Query 038616
Match_columns 431
No_of_seqs 22 out of 24
Neff 1.8
Searched_HMMs 46136
Date Fri Mar 29 12:51:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038616.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038616hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA00616 hypothetical protein 97.1 0.00028 6E-09 52.6 1.8 27 321-347 1-27 (44)
2 PF00096 zf-C2H2: Zinc finger, 97.0 0.00026 5.7E-09 43.3 0.9 23 322-345 1-23 (23)
3 PF13912 zf-C2H2_6: C2H2-type 96.8 0.00044 9.6E-09 43.7 0.9 26 321-347 1-26 (27)
4 PF13894 zf-C2H2_4: C2H2-type 96.6 0.0011 2.4E-08 39.2 1.4 24 322-345 1-24 (24)
5 PHA02768 hypothetical protein; 95.9 0.004 8.7E-08 48.3 1.7 27 322-349 6-32 (55)
6 smart00355 ZnF_C2H2 zinc finge 94.6 0.027 5.7E-07 33.1 1.9 24 322-346 1-24 (26)
7 smart00451 ZnF_U1 U1-like zinc 94.2 0.028 6.1E-07 36.9 1.5 24 320-343 2-25 (35)
8 PF13465 zf-H2C2_2: Zinc-finge 93.3 0.023 4.9E-07 36.9 -0.1 21 313-333 6-26 (26)
9 KOG3623 Homeobox transcription 93.3 0.028 6E-07 61.6 0.4 31 309-343 301-331 (1007)
10 PF12756 zf-C2H2_2: C2H2 type 92.8 0.064 1.4E-06 40.2 1.7 30 321-350 50-80 (100)
11 PF12874 zf-met: Zinc-finger o 92.6 0.052 1.1E-06 33.7 0.9 22 322-343 1-22 (25)
12 PF12171 zf-C2H2_jaz: Zinc-fin 92.1 0.044 9.5E-07 35.3 -0.0 22 322-343 2-23 (27)
13 COG4049 Uncharacterized protei 91.6 0.11 2.5E-06 41.9 1.8 43 322-367 18-60 (65)
14 PF09237 GAGA: GAGA factor; I 91.4 0.13 2.7E-06 40.6 1.9 31 317-347 20-50 (54)
15 PHA00732 hypothetical protein 87.9 0.31 6.6E-06 39.4 1.7 26 321-346 1-26 (79)
16 KOG2462 C2H2-type Zn-finger pr 86.5 0.47 1E-05 46.8 2.4 33 316-349 210-242 (279)
17 PHA00733 hypothetical protein 85.9 0.55 1.2E-05 40.4 2.2 30 314-343 66-95 (128)
18 KOG3623 Homeobox transcription 78.6 0.56 1.2E-05 51.9 -0.5 28 315-342 944-971 (1007)
19 PF08209 Sgf11: Sgf11 (transcr 78.3 1.1 2.3E-05 31.9 1.0 21 321-342 4-24 (33)
20 PF07754 DUF1610: Domain of un 74.5 1.4 3.1E-05 29.7 0.8 15 315-329 10-24 (24)
21 PF05605 zf-Di19: Drought indu 73.4 2.6 5.5E-05 31.0 1.9 27 321-348 2-28 (54)
22 PF13913 zf-C2HC_2: zinc-finge 72.7 2.5 5.5E-05 27.7 1.6 20 322-342 3-22 (25)
23 PF13909 zf-H2C2_5: C2H2-type 72.6 2.3 5E-05 26.3 1.3 21 322-343 1-21 (24)
24 PF12756 zf-C2H2_2: C2H2 type 72.4 1.2 2.6E-05 33.4 0.0 26 323-348 1-26 (100)
25 PF05605 zf-Di19: Drought indu 70.2 3.2 7E-05 30.4 1.9 23 321-345 31-53 (54)
26 PHA00733 hypothetical protein 69.4 3.3 7.2E-05 35.7 2.1 26 320-345 98-123 (128)
27 COG5188 PRP9 Splicing factor 3 67.1 4.5 9.7E-05 42.2 2.8 33 322-354 239-272 (470)
28 PTZ00448 hypothetical protein; 65.8 3.5 7.6E-05 42.3 1.7 26 318-343 311-336 (373)
29 KOG1074 Transcriptional repres 65.2 2 4.3E-05 48.1 -0.1 37 311-348 623-659 (958)
30 PHA00732 hypothetical protein 64.0 3 6.5E-05 33.7 0.7 25 321-349 27-51 (79)
31 PF12230 PRP21_like_P: Pre-mRN 62.9 2.4 5.3E-05 38.6 0.0 41 322-364 169-209 (229)
32 KOG3800 Predicted E3 ubiquitin 61.8 4.9 0.00011 40.3 1.9 53 318-380 37-92 (300)
33 KOG4167 Predicted DNA-binding 61.6 4.3 9.4E-05 45.2 1.6 30 319-349 790-819 (907)
34 KOG3993 Transcription factor ( 60.6 3.7 8E-05 43.3 0.8 28 318-346 292-319 (500)
35 KOG0717 Molecular chaperone (D 59.8 7.3 0.00016 41.4 2.8 26 318-343 288-314 (508)
36 PF13878 zf-C2H2_3: zinc-finge 57.8 6.2 0.00013 28.5 1.4 22 313-334 5-26 (41)
37 KOG1146 Homeobox protein [Gene 57.1 5.8 0.00012 46.3 1.6 42 308-350 453-494 (1406)
38 PF09723 Zn-ribbon_8: Zinc rib 56.1 1.8 3.9E-05 31.0 -1.7 18 322-339 6-23 (42)
39 PF09538 FYDLN_acid: Protein o 56.0 5.1 0.00011 34.4 0.8 17 317-334 23-39 (108)
40 TIGR03826 YvyF flagellar opero 52.5 10 0.00022 33.9 2.1 63 323-396 5-70 (137)
41 KOG2785 C2H2-type Zn-finger pr 52.4 6.4 0.00014 40.7 1.0 24 320-350 2-27 (390)
42 smart00834 CxxC_CXXC_SSSS Puta 52.4 4.7 0.0001 27.3 -0.0 17 322-338 6-22 (41)
43 TIGR02605 CxxC_CxxC_SSSS putat 52.2 2.6 5.6E-05 30.3 -1.3 18 322-339 6-23 (52)
44 PLN02748 tRNA dimethylallyltra 51.9 13 0.00027 38.7 2.9 29 315-343 412-441 (468)
45 PHA02768 hypothetical protein; 51.6 5.1 0.00011 31.4 0.1 16 320-335 30-45 (55)
46 PF14353 CpXC: CpXC protein 48.5 6.5 0.00014 32.7 0.2 20 321-340 38-57 (128)
47 COG1885 Uncharacterized protei 47.7 7.7 0.00017 34.5 0.6 16 319-334 47-62 (115)
48 COG2888 Predicted Zn-ribbon RN 46.5 7.6 0.00017 31.4 0.4 8 321-328 50-57 (61)
49 KOG3576 Ovo and related transc 46.1 12 0.00025 37.0 1.6 42 307-348 159-200 (267)
50 PRK14890 putative Zn-ribbon RN 45.2 8.3 0.00018 30.9 0.4 10 320-329 47-56 (59)
51 PF09855 DUF2082: Nucleic-acid 43.9 9.4 0.0002 30.4 0.5 9 322-330 1-9 (64)
52 PF14753 DUF4475: Domain of un 42.5 11 0.00024 35.9 0.8 35 320-358 118-160 (196)
53 KOG1280 Uncharacterized conser 42.1 16 0.00035 37.8 2.0 40 305-346 65-104 (381)
54 PF06524 NOA36: NOA36 protein; 41.7 8.1 0.00018 38.9 -0.2 28 313-342 201-228 (314)
55 PF09986 DUF2225: Uncharacteri 40.6 9.5 0.00021 35.2 0.1 21 320-340 4-24 (214)
56 PLN02294 cytochrome c oxidase 40.2 18 0.00038 34.1 1.8 27 306-332 126-152 (174)
57 KOG2907 RNA polymerase I trans 39.7 10 0.00022 33.9 0.1 12 322-333 103-114 (116)
58 PF04423 Rad50_zn_hook: Rad50 39.2 17 0.00036 26.8 1.2 25 323-350 22-46 (54)
59 KOG2462 C2H2-type Zn-finger pr 38.9 12 0.00026 37.3 0.5 34 310-343 232-265 (279)
60 KOG4317 Predicted Zn-finger pr 36.4 14 0.0003 38.1 0.5 12 322-333 20-31 (383)
61 PF08646 Rep_fac-A_C: Replicat 35.2 11 0.00024 31.8 -0.3 13 319-331 35-47 (146)
62 PF04438 zf-HIT: HIT zinc fing 35.0 12 0.00025 25.9 -0.2 13 319-331 11-23 (30)
63 PF04641 Rtf2: Rtf2 RING-finge 35.0 9.7 0.00021 35.7 -0.8 59 285-350 80-142 (260)
64 KOG1814 Predicted E3 ubiquitin 34.8 36 0.00078 36.0 3.2 44 323-367 295-351 (445)
65 PF09776 Mitoc_L55: Mitochondr 34.3 24 0.00051 31.4 1.5 22 345-366 73-94 (116)
66 PF07975 C1_4: TFIIH C1-like d 32.6 15 0.00032 28.4 -0.0 15 319-333 19-33 (51)
67 PF01927 Mut7-C: Mut7-C RNAse 32.6 16 0.00034 31.6 0.1 12 321-332 124-135 (147)
68 KOG1074 Transcriptional repres 32.4 16 0.00034 41.5 0.1 43 311-354 897-939 (958)
69 PF04780 DUF629: Protein of un 32.0 26 0.00055 37.0 1.6 31 317-347 53-83 (466)
70 smart00531 TFIIE Transcription 31.1 17 0.00036 31.5 0.1 13 321-333 99-111 (147)
71 PF10571 UPF0547: Uncharacteri 30.7 17 0.00036 24.6 0.0 15 323-337 2-16 (26)
72 TIGR02300 FYDLN_acid conserved 29.2 22 0.00047 32.2 0.5 15 320-334 25-39 (129)
73 COG4640 Predicted membrane pro 28.9 27 0.00058 37.0 1.1 34 316-354 10-43 (465)
74 PRK00398 rpoP DNA-directed RNA 28.8 19 0.0004 25.8 -0.0 14 321-334 3-16 (46)
75 smart00154 ZnF_AN1 AN1-like Zi 28.2 23 0.0005 25.4 0.4 16 321-336 12-27 (39)
76 TIGR00373 conserved hypothetic 27.7 40 0.00086 29.9 1.8 10 321-330 128-137 (158)
77 KOG2636 Splicing factor 3a, su 26.6 20 0.00043 38.2 -0.2 43 309-352 260-303 (497)
78 COG0777 AccD Acetyl-CoA carbox 26.2 51 0.0011 33.3 2.5 32 376-407 72-110 (294)
79 PF05191 ADK_lid: Adenylate ki 26.1 18 0.0004 25.7 -0.4 12 322-333 2-13 (36)
80 PRK06266 transcription initiat 26.0 53 0.0012 29.9 2.4 12 321-332 136-147 (178)
81 COG1813 Predicted transcriptio 25.5 79 0.0017 29.5 3.4 44 382-425 114-161 (165)
82 PLN03086 PRLI-interacting fact 25.5 41 0.00088 36.3 1.7 21 320-342 477-497 (567)
83 PF13719 zinc_ribbon_5: zinc-r 25.2 30 0.00064 24.3 0.5 15 318-332 22-36 (37)
84 PF12760 Zn_Tnp_IS1595: Transp 25.2 34 0.00073 24.7 0.8 11 319-330 17-27 (46)
85 PF08790 zf-LYAR: LYAR-type C2 25.0 12 0.00026 26.2 -1.4 20 322-342 1-20 (28)
86 PRK03922 hypothetical protein; 25.0 30 0.00065 30.9 0.6 16 319-334 47-62 (113)
87 COG3809 Uncharacterized protei 24.6 75 0.0016 27.4 2.8 18 323-340 23-40 (88)
