYRL------GSSVGDGVIIKD---G---KFECQFCHKVF 404 (790)
Q Consensus 347 PyeC~~--CgKtF~~kSsLkrH~l~~H~r~--------hK~F~~------sssLk~H~RtHt---G---PYkC~~CGKsF 404 (790)
.|.|+. |..+......|+.|.+..|-.- .|.|.+ +..|+.|..... | .-.|.+|.+.|
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~F 230 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYF 230 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCcEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhcccee
Confidence 478875 7776666788999987666543 244543 566777765443 2 44799999999
Q ss_pred CCchhhhhhcccc
Q 003869 405 HERRRYNGHVGIH 417 (790)
Q Consensus 405 s~ks~L~rH~RtH 417 (790)
.....|.+|+|..
T Consensus 231 YdDDEL~~HcR~~ 243 (493)
T COG5236 231 YDDDELRRHCRLR 243 (493)
T ss_pred cChHHHHHHHHhh
Confidence 9999999999863
No 69
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=50.87 E-value=6.5 Score=32.49 Aligned_cols=30 Identities=33% Similarity=0.863 Sum_probs=22.8
Q ss_pred eeeEEeeeCCccchhhhccccCCCccccccccccccc
Q 003869 744 LTTLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAKI 780 (790)
Q Consensus 744 ~~~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k~ 780 (790)
..-.|.-||.+| |.=....|.-||.|.-||
T Consensus 5 ~~Y~C~~Cg~~~-------~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGREV-------ELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCee-------ehhhccCceeCCCCCcEE
Confidence 456899999999 322345689999998876
No 70
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=48.13 E-value=4.7 Score=44.68 Aligned_cols=24 Identities=13% Similarity=0.412 Sum_probs=21.7
Q ss_pred CcccccCCCCcccCChhHHHHHHH
Q 003869 345 RDLFECHKCEMTFDEKDTYLQHLL 368 (790)
Q Consensus 345 EKPyeC~~CgKtF~~kSsLkrH~l 368 (790)
.|||.|.+|+|.|.....|+.|+.
T Consensus 396 ~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 396 DKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CCceeccccchhhccCccceeccc
Confidence 499999999999999999999844
No 71
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=47.69 E-value=5.7 Score=44.57 Aligned_cols=65 Identities=17% Similarity=0.385 Sum_probs=44.0
Q ss_pred CCcccccCC--CCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccC------CcccCCcCccccCCchhhhhhc
Q 003869 344 VRDLFECHK--CEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKD------GKFECQFCHKVFHERRRYNGHV 414 (790)
Q Consensus 344 ~EKPyeC~~--CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHt------GPYkC~~CGKsFs~ks~L~rH~ 414 (790)
..++|+|++ |.+.+.....|+.|.+..|... ...... --|-|+ +||+|++|.|++.-..+|+-|.
T Consensus 346 ~~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~---i~~~s~---~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 346 VDKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSP---ITTPTP---APIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred ecCCCCCCCCcchhhcccCcceeeccccCcCCC---CCCCCC---CCCCcceeeeccCcccChhhhhhhccCCCCCcee
Confidence 368999976 9999999999999876444322 000000 012344 3999999999998877776553
No 72
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=47.42 E-value=9.3 Score=30.68 Aligned_cols=28 Identities=25% Similarity=0.445 Sum_probs=22.2
Q ss_pred eeEEeeeCCccchhhhccccCCCccccccccccccc
Q 003869 745 TTLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAKI 780 (790)
Q Consensus 745 ~~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k~ 780 (790)
.-.|.-||.||.-+ ..-+.-||.|..+|
T Consensus 2 ~Y~C~~Cg~~~~~~--------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK--------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC--------CCCceECCCCCceE
Confidence 45799999999865 34668999998876
No 73
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=44.06 E-value=9.9 Score=30.26 Aligned_cols=30 Identities=30% Similarity=0.654 Sum_probs=21.1
Q ss_pred eeeEEeeeCCccchhhhccccCCCccccccccccccc
Q 003869 744 LTTLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAKI 780 (790)
Q Consensus 744 ~~~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k~ 780 (790)
....|.-||.+|.-+... + .+-||.|..++
T Consensus 2 ~~y~C~~CG~~~~~~~~~---~----~~~Cp~CG~~~ 31 (46)
T PRK00398 2 AEYKCARCGREVELDEYG---T----GVRCPYCGYRI 31 (46)
T ss_pred CEEECCCCCCEEEECCCC---C----ceECCCCCCeE
Confidence 456888999888654221 1 68899998765
No 74
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=42.64 E-value=11 Score=30.42 Aligned_cols=25 Identities=20% Similarity=0.555 Sum_probs=20.2
Q ss_pred cccCCcCccccCCc-----hhhhhhcc-ccc
Q 003869 394 KFECQFCHKVFHER-----RRYNGHVG-IHV 418 (790)
Q Consensus 394 PYkC~~CGKsFs~k-----s~L~rH~R-tHt 418 (790)
--.|..|++.+... ++|.+|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 35799999999876 59999988 564
No 75
>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=41.68 E-value=14 Score=35.04 Aligned_cols=31 Identities=19% Similarity=0.468 Sum_probs=24.1
Q ss_pred ccccCCCCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccCCcccCCcCccccCCc
Q 003869 347 LFECHKCEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKDGKFECQFCHKVFHER 407 (790)
Q Consensus 347 PyeC~~CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHtGPYkC~~CGKsFs~k 407 (790)
...|+.||+.|.... ..|-.|+.||..|.-.
