Query 045333
Match_columns 225
No_of_seqs 162 out of 753
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 12:11:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045333.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045333hhsearch_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 98.4 1.2E-07 2.5E-12 86.7 2.2 37 62-98 207-243 (279)
2 KOG1074 Transcriptional repres 98.4 1.2E-07 2.5E-12 96.8 1.3 40 61-100 624-663 (958)
3 PHA02768 hypothetical protein; 98.1 1.4E-06 2.9E-11 62.8 1.5 25 70-94 5-29 (55)
4 PF00096 zf-C2H2: Zinc finger, 98.0 2.8E-06 6E-11 49.1 1.1 23 71-93 1-23 (23)
5 PHA00616 hypothetical protein 97.9 2.6E-06 5.6E-11 58.9 0.7 29 70-98 1-29 (44)
6 KOG2462 C2H2-type Zn-finger pr 97.9 3.3E-06 7.1E-11 77.3 1.0 31 69-99 186-216 (279)
7 KOG3623 Homeobox transcription 97.9 3.9E-06 8.4E-11 85.4 1.2 36 64-99 916-951 (1007)
8 PF13912 zf-C2H2_6: C2H2-type 97.8 7.9E-06 1.7E-10 48.8 1.2 26 70-95 1-26 (27)
9 KOG1074 Transcriptional repres 97.7 7.1E-05 1.5E-09 77.0 6.5 38 61-98 372-409 (958)
10 PF13894 zf-C2H2_4: C2H2-type 97.6 2.7E-05 5.8E-10 44.0 1.5 24 71-94 1-24 (24)
11 PF13465 zf-H2C2_2: Zinc-finge 97.6 8.2E-06 1.8E-10 49.6 -1.2 20 63-82 7-26 (26)
12 smart00355 ZnF_C2H2 zinc finge 97.4 9.8E-05 2.1E-09 41.7 1.6 25 71-95 1-25 (26)
13 KOG3623 Homeobox transcription 97.3 6.1E-05 1.3E-09 77.0 0.7 33 67-99 278-310 (1007)
14 PF09237 GAGA: GAGA factor; I 96.9 0.00057 1.2E-08 49.3 1.7 34 66-99 20-53 (54)
15 PF12874 zf-met: Zinc-finger o 96.8 0.00038 8.3E-09 40.8 0.7 24 71-94 1-24 (25)
16 KOG3576 Ovo and related transc 96.8 0.00028 6E-09 63.6 -0.5 39 61-99 136-174 (267)
17 PHA00732 hypothetical protein 96.4 0.0017 3.7E-08 49.2 1.7 27 70-96 1-28 (79)
18 PHA00733 hypothetical protein 96.0 0.0041 8.9E-08 50.6 2.1 29 66-94 69-97 (128)
19 PF12171 zf-C2H2_jaz: Zinc-fin 95.7 0.0033 7.1E-08 38.0 0.3 24 70-93 1-24 (27)
20 KOG3576 Ovo and related transc 95.6 0.0041 9E-08 56.2 0.8 37 59-95 162-198 (267)
21 PF12756 zf-C2H2_2: C2H2 type 94.9 0.015 3.2E-07 42.2 1.7 25 69-93 49-73 (100)
22 PF13909 zf-H2C2_5: C2H2-type 94.5 0.017 3.7E-07 33.7 1.0 23 71-94 1-23 (24)
23 PF13913 zf-C2HC_2: zinc-finge 94.0 0.029 6.2E-07 34.1 1.2 21 71-92 3-23 (25)
24 smart00451 ZnF_U1 U1-like zinc 93.8 0.036 7.9E-07 34.3 1.4 23 70-92 3-25 (35)
25 PHA00733 hypothetical protein 93.0 0.06 1.3E-06 43.8 1.9 28 68-95 97-124 (128)
26 PF13465 zf-H2C2_2: Zinc-finge 92.7 0.06 1.3E-06 32.6 1.2 15 85-99 1-15 (26)
27 KOG3993 Transcription factor ( 92.1 0.065 1.4E-06 52.6 1.3 26 70-95 295-320 (500)
28 KOG2893 Zn finger protein [Gen 91.4 0.037 7.9E-07 51.3 -1.2 36 60-95 24-60 (341)
29 PHA02768 hypothetical protein; 89.9 0.092 2E-06 38.0 -0.0 24 62-87 25-48 (55)
30 KOG3608 Zn finger proteins [Ge 88.0 0.26 5.5E-06 47.9 1.5 37 59-95 281-317 (467)
31 KOG3993 Transcription factor ( 87.1 0.24 5.2E-06 48.7 0.8 29 67-95 353-381 (500)
32 PF02892 zf-BED: BED zinc fing 85.8 0.53 1.1E-05 30.9 1.7 27 67-93 13-44 (45)
33 PF05605 zf-Di19: Drought indu 85.7 0.54 1.2E-05 32.5 1.8 27 70-97 2-29 (54)
34 COG5189 SFP1 Putative transcri 84.0 0.34 7.4E-06 46.5 0.1 24 67-90 395-418 (423)
35 smart00614 ZnF_BED BED zinc fi 83.9 0.64 1.4E-05 31.7 1.4 25 70-94 18-48 (50)
36 PF05605 zf-Di19: Drought indu 83.2 0.75 1.6E-05 31.8 1.6 26 68-95 29-54 (54)
37 PLN03086 PRLI-interacting fact 82.3 0.81 1.8E-05 46.1 2.0 28 69-98 477-504 (567)
38 PRK04860 hypothetical protein; 82.2 0.76 1.6E-05 39.1 1.5 27 69-99 118-144 (160)
39 PF12756 zf-C2H2_2: C2H2 type 81.5 0.46 1E-05 34.3 0.0 24 72-95 1-24 (100)
40 COG5048 FOG: Zn-finger [Genera 80.0 0.71 1.5E-05 39.8 0.6 36 64-99 313-352 (467)
41 COG4049 Uncharacterized protei 76.6 1 2.2E-05 33.5 0.5 27 66-92 13-39 (65)
42 KOG2071 mRNA cleavage and poly 76.0 1.3 2.9E-05 44.7 1.4 32 67-98 415-446 (579)
43 KOG4167 Predicted DNA-binding 75.7 0.72 1.6E-05 48.2 -0.6 29 67-95 789-817 (907)
44 PLN03086 PRLI-interacting fact 75.0 1.6 3.5E-05 44.0 1.6 28 66-94 449-476 (567)
45 PHA00732 hypothetical protein 74.3 1.6 3.4E-05 33.1 1.1 22 70-94 27-48 (79)
46 KOG2482 Predicted C2H2-type Zn 71.1 2.3 5E-05 41.2 1.6 29 70-98 195-225 (423)
47 COG5189 SFP1 Putative transcri 71.1 2 4.3E-05 41.4 1.2 30 66-95 345-377 (423)
48 KOG3608 Zn finger proteins [Ge 65.9 3.7 8E-05 40.1 1.8 28 68-95 350-378 (467)
49 PF12013 DUF3505: Protein of u 65.1 3.9 8.3E-05 31.7 1.5 27 69-95 79-109 (109)
50 PRK04860 hypothetical protein; 64.1 2.9 6.3E-05 35.5 0.7 22 63-84 136-157 (160)
51 PF09986 DUF2225: Uncharacteri 61.3 2 4.4E-05 37.5 -0.8 25 68-92 3-27 (214)
52 PF05443 ROS_MUCR: ROS/MUCR tr 52.3 6.7 0.00015 32.7 0.9 28 68-98 70-97 (132)
53 PF09845 DUF2072: Zn-ribbon co 51.2 6.8 0.00015 32.9 0.8 15 70-84 1-15 (131)
54 COG4957 Predicted transcriptio 49.2 7 0.00015 33.5 0.6 28 70-100 76-103 (148)
55 smart00154 ZnF_AN1 AN1-like Zi 43.5 11 0.00024 25.0 0.7 15 70-84 12-26 (39)
56 smart00834 CxxC_CXXC_SSSS Puta 43.2 10 0.00022 24.1 0.5 16 70-85 5-20 (41)
57 PF13878 zf-C2H2_3: zinc-finge 43.2 14 0.00031 24.7 1.3 25 70-94 13-39 (41)
58 smart00734 ZnF_Rad18 Rad18-lik 42.1 16 0.00034 22.4 1.2 20 71-91 2-21 (26)
59 KOG3408 U1-like Zn-finger-cont 41.0 15 0.00033 30.9 1.3 38 68-108 55-94 (129)
60 COG5048 FOG: Zn-finger [Genera 38.7 15 0.00032 31.7 1.0 34 63-96 54-89 (467)
61 PF10276 zf-CHCC: Zinc-finger 38.2 12 0.00027 25.3 0.3 12 69-80 28-39 (40)
62 PF02748 PyrI_C: Aspartate car 36.1 14 0.00031 26.1 0.4 16 67-82 32-47 (52)
63 TIGR02605 CxxC_CxxC_SSSS putat 35.4 15 0.00033 24.7 0.5 14 70-83 5-18 (52)
64 KOG1146 Homeobox protein [Gene 34.6 28 0.0006 38.9 2.4 28 65-92 460-487 (1406)
65 PF01428 zf-AN1: AN1-like Zinc 33.3 15 0.00032 24.5 0.1 16 69-84 12-27 (43)
66 PF09723 Zn-ribbon_8: Zinc rib 33.0 17 0.00038 24.1 0.4 18 70-87 5-22 (42)