88 COG1675 TFA1 Transcription ini 24.3 31 0.00067 32.1 0.6 11 322-332 133-143 (176)
89 COG3364 Zn-ribbon containing p 24.3 28 0.0006 31.0 0.3 14 321-334 2-15 (112)
90 PF09965 DUF2199: Uncharacteri 24.3 24 0.00052 31.8 -0.2 36 322-358 1-36 (148)
91 COG4888 Uncharacterized Zn rib 24.2 28 0.00062 30.7 0.3 13 320-332 21-33 (104)
92 cd00924 Cyt_c_Oxidase_Vb Cytoc 23.6 32 0.0007 29.2 0.5 23 310-332 68-90 (97)
93 COG1656 Uncharacterized conser 23.4 30 0.00066 32.3 0.3 12 322-333 131-142 (165)
94 PF13248 zf-ribbon_3: zinc-rib 23.3 27 0.00058 22.9 -0.0 18 322-339 3-20 (26)
95 PF01428 zf-AN1: AN1-like Zinc 23.0 25 0.00054 25.2 -0.3 19 320-338 12-30 (43)
96 PRK06921 hypothetical protein; 22.8 39 0.00084 31.8 0.9 10 321-330 32-41 (266)
97 PF12013 DUF3505: Protein of u 22.7 62 0.0013 26.4 2.0 24 322-345 81-108 (109)
98 smart00734 ZnF_Rad18 Rad18-lik 22.7 61 0.0013 21.6 1.6 19 323-342 3-21 (26)
99 COG4338 Uncharacterized protei 22.7 76 0.0017 25.3 2.3 34 323-360 14-47 (54)
100 cd04476 RPA1_DBD_C RPA1_DBD_C: 22.3 35 0.00075 29.4 0.4 12 320-331 50-61 (166)
101 PF09845 DUF2072: Zn-ribbon co 21.8 35 0.00076 30.9 0.4 15 321-335 1-15 (131)
102 KOG3993 Transcription factor ( 20.8 52 0.0011 35.2 1.4 36 318-354 353-388 (500)
103 PTZ00222 60S ribosomal protein 20.3 74 0.0016 31.8 2.3 23 344-366 96-118 (263)
104 KOG1146 Homeobox protein [Gene 20.3 59 0.0013 38.6 1.8 27 318-344 515-541 (1406)
No 1
>PHA00616 hypothetical protein
Probab=97.08 E-value=0.00028 Score=52.62 Aligned_cols=27 Identities=26% Similarity=0.482 Sum_probs=24.4
Q ss_pred cccCcccchhhhhhHHHHHHHhhhccc
Q 038616 321 PYICPKCIQEFLTSQSFAAHVASAHYR 347 (431)
Q Consensus 321 PYtCPKCN~VFdTSQkFAAHmsS~HYK 347 (431)
||.||.|+++|...+.+..|+.+.|-.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCC
Confidence 899999999999999999999985543
No 2
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.01 E-value=0.00026 Score=43.25 Aligned_cols=23 Identities=30% Similarity=0.765 Sum_probs=21.8
Q ss_pred ccCcccchhhhhhHHHHHHHhhhc
Q 038616 322 YICPKCIQEFLTSQSFAAHVASAH 345 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAAHmsS~H 345 (431)
|+|+.|+++|.+...|..||.. |
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~-H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR-H 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH-H
T ss_pred CCCCCCCCccCCHHHHHHHHhH-C
Confidence 7999999999999999999986 6
No 3
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=96.83 E-value=0.00044 Score=43.69 Aligned_cols=26 Identities=27% Similarity=0.623 Sum_probs=23.5
Q ss_pred cccCcccchhhhhhHHHHHHHhhhccc
Q 038616 321 PYICPKCIQEFLTSQSFAAHVASAHYR 347 (431)
Q Consensus 321 PYtCPKCN~VFdTSQkFAAHmsS~HYK 347 (431)
||+|..|++.|.+.+.|.+|+.. |.+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~-h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRS-HCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCT-TTT
T ss_pred CCCCCccCCccCChhHHHHHhHH-hcC
Confidence 79999999999999999999985 653
No 4
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.59 E-value=0.0011 Score=39.19 Aligned_cols=24 Identities=25% Similarity=0.703 Sum_probs=20.1
Q ss_pred ccCcccchhhhhhHHHHHHHhhhc
Q 038616 322 YICPKCIQEFLTSQSFAAHVASAH 345 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAAHmsS~H 345 (431)
|.|+.|++.|.+...+..||...|
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 789999999999999999999744
No 5
>PHA02768 hypothetical protein; Provisional
Probab=95.93 E-value=0.004 Score=48.31 Aligned_cols=27 Identities=26% Similarity=0.578 Sum_probs=24.3
Q ss_pred ccCcccchhhhhhHHHHHHHhhhccccc
Q 038616 322 YICPKCIQEFLTSQSFAAHVASAHYRFE 349 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAAHmsS~HYK~E 349 (431)
|.|++|++.|..++.+..||.. |-|.+
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~-H~k~~ 32 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRK-HNTNL 32 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHh-cCCcc
Confidence 7999999999999999999996 87543
No 6
>smart00355 ZnF_C2H2 zinc finger.
Probab=94.60 E-value=0.027 Score=33.15 Aligned_cols=24 Identities=29% Similarity=0.769 Sum_probs=21.9
Q ss_pred ccCcccchhhhhhHHHHHHHhhhcc
Q 038616 322 YICPKCIQEFLTSQSFAAHVASAHY 346 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAAHmsS~HY 346 (431)
|.|+.|.+.|.+...|..||. .|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH-Hhc
Confidence 789999999999999999998 475
No 7
>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=94.18 E-value=0.028 Score=36.87 Aligned_cols=24 Identities=29% Similarity=0.581 Sum_probs=22.2
Q ss_pred CcccCcccchhhhhhHHHHHHHhh
Q 038616 320 GPYICPKCIQEFLTSQSFAAHVAS 343 (431)
Q Consensus 320 GPYtCPKCN~VFdTSQkFAAHmsS 343 (431)
|+|.|.-|++.|..+..+.+|+.+
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHCh
Confidence 689999999999999999999886
No 8
>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=93.29 E-value=0.023 Score=36.95 Aligned_cols=21 Identities=29% Similarity=0.605 Sum_probs=17.1
Q ss_pred eccccccCcccCcccchhhhh
Q 038616 313 SLSRKKYGPYICPKCIQEFLT 333 (431)
Q Consensus 313 SLP~~KyGPYtCPKCN~VFdT 333 (431)
-.-|.+..||.|+.|++.|.+
T Consensus 6 ~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 6 MRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHSSSSSEEESSSSEEESS
T ss_pred hhhcCCCCCCCCCCCcCeeCc
Confidence 334678899999999999864
No 9
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.26 E-value=0.028 Score=61.60 Aligned_cols=31 Identities=39% Similarity=0.734 Sum_probs=28.3
Q ss_pred CeeeeccccccCcccCcccchhhhhhHHHHHHHhh
Q 038616 309 GVIHSLSRKKYGPYICPKCIQEFLTSQSFAAHVAS 343 (431)
Q Consensus 309 GrtHSLP~~KyGPYtCPKCN~VFdTSQkFAAHmsS 343 (431)
=|||| +..||.||-|.|.|..|-.|.+||+|
T Consensus 301 lRIHS----GEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 301 LRIHS----GEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred heeec----CCCCcCCcccccccccCCcccccccc
Confidence 36666 78899999999999999999999999
No 10
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=92.79 E-value=0.064 Score=40.20 Aligned_cols=30 Identities=23% Similarity=0.617 Sum_probs=23.8
Q ss_pred cccCcccchhhhhhHHHHHHHhhh-cccccc
Q 038616 321 PYICPKCIQEFLTSQSFAAHVASA-HYRFET 350 (431)
Q Consensus 321 PYtCPKCN~VFdTSQkFAAHmsS~-HYK~ET 350 (431)
+++|+.|++.|.+...+..||.+. |.+...
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 799999999999999999999963 555543
No 11
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=92.65 E-value=0.052 Score=33.66 Aligned_cols=22 Identities=27% Similarity=0.661 Sum_probs=21.0
Q ss_pred ccCcccchhhhhhHHHHHHHhh
Q 038616 322 YICPKCIQEFLTSQSFAAHVAS 343 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAAHmsS 343 (431)
|.|.-|++.|.+...|.+|+.|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 7899999999999999999986
No 12
>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=92.05 E-value=0.044 Score=35.29 Aligned_cols=22 Identities=23% Similarity=0.600 Sum_probs=20.9
Q ss_pred ccCcccchhhhhhHHHHHHHhh
Q 038616 322 YICPKCIQEFLTSQSFAAHVAS 343 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAAHmsS 343 (431)
|.|.-|++.|.+...|..||.|
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 7899999999999999999986
No 13
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=91.58 E-value=0.11 Score=41.85 Aligned_cols=43 Identities=30% Similarity=0.407 Sum_probs=34.5
Q ss_pred ccCcccchhhhhhHHHHHHHhhhccccccHHHHHHHHHHHhhhhhH
Q 038616 322 YICPKCIQEFLTSQSFAAHVASAHYRFETAAERKKRLAAKYKKKNI 367 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAAHmsS~HYK~ET~eERKKRl~Ar~kKr~~ 367 (431)
+.||+|+++|..+-....|+--+|-- ...|-||.-.|.||++.
