Query 041626
Match_columns 193
No_of_seqs 164 out of 1042
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 09:06:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041626.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041626hhsearch_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 98.0 2.1E-06 4.5E-11 76.9 2.3 35 59-93 209-243 (279)
2 PHA00616 hypothetical protein 98.0 1.7E-06 3.6E-11 58.5 0.8 29 65-93 1-29 (44)
3 PF00096 zf-C2H2: Zinc finger, 97.9 3.4E-06 7.4E-11 47.6 0.7 23 66-88 1-23 (23)
4 PHA02768 hypothetical protein; 97.9 4.2E-06 9.2E-11 58.9 1.3 24 66-89 6-29 (55)
5 PF13912 zf-C2H2_6: C2H2-type 97.7 1.7E-05 3.6E-10 46.4 1.0 26 65-90 1-26 (27)
6 PF13894 zf-C2H2_4: C2H2-type 97.6 3E-05 6.5E-10 42.8 1.0 24 66-89 1-24 (24)
7 KOG2462 C2H2-type Zn-finger pr 97.5 2.8E-05 6.1E-10 69.7 1.1 30 64-93 186-215 (279)
8 KOG1074 Transcriptional repres 97.5 4E-05 8.6E-10 77.2 1.4 35 58-92 626-660 (958)
9 KOG3623 Homeobox transcription 97.5 4.4E-05 9.6E-10 76.3 1.4 35 59-93 916-950 (1007)
10 smart00355 ZnF_C2H2 zinc finge 97.3 0.00013 2.8E-09 40.3 1.5 24 66-89 1-24 (26)
11 KOG3623 Homeobox transcription 96.9 0.0003 6.6E-09 70.5 0.6 33 61-93 277-309 (1007)
12 PF13465 zf-H2C2_2: Zinc-finge 96.7 0.00047 1E-08 40.9 0.4 18 60-77 9-26 (26)
13 PF12874 zf-met: Zinc-finger o 96.4 0.0013 2.8E-08 37.6 0.7 23 66-88 1-23 (25)
14 PF09237 GAGA: GAGA factor; I 96.3 0.0019 4.1E-08 45.5 1.3 34 60-93 19-52 (54)
15 KOG3576 Ovo and related transc 96.3 0.001 2.2E-08 58.7 -0.2 34 60-93 140-173 (267)
16 PHA00732 hypothetical protein 96.1 0.0031 6.8E-08 46.7 1.6 26 65-90 1-27 (79)
17 PF12171 zf-C2H2_jaz: Zinc-fin 95.7 0.0034 7.4E-08 37.0 0.4 24 65-88 1-24 (27)
18 KOG1074 Transcriptional repres 95.6 0.0054 1.2E-07 62.3 1.7 28 66-93 880-907 (958)
19 PHA00733 hypothetical protein 95.2 0.012 2.6E-07 46.9 1.9 28 61-88 69-96 (128)
20 PF13909 zf-H2C2_5: C2H2-type 95.1 0.0076 1.6E-07 34.4 0.4 23 66-89 1-23 (24)
21 COG5189 SFP1 Putative transcri 94.6 0.012 2.6E-07 54.8 0.7 35 52-86 385-419 (423)
22 PF12756 zf-C2H2_2: C2H2 type 93.7 0.033 7.1E-07 39.6 1.3 25 65-89 50-74 (100)
23 PF13913 zf-C2HC_2: zinc-finge 92.7 0.059 1.3E-06 31.9 1.1 21 66-87 3-23 (25)
24 smart00451 ZnF_U1 U1-like zinc 92.6 0.058 1.3E-06 32.7 1.1 23 65-87 3-25 (35)
25 PHA00733 hypothetical protein 92.2 0.083 1.8E-06 42.0 1.8 27 63-89 97-123 (128)
26 KOG3576 Ovo and related transc 91.8 0.064 1.4E-06 47.6 0.8 32 58-89 166-198 (267)
27 KOG3993 Transcription factor ( 91.5 0.1 2.2E-06 50.1 1.7 25 65-89 295-319 (500)
28 PF13465 zf-H2C2_2: Zinc-finge 91.1 0.13 2.8E-06 30.3 1.4 14 80-93 1-14 (26)
29 KOG3993 Transcription factor ( 89.8 0.11 2.5E-06 49.8 0.5 34 57-90 348-381 (500)
30 PF05605 zf-Di19: Drought indu 83.3 0.84 1.8E-05 30.8 1.8 26 65-91 2-28 (54)
31 PF05605 zf-Di19: Drought indu 83.1 0.88 1.9E-05 30.7 1.9 21 67-89 33-53 (54)
32 KOG3608 Zn finger proteins [Ge 81.2 0.78 1.7E-05 43.6 1.3 32 58-89 285-316 (467)
33 PF12756 zf-C2H2_2: C2H2 type 79.2 0.61 1.3E-05 32.9 0.0 24 67-90 1-24 (100)
34 PRK04860 hypothetical protein; 78.3 1.2 2.5E-05 37.1 1.4 26 64-93 118-143 (160)
35 PHA02768 hypothetical protein; 74.3 1.3 2.8E-05 31.3 0.6 19 64-82 30-48 (55)
36 PLN03086 PRLI-interacting fact 73.1 2.1 4.6E-05 42.2 1.9 25 64-89 452-476 (567)
37 PHA00732 hypothetical protein 72.4 1.7 3.8E-05 32.1 0.9 22 65-89 27-48 (79)
38 smart00614 ZnF_BED BED zinc fi 72.0 2.4 5.2E-05 28.2 1.4 23 67-89 20-48 (50)
39 KOG4167 Predicted DNA-binding 70.3 1.1 2.4E-05 45.8 -0.7 33 58-90 785-817 (907)
40 PF02892 zf-BED: BED zinc fing 70.3 2.6 5.7E-05 26.8 1.3 26 63-88 14-44 (45)
41 KOG2893 Zn finger protein [Gen 68.3 1.1 2.4E-05 40.8 -1.1 40 50-89 19-59 (341)
42 PF12013 DUF3505: Protein of u 67.4 2.9 6.3E-05 31.6 1.2 25 66-90 81-109 (109)
43 COG4049 Uncharacterized protei 66.4 2 4.4E-05 31.1 0.1 28 62-89 14-42 (65)
44 PLN03086 PRLI-interacting fact 62.9 4.4 9.6E-05 40.1 1.8 28 64-93 477-504 (567)
45 KOG2071 mRNA cleavage and poly 60.9 4.7 0.0001 40.0 1.6 33 61-93 414-446 (579)
46 COG5048 FOG: Zn-finger [Genera 58.4 4.6 9.9E-05 34.2 0.9 35 59-93 313-351 (467)
47 PF05443 ROS_MUCR: ROS/MUCR tr 55.1 5.7 0.00012 32.3 0.9 25 66-93 73-97 (132)
48 KOG3608 Zn finger proteins [Ge 53.9 7 0.00015 37.4 1.4 26 62-87 349-374 (467)
49 COG5189 SFP1 Putative transcri 52.2 10 0.00023 35.8 2.2 31 62-92 346-379 (423)
50 PF09986 DUF2225: Uncharacteri 51.9 3.7 8E-05 35.1 -0.7 25 63-87 3-27 (214)
51 KOG2482 Predicted C2H2-type Zn 50.6 10 0.00022 36.1 1.9 29 65-93 195-225 (423)
52 PF09845 DUF2072: Zn-ribbon co 47.4 9 0.00019 31.4 0.9 15 65-79 1-15 (131)
53 smart00734 ZnF_Rad18 Rad18-lik 46.0 12 0.00026 22.3 1.1 19 67-86 3-21 (26)
54 COG3677 Transposase and inacti 39.6 16 0.00034 29.3 1.2 23 56-78 44-66 (129)
55 smart00834 CxxC_CXXC_SSSS Puta 38.2 12 0.00026 23.1 0.3 17 65-81 5-21 (41)
56 PF13878 zf-C2H2_3: zinc-finge 38.1 18 0.00039 23.6 1.1 24 66-89 14-39 (41)
57 PF09538 FYDLN_acid: Protein o 37.6 16 0.00034 28.7 0.9 17 61-78 6-22 (108)
58 COG4957 Predicted transcriptio 37.0 15 0.00032 30.7 0.7 24 67-93 78-101 (148)
59 PF12230 PRP21_like_P: Pre-mRN 34.1 13 0.00029 31.6 0.0 29 62-91 165-193 (229)