67 PF04959 ARS2: Arsenite-resist 31.4 19 0.00041 32.3 0.5 31 67-97 74-104 (214)
68 PLN02748 tRNA dimethylallyltra 30.1 21 0.00046 35.2 0.6 28 69-96 417-447 (468)
69 KOG1842 FYVE finger-containing 30.0 23 0.0005 35.5 0.8 28 69-96 14-42 (505)
70 PF13451 zf-trcl: Probable zin 30.0 22 0.00047 25.3 0.5 15 68-82 2-16 (49)
71 KOG2785 C2H2-type Zn-finger pr 29.2 25 0.00055 34.3 1.0 26 67-92 65-90 (390)
72 COG3364 Zn-ribbon containing p 28.9 26 0.00056 28.8 0.8 15 70-84 2-16 (112)
73 KOG1146 Homeobox protein [Gene 28.0 25 0.00054 39.2 0.8 27 68-95 1327-1353(1406)
74 PF04780 DUF629: Protein of un 25.8 47 0.001 33.1 2.2 28 69-96 56-84 (466)
75 PF04423 Rad50_zn_hook: Rad50 25.6 25 0.00054 24.2 0.2 11 72-82 22-32 (54)
76 PF14353 CpXC: CpXC protein 24.5 18 0.00039 28.6 -0.8 25 69-93 37-61 (128)
77 COG1773 Rubredoxin [Energy pro 24.1 31 0.00068 25.1 0.5 13 69-81 2-14 (55)
78 PTZ00448 hypothetical protein; 23.8 42 0.00091 32.7 1.4 23 70-92 314-336 (373)
79 TIGR00240 ATCase_reg aspartate 23.8 27 0.00059 30.0 0.1 14 70-83 132-145 (150)
80 cd00924 Cyt_c_Oxidase_Vb Cytoc 23.6 37 0.0008 26.9 0.8 16 65-81 75-90 (97)
81 PRK00893 aspartate carbamoyltr 23.0 35 0.00076 29.3 0.6 17 67-83 131-147 (152)
82 PRK00398 rpoP DNA-directed RNA 23.0 37 0.0008 22.7 0.6 18 69-86 2-19 (46)
83 COG4391 Uncharacterized protei 22.7 38 0.00082 25.4 0.7 14 68-81 46-59 (62)
84 KOG2636 Splicing factor 3a, su 22.5 53 0.0011 33.0 1.8 25 67-91 398-423 (497)
85 PF10571 UPF0547: Uncharacteri 22.4 40 0.00087 20.8 0.6 13 69-81 13-25 (26)
86 PLN02294 cytochrome c oxidase 21.5 43 0.00094 29.5 0.9 15 68-82 139-153 (174)
87 PRK00464 nrdR transcriptional 21.5 37 0.0008 28.9 0.4 22 69-90 27-48 (154)
88 KOG3352 Cytochrome c oxidase, 21.3 45 0.00098 28.8 0.9 14 68-81 131-144 (153)
89 COG4640 Predicted membrane pro 21.1 54 0.0012 32.6 1.5 23 67-89 12-34 (465)
90 KOG0717 Molecular chaperone (D 20.8 46 0.001 33.5 1.0 25 71-95 293-319 (508)
91 COG3677 Transposase and inacti 20.6 39 0.00085 27.7 0.4 16 67-82 50-65 (129)
92 PLN03238 probable histone acet 20.3 68 0.0015 30.3 1.9 28 68-95 46-73 (290)
93 KOG2231 Predicted E3 ubiquitin 20.2 45 0.00097 34.7 0.8 25 71-95 100-140 (669)
94 COG1781 PyrI Aspartate carbamo 20.0 38 0.00083 29.3 0.3 16 70-85 135-150 (153)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=98.40 E-value=1.2e-07 Score=86.67 Aligned_cols=37 Identities=22% Similarity=0.524 Sum_probs=31.9
Q ss_pred CCCCCCCcceeCCccccccCCchhHHHHhhhcCCcch
Q 045333 62 MGTTWPPRSYTCTFCRREFRSAQALGGHMNVHRRDRA 98 (225)
Q Consensus 62 ~~~~~geKpy~C~~CgK~FsS~qALgGHmr~HtgERp 98 (225)
++||+|||||.|..|+|.|.-+++|.-||++|.+.|+
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~ 243 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKK 243 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhhcCCcc
Confidence 4788889999999999999999999999999888874
No 2
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.36 E-value=1.2e-07 Score=96.84 Aligned_cols=40 Identities=28% Similarity=0.510 Sum_probs=36.2
Q ss_pred cCCCCCCCcceeCCccccccCCchhHHHHhhhcCCcchhc
Q 045333 61 IMGTTWPPRSYTCTFCRREFRSAQALGGHMNVHRRDRARL 100 (225)
Q Consensus 61 ~~~~~~geKpy~C~~CgK~FsS~qALgGHmr~HtgERp~~ 100 (225)
-++||+|||||+|++|||.|..+-+|+-||-+|+..-+..
T Consensus 624 HyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R 663 (958)
T KOG1074|consen 624 HYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPAR 663 (958)
T ss_pred hhhcccCcCccccccccchhccccchhhcccccccCcccc
Confidence 4689999999999999999999999999999999875543
No 3
>PHA02768 hypothetical protein; Provisional
Probab=98.09 E-value=1.4e-06 Score=62.81 Aligned_cols=25 Identities=20% Similarity=0.595 Sum_probs=24.2
Q ss_pred ceeCCccccccCCchhHHHHhhhcC
Q 045333 70 SYTCTFCRREFRSAQALGGHMNVHR 94 (225)
Q Consensus 70 py~C~~CgK~FsS~qALgGHmr~Ht 94 (225)
.|+|+.|||.|.+.++|.+|||+|+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC
Confidence 5899999999999999999999999
No 4
>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=97.97 E-value=2.8e-06 Score=49.10 Aligned_cols=23 Identities=39% Similarity=0.853 Sum_probs=22.0
Q ss_pred eeCCccccccCCchhHHHHhhhc
Q 045333 71 YTCTFCRREFRSAQALGGHMNVH 93 (225)
Q Consensus 71 y~C~~CgK~FsS~qALgGHmr~H 93 (225)
|+|.+|+|.|.+...|..||+.|
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 79999999999999999999986
No 5
>PHA00616 hypothetical protein
Probab=97.94 E-value=2.6e-06 Score=58.95 Aligned_cols=29 Identities=21% Similarity=0.421 Sum_probs=27.7
Q ss_pred ceeCCccccccCCchhHHHHhhhcCCcch
Q 045333 70 SYTCTFCRREFRSAQALGGHMNVHRRDRA 98 (225)
Q Consensus 70 py~C~~CgK~FsS~qALgGHmr~HtgERp 98 (225)
||+|..||+.|..++.|..|++.|+++++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 69999999999999999999999999975
No 6
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=97.91 E-value=3.3e-06 Score=77.32 Aligned_cols=31 Identities=23% Similarity=0.548 Sum_probs=29.4
Q ss_pred cceeCCccccccCCchhHHHHhhhcCCcchh
Q 045333 69 RSYTCTFCRREFRSAQALGGHMNVHRRDRAR 99 (225)
Q Consensus 69 Kpy~C~~CgK~FsS~qALgGHmr~HtgERp~ 99 (225)
-+++|.+|||.|++..-|.||+|+||||||-
T Consensus 186 l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF 216 (279)
T KOG2462|consen 186 LPCECGICGKAFSRPWLLQGHIRTHTGEKPF 216 (279)
T ss_pred CCcccccccccccchHHhhcccccccCCCCc
Confidence 5999999999999999999999999999983
No 7
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=97.89 E-value=3.9e-06 Score=85.42 Aligned_cols=36 Identities=22% Similarity=0.573 Sum_probs=34.2
Q ss_pred CCCCCcceeCCccccccCCchhHHHHhhhcCCcchh
Q 045333 64 TTWPPRSYTCTFCRREFRSAQALGGHMNVHRRDRAR 99 (225)
Q Consensus 64 ~~~geKpy~C~~CgK~FsS~qALgGHmr~HtgERp~ 99 (225)
-|+|.|||+|.+|.|.|..+.+|.-|||.|.||||.