T Consensus 18 lrCPRC~~~FR~~K~Y~RHVNKaH~~---~~~r~k~~~k~~Kk~~d 60 (65)
T COG4049 18 LRCPRCGMVFRRRKDYIRHVNKAHGW---LFGRGKPKGKRLKKKYD 60 (65)
T ss_pred eeCCchhHHHHHhHHHHHHhhHHhhh---hhcCCchhHHHHHHhhh
Confidence 68999999999999999999876742 23456777777788874
No 14
>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=91.40 E-value=0.13 Score=40.57 Aligned_cols=31 Identities=23% Similarity=0.517 Sum_probs=23.0
Q ss_pred cccCcccCcccchhhhhhHHHHHHHhhhccc
Q 038616 317 KKYGPYICPKCIQEFLTSQSFAAHVASAHYR 347 (431)
Q Consensus 317 ~KyGPYtCPKCN~VFdTSQkFAAHmsS~HYK 347 (431)
+-+-|-|||.|..++..|..+-.||.+.|.+
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 4467999999999999999999999988865
No 15
>PHA00732 hypothetical protein
Probab=87.92 E-value=0.31 Score=39.36 Aligned_cols=26 Identities=23% Similarity=0.397 Sum_probs=22.9
Q ss_pred cccCcccchhhhhhHHHHHHHhhhcc
Q 038616 321 PYICPKCIQEFLTSQSFAAHVASAHY 346 (431)
Q Consensus 321 PYtCPKCN~VFdTSQkFAAHmsS~HY 346 (431)
||.|+.|++.|.+...+..||...|-
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~ 26 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT 26 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC
Confidence 79999999999999999999984353
No 16
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=86.53 E-value=0.47 Score=46.84 Aligned_cols=33 Identities=24% Similarity=0.591 Sum_probs=28.9
Q ss_pred ccccCcccCcccchhhhhhHHHHHHHhhhccccc
Q 038616 316 RKKYGPYICPKCIQEFLTSQSFAAHVASAHYRFE 349 (431)
Q Consensus 316 ~~KyGPYtCPKCN~VFdTSQkFAAHmsS~HYK~E 349 (431)
|.+..||-||-|+|.|.-...+-|||- +|.-.+
T Consensus 210 HTGEKPF~C~hC~kAFADRSNLRAHmQ-THS~~K 242 (279)
T KOG2462|consen 210 HTGEKPFSCPHCGKAFADRSNLRAHMQ-THSDVK 242 (279)
T ss_pred ccCCCCccCCcccchhcchHHHHHHHH-hhcCCc
Confidence 467899999999999999999999999 576543
No 17
>PHA00733 hypothetical protein
Probab=85.87 E-value=0.55 Score=40.36 Aligned_cols=30 Identities=37% Similarity=0.811 Sum_probs=26.1
Q ss_pred ccccccCcccCcccchhhhhhHHHHHHHhh
Q 038616 314 LSRKKYGPYICPKCIQEFLTSQSFAAHVAS 343 (431)
Q Consensus 314 LP~~KyGPYtCPKCN~VFdTSQkFAAHmsS 343 (431)
++.....||+|+.|++.|.+...+..|+..
T Consensus 66 ~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~ 95 (128)
T PHA00733 66 LTSKAVSPYVCPLCLMPFSSSVSLKQHIRY 95 (128)
T ss_pred cccCCCCCccCCCCCCcCCCHHHHHHHHhc
Confidence 566667899999999999999999999984
No 18
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=78.61 E-value=0.56 Score=51.95 Aligned_cols=28 Identities=29% Similarity=0.667 Sum_probs=22.7
Q ss_pred cccccCcccCcccchhhhhhHHHHHHHh
Q 038616 315 SRKKYGPYICPKCIQEFLTSQSFAAHVA 342 (431)
Q Consensus 315 P~~KyGPYtCPKCN~VFdTSQkFAAHms 342 (431)
=|-+..||.|.||.|.|..|-...-||-
T Consensus 944 LHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 944 LHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred hccCCCcchhhhhhhhcccccchHhhhc
Confidence 3456788888888888888888888887
No 19
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=78.28 E-value=1.1 Score=31.92 Aligned_cols=21 Identities=33% Similarity=0.635 Sum_probs=16.6
Q ss_pred cccCcccchhhhhhHHHHHHHh
Q 038616 321 PYICPKCIQEFLTSQSFAAHVA 342 (431)
Q Consensus 321 PYtCPKCN~VFdTSQkFAAHms 342 (431)
-++||.|++.+..+ +||+|..
T Consensus 4 ~~~C~nC~R~v~a~-RfA~HLe 24 (33)
T PF08209_consen 4 YVECPNCGRPVAAS-RFAPHLE 24 (33)
T ss_dssp EEE-TTTSSEEEGG-GHHHHHH
T ss_pred eEECCCCcCCcchh-hhHHHHH
Confidence 37899999988755 7999986
No 20
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=74.49 E-value=1.4 Score=29.68 Aligned_cols=15 Identities=33% Similarity=0.815 Sum_probs=13.3
Q ss_pred cccccCcccCcccch
Q 038616 315 SRKKYGPYICPKCIQ 329 (431)
Q Consensus 315 P~~KyGPYtCPKCN~ 329 (431)
|.++.-+|.||+|+.
T Consensus 10 ~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 10 PREQAVPFPCPNCGF 24 (24)
T ss_pred CcccCceEeCCCCCC
Confidence 788899999999974
No 21
>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=73.40 E-value=2.6 Score=30.97 Aligned_cols=27 Identities=26% Similarity=0.566 Sum_probs=21.9
Q ss_pred cccCcccchhhhhhHHHHHHHhhhcccc
Q 038616 321 PYICPKCIQEFLTSQSFAAHVASAHYRF 348 (431)
Q Consensus 321 PYtCPKCN~VFdTSQkFAAHmsS~HYK~ 348 (431)
.|+||-|++.|+ -+.|..|+...|...
T Consensus 2 ~f~CP~C~~~~~-~~~L~~H~~~~H~~~ 28 (54)
T PF05605_consen 2 SFTCPYCGKGFS-ESSLVEHCEDEHRSE 28 (54)
T ss_pred CcCCCCCCCccC-HHHHHHHHHhHCcCC
Confidence 489999999665 468999999878753
No 22
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=72.72 E-value=2.5 Score=27.68 Aligned_cols=20 Identities=25% Similarity=0.615 Sum_probs=17.0
Q ss_pred ccCcccchhhhhhHHHHHHHh
Q 038616 322 YICPKCIQEFLTSQSFAAHVA 342 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAAHms 342 (431)
..||.|++-| ....++.|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3799999999 6778899876
No 23
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=72.63 E-value=2.3 Score=26.34 Aligned_cols=21 Identities=24% Similarity=0.615 Sum_probs=15.4
Q ss_pred ccCcccchhhhhhHHHHHHHhh
Q 038616 322 YICPKCIQEFLTSQSFAAHVAS 343 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAAHmsS 343 (431)
|.|+.|+-... ...|..||..
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 78999997665 6778888875
No 24
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=72.41 E-value=1.2 Score=33.38 Aligned_cols=26 Identities=19% Similarity=0.286 Sum_probs=0.0
Q ss_pred cCcccchhhhhhHHHHHHHhhhcccc
Q 038616 323 ICPKCIQEFLTSQSFAAHVASAHYRF 348 (431)
Q Consensus 323 tCPKCN~VFdTSQkFAAHmsS~HYK~ 348 (431)
.|+-|+..|++-+.+..||...|--.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~ 26 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFD 26 (100)
T ss_dssp --------------------------
T ss_pred Cccccccccccccccccccccccccc
Confidence 39999999999999999999877654
No 25
>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=70.19 E-value=3.2 Score=30.43 Aligned_cols=23 Identities=26% Similarity=0.694 Sum_probs=18.8
Q ss_pred cccCcccchhhhhhHHHHHHHhhhc
Q 038616 321 PYICPKCIQEFLTSQSFAAHVASAH 345 (431)
Q Consensus 321 PYtCPKCN~VFdTSQkFAAHmsS~H 345 (431)
.+.||.|..-+ +..|..||.+.|
T Consensus 31 ~v~CPiC~~~~--~~~l~~Hl~~~H 53 (54)
T PF05605_consen 31 NVVCPICSSRV--TDNLIRHLNSQH 53 (54)
T ss_pred CccCCCchhhh--hhHHHHHHHHhc
Confidence 58999999854 459999999766
No 26
>PHA00733 hypothetical protein
Probab=69.41 E-value=3.3 Score=35.65 Aligned_cols=26 Identities=35% Similarity=0.658 Sum_probs=23.0
Q ss_pred CcccCcccchhhhhhHHHHHHHhhhc
Q 038616 320 GPYICPKCIQEFLTSQSFAAHVASAH 345 (431)
Q Consensus 320 GPYtCPKCN~VFdTSQkFAAHmsS~H 345 (431)
.||+|+.|.+.|..+..|..|+.-.|
T Consensus 98 ~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 98 HSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred cCccCCCCCCccCCHHHHHHHHHHhc
Confidence 36999999999999999999998644
No 27
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=67.08 E-value=4.5 Score=42.16 Aligned_cols=33 Identities=30% Similarity=0.509 Sum_probs=27.6
Q ss_pred ccCcccchhhhhhHHHHHHHh-hhccccccHHHH
Q 038616 322 YICPKCIQEFLTSQSFAAHVA-SAHYRFETAAER 354 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAAHms-S~HYK~ET~eER 354 (431)
+-|++|.+.|.||.-|-+|.. -.|.|.+...+-
T Consensus 239 ~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~~~ 272 (470)
T COG5188 239 VYCVKCGREFSRSKVFEYHLEGKRHCKEGQGKEE 272 (470)
T ss_pred eeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhhhH
Confidence 569999999999999999987 468887775444
No 28
>PTZ00448 hypothetical protein; Provisional
Probab=65.82 E-value=3.5 Score=42.28 Aligned_cols=26 Identities=27% Similarity=0.561 Sum_probs=22.5
Q ss_pred ccCcccCcccchhhhhhHHHHHHHhh
Q 038616 318 KYGPYICPKCIQEFLTSQSFAAHVAS 343 (431)
Q Consensus 318 KyGPYtCPKCN~VFdTSQkFAAHmsS 343 (431)
+-++|+|..|+-.|.+++.+-.||.|
T Consensus 311 ~~~~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 311 KSNMLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred ccCCccccccccccCCHHHHHHHhhh
Confidence 34689999999999999998888776
No 29
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=65.25 E-value=2 Score=48.12 Aligned_cols=37 Identities=24% Similarity=0.448 Sum_probs=32.3
Q ss_pred eeeccccccCcccCcccchhhhhhHHHHHHHhhhcccc
Q 038616 311 IHSLSRKKYGPYICPKCIQEFLTSQSFAAHVASAHYRF 348 (431)
Q Consensus 311 tHSLP~~KyGPYtCPKCN~VFdTSQkFAAHmsS~HYK~ 348 (431)
+|---|....||.|-.|++.|.|.-.+-|||+- |--.