60 PF04959 ARS2: Arsenite-resist 31.0 13 0.00029 32.4 -0.5 31 62-92 74-104 (214)
61 PRK00464 nrdR transcriptional 30.6 18 0.00038 30.0 0.2 21 65-85 28-48 (154)
62 PF10571 UPF0547: Uncharacteri 30.1 24 0.00052 21.2 0.6 11 66-76 15-25 (26)
63 PRK04860 hypothetical protein; 30.0 20 0.00044 29.7 0.4 22 58-79 136-157 (160)
64 TIGR02605 CxxC_CxxC_SSSS putat 30.0 19 0.00042 23.6 0.2 16 65-80 5-20 (52)
65 smart00154 ZnF_AN1 AN1-like Zi 29.1 24 0.00052 22.8 0.5 14 65-78 12-25 (39)
66 PF09723 Zn-ribbon_8: Zinc rib 29.1 20 0.00043 23.2 0.2 19 65-83 5-23 (42)
67 COG5048 FOG: Zn-finger [Genera 28.0 38 0.00083 28.6 1.7 34 60-93 28-61 (467)
68 KOG2636 Splicing factor 3a, su 28.0 31 0.00067 33.8 1.3 24 63-86 399-423 (497)
69 KOG3408 U1-like Zn-finger-cont 27.4 27 0.00058 28.7 0.7 26 62-87 54-79 (129)
70 KOG1146 Homeobox protein [Gene 26.2 39 0.00085 37.0 1.8 37 64-101 1328-1365(1406)
71 COG3364 Zn-ribbon containing p 26.1 32 0.00069 27.6 0.9 16 65-80 2-17 (112)
72 KOG0717 Molecular chaperone (D 26.1 28 0.00062 34.2 0.7 22 66-87 293-314 (508)
73 PTZ00448 hypothetical protein; 26.1 35 0.00075 32.4 1.3 23 65-87 314-336 (373)
74 PF15269 zf-C2H2_7: Zinc-finge 25.8 53 0.0012 23.0 1.8 25 65-89 20-44 (54)
75 PLN03239 histone acetyltransfe 25.7 31 0.00068 32.5 0.9 47 37-86 81-127 (351)
76 COG5188 PRP9 Splicing factor 3 25.5 25 0.00054 33.8 0.2 35 56-91 230-266 (470)
77 PHA00626 hypothetical protein 25.4 30 0.00064 25.0 0.5 20 63-83 21-40 (59)
78 KOG4124 Putative transcription 25.2 36 0.00079 32.6 1.2 28 64-92 212-240 (442)
79 PF07754 DUF1610: Domain of un 25.1 29 0.00062 20.8 0.3 10 64-73 15-24 (24)
80 PF01428 zf-AN1: AN1-like Zinc 24.4 23 0.0005 22.9 -0.2 15 64-78 12-26 (43)
81 PF04423 Rad50_zn_hook: Rad50 24.2 26 0.00057 23.5 0.1 11 67-77 22-32 (54)
82 PF04780 DUF629: Protein of un 24.0 38 0.00081 33.0 1.1 26 66-91 58-84 (466)
83 smart00064 FYVE Protein presen 22.8 50 0.0011 22.6 1.2 14 63-76 24-37 (68)
84 TIGR02300 FYDLN_acid conserved 22.7 40 0.00086 27.7 0.8 12 66-77 10-21 (129)
85 COG4640 Predicted membrane pro 22.3 50 0.0011 32.1 1.5 23 62-84 12-34 (465)
86 KOG1842 FYVE finger-containing 22.1 38 0.00083 33.2 0.7 27 66-92 16-43 (505)
87 PF14353 CpXC: CpXC protein 21.4 22 0.00047 27.5 -0.9 23 65-87 38-60 (128)
88 PF10276 zf-CHCC: Zinc-finger 21.1 32 0.00069 22.7 0.0 12 65-76 29-40 (40)
89 KOG4173 Alpha-SNAP protein [In 20.5 30 0.00066 31.0 -0.3 20 67-86 108-127 (253)
90 KOG2593 Transcription initiati 20.1 41 0.00088 32.6 0.5 21 62-82 125-145 (436)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=98.05 E-value=2.1e-06 Score=76.89 Aligned_cols=35 Identities=20% Similarity=0.498 Sum_probs=28.3
Q ss_pred CCCCCcccccCcccccccCcchHHHHhhhcCCcCc
Q 041626 59 FSWPPRSYTCSFCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 59 ~~~~eKpYkC~~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
.+++||||.|+.|+|+|..+++|+.||++|.+.|.
T Consensus 209 THTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~ 243 (279)
T KOG2462|consen 209 THTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKK 243 (279)
T ss_pred cccCCCCccCCcccchhcchHHHHHHHHhhcCCcc
Confidence 56788888888888888888888888888887764
No 2
>PHA00616 hypothetical protein
Probab=98.02 E-value=1.7e-06 Score=58.48 Aligned_cols=29 Identities=21% Similarity=0.410 Sum_probs=27.5
Q ss_pred ccccCcccccccCcchHHHHhhhcCCcCc
Q 041626 65 SYTCSFCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
||+|..||+.|..++.|..|++.|+++++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 69999999999999999999999999875
No 3
>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=97.91 E-value=3.4e-06 Score=47.64 Aligned_cols=23 Identities=39% Similarity=0.856 Sum_probs=21.8
Q ss_pred cccCcccccccCcchHHHHhhhc
Q 041626 66 YTCSFCKREFRSAQALGGHMNVH 88 (193)
Q Consensus 66 YkC~~CgKsF~skqaL~~Hmr~H 88 (193)
|+|+.|++.|+++..|..||+.|
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 78999999999999999999876
No 4
>PHA02768 hypothetical protein; Provisional
Probab=97.90 E-value=4.2e-06 Score=58.87 Aligned_cols=24 Identities=21% Similarity=0.617 Sum_probs=23.5
Q ss_pred cccCcccccccCcchHHHHhhhcC
Q 041626 66 YTCSFCKREFRSAQALGGHMNVHR 89 (193)
Q Consensus 66 YkC~~CgKsF~skqaL~~Hmr~Ht 89 (193)
|+|+.|||.|++.++|..||++|+
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC
Confidence 799999999999999999999999
No 5
>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=97.67 E-value=1.7e-05 Score=46.40 Aligned_cols=26 Identities=31% Similarity=0.598 Sum_probs=24.2
Q ss_pred ccccCcccccccCcchHHHHhhhcCC
Q 041626 65 SYTCSFCKREFRSAQALGGHMNVHRR 90 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~Hmr~Htg 90 (193)
||+|..|++.|.+..+|..|++.|..
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 68999999999999999999999864
No 6
>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=97.56 E-value=3e-05 Score=42.85 Aligned_cols=24 Identities=38% Similarity=0.891 Sum_probs=20.3
Q ss_pred cccCcccccccCcchHHHHhhhcC
Q 041626 66 YTCSFCKREFRSAQALGGHMNVHR 89 (193)
Q Consensus 66 YkC~~CgKsF~skqaL~~Hmr~Ht 89 (193)
|.|++|++.|.+...|..|++.|.