T Consensus 9 KR~Cp~CG~kFYDLn------------------------------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLN------------------------------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhccCC------------------------------CCCccCCCCCCccCcc
Confidence 468999999887432 1288999999999866
No 76
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=41.62 E-value=19 Score=28.07 Aligned_cols=27 Identities=19% Similarity=0.363 Sum_probs=17.8
Q ss_pred CcccccCCCCcccCCh----hHHHHHHHhhh
Q 003869 345 RDLFECHKCEMTFDEK----DTYLQHLLSFH 371 (790)
Q Consensus 345 EKPyeC~~CgKtF~~k----SsLkrH~l~~H 371 (790)
....+|.+|++.+... ++|.+|++..|
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 4668999999998764 89999985344
No 77
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=39.43 E-value=11 Score=37.14 Aligned_cols=24 Identities=25% Similarity=0.379 Sum_probs=15.6
Q ss_pred cccCCcCccccCCchhhhhhccccccC
Q 003869 394 KFECQFCHKVFHERRRYNGHVGIHVRN 420 (790)
Q Consensus 394 PYkC~~CGKsFs~ks~L~rH~RtHtgE 420 (790)
--.|-+|||.|. .|++|++.|+|-
T Consensus 72 ~i~clecGk~~k---~LkrHL~~~~gl 95 (132)
T PF05443_consen 72 YIICLECGKKFK---TLKRHLRTHHGL 95 (132)
T ss_dssp -EE-TBT--EES---BHHHHHHHTT-S
T ss_pred eeEEccCCcccc---hHHHHHHHccCC
Confidence 567999999998 458999999653
No 78
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=38.21 E-value=15 Score=36.26 Aligned_cols=39 Identities=13% Similarity=0.408 Sum_probs=25.7
Q ss_pred cceeeEEeeeCCccchhhhccccCCCcccccccccccccc
Q 003869 742 HHLTTLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAKIS 781 (790)
Q Consensus 742 ~~~~~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k~s 781 (790)
.....+|.-|+..|.-.-... ....+--|.||.|.+.+-
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~-~~d~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQ-LLDMDGTFTCPRCGEELE 134 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHH-hcCCCCcEECCCCCCEEE
Confidence 345789999999999543211 111122299999998763
No 79
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=38.15 E-value=7.2 Score=29.05 Aligned_cols=26 Identities=31% Similarity=0.763 Sum_probs=14.6
Q ss_pred EEeeeCCccchhhhccccCCCccccccccccccc
Q 003869 747 LCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAKI 780 (790)
Q Consensus 747 ~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k~ 780 (790)
-|.-|+.++.+ .|..-|+||+|..-|
T Consensus 4 ~Cp~C~se~~y--------~D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTY--------EDGELLVCPECGHEW 29 (30)
T ss_dssp --TTT-----E--------E-SSSEEETTTTEEE
T ss_pred CCCCCCCccee--------ccCCEEeCCcccccC
Confidence 58889999988 667779999998644
No 80
>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=37.85 E-value=18 Score=29.60 Aligned_cols=24 Identities=25% Similarity=0.515 Sum_probs=18.7
Q ss_pred cccCCcCccccCCchhhhhhccccc
Q 003869 394 KFECQFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 394 PYkC~~CGKsFs~ks~L~rH~RtHt 418 (790)
-|.|++|++.|. ...|..|....+
T Consensus 2 ~f~CP~C~~~~~-~~~L~~H~~~~H 25 (54)
T PF05605_consen 2 SFTCPYCGKGFS-ESSLVEHCEDEH 25 (54)
T ss_pred CcCCCCCCCccC-HHHHHHHHHhHC
Confidence 389999999555 578999977644
No 81
>PHA03230 nuclear protein UL55; Provisional
Probab=35.71 E-value=18 Score=37.25 Aligned_cols=31 Identities=26% Similarity=0.628 Sum_probs=23.3
Q ss_pred eeCCccchhhhccccCCCc-------ccccccccccccc
Q 003869 750 WCGMEFSHEVVDSEMQPDS-------VGYMCPTCKAKIS 781 (790)
Q Consensus 750 wc~~ef~~~~~~~e~q~~s-------~g~~c~~ck~k~s 781 (790)
-|+..|+|-..-..-+.+. |||-| +||-+||
T Consensus 111 lC~aPFSaaTi~d~~~~~~~~~~I~Gl~yHC-HCk~PFS 148 (180)
T PHA03230 111 LCSAPFSAATIKDSLDDGYLEYTINGLCYHC-HCKNPFS 148 (180)
T ss_pred CCCCCcchheeeccCCCCcceeEEeEEEEee-ccCCCCC
Confidence 4888888876666555554 78888 7888887
No 82
>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=34.68 E-value=58 Score=30.31 Aligned_cols=72 Identities=15% Similarity=0.334 Sum_probs=46.3
Q ss_pred cccccCCCCcccCChhHHHHHHHhhhccc-C-------ccccC-------CCCC---------CccccccCCcccC----
Q 003869 346 DLFECHKCEMTFDEKDTYLQHLLSFHQRT-T-------RRYRL-------GSSV---------GDGVIIKDGKFEC---- 397 (790)