T Consensus 623 mHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~v-Hka~ 659 (958)
T KOG1074|consen 623 MHYRTHTGERPFKCKICGRAFTTKGNLKAHMSV-HKAK 659 (958)
T ss_pred hhhhcccCcCccccccccchhccccchhhcccc-cccC
Confidence 566678899999999999999999999999994 8543
No 30
>PHA00732 hypothetical protein
Probab=64.01 E-value=3 Score=33.74 Aligned_cols=25 Identities=28% Similarity=0.602 Sum_probs=19.7
Q ss_pred cccCcccchhhhhhHHHHHHHhhhccccc
Q 038616 321 PYICPKCIQEFLTSQSFAAHVASAHYRFE 349 (431)
Q Consensus 321 PYtCPKCN~VFdTSQkFAAHmsS~HYK~E 349 (431)
+|+|+.|++.|. ..+.|+.+ +|-.|
T Consensus 27 ~~~C~~CgKsF~---~l~~H~~~-~~~~~ 51 (79)
T PHA00732 27 LTKCPVCNKSYR---RLNQHFYS-QYDIE 51 (79)
T ss_pred CCccCCCCCEeC---Chhhhhcc-cCCcc
Confidence 579999999998 58888864 66554
No 31
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=62.88 E-value=2.4 Score=38.60 Aligned_cols=41 Identities=22% Similarity=0.262 Sum_probs=0.0
Q ss_pred ccCcccchhhhhhHHHHHHHhhhccccccHHHHHHHHHHHhhh
Q 038616 322 YICPKCIQEFLTSQSFAAHVASAHYRFETAAERKKRLAAKYKK 364 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAAHmsS~HYK~ET~eERKKRl~Ar~kK 364 (431)
.+||.|+..+.-+ +|+.||-. .---=.=+|-++|+.+|.+.
T Consensus 169 ~~cPitGe~IP~~-e~~eHmRi-~LlDP~wkEqr~~~~~k~~~ 209 (229)
T PF12230_consen 169 IICPITGEMIPAD-EMDEHMRI-ELLDPRWKEQRDRYEAKRKQ 209 (229)
T ss_dssp -------------------------------------------
T ss_pred ccccccccccccc-cccccccc-cccccccccccccccccccc
Confidence 6899999999876 47777763 22222223445666666655
No 32
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=61.79 E-value=4.9 Score=40.32 Aligned_cols=53 Identities=19% Similarity=0.424 Sum_probs=36.1
Q ss_pred ccCcccCcccchhhhhhHHHHHHHhhhccccccHHHHHHHHHHHhhhhhHHHHhhh---cCCCcee
Q 038616 318 KYGPYICPKCIQEFLTSQSFAAHVASAHYRFETAAERKKRLAAKYKKKNILRMARS---SNGSLTI 380 (431)
Q Consensus 318 KyGPYtCPKCN~VFdTSQkFAAHmsS~HYK~ET~eERKKRl~Ar~kKr~~l~i~~K---lnG~lqe 380 (431)
-+|||.||.|+.+.-- .-++.++-|+--++..-.+|||-++...++ +.|+|.+
T Consensus 37 ~~g~~~CpeC~~iLRk----------~nfr~q~fED~~vekEv~iRrri~~~~nk~~eeF~~~Lae 92 (300)
T KOG3800|consen 37 SLGPAQCPECMVILRK----------NNFRVQTFEDPTVEKEVDIRRRILRIFNKKEEEFTGSLAE 92 (300)
T ss_pred hcCCCCCCcccchhhh----------cccchhhcchhHHHHHHHHHHHHHHHhccchhhhhhhHHH
Confidence 3799999999987542 367777777777777777777765444333 5555544
No 33
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=61.58 E-value=4.3 Score=45.20 Aligned_cols=30 Identities=30% Similarity=0.537 Sum_probs=26.3
Q ss_pred cCcccCcccchhhhhhHHHHHHHhhhccccc
Q 038616 319 YGPYICPKCIQEFLTSQSFAAHVASAHYRFE 349 (431)
Q Consensus 319 yGPYtCPKCN~VFdTSQkFAAHmsS~HYK~E 349 (431)
.|=|.|-.|.|||+---..-|||.+ |---|
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~-Hr~q~ 819 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKT-HRQQE 819 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHH-HHHHH
Confidence 6779999999999999999999996 76544
No 34
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=60.62 E-value=3.7 Score=43.33 Aligned_cols=28 Identities=29% Similarity=0.481 Sum_probs=23.9
Q ss_pred ccCcccCcccchhhhhhHHHHHHHhhhcc
Q 038616 318 KYGPYICPKCIQEFLTSQSFAAHVASAHY 346 (431)
Q Consensus 318 KyGPYtCPKCN~VFdTSQkFAAHmsS~HY 346 (431)
-.--|.||.|.|||.---.+|+|--. |-
T Consensus 292 V~vEYrCPEC~KVFsCPANLASHRRW-HK 319 (500)
T KOG3993|consen 292 VHVEYRCPECDKVFSCPANLASHRRW-HK 319 (500)
T ss_pred EEeeecCCcccccccCchhhhhhhcc-cC
Confidence 34468999999999999999999985 63
No 35
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=59.81 E-value=7.3 Score=41.42 Aligned_cols=26 Identities=23% Similarity=0.482 Sum_probs=23.2
Q ss_pred ccCc-ccCcccchhhhhhHHHHHHHhh
Q 038616 318 KYGP-YICPKCIQEFLTSQSFAAHVAS 343 (431)
Q Consensus 318 KyGP-YtCPKCN~VFdTSQkFAAHmsS 343 (431)
.+|+ +-|+-|||.|-|--.++.|.-|
T Consensus 288 ~~ge~lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 288 NEGEVLYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred hcCCceEEeeccccccchHHHHhhHHH
Confidence 5666 8899999999999999999887
No 36
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=57.85 E-value=6.2 Score=28.49 Aligned_cols=22 Identities=27% Similarity=0.683 Sum_probs=17.1
Q ss_pred eccccccCcccCcccchhhhhh
Q 038616 313 SLSRKKYGPYICPKCIQEFLTS 334 (431)
Q Consensus 313 SLP~~KyGPYtCPKCN~VFdTS 334 (431)
.|.-++.|.-+|++|+.++...
T Consensus 5 d~gq~~~~~~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 5 DLGQKSFGATTCPTCGMLYSPG 26 (41)
T ss_pred eCCCCccCCcCCCCCCCEECCC
Confidence 3455667899999999988654
No 37
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=57.07 E-value=5.8 Score=46.30 Aligned_cols=42 Identities=24% Similarity=0.389 Sum_probs=36.1
Q ss_pred CCeeeeccccccCcccCcccchhhhhhHHHHHHHhhhcccccc
Q 038616 308 DGVIHSLSRKKYGPYICPKCIQEFLTSQSFAAHVASAHYRFET 350 (431)
Q Consensus 308 DGrtHSLP~~KyGPYtCPKCN~VFdTSQkFAAHmsS~HYK~ET 350 (431)
.|-|.-|+.-+ .-|.|||||.++.-.+.+..||.+.|--++.
T Consensus 453 ~~~t~~L~S~~-kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~ 494 (1406)
T KOG1146|consen 453 EGQTVVLHSFF-KTLKCPKCNWHYKLAQTLGVHMRSKHPESQS 494 (1406)
T ss_pred ccceeeeeccc-ccccCCccchhhhhHHHhhhcccccccccch
Confidence 45566677666 7899999999999999999999999988777
No 38
>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=56.08 E-value=1.8 Score=31.02 Aligned_cols=18 Identities=39% Similarity=0.713 Sum_probs=16.1
Q ss_pred ccCcccchhhhhhHHHHH
Q 038616 322 YICPKCIQEFLTSQSFAA 339 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAA 339 (431)
|.|++|+.+|+.-++++.
T Consensus 6 y~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE 23 (42)
T ss_pred EEeCCCCCEEEEEEEcCC
Confidence 899999999999887766
No 39
>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=55.99 E-value=5.1 Score=34.37 Aligned_cols=17 Identities=47% Similarity=1.019 Sum_probs=15.1
Q ss_pred cccCcccCcccchhhhhh
Q 038616 317 KKYGPYICPKCIQEFLTS 334 (431)
Q Consensus 317 ~KyGPYtCPKCN~VFdTS 334 (431)
+| .|-+||||+.+|.-+
T Consensus 23 nk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 23 NK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred CC-CCccCCCCCCccCcc
Confidence 55 899999999999887
No 40
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=52.49 E-value=10 Score=33.88 Aligned_cols=63 Identities=24% Similarity=0.346 Sum_probs=31.8
Q ss_pred cCcccchhhhhhHHHHHHHhhhcc-ccccHHHHHHHHHHHhhh--hhHHHHhhhcCCCceeecCCccchhHHHHHHH
Q 038616 323 ICPKCIQEFLTSQSFAAHVASAHY-RFETAAERKKRLAAKYKK--KNILRMARSSNGSLTIVHGRSFKNIADWRRKE 396 (431)
Q Consensus 323 tCPKCN~VFdTSQkFAAHmsS~HY-K~ET~eERKKRl~Ar~kK--r~~l~i~~KlnG~lqeVhg~S~kiikd~~r~~ 396 (431)
.||+|+++|..+ +. -+=..=| +-|..-++-+.|...+.. -....|+.. =|-|.+.|..|.|..
T Consensus 5 nC~~CgklF~~~--~~-~iCp~C~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~--------tgVs~~~I~~~IreG 70 (137)
T TIGR03826 5 NCPKCGRLFVKT--GR-DVCPSCYEEEEREFEKVYKFLRKHENRQATVSEIVEE--------TGVSEKLILKFIREG 70 (137)
T ss_pred cccccchhhhhc--CC-ccCHHHhHHHHHHHHHHHHHHHHCCCCCCCHHHHHHH--------HCcCHHHHHHHHHcC
Confidence 699999999762 11 1111112 223344445555444443 222333222 245677788888754
No 41
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=52.44 E-value=6.4 Score=40.73 Aligned_cols=24 Identities=33% Similarity=0.628 Sum_probs=19.0
Q ss_pred CcccCcccchhhhhh--HHHHHHHhhhcccccc
Q 038616 320 GPYICPKCIQEFLTS--QSFAAHVASAHYRFET 350 (431)
Q Consensus 320 GPYtCPKCN~VFdTS--QkFAAHmsS~HYK~ET 350 (431)
+-|||.-|+..|+++ |+ .|||+|=
T Consensus 2 t~ftC~tC~v~F~~ad~Qr-------~HyKSdW 27 (390)
T KOG2785|consen 2 TGFTCNTCNVEFDDADEQR-------AHYKSDW 27 (390)
T ss_pred CcceeeceeeeeccHHHHH-------HHhhhhH
Confidence 359999999999999 65 3666663
No 42
>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=52.35 E-value=4.7 Score=27.27 Aligned_cols=17 Identities=29% Similarity=0.628 Sum_probs=14.0
Q ss_pred ccCcccchhhhhhHHHH
Q 038616 322 YICPKCIQEFLTSQSFA 338 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFA 338 (431)
|.|++|+.+|+.-+.++
T Consensus 6 y~C~~Cg~~fe~~~~~~ 22 (41)
T smart00834 6 YRCEDCGHTFEVLQKIS 22 (41)
T ss_pred EEcCCCCCEEEEEEecC
Confidence 78999999998766554
No 43
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=52.21 E-value=2.6 Score=30.25 Aligned_cols=18 Identities=28% Similarity=0.602 Sum_probs=14.7
Q ss_pred ccCcccchhhhhhHHHHH
Q 038616 322 YICPKCIQEFLTSQSFAA 339 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAA 339 (431)
|.|++|+.+|+.-+.++.