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 689999999999999999998873
No 7
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=97.54 E-value=2.8e-05 Score=69.72 Aligned_cols=30 Identities=23% Similarity=0.617 Sum_probs=25.8
Q ss_pred cccccCcccccccCcchHHHHhhhcCCcCc
Q 041626 64 RSYTCSFCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 64 KpYkC~~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
-+++|.+|||.|.+.--|++|+|+|+||||
T Consensus 186 l~c~C~iCGKaFSRPWLLQGHiRTHTGEKP 215 (279)
T KOG2462|consen 186 LPCECGICGKAFSRPWLLQGHIRTHTGEKP 215 (279)
T ss_pred CCcccccccccccchHHhhcccccccCCCC
Confidence 467888888888888888888888988887
No 8
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=97.48 E-value=4e-05 Score=77.17 Aligned_cols=35 Identities=29% Similarity=0.584 Sum_probs=32.1
Q ss_pred CCCCCCcccccCcccccccCcchHHHHhhhcCCcC
Q 041626 58 GFSWPPRSYTCSFCKREFRSAQALGGHMNVHRRDR 92 (193)
Q Consensus 58 ~~~~~eKpYkC~~CgKsF~skqaL~~Hmr~HtgER 92 (193)
+.+.+||||+|++|||+|+++.+|+.||-+|....
T Consensus 626 rtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p 660 (958)
T KOG1074|consen 626 RTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKP 660 (958)
T ss_pred hcccCcCccccccccchhccccchhhcccccccCc
Confidence 56889999999999999999999999999998554
No 9
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=97.45 E-value=4.4e-05 Score=76.30 Aligned_cols=35 Identities=26% Similarity=0.578 Sum_probs=33.0
Q ss_pred CCCCCcccccCcccccccCcchHHHHhhhcCCcCc
Q 041626 59 FSWPPRSYTCSFCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 59 ~~~~eKpYkC~~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
.+++.|||+|.+|.|+|..+.+|..|+|.|.||||
T Consensus 916 EHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKP 950 (1007)
T KOG3623|consen 916 EHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKP 950 (1007)
T ss_pred hhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCc
Confidence 47889999999999999999999999999999998
No 10
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.29 E-value=0.00013 Score=40.34 Aligned_cols=24 Identities=42% Similarity=0.823 Sum_probs=22.5
Q ss_pred cccCcccccccCcchHHHHhhhcC
Q 041626 66 YTCSFCKREFRSAQALGGHMNVHR 89 (193)
Q Consensus 66 YkC~~CgKsF~skqaL~~Hmr~Ht 89 (193)
|+|+.|++.|.+...|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 689999999999999999999885
No 11
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=96.87 E-value=0.0003 Score=70.52 Aligned_cols=33 Identities=21% Similarity=0.563 Sum_probs=30.8
Q ss_pred CCCcccccCcccccccCcchHHHHhhhcCCcCc
Q 041626 61 WPPRSYTCSFCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 61 ~~eKpYkC~~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
+..|.|+|..|+|+|.-+.+|+.|.|+|.||||
T Consensus 277 a~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKP 309 (1007)
T KOG3623|consen 277 ALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKP 309 (1007)
T ss_pred hhhccccccccchhhhhHHHHHhhheeecCCCC
Confidence 455889999999999999999999999999998
No 12
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=96.72 E-value=0.00047 Score=40.87 Aligned_cols=18 Identities=22% Similarity=0.800 Sum_probs=16.1
Q ss_pred CCCCcccccCcccccccC
Q 041626 60 SWPPRSYTCSFCKREFRS 77 (193)
Q Consensus 60 ~~~eKpYkC~~CgKsF~s 77 (193)
+.+++||+|++|+|.|.+
T Consensus 9 H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 9 HTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HSSSSSEEESSSSEEESS
T ss_pred cCCCCCCCCCCCcCeeCc
Confidence 578999999999999974
No 13
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.37 E-value=0.0013 Score=37.64 Aligned_cols=23 Identities=26% Similarity=0.767 Sum_probs=21.4
Q ss_pred cccCcccccccCcchHHHHhhhc
Q 041626 66 YTCSFCKREFRSAQALGGHMNVH 88 (193)
Q Consensus 66 YkC~~CgKsF~skqaL~~Hmr~H 88 (193)
|.|.+|++.|.+...|..|++.|
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 67999999999999999999875
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=96.29 E-value=0.0019 Score=45.47 Aligned_cols=34 Identities=21% Similarity=0.461 Sum_probs=24.1
Q ss_pred CCCCcccccCcccccccCcchHHHHhhhcCCcCc
Q 041626 60 SWPPRSYTCSFCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 60 ~~~eKpYkC~~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
..-+.|..|++|+..+++..+|.+|+.++++.||
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 3456788999999999999999999988777765
No 15
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=96.26 E-value=0.001 Score=58.70 Aligned_cols=34 Identities=24% Similarity=0.445 Sum_probs=28.5
Q ss_pred CCCCcccccCcccccccCcchHHHHhhhcCCcCc
Q 041626 60 SWPPRSYTCSFCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 60 ~~~eKpYkC~~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
+..-|.|.|.+|||.|...-+|.+|+|+|+|.||
T Consensus 140 h~~vkr~lct~cgkgfndtfdlkrh~rthtgvrp 173 (267)
T KOG3576|consen 140 HSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRP 173 (267)
T ss_pred ccHHHHHHHhhccCcccchhhhhhhhccccCccc
Confidence 4455778888999999999999999999998887
No 16
>PHA00732 hypothetical protein
Probab=96.06 E-value=0.0031 Score=46.70 Aligned_cols=26 Identities=23% Similarity=0.371 Sum_probs=23.3
Q ss_pred ccccCcccccccCcchHHHHhhh-cCC
Q 041626 65 SYTCSFCKREFRSAQALGGHMNV-HRR 90 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~Hmr~-Htg 90 (193)
||.|+.|++.|.+...|..|++. |++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~ 27 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL 27 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC
Confidence 68999999999999999999984 653
No 17
>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=95.70 E-value=0.0034 Score=37.02 Aligned_cols=24 Identities=29% Similarity=0.656 Sum_probs=21.2
Q ss_pred ccccCcccccccCcchHHHHhhhc
Q 041626 65 SYTCSFCKREFRSAQALGGHMNVH 88 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~Hmr~H 88 (193)
.|-|..|++.|.+..++..|++.+
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCCcccCCCCcCCHHHHHHHHccC
Confidence 378999999999999999999753
No 18
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=95.64 E-value=0.0054 Score=62.34 Aligned_cols=28 Identities=32% Similarity=0.641 Sum_probs=23.0
Q ss_pred cccCcccccccCcchHHHHhhhcCCcCc
Q 041626 66 YTCSFCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 66 YkC~~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
+.|..|+|.|.+..+|..|||+|+++|+
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KP 907 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKP 907 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCC
Confidence 6788888888888888888888888877
No 19
>PHA00733 hypothetical protein
Probab=95.18 E-value=0.012 Score=46.87 Aligned_cols=28 Identities=25% Similarity=0.514 Sum_probs=25.4
Q ss_pred CCCcccccCcccccccCcchHHHHhhhc
Q 041626 61 WPPRSYTCSFCKREFRSAQALGGHMNVH 88 (193)
Q Consensus 61 ~~eKpYkC~~CgKsF~skqaL~~Hmr~H 88 (193)
.+.+||.|+.|++.|.+...|..|++.|
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h 96 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYT 96 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcC
Confidence 3478999999999999999999999977
No 20
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.06 E-value=0.0076 Score=34.37 Aligned_cols=23 Identities=26% Similarity=0.622 Sum_probs=18.7
Q ss_pred cccCcccccccCcchHHHHhhhcC
Q 041626 66 YTCSFCKREFRSAQALGGHMNVHR 89 (193)
Q Consensus 66 YkC~~CgKsF~skqaL~~Hmr~Ht 89 (193)
|+|+.|..... ...|..|++.|.
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 78999999998 889999998864
No 21
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=94.59 E-value=0.012 Score=54.79 Aligned_cols=35 Identities=23% Similarity=0.526 Sum_probs=31.8
Q ss_pred cccccCCCCCCCcccccCcccccccCcchHHHHhh
Q 041626 52 GEEYLSGFSWPPRSYTCSFCKREFRSAQALGGHMN 86 (193)
Q Consensus 52 ~~~~~~~~~~~eKpYkC~~CgKsF~skqaL~~Hmr 86 (193)
+++-+++|.+..|||.|++|+|.+....-|+-|+.