T Consensus 916 EHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPf 951 (1007)
T KOG3623|consen 916 EHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPF 951 (1007)
T ss_pred hhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcc
Confidence 578999999999999999999999999999999984
No 8
>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=97.81 E-value=7.9e-06 Score=48.85 Aligned_cols=26 Identities=31% Similarity=0.593 Sum_probs=24.4
Q ss_pred ceeCCccccccCCchhHHHHhhhcCC
Q 045333 70 SYTCTFCRREFRSAQALGGHMNVHRR 95 (225)
Q Consensus 70 py~C~~CgK~FsS~qALgGHmr~Htg 95 (225)
+|+|..|++.|.+..+|..||+.|.+
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 69999999999999999999999964
No 9
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=97.68 E-value=7.1e-05 Score=77.03 Aligned_cols=38 Identities=21% Similarity=0.451 Sum_probs=29.5
Q ss_pred cCCCCCCCcceeCCccccccCCchhHHHHhhhcCCcch
Q 045333 61 IMGTTWPPRSYTCTFCRREFRSAQALGGHMNVHRRDRA 98 (225)
Q Consensus 61 ~~~~~~geKpy~C~~CgK~FsS~qALgGHmr~HtgERp 98 (225)
.++.|+|||||+|++||..|+++-+|+-|...|+.+-|
T Consensus 372 HlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~e~~p 409 (958)
T KOG1074|consen 372 HLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHREKYP 409 (958)
T ss_pred hhhccCCCCCeeecccccccccccceeeeeeeccccCC
Confidence 34677888888888888888888888888888876654
No 10
>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=97.62 E-value=2.7e-05 Score=43.96 Aligned_cols=24 Identities=38% Similarity=0.888 Sum_probs=20.5
Q ss_pred eeCCccccccCCchhHHHHhhhcC
Q 045333 71 YTCTFCRREFRSAQALGGHMNVHR 94 (225)
Q Consensus 71 y~C~~CgK~FsS~qALgGHmr~Ht 94 (225)
|.|.+|++.|.+...|..||+.|.
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 789999999999999999999873
No 11
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=97.58 E-value=8.2e-06 Score=49.62 Aligned_cols=20 Identities=25% Similarity=0.740 Sum_probs=17.7
Q ss_pred CCCCCCcceeCCccccccCC
Q 045333 63 GTTWPPRSYTCTFCRREFRS 82 (225)
Q Consensus 63 ~~~~geKpy~C~~CgK~FsS 82 (225)
.+|+++|||+|++|+|.|.+
T Consensus 7 ~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 7 RTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHSSSSSEEESSSSEEESS
T ss_pred hhcCCCCCCCCCCCcCeeCc
Confidence 36889999999999999974
No 12
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.37 E-value=9.8e-05 Score=41.72 Aligned_cols=25 Identities=40% Similarity=0.784 Sum_probs=23.0
Q ss_pred eeCCccccccCCchhHHHHhhhcCC
Q 045333 71 YTCTFCRREFRSAQALGGHMNVHRR 95 (225)
Q Consensus 71 y~C~~CgK~FsS~qALgGHmr~Htg 95 (225)
|+|..|++.|.....|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 6899999999999999999998853
No 13
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=97.33 E-value=6.1e-05 Score=76.97 Aligned_cols=33 Identities=24% Similarity=0.578 Sum_probs=30.5
Q ss_pred CCcceeCCccccccCCchhHHHHhhhcCCcchh
Q 045333 67 PPRSYTCTFCRREFRSAQALGGHMNVHRRDRAR 99 (225)
Q Consensus 67 geKpy~C~~CgK~FsS~qALgGHmr~HtgERp~ 99 (225)
.-|.|+|..|||.|.-+.+|+-|.|+|.||||.
T Consensus 278 ~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPf 310 (1007)
T KOG3623|consen 278 LLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPF 310 (1007)
T ss_pred hhccccccccchhhhhHHHHHhhheeecCCCCc
Confidence 458999999999999999999999999999984
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=96.86 E-value=0.00057 Score=49.31 Aligned_cols=34 Identities=18% Similarity=0.428 Sum_probs=24.6
Q ss_pred CCCcceeCCccccccCCchhHHHHhhhcCCcchh
Q 045333 66 WPPRSYTCTFCRREFRSAQALGGHMNVHRRDRAR 99 (225)
Q Consensus 66 ~geKpy~C~~CgK~FsS~qALgGHmr~HtgERp~ 99 (225)
-.+.|..|++|++.+++..+|.+||.++++.||.
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~~ 53 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKPG 53 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS--
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccCC
Confidence 3578999999999999999999999988888763
No 15
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.85 E-value=0.00038 Score=40.77 Aligned_cols=24 Identities=25% Similarity=0.758 Sum_probs=22.1
Q ss_pred eeCCccccccCCchhHHHHhhhcC
Q 045333 71 YTCTFCRREFRSAQALGGHMNVHR 94 (225)
Q Consensus 71 y~C~~CgK~FsS~qALgGHmr~Ht 94 (225)
|.|++|++.|.+...|..|++.|+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~ 24 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKK 24 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCC
Confidence 789999999999999999998763
No 16
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=96.77 E-value=0.00028 Score=63.60 Aligned_cols=39 Identities=23% Similarity=0.373 Sum_probs=30.9
Q ss_pred cCCCCCCCcceeCCccccccCCchhHHHHhhhcCCcchh
Q 045333 61 IMGTTWPPRSYTCTFCRREFRSAQALGGHMNVHRRDRAR 99 (225)
Q Consensus 61 ~~~~~~geKpy~C~~CgK~FsS~qALgGHmr~HtgERp~ 99 (225)
-+.+|..-|-|-|.+|||.|...-.|++|+|+|+|.||.
T Consensus 136 h~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpy 174 (267)
T KOG3576|consen 136 HLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPY 174 (267)
T ss_pred HhhhccHHHHHHHhhccCcccchhhhhhhhccccCcccc
Confidence 456777777888888888888888888888888888874
No 17
>PHA00732 hypothetical protein
Probab=96.40 E-value=0.0017 Score=49.21 Aligned_cols=27 Identities=22% Similarity=0.352 Sum_probs=24.0
Q ss_pred ceeCCccccccCCchhHHHHhh-hcCCc
Q 045333 70 SYTCTFCRREFRSAQALGGHMN-VHRRD 96 (225)
Q Consensus 70 py~C~~CgK~FsS~qALgGHmr-~HtgE 96 (225)
||+|..|++.|.+..+|..||+ .|++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~ 28 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLT 28 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCC
Confidence 6899999999999999999998 47653
No 18
>PHA00733 hypothetical protein
Probab=95.99 E-value=0.0041 Score=50.58 Aligned_cols=29 Identities=24% Similarity=0.496 Sum_probs=26.3
Q ss_pred CCCcceeCCccccccCCchhHHHHhhhcC
Q 045333 66 WPPRSYTCTFCRREFRSAQALGGHMNVHR 94 (225)
Q Consensus 66 ~geKpy~C~~CgK~FsS~qALgGHmr~Ht 94 (225)
.++++|.|..|++.|.+...|..|++.|.
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~ 97 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYTE 97 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcCC
Confidence 35899999999999999999999999873
No 19
>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=95.68 E-value=0.0033 Score=37.99 Aligned_cols=24 Identities=29% Similarity=0.638 Sum_probs=21.3
Q ss_pred ceeCCccccccCCchhHHHHhhhc
Q 045333 70 SYTCTFCRREFRSAQALGGHMNVH 93 (225)
Q Consensus 70 py~C~~CgK~FsS~qALgGHmr~H 93 (225)
.|-|.+|+|.|.+..+|..||+.+
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 378999999999999999999863
No 20
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=95.63 E-value=0.0041 Score=56.22 Aligned_cols=37 Identities=22% Similarity=0.429 Sum_probs=31.7
Q ss_pred cCcCCCCCCCcceeCCccccccCCchhHHHHhhhcCC
Q 045333 59 GNIMGTTWPPRSYTCTFCRREFRSAQALGGHMNVHRR 95 (225)
Q Consensus 59 ~~~~~~~~geKpy~C~~CgK~FsS~qALgGHmr~Htg 95 (225)
..-+.||+|-|||+|..|+|.|..+-.|..|.+.-.|
T Consensus 162 krh~rthtgvrpykc~~c~kaftqrcsleshl~kvhg 198 (267)
T KOG3576|consen 162 KRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHG 198 (267)
T ss_pred hhhhccccCccccchhhhhHHHHhhccHHHHHHHHcC
Confidence 3456899999999999999999999999999764333
No 21
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.92 E-value=0.015 Score=42.19 Aligned_cols=25 Identities=40% Similarity=0.911 Sum_probs=22.2
Q ss_pred cceeCCccccccCCchhHHHHhhhc
Q 045333 69 RSYTCTFCRREFRSAQALGGHMNVH 93 (225)
Q Consensus 69 Kpy~C~~CgK~FsS~qALgGHmr~H 93 (225)
+.+.|.+|++.|.+..+|..||+.+
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCCccCCCCcCHHHHHHHHcCc
Confidence 3799999999999999999999975
No 22
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.53 E-value=0.017 Score=33.65 Aligned_cols=23 Identities=26% Similarity=0.613 Sum_probs=19.0
Q ss_pred eeCCccccccCCchhHHHHhhhcC
Q 045333 71 YTCTFCRREFRSAQALGGHMNVHR 94 (225)
Q Consensus 71 y~C~~CgK~FsS~qALgGHmr~Ht 94 (225)
|+|+.|.-... ...|..|++.|.