Q Consensus 346 KPyeC~~CgKtF~~kSsLkrH~l~~H~r~-h-------K~F~~-------sssL---------k~H~RtHtGPYkC---- 397 (790)
+-..|..|+..... +.+..|++..|... . +.+.. ...+ ...+.++. -|.|
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~~-G~~C~~~~ 87 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVYD-GYRCQCDP 87 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCCC-CeeeecCC
Confidence 45789999987665 88888987555322 1 11111 0011 11122232 4899
Q ss_pred CcCccccCCchhhhhhcccccc
Q 003869 398 QFCHKVFHERRRYNGHVGIHVR 419 (790)
Q Consensus 398 ~~CGKsFs~ks~L~rH~RtHtg 419 (790)
..|+..+.....+.+|.+.++|
T Consensus 88 ~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 88 PHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCCcEeccHHHHHHHHHHhcC
Confidence 9999999999999999998764
No 83
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=34.37 E-value=26 Score=28.29 Aligned_cols=25 Identities=20% Similarity=0.397 Sum_probs=19.6
Q ss_pred ccccCCCCcccCCh-----hHHHHHHHhhh
Q 003869 347 LFECHKCEMTFDEK-----DTYLQHLLSFH 371 (790)
Q Consensus 347 PyeC~~CgKtF~~k-----SsLkrH~l~~H 371 (790)
.-.|.+|++.+... ++|.+|+...|
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 46899999998765 68999987444
No 84
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=33.96 E-value=15 Score=41.04 Aligned_cols=10 Identities=80% Similarity=1.843 Sum_probs=0.0
Q ss_pred cccccccccc
Q 003869 770 GYMCPTCKAK 779 (790)
Q Consensus 770 g~~c~~ck~k 779 (790)
||+||.||||
T Consensus 276 Gy~CP~Ckak 285 (378)
T KOG2807|consen 276 GYFCPQCKAK 285 (378)
T ss_pred ceeCCcccCe
No 85
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=33.39 E-value=17 Score=36.44 Aligned_cols=18 Identities=11% Similarity=0.587 Sum_probs=15.0
Q ss_pred cCCCcccccccccccccc
Q 003869 764 MQPDSVGYMCPTCKAKIS 781 (790)
Q Consensus 764 ~q~~s~g~~c~~ck~k~s 781 (790)
.-.+..+|+||.|+.|+|
T Consensus 103 ~e~~~~~Y~Cp~c~~r~t 120 (158)
T TIGR00373 103 FETNNMFFICPNMCVRFT 120 (158)
T ss_pred hccCCCeEECCCCCcEee
Confidence 345779999999999986
No 86
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=32.96 E-value=20 Score=30.17 Aligned_cols=15 Identities=33% Similarity=1.143 Sum_probs=11.6
Q ss_pred eeeEEeeeCCccchh
Q 003869 744 LTTLCVWCGMEFSHE 758 (790)
Q Consensus 744 ~~~~cvwc~~ef~~~ 758 (790)
.-..|.|||.+|.=+
T Consensus 26 ~~~YC~~Cg~~Y~d~ 40 (55)
T PF13821_consen 26 EHNYCFWCGTKYDDE 40 (55)
T ss_pred hCceeeeeCCccCCH
Confidence 357899999998643
No 87
>PRK04860 hypothetical protein; Provisional
Probab=32.87 E-value=18 Score=36.53 Aligned_cols=30 Identities=13% Similarity=0.328 Sum_probs=24.8
Q ss_pred cccCCcCccccCCchhhhhhccccccCcccCcCC
Q 003869 394 KFECQFCHKVFHERRRYNGHVGIHVRNYVRGIEE 427 (790)
Q Consensus 394 PYkC~~CGKsFs~ks~L~rH~RtHtgE~~~~~~~ 427 (790)
+|.|. |++ ....+++|.++|+++....+..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~ 148 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRR 148 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCC
Confidence 89998 998 7788999999999887655443
No 88
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.40 E-value=62 Score=31.19 Aligned_cols=72 Identities=15% Similarity=0.263 Sum_probs=46.7
Q ss_pred CcccccCCCCcccCChhHHHHHHHhhhcccCc---------------cccCCCCCCccc------cccCCcccCCcCccc
Q 003869 345 RDLFECHKCEMTFDEKDTYLQHLLSFHQRTTR---------------RYRLGSSVGDGV------IIKDGKFECQFCHKV 403 (790)
Q Consensus 345 EKPyeC~~CgKtF~~kSsLkrH~l~~H~r~hK---------------~F~~sssLk~H~------RtHtGPYkC~~CGKs 403 (790)
+-|-+|+.||-+.-...+|.|.. .|.-.-+ -|.....+..-. ..-.+.|+|+.|.+.
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSy--HHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~ 90 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSY--HHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNV 90 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhh--hccCCCcccccccccccCCCCcccCcCCCCCCcccccccccccccceeCCCCCCc
Confidence 36789999999999998887752 1221111 222222221110 011227999999999
Q ss_pred cCCchhhhhhccccc
Q 003869 404 FHERRRYNGHVGIHV 418 (790)
Q Consensus 404 Fs~ks~L~rH~RtHt 418 (790)
|-..-....|...|.
