Query 041240
Match_columns 113
No_of_seqs 107 out of 284
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 05:08:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041240.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041240hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14392 zf-CCHC_4: Zinc knuck 99.7 3.6E-17 7.7E-22 98.3 3.1 44 43-86 1-49 (49)
2 PF14111 DUF4283: Domain of un 99.1 9.4E-11 2E-15 82.6 4.0 42 1-42 112-153 (153)
3 PF00098 zf-CCHC: Zinc knuckle 97.4 6.6E-05 1.4E-09 36.3 1.2 17 70-86 2-18 (18)
4 PF13696 zf-CCHC_2: Zinc knuck 95.5 0.0063 1.4E-07 33.6 1.0 20 69-88 9-28 (32)
5 PF15288 zf-CCHC_6: Zinc knuck 95.0 0.023 5.1E-07 32.8 2.3 20 69-88 2-23 (40)
6 smart00343 ZnF_C2HC zinc finge 94.6 0.015 3.2E-07 29.9 0.7 18 70-87 1-18 (26)
7 COG5082 AIR1 Arginine methyltr 91.0 0.12 2.5E-06 39.2 1.3 16 69-84 98-113 (190)
8 COG5082 AIR1 Arginine methyltr 91.0 0.099 2.1E-06 39.6 0.9 22 64-85 56-77 (190)
9 PF13917 zf-CCHC_3: Zinc knuck 89.7 0.18 3.8E-06 29.4 1.1 19 68-86 4-22 (42)
10 PTZ00368 universal minicircle 88.9 0.23 5E-06 35.2 1.4 18 69-86 130-147 (148)
11 KOG4400 E3 ubiquitin ligase in 84.5 0.45 9.9E-06 36.7 1.0 25 62-87 138-162 (261)
12 PF10083 DUF2321: Uncharacteri 81.9 0.54 1.2E-05 34.6 0.5 31 45-76 45-76 (158)
13 PF14787 zf-CCHC_5: GAG-polypr 80.6 1.2 2.5E-05 25.2 1.5 25 68-92 2-26 (36)
14 KOG0109 RNA-binding protein LA 79.7 1.2 2.5E-05 36.3 1.7 23 68-90 160-182 (346)
15 PTZ00368 universal minicircle 78.5 1.1 2.4E-05 31.6 1.2 16 71-86 30-45 (148)
16 COG4306 Uncharacterized protei 74.3 1.1 2.4E-05 32.3 0.2 30 46-76 46-76 (160)
17 PLN00032 DNA-directed RNA poly 72.8 1.5 3.3E-05 28.2 0.6 15 67-81 3-18 (71)
18 PF01194 RNA_pol_N: RNA polyme 71.9 1.8 3.8E-05 27.1 0.7 14 67-80 3-17 (60)
19 PRK04016 DNA-directed RNA poly 71.1 1.8 3.9E-05 27.2 0.6 13 67-79 3-16 (62)
20 COG5222 Uncharacterized conser 69.8 2.2 4.8E-05 35.0 1.0 20 69-88 177-196 (427)
21 KOG4400 E3 ubiquitin ligase in 68.9 3.8 8.3E-05 31.6 2.2 25 67-91 163-187 (261)
22 COG1644 RPB10 DNA-directed RNA 67.7 2.2 4.9E-05 26.8 0.5 16 67-82 3-19 (63)
23 KOG0341 DEAD-box protein abstr 64.0 3 6.6E-05 35.6 0.8 21 68-88 570-590 (610)
24 KOG3497 DNA-directed RNA polym 63.9 2.5 5.5E-05 26.7 0.2 11 67-77 3-13 (69)
25 smart00647 IBR In Between Ring 63.4 4.2 9.1E-05 24.0 1.1 18 67-84 47-64 (64)
26 PF01191 RNA_pol_Rpb5_C: RNA p 63.1 11 0.00024 24.3 3.1 40 1-40 34-73 (74)
27 COG2012 RPB5 DNA-directed RNA 61.7 14 0.0003 24.3 3.4 40 1-40 40-79 (80)
