Query 034948
Match_columns 78
No_of_seqs 103 out of 155
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 07:56:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034948.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034948hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12907 zf-met2: Zinc-binding 99.9 1.3E-25 2.8E-30 128.1 3.0 40 37-76 1-40 (40)
2 KOG4118 Uncharacterized conser 99.8 1.2E-20 2.5E-25 118.8 5.3 65 1-70 1-68 (74)
3 PF04419 4F5: 4F5 protein fami 98.1 1.3E-07 2.8E-12 53.1 -2.9 35 1-37 1-38 (38)
4 PF12874 zf-met: Zinc-finger o 95.7 0.0051 1.1E-07 30.0 1.0 23 38-63 1-23 (25)
5 PF13894 zf-C2H2_4: C2H2-type 95.4 0.0088 1.9E-07 27.9 1.1 24 38-64 1-24 (24)
6 KOG4488 Small EDRK-rich protei 94.9 0.038 8.2E-07 34.9 3.2 20 1-22 1-20 (70)
7 PF00096 zf-C2H2: Zinc finger, 94.2 0.022 4.7E-07 27.2 0.8 22 38-62 1-22 (23)
8 PF13909 zf-H2C2_5: C2H2-type 93.5 0.026 5.7E-07 27.4 0.4 24 38-65 1-24 (24)
9 PF13912 zf-C2H2_6: C2H2-type 93.5 0.038 8.2E-07 27.3 1.0 25 38-65 2-26 (27)
10 PF09237 GAGA: GAGA factor; I 90.7 0.19 4.2E-06 30.4 1.8 27 38-67 25-51 (54)
11 PF02892 zf-BED: BED zinc fing 90.2 0.15 3.2E-06 27.9 1.0 29 37-65 16-45 (45)
12 PF05605 zf-Di19: Drought indu 89.2 0.31 6.8E-06 28.0 1.9 28 37-68 2-29 (54)
13 smart00355 ZnF_C2H2 zinc finge 88.9 0.3 6.6E-06 22.4 1.4 24 38-65 1-24 (26)
14 smart00451 ZnF_U1 U1-like zinc 88.4 0.26 5.7E-06 25.3 1.0 24 37-63 3-26 (35)
15 PF12171 zf-C2H2_jaz: Zinc-fin 85.5 0.18 4E-06 25.1 -0.5 23 38-63 2-24 (27)
16 PF12756 zf-C2H2_2: C2H2 type 83.9 0.89 1.9E-05 27.2 1.9 28 37-67 50-78 (100)
17 smart00614 ZnF_BED BED zinc fi 81.0 1 2.2E-05 25.5 1.3 30 37-66 18-49 (50)
18 PHA00616 hypothetical protein 80.8 1.7 3.8E-05 25.0 2.3 29 38-69 2-30 (44)
19 KOG1842 FYVE finger-containing 79.1 1.4 2.9E-05 36.6 1.9 29 37-68 15-43 (505)
20 PF13913 zf-C2HC_2: zinc-finge 79.1 1.2 2.6E-05 22.3 1.1 20 38-61 3-22 (25)
21 PHA02768 hypothetical protein; 78.9 1.7 3.7E-05 26.1 1.9 28 35-66 3-30 (55)
22 smart00734 ZnF_Rad18 Rad18-lik 77.6 1.6 3.6E-05 22.1 1.3 20 38-61 2-21 (26)
23 PF04780 DUF629: Protein of un 73.5 1.7 3.6E-05 35.7 1.1 27 38-67 58-84 (466)
24 PF12756 zf-C2H2_2: C2H2 type 69.1 1.6 3.4E-05 26.1 0.0 26 39-67 1-26 (100)
25 PHA00733 hypothetical protein 63.4 4.6 0.0001 27.2 1.4 21 38-61 74-94 (128)
26 PHA00732 hypothetical protein 58.3 8.6 0.00019 24.1 1.9 9 39-47 29-37 (79)
27 COG2879 Uncharacterized small 56.4 11 0.00024 23.5 2.2 20 49-68 21-40 (65)
28 PF04988 AKAP95: A-kinase anch 54.6 6.4 0.00014 28.5 1.0 23 38-63 1-23 (165)
29 PF09986 DUF2225: Uncharacteri 49.9 4.6 0.0001 29.2 -0.4 13 37-49 5-17 (214)
30 PF12013 DUF3505: Protein of u 46.8 12 0.00025 23.9 1.2 25 37-64 80-108 (109)
31 PF13719 zinc_ribbon_5: zinc-r 43.6 4.5 9.7E-05 21.8 -1.0 16 36-51 1-16 (37)
32 PF13465 zf-H2C2_2: Zinc-finge 42.9 5 0.00011 19.9 -0.8 12 37-48 14-25 (26)
33 PF03884 DUF329: Domain of unk 41.4 7.7 0.00017 23.4 -0.2 14 36-49 1-14 (57)
34 smart00586 ZnF_DBF Zinc finger 40.8 12 0.00025 22.0 0.5 20 38-63 6-25 (49)
35 TIGR02098 MJ0042_CXXC MJ0042 f 40.8 4.6 0.0001 21.3 -1.2 16 36-51 1-16 (38)
36 KOG3214 Uncharacterized Zn rib 40.5 8.8 0.00019 26.1 -0.1 16 38-53 48-63 (109)
37 COG0299 PurN Folate-dependent 40.0 18 0.0004 26.8 1.5 32 42-76 83-118 (200)
38 PTZ00448 hypothetical protein; 39.0 17 0.00037 29.3 1.3 24 37-63 314-337 (373)
39 PF07535 zf-DBF: DBF zinc fing 38.6 11 0.00024 22.0 0.1 19 39-63 7-25 (49)
40 PF03194 LUC7: LUC7 N_terminus 38.6 19 0.00042 26.9 1.5 26 38-63 191-216 (254)
41 PF05290 Baculo_IE-1: Baculovi 38.4 9.9 0.00021 26.9 -0.1 16 36-51 120-135 (140)
42 KOG3576 Ovo and related transc 34.6 25 0.00053 27.0 1.5 32 34-68 209-240 (267)
43 PF04423 Rad50_zn_hook: Rad50 34.2 12 0.00026 21.3 -0.2 23 39-62 22-44 (54)
44 KOG2482 Predicted C2H2-type Zn 33.6 25 0.00053 28.7 1.4 29 37-68 195-228 (423)
45 KOG1280 Uncharacterized conser 29.8 37 0.0008 27.5 1.8 37 35-74 77-113 (381)
46 PF14357 DUF4404: Domain of un 28.6 41 0.00089 21.2 1.6 14 54-67 56-69 (85)
47 KOG3623 Homeobox transcription 27.8 39 0.00085 30.2 1.7 31 38-72 923-953 (1007)
48 KOG3608 Zn finger proteins [Ge 26.8 50 0.0011 27.2 2.1 29 37-68 263-291 (467)
49 PF13445 zf-RING_UBOX: RING-ty 26.8 24 0.00051 19.7 0.2 13 40-53 1-13 (43)
50 PF13717 zinc_ribbon_4: zinc-r 26.7 17 0.00036 19.5 -0.5 13 36-48 1-13 (36)
51 PF10146 zf-C4H2: Zinc finger- 25.6 27 0.00058 26.0 0.3 18 38-68 209-226 (230)
52 cd00066 G-alpha G protein alph 25.4 44 0.00095 25.2 1.5 18 60-77 241-258 (317)