T Consensus 385 ~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 385 SPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CccccccccccCCceeccccchhhccCccceeccc
Confidence 56678999999999999999999999999999954
No 22
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=93.74 E-value=0.033 Score=39.56 Aligned_cols=25 Identities=40% Similarity=0.925 Sum_probs=21.9
Q ss_pred ccccCcccccccCcchHHHHhhhcC
Q 041626 65 SYTCSFCKREFRSAQALGGHMNVHR 89 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~Hmr~Ht 89 (193)
.+.|.+|++.|.+..+|..||+.|.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 6899999999999999999999753
No 23
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.68 E-value=0.059 Score=31.90 Aligned_cols=21 Identities=29% Similarity=0.741 Sum_probs=17.7
Q ss_pred cccCcccccccCcchHHHHhhh
Q 041626 66 YTCSFCKREFRSAQALGGHMNV 87 (193)
Q Consensus 66 YkC~~CgKsF~skqaL~~Hmr~ 87 (193)
..|+.|++.| ...+|..|+.+
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 67779999864
No 24
>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=92.65 E-value=0.058 Score=32.66 Aligned_cols=23 Identities=17% Similarity=0.605 Sum_probs=20.8
Q ss_pred ccccCcccccccCcchHHHHhhh
Q 041626 65 SYTCSFCKREFRSAQALGGHMNV 87 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~Hmr~ 87 (193)
+|.|.+|++.|.+..++..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999999864
No 25
>PHA00733 hypothetical protein
Probab=92.24 E-value=0.083 Score=42.04 Aligned_cols=27 Identities=26% Similarity=0.541 Sum_probs=23.9
Q ss_pred CcccccCcccccccCcchHHHHhhhcC
Q 041626 63 PRSYTCSFCKREFRSAQALGGHMNVHR 89 (193)
Q Consensus 63 eKpYkC~~CgKsF~skqaL~~Hmr~Ht 89 (193)
+.+|.|+.|++.|....+|..|++.++
T Consensus 97 ~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 97 EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 457999999999999999999997654
No 26
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=91.84 E-value=0.064 Score=47.59 Aligned_cols=32 Identities=31% Similarity=0.631 Sum_probs=27.9
Q ss_pred CCCCCCcccccCcccccccCcchHHHHhh-hcC
Q 041626 58 GFSWPPRSYTCSFCKREFRSAQALGGHMN-VHR 89 (193)
Q Consensus 58 ~~~~~eKpYkC~~CgKsF~skqaL~~Hmr-~Ht 89 (193)
-.+++-+||+|..|+|+|+++-.|..|.+ +|.
T Consensus 166 rthtgvrpykc~~c~kaftqrcsleshl~kvhg 198 (267)
T KOG3576|consen 166 RTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHG 198 (267)
T ss_pred ccccCccccchhhhhHHHHhhccHHHHHHHHcC
Confidence 35778899999999999999999999975 453
No 27
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=91.49 E-value=0.1 Score=50.13 Aligned_cols=25 Identities=28% Similarity=0.679 Sum_probs=23.7
Q ss_pred ccccCcccccccCcchHHHHhhhcC
Q 041626 65 SYTCSFCKREFRSAQALGGHMNVHR 89 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~Hmr~Ht 89 (193)
-|+|+.|+|.|....+|--|+|.|.
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred eecCCcccccccCchhhhhhhcccC
Confidence 4999999999999999999999995
No 28
>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=91.11 E-value=0.13 Score=30.28 Aligned_cols=14 Identities=29% Similarity=0.544 Sum_probs=12.7
Q ss_pred hHHHHhhhcCCcCc
Q 041626 80 ALGGHMNVHRRDRA 93 (193)
Q Consensus 80 aL~~Hmr~HtgER~ 93 (193)
+|..||++|+++|+
T Consensus 1 ~l~~H~~~H~~~k~ 14 (26)
T PF13465_consen 1 NLRRHMRTHTGEKP 14 (26)
T ss_dssp HHHHHHHHHSSSSS
T ss_pred CHHHHhhhcCCCCC
Confidence 58999999999987
No 29
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=89.76 E-value=0.11 Score=49.77 Aligned_cols=34 Identities=29% Similarity=0.535 Sum_probs=27.7
Q ss_pred CCCCCCCcccccCcccccccCcchHHHHhhhcCC
Q 041626 57 SGFSWPPRSYTCSFCKREFRSAQALGGHMNVHRR 90 (193)
Q Consensus 57 ~~~~~~eKpYkC~~CgKsF~skqaL~~Hmr~Htg 90 (193)
.|..+..--|.|.+|+|.|++...|+.|+.+|..
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 4444444479999999999999999999988763
No 30
>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=83.31 E-value=0.84 Score=30.80 Aligned_cols=26 Identities=38% Similarity=0.856 Sum_probs=17.1
Q ss_pred ccccCcccccccCcchHHHHhh-hcCCc
Q 041626 65 SYTCSFCKREFRSAQALGGHMN-VHRRD 91 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~Hmr-~HtgE 91 (193)
.|.|++|++.| +...|..|.. .|..+
T Consensus 2 ~f~CP~C~~~~-~~~~L~~H~~~~H~~~ 28 (54)
T PF05605_consen 2 SFTCPYCGKGF-SESSLVEHCEDEHRSE 28 (54)
T ss_pred CcCCCCCCCcc-CHHHHHHHHHhHCcCC
Confidence 37788888844 4567888854 45544
No 31
>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=83.11 E-value=0.88 Score=30.69 Aligned_cols=21 Identities=24% Similarity=0.583 Sum_probs=17.0
Q ss_pred ccCcccccccCcchHHHHhhhcC
Q 041626 67 TCSFCKREFRSAQALGGHMNVHR 89 (193)
Q Consensus 67 kC~~CgKsF~skqaL~~Hmr~Ht 89 (193)
.|++|...++. .|..|++.+.
T Consensus 33 ~CPiC~~~~~~--~l~~Hl~~~H 53 (54)
T PF05605_consen 33 VCPICSSRVTD--NLIRHLNSQH 53 (54)
T ss_pred cCCCchhhhhh--HHHHHHHHhc
Confidence 49999997664 8999998764
No 32
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=81.15 E-value=0.78 Score=43.64 Aligned_cols=32 Identities=19% Similarity=0.360 Sum_probs=25.8
Q ss_pred CCCCCCcccccCcccccccCcchHHHHhhhcC
Q 041626 58 GFSWPPRSYTCSFCKREFRSAQALGGHMNVHR 89 (193)
Q Consensus 58 ~~~~~eKpYkC~~CgKsF~skqaL~~Hmr~Ht 89 (193)
-.++..|||+|..|++.|.+-+.|.+|..+|.
T Consensus 285 ~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 285 YRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred hhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 34566788888888888888888888888886
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=79.20 E-value=0.61 Score=32.94 Aligned_cols=24 Identities=33% Similarity=0.652 Sum_probs=0.0
Q ss_pred ccCcccccccCcchHHHHhhhcCC
Q 041626 67 TCSFCKREFRSAQALGGHMNVHRR 90 (193)
Q Consensus 67 kC~~CgKsF~skqaL~~Hmr~Htg 90 (193)
+|.+|+..|.+...|..||...++
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~ 24 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHG 24 (100)
T ss_dssp ------------------------
T ss_pred Cccccccccccccccccccccccc
Confidence 599999999999999999965443
No 34
>PRK04860 hypothetical protein; Provisional
Probab=78.31 E-value=1.2 Score=37.07 Aligned_cols=26 Identities=23% Similarity=0.509 Sum_probs=22.6
Q ss_pred cccccCcccccccCcchHHHHhhhcCCcCc
Q 041626 64 RSYTCSFCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 64 KpYkC~~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
-+|.|. |++ ....+..|.++|+++++
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~ 143 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAV 143 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCcc
Confidence 469998 998 77789999999999874
No 35
>PHA02768 hypothetical protein; Provisional
Probab=74.33 E-value=1.3 Score=31.28 Aligned_cols=19 Identities=21% Similarity=0.090 Sum_probs=16.5
Q ss_pred cccccCcccccccCcchHH
Q 041626 64 RSYTCSFCKREFRSAQALG 82 (193)
Q Consensus 64 KpYkC~~CgKsF~skqaL~ 82 (193)
++|+|..|+|.|...+.|.