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 79999999998 999999999864
No 23
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.01 E-value=0.029 Score=34.11 Aligned_cols=21 Identities=29% Similarity=0.738 Sum_probs=18.7
Q ss_pred eeCCccccccCCchhHHHHhhh
Q 045333 71 YTCTFCRREFRSAQALGGHMNV 92 (225)
Q Consensus 71 y~C~~CgK~FsS~qALgGHmr~ 92 (225)
..|.+|||.| ...+|..|+.+
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 88999999875
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=93.78 E-value=0.036 Score=34.35 Aligned_cols=23 Identities=17% Similarity=0.598 Sum_probs=21.1
Q ss_pred ceeCCccccccCCchhHHHHhhh
Q 045333 70 SYTCTFCRREFRSAQALGGHMNV 92 (225)
Q Consensus 70 py~C~~CgK~FsS~qALgGHmr~ 92 (225)
+|.|.+|++.|.+..++..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 68999999999999999999864
No 25
>PHA00733 hypothetical protein
Probab=92.99 E-value=0.06 Score=43.80 Aligned_cols=28 Identities=25% Similarity=0.523 Sum_probs=24.3
Q ss_pred CcceeCCccccccCCchhHHHHhhhcCC
Q 045333 68 PRSYTCTFCRREFRSAQALGGHMNVHRR 95 (225)
Q Consensus 68 eKpy~C~~CgK~FsS~qALgGHmr~Htg 95 (225)
+++|+|.+|+|.|....+|..|++-..+
T Consensus 97 ~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 97 EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 4689999999999999999999976543
No 26
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=92.69 E-value=0.06 Score=32.56 Aligned_cols=15 Identities=27% Similarity=0.468 Sum_probs=13.3
Q ss_pred hHHHHhhhcCCcchh
Q 045333 85 ALGGHMNVHRRDRAR 99 (225)
Q Consensus 85 ALgGHmr~HtgERp~ 99 (225)
+|..||++|+++||.
T Consensus 1 ~l~~H~~~H~~~k~~ 15 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPY 15 (26)
T ss_dssp HHHHHHHHHSSSSSE
T ss_pred CHHHHhhhcCCCCCC
Confidence 589999999999973
No 27
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=92.13 E-value=0.065 Score=52.55 Aligned_cols=26 Identities=27% Similarity=0.627 Sum_probs=24.8
Q ss_pred ceeCCccccccCCchhHHHHhhhcCC
Q 045333 70 SYTCTFCRREFRSAQALGGHMNVHRR 95 (225)
Q Consensus 70 py~C~~CgK~FsS~qALgGHmr~Htg 95 (225)
.|+|..|+|.|...-+|-.|.|.|+-
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKP 320 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKP 320 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCC
Confidence 79999999999999999999999964
No 28
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=91.42 E-value=0.037 Score=51.30 Aligned_cols=36 Identities=25% Similarity=0.564 Sum_probs=29.9
Q ss_pred CcCCCCCCCcceeCCccccccCCchhHHHH-hhhcCC
Q 045333 60 NIMGTTWPPRSYTCTFCRREFRSAQALGGH-MNVHRR 95 (225)
Q Consensus 60 ~~~~~~~geKpy~C~~CgK~FsS~qALgGH-mr~Htg 95 (225)
.|+--|-..|-|+|.+|.|+..+..-|..| |++|+.
T Consensus 24 kiliqhqkakhfkchichkkl~sgpglsihcmqvhke 60 (341)
T KOG2893|consen 24 KILIQHQKAKHFKCHICHKKLFSGPGLSIHCMQVHKE 60 (341)
T ss_pred hhhhhhhhhccceeeeehhhhccCCCceeehhhhhhh
Confidence 444456678999999999999999999999 778864
No 29
>PHA02768 hypothetical protein; Provisional
Probab=89.95 E-value=0.092 Score=37.99 Aligned_cols=24 Identities=8% Similarity=0.027 Sum_probs=19.8
Q ss_pred CCCCCCCcceeCCccccccCCchhHH
Q 045333 62 MGTTWPPRSYTCTFCRREFRSAQALG 87 (225)
Q Consensus 62 ~~~~~geKpy~C~~CgK~FsS~qALg 87 (225)
+.+|+ |+|+|..|+|.|...+.|-
T Consensus 25 ~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 25 LRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred HHhcC--CcccCCcccceecccceeE
Confidence 45676 7999999999999887763
No 30
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=88.05 E-value=0.26 Score=47.87 Aligned_cols=37 Identities=19% Similarity=0.371 Sum_probs=31.6
Q ss_pred cCcCCCCCCCcceeCCccccccCCchhHHHHhhhcCC
Q 045333 59 GNIMGTTWPPRSYTCTFCRREFRSAQALGGHMNVHRR 95 (225)
Q Consensus 59 ~~~~~~~~geKpy~C~~CgK~FsS~qALgGHmr~Htg 95 (225)
..++-.|...|||+|+.|++.|.+-..|.+|..+|+.
T Consensus 281 ~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~ 317 (467)
T KOG3608|consen 281 THIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSK 317 (467)
T ss_pred HHHHhhhccCCCccccchhhhhccHHHHHHHHHhccc
Confidence 3455567789999999999999999999999999984
No 31
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=87.11 E-value=0.24 Score=48.74 Aligned_cols=29 Identities=28% Similarity=0.610 Sum_probs=25.3
Q ss_pred CCcceeCCccccccCCchhHHHHhhhcCC
Q 045333 67 PPRSYTCTFCRREFRSAQALGGHMNVHRR 95 (225)
Q Consensus 67 geKpy~C~~CgK~FsS~qALgGHmr~Htg 95 (225)
.+-.|.|.+|+|+|++.-.|++|+-+|..
T Consensus 353 s~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 353 SSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred cCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 34599999999999999999999877753
No 32
>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=85.80 E-value=0.53 Score=30.86 Aligned_cols=27 Identities=19% Similarity=0.568 Sum_probs=17.7
Q ss_pred CCcceeCCccccccCCc----hhHHHHh-hhc
Q 045333 67 PPRSYTCTFCRREFRSA----QALGGHM-NVH 93 (225)
Q Consensus 67 geKpy~C~~CgK~FsS~----qALgGHm-r~H 93 (225)
+.+..+|++|++.|... ..|..|+ +.|
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 35678999999999985 7888898 444
No 33
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=85.72 E-value=0.54 Score=32.48 Aligned_cols=27 Identities=37% Similarity=0.835 Sum_probs=20.6
Q ss_pred ceeCCccccccCCchhHHHHh-hhcCCcc
Q 045333 70 SYTCTFCRREFRSAQALGGHM-NVHRRDR 97 (225)
Q Consensus 70 py~C~~CgK~FsS~qALgGHm-r~HtgER 97 (225)
.|.|++|++.| +...|..|. ..|..++
T Consensus 2 ~f~CP~C~~~~-~~~~L~~H~~~~H~~~~ 29 (54)
T PF05605_consen 2 SFTCPYCGKGF-SESSLVEHCEDEHRSES 29 (54)
T ss_pred CcCCCCCCCcc-CHHHHHHHHHhHCcCCC
Confidence 58999999955 568899996 5666553
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=83.99 E-value=0.34 Score=46.49 Aligned_cols=24 Identities=21% Similarity=0.654 Sum_probs=21.7
Q ss_pred CCcceeCCccccccCCchhHHHHh
Q 045333 67 PPRSYTCTFCRREFRSAQALGGHM 90 (225)
Q Consensus 67 geKpy~C~~CgK~FsS~qALgGHm 90 (225)
..|||+|.+|+|.+..-.-|+-|.