53 KOG1493 Anaphase-promoting com 24.5 24 0.00052 23.0 -0.1 11 38-48 71-81 (84)
54 KOG2785 C2H2-type Zn-finger pr 22.3 81 0.0018 25.7 2.5 29 32-63 63-91 (390)
55 KOG1074 Transcriptional repres 21.4 40 0.00086 30.3 0.6 33 38-73 634-666 (958)
56 KOG3623 Homeobox transcription 21.0 60 0.0013 29.1 1.6 33 37-73 281-313 (1007)
57 PF12230 PRP21_like_P: Pre-mRN 20.9 33 0.00071 24.7 0.0 23 35-61 166-188 (229)
58 PRK11088 rrmA 23S rRNA methylt 20.7 33 0.00072 24.8 0.0 12 37-48 2-13 (272)
No 1
>PF12907 zf-met2: Zinc-binding
Probab=99.91 E-value=1.3e-25 Score=128.05 Aligned_cols=40 Identities=58% Similarity=1.007 Sum_probs=38.8
Q ss_pred cccchhhhhhhhccCChhHHHHHHHhcCCCCCccccCCCC
Q 034948 37 SIQCKVCMQTFMCTTSEVKCREHAEAKHPKSDIYACFPHL 76 (78)
Q Consensus 37 ~i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~~~~~CFP~~ 76 (78)
+|+|+||||+||+|+++++|++|+||||||++|++|||+|
T Consensus 1 ~i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~~CFP~l 40 (40)
T PF12907_consen 1 NIICKICRQTFMQTTNEPQLKEHAENKHPKNTFEECFPNL 40 (40)
T ss_pred CcCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHHHcCCCC
Confidence 5899999999999999999999999999999999999986
No 2
>KOG4118 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.82 E-value=1.2e-20 Score=118.84 Aligned_cols=65 Identities=31% Similarity=0.453 Sum_probs=58.3
Q ss_pred CCCccHHHHHHHHHHHHHHHhh---hcccCcHHHHHhhccccchhhhhhhhccCChhHHHHHHHhcCCCCCcc
Q 034948 1 MGGGNGQKAKMAREKNLEKQKA---ANKGSQLETNKKAMSIQCKVCMQTFMCTTSEVKCREHAEAKHPKSDIY 70 (78)
Q Consensus 1 Mg~GNg~ka~~~r~rn~kk~~k---~~~~SQlkan~~A~~i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~~~~ 70 (78)
|.||.+ | .++|+||++|+++ +.+++|+.++.+||+++|.||+.+ |+|+.++++||||||||++|.
T Consensus 1 MARGhQ-K-iqSQqknaeKqAkakk~~G~DQK~AA~~aL~~kCtVC~~~---mpdpktfkqhfe~kHpk~~~P 68 (74)
T KOG4118|consen 1 MARGHQ-K-IQSQQKNAEKQAKAKKKQGHDQKAAAMAALHHKCTVCMVQ---MPDPKTFKQHFENKHPKEPLP 68 (74)
T ss_pred CcchHH-H-HHHHHHHHHHHHHHHHHcCccHHHHHHHHHHhhhHhhHhh---CCCCchHHHHHhhcCCCCCCC
Confidence 777744 4 8999999999766 567899999999999999999999 999999999999999999864
No 3
>PF04419 4F5: 4F5 protein family; InterPro: IPR007513 Members of this family are short proteins that are rich in aspartate, glutamate, lysine and arginine. Although the function of these proteins is unknown, they are found to be ubiquitously expressed [].; PDB: 1WVK_A.
Probab=98.09 E-value=1.3e-07 Score=53.11 Aligned_cols=35 Identities=37% Similarity=0.482 Sum_probs=17.5
Q ss_pred CCCccHHHHHHHHHHHHHHHhh---hcccCcHHHHHhhcc
Q 034948 1 MGGGNGQKAKMAREKNLEKQKA---ANKGSQLETNKKAMS 37 (78)
Q Consensus 1 Mg~GNg~ka~~~r~rn~kk~~k---~~~~SQlkan~~A~~ 37 (78)
|++||++ +++|+||++++++ +.++|||++++++|+
T Consensus 1 MtRGnQr--~~aRekn~Kk~~~~~~k~~~s~l~~~~~~l~ 38 (38)
T PF04419_consen 1 MTRGNQR--EQAREKNQKKQAKQKKKGGKSGLKAAQRALN 38 (38)
T ss_dssp ---SGGG--TTTSTTT---SS---SS-SS-SS----TT--
T ss_pred CccHhHH--HHHHHHHHHHhhccccCCCccchhHHHHhcC
Confidence 8888886 8999999999963 567899999999875
No 4
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.69 E-value=0.0051 Score=30.00 Aligned_cols=23 Identities=30% Similarity=0.639 Sum_probs=20.2
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhc
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAK 63 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~K 63 (78)
+.|.||..+ ..++.+|.+|..++
T Consensus 1 ~~C~~C~~~---f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKS---FSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEE---ESSHHHHHHHHTTH
T ss_pred CCCCCCCCC---cCCHHHHHHHHCcC
Confidence 469999999 67999999999876
No 5
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=95.39 E-value=0.0088 Score=27.93 Aligned_cols=24 Identities=29% Similarity=0.663 Sum_probs=19.0
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhcC
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAKH 64 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~KH 64 (78)
++|++|..+ ..+...|..|....|
T Consensus 1 ~~C~~C~~~---~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKS---FRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-E---ESSHHHHHHHHHHHS
T ss_pred CCCcCCCCc---CCcHHHHHHHHHhhC
Confidence 479999999 568899999998876
No 6
>KOG4488 consensus Small EDRK-rich protein H4F5 [General function prediction only]
Probab=94.87 E-value=0.038 Score=34.90 Aligned_cols=20 Identities=45% Similarity=0.722 Sum_probs=18.0
Q ss_pred CCCccHHHHHHHHHHHHHHHhh
Q 034948 1 MGGGNGQKAKMAREKNLEKQKA 22 (78)
Q Consensus 1 Mg~GNg~ka~~~r~rn~kk~~k 22 (78)
|.+||++ .-+|++|++|.+.