T Consensus 30 k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 30 TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred CcccCCcccceecccceeE
Confidence 6899999999999887664
No 36
>PLN03086 PRLI-interacting factor K; Provisional
Probab=73.12 E-value=2.1 Score=42.25 Aligned_cols=25 Identities=24% Similarity=0.563 Sum_probs=14.5
Q ss_pred cccccCcccccccCcchHHHHhhhcC
Q 041626 64 RSYTCSFCKREFRSAQALGGHMNVHR 89 (193)
Q Consensus 64 KpYkC~~CgKsF~skqaL~~Hmr~Ht 89 (193)
+.+.|++|++.|. ...|..|+++|+
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~~H 476 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKVFH 476 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHhcC
Confidence 4456666666664 455666666543
No 37
>PHA00732 hypothetical protein
Probab=72.37 E-value=1.7 Score=32.10 Aligned_cols=22 Identities=23% Similarity=0.614 Sum_probs=17.4
Q ss_pred ccccCcccccccCcchHHHHhhhcC
Q 041626 65 SYTCSFCKREFRSAQALGGHMNVHR 89 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~Hmr~Ht 89 (193)
++.|+.|++.|. .|..|.+++.
T Consensus 27 ~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 27 LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CCccCCCCCEeC---ChhhhhcccC
Confidence 468999999998 4888886543
No 38
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=72.01 E-value=2.4 Score=28.17 Aligned_cols=23 Identities=22% Similarity=0.699 Sum_probs=19.1
Q ss_pred ccCcccccccCc-----chHHHHhh-hcC
Q 041626 67 TCSFCKREFRSA-----QALGGHMN-VHR 89 (193)
Q Consensus 67 kC~~CgKsF~sk-----qaL~~Hmr-~Ht 89 (193)
.|.+|++.+... ++|.+|++ .|.
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 699999999876 58999987 564
No 39
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=70.34 E-value=1.1 Score=45.77 Aligned_cols=33 Identities=27% Similarity=0.560 Sum_probs=27.5
Q ss_pred CCCCCCcccccCcccccccCcchHHHHhhhcCC
Q 041626 58 GFSWPPRSYTCSFCKREFRSAQALGGHMNVHRR 90 (193)
Q Consensus 58 ~~~~~eKpYkC~~CgKsF~skqaL~~Hmr~Htg 90 (193)
|...+.--|.|..|+|.|-.-..+..||+.|+-
T Consensus 785 ~~~~~~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 785 GETDPTGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CCCCCCceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 344445559999999999999999999999984
No 40
>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=70.34 E-value=2.6 Score=26.85 Aligned_cols=26 Identities=19% Similarity=0.598 Sum_probs=16.2
Q ss_pred CcccccCcccccccCc----chHHHHh-hhc
Q 041626 63 PRSYTCSFCKREFRSA----QALGGHM-NVH 88 (193)
Q Consensus 63 eKpYkC~~CgKsF~sk----qaL~~Hm-r~H 88 (193)
.....|.+|++.+... ..|..|+ +.|
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 3446899999999885 6888888 444
No 41
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=68.34 E-value=1.1 Score=40.83 Aligned_cols=40 Identities=23% Similarity=0.507 Sum_probs=30.8
Q ss_pred cccccccCCCCCCCcccccCcccccccCcchHHHH-hhhcC
Q 041626 50 SYGEEYLSGFSWPPRSYTCSFCKREFRSAQALGGH-MNVHR 89 (193)
Q Consensus 50 ~~~~~~~~~~~~~eKpYkC~~CgKsF~skqaL~~H-mr~Ht 89 (193)
.|+.+-+--.+-+.|.|+|.+|.|...+..-|..| |++|.
T Consensus 19 efddekiliqhqkakhfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 19 EFDDEKILIQHQKAKHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred ccchhhhhhhhhhhccceeeeehhhhccCCCceeehhhhhh
Confidence 46555554566788899999999999999888888 56664
No 42
>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=67.40 E-value=2.9 Score=31.62 Aligned_cols=25 Identities=24% Similarity=0.481 Sum_probs=22.9
Q ss_pred ccc----CcccccccCcchHHHHhhhcCC
Q 041626 66 YTC----SFCKREFRSAQALGGHMNVHRR 90 (193)
Q Consensus 66 YkC----~~CgKsF~skqaL~~Hmr~Htg 90 (193)
|.| ..|+..+++...|..|++.+++
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 799 9999999999999999987754
No 43
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=66.40 E-value=2 Score=31.14 Aligned_cols=28 Identities=25% Similarity=0.405 Sum_probs=23.0
Q ss_pred CCcccccCcccccccCcchHHHHhh-hcC
Q 041626 62 PPRSYTCSFCKREFRSAQALGGHMN-VHR 89 (193)
Q Consensus 62 ~eKpYkC~~CgKsF~skqaL~~Hmr-~Ht 89 (193)
+|--+.|+.|++.|+...+..+|.+ .|.
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 3445799999999999999999985 454
No 44
>PLN03086 PRLI-interacting factor K; Provisional
Probab=62.94 E-value=4.4 Score=40.05 Aligned_cols=28 Identities=14% Similarity=0.249 Sum_probs=24.3
Q ss_pred cccccCcccccccCcchHHHHhhhcCCcCc
Q 041626 64 RSYTCSFCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 64 KpYkC~~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
++|.|+ |++.| .+..|..|+++|..+|+
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kp 504 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRL 504 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCc
Confidence 899999 99866 67899999999987776
No 45
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=60.87 E-value=4.7 Score=40.03 Aligned_cols=33 Identities=18% Similarity=0.424 Sum_probs=27.5
Q ss_pred CCCcccccCcccccccCcchHHHHhhhcCCcCc
Q 041626 61 WPPRSYTCSFCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 61 ~~eKpYkC~~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
...+|.+|..||+.|........||..|...+.
T Consensus 414 y~~~pnqC~~CG~R~~~~ee~sk~md~H~dwh~ 446 (579)
T KOG2071|consen 414 YKDSPNQCKSCGLRFDDSEERSKHMDIHDDWHR 446 (579)
T ss_pred ccCCcchhcccccccccchhhhhHhhhhhhhhh
Confidence 456778999999999999999999988875543
No 46
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=58.40 E-value=4.6 Score=34.17 Aligned_cols=35 Identities=20% Similarity=0.438 Sum_probs=21.9
Q ss_pred CCCCC--cccccC--cccccccCcchHHHHhhhcCCcCc
Q 041626 59 FSWPP--RSYTCS--FCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 59 ~~~~e--KpYkC~--~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
.+..+ ++|.|+ .|++.|.....+..|...|++.++
T Consensus 313 ~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~ 351 (467)
T COG5048 313 NHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP 351 (467)
T ss_pred ccccccCCceeeeccCCCccccccccccCCcccccCCCc
Confidence 34444 666666 566666666666666666665553
No 47
>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=55.14 E-value=5.7 Score=32.32 Aligned_cols=25 Identities=24% Similarity=0.566 Sum_probs=16.3
Q ss_pred cccCcccccccCcchHHHHhhhcCCcCc
Q 041626 66 YTCSFCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 66 YkC~~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
-.|-+|||.|.. |.+|.+.|+|-.+
T Consensus 73 i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eEEccCCcccch---HHHHHHHccCCCH
Confidence 469999999975 6999999976544
No 48
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=53.88 E-value=7 Score=37.43 Aligned_cols=26 Identities=35% Similarity=0.715 Sum_probs=22.6
Q ss_pred CCcccccCcccccccCcchHHHHhhh
Q 041626 62 PPRSYTCSFCKREFRSAQALGGHMNV 87 (193)
Q Consensus 62 ~eKpYkC~~CgKsF~skqaL~~Hmr~ 87 (193)
.+-+|.|..|+|.|++..+|+.|.+.