T Consensus 6 y~C~~Cg~~fe~~~~~~~ 23 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD 23 (52)
T ss_pred EEeCCCCCEeEEEEecCC
Confidence 789999999998766553
No 44
>PLN02748 tRNA dimethylallyltransferase
Probab=51.90 E-value=13 Score=38.73 Aligned_cols=29 Identities=21% Similarity=0.520 Sum_probs=25.1
Q ss_pred cccccCcccCcccch-hhhhhHHHHHHHhh
Q 038616 315 SRKKYGPYICPKCIQ-EFLTSQSFAAHVAS 343 (431)
Q Consensus 315 P~~KyGPYtCPKCN~-VFdTSQkFAAHmsS 343 (431)
+-+....|+|.-|++ ++-+-.....|+.|
T Consensus 412 ~~~~~~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 412 SRELWTQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred cccccccccccCCCCcccCCHHHHHHHhcc
Confidence 445567899999997 99999999999997
No 45
>PHA02768 hypothetical protein; Provisional
Probab=51.55 E-value=5.1 Score=31.39 Aligned_cols=16 Identities=13% Similarity=0.112 Sum_probs=13.4
Q ss_pred CcccCcccchhhhhhH
Q 038616 320 GPYICPKCIQEFLTSQ 335 (431)
Q Consensus 320 GPYtCPKCN~VFdTSQ 335 (431)
.||.|.+|.++|.+..
T Consensus 30 k~~kc~~C~k~f~~~s 45 (55)
T PHA02768 30 TNLKLSNCKRISLRTG 45 (55)
T ss_pred CcccCCcccceecccc
Confidence 3999999999998643
No 46
>PF14353 CpXC: CpXC protein
Probab=48.46 E-value=6.5 Score=32.71 Aligned_cols=20 Identities=25% Similarity=0.675 Sum_probs=15.1
Q ss_pred cccCcccchhhhhhHHHHHH
Q 038616 321 PYICPKCIQEFLTSQSFAAH 340 (431)
Q Consensus 321 PYtCPKCN~VFdTSQkFAAH 340 (431)
-|+||.|+..|.-...|.-|
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred EEECCCCCCceecCCCEEEE
Confidence 48999999998766555444
No 47
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=47.69 E-value=7.7 Score=34.52 Aligned_cols=16 Identities=38% Similarity=0.823 Sum_probs=13.2
Q ss_pred cCcccCcccchhhhhh
Q 038616 319 YGPYICPKCIQEFLTS 334 (431)
Q Consensus 319 yGPYtCPKCN~VFdTS 334 (431)
-|.+.||+|+.-|+.-
T Consensus 47 ~G~t~CP~Cg~~~e~~ 62 (115)
T COG1885 47 VGSTSCPKCGEPFESA 62 (115)
T ss_pred cccccCCCCCCcccee
Confidence 4889999999988753
No 48
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=46.55 E-value=7.6 Score=31.44 Aligned_cols=8 Identities=75% Similarity=1.759 Sum_probs=5.9
Q ss_pred cccCcccc
Q 038616 321 PYICPKCI 328 (431)
Q Consensus 321 PYtCPKCN 328 (431)
||+||||+
T Consensus 50 ~Y~Cp~CG 57 (61)
T COG2888 50 PYRCPKCG 57 (61)
T ss_pred ceECCCcC
Confidence 67777776
No 49
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=46.13 E-value=12 Score=36.97 Aligned_cols=42 Identities=24% Similarity=0.335 Sum_probs=34.8
Q ss_pred CCCeeeeccccccCcccCcccchhhhhhHHHHHHHhhhcccc
Q 038616 307 GDGVIHSLSRKKYGPYICPKCIQEFLTSQSFAAHVASAHYRF 348 (431)
Q Consensus 307 ~DGrtHSLP~~KyGPYtCPKCN~VFdTSQkFAAHmsS~HYK~ 348 (431)
.|=..|.--|..-.||.|.-|+|.|...-.+-+|..-+|---
T Consensus 159 fdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~ 200 (267)
T KOG3576|consen 159 FDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQ 200 (267)
T ss_pred hhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCch
Confidence 344556666789999999999999999999999999878543
No 50
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=45.16 E-value=8.3 Score=30.88 Aligned_cols=10 Identities=60% Similarity=1.394 Sum_probs=7.8
Q ss_pred CcccCcccch
Q 038616 320 GPYICPKCIQ 329 (431)
Q Consensus 320 GPYtCPKCN~ 329 (431)
-+|+||+|+-
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 4789999973
No 51
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=43.91 E-value=9.4 Score=30.40 Aligned_cols=9 Identities=67% Similarity=1.453 Sum_probs=7.6
Q ss_pred ccCcccchh
Q 038616 322 YICPKCIQE 330 (431)
Q Consensus 322 YtCPKCN~V 330 (431)
|.||||+..
T Consensus 1 y~C~KCg~~ 9 (64)
T PF09855_consen 1 YKCPKCGNE 9 (64)
T ss_pred CCCCCCCCc
Confidence 899999873
No 52
>PF14753 DUF4475: Domain of unknown function (DUF4475)
Probab=42.46 E-value=11 Score=35.85 Aligned_cols=35 Identities=46% Similarity=0.736 Sum_probs=24.8
Q ss_pred CcccCcccch--hhhhh------HHHHHHHhhhccccccHHHHHHHH
Q 038616 320 GPYICPKCIQ--EFLTS------QSFAAHVASAHYRFETAAERKKRL 358 (431)
Q Consensus 320 GPYtCPKCN~--VFdTS------QkFAAHmsS~HYK~ET~eERKKRl 358 (431)
+||.|.||.+ -|+++ |.+++|.-. +||++||.+|=
T Consensus 118 ~~~~C~k~~~C~~F~S~f~C~Cd~~~~~HeTv----~ET~~eR~~~G 160 (196)
T PF14753_consen 118 GPHKCKKCCGCSGFESSFLCACDQPWEAHETV----FETEEERRARG 160 (196)
T ss_pred CCccCCCCCCCCCCCCCceecCcCchhheeee----EecHHHHHHcC
Confidence 6677777642 24443 678889875 89999998763
No 53
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=42.12 E-value=16 Score=37.80 Aligned_cols=40 Identities=28% Similarity=0.257 Sum_probs=29.5
Q ss_pred cCCCCeeeeccccccCcccCcccchhhhhhHHHHHHHhhhcc
Q 038616 305 EEGDGVIHSLSRKKYGPYICPKCIQEFLTSQSFAAHVASAHY 346 (431)
Q Consensus 305 ~~~DGrtHSLP~~KyGPYtCPKCN~VFdTSQkFAAHmsS~HY 346 (431)
-.+.|--.|.=+ .-.||||-|+.-=-|-..|--|+++.|-
T Consensus 65 L~f~Ge~i~~y~--~qSftCPyC~~~Gfte~~f~~Hv~s~Hp 104 (381)
T KOG1280|consen 65 LYFGGEPISHYD--PQSFTCPYCGIMGFTERQFGTHVLSQHP 104 (381)
T ss_pred eEecCccccccc--cccccCCcccccccchhHHHHHhhhcCc
Confidence 344444433322 2399999999998899999999999885
No 54
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=41.68 E-value=8.1 Score=38.90 Aligned_cols=28 Identities=25% Similarity=0.471 Sum_probs=21.3
Q ss_pred eccccccCcccCcccchhhhhhHHHHHHHh
Q 038616 313 SLSRKKYGPYICPKCIQEFLTSQSFAAHVA 342 (431)
Q Consensus 313 SLP~~KyGPYtCPKCN~VFdTSQkFAAHms 342 (431)
-+.|+|..|++||||+ |+|+++----||
T Consensus 201 g~ky~k~k~~PCPKCg--~et~eTkdLSmS 228 (314)
T PF06524_consen 201 GFKYEKGKPIPCPKCG--YETQETKDLSMS 228 (314)
T ss_pred ccccccCCCCCCCCCC--Ccccccccceee
Confidence 3678999999999998 567666544454
No 55
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=40.64 E-value=9.5 Score=35.17 Aligned_cols=21 Identities=29% Similarity=0.532 Sum_probs=16.0
Q ss_pred CcccCcccchhhhhhHHHHHH
Q 038616 320 GPYICPKCIQEFLTSQSFAAH 340 (431)
Q Consensus 320 GPYtCPKCN~VFdTSQkFAAH 340 (431)
..++||-|++.|.|..-+...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~ 24 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGK 24 (214)
T ss_pred CceECCCCCCeeeeeEEEcCC
Confidence 358999999999987654433
No 56
>PLN02294 cytochrome c oxidase subunit Vb
Probab=40.22 E-value=18 Score=34.15 Aligned_cols=27 Identities=26% Similarity=0.384 Sum_probs=20.6
Q ss_pred CCCCeeeeccccccCcccCcccchhhh
Q 038616 306 EGDGVIHSLSRKKYGPYICPKCIQEFL 332 (431)
Q Consensus 306 ~~DGrtHSLP~~KyGPYtCPKCN~VFd 332 (431)
+|+--++-+=-+|-.|+.||.|+.+|.
T Consensus 126 eDsh~v~Wf~L~kGkp~RCpeCG~~fk 152 (174)
T PLN02294 126 EDEHDVVWFWLEKGKSFECPVCTQYFE 152 (174)
T ss_pred CCCceeEEEEecCCCceeCCCCCCEEE
Confidence 345556666667778999999999984
No 57
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=39.68 E-value=10 Score=33.88 Aligned_cols=12 Identities=50% Similarity=1.220 Sum_probs=9.7
Q ss_pred ccCcccchhhhh
Q 038616 322 YICPKCIQEFLT 333 (431)
Q Consensus 322 YtCPKCN~VFdT 333 (431)
||||||..-|.+
T Consensus 103 YTC~kC~~k~~e 114 (116)
T KOG2907|consen 103 YTCPKCKYKFTE 114 (116)
T ss_pred EEcCccceeeec
Confidence 899999887754
No 58
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=39.21 E-value=17 Score=26.78 Aligned_cols=25 Identities=20% Similarity=0.476 Sum_probs=13.1
Q ss_pred cCcccchhhhhhHHHHHHHhhhcccccc
Q 038616 323 ICPKCIQEFLTSQSFAAHVASAHYRFET 350 (431)
Q Consensus 323 tCPKCN~VFdTSQkFAAHmsS~HYK~ET 350 (431)
.||-|++-|+.-.+ ..... +|+.+.