T Consensus 1 MtRGNQR--dLaRqKN~KK~~d 20 (70)
T KOG4488|consen 1 MTRGNQR--DLARQKNMKKQQD 20 (70)
T ss_pred CCcchHH--HHHHHHHHHHHHH
Confidence 8999998 8899999999874
No 7
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=94.19 E-value=0.022 Score=27.16 Aligned_cols=22 Identities=23% Similarity=0.670 Sum_probs=19.2
Q ss_pred ccchhhhhhhhccCChhHHHHHHHh
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEA 62 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~ 62 (78)
++|.+|..+| .++..|..|...
T Consensus 1 y~C~~C~~~f---~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSF---SSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEE---SSHHHHHHHHHH
T ss_pred CCCCCCCCcc---CCHHHHHHHHhH
Confidence 5799999995 588999999886
No 8
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=93.52 E-value=0.026 Score=27.40 Aligned_cols=24 Identities=25% Similarity=0.636 Sum_probs=18.3
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhcCC
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAKHP 65 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~KHp 65 (78)
+.|+.|--. +. +..|.+|.+..||
T Consensus 1 y~C~~C~y~---t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYS---TS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-E---ES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCc---CC-HHHHHHHHHhhCc
Confidence 579999844 55 8899999999886
No 9
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=93.50 E-value=0.038 Score=27.26 Aligned_cols=25 Identities=32% Similarity=0.561 Sum_probs=21.1
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhcCC
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAKHP 65 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~KHp 65 (78)
+.|.+|..+|. +...|.+|-...|+
T Consensus 2 ~~C~~C~~~F~---~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 2 FECDECGKTFS---SLSALREHKRSHCS 26 (27)
T ss_dssp EEETTTTEEES---SHHHHHHHHCTTTT
T ss_pred CCCCccCCccC---ChhHHHHHhHHhcC
Confidence 68999999975 78899999976665
No 10
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=90.74 E-value=0.19 Score=30.35 Aligned_cols=27 Identities=26% Similarity=0.480 Sum_probs=21.2
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhcCCCC
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAKHPKS 67 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~ 67 (78)
.+|+||..+ ......|+.|.|..|-+.
T Consensus 25 atCP~C~a~---~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 25 ATCPICGAV---IRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp EE-TTT--E---ESSHHHHHHHHHHHTTTS
T ss_pred CCCCcchhh---ccchhhHHHHHHHHhccc
Confidence 589999999 778899999999999665
No 11
>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=90.21 E-value=0.15 Score=27.90 Aligned_cols=29 Identities=24% Similarity=0.547 Sum_probs=21.2
Q ss_pred cccchhhhhhhhcc-CChhHHHHHHHhcCC
Q 034948 37 SIQCKVCMQTFMCT-TSEVKCREHAEAKHP 65 (78)
Q Consensus 37 ~i~C~vC~~~Fm~t-~~~~~L~~H~e~KHp 65 (78)
..+|..|...|-.. ..-..|..|...+||
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL~~~hp 45 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHLKKKHP 45 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHHHHTTH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhhhhhCc
Confidence 46899999998764 456899999999997
No 12
>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=89.22 E-value=0.31 Score=27.97 Aligned_cols=28 Identities=36% Similarity=0.599 Sum_probs=22.4
Q ss_pred cccchhhhhhhhccCChhHHHHHHHhcCCCCC
Q 034948 37 SIQCKVCMQTFMCTTSEVKCREHAEAKHPKSD 68 (78)
Q Consensus 37 ~i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~~ 68 (78)
.+.|+.|...| +...|.+|.+..|+.+.
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 47899999963 56789999999998653
No 13
>smart00355 ZnF_C2H2 zinc finger.
Probab=88.92 E-value=0.3 Score=22.45 Aligned_cols=24 Identities=29% Similarity=0.641 Sum_probs=19.5
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhcCC
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAKHP 65 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~KHp 65 (78)
+.|.+|..+| .....|..|.. .|.
T Consensus 1 ~~C~~C~~~f---~~~~~l~~H~~-~H~ 24 (26)
T smart00355 1 YRCPECGKVF---KSKSALKEHMR-THX 24 (26)
T ss_pred CCCCCCcchh---CCHHHHHHHHH-Hhc
Confidence 4799999995 57789999988 554
No 14
>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=88.36 E-value=0.26 Score=25.28 Aligned_cols=24 Identities=33% Similarity=0.699 Sum_probs=20.5
Q ss_pred cccchhhhhhhhccCChhHHHHHHHhc
Q 034948 37 SIQCKVCMQTFMCTTSEVKCREHAEAK 63 (78)
Q Consensus 37 ~i~C~vC~~~Fm~t~~~~~L~~H~e~K 63 (78)
.+.|.+|..+|- +...|.+|..++
T Consensus 3 ~~~C~~C~~~~~---~~~~~~~H~~gk 26 (35)
T smart00451 3 GFYCKLCNVTFT---DEISVEAHLKGK 26 (35)
T ss_pred CeEccccCCccC---CHHHHHHHHChH
Confidence 367999999963 888999999987
No 15
>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=85.46 E-value=0.18 Score=25.14 Aligned_cols=23 Identities=26% Similarity=0.545 Sum_probs=19.7
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhc
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAK 63 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~K 63 (78)
+.|.+|.-. ..+...|.+|..+|
T Consensus 2 ~~C~~C~k~---f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 2 FYCDACDKY---FSSENQLKQHMKSK 24 (27)
T ss_dssp CBBTTTTBB---BSSHHHHHCCTTSH
T ss_pred CCcccCCCC---cCCHHHHHHHHccC
Confidence 579999999 46889999998875
No 16
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=83.87 E-value=0.89 Score=27.19 Aligned_cols=28 Identities=39% Similarity=0.678 Sum_probs=22.0
Q ss_pred cccchhhhhhhhccCChhHHHHHHHhc-CCCC
Q 034948 37 SIQCKVCMQTFMCTTSEVKCREHAEAK-HPKS 67 (78)
Q Consensus 37 ~i~C~vC~~~Fm~t~~~~~L~~H~e~K-HpK~ 67 (78)
.+.|.+|...| .+...|.+|..++ |.+.