T Consensus 349 np~~Y~CH~Cdr~ft~G~~L~~HL~k 374 (467)
T KOG3608|consen 349 NPILYACHCCDRFFTSGKSLSAHLMK 374 (467)
T ss_pred CCCceeeecchhhhccchhHHHHHHH
Confidence 45679999999999999999999753
No 49
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=52.23 E-value=10 Score=35.84 Aligned_cols=31 Identities=23% Similarity=0.612 Sum_probs=24.9
Q ss_pred CCcccccC--cccccccCcchHHHHhhh-cCCcC
Q 041626 62 PPRSYTCS--FCKREFRSAQALGGHMNV-HRRDR 92 (193)
Q Consensus 62 ~eKpYkC~--~CgKsF~skqaL~~Hmr~-HtgER 92 (193)
.+|||+|+ -|.|.++...-|+-||.- |...+
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~ 379 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQK 379 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcc
Confidence 35999997 599999999999999863 43333
No 50
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=51.92 E-value=3.7 Score=35.13 Aligned_cols=25 Identities=28% Similarity=0.755 Sum_probs=20.7
Q ss_pred CcccccCcccccccCcchHHHHhhh
Q 041626 63 PRSYTCSFCKREFRSAQALGGHMNV 87 (193)
Q Consensus 63 eKpYkC~~CgKsF~skqaL~~Hmr~ 87 (193)
.+.+.|++|++.|.+..-+.+..++
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 3567999999999999888777764
No 51
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=50.63 E-value=10 Score=36.11 Aligned_cols=29 Identities=34% Similarity=0.725 Sum_probs=24.0
Q ss_pred ccccCcccccccCcchHHHHhhh--cCCcCc
Q 041626 65 SYTCSFCKREFRSAQALGGHMNV--HRRDRA 93 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~Hmr~--HtgER~ 93 (193)
.+.|-+|.|.|+.+..|..|||. |.+-.|
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinP 225 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINP 225 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCC
Confidence 47899999999999999999974 554434
No 52
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=47.38 E-value=9 Score=31.44 Aligned_cols=15 Identities=27% Similarity=0.660 Sum_probs=13.7
Q ss_pred ccccCcccccccCcc
Q 041626 65 SYTCSFCKREFRSAQ 79 (193)
Q Consensus 65 pYkC~~CgKsF~skq 79 (193)
||+|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 799999999999876
No 53
>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=46.04 E-value=12 Score=22.28 Aligned_cols=19 Identities=26% Similarity=0.756 Sum_probs=15.4
Q ss_pred ccCcccccccCcchHHHHhh
Q 041626 67 TCSFCKREFRSAQALGGHMN 86 (193)
Q Consensus 67 kC~~CgKsF~skqaL~~Hmr 86 (193)
.|++|++.+ ....+..|.-
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 699999999 5567888864
No 54
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.62 E-value=16 Score=29.30 Aligned_cols=23 Identities=22% Similarity=0.583 Sum_probs=17.8
Q ss_pred cCCCCCCCcccccCcccccccCc
Q 041626 56 LSGFSWPPRSYTCSFCKREFRSA 78 (193)
Q Consensus 56 ~~~~~~~eKpYkC~~CgKsF~sk 78 (193)
.++...+...|.|+.|++.|...
T Consensus 44 ~g~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 44 IGGIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred ECCccccccccccCCcCcceeee
Confidence 35566667789999999999753
No 55
>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=38.16 E-value=12 Score=23.10 Aligned_cols=17 Identities=29% Similarity=0.710 Sum_probs=13.2
Q ss_pred ccccCcccccccCcchH
Q 041626 65 SYTCSFCKREFRSAQAL 81 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL 81 (193)
.|+|..||+.|.-.+..
T Consensus 5 ~y~C~~Cg~~fe~~~~~ 21 (41)
T smart00834 5 EYRCEDCGHTFEVLQKI 21 (41)
T ss_pred EEEcCCCCCEEEEEEec
Confidence 48999999999755543
No 56
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=38.13 E-value=18 Score=23.59 Aligned_cols=24 Identities=21% Similarity=0.350 Sum_probs=18.5
Q ss_pred cccCcccccccCc--chHHHHhhhcC
Q 041626 66 YTCSFCKREFRSA--QALGGHMNVHR 89 (193)
Q Consensus 66 YkC~~CgKsF~sk--qaL~~Hmr~Ht 89 (193)
-.|+.||..|... .+-..|.+-|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 4899999999864 45677877774
No 57
>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=37.58 E-value=16 Score=28.72 Aligned_cols=17 Identities=24% Similarity=0.507 Sum_probs=12.6
Q ss_pred CCCcccccCcccccccCc
Q 041626 61 WPPRSYTCSFCKREFRSA 78 (193)
Q Consensus 61 ~~eKpYkC~~CgKsF~sk 78 (193)
||-| ..|+.||+.|+..
T Consensus 6 lGtK-R~Cp~CG~kFYDL 22 (108)
T PF09538_consen 6 LGTK-RTCPSCGAKFYDL 22 (108)
T ss_pred cCCc-ccCCCCcchhccC
Confidence 4444 4799999999764
No 58
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=37.00 E-value=15 Score=30.72 Aligned_cols=24 Identities=25% Similarity=0.375 Sum_probs=19.9
Q ss_pred ccCcccccccCcchHHHHhhhcCCcCc
Q 041626 67 TCSFCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 67 kC~~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
.|-+|||.|.+ |.+|..+|.+--|
T Consensus 78 icLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 78 ICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEeccCcchHH---HHHHHhcccCCCH
Confidence 59999999964 9999999986443
No 59
>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=34.09 E-value=13 Score=31.55 Aligned_cols=29 Identities=14% Similarity=0.320 Sum_probs=0.0
Q ss_pred CCcccccCcccccccCcchHHHHhhhcCCc
Q 041626 62 PPRSYTCSFCKREFRSAQALGGHMNVHRRD 91 (193)
Q Consensus 62 ~eKpYkC~~CgKsF~skqaL~~Hmr~HtgE 91 (193)
+.+...|++||+...-.. |..|||+...+
T Consensus 165 ~~~~~~cPitGe~IP~~e-~~eHmRi~LlD 193 (229)
T PF12230_consen 165 KEKMIICPITGEMIPADE-MDEHMRIELLD 193 (229)
T ss_dssp ------------------------------
T ss_pred cccccccccccccccccc-ccccccccccc
Confidence 334578999999987665 99999998754
No 60
>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=31.03 E-value=13 Score=32.39 Aligned_cols=31 Identities=13% Similarity=0.486 Sum_probs=22.2
Q ss_pred CCcccccCcccccccCcchHHHHhhhcCCcC
Q 041626 62 PPRSYTCSFCKREFRSAQALGGHMNVHRRDR 92 (193)
Q Consensus 62 ~eKpYkC~~CgKsF~skqaL~~Hmr~HtgER 92 (193)
.+..|.|..|+|.|.-..-...|...-+.|+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 4456999999999999999999986544443
No 61
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=30.65 E-value=18 Score=30.05 Aligned_cols=21 Identities=14% Similarity=0.284 Sum_probs=16.6
Q ss_pred ccccCcccccccCcchHHHHh
Q 041626 65 SYTCSFCKREFRSAQALGGHM 85 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~Hm 85 (193)
.|+|+.||+.|.+--.+..=|
T Consensus 28 ~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 28 RRECLACGKRFTTFERVELVP 48 (154)
T ss_pred eeeccccCCcceEeEeccCcc
Confidence 399999999999876655544
No 62
>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=30.06 E-value=24 Score=21.17 Aligned_cols=11 Identities=27% Similarity=0.794 Sum_probs=9.2
Q ss_pred cccCccccccc
Q 041626 66 YTCSFCKREFR 76 (193)
Q Consensus 66 YkC~~CgKsF~ 76 (193)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 46999999985
No 63
>PRK04860 hypothetical protein; Provisional
Probab=30.00 E-value=20 Score=29.73 Aligned_cols=22 Identities=14% Similarity=0.229 Sum_probs=17.8
Q ss_pred CCCCCCcccccCcccccccCcc
Q 041626 58 GFSWPPRSYTCSFCKREFRSAQ 79 (193)
Q Consensus 58 ~~~~~eKpYkC~~CgKsF~skq 79 (193)
-...++++|.|..|++.|.-..