T Consensus 22 ~CPlC~r~l~~e~~--~~li~-~~~~~i 46 (54)
T PF04423_consen 22 CCPLCGRPLDEEHR--QELIK-KYKSEI 46 (54)
T ss_dssp E-TTT--EE-HHHH--HHHHH-HHHHHH
T ss_pred cCCCCCCCCCHHHH--HHHHH-HHHHHH
Confidence 89999999987655 44443 554444
No 59
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=38.90 E-value=12 Score=37.35 Aligned_cols=34 Identities=21% Similarity=0.373 Sum_probs=28.0
Q ss_pred eeeeccccccCcccCcccchhhhhhHHHHHHHhh
Q 038616 310 VIHSLSRKKYGPYICPKCIQEFLTSQSFAAHVAS 343 (431)
Q Consensus 310 rtHSLP~~KyGPYtCPKCN~VFdTSQkFAAHmsS 343 (431)
|-|-.-|-...+|.|++|+|.|.--.-+..|-.|
T Consensus 232 RAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 232 RAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred HHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 5555556677799999999999998888888876
No 60
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=36.36 E-value=14 Score=38.15 Aligned_cols=12 Identities=33% Similarity=1.065 Sum_probs=9.9
Q ss_pred ccCcccchhhhh
Q 038616 322 YICPKCIQEFLT 333 (431)
Q Consensus 322 YtCPKCN~VFdT 333 (431)
||||+||-.+-|
T Consensus 20 YtCPRCn~~YCs 31 (383)
T KOG4317|consen 20 YTCPRCNLLYCS 31 (383)
T ss_pred ccCCCCCcccee
Confidence 999999976644
No 61
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=35.20 E-value=11 Score=31.76 Aligned_cols=13 Identities=38% Similarity=0.871 Sum_probs=11.4
Q ss_pred cCcccCcccchhh
Q 038616 319 YGPYICPKCIQEF 331 (431)
Q Consensus 319 yGPYtCPKCN~VF 331 (431)
.|.|.|++|++..
T Consensus 35 ~~~y~C~~C~~~~ 47 (146)
T PF08646_consen 35 DGSYRCEKCNKTV 47 (146)
T ss_dssp TTEEEETTTTEEE
T ss_pred CcEEECCCCCCcC
Confidence 5779999999986
No 62
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=35.04 E-value=12 Score=25.87 Aligned_cols=13 Identities=31% Similarity=0.930 Sum_probs=8.1
Q ss_pred cCcccCcccchhh
Q 038616 319 YGPYICPKCIQEF 331 (431)
Q Consensus 319 yGPYtCPKCN~VF 331 (431)
.+.|+||+|+..+
T Consensus 11 ~~kY~Cp~C~~~~ 23 (30)
T PF04438_consen 11 PAKYRCPRCGARY 23 (30)
T ss_dssp EESEE-TTT--EE
T ss_pred CCEEECCCcCCce
Confidence 6789999998653
No 63
>PF04641 Rtf2: Rtf2 RING-finger
Probab=35.02 E-value=9.7 Score=35.74 Aligned_cols=59 Identities=20% Similarity=0.274 Sum_probs=38.1
Q ss_pred ccccccccc----ccccCCccccccCCCCeeeeccccccCcccCcccchhhhhhHHHHHHHhhhcccccc
Q 038616 285 DLIYAPRKM----SEESSDDEDEDEEGDGVIHSLSRKKYGPYICPKCIQEFLTSQSFAAHVASAHYRFET 350 (431)
Q Consensus 285 ~~grslKki----~E~t~dyi~dd~~~DGrtHSLP~~KyGPYtCPKCN~VFdTSQkFAAHmsS~HYK~ET 350 (431)
..+++||.+ |+...++.+++. +.--...++|.||-+.++|.-+.+|++-...-|--+|.
T Consensus 80 ~hI~~LKDl~~l~~~~n~~~~~~~~-------~~~~~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~ 142 (260)
T PF04641_consen 80 SHIKSLKDLVELKFTKNPSYKEEDK-------SSGDNSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEK 142 (260)
T ss_pred ccccCccceeeEEeEecCccccccc-------cccccCCceeECCCCCcccCCceeEEEEcCCCCEeeHH
Confidence 456777775 555444432222 33445789999999999998888888765555544443
No 64
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.80 E-value=36 Score=35.98 Aligned_cols=44 Identities=30% Similarity=0.503 Sum_probs=35.7
Q ss_pred cCcccchhhhhhHHHHHHHhhhccccc-------------cHHHHHHHHHHHhhhhhH
Q 038616 323 ICPKCIQEFLTSQSFAAHVASAHYRFE-------------TAAERKKRLAAKYKKKNI 367 (431)
Q Consensus 323 tCPKCN~VFdTSQkFAAHmsS~HYK~E-------------T~eERKKRl~Ar~kKr~~ 367 (431)
+|.|||-+|=|-=+.+-|..| -.|.+ +.++||.-+.+|+-||.+
T Consensus 295 ~CskCnFaFCtlCk~t~HG~s-~Ck~~~~~~~~l~~~~~~~d~a~k~ele~Ryg~rvv 351 (445)
T KOG1814|consen 295 ICSKCNFAFCTLCKLTWHGVS-PCKVKAEKLIELYLEYLEADEARKRELEKRYGKRVV 351 (445)
T ss_pred hhccCccHHHHHHHHhhcCCC-cccCchHHHHHHHHHHhhcCHHHHHHHHHHhhHHHH
Confidence 899999999999999999865 66655 667788778788877753
No 65
>PF09776 Mitoc_L55: Mitochondrial ribosomal protein L55; InterPro: IPR018615 Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.
Probab=34.32 E-value=24 Score=31.36 Aligned_cols=22 Identities=32% Similarity=0.344 Sum_probs=17.5
Q ss_pred ccccccHHHHHHHHHHHhhhhh
Q 038616 345 HYRFETAAERKKRLAAKYKKKN 366 (431)
Q Consensus 345 HYK~ET~eERKKRl~Ar~kKr~ 366 (431)
--..=|+|||+.|+++|.+|+.
T Consensus 73 Dl~~LSeeERk~rl~kR~pk~k 94 (116)
T PF09776_consen 73 DLDTLSEEERKARLRKRKPKKK 94 (116)
T ss_pred CcccCCHHHHHHHHHHhCCccc
Confidence 3455689999999999888654
No 66
>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=32.59 E-value=15 Score=28.39 Aligned_cols=15 Identities=40% Similarity=0.904 Sum_probs=7.7
Q ss_pred cCcccCcccchhhhh
Q 038616 319 YGPYICPKCIQEFLT 333 (431)
Q Consensus 319 yGPYtCPKCN~VFdT 333 (431)
.+.|.||+|+++|=-
T Consensus 19 ~~~y~C~~C~~~FC~ 33 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCI 33 (51)
T ss_dssp -EEE--TTTT--B-H
T ss_pred CCeEECCCCCCcccc
Confidence 578999999999843
No 67
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=32.56 E-value=16 Score=31.65 Aligned_cols=12 Identities=25% Similarity=0.725 Sum_probs=10.3
Q ss_pred cccCcccchhhh
Q 038616 321 PYICPKCIQEFL 332 (431)
Q Consensus 321 PYtCPKCN~VFd 332 (431)
=|.||+|+++|=
T Consensus 124 f~~C~~C~kiyW 135 (147)
T PF01927_consen 124 FWRCPGCGKIYW 135 (147)
T ss_pred EEECCCCCCEec
Confidence 478999999984
No 68
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=32.37 E-value=16 Score=41.46 Aligned_cols=43 Identities=23% Similarity=0.509 Sum_probs=34.8
Q ss_pred eeeccccccCcccCcccchhhhhhHHHHHHHhhhccccccHHHH
Q 038616 311 IHSLSRKKYGPYICPKCIQEFLTSQSFAAHVASAHYRFETAAER 354 (431)
Q Consensus 311 tHSLP~~KyGPYtCPKCN~VFdTSQkFAAHmsS~HYK~ET~eER 354 (431)
||.--|.+.+||.|--|.+-|-|.-.+-.||. +|.-.-+-..|
T Consensus 897 iH~rTHtg~KPF~C~fC~~aFttrgnLKvHMg-tH~w~q~~srr 939 (958)
T KOG1074|consen 897 IHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMG-THMWVQPPSRR 939 (958)
T ss_pred HhhhcCCCCCCccchhhhhhhhhhhhhhhhhc-cccccCCCccC
Confidence 34444567899999999999999999999999 69887765443
No 69
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=31.98 E-value=26 Score=36.96 Aligned_cols=31 Identities=29% Similarity=0.688 Sum_probs=25.4
Q ss_pred cccCcccCcccchhhhhhHHHHHHHhhhccc
Q 038616 317 KKYGPYICPKCIQEFLTSQSFAAHVASAHYR 347 (431)
Q Consensus 317 ~KyGPYtCPKCN~VFdTSQkFAAHmsS~HYK 347 (431)
.+..=.+||.|.+.|.....|-.||..-|--
T Consensus 53 ~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 53 KSWRFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred CceeEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 3444568999999999999999999985643
No 70
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=31.08 E-value=17 Score=31.54 Aligned_cols=13 Identities=31% Similarity=0.899 Sum_probs=11.5
Q ss_pred cccCcccchhhhh
Q 038616 321 PYICPKCIQEFLT 333 (431)
Q Consensus 321 PYtCPKCN~VFdT 333 (431)
-|.||.|+..|+.