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCCceeccccchhhccCccceecc
Confidence 469999999999999999998885
No 35
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=83.90 E-value=0.64 Score=31.71 Aligned_cols=25 Identities=20% Similarity=0.612 Sum_probs=20.5
Q ss_pred ceeCCccccccCCc-----hhHHHHhh-hcC
Q 045333 70 SYTCTFCRREFRSA-----QALGGHMN-VHR 94 (225)
Q Consensus 70 py~C~~CgK~FsS~-----qALgGHmr-~Ht 94 (225)
.=.|++|++.++.. .+|..|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 45899999999876 58999988 564
No 36
>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=83.24 E-value=0.75 Score=31.77 Aligned_cols=26 Identities=23% Similarity=0.561 Sum_probs=21.0
Q ss_pred CcceeCCccccccCCchhHHHHhhhcCC
Q 045333 68 PRSYTCTFCRREFRSAQALGGHMNVHRR 95 (225)
Q Consensus 68 eKpy~C~~CgK~FsS~qALgGHmr~Htg 95 (225)
.+.+.|++|.+.+.. .|..||+.+.+
T Consensus 29 ~~~v~CPiC~~~~~~--~l~~Hl~~~H~ 54 (54)
T PF05605_consen 29 SKNVVCPICSSRVTD--NLIRHLNSQHR 54 (54)
T ss_pred CCCccCCCchhhhhh--HHHHHHHHhcC
Confidence 357999999997664 99999987653
No 37
>PLN03086 PRLI-interacting factor K; Provisional
Probab=82.34 E-value=0.81 Score=46.09 Aligned_cols=28 Identities=14% Similarity=0.247 Sum_probs=21.2
Q ss_pred cceeCCccccccCCchhHHHHhhhcCCcch
Q 045333 69 RSYTCTFCRREFRSAQALGGHMNVHRRDRA 98 (225)
Q Consensus 69 Kpy~C~~CgK~FsS~qALgGHmr~HtgERp 98 (225)
++|.|+ |++.| .+..|..|++.|..+|+
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 678888 88655 55788888888887776
No 38
>PRK04860 hypothetical protein; Provisional
Probab=82.18 E-value=0.76 Score=39.08 Aligned_cols=27 Identities=22% Similarity=0.468 Sum_probs=23.7
Q ss_pred cceeCCccccccCCchhHHHHhhhcCCcchh
Q 045333 69 RSYTCTFCRREFRSAQALGGHMNVHRRDRAR 99 (225)
Q Consensus 69 Kpy~C~~CgK~FsS~qALgGHmr~HtgERp~ 99 (225)
-+|.|. |++ ....+..|+++|+++++.
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~Y 144 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVY 144 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccE
Confidence 379998 998 888899999999999863
No 39
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=81.51 E-value=0.46 Score=34.28 Aligned_cols=24 Identities=33% Similarity=0.652 Sum_probs=0.0
Q ss_pred eCCccccccCCchhHHHHhhhcCC
Q 045333 72 TCTFCRREFRSAQALGGHMNVHRR 95 (225)
Q Consensus 72 ~C~~CgK~FsS~qALgGHmr~Htg 95 (225)
+|.+|+..|.+...|..||+...+
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 599999999999999999965444
No 40
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=80.00 E-value=0.71 Score=39.77 Aligned_cols=36 Identities=19% Similarity=0.451 Sum_probs=30.2
Q ss_pred CCCCC--cceeCC--ccccccCCchhHHHHhhhcCCcchh
Q 045333 64 TTWPP--RSYTCT--FCRREFRSAQALGGHMNVHRRDRAR 99 (225)
Q Consensus 64 ~~~ge--Kpy~C~--~CgK~FsS~qALgGHmr~HtgERp~ 99 (225)
.|.++ ++|.|. +|++.|.+..+|..|...|.+.++.
T Consensus 313 ~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (467)
T COG5048 313 NHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPA 352 (467)
T ss_pred ccccccCCceeeeccCCCccccccccccCCcccccCCCcc
Confidence 57778 899999 7999999999999999988887654
No 41
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=76.60 E-value=1 Score=33.52 Aligned_cols=27 Identities=22% Similarity=0.270 Sum_probs=24.5
Q ss_pred CCCcceeCCccccccCCchhHHHHhhh
Q 045333 66 WPPRSYTCTFCRREFRSAQALGGHMNV 92 (225)
Q Consensus 66 ~geKpy~C~~CgK~FsS~qALgGHmr~ 92 (225)
.||--++|+-|++.|+......+|.+.
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 477889999999999999999999874
No 42
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=75.97 E-value=1.3 Score=44.72 Aligned_cols=32 Identities=19% Similarity=0.396 Sum_probs=27.9
Q ss_pred CCcceeCCccccccCCchhHHHHhhhcCCcch
Q 045333 67 PPRSYTCTFCRREFRSAQALGGHMNVHRRDRA 98 (225)
Q Consensus 67 geKpy~C~~CgK~FsS~qALgGHmr~HtgERp 98 (225)
..++.+|+.||+.|....-...||..|-..+-
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~dwh~ 446 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHDDWHR 446 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhhhhhh
Confidence 46889999999999999999999998876544
No 43
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=75.69 E-value=0.72 Score=48.15 Aligned_cols=29 Identities=28% Similarity=0.650 Sum_probs=26.2
Q ss_pred CCcceeCCccccccCCchhHHHHhhhcCC
Q 045333 67 PPRSYTCTFCRREFRSAQALGGHMNVHRR 95 (225)
Q Consensus 67 geKpy~C~~CgK~FsS~qALgGHmr~Htg 95 (225)
..--|-|..|+|.|..-..++-||+.|+-
T Consensus 789 ~~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 789 PTGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CCceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 34579999999999999999999999974
No 44
>PLN03086 PRLI-interacting factor K; Provisional
Probab=75.00 E-value=1.6 Score=44.00 Aligned_cols=28 Identities=21% Similarity=0.446 Sum_probs=23.6
Q ss_pred CCCcceeCCccccccCCchhHHHHhhhcC
Q 045333 66 WPPRSYTCTFCRREFRSAQALGGHMNVHR 94 (225)
Q Consensus 66 ~geKpy~C~~CgK~FsS~qALgGHmr~Ht 94 (225)
..++.+.|++|++.|. ...|..|+++|+
T Consensus 449 el~~H~~C~~Cgk~f~-~s~LekH~~~~H 476 (567)
T PLN03086 449 EAKNHVHCEKCGQAFQ-QGEMEKHMKVFH 476 (567)
T ss_pred ccccCccCCCCCCccc-hHHHHHHHHhcC
Confidence 3467889999999996 678999999875
No 45
>PHA00732 hypothetical protein
Probab=74.33 E-value=1.6 Score=33.13 Aligned_cols=22 Identities=23% Similarity=0.602 Sum_probs=17.5
Q ss_pred ceeCCccccccCCchhHHHHhhhcC
Q 045333 70 SYTCTFCRREFRSAQALGGHMNVHR 94 (225)
Q Consensus 70 py~C~~CgK~FsS~qALgGHmr~Ht 94 (225)
+++|+.|+|.|. .|..|++.+.
T Consensus 27 ~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 27 LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CCccCCCCCEeC---ChhhhhcccC
Confidence 568999999998 4888886543
No 46
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=71.14 E-value=2.3 Score=41.24 Aligned_cols=29 Identities=34% Similarity=0.722 Sum_probs=24.6
Q ss_pred ceeCCccccccCCchhHHHHhh--hcCCcch
Q 045333 70 SYTCTFCRREFRSAQALGGHMN--VHRRDRA 98 (225)
Q Consensus 70 py~C~~CgK~FsS~qALgGHmr--~HtgERp 98 (225)
.++|-+|.|.|+.+..|.-||| .|++-.|
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinP 225 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINP 225 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCC
Confidence 5899999999999999999997 5655444
No 47
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=71.11 E-value=2 Score=41.45 Aligned_cols=30 Identities=23% Similarity=0.589 Sum_probs=25.0
Q ss_pred CCCcceeCCc--cccccCCchhHHHHhh-hcCC
Q 045333 66 WPPRSYTCTF--CRREFRSAQALGGHMN-VHRR 95 (225)
Q Consensus 66 ~geKpy~C~~--CgK~FsS~qALgGHmr-~Htg 95 (225)
.++|||+|++ |.|++....-|+-||. .|..
T Consensus 345 ~d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~ 377 (423)
T COG5189 345 KDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQN 377 (423)
T ss_pred ecCceecCCCCCchhhhccccchhhhhhccccC
Confidence 3469999998 9999999999999985 4433
No 48
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=65.89 E-value=3.7 Score=40.15 Aligned_cols=28 Identities=36% Similarity=0.686 Sum_probs=23.5
Q ss_pred CcceeCCccccccCCchhHHHHhh-hcCC
Q 045333 68 PRSYTCTFCRREFRSAQALGGHMN-VHRR 95 (225)
Q Consensus 68 eKpy~C~~CgK~FsS~qALgGHmr-~Htg 95 (225)
+-+|+|..|+|.|.++.+|+.|.+ .|.-
T Consensus 350 p~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f 378 (467)
T KOG3608|consen 350 PILYACHCCDRFFTSGKSLSAHLMKKHGF 378 (467)
T ss_pred CCceeeecchhhhccchhHHHHHHHhhcc
Confidence 568999999999999999999964 4543
No 49
>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=65.14 E-value=3.9 Score=31.66 Aligned_cols=27 Identities=22% Similarity=0.444 Sum_probs=24.4
Q ss_pred cceeC----CccccccCCchhHHHHhhhcCC
Q 045333 69 RSYTC----TFCRREFRSAQALGGHMNVHRR 95 (225)
Q Consensus 69 Kpy~C----~~CgK~FsS~qALgGHmr~Htg 95 (225)
.-|.| ..|+..+++...|..|++.+.|
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 46999 9999999999999999998764
No 50
>PRK04860 hypothetical protein; Provisional
Probab=64.12 E-value=2.9 Score=35.55 Aligned_cols=22 Identities=14% Similarity=0.244 Sum_probs=18.0
Q ss_pred CCCCCCcceeCCccccccCCch
Q 045333 63 GTTWPPRSYTCTFCRREFRSAQ 84 (225)
Q Consensus 63 ~~~~geKpy~C~~CgK~FsS~q 84 (225)
.+|.++++|.|..|++.|.-..