T Consensus 50 ~~~C~~C~~~f---~s~~~l~~Hm~~~~H~~~ 78 (100)
T PF12756_consen 50 SFRCPYCNKTF---RSREALQEHMRSKHHKKR 78 (100)
T ss_dssp SEEBSSSS-EE---SSHHHHHHHHHHTTTTC-
T ss_pred CCCCCccCCCC---cCHHHHHHHHcCccCCCc
Confidence 58999999995 4889999999987 5443
No 17
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=80.98 E-value=1 Score=25.49 Aligned_cols=30 Identities=27% Similarity=0.525 Sum_probs=24.7
Q ss_pred cccchhhhhhhhcc--CChhHHHHHHHhcCCC
Q 034948 37 SIQCKVCMQTFMCT--TSEVKCREHAEAKHPK 66 (78)
Q Consensus 37 ~i~C~vC~~~Fm~t--~~~~~L~~H~e~KHpK 66 (78)
..+|..|...+-.. ..-+.|..|..++||.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~~ 49 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHPA 49 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCcC
Confidence 46899999997654 4568999999999986
No 18
>PHA00616 hypothetical protein
Probab=80.84 E-value=1.7 Score=25.02 Aligned_cols=29 Identities=24% Similarity=0.410 Sum_probs=23.7
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhcCCCCCc
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAKHPKSDI 69 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~~~ 69 (78)
++|.-|...|. +.+.|..|..+.|--+++
T Consensus 2 YqC~~CG~~F~---~~s~l~~H~r~~hg~~~~ 30 (44)
T PHA00616 2 YQCLRCGGIFR---KKKEVIEHLLSVHKQNKL 30 (44)
T ss_pred CccchhhHHHh---hHHHHHHHHHHhcCCCcc
Confidence 68999999975 889999999877765543
No 19
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=79.11 E-value=1.4 Score=36.57 Aligned_cols=29 Identities=17% Similarity=0.468 Sum_probs=25.8
Q ss_pred cccchhhhhhhhccCChhHHHHHHHhcCCCCC
Q 034948 37 SIQCKVCMQTFMCTTSEVKCREHAEAKHPKSD 68 (78)
Q Consensus 37 ~i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~~ 68 (78)
++.|+||+.- .++...|..|++.-|+-++
T Consensus 15 gflCPiC~~d---l~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 15 GFLCPICLLD---LPNLSALNDHLDVEHFEED 43 (505)
T ss_pred cccCchHhhh---hhhHHHHHHHHhhhccccc
Confidence 5889999999 5689999999999999775
No 20
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=79.10 E-value=1.2 Score=22.32 Aligned_cols=20 Identities=20% Similarity=0.683 Sum_probs=16.1
Q ss_pred ccchhhhhhhhccCChhHHHHHHH
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAE 61 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e 61 (78)
+.|.+|..+| .+..|..|..
T Consensus 3 ~~C~~CgR~F----~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF----NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE----CHHHHHHHHH
Confidence 6799999999 5667888864
No 21
>PHA02768 hypothetical protein; Provisional
Probab=78.92 E-value=1.7 Score=26.12 Aligned_cols=28 Identities=14% Similarity=0.468 Sum_probs=22.7
Q ss_pred hccccchhhhhhhhccCChhHHHHHHHhcCCC
Q 034948 35 AMSIQCKVCMQTFMCTTSEVKCREHAEAKHPK 66 (78)
Q Consensus 35 A~~i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK 66 (78)
-|.+.|++|...|. ....|..|... |.|
T Consensus 3 ~~~y~C~~CGK~Fs---~~~~L~~H~r~-H~k 30 (55)
T PHA02768 3 LLGYECPICGEIYI---KRKSMITHLRK-HNT 30 (55)
T ss_pred ccccCcchhCCeec---cHHHHHHHHHh-cCC
Confidence 36789999999985 56779999997 553
No 22
>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=77.59 E-value=1.6 Score=22.14 Aligned_cols=20 Identities=30% Similarity=0.689 Sum_probs=16.3
Q ss_pred ccchhhhhhhhccCChhHHHHHHH
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAE 61 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e 61 (78)
+.|+||.+.+ ....+..|.+
T Consensus 2 v~CPiC~~~v----~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV----PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc----cHHHHHHHHH
Confidence 5799999994 5578888887
No 23
>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=73.49 E-value=1.7 Score=35.69 Aligned_cols=27 Identities=30% Similarity=0.669 Sum_probs=23.1
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhcCCCC
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAKHPKS 67 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~ 67 (78)
-+|.+|-..|+ +...|..|++++|+..
T Consensus 58 WiCp~CskkF~---d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 58 WICPRCSKKFS---DAESCLSHMEQEHPAG 84 (466)
T ss_pred eeCCcccceeC---CHHHHHHHHHHhhhhh
Confidence 57999998876 6678999999999865
No 24
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=69.13 E-value=1.6 Score=26.11 Aligned_cols=26 Identities=31% Similarity=0.503 Sum_probs=0.0
Q ss_pred cchhhhhhhhccCChhHHHHHHHhcCCCC
Q 034948 39 QCKVCMQTFMCTTSEVKCREHAEAKHPKS 67 (78)
Q Consensus 39 ~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~ 67 (78)
+|.+|..+| ++...|.+|....|.-.