T Consensus 91 FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 91 FCVDCDVFVHESLHC 105 (112)
T ss_pred cccccchhhhhhccC
Confidence 999999999998885
No 89
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=30.67 E-value=15 Score=31.27 Aligned_cols=23 Identities=35% Similarity=0.668 Sum_probs=20.9
Q ss_pred cccCCcCccccCCchhhhhhccc
Q 003869 394 KFECQFCHKVFHERRRYNGHVGI 416 (790)
Q Consensus 394 PYkC~~CGKsFs~ks~L~rH~Rt 416 (790)
-+.|+-||+.|.....+.+|...
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhH
Confidence 78999999999999999999754
No 90
>PF14621 RFX5_DNA_bdg: RFX5 DNA-binding domain
Probab=30.60 E-value=21 Score=36.75 Aligned_cols=16 Identities=44% Similarity=0.412 Sum_probs=12.1
Q ss_pred HHHHHhhhcCCCCCcc
Q 003869 145 HVLMRKRKRGRKPKTK 160 (790)
Q Consensus 145 ~~~~~krkrgr~~~~~ 160 (790)
..+--|||||||+|.-
T Consensus 63 t~sdAKRKRGRPRKKs 78 (219)
T PF14621_consen 63 TGSDAKRKRGRPRKKS 78 (219)
T ss_pred ccchhhhhcCCCccCC
Confidence 3446799999999763
No 91
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=30.44 E-value=23 Score=32.83 Aligned_cols=19 Identities=21% Similarity=0.441 Sum_probs=15.1
Q ss_pred ccCCcccCCcCccccCCch
Q 003869 390 IKDGKFECQFCHKVFHERR 408 (790)
Q Consensus 390 tHtGPYkC~~CGKsFs~ks 408 (790)
..+|.++|..|++.|.--.
T Consensus 49 ~a~GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 49 GSTGIWTCRKCGAKFAGGA 67 (91)
T ss_pred EeeEEEEcCCCCCEEeCCc
Confidence 4567899999999997543
No 92
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 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 DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=29.95 E-value=14 Score=38.06 Aligned_cols=40 Identities=33% Similarity=0.585 Sum_probs=22.6
Q ss_pred ceeeEEeeeCCccchhhhccc--cCCCccccccccccccccc
Q 003869 743 HLTTLCVWCGMEFSHEVVDSE--MQPDSVGYMCPTCKAKISG 782 (790)
Q Consensus 743 ~~~~~cvwc~~ef~~~~~~~e--~q~~s~g~~c~~ck~k~sg 782 (790)
-+...|.-|+.+|.-.++-.+ ...-..|.+||.|+..++.
T Consensus 16 ~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~~~~ 57 (188)
T PF08996_consen 16 PLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTPLSP 57 (188)
T ss_dssp -EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B--H
T ss_pred ceEeECCCCCCCccccccccCCccccccCcCcCCCCCCcCCH
Confidence 567899999999998887552 2233569999999997763
No 93
>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=29.88 E-value=32 Score=33.76 Aligned_cols=36 Identities=8% Similarity=0.101 Sum_probs=25.6
Q ss_pred cccccCCCCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccCCcccCCcCccccCCchhhh
Q 003869 346 DLFECHKCEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKDGKFECQFCHKVFHERRRYN 411 (790)
Q Consensus 346 KPyeC~~CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHtGPYkC~~CGKsFs~ks~L~ 411 (790)
....|+.||+.|.... ..|-.|+.||..|.....++
T Consensus 8 tKr~Cp~cg~kFYDLn------------------------------k~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 8 TKRICPNTGSKFYDLN------------------------------RRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred ccccCCCcCccccccC------------------------------CCCccCCCcCCccCcchhhc
Confidence 3468999999886322 02889999999987664443
No 94
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=29.69 E-value=26 Score=32.52 Aligned_cols=19 Identities=21% Similarity=0.410 Sum_probs=14.8
Q ss_pred ccCCcccCCcCccccCCch
Q 003869 390 IKDGKFECQFCHKVFHERR 408 (790)
Q Consensus 390 tHtGPYkC~~CGKsFs~ks 408 (790)
..+|.+.|..|++.|.--.
T Consensus 50 ~a~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 50 QAVGIWRCKGCKKTVAGGA 68 (90)
T ss_pred eeeEEEEcCCCCCEEeCCc
Confidence 3557899999999997543
No 95
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.16 E-value=17 Score=31.49 Aligned_cols=17 Identities=41% Similarity=1.075 Sum_probs=13.5
Q ss_pred ccccccccccc---------cccccC
Q 003869 770 GYMCPTCKAKI---------SGQLGG 786 (790)
Q Consensus 770 g~~c~~ck~k~---------sg~~~~ 786 (790)
-||||+|+.++ +|+||.