T Consensus 99 ~Y~Cp~C~~~y~~ 111 (147)
T smart00531 99 YYKCPNCQSKYTF 111 (147)
T ss_pred EEECcCCCCEeeH
Confidence 5999999999984
No 71
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=30.73 E-value=17 Score=24.55 Aligned_cols=15 Identities=40% Similarity=0.820 Sum_probs=10.3
Q ss_pred cCcccchhhhhhHHH
Q 038616 323 ICPKCIQEFLTSQSF 337 (431)
Q Consensus 323 tCPKCN~VFdTSQkF 337 (431)
+||.|.++...+.++
T Consensus 2 ~CP~C~~~V~~~~~~ 16 (26)
T PF10571_consen 2 TCPECGAEVPESAKF 16 (26)
T ss_pred cCCCCcCCchhhcCc
Confidence 577777777666554
No 72
>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=29.16 E-value=22 Score=32.21 Aligned_cols=15 Identities=20% Similarity=0.368 Sum_probs=13.5
Q ss_pred CcccCcccchhhhhh
Q 038616 320 GPYICPKCIQEFLTS 334 (431)
Q Consensus 320 GPYtCPKCN~VFdTS 334 (431)
-|-+||||+.+|.-+
T Consensus 25 ~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 25 RPAVSPYTGEQFPPE 39 (129)
T ss_pred CCccCCCcCCccCcc
Confidence 799999999998776
No 73
>COG4640 Predicted membrane protein [Function unknown]
Probab=28.85 E-value=27 Score=36.97 Aligned_cols=34 Identities=26% Similarity=0.350 Sum_probs=26.2
Q ss_pred ccccCcccCcccchhhhhhHHHHHHHhhhccccccHHHH
Q 038616 316 RKKYGPYICPKCIQEFLTSQSFAAHVASAHYRFETAAER 354 (431)
Q Consensus 316 ~~KyGPYtCPKCN~VFdTSQkFAAHmsS~HYK~ET~eER 354 (431)
++-.+.+.|++|++.|..-|+.|.-.. +|+.++|
T Consensus 10 qk~Ed~~qC~qCG~~~t~~~sqan~~t-----n~i~~tr 43 (465)
T COG4640 10 QKAEDDVQCTQCGHKFTSRQSQANKST-----NEIIQTR 43 (465)
T ss_pred ccccccccccccCCcCCchhhhhhHHH-----HHHHHhh
Confidence 344567789999999999999887544 4677777
No 74
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=28.82 E-value=19 Score=25.81 Aligned_cols=14 Identities=29% Similarity=0.674 Sum_probs=11.0
Q ss_pred cccCcccchhhhhh
Q 038616 321 PYICPKCIQEFLTS 334 (431)
Q Consensus 321 PYtCPKCN~VFdTS 334 (431)
.|.|+.|+..|+-.
T Consensus 3 ~y~C~~CG~~~~~~ 16 (46)
T PRK00398 3 EYKCARCGREVELD 16 (46)
T ss_pred EEECCCCCCEEEEC
Confidence 58899999888654
No 75
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=28.20 E-value=23 Score=25.41 Aligned_cols=16 Identities=19% Similarity=0.482 Sum_probs=13.1
Q ss_pred cccCcccchhhhhhHH
Q 038616 321 PYICPKCIQEFLTSQS 336 (431)
Q Consensus 321 PYtCPKCN~VFdTSQk 336 (431)
|++|..|+++|=.+..
T Consensus 12 ~f~C~~C~~~FC~~HR 27 (39)
T smart00154 12 GFKCRHCGNLFCGEHR 27 (39)
T ss_pred CeECCccCCccccccC
Confidence 8899999999965543
No 76
>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=27.69 E-value=40 Score=29.95 Aligned_cols=10 Identities=30% Similarity=1.006 Sum_probs=7.9
Q ss_pred cccCcccchh
Q 038616 321 PYICPKCIQE 330 (431)
Q Consensus 321 PYtCPKCN~V 330 (431)
-|+||.|+.+
T Consensus 128 ~F~Cp~Cg~~ 137 (158)
T TIGR00373 128 NFTCPRCGAM 137 (158)
T ss_pred CCcCCCCCCE
Confidence 4888888877
No 77
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=26.56 E-value=20 Score=38.18 Aligned_cols=43 Identities=14% Similarity=0.129 Sum_probs=31.3
Q ss_pred CeeeeccccccCcccCcccchhhhhhHHHHHHHh-hhccccccHH
Q 038616 309 GVIHSLSRKKYGPYICPKCIQEFLTSQSFAAHVA-SAHYRFETAA 352 (431)
Q Consensus 309 GrtHSLP~~KyGPYtCPKCN~VFdTSQkFAAHms-S~HYK~ET~e 352 (431)
|+.-+|-.+.-|-+ |++|.+.|.|+.++-.|.- ..|-|+++++
T Consensus 260 ~al~alglk~gGt~-~~ra~rlf~Tk~~~l~~L~~~~~~kn~s~~ 303 (497)
T KOG2636|consen 260 SALTALGLKCGGTL-HERAQRLFSTKSKSLSHLDTKLFAKNPSKK 303 (497)
T ss_pred HHHHHHHHhcCCee-cHHHHhhhhhcCcchhhhhhhhhccCcccc
Confidence 45556666666654 8899999999999977765 3466677766
No 78
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=26.20 E-value=51 Score=33.34 Aligned_cols=32 Identities=19% Similarity=0.277 Sum_probs=18.5
Q ss_pred CCceeecCC-------ccchhHHHHHHHhhhccccccch
Q 038616 376 GSLTIVHGR-------SFKNIADWRRKEKRAAVKIEDGD 407 (431)
Q Consensus 376 G~lqeVhg~-------S~kiikd~~r~~k~a~~k~e~~~ 407 (431)
|+..|+-.. .++-.|.|..|-++|..|-...|
T Consensus 72 gsf~el~~~l~~~dPL~F~d~k~Y~~rL~~a~~~tg~~d 110 (294)
T COG0777 72 GSFEELDSPLEPKDPLKFPDSKKYKDRLEAARKKTGLDD 110 (294)
T ss_pred CcceecccCCCcCCcccCCcchhhHHHHHHHHhhcCCCc
Confidence 566666553 33334668877777765554433
No 79
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=26.11 E-value=18 Score=25.75 Aligned_cols=12 Identities=42% Similarity=0.913 Sum_probs=9.6
Q ss_pred ccCcccchhhhh
Q 038616 322 YICPKCIQEFLT 333 (431)
Q Consensus 322 YtCPKCN~VFdT 333 (431)
.+||+|+++|..
T Consensus 2 r~C~~Cg~~Yh~ 13 (36)
T PF05191_consen 2 RICPKCGRIYHI 13 (36)
T ss_dssp EEETTTTEEEET
T ss_pred cCcCCCCCcccc
Confidence 479999998853
No 80
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=26.04 E-value=53 Score=29.90 Aligned_cols=12 Identities=25% Similarity=0.766 Sum_probs=9.0
Q ss_pred cccCcccchhhh
Q 038616 321 PYICPKCIQEFL 332 (431)
Q Consensus 321 PYtCPKCN~VFd 332 (431)
-|+||.|+.+..
T Consensus 136 ~F~Cp~Cg~~L~ 147 (178)
T PRK06266 136 GFRCPQCGEMLE 147 (178)
T ss_pred CCcCCCCCCCCe
Confidence 488888887754
No 81
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=25.51 E-value=79 Score=29.55 Aligned_cols=44 Identities=27% Similarity=0.435 Sum_probs=29.8
Q ss_pred cCCccchhHHHHHHHhhhcccccc-c-hh--hHhhcCCCcceeeceee
Q 038616 382 HGRSFKNIADWRRKEKRAAVKIED-G-DD--QVQKQGEDGLTIGGIAV 425 (431)
Q Consensus 382 hg~S~kiikd~~r~~k~a~~k~e~-~-~d--~vqk~g~~~~~~~~~~~ 425 (431)
+|+....++.-+.=||.-++|.-. + ++ .--.-+.+|||+|-|++
T Consensus 114 ~g~~~P~~~~akkLEk~LgIkL~e~~~~~~~~~~~~~~~~~TLGdiv~ 161 (165)
T COG1813 114 RGEATPNIKVAKKLEKLLGIKLVEKVDEEEEGPKGKDDDGLTLGDIVR 161 (165)
T ss_pred hcccCccHHHHHHHHHHhCceeeeeccccccccccCCcCCCcccceEE
Confidence 667777777777777777776422 1 11 13456789999999985
No 82
>PLN03086 PRLI-interacting factor K; Provisional
Probab=25.46 E-value=41 Score=36.26 Aligned_cols=21 Identities=29% Similarity=0.634 Sum_probs=12.1
Q ss_pred CcccCcccchhhhhhHHHHHHHh
Q 038616 320 GPYICPKCIQEFLTSQSFAAHVA 342 (431)
Q Consensus 320 GPYtCPKCN~VFdTSQkFAAHms 342 (431)
.||.|| |++.| ....++.|+.
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~ 497 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQA 497 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhh
Confidence 466666 66544 4456666654
No 83
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=25.21 E-value=30 Score=24.31 Aligned_cols=15 Identities=33% Similarity=0.516 Sum_probs=11.9
Q ss_pred ccCcccCcccchhhh
Q 038616 318 KYGPYICPKCIQEFL 332 (431)
Q Consensus 318 KyGPYtCPKCN~VFd 332 (431)
+-+.-.||+|+.+|.
T Consensus 22 ~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 22 GGRKVRCPKCGHVFR 36 (37)
T ss_pred CCcEEECCCCCcEee
Confidence 345678999999985
No 84
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=25.20 E-value=34 Score=24.66 Aligned_cols=11 Identities=36% Similarity=1.174 Sum_probs=8.2
Q ss_pred cCcccCcccchh
Q 038616 319 YGPYICPKCIQE 330 (431)
Q Consensus 319 yGPYtCPKCN~V 330 (431)
.| ++||+|+..
T Consensus 17 ~g-~~CP~Cg~~ 27 (46)
T PF12760_consen 17 DG-FVCPHCGST 27 (46)
T ss_pred CC-CCCCCCCCe
Confidence 45 669999964
No 85
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=25.04 E-value=12 Score=26.18 Aligned_cols=20 Identities=25% Similarity=0.833 Sum_probs=14.7
Q ss_pred ccCcccchhhhhhHHHHHHHh
Q 038616 322 YICPKCIQEFLTSQSFAAHVA 342 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAAHms 342 (431)
|+|--|++.| +...+.+|.+
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 6899999999 6677788876
No 86
>PRK03922 hypothetical protein; Provisional
Probab=25.03 E-value=30 Score=30.89 Aligned_cols=16 Identities=44% Similarity=0.862 Sum_probs=13.1
Q ss_pred cCcccCcccchhhhhh
Q 038616 319 YGPYICPKCIQEFLTS 334 (431)
Q Consensus 319 yGPYtCPKCN~VFdTS 334 (431)
-|-.+||+|+..|+.-
T Consensus 47 vG~~~cP~cge~~~~a 62 (113)
T PRK03922 47 VGLTICPKCGEPFDSA 62 (113)
T ss_pred cCcccCCCCCCcCCcE
Confidence 3678999999999854
No 87
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.63 E-value=75 Score=27.41 Aligned_cols=18 Identities=22% Similarity=0.617 Sum_probs=12.2
Q ss_pred cCcccchhhhhhHHHHHH
Q 038616 323 ICPKCIQEFLTSQSFAAH 340 (431)
Q Consensus 323 tCPKCN~VFdTSQkFAAH 340 (431)
-||+|.+|.-.--.+-.=
T Consensus 23 ~CPrCrGVWLDrGELdKl 40 (88)
T COG3809 23 YCPRCRGVWLDRGELDKL 40 (88)
T ss_pred eCCccccEeecchhHHHH
Confidence 399999987655444333
No 88
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.34 E-value=31 Score=32.10 Aligned_cols=11 Identities=36% Similarity=1.132 Sum_probs=9.5
Q ss_pred ccCcccchhhh
Q 038616 322 YICPKCIQEFL 332 (431)
Q Consensus 322 YtCPKCN~VFd 332 (431)
|+||+||....