T Consensus 136 ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 136 RVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred HHhcCCccEECCCCCceeEEec
Confidence 4567899999999999997543
No 51
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=61.28 E-value=2 Score=37.54 Aligned_cols=25 Identities=28% Similarity=0.752 Sum_probs=21.5
Q ss_pred CcceeCCccccccCCchhHHHHhhh
Q 045333 68 PRSYTCTFCRREFRSAQALGGHMNV 92 (225)
Q Consensus 68 eKpy~C~~CgK~FsS~qALgGHmr~ 92 (225)
+|.++|++|++.|.++.-+.+..|+
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 5789999999999998888777665
No 52
>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=52.35 E-value=6.7 Score=32.69 Aligned_cols=28 Identities=25% Similarity=0.580 Sum_probs=18.5
Q ss_pred CcceeCCccccccCCchhHHHHhhhcCCcch
Q 045333 68 PRSYTCTFCRREFRSAQALGGHMNVHRRDRA 98 (225)
Q Consensus 68 eKpy~C~~CgK~FsS~qALgGHmr~HtgERp 98 (225)
+..-.|-+|||.|.. |++|.+.|+|-.|
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCH
Confidence 456799999999975 6999999988765
No 53
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=51.16 E-value=6.8 Score=32.93 Aligned_cols=15 Identities=33% Similarity=0.685 Sum_probs=13.7
Q ss_pred ceeCCccccccCCch
Q 045333 70 SYTCTFCRREFRSAQ 84 (225)
Q Consensus 70 py~C~~CgK~FsS~q 84 (225)
||+|.-||+.|....
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 799999999999876
No 54
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=49.24 E-value=7 Score=33.46 Aligned_cols=28 Identities=21% Similarity=0.265 Sum_probs=23.3
Q ss_pred ceeCCccccccCCchhHHHHhhhcCCcchhc
Q 045333 70 SYTCTFCRREFRSAQALGGHMNVHRRDRARL 100 (225)
Q Consensus 70 py~C~~CgK~FsS~qALgGHmr~HtgERp~~ 100 (225)
---|-.|||.|.+ |++|.++|.+--|..
T Consensus 76 ~IicLEDGkkfKS---LKRHL~t~~gmTPd~ 103 (148)
T COG4957 76 YIICLEDGKKFKS---LKRHLTTHYGLTPDE 103 (148)
T ss_pred eEEEeccCcchHH---HHHHHhcccCCCHHH
Confidence 4579999999975 999999999876643
No 55
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=43.53 E-value=11 Score=25.01 Aligned_cols=15 Identities=20% Similarity=0.693 Sum_probs=13.0
Q ss_pred ceeCCccccccCCch
Q 045333 70 SYTCTFCRREFRSAQ 84 (225)
Q Consensus 70 py~C~~CgK~FsS~q 84 (225)
+|+|..|++.|-...
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 899999999997653
No 56
>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=43.24 E-value=10 Score=24.06 Aligned_cols=16 Identities=31% Similarity=0.692 Sum_probs=12.6
Q ss_pred ceeCCccccccCCchh
Q 045333 70 SYTCTFCRREFRSAQA 85 (225)
Q Consensus 70 py~C~~CgK~FsS~qA 85 (225)
.|+|..||+.|.--+.
T Consensus 5 ~y~C~~Cg~~fe~~~~ 20 (41)
T smart00834 5 EYRCEDCGHTFEVLQK 20 (41)
T ss_pred EEEcCCCCCEEEEEEe
Confidence 5899999999975443
No 57
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=43.19 E-value=14 Score=24.66 Aligned_cols=25 Identities=20% Similarity=0.348 Sum_probs=19.2
Q ss_pred ceeCCccccccCCc--hhHHHHhhhcC
Q 045333 70 SYTCTFCRREFRSA--QALGGHMNVHR 94 (225)
Q Consensus 70 py~C~~CgK~FsS~--qALgGHmr~Ht 94 (225)
.-+|+.||..|... ..-.-|.+.|.
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 35999999999874 45567887775
No 58
>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=42.09 E-value=16 Score=22.36 Aligned_cols=20 Identities=25% Similarity=0.697 Sum_probs=16.1
Q ss_pred eeCCccccccCCchhHHHHhh
Q 045333 71 YTCTFCRREFRSAQALGGHMN 91 (225)
Q Consensus 71 y~C~~CgK~FsS~qALgGHmr 91 (225)
..|++|++.+ ....+..|..
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999999 6678888865
No 59
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=40.98 E-value=15 Score=30.87 Aligned_cols=38 Identities=32% Similarity=0.569 Sum_probs=28.1
Q ss_pred CcceeCCccccccCCchhHHHHhh--hcCCcchhcccccCCCC
Q 045333 68 PRSYTCTFCRREFRSAQALGGHMN--VHRRDRARLHHHQAQPH 108 (225)
Q Consensus 68 eKpy~C~~CgK~FsS~qALgGHmr--~HtgERp~~~~~~~~p~ 108 (225)
--.|-|=.|.|-|....+|.-|.+ .|+ .+++.....|.
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~ktK~HK---rRvK~l~~~Py 94 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKTKVHK---RRVKELREVPY 94 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhccHHH---HHHHhcccCCc
Confidence 348999999999999999999997 453 34444444444
No 60
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=38.70 E-value=15 Score=31.69 Aligned_cols=34 Identities=18% Similarity=0.539 Sum_probs=18.7
Q ss_pred CCCCCCcceeCCc--cccccCCchhHHHHhhhcCCc
Q 045333 63 GTTWPPRSYTCTF--CRREFRSAQALGGHMNVHRRD 96 (225)
Q Consensus 63 ~~~~geKpy~C~~--CgK~FsS~qALgGHmr~HtgE 96 (225)
..+.+++++.|.. |.+.|.....+..|.+.|...
T Consensus 54 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (467)
T COG5048 54 RSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNN 89 (467)
T ss_pred ccccccCCccccccccccccCCcchhhhhccccccc
Confidence 4455566666655 445555555555555555543
No 61
>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=38.25 E-value=12 Score=25.34 Aligned_cols=12 Identities=17% Similarity=0.855 Sum_probs=10.8
Q ss_pred cceeCCcccccc
Q 045333 69 RSYTCTFCRREF 80 (225)
Q Consensus 69 Kpy~C~~CgK~F 80 (225)
++-.|++|++.|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 578999999988
No 62
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=36.12 E-value=14 Score=26.11 Aligned_cols=16 Identities=25% Similarity=0.746 Sum_probs=11.3
Q ss_pred CCcceeCCccccccCC
Q 045333 67 PPRSYTCTFCRREFRS 82 (225)
Q Consensus 67 geKpy~C~~CgK~FsS 82 (225)
....|+|.||++.|..
T Consensus 32 ~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 32 EPIKLRCHYCERIITE 47 (52)
T ss_dssp TTCEEEETTT--EEEH
T ss_pred CCCEEEeeCCCCEecc
Confidence 4578999999998864
No 63
>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=35.35 E-value=15 Score=24.67 Aligned_cols=14 Identities=36% Similarity=0.861 Sum_probs=11.9
Q ss_pred ceeCCccccccCCc
Q 045333 70 SYTCTFCRREFRSA 83 (225)
Q Consensus 70 py~C~~CgK~FsS~ 83 (225)
.|+|..||..|..-
T Consensus 5 ey~C~~Cg~~fe~~ 18 (52)
T TIGR02605 5 EYRCTACGHRFEVL 18 (52)
T ss_pred EEEeCCCCCEeEEE
Confidence 58999999999854
No 64
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=34.64 E-value=28 Score=38.91 Aligned_cols=28 Identities=29% Similarity=0.481 Sum_probs=25.4
Q ss_pred CCCCcceeCCccccccCCchhHHHHhhh
Q 045333 65 TWPPRSYTCTFCRREFRSAQALGGHMNV 92 (225)
Q Consensus 65 ~~geKpy~C~~CgK~FsS~qALgGHmr~ 92 (225)
++-.|-|+|..|+..|+..+.|+.|||.