T Consensus 31 tymC~eC~~Rva~kt~~R~~~g~f~f 56 (68)
T COG4896 31 TYMCPECEHRVAIKTISRVNSGHFNF 56 (68)
T ss_pred eEechhhHhhhchhhHHHhccCCccc
Confidence 59999998765 677775
No 96
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=29.16 E-value=26 Score=33.44 Aligned_cols=28 Identities=32% Similarity=0.615 Sum_probs=21.9
Q ss_pred ceeeEEeeeCCccchhhhccccCCCcccccccccccc
Q 003869 743 HLTTLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAK 779 (790)
Q Consensus 743 ~~~~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k 779 (790)
-+...|--||.+|..... .|.||.|+..
T Consensus 68 p~~~~C~~Cg~~~~~~~~---------~~~CP~Cgs~ 95 (115)
T TIGR00100 68 PVECECEDCSEEVSPEID---------LYRCPKCHGI 95 (115)
T ss_pred CcEEEcccCCCEEecCCc---------CccCcCCcCC
Confidence 356889999999987644 5889999953
No 97
>smart00349 KRAB krueppel associated box.
Probab=28.71 E-value=35 Score=23.60 Aligned_cols=45 Identities=20% Similarity=0.248 Sum_probs=26.5
Q ss_pred CeEEeeeccC-CCCCchHHHHhhhhc----------ccccChHHHHhhhhccCCcc
Q 003869 175 GSVVDIVDLG-SLEDPYGEELRRRTE----------GISANEEALLGFLRDLGGQW 219 (790)
Q Consensus 175 gv~vd~~~~~-~~~dp~~~el~r~~~----------Gl~~~kpeli~~LEq~~g~W 219 (790)
.+.+++.... ...++...+++...+ |+...+|+++..++++..+|
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 (61)
T smart00349 5 DVAVYFSQEEWEQLDPAQRNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEPW 60 (61)
T ss_pred cceeecCHHHHhccCHHHHHHHHHHHHHhhccccccCCCcCCcchhhhhhccCcCC
Confidence 3444544432 345555555544322 66666788888888777776
No 98
>KOG4451 consensus Uncharacterized conserved protein (tumor-associated antigen HCA127 in humans) [Function unknown]
Probab=28.42 E-value=16 Score=39.08 Aligned_cols=58 Identities=26% Similarity=0.461 Sum_probs=34.4
Q ss_pred ccccCCCCCCCCCccccccCCcccCCCCCCccccchhhhccccccceeeEEeeeCCccchhhhccccCCCcccccccccc
Q 003869 698 FGTGQESGPLPEAPIQMSNNAGMDGSYGSSTQVESEVLLNSTSRHHLTTLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCK 777 (790)
Q Consensus 698 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck 777 (790)
+.--|-+.|-.+.+-.+-+..+|.-+|- +--|+| -+|.-|+..++--|- +||-||
T Consensus 216 ~a~~~p~~~~v~r~Q~~~~~~~~~psFr-------qqpppM-------K~ClsChqqIHRNAP-----------iCPlCK 270 (286)
T KOG4451|consen 216 AAMQQPSGSQVDRPQNLINRHRMPPSFR-------QQPPPM-------KVCLSCHQQIHRNAP-----------ICPLCK 270 (286)
T ss_pred cccCCCCCCcccchhhcccccCCCcchh-------cCCCcc-------hHHHHHHHHHhcCCC-----------CCcchh
Confidence 3334445455555555555555554443 112223 359999988766554 899999
Q ss_pred ccc
Q 003869 778 AKI 780 (790)
Q Consensus 778 ~k~ 780 (790)
+|-
T Consensus 271 aKs 273 (286)
T KOG4451|consen 271 AKS 273 (286)
T ss_pred hcc
Confidence 985
No 99
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.27 E-value=26 Score=33.53 Aligned_cols=28 Identities=25% Similarity=0.622 Sum_probs=20.7
Q ss_pred ceeeEEeeeCCccchhhhccccCCCccccc-ccccccc
Q 003869 743 HLTTLCVWCGMEFSHEVVDSEMQPDSVGYM-CPTCKAK 779 (790)
Q Consensus 743 ~~~~~cvwc~~ef~~~~~~~e~q~~s~g~~-c~~ck~k 779 (790)
-+...|--||.+|.-... .|. ||.|+..