28 KOG2044 5'-3' exonuclease HKE1 59.7 5.5 0.00012 36.3 1.6 28 62-89 254-281 (931)
29 COG1998 RPS31 Ribosomal protei 56.7 6.7 0.00015 23.7 1.2 17 59-75 7-26 (51)
30 COG1940 NagC Transcriptional r 56.2 14 0.0003 28.6 3.2 82 3-88 90-192 (314)
31 PRK09570 rpoH DNA-directed RNA 55.2 23 0.00049 23.2 3.6 41 1-41 37-77 (79)
32 KOG2560 RNA splicing factor - 50.8 5.5 0.00012 34.2 0.2 20 69-88 113-132 (529)
33 PF00567 TUDOR: Tudor domain; 45.5 37 0.0008 21.5 3.5 46 33-78 65-121 (121)
34 COG5179 TAF1 Transcription ini 40.8 15 0.00032 33.2 1.2 25 68-92 937-963 (968)
35 PF01485 IBR: IBR domain; Int 40.6 11 0.00024 22.0 0.4 18 67-84 47-64 (64)
36 KOG0119 Splicing factor 1/bran 36.9 16 0.00035 31.7 0.9 18 70-87 287-304 (554)
37 KOG2673 Uncharacterized conser 33.7 22 0.00047 30.5 1.2 18 71-88 131-148 (485)
38 PF01188 MR_MLE: Mandelate rac 32.7 53 0.0012 19.8 2.6 24 2-25 44-67 (67)
39 KOG2985 Uncharacterized conser 31.0 11 0.00025 30.1 -0.9 29 65-93 78-106 (306)
40 PF14205 Cys_rich_KTR: Cystein 30.0 24 0.00051 21.7 0.6 15 62-76 22-36 (55)
41 PF05515 Viral_NABP: Viral nuc 30.0 32 0.00069 24.4 1.3 19 69-87 63-81 (124)
42 KOG4399 C2HC-type Zn-finger pr 29.9 25 0.00054 28.3 0.9 20 68-87 261-280 (325)
43 PF13248 zf-ribbon_3: zinc-rib 28.8 20 0.00043 18.2 0.1 9 68-76 16-24 (26)
44 PRK09698 D-allose kinase; Prov 28.0 1.1E+02 0.0023 23.5 4.1 78 8-86 94-188 (302)
45 PF09297 zf-NADH-PPase: NADH p 27.6 26 0.00057 18.4 0.5 13 68-80 3-15 (32)
46 PF10741 T2SM_b: Type II secre 26.5 1.2E+02 0.0025 20.1 3.6 42 9-50 20-61 (110)
47 PF14599 zinc_ribbon_6: Zinc-r 25.9 41 0.00089 20.8 1.2 20 58-77 38-57 (61)
48 PF13821 DUF4187: Domain of un 25.4 40 0.00088 20.3 1.1 25 67-91 26-54 (55)
49 PF02591 DUF164: Putative zinc 25.1 29 0.00063 20.5 0.4 11 67-77 45-55 (56)
50 smart00769 WHy Water Stress an 24.1 93 0.002 20.1 2.7 33 35-67 13-45 (100)
51 PRK15329 chaperone protein Sic 24.0 71 0.0015 23.1 2.2 22 8-29 5-26 (138)
52 COG1867 TRM1 N2,N2-dimethylgua 23.4 40 0.00088 28.2 1.0 39 4-45 180-225 (380)
53 KOG3794 CBF1-interacting corep 22.6 40 0.00086 28.6 0.8 22 68-89 124-147 (453)
54 PF14803 Nudix_N_2: Nudix N-te 22.6 33 0.00072 18.8 0.3 8 69-76 1-8 (34)
55 PF04246 RseC_MucC: Positive r 22.2 2.5E+02 0.0054 19.2 4.7 26 55-85 4-29 (135)
56 PF05037 DUF669: Protein of un 21.3 51 0.0011 23.1 1.1 39 6-44 71-113 (141)
57 PRK00432 30S ribosomal protein 20.1 60 0.0013 19.1 1.0 11 66-76 18-28 (50)
58 cd07153 Fur_like Ferric uptake 20.1 1.5E+02 0.0032 19.3 3.1 15 67-81 72-86 (116)