T Consensus 1 ~C~~C~~~f---~~~~~l~~H~~~~H~~~ 26 (100)
T PF12756_consen 1 QCLFCDESF---SSVDDLLQHMKKKHGFD 26 (100)
T ss_dssp -----------------------------
T ss_pred Ccccccccc---ccccccccccccccccc
Confidence 599999995 46788999999999644
No 25
>PHA00733 hypothetical protein
Probab=63.40 E-value=4.6 Score=27.19 Aligned_cols=21 Identities=29% Similarity=0.743 Sum_probs=11.4
Q ss_pred ccchhhhhhhhccCChhHHHHHHH
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAE 61 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e 61 (78)
++|.+|...| .....|.+|.+
T Consensus 74 y~C~~Cgk~F---ss~s~L~~H~r 94 (128)
T PHA00733 74 YVCPLCLMPF---SSSVSLKQHIR 94 (128)
T ss_pred ccCCCCCCcC---CCHHHHHHHHh
Confidence 5566665553 34455555555
No 26
>PHA00732 hypothetical protein
Probab=58.33 E-value=8.6 Score=24.08 Aligned_cols=9 Identities=33% Similarity=1.228 Sum_probs=4.4
Q ss_pred cchhhhhhh
Q 034948 39 QCKVCMQTF 47 (78)
Q Consensus 39 ~C~vC~~~F 47 (78)
.|++|..+|
T Consensus 29 ~C~~CgKsF 37 (79)
T PHA00732 29 KCPVCNKSY 37 (79)
T ss_pred ccCCCCCEe
Confidence 455555544
No 27
>COG2879 Uncharacterized small protein [Function unknown]
Probab=56.36 E-value=11 Score=23.49 Aligned_cols=20 Identities=25% Similarity=0.283 Sum_probs=18.1
Q ss_pred ccCChhHHHHHHHhcCCCCC
Q 034948 49 CTTSEVKCREHAEAKHPKSD 68 (78)
Q Consensus 49 ~t~~~~~L~~H~e~KHpK~~ 68 (78)
.++|...|-+|...|||..+
T Consensus 21 GvpdYdnYVehmr~~hPd~p 40 (65)
T COG2879 21 GVPDYDNYVEHMRKKHPDKP 40 (65)
T ss_pred CCCcHHHHHHHHHHhCcCCC
Confidence 47899999999999999876
No 28
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=54.57 E-value=6.4 Score=28.47 Aligned_cols=23 Identities=30% Similarity=0.534 Sum_probs=21.1
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhc
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAK 63 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~K 63 (78)
+.|.+|+-. |-....+..|+||+
T Consensus 1 F~Cs~CKfr---tf~~~ei~~HleS~ 23 (165)
T PF04988_consen 1 FTCSFCKFR---TFEEKEIEKHLESK 23 (165)
T ss_pred Cccceeeee---cccHHHHHHHHccc
Confidence 479999988 88999999999998
No 29
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=49.87 E-value=4.6 Score=29.22 Aligned_cols=13 Identities=38% Similarity=0.843 Sum_probs=11.3
Q ss_pred cccchhhhhhhhc
Q 034948 37 SIQCKVCMQTFMC 49 (78)
Q Consensus 37 ~i~C~vC~~~Fm~ 49 (78)
+++|+||.+.|..
T Consensus 5 ~~~CPvC~~~F~~ 17 (214)
T PF09986_consen 5 KITCPVCGKEFKT 17 (214)
T ss_pred ceECCCCCCeeee
Confidence 5899999999964
No 30
>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=46.76 E-value=12 Score=23.91 Aligned_cols=25 Identities=28% Similarity=0.461 Sum_probs=22.0
Q ss_pred cccc----hhhhhhhhccCChhHHHHHHHhcC
Q 034948 37 SIQC----KVCMQTFMCTTSEVKCREHAEAKH 64 (78)
Q Consensus 37 ~i~C----~vC~~~Fm~t~~~~~L~~H~e~KH 64 (78)
.+.| ..|.-. +.+..++..|+..+|
T Consensus 80 G~~C~~~~~~C~y~---~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 80 GYRCQCDPPHCGYI---TRSKKTMRKHWRKEH 108 (109)
T ss_pred CeeeecCCCCCCcE---eccHHHHHHHHHHhc
Confidence 5889 999666 888999999999988
No 31
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=43.58 E-value=4.5 Score=21.82 Aligned_cols=16 Identities=31% Similarity=0.644 Sum_probs=12.2
Q ss_pred ccccchhhhhhhhccC
Q 034948 36 MSIQCKVCMQTFMCTT 51 (78)
Q Consensus 36 ~~i~C~vC~~~Fm~t~ 51 (78)
|.|+|+-|.+.|-...
T Consensus 1 M~i~CP~C~~~f~v~~ 16 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPD 16 (37)
T ss_pred CEEECCCCCceEEcCH
Confidence 5688999999886443
No 32
>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=42.88 E-value=5 Score=19.86 Aligned_cols=12 Identities=25% Similarity=0.766 Sum_probs=9.8
Q ss_pred cccchhhhhhhh
Q 034948 37 SIQCKVCMQTFM 48 (78)
Q Consensus 37 ~i~C~vC~~~Fm 48 (78)
.+.|++|...|-
T Consensus 14 ~~~C~~C~k~F~ 25 (26)
T PF13465_consen 14 PYKCPYCGKSFS 25 (26)
T ss_dssp SEEESSSSEEES
T ss_pred CCCCCCCcCeeC
Confidence 389999998873
No 33
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=41.41 E-value=7.7 Score=23.35 Aligned_cols=14 Identities=21% Similarity=0.740 Sum_probs=7.5
Q ss_pred ccccchhhhhhhhc
Q 034948 36 MSIQCKVCMQTFMC 49 (78)
Q Consensus 36 ~~i~C~vC~~~Fm~ 49 (78)
|++.|+||+..+.-
T Consensus 1 m~v~CP~C~k~~~~ 14 (57)
T PF03884_consen 1 MTVKCPICGKPVEW 14 (57)
T ss_dssp -EEE-TTT--EEE-
T ss_pred CcccCCCCCCeecc
Confidence 67899999998554
No 34
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=40.76 E-value=12 Score=21.98 Aligned_cols=20 Identities=15% Similarity=0.363 Sum_probs=15.6
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhc
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAK 63 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~K 63 (78)
--|.+|+..| ..|.+|..++
T Consensus 6 GYCE~Cr~kf------d~l~~Hi~s~ 25 (49)
T smart00586 6 GYCENCREKY------DDLETHLLSE 25 (49)
T ss_pred cccccHhHHH------hhHHHHhccH
Confidence 3599999997 3588888775
No 35
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=40.75 E-value=4.6 Score=21.27 Aligned_cols=16 Identities=38% Similarity=0.758 Sum_probs=11.9
Q ss_pred ccccchhhhhhhhccC
Q 034948 36 MSIQCKVCMQTFMCTT 51 (78)
Q Consensus 36 ~~i~C~vC~~~Fm~t~ 51 (78)
|.+.|+-|.++|....