T Consensus 136 ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 136 RVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred HHhcCCccEECCCCCceeEEec
Confidence 4577889999999999987543
No 64
>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=30.00 E-value=19 Score=23.58 Aligned_cols=16 Identities=31% Similarity=0.779 Sum_probs=12.7
Q ss_pred ccccCcccccccCcch
Q 041626 65 SYTCSFCKREFRSAQA 80 (193)
Q Consensus 65 pYkC~~CgKsF~skqa 80 (193)
-|+|..|+..|.-.+.
T Consensus 5 ey~C~~Cg~~fe~~~~ 20 (52)
T TIGR02605 5 EYRCTACGHRFEVLQK 20 (52)
T ss_pred EEEeCCCCCEeEEEEe
Confidence 4899999999986543
No 65
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=29.06 E-value=24 Score=22.79 Aligned_cols=14 Identities=21% Similarity=0.712 Sum_probs=11.9
Q ss_pred ccccCcccccccCc
Q 041626 65 SYTCSFCKREFRSA 78 (193)
Q Consensus 65 pYkC~~CgKsF~sk 78 (193)
||+|..|++.|=..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78999999999654
No 66
>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=29.05 E-value=20 Score=23.21 Aligned_cols=19 Identities=32% Similarity=0.730 Sum_probs=14.5
Q ss_pred ccccCcccccccCcchHHH
Q 041626 65 SYTCSFCKREFRSAQALGG 83 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~ 83 (193)
.|.|..||..|-..+.+..
T Consensus 5 ey~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISE 23 (42)
T ss_pred EEEeCCCCCEEEEEEEcCC
Confidence 4899999999977665443
No 67
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=27.97 E-value=38 Score=28.62 Aligned_cols=34 Identities=26% Similarity=0.561 Sum_probs=22.7
Q ss_pred CCCCcccccCcccccccCcchHHHHhhhcCCcCc
Q 041626 60 SWPPRSYTCSFCKREFRSAQALGGHMNVHRRDRA 93 (193)
Q Consensus 60 ~~~eKpYkC~~CgKsF~skqaL~~Hmr~HtgER~ 93 (193)
....+++.|..|...|........|.+.|.++++
T Consensus 28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (467)
T COG5048 28 SNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKP 61 (467)
T ss_pred ccCCchhhcccccccccccchhhhhcccccccCC
Confidence 3444556677777777777777777777776665
No 68
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=27.96 E-value=31 Score=33.79 Aligned_cols=24 Identities=25% Similarity=0.678 Sum_probs=20.9
Q ss_pred CcccccCccc-ccccCcchHHHHhh
Q 041626 63 PRSYTCSFCK-REFRSAQALGGHMN 86 (193)
Q Consensus 63 eKpYkC~~Cg-KsF~skqaL~~Hmr 86 (193)
.+.|.|.+|| +++.-..++.+|-.
T Consensus 399 ~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 399 DIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred CcccceeeccCccccCcHHHHHHhH
Confidence 3678999999 99999999999964
No 69
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=27.35 E-value=27 Score=28.69 Aligned_cols=26 Identities=31% Similarity=0.510 Sum_probs=22.6
Q ss_pred CCcccccCcccccccCcchHHHHhhh
Q 041626 62 PPRSYTCSFCKREFRSAQALGGHMNV 87 (193)
Q Consensus 62 ~eKpYkC~~CgKsF~skqaL~~Hmr~ 87 (193)
+--.|-|-.|.+-|.+..+|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 33568999999999999999999874
No 70
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=26.16 E-value=39 Score=36.96 Aligned_cols=37 Identities=22% Similarity=0.297 Sum_probs=0.0
Q ss_pred cccccCcccccccCcchHHHHhhh-cCCcCcCCCCCCCC
Q 041626 64 RSYTCSFCKREFRSAQALGGHMNV-HRRDRARLRISPPT 101 (193)
Q Consensus 64 KpYkC~~CgKsF~skqaL~~Hmr~-HtgER~~~~~spp~ 101 (193)
+.| |.+|...|+..++|..||++ |+..|.+.....++
T Consensus 1328 ~~~-c~~c~~~~~~~~alqihm~~~~~~~kt~~~~p~~~ 1365 (1406)
T KOG1146|consen 1328 TYH-CLACEVLLSGREALQIHMRSSAHRRKTAPPQPGPP 1365 (1406)
T ss_pred ccc-chHHHhhcchhHHHHHHHHHhhhcccCCCCCCCCc
No 71
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=26.08 E-value=32 Score=27.59 Aligned_cols=16 Identities=19% Similarity=0.517 Sum_probs=13.7
Q ss_pred ccccCcccccccCcch
Q 041626 65 SYTCSFCKREFRSAQA 80 (193)
Q Consensus 65 pYkC~~CgKsF~skqa 80 (193)
||.|..||..|.+.+.
T Consensus 2 pH~CtrCG~vf~~g~~ 17 (112)
T COG3364 2 PHQCTRCGEVFDDGSE 17 (112)
T ss_pred CceecccccccccccH
Confidence 6899999999998643
No 72
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=26.07 E-value=28 Score=34.17 Aligned_cols=22 Identities=32% Similarity=0.715 Sum_probs=20.2
Q ss_pred cccCcccccccCcchHHHHhhh
Q 041626 66 YTCSFCKREFRSAQALGGHMNV 87 (193)
Q Consensus 66 YkC~~CgKsF~skqaL~~Hmr~ 87 (193)
+-|..|.|+|.+--+|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999999864
No 73
>PTZ00448 hypothetical protein; Provisional
Probab=26.06 E-value=35 Score=32.43 Aligned_cols=23 Identities=17% Similarity=0.364 Sum_probs=21.2
Q ss_pred ccccCcccccccCcchHHHHhhh
Q 041626 65 SYTCSFCKREFRSAQALGGHMNV 87 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~Hmr~ 87 (193)
.|.|..|+-.|.+....+.|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999999999999985
No 74
>PF15269 zf-C2H2_7: Zinc-finger
Probab=25.80 E-value=53 Score=22.99 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=21.4
Q ss_pred ccccCcccccccCcchHHHHhhhcC
Q 041626 65 SYTCSFCKREFRSAQALGGHMNVHR 89 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~Hmr~Ht 89 (193)
.|+|-+|.-....++.|-.||+--.
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky~l 44 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKYSL 44 (54)
T ss_pred cceeecCCcccchHHHHHHHHHHHh
Confidence 4789999999999999999997543
No 75
>PLN03239 histone acetyltransferase; Provisional
Probab=25.71 E-value=31 Score=32.47 Aligned_cols=47 Identities=15% Similarity=0.101 Sum_probs=35.1
Q ss_pred CCcchhhhhhhcccccccccCCCCCCCcccccCcccccccCcchHHHHhh
Q 041626 37 NKMKDSCQQRQQQSYGEEYLSGFSWPPRSYTCSFCKREFRSAQALGGHMN 86 (193)
Q Consensus 37 ~~~~d~w~~~~~~~~~~~~~~~~~~~eKpYkC~~CgKsF~skqaL~~Hmr 86 (193)
...=+.|-.++ +.+++.....+-..-|.|++|-|=|.+...|.+|+.