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRs 487 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRS 487 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccc
Confidence 3445999999999999999999999997
No 65
>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=33.34 E-value=15 Score=24.45 Aligned_cols=16 Identities=19% Similarity=0.663 Sum_probs=10.6
Q ss_pred cceeCCccccccCCch
Q 045333 69 RSYTCTFCRREFRSAQ 84 (225)
Q Consensus 69 Kpy~C~~CgK~FsS~q 84 (225)
-+|+|+.|++.|=...
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 4899999999997643
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=33.04 E-value=17 Score=24.14 Aligned_cols=18 Identities=33% Similarity=0.781 Sum_probs=13.8
Q ss_pred ceeCCccccccCCchhHH
Q 045333 70 SYTCTFCRREFRSAQALG 87 (225)
Q Consensus 70 py~C~~CgK~FsS~qALg 87 (225)
.|+|..||..|-.-+.+.
T Consensus 5 ey~C~~Cg~~fe~~~~~~ 22 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSIS 22 (42)
T ss_pred EEEeCCCCCEEEEEEEcC
Confidence 589999999997655443
No 67
>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=31.43 E-value=19 Score=32.25 Aligned_cols=31 Identities=13% Similarity=0.484 Sum_probs=22.4
Q ss_pred CCcceeCCccccccCCchhHHHHhhhcCCcc
Q 045333 67 PPRSYTCTFCRREFRSAQALGGHMNVHRRDR 97 (225)
Q Consensus 67 geKpy~C~~CgK~FsS~qALgGHmr~HtgER 97 (225)
.+..|.|..|+|.|.-..=-.+|...=+.|+
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 5668999999999999999999975444443
No 68
>PLN02748 tRNA dimethylallyltransferase
Probab=30.12 E-value=21 Score=35.24 Aligned_cols=28 Identities=29% Similarity=0.580 Sum_probs=22.2
Q ss_pred cceeCCcccc-ccCCchhHHHHh--hhcCCc
Q 045333 69 RSYTCTFCRR-EFRSAQALGGHM--NVHRRD 96 (225)
Q Consensus 69 Kpy~C~~CgK-~FsS~qALgGHm--r~HtgE 96 (225)
+.|.|.+|++ .|..-..-..|+ |.|+..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~ 447 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKR 447 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHH
Confidence 7899999997 799888888887 456543
No 69
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=30.01 E-value=23 Score=35.52 Aligned_cols=28 Identities=21% Similarity=0.542 Sum_probs=24.6
Q ss_pred cceeCCccccccCCchhHHHHh-hhcCCc
Q 045333 69 RSYTCTFCRREFRSAQALGGHM-NVHRRD 96 (225)
Q Consensus 69 Kpy~C~~CgK~FsS~qALgGHm-r~HtgE 96 (225)
+-|.|++|.+.|.+-++|.-|. +-|-+|
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 5799999999999999999998 567655
No 70
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=29.98 E-value=22 Score=25.30 Aligned_cols=15 Identities=33% Similarity=0.640 Sum_probs=12.6
Q ss_pred CcceeCCccccccCC
Q 045333 68 PRSYTCTFCRREFRS 82 (225)
Q Consensus 68 eKpy~C~~CgK~FsS 82 (225)
+|.+.|.-||+.|.=
T Consensus 2 Dk~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVF 16 (49)
T ss_pred CeeEEcccCCCeEEE
Confidence 578999999999853
No 71
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=29.25 E-value=25 Score=34.33 Aligned_cols=26 Identities=23% Similarity=0.494 Sum_probs=23.2
Q ss_pred CCcceeCCccccccCCchhHHHHhhh
Q 045333 67 PPRSYTCTFCRREFRSAQALGGHMNV 92 (225)
Q Consensus 67 geKpy~C~~CgK~FsS~qALgGHmr~ 92 (225)
++-++.|.+|.|.|.+..|...|+..
T Consensus 65 ~~~~~~c~~c~k~~~s~~a~~~hl~S 90 (390)
T KOG2785|consen 65 AESVVYCEACNKSFASPKAHENHLKS 90 (390)
T ss_pred cccceehHHhhccccChhhHHHHHHH
Confidence 45689999999999999999999853
No 72
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=28.87 E-value=26 Score=28.85 Aligned_cols=15 Identities=27% Similarity=0.576 Sum_probs=13.4
Q ss_pred ceeCCccccccCCch
Q 045333 70 SYTCTFCRREFRSAQ 84 (225)
Q Consensus 70 py~C~~CgK~FsS~q 84 (225)
||+|.-||+.|...+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 799999999999853
No 73
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=28.01 E-value=25 Score=39.22 Aligned_cols=27 Identities=22% Similarity=0.263 Sum_probs=22.8
Q ss_pred CcceeCCccccccCCchhHHHHhhhcCC
Q 045333 68 PRSYTCTFCRREFRSAQALGGHMNVHRR 95 (225)
Q Consensus 68 eKpy~C~~CgK~FsS~qALgGHmr~Htg 95 (225)
-++| |.+|...|+..++|..|||.-..
T Consensus 1327 ~~~~-c~~c~~~~~~~~alqihm~~~~~ 1353 (1406)
T KOG1146|consen 1327 CTYH-CLACEVLLSGREALQIHMRSSAH 1353 (1406)
T ss_pred cccc-chHHHhhcchhHHHHHHHHHhhh
Confidence 3566 99999999999999999985433
No 74
>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=25.79 E-value=47 Score=33.11 Aligned_cols=28 Identities=29% Similarity=0.595 Sum_probs=24.3
Q ss_pred cceeCCccccccCCchhHHHHhh-hcCCc
Q 045333 69 RSYTCTFCRREFRSAQALGGHMN-VHRRD 96 (225)
Q Consensus 69 Kpy~C~~CgK~FsS~qALgGHmr-~HtgE 96 (225)
|--.|.+|.+.|.....+..||. -|-+.
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 56789999999999999999995 67654
No 75
>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=25.55 E-value=25 Score=24.20 Aligned_cols=11 Identities=27% Similarity=0.899 Sum_probs=6.5
Q ss_pred eCCccccccCC
Q 045333 72 TCTFCRREFRS 82 (225)
Q Consensus 72 ~C~~CgK~FsS 82 (225)
.|++|+|.|..
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 99999999986
No 76
>PF14353 CpXC: CpXC protein
Probab=24.52 E-value=18 Score=28.56 Aligned_cols=25 Identities=32% Similarity=0.432 Sum_probs=19.6
Q ss_pred cceeCCccccccCCchhHHHHhhhc
Q 045333 69 RSYTCTFCRREFRSAQALGGHMNVH 93 (225)
Q Consensus 69 Kpy~C~~CgK~FsS~qALgGHmr~H 93 (225)
-.|.|+.||+.|.-...+--|-..|
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~D~~~ 61 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYHDPEK 61 (128)
T ss_pred CEEECCCCCCceecCCCEEEEcCCC
Confidence 4799999999998877776665543
No 77
>COG1773 Rubredoxin [Energy production and conversion]
Probab=24.15 E-value=31 Score=25.09 Aligned_cols=13 Identities=15% Similarity=0.797 Sum_probs=11.1
Q ss_pred cceeCCccccccC
Q 045333 69 RSYTCTFCRREFR 81 (225)
Q Consensus 69 Kpy~C~~CgK~Fs 81 (225)
+.|+|+.||..|.
T Consensus 2 ~~~~C~~CG~vYd 14 (55)
T COG1773 2 KRWRCSVCGYVYD 14 (55)
T ss_pred CceEecCCceEec
Confidence 4689999999985
No 78
>PTZ00448 hypothetical protein; Provisional
Probab=23.84 E-value=42 Score=32.68 Aligned_cols=23 Identities=17% Similarity=0.356 Sum_probs=21.1
Q ss_pred ceeCCccccccCCchhHHHHhhh
Q 045333 70 SYTCTFCRREFRSAQALGGHMNV 92 (225)
Q Consensus 70 py~C~~CgK~FsS~qALgGHmr~ 92 (225)
.|.|..|+-.|.+......|++.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 68899999999999999999983
No 79
>TIGR00240 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff.
Probab=23.79 E-value=27 Score=29.97 Aligned_cols=14 Identities=21% Similarity=0.826 Sum_probs=11.9
Q ss_pred ceeCCccccccCCc
Q 045333 70 SYTCTFCRREFRSA 83 (225)
Q Consensus 70 py~C~~CgK~FsS~ 83 (225)
.|+|.||++.|...