T Consensus 1 M~~~CP~C~~~~~v~~ 16 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVD 16 (38)
T ss_pred CEEECCCCCCEEEeCH
Confidence 5678888888886543
No 36
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=40.48 E-value=8.8 Score=26.06 Aligned_cols=16 Identities=25% Similarity=0.798 Sum_probs=13.6
Q ss_pred ccchhhhhhhhccCCh
Q 034948 38 IQCKVCMQTFMCTTSE 53 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~ 53 (78)
+-|.||.+.|.++.+.
T Consensus 48 ~sC~iC~esFqt~it~ 63 (109)
T KOG3214|consen 48 ASCRICEESFQTTITA 63 (109)
T ss_pred eeeeehhhhhccchHh
Confidence 6799999999987764
No 37
>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]
Probab=40.01 E-value=18 Score=26.80 Aligned_cols=32 Identities=25% Similarity=0.438 Sum_probs=26.3
Q ss_pred hhhhhhhccCChhHHHHHHHh----cCCCCCccccCCCC
Q 034948 42 VCMQTFMCTTSEVKCREHAEA----KHPKSDIYACFPHL 76 (78)
Q Consensus 42 vC~~~Fm~t~~~~~L~~H~e~----KHpK~~~~~CFP~~ 76 (78)
||.+.||..-. +.+-+||+. =||- |-.|||++
T Consensus 83 vvLAGyMrIL~-~~fl~~~~grIlNIHPS--LLP~f~G~ 118 (200)
T COG0299 83 VVLAGYMRILG-PEFLSRFEGRILNIHPS--LLPAFPGL 118 (200)
T ss_pred EEEcchHHHcC-HHHHHHhhcceEecCcc--cccCCCCc
Confidence 78999998877 788999995 4995 55899985
No 38
>PTZ00448 hypothetical protein; Provisional
Probab=38.99 E-value=17 Score=29.27 Aligned_cols=24 Identities=13% Similarity=0.411 Sum_probs=20.4
Q ss_pred cccchhhhhhhhccCChhHHHHHHHhc
Q 034948 37 SIQCKVCMQTFMCTTSEVKCREHAEAK 63 (78)
Q Consensus 37 ~i~C~vC~~~Fm~t~~~~~L~~H~e~K 63 (78)
.+.|..|.-+| .+....++|+.+-
T Consensus 314 ~~tC~~C~v~F---~~~~~qR~H~KSD 337 (373)
T PTZ00448 314 MLLCRKCNIQL---MDHNAFKQHYRSE 337 (373)
T ss_pred Ccccccccccc---CCHHHHHHHhhhh
Confidence 46799999998 4778899999875
No 39
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=38.62 E-value=11 Score=21.99 Aligned_cols=19 Identities=21% Similarity=0.555 Sum_probs=15.5
Q ss_pred cchhhhhhhhccCChhHHHHHHHhc
Q 034948 39 QCKVCMQTFMCTTSEVKCREHAEAK 63 (78)
Q Consensus 39 ~C~vC~~~Fm~t~~~~~L~~H~e~K 63 (78)
-|.+|+..| ..|.+|..+.
T Consensus 7 YCE~C~~ky------~~l~~Hi~s~ 25 (49)
T PF07535_consen 7 YCENCRVKY------DDLEEHIQSE 25 (49)
T ss_pred cCccccchh------hhHHHHhCCH
Confidence 599999987 4688998876
No 40
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=38.57 E-value=19 Score=26.87 Aligned_cols=26 Identities=19% Similarity=0.367 Sum_probs=20.5
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhc
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAK 63 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~K 63 (78)
.+|.||.+--...-+..=|.+||.-|
T Consensus 191 ~VCeVCGA~Ls~~D~d~RladH~~GK 216 (254)
T PF03194_consen 191 EVCEVCGAFLSVGDNDRRLADHFGGK 216 (254)
T ss_pred cchhhhhhHHhccchHHHHHHHhccc
Confidence 68999998655556666799999877
No 41
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=38.39 E-value=9.9 Score=26.88 Aligned_cols=16 Identities=25% Similarity=0.654 Sum_probs=12.3
Q ss_pred ccccchhhhhhhhccC
Q 034948 36 MSIQCKVCMQTFMCTT 51 (78)
Q Consensus 36 ~~i~C~vC~~~Fm~t~ 51 (78)
+--+|+||+++|-...
T Consensus 120 ~ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 120 LYPVCPVCKTSFKSSS 135 (140)
T ss_pred cCCCCCcccccccccc
Confidence 4568999999997443
No 42
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=34.57 E-value=25 Score=26.99 Aligned_cols=32 Identities=25% Similarity=0.285 Sum_probs=28.4
Q ss_pred hhccccchhhhhhhhccCChhHHHHHHHhcCCCCC
Q 034948 34 KAMSIQCKVCMQTFMCTTSEVKCREHAEAKHPKSD 68 (78)
Q Consensus 34 ~A~~i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~~ 68 (78)
-+.-++|.-|.-| +..+..|-.|..+-||-++
T Consensus 209 r~kl~vcedcg~t---~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 209 RAKLYVCEDCGYT---SERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred hhheeeecccCCC---CCChhHHHHHHHhcCCCCH
Confidence 4556999999999 9999999999999999875
No 43
>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=34.19 E-value=12 Score=21.30 Aligned_cols=23 Identities=9% Similarity=0.190 Sum_probs=11.0
Q ss_pred cchhhhhhhhccCChhHHHHHHHh
Q 034948 39 QCKVCMQTFMCTTSEVKCREHAEA 62 (78)
Q Consensus 39 ~C~vC~~~Fm~t~~~~~L~~H~e~ 62 (78)
.|+||...|----. ..|..++.+
T Consensus 22 ~CPlC~r~l~~e~~-~~li~~~~~ 44 (54)
T PF04423_consen 22 CCPLCGRPLDEEHR-QELIKKYKS 44 (54)
T ss_dssp E-TTT--EE-HHHH-HHHHHHHHH
T ss_pred cCCCCCCCCCHHHH-HHHHHHHHH
Confidence 89999999753322 445444443
No 44
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=33.59 E-value=25 Score=28.70 Aligned_cols=29 Identities=31% Similarity=0.689 Sum_probs=24.5
Q ss_pred cccchhhhhhhhccCChhHHHHHHHhc-C----CCCC
Q 034948 37 SIQCKVCMQTFMCTTSEVKCREHAEAK-H----PKSD 68 (78)
Q Consensus 37 ~i~C~vC~~~Fm~t~~~~~L~~H~e~K-H----pK~~ 68 (78)
...|--|-..| .++++|++|..+| | ||+.