T Consensus 69 p~~~~C~~Cg~~~~~~~~---------~~~~CP~Cgs~ 97 (117)
T PRK00564 69 KVELECKDCSHVFKPNAL---------DYGVCEKCHSK 97 (117)
T ss_pred CCEEEhhhCCCccccCCc---------cCCcCcCCCCC
Confidence 457889999988865432 566 9999964
No 100
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=28.25 E-value=25 Score=37.14 Aligned_cols=32 Identities=22% Similarity=0.602 Sum_probs=27.2
Q ss_pred eEEeeeCCccchhhhccccCCCccccccccccccc
Q 003869 746 TLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAKI 780 (790)
Q Consensus 746 ~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k~ 780 (790)
-.|.-| |+|-++.+=.--++.-|+||.|++++
T Consensus 193 lIC~~C---~hhngl~~~~ek~~~efiC~~Cn~~n 224 (251)
T COG5415 193 LICPQC---HHHNGLYRLAEKPIIEFICPHCNHKN 224 (251)
T ss_pred hccccc---cccccccccccccchheecccchhhc
Confidence 346655 78999998888888899999999987
No 101
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=27.23 E-value=24 Score=32.65 Aligned_cols=18 Identities=28% Similarity=0.698 Sum_probs=13.8
Q ss_pred ccCCcccCCcCccccCCc
Q 003869 390 IKDGKFECQFCHKVFHER 407 (790)
Q Consensus 390 tHtGPYkC~~CGKsFs~k 407 (790)
..+|-++|..|++.|.--
T Consensus 49 ~a~GIW~C~~C~~~~AGG 66 (90)
T PF01780_consen 49 VATGIWKCKKCGKKFAGG 66 (90)
T ss_dssp EETTEEEETTTTEEEE-B
T ss_pred eeeEEeecCCCCCEEeCC
Confidence 456789999999998743
No 102
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=26.95 E-value=11 Score=45.87 Aligned_cols=26 Identities=38% Similarity=0.736 Sum_probs=24.1
Q ss_pred CcccCCcCccccCCchhhhhhccccc
Q 003869 393 GKFECQFCHKVFHERRRYNGHVGIHV 418 (790)
Q Consensus 393 GPYkC~~CGKsFs~ks~L~rH~RtHt 418 (790)
|-|-|..|+|.|-.-..++.||++|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 36999999999999999999999995
No 103
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=26.39 E-value=13 Score=30.74 Aligned_cols=37 Identities=30% Similarity=0.529 Sum_probs=24.2
Q ss_pred eeEEeeeCCccchhhhcc----ccCCCcccccccccccccc
Q 003869 745 TTLCVWCGMEFSHEVVDS----EMQPDSVGYMCPTCKAKIS 781 (790)
Q Consensus 745 ~~~cvwc~~ef~~~~~~~----e~q~~s~g~~c~~ck~k~s 781 (790)
+-+|+-||.+|--.|-+- |-.-++----|++|..+--
T Consensus 4 ~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR~~rk 44 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCRQARK 44 (49)
T ss_pred eEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHHHHHH
Confidence 568999999996554332 3333444446999987643
No 104
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=26.26 E-value=23 Score=25.11 Aligned_cols=24 Identities=38% Similarity=0.966 Sum_probs=15.1
Q ss_pred eEEeeeCCccchhhhccccCCCccccccccccccc
Q 003869 746 TLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAKI 780 (790)
Q Consensus 746 ~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k~ 780 (790)
..|..||.+..-++ -.||.|.++|
T Consensus 3 ~~Cp~Cg~~~~~~~-----------~fC~~CG~~L 26 (26)
T PF13248_consen 3 MFCPNCGAEIDPDA-----------KFCPNCGAKL 26 (26)
T ss_pred CCCcccCCcCCccc-----------ccChhhCCCC
Confidence 46788887543322 2688887765
No 105
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=26.17 E-value=30 Score=32.07 Aligned_cols=19 Identities=26% Similarity=0.618 Sum_probs=15.0
Q ss_pred ccCCcccCCcCccccCCch
Q 003869 390 IKDGKFECQFCHKVFHERR 408 (790)
Q Consensus 390 tHtGPYkC~~CGKsFs~ks 408 (790)
..+|.+.|..|++.|.--.
T Consensus 50 ~a~GIW~C~~C~~~~AGGA 68 (90)
T PRK03976 50 VGTGIWECRKCGAKFAGGA 68 (90)
T ss_pred EEEEEEEcCCCCCEEeCCc
Confidence 4567899999999997543
No 106
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=25.91 E-value=27 Score=34.65 Aligned_cols=24 Identities=21% Similarity=0.187 Sum_probs=20.3
Q ss_pred cccCCcCccccCCchhhhhhccccccC
Q 003869 394 KFECQFCHKVFHERRRYNGHVGIHVRN 420 (790)
Q Consensus 394 PYkC~~CGKsFs~ks~L~rH~RtHtgE 420 (790)
-..|-+|||.|. .|+||+.+|.+-
T Consensus 76 ~IicLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 76 YIICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred eEEEeccCcchH---HHHHHHhcccCC
Confidence 467999999997 789999998653
No 107
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=25.50 E-value=29 Score=35.61 Aligned_cols=16 Identities=19% Similarity=0.870 Sum_probs=12.4
Q ss_pred CCcccccccccccccc
Q 003869 766 PDSVGYMCPTCKAKIS 781 (790)
Q Consensus 766 ~~s~g~~c~~ck~k~s 781 (790)
.+..+|+||.|+.+++
T Consensus 113 ~~~~~Y~Cp~C~~ryt 128 (178)
T PRK06266 113 ENNMFFFCPNCHIRFT 128 (178)
T ss_pred cCCCEEECCCCCcEEe
Confidence 3567888888888875
No 108
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=25.41 E-value=45 Score=35.43 Aligned_cols=29 Identities=21% Similarity=0.492 Sum_probs=22.7
Q ss_pred CcccccCCCCcccCChhHHHHHHHhhhcc
Q 003869 345 RDLFECHKCEMTFDEKDTYLQHLLSFHQR 373 (790)
Q Consensus 345 EKPyeC~~CgKtF~~kSsLkrH~l~~H~r 373 (790)
+..|.|..|+|.|.-..-...|+...|..