T Consensus 133 F~Cp~Cg~~L~ 143 (176)
T COG1675 133 FTCPKCGEDLE 143 (176)
T ss_pred CCCCCCCchhh
Confidence 99999998754
No 89
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=24.32 E-value=28 Score=31.03 Aligned_cols=14 Identities=29% Similarity=0.667 Sum_probs=12.2
Q ss_pred cccCcccchhhhhh
Q 038616 321 PYICPKCIQEFLTS 334 (431)
Q Consensus 321 PYtCPKCN~VFdTS 334 (431)
|..|-+|+.||++-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 67899999999983
No 90
>PF09965 DUF2199: Uncharacterized protein conserved in bacteria (DUF2199); InterPro: IPR018697 This domain has no known function.
Probab=24.29 E-value=24 Score=31.82 Aligned_cols=36 Identities=25% Similarity=0.333 Sum_probs=28.6
Q ss_pred ccCcccchhhhhhHHHHHHHhhhccccccHHHHHHHH
Q 038616 322 YICPKCIQEFLTSQSFAAHVASAHYRFETAAERKKRL 358 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAAHmsS~HYK~ET~eERKKRl 358 (431)
|+|..|+..++..-.|+.-.-- .|---.++||.+|.
T Consensus 1 y~C~~Cg~~h~~~P~~~~~~Pd-~~~~~~~~er~~r~ 36 (148)
T PF09965_consen 1 YTCSCCGEEHEGLPSLGFDAPD-YYYELPEEEREARA 36 (148)
T ss_pred CCCCcCCccCCCCcccccCCCh-hhhhCCHHHhhhhc
Confidence 8999999999988877765553 66666788888876
No 91
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=24.15 E-value=28 Score=30.65 Aligned_cols=13 Identities=31% Similarity=0.912 Sum_probs=10.0
Q ss_pred CcccCcccchhhh
Q 038616 320 GPYICPKCIQEFL 332 (431)
Q Consensus 320 GPYtCPKCN~VFd 332 (431)
.-||||.||++-.
T Consensus 21 k~FtCp~Cghe~v 33 (104)
T COG4888 21 KTFTCPRCGHEKV 33 (104)
T ss_pred ceEecCccCCeee
Confidence 3499999997643
No 92
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=23.63 E-value=32 Score=29.24 Aligned_cols=23 Identities=26% Similarity=0.376 Sum_probs=16.8
Q ss_pred eeeeccccccCcccCcccchhhh
Q 038616 310 VIHSLSRKKYGPYICPKCIQEFL 332 (431)
Q Consensus 310 rtHSLP~~KyGPYtCPKCN~VFd 332 (431)
-++-+=-+|..|+.|+.|+.+|.
T Consensus 68 ~v~W~~l~~g~~~rC~eCG~~fk 90 (97)
T cd00924 68 DVIWMWLEKGKPKRCPECGHVFK 90 (97)
T ss_pred eEEEEEEeCCCceeCCCCCcEEE
Confidence 34444445558999999999984
No 93
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=23.39 E-value=30 Score=32.27 Aligned_cols=12 Identities=42% Similarity=1.054 Sum_probs=10.0
Q ss_pred ccCcccchhhhh
Q 038616 322 YICPKCIQEFLT 333 (431)
Q Consensus 322 YtCPKCN~VFdT 333 (431)
|.||+|+++|=-
T Consensus 131 ~~C~~CgkiYW~ 142 (165)
T COG1656 131 YRCPKCGKIYWK 142 (165)
T ss_pred eECCCCcccccC
Confidence 679999999853
No 94
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=23.25 E-value=27 Score=22.89 Aligned_cols=18 Identities=28% Similarity=0.674 Sum_probs=13.6
Q ss_pred ccCcccchhhhhhHHHHH
Q 038616 322 YICPKCIQEFLTSQSFAA 339 (431)
Q Consensus 322 YtCPKCN~VFdTSQkFAA 339 (431)
-+||.|+...+...+|-.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~ 20 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCP 20 (26)
T ss_pred CCCcccCCcCCcccccCh
Confidence 479999998777776643
No 95
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=22.99 E-value=25 Score=25.16 Aligned_cols=19 Identities=21% Similarity=0.597 Sum_probs=12.1
Q ss_pred CcccCcccchhhhhhHHHH
Q 038616 320 GPYICPKCIQEFLTSQSFA 338 (431)
Q Consensus 320 GPYtCPKCN~VFdTSQkFA 338 (431)
=|++|+.|++.|=....+.
T Consensus 12 ~~~~C~~C~~~FC~~Hr~~ 30 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRLP 30 (43)
T ss_dssp SHEE-TTTS-EE-TTTHST
T ss_pred CCeECCCCCcccCccccCc
Confidence 3899999999997665543
No 96
>PRK06921 hypothetical protein; Provisional
Probab=22.79 E-value=39 Score=31.83 Aligned_cols=10 Identities=50% Similarity=1.202 Sum_probs=8.4
Q ss_pred cccCcccchh
Q 038616 321 PYICPKCIQE 330 (431)
Q Consensus 321 PYtCPKCN~V 330 (431)
.|+||+|+..
T Consensus 32 ~~~Cp~C~dt 41 (266)
T PRK06921 32 RYDCPKCKDR 41 (266)
T ss_pred CCCCCCCCCC
Confidence 6999999864
No 97
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=22.73 E-value=62 Score=26.37 Aligned_cols=24 Identities=25% Similarity=0.520 Sum_probs=22.2
Q ss_pred ccC----cccchhhhhhHHHHHHHhhhc
Q 038616 322 YIC----PKCIQEFLTSQSFAAHVASAH 345 (431)
Q Consensus 322 YtC----PKCN~VFdTSQkFAAHmsS~H 345 (431)
|.| +.|.-++.+..+.-.|+...|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 999 999999999999999998755
No 98
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=22.70 E-value=61 Score=21.60 Aligned_cols=19 Identities=26% Similarity=0.726 Sum_probs=15.1
Q ss_pred cCcccchhhhhhHHHHHHHh
Q 038616 323 ICPKCIQEFLTSQSFAAHVA 342 (431)
Q Consensus 323 tCPKCN~VFdTSQkFAAHms 342 (431)
.||-|++-+ +...+-+|.-
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 699999998 6667777765
No 99
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.66 E-value=76 Score=25.32 Aligned_cols=34 Identities=32% Similarity=0.560 Sum_probs=27.0
Q ss_pred cCcccchhhhhhHHHHHHHhhhccccccHHHHHHHHHH
Q 038616 323 ICPKCIQEFLTSQSFAAHVASAHYRFETAAERKKRLAA 360 (431)
Q Consensus 323 tCPKCN~VFdTSQkFAAHmsS~HYK~ET~eERKKRl~A 360 (431)
+||-|.+-|.-.-|.|.---++-|-+ ||=+|+++
T Consensus 14 ICpvCqRPFsWRkKW~~cWDeVKyCS----eRCrr~Rs 47 (54)
T COG4338 14 ICPVCQRPFSWRKKWARCWDEVKYCS----ERCRRLRS 47 (54)
T ss_pred hhhhhcCchHHHHHHHHHHHHHHHHH----HHHHHHhc
Confidence 89999999999999998877755544 56667754
No 100
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=22.29 E-value=35 Score=29.35 Aligned_cols=12 Identities=42% Similarity=1.021 Sum_probs=11.0
Q ss_pred CcccCcccchhh
Q 038616 320 GPYICPKCIQEF 331 (431)
Q Consensus 320 GPYtCPKCN~VF 331 (431)
|-|.|++|++.+
T Consensus 50 ~~~~C~~C~~~~ 61 (166)
T cd04476 50 GTYRCEKCNKSV 61 (166)
T ss_pred CcEECCCCCCcC
Confidence 789999999986
No 101
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=21.80 E-value=35 Score=30.89 Aligned_cols=15 Identities=33% Similarity=0.660 Sum_probs=12.8
Q ss_pred cccCcccchhhhhhH
Q 038616 321 PYICPKCIQEFLTSQ 335 (431)
Q Consensus 321 PYtCPKCN~VFdTSQ 335 (431)
|..|-+|+++|+...
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678999999999764
No 102
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=20.85 E-value=52 Score=35.19 Aligned_cols=36 Identities=25% Similarity=0.440 Sum_probs=30.5
Q ss_pred ccCcccCcccchhhhhhHHHHHHHhhhccccccHHHH
Q 038616 318 KYGPYICPKCIQEFLTSQSFAAHVASAHYRFETAAER 354 (431)
Q Consensus 318 KyGPYtCPKCN~VFdTSQkFAAHmsS~HYK~ET~eER 354 (431)
-.|-|.|..|.|-|.+--.+--|.++ |-+.+..++.
T Consensus 353 s~gi~~C~~C~KkFrRqAYLrKHqlt-hq~~~~~k~~ 388 (500)
T KOG3993|consen 353 SSGIFSCHTCGKKFRRQAYLRKHQLT-HQRAPLAKEK 388 (500)
T ss_pred cCceeecHHhhhhhHHHHHHHHhHHh-hhccccchhc
Confidence 34579999999999999999999996 8888876653
No 103
>PTZ00222 60S ribosomal protein L7a; Provisional
Probab=20.33 E-value=74 Score=31.76 Aligned_cols=23 Identities=30% Similarity=0.387 Sum_probs=19.4
Q ss_pred hccccccHHHHHHHHHHHhhhhh
Q 038616 344 AHYRFETAAERKKRLAAKYKKKN 366 (431)
Q Consensus 344 ~HYK~ET~eERKKRl~Ar~kKr~ 366 (431)
..|+-||..|+|.||.++-.++-
T Consensus 96 ~KYrPEtk~~kk~Rl~~~A~~~~ 118 (263)
T PTZ00222 96 KKYAPETRKARRDRLHKVAEEKK 118 (263)
T ss_pred HHcCCccHHHHHHHHHHHHHHHh
Confidence 48999999999999998766543
No 104
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=20.31 E-value=59 Score=38.59 Aligned_cols=27 Identities=26% Similarity=0.447 Sum_probs=24.6
Q ss_pred ccCcccCcccchhhhhhHHHHHHHhhh
Q 038616 318 KYGPYICPKCIQEFLTSQSFAAHVASA 344 (431)
Q Consensus 318 KyGPYtCPKCN~VFdTSQkFAAHmsS~ 344 (431)
.|+||.|-.|+-.+.|-+.+..||-|.
T Consensus 515 ~~~p~~C~~C~~stttng~LsihlqS~ 541 (1406)
T KOG1146|consen 515 PGKPYPCRACNYSTTTNGNLSIHLQSD 541 (1406)
T ss_pred CCCcccceeeeeeeecchHHHHHHHHH
Confidence 468999999999999999999999973
Done!