T Consensus 195 r~~CLyCekif---rdkntLkeHMrkK~HrrinPknr 228 (423)
T KOG2482|consen 195 RLRCLYCEKIF---RDKNTLKEHMRKKRHRRINPKNR 228 (423)
T ss_pred hheeeeecccc---CCcHHHHHHHHhccCcccCCCcc
Confidence 47899999996 5999999999998 5 7764
No 45
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=29.79 E-value=37 Score=27.49 Aligned_cols=37 Identities=22% Similarity=0.387 Sum_probs=29.1
Q ss_pred hccccchhhhhhhhccCChhHHHHHHHhcCCCCCccccCC
Q 034948 35 AMSIQCKVCMQTFMCTTSEVKCREHAEAKHPKSDIYACFP 74 (78)
Q Consensus 35 A~~i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~~~~~CFP 74 (78)
...+.|+.|... --...+|..|+.+-||-.....-||
T Consensus 77 ~qSftCPyC~~~---Gfte~~f~~Hv~s~Hpda~~~~icp 113 (381)
T KOG1280|consen 77 PQSFTCPYCGIM---GFTERQFGTHVLSQHPEASTSVICP 113 (381)
T ss_pred cccccCCccccc---ccchhHHHHHhhhcCcccCcceeee
Confidence 347999999988 6678999999999999876433333
No 46
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=28.61 E-value=41 Score=21.21 Aligned_cols=14 Identities=43% Similarity=0.482 Sum_probs=11.7
Q ss_pred hHHHHHHHhcCCCC
Q 034948 54 VKCREHAEAKHPKS 67 (78)
Q Consensus 54 ~~L~~H~e~KHpK~ 67 (78)
..+-+|||..||+-
T Consensus 56 ~~av~~FE~~HP~l 69 (85)
T PF14357_consen 56 NEAVERFEASHPKL 69 (85)
T ss_pred HHHHHHHHHhCCcH
Confidence 45788999999974
No 47
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=27.75 E-value=39 Score=30.19 Aligned_cols=31 Identities=26% Similarity=0.619 Sum_probs=19.0
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhcCCCCCcccc
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAKHPKSDIYAC 72 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~~~~~C 72 (78)
++|.||...|- -.-.|.+|.+ -|+.+..-+|
T Consensus 923 yqC~iCkKAFK---HKHHLtEHkR-LHSGEKPfQC 953 (1007)
T KOG3623|consen 923 YQCIICKKAFK---HKHHLTEHKR-LHSGEKPFQC 953 (1007)
T ss_pred cccchhhHhhh---hhhhhhhhhh-hccCCCcchh
Confidence 66777777764 4556677765 4666554454
No 48
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=26.79 E-value=50 Score=27.20 Aligned_cols=29 Identities=24% Similarity=0.470 Sum_probs=23.9
Q ss_pred cccchhhhhhhhccCChhHHHHHHHhcCCCCC
Q 034948 37 SIQCKVCMQTFMCTTSEVKCREHAEAKHPKSD 68 (78)
Q Consensus 37 ~i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~~ 68 (78)
.++|+.|--+ -+.++.|.-|..-+|++..
T Consensus 263 ~ykCplCdmt---c~~~ssL~~H~r~rHs~dk 291 (467)
T KOG3608|consen 263 CYKCPLCDMT---CSSASSLTTHIRYRHSKDK 291 (467)
T ss_pred cccccccccC---CCChHHHHHHHHhhhccCC
Confidence 4788888877 7888899999999998764
No 49
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=26.76 E-value=24 Score=19.72 Aligned_cols=13 Identities=23% Similarity=0.797 Sum_probs=4.4
Q ss_pred chhhhhhhhccCCh
Q 034948 40 CKVCMQTFMCTTSE 53 (78)
Q Consensus 40 C~vC~~~Fm~t~~~ 53 (78)
|+||+. |....++
T Consensus 1 CpIc~e-~~~~~n~ 13 (43)
T PF13445_consen 1 CPICKE-FSTEENP 13 (43)
T ss_dssp -TTT-----TTSS-
T ss_pred CCcccc-ccCCCCC
Confidence 889998 7544443
No 50
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=26.67 E-value=17 Score=19.54 Aligned_cols=13 Identities=31% Similarity=0.736 Sum_probs=10.4
Q ss_pred ccccchhhhhhhh
Q 034948 36 MSIQCKVCMQTFM 48 (78)
Q Consensus 36 ~~i~C~vC~~~Fm 48 (78)
|.|.|+-|.+.|.