T Consensus 132 ~lrC~YCe~~~~~~ 145 (150)
T TIGR00240 132 ALRCYYCEKEIEHN 145 (150)
T ss_pred EEEEECCCCEEecc
Confidence 59999999999643
No 80
>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=23.62 E-value=37 Score=26.95 Aligned_cols=16 Identities=19% Similarity=0.464 Sum_probs=13.2
Q ss_pred CCCCcceeCCccccccC
Q 045333 65 TWPPRSYTCTFCRREFR 81 (225)
Q Consensus 65 ~~geKpy~C~~CgK~Fs 81 (225)
+.+ ++++|..||.-|.
T Consensus 75 ~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 75 EKG-KPKRCPECGHVFK 90 (97)
T ss_pred eCC-CceeCCCCCcEEE
Confidence 344 7999999999885
No 81
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=23.00 E-value=35 Score=29.30 Aligned_cols=17 Identities=29% Similarity=0.905 Sum_probs=13.7
Q ss_pred CCcceeCCccccccCCc
Q 045333 67 PPRSYTCTFCRREFRSA 83 (225)
Q Consensus 67 geKpy~C~~CgK~FsS~ 83 (225)
....|+|.||++.|...
T Consensus 131 ~~~~~rC~YCe~~~~~~ 147 (152)
T PRK00893 131 EPIKLRCKYCEKEFSED 147 (152)
T ss_pred CCCEEEeeCCCCEechh
Confidence 34579999999999753
No 82
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=22.98 E-value=37 Score=22.65 Aligned_cols=18 Identities=28% Similarity=0.527 Sum_probs=13.2
Q ss_pred cceeCCccccccCCchhH
Q 045333 69 RSYTCTFCRREFRSAQAL 86 (225)
Q Consensus 69 Kpy~C~~CgK~FsS~qAL 86 (225)
..|+|..||..|.-...-
T Consensus 2 ~~y~C~~CG~~~~~~~~~ 19 (46)
T PRK00398 2 AEYKCARCGREVELDEYG 19 (46)
T ss_pred CEEECCCCCCEEEECCCC
Confidence 468999999988664443
No 83
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.71 E-value=38 Score=25.35 Aligned_cols=14 Identities=21% Similarity=0.847 Sum_probs=11.7
Q ss_pred CcceeCCccccccC
Q 045333 68 PRSYTCTFCRREFR 81 (225)
Q Consensus 68 eKpy~C~~CgK~Fs 81 (225)
+..-.|++|++.|+
T Consensus 46 ~gev~CPYC~t~y~ 59 (62)
T COG4391 46 EGEVVCPYCSTRYR 59 (62)
T ss_pred CCcEecCccccEEE
Confidence 45679999999986
No 84
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=22.48 E-value=53 Score=33.04 Aligned_cols=25 Identities=24% Similarity=0.618 Sum_probs=22.0
Q ss_pred CCcceeCCccc-cccCCchhHHHHhh
Q 045333 67 PPRSYTCTFCR-REFRSAQALGGHMN 91 (225)
Q Consensus 67 geKpy~C~~Cg-K~FsS~qALgGHmr 91 (225)
=.+.|.|.||| +++.-..|+.+|..
T Consensus 398 L~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 398 LDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred CCcccceeeccCccccCcHHHHHHhH
Confidence 35789999999 99999999999964
No 85
>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=22.35 E-value=40 Score=20.79 Aligned_cols=13 Identities=23% Similarity=0.690 Sum_probs=10.4
Q ss_pred cceeCCccccccC
Q 045333 69 RSYTCTFCRREFR 81 (225)
Q Consensus 69 Kpy~C~~CgK~Fs 81 (225)
..-.|+.||..|.
T Consensus 13 ~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 13 SAKFCPHCGYDFE 25 (26)
T ss_pred hcCcCCCCCCCCc
Confidence 3458999999995
No 86
>PLN02294 cytochrome c oxidase subunit Vb
Probab=21.53 E-value=43 Score=29.49 Aligned_cols=15 Identities=27% Similarity=0.786 Sum_probs=12.8
Q ss_pred CcceeCCccccccCC
Q 045333 68 PRSYTCTFCRREFRS 82 (225)
Q Consensus 68 eKpy~C~~CgK~FsS 82 (225)
.|+++|..||..|.-
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 379999999999863
No 87
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=21.49 E-value=37 Score=28.88 Aligned_cols=22 Identities=18% Similarity=0.356 Sum_probs=17.9
Q ss_pred cceeCCccccccCCchhHHHHh
Q 045333 69 RSYTCTFCRREFRSAQALGGHM 90 (225)
Q Consensus 69 Kpy~C~~CgK~FsS~qALgGHm 90 (225)
|-|+|.-||+.|.....+..=|
T Consensus 27 ~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 27 RRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred eeeeccccCCcceEeEeccCcc
Confidence 3499999999999877766655
No 88
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=21.27 E-value=45 Score=28.85 Aligned_cols=14 Identities=21% Similarity=0.577 Sum_probs=11.4
Q ss_pred CcceeCCccccccC
Q 045333 68 PRSYTCTFCRREFR 81 (225)
Q Consensus 68 eKpy~C~~CgK~Fs 81 (225)
.+.++|..||.-|.
T Consensus 131 ge~~rc~eCG~~fk 144 (153)
T KOG3352|consen 131 GETQRCPECGHYFK 144 (153)
T ss_pred CCcccCCcccceEE
Confidence 35788999998885
No 89
>COG4640 Predicted membrane protein [Function unknown]
Probab=21.07 E-value=54 Score=32.62 Aligned_cols=23 Identities=26% Similarity=0.504 Sum_probs=18.6
Q ss_pred CCcceeCCccccccCCchhHHHH
Q 045333 67 PPRSYTCTFCRREFRSAQALGGH 89 (225)
Q Consensus 67 geKpy~C~~CgK~FsS~qALgGH 89 (225)
.|-.+.|+.||..|..++++..-
T Consensus 12 ~Ed~~qC~qCG~~~t~~~sqan~ 34 (465)
T COG4640 12 AEDDVQCTQCGHKFTSRQSQANK 34 (465)
T ss_pred ccccccccccCCcCCchhhhhhH
Confidence 34455699999999999998873
No 90
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=20.76 E-value=46 Score=33.54 Aligned_cols=25 Identities=32% Similarity=0.748 Sum_probs=21.6
Q ss_pred eeCCccccccCCchhHHHHhh--hcCC
Q 045333 71 YTCTFCRREFRSAQALGGHMN--VHRR 95 (225)
Q Consensus 71 y~C~~CgK~FsS~qALgGHmr--~Htg 95 (225)
+-|-+|.|.|.+--+|..|.+ .|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHke 319 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKE 319 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHH
Confidence 889999999999999999975 4543
No 91
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.64 E-value=39 Score=27.72 Aligned_cols=16 Identities=25% Similarity=0.652 Sum_probs=13.3
Q ss_pred CCcceeCCccccccCC
Q 045333 67 PPRSYTCTFCRREFRS 82 (225)
Q Consensus 67 geKpy~C~~CgK~FsS 82 (225)
+.--|+|+-|++.|.-
T Consensus 50 ~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 50 GHQRYKCKSCGSTFTV 65 (129)
T ss_pred cccccccCCcCcceee
Confidence 3557999999999975
No 92
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=20.27 E-value=68 Score=30.28 Aligned_cols=28 Identities=21% Similarity=0.521 Sum_probs=24.7
Q ss_pred CcceeCCccccccCCchhHHHHhhhcCC
Q 045333 68 PRSYTCTFCRREFRSAQALGGHMNVHRR 95 (225)
Q Consensus 68 eKpy~C~~CgK~FsS~qALgGHmr~Htg 95 (225)
++-|-|.+|-|=|.+...|..|+...+-
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~C~~ 73 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAKCDI 73 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHhCCC
Confidence 5789999999999999999999985543
No 93
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.23 E-value=45 Score=34.72 Aligned_cols=25 Identities=40% Similarity=0.853 Sum_probs=18.8
Q ss_pred eeCCccccccC---------------CchhHHHHh-hhcCC
Q 045333 71 YTCTFCRREFR---------------SAQALGGHM-NVHRR 95 (225)
Q Consensus 71 y~C~~CgK~Fs---------------S~qALgGHm-r~Htg 95 (225)
|.|.+|++.|. +...|..|| ..|..
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~~ 140 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHKL 140 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhhh
Confidence 67777777774 889999999 46654
No 94
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=20.01 E-value=38 Score=29.26 Aligned_cols=16 Identities=19% Similarity=0.845 Sum_probs=12.9
Q ss_pred ceeCCccccccCCchh
Q 045333 70 SYTCTFCRREFRSAQA 85 (225)
Q Consensus 70 py~C~~CgK~FsS~qA 85 (225)
.|+|.||+|.|.....
T Consensus 135 ~lrC~YCe~~~~~~~v 150 (153)
T COG1781 135 ALRCKYCEKTFSEDEV 150 (153)
T ss_pred EEEEEecCcEechhhh
Confidence 3999999999976543
Done!