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 56799999999999999999999766753
No 109
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=24.90 E-value=40 Score=34.52 Aligned_cols=11 Identities=27% Similarity=0.779 Sum_probs=8.9
Q ss_pred cccccCCCCcc
Q 003869 346 DLFECHKCEMT 356 (790)
Q Consensus 346 KPyeC~~CgKt 356 (790)
+-|.|++||.+
T Consensus 133 ~~~vC~vCGy~ 143 (166)
T COG1592 133 KVWVCPVCGYT 143 (166)
T ss_pred CEEEcCCCCCc
Confidence 36999999864
No 110
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.40 E-value=45 Score=32.25 Aligned_cols=30 Identities=27% Similarity=0.505 Sum_probs=20.0
Q ss_pred ceeeEEeeeCCccchhhhccccCCCccc--ccccccc
Q 003869 743 HLTTLCVWCGMEFSHEVVDSEMQPDSVG--YMCPTCK 777 (790)
Q Consensus 743 ~~~~~cvwc~~ef~~~~~~~e~q~~s~g--~~c~~ck 777 (790)
.....| -||.+|.-... ..+... |-||.|+
T Consensus 68 p~~~~C-~Cg~~~~~~~~----~~~~~~~~~~CP~Cg 99 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDED----EIDHYAAVIECPVCG 99 (124)
T ss_pred CeeEEe-eCcCccccccc----chhccccCCcCcCCC
Confidence 467899 99988875432 111223 6799998
No 111
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.77 E-value=33 Score=33.83 Aligned_cols=16 Identities=31% Similarity=0.903 Sum_probs=14.2
Q ss_pred CCcccccccccccccc
Q 003869 766 PDSVGYMCPTCKAKIS 781 (790)
Q Consensus 766 ~~s~g~~c~~ck~k~s 781 (790)
.+...|+||.|+.+++
T Consensus 95 ~~~~~Y~Cp~C~~~y~ 110 (147)
T smart00531 95 TNNAYYKCPNCQSKYT 110 (147)
T ss_pred cCCcEEECcCCCCEee
Confidence 4678999999999987
No 112
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=22.49 E-value=42 Score=26.44 Aligned_cols=30 Identities=33% Similarity=0.516 Sum_probs=23.9
Q ss_pred eeEEeeeCCccchhhhccccCCCccccccccccc
Q 003869 745 TTLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKA 778 (790)
Q Consensus 745 ~~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~ 778 (790)
...|.-||.+|....--+| ...-.||.|+.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~----~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISE----DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEcCC----CCCCcCCCCCC
Confidence 4579999999988877666 34568999998
No 113
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=21.79 E-value=47 Score=36.15 Aligned_cols=45 Identities=24% Similarity=0.530 Sum_probs=32.2
Q ss_pred cccCCCCcccCChhHHHHHHHhhhcccCccccCCCCCCccccccCC-cccCCcCccccCCchhhhhhcc
Q 003869 348 FECHKCEMTFDEKDTYLQHLLSFHQRTTRRYRLGSSVGDGVIIKDG-KFECQFCHKVFHERRRYNGHVG 415 (790)
Q Consensus 348 yeC~~CgKtF~~kSsLkrH~l~~H~r~hK~F~~sssLk~H~RtHtG-PYkC~~CGKsFs~ks~L~rH~R 415 (790)
|.|..||.+-.. -.+-+|+- ..++ -|.|--|++.|.+ ..+..|..
T Consensus 4 FtCnvCgEsvKK-p~vekH~s---------------------rCrn~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMS---------------------RCRNAYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhccc-cchHHHHH---------------------hccCCeeEEeeccccccc-chhhhhhh
Confidence 789999987543 33445644 2333 8999999999999 67778855
No 114
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=21.72 E-value=42 Score=29.96 Aligned_cols=46 Identities=30% Similarity=0.544 Sum_probs=34.6
Q ss_pred cccccceeecccccccCccCcccccccCCCCccccccccccccccc
Q 003869 237 TLPVGWKLLLGLKRREGRASVYCRRYISPGGQHFVSCKEVSGYLQS 282 (790)
Q Consensus 237 ~l~~~~kl~~glKr~e~r~~~~CR~~iSPkGqqf~TCkE~SSyf~S 282 (790)
.++.||+..+.+++-........-.|.+|.|.++-+-.++..|+..
T Consensus 7 Plp~GW~R~~~~r~~g~~~~~~dV~Y~sP~GkklRs~~ev~~YL~~ 52 (77)
T smart00391 7 PLPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHK 52 (77)
T ss_pred CCCCCcEEEEEEecCCCCCCcccEEEECCCCCeeeCHHHHHHHHHh
Confidence 4677999988887554333333366899999999998999888765
No 115
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=21.65 E-value=48 Score=27.83 Aligned_cols=35 Identities=29% Similarity=0.697 Sum_probs=25.5
Q ss_pred cceeeEEeeeCCccchhhhccccCCCcccccccccccc
Q 003869 742 HHLTTLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAK 779 (790)
Q Consensus 742 ~~~~~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k 779 (790)
+..+-.|.-| |+|-++.-..-...+-|.||.|++.