T Consensus 1 M~i~Cp~C~~~y~ 13 (36)
T PF13717_consen 1 MIITCPNCQAKYE 13 (36)
T ss_pred CEEECCCCCCEEe
Confidence 5678888888886
No 51
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 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 family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=25.59 E-value=27 Score=25.99 Aligned_cols=18 Identities=22% Similarity=0.647 Sum_probs=11.5
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhcCCCCC
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAKHPKSD 68 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~~ 68 (78)
-+|++|++- ..|||||.+
T Consensus 209 PiCPlCK~K-------------sRSrnpKk~ 226 (230)
T PF10146_consen 209 PICPLCKAK-------------SRSRNPKKP 226 (230)
T ss_pred CCCcccccc-------------cccCCCCCc
Confidence 356666655 346888874
No 52
>cd00066 G-alpha G protein alpha subunit. The alpha subunit of G proteins contains the guanine nucleotide binding site. The heterotrimeric GNP-binding proteins are signal transducers that communicate signals from many hormones, neurotransmitters, chemokines, and autocrine and paracrine factors. Extracellular signals are received by receptors, which activate the G proteins, which in turn route the signals to several distinct intracellular signaling pathways. The alpha subunit of G proteins is a weak GTPase. In the resting state, heterotrimeric G proteins are associated at the cytosolic face of the plasma membrane and the alpha subunit binds to GDP. Upon activation by a receptor GDP is replaced with GTP, and the G-alpha/GTP complex dissociates from the beta and gamma subunits. This results in activation of downstream signaling pathways, such as cAMP synthesis by adenylyl cyclase, which is terminated when GTP is hydrolized and the heterotrimers reconstitute.
Probab=25.43 E-value=44 Score=25.17 Aligned_cols=18 Identities=33% Similarity=0.401 Sum_probs=13.3
Q ss_pred HHhcCCCCCccccCCCCC
Q 034948 60 AEAKHPKSDIYACFPHLK 77 (78)
Q Consensus 60 ~e~KHpK~~~~~CFP~~~ 77 (78)
++.|=++.+|..|||++.
T Consensus 241 f~~ki~~~~l~~~fp~y~ 258 (317)
T cd00066 241 FEEKIKKSPLTDYFPDYT 258 (317)
T ss_pred HHHhhcCCCccccCCCCC
Confidence 445555668999999985
No 53
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=24.46 E-value=24 Score=22.98 Aligned_cols=11 Identities=45% Similarity=0.857 Sum_probs=9.4
Q ss_pred ccchhhhhhhh
Q 034948 38 IQCKVCMQTFM 48 (78)
Q Consensus 38 i~C~vC~~~Fm 48 (78)
-+|+.|||+|.
T Consensus 71 ~~CPmcRq~~~ 81 (84)
T KOG1493|consen 71 GQCPMCRQTWQ 81 (84)
T ss_pred ccCCcchheeE
Confidence 47999999985
No 54
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=22.29 E-value=81 Score=25.67 Aligned_cols=29 Identities=21% Similarity=0.499 Sum_probs=23.4
Q ss_pred HHhhccccchhhhhhhhccCChhHHHHHHHhc
Q 034948 32 NKKAMSIQCKVCMQTFMCTTSEVKCREHAEAK 63 (78)
Q Consensus 32 n~~A~~i~C~vC~~~Fm~t~~~~~L~~H~e~K 63 (78)
.++-+.+.|.||+..| ..+...++|.-+|
T Consensus 63 e~~~~~~~c~~c~k~~---~s~~a~~~hl~Sk 91 (390)
T KOG2785|consen 63 EEAESVVYCEACNKSF---ASPKAHENHLKSK 91 (390)
T ss_pred hhcccceehHHhhccc---cChhhHHHHHHHh
Confidence 3445668899999995 5888899999887
No 55
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=21.36 E-value=40 Score=30.26 Aligned_cols=33 Identities=27% Similarity=0.539 Sum_probs=0.0
Q ss_pred ccchhhhhhhhccCChhHHHHHHHhcCCCCCccccC
Q 034948 38 IQCKVCMQTFMCTTSEVKCREHAEAKHPKSDIYACF 73 (78)
Q Consensus 38 i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~~~~~CF 73 (78)
++|+||.--| |++ --|+-|+-....|-++--||
T Consensus 634 FkCKiCgRAF--tTk-GNLkaH~~vHka~p~~R~q~ 666 (958)
T KOG1074|consen 634 FKCKICGRAF--TTK-GNLKAHMSVHKAKPPARVQF 666 (958)
T ss_pred cccccccchh--ccc-cchhhcccccccCccccccc
No 56
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=21.03 E-value=60 Score=29.09 Aligned_cols=33 Identities=21% Similarity=0.510 Sum_probs=27.2
Q ss_pred cccchhhhhhhhccCChhHHHHHHHhcCCCCCccccC
Q 034948 37 SIQCKVCMQTFMCTTSEVKCREHAEAKHPKSDIYACF 73 (78)
Q Consensus 37 ~i~C~vC~~~Fm~t~~~~~L~~H~e~KHpK~~~~~CF 73 (78)
+++|+.|...|- =.-.|++|.+. |+.+..-+|.
T Consensus 281 KFKCtECgKAFK---fKHHLKEHlRI-HSGEKPfeCp 313 (1007)
T KOG3623|consen 281 KFKCTECGKAFK---FKHHLKEHLRI-HSGEKPFECP 313 (1007)
T ss_pred cccccccchhhh---hHHHHHhhhee-ecCCCCcCCc
Confidence 599999999985 46789999984 8888777774
No 57
>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=20.87 E-value=33 Score=24.66 Aligned_cols=23 Identities=17% Similarity=0.238 Sum_probs=0.0
Q ss_pred hccccchhhhhhhhccCChhHHHHHHH
Q 034948 35 AMSIQCKVCMQTFMCTTSEVKCREHAE 61 (78)
Q Consensus 35 A~~i~C~vC~~~Fm~t~~~~~L~~H~e 61 (78)
..-++|+||++. .+ ...|.+|..
T Consensus 166 ~~~~~cPitGe~---IP-~~e~~eHmR 188 (229)
T PF12230_consen 166 EKMIICPITGEM---IP-ADEMDEHMR 188 (229)
T ss_dssp ---------------------------
T ss_pred cccccccccccc---cc-ccccccccc
Confidence 345899999998 33 366788865
No 58
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=20.73 E-value=33 Score=24.81 Aligned_cols=12 Identities=42% Similarity=0.869 Sum_probs=10.0
Q ss_pred cccchhhhhhhh
Q 034948 37 SIQCKVCMQTFM 48 (78)
Q Consensus 37 ~i~C~vC~~~Fm 48 (78)
.++|+||++.+.
T Consensus 2 ~~~CP~C~~~l~ 13 (272)
T PRK11088 2 SYQCPLCHQPLT 13 (272)
T ss_pred cccCCCCCcchh
Confidence 478999999963
Done!