T Consensus 81 ~y~i~tWYfSP---yP~e~~~~~~~~~~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 81 PYQMDTWYFSP---LPKELFKAGGFIDVLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred CeeecCCCCCC---CcHHHhcccccCceEEEeccchhhhcCHHHHHHHHH
Confidence 44456677643 666665444456678999999999999999999975
No 76
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=25.55 E-value=25 Score=33.80 Aligned_cols=35 Identities=29% Similarity=0.710 Sum_probs=27.4
Q ss_pred cCCCCCCCcccccCcccccccCcchHHHHh--hhcCCc
Q 041626 56 LSGFSWPPRSYTCSFCKREFRSAQALGGHM--NVHRRD 91 (193)
Q Consensus 56 ~~~~~~~eKpYkC~~CgKsF~skqaL~~Hm--r~HtgE 91 (193)
+.|-.|.++- -|..|++-|.+..-+..|. +.|..+
T Consensus 230 ~~g~~~~~~~-YC~~C~r~f~~~~VFe~Hl~gK~H~k~ 266 (470)
T COG5188 230 MEGAEWFPKV-YCVKCGREFSRSKVFEYHLEGKRHCKE 266 (470)
T ss_pred cchhhhccce-eeHhhhhHhhhhHHHHHHHhhhhhhhh
Confidence 5666777664 5999999999999999998 456644
No 77
>PHA00626 hypothetical protein
Probab=25.36 E-value=30 Score=24.99 Aligned_cols=20 Identities=25% Similarity=0.517 Sum_probs=14.6
Q ss_pred CcccccCcccccccCcchHHH
Q 041626 63 PRSYTCSFCKREFRSAQALGG 83 (193)
Q Consensus 63 eKpYkC~~CgKsF~skqaL~~ 83 (193)
...|+|+.||..|+ +.+++.
T Consensus 21 snrYkCkdCGY~ft-~~~~~~ 40 (59)
T PHA00626 21 SDDYVCCDCGYNDS-KDAFGE 40 (59)
T ss_pred CcceEcCCCCCeec-hhhhhh
Confidence 34699999999885 445543
No 78
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=25.16 E-value=36 Score=32.62 Aligned_cols=28 Identities=14% Similarity=0.201 Sum_probs=24.1
Q ss_pred cccccCcccccccCcchHHHH-hhhcCCcC
Q 041626 64 RSYTCSFCKREFRSAQALGGH-MNVHRRDR 92 (193)
Q Consensus 64 KpYkC~~CgKsF~skqaL~~H-mr~HtgER 92 (193)
+||+|. |++.+.+++.|..| +.+|.++-
T Consensus 212 ~p~k~~-~~~~~~T~~~l~~HS~N~~~~~S 240 (442)
T KOG4124|consen 212 TPKKMP-ESLVMDTSSPLSDHSMNIDVGES 240 (442)
T ss_pred CCccCc-ccccccccchhhhccccCCCCcc
Confidence 789998 99999999999999 57777654
No 79
>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=25.13 E-value=29 Score=20.80 Aligned_cols=10 Identities=20% Similarity=0.654 Sum_probs=8.1
Q ss_pred cccccCcccc
Q 041626 64 RSYTCSFCKR 73 (193)
Q Consensus 64 KpYkC~~CgK 73 (193)
-+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 3599999985
No 80
>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=24.38 E-value=23 Score=22.93 Aligned_cols=15 Identities=20% Similarity=0.678 Sum_probs=9.7
Q ss_pred cccccCcccccccCc
Q 041626 64 RSYTCSFCKREFRSA 78 (193)
Q Consensus 64 KpYkC~~CgKsF~sk 78 (193)
-|+.|+.|++.|=..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 378999999999654
No 81
>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=24.21 E-value=26 Score=23.46 Aligned_cols=11 Identities=27% Similarity=0.905 Sum_probs=6.3
Q ss_pred ccCcccccccC
Q 041626 67 TCSFCKREFRS 77 (193)
Q Consensus 67 kC~~CgKsF~s 77 (193)
.|+.|++.|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 79999999976
No 82
>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=23.96 E-value=38 Score=33.00 Aligned_cols=26 Identities=27% Similarity=0.623 Sum_probs=22.7
Q ss_pred cccCcccccccCcchHHHHhh-hcCCc
Q 041626 66 YTCSFCKREFRSAQALGGHMN-VHRRD 91 (193)
Q Consensus 66 YkC~~CgKsF~skqaL~~Hmr-~HtgE 91 (193)
-.|+.|.+.|.+...+..|+. .|.+.
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 579999999999999999996 57654
No 83
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the 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=22.68 E-value=40 Score=27.72 Aligned_cols=12 Identities=17% Similarity=0.321 Sum_probs=8.2
Q ss_pred cccCcccccccC
Q 041626 66 YTCSFCKREFRS 77 (193)
Q Consensus 66 YkC~~CgKsF~s 77 (193)
+.|+.||+.|+.
T Consensus 10 r~Cp~cg~kFYD 21 (129)
T TIGR02300 10 RICPNTGSKFYD 21 (129)
T ss_pred ccCCCcCccccc
Confidence 367777777764
No 85
>COG4640 Predicted membrane protein [Function unknown]
Probab=22.26 E-value=50 Score=32.09 Aligned_cols=23 Identities=22% Similarity=0.488 Sum_probs=18.0
Q ss_pred CCcccccCcccccccCcchHHHH
Q 041626 62 PPRSYTCSFCKREFRSAQALGGH 84 (193)
Q Consensus 62 ~eKpYkC~~CgKsF~skqaL~~H 84 (193)
.|-.++|+.||..|...+++...
T Consensus 12 ~Ed~~qC~qCG~~~t~~~sqan~ 34 (465)
T COG4640 12 AEDDVQCTQCGHKFTSRQSQANK 34 (465)
T ss_pred ccccccccccCCcCCchhhhhhH
Confidence 33445699999999999987764
No 86
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=22.05 E-value=38 Score=33.22 Aligned_cols=27 Identities=22% Similarity=0.554 Sum_probs=23.3
Q ss_pred cccCcccccccCcchHHHHh-hhcCCcC
Q 041626 66 YTCSFCKREFRSAQALGGHM-NVHRRDR 92 (193)
Q Consensus 66 YkC~~CgKsF~skqaL~~Hm-r~HtgER 92 (193)
|.|++|.+.|.+-++|..|. ..|..+-
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 78999999999999999998 4576553
No 87
>PF14353 CpXC: CpXC protein
Probab=21.37 E-value=22 Score=27.46 Aligned_cols=23 Identities=35% Similarity=0.509 Sum_probs=17.4
Q ss_pred ccccCcccccccCcchHHHHhhh
Q 041626 65 SYTCSFCKREFRSAQALGGHMNV 87 (193)
Q Consensus 65 pYkC~~CgKsF~skqaL~~Hmr~ 87 (193)
.|.|+.||+.|.-...+.-|-..
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCC
Confidence 47999999999876666666443
No 88
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=21.13 E-value=32 Score=22.71 Aligned_cols=12 Identities=17% Similarity=0.833 Sum_probs=10.1
Q ss_pred ccccCccccccc
Q 041626 65 SYTCSFCKREFR 76 (193)
Q Consensus 65 pYkC~~CgKsF~ 76 (193)
+-.|++|+..|.
T Consensus 29 ~~~CpYCg~~yv 40 (40)
T PF10276_consen 29 PVVCPYCGTRYV 40 (40)
T ss_dssp EEEETTTTEEEE
T ss_pred eEECCCCCCEEC
Confidence 578999999883
No 89
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.52 E-value=30 Score=30.96 Aligned_cols=20 Identities=45% Similarity=0.996 Sum_probs=18.7
Q ss_pred ccCcccccccCcchHHHHhh
Q 041626 67 TCSFCKREFRSAQALGGHMN 86 (193)
Q Consensus 67 kC~~CgKsF~skqaL~~Hmr 86 (193)
.|.+|.|.|.+..-|..|..
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~ 127 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHIL 127 (253)
T ss_pred hhHHHHHhCCchhhhhHHHH
Confidence 89999999999999999975
No 90
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.11 E-value=41 Score=32.60 Aligned_cols=21 Identities=29% Similarity=0.692 Sum_probs=16.5
Q ss_pred CCcccccCcccccccCcchHH
Q 041626 62 PPRSYTCSFCKREFRSAQALG 82 (193)
Q Consensus 62 ~eKpYkC~~CgKsF~skqaL~ 82 (193)
...-|.|+.|.+.|+.-.++.
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~ 145 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQ 145 (436)
T ss_pred ccccccCCccccchhhhHHHH
Confidence 345599999999999876654
Done!