T Consensus 19 ~r~aLIC~~C---~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 19 NRYALICSKC---FSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred CceeEECccc---chhhcccccccCCceEEEcCCCCCc
Confidence 4456666666 6799988544566789999999864
No 116
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=21.53 E-value=38 Score=39.28 Aligned_cols=61 Identities=16% Similarity=0.335 Sum_probs=43.9
Q ss_pred ccccccCCcccCCCCCCccccchhhhccccccceeeEEeeeCCccchhhhccccCCCcccccccccccccccc
Q 003869 711 PIQMSNNAGMDGSYGSSTQVESEVLLNSTSRHHLTTLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAKISGQ 783 (790)
Q Consensus 711 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k~sg~ 783 (790)
..+--|+++-++. +-+||-.+.+.+--.-...+|--||.. +.|-.|. ||-|+.|+-++..-
T Consensus 320 D~i~~~G~~~~~~----~n~ek~~v~~l~~~~~~~p~Cp~Cg~~-----m~S~G~~---g~rC~kCg~~~~~~ 380 (421)
T COG1571 320 DEITVYGSVKPGT----LNLEKFQVLKLARYERVNPVCPRCGGR-----MKSAGRN---GFRCKKCGTRARET 380 (421)
T ss_pred CEEEEecCccccc----eeEEEEEEEEeeeeEEcCCCCCccCCc-----hhhcCCC---CcccccccccCCcc
Confidence 3344566666666 778888555554445567799999986 4566666 99999999998764
No 117
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=21.21 E-value=59 Score=24.30 Aligned_cols=9 Identities=22% Similarity=0.822 Sum_probs=7.8
Q ss_pred cccCCcCcc
Q 003869 394 KFECQFCHK 402 (790)
Q Consensus 394 PYkC~~CGK 402 (790)
|+.|+.||-
T Consensus 17 ~~~CP~Cg~ 25 (33)
T cd00350 17 PWVCPVCGA 25 (33)
T ss_pred CCcCcCCCC
Confidence 889999985
No 118
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=21.13 E-value=47 Score=31.62 Aligned_cols=52 Identities=13% Similarity=0.271 Sum_probs=30.3
Q ss_pred ccccccCCcccCCCCCCccccchhhhccccccceeeEEeeeCCccchhhhccccCCCccccccccccc
Q 003869 711 PIQMSNNAGMDGSYGSSTQVESEVLLNSTSRHHLTTLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKA 778 (790)
Q Consensus 711 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~ 778 (790)
.+.+.|++...++.-.-..|+=+. .-+...|--||.+|..+. ..|.||.|+.
T Consensus 43 ~L~f~f~~~~~~T~~egA~L~I~~-------vp~~~~C~~Cg~~~~~~~---------~~~~CP~Cgs 94 (113)
T PRK12380 43 AVRFSFEIVCHGTVAQGCDLHIVY-------KPAQAWCWDCSQVVEIHQ---------HDAQCPHCHG 94 (113)
T ss_pred HHHHHHHHHhCCCccCCCEEEEEe-------eCcEEEcccCCCEEecCC---------cCccCcCCCC
Confidence 344444444444443333444332 234678999998887654 4566999994
No 119
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=20.53 E-value=29 Score=28.92 Aligned_cols=30 Identities=37% Similarity=0.795 Sum_probs=12.7
Q ss_pred EeeeCCccchhhhccccCCCccccccccccccc
Q 003869 748 CVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAKI 780 (790)
Q Consensus 748 cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k~ 780 (790)
|.-|..+|.--. +...+|..|.||.||.-|
T Consensus 2 CfgC~~~~~~~~---~~~~~~~~y~C~~C~~~F 31 (51)
T PF07975_consen 2 CFGCQKPFPDGP---EKKADSSRYRCPKCKNHF 31 (51)
T ss_dssp ETTTTEE-TTS----------EEE--TTTT--B
T ss_pred CccCCCCCCCcc---cccccCCeEECCCCCCcc
Confidence 556666665432 222338889999998754
No 120
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=20.44 E-value=39 Score=32.27 Aligned_cols=31 Identities=23% Similarity=0.522 Sum_probs=24.1
Q ss_pred eEEeeeCCccchhhhccccCCCccccccccccccccccc
Q 003869 746 TLCVWCGMEFSHEVVDSEMQPDSVGYMCPTCKAKISGQL 784 (790)
Q Consensus 746 ~~cvwc~~ef~~~~~~~e~q~~s~g~~c~~ck~k~sg~~ 784 (790)
..|.-|+.||-++- +.-|+||.|....+++-
T Consensus 4 p~cp~c~sEytYed--------~~~~~cpec~~ew~~~~ 34 (112)
T COG2824 4 PPCPKCNSEYTYED--------GGQLICPECAHEWNENE 34 (112)
T ss_pred CCCCccCCceEEec--------CceEeCchhcccccccc
Confidence 46889999998763 34699999999888543
No 121
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=20.39 E-value=76 Score=27.47 Aligned_cols=12 Identities=25% Similarity=0.487 Sum_probs=9.2
Q ss_pred cccccCCCCccc
Q 003869 346 DLFECHKCEMTF 357 (790)
Q Consensus 346 KPyeC~~CgKtF 357 (790)
-.|.|+.||+.-
T Consensus 26 v~F~CPnCGe~~ 37 (61)
T COG2888 26 VKFPCPNCGEVE 37 (61)
T ss_pred eEeeCCCCCcee
Confidence 358999999753
Done!