No 1
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=99.67 E-value=3.6e-17 Score=98.29 Aligned_cols=44 Identities=45% Similarity=0.859 Sum_probs=40.2
Q ss_pred ecCCCCceeEEEEc---Ce--EEEEEEccccccccccCccccCCCCCCC
Q 041240 43 IDPNKPLISQFFLD---GK--LQKVEYEGLPNTSFLCGKYGHSKDICPN 86 (113)
Q Consensus 43 iDl~kpL~~~v~v~---g~--~~~v~YE~Lp~fC~~Cg~iGH~~~~C~~ 86 (113)
||++|||.+++.|+ |. ++.|+|||||.||++||.+||..++|++
T Consensus 1 id~~kPL~~~i~v~~~~g~~~~~~v~YE~lp~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 1 IDVSKPLRREIKVKFPEGESFWVKVKYERLPRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred CCCCCcccceEEEEeCCCcEEEEEEEECCcChhhcCCCCcCcCHhHcCC
Confidence 69999999999884 32 8999999999999999999999999985
No 2
>PF14111 DUF4283: Domain of unknown function (DUF4283)
Probab=99.09 E-value=9.4e-11 Score=82.59 Aligned_cols=42 Identities=33% Similarity=0.592 Sum_probs=41.0
Q ss_pred CCcccccHHHHHHHhhccCceEEEecCCCcccccceeEEEEE
Q 041240 1 MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVE 42 (113)
Q Consensus 1 LP~~y~~~~~l~~I~~~iG~~l~vD~~t~~~~~g~faRV~Ve 42 (113)
||+.||+++++++||+.+|+|+++|.+|.+..+++||||+|+
T Consensus 112 lP~~~~~~~~~~~i~~~iG~~i~vD~~t~~~~~~~~~Rv~V~ 153 (153)
T PF14111_consen 112 LPLHLWSEEILKAIGSKIGEPIEVDENTLKRTRLDFARVRVE 153 (153)
T ss_pred CCHHHhhhHHHHHHHHhcCCeEEEEcCCCCcccccEEEEEEC
Confidence 799999999999999999999999999999999999999996
No 3
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=97.43 E-value=6.6e-05 Score=36.32 Aligned_cols=17 Identities=41% Similarity=0.913 Sum_probs=15.8
Q ss_pred cccccCccccCCCCCCC
Q 041240 70 TSFLCGKYGHSKDICPN 86 (113)
Q Consensus 70 fC~~Cg~iGH~~~~C~~ 86 (113)
.||+||..||...+||.
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 69999999999999984
No 4
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=95.54 E-value=0.0063 Score=33.58 Aligned_cols=20 Identities=30% Similarity=0.637 Sum_probs=17.9
Q ss_pred ccccccCccccCCCCCCCCC
Q 041240 69 NTSFLCGKYGHSKDICPNRT 88 (113)
Q Consensus 69 ~fC~~Cg~iGH~~~~C~~~~ 88 (113)
..|+.|+.-||..++||...
T Consensus 9 Y~C~~C~~~GH~i~dCP~~~ 28 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPTNK 28 (32)
T ss_pred CEeecCCCCCccHhHCCCCC
Confidence 47999999999999999943
No 5
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=95.02 E-value=0.023 Score=32.82 Aligned_cols=20 Identities=30% Similarity=0.685 Sum_probs=17.0
Q ss_pred ccccccCccccCC--CCCCCCC
Q 041240 69 NTSFLCGKYGHSK--DICPNRT 88 (113)
Q Consensus 69 ~fC~~Cg~iGH~~--~~C~~~~ 88 (113)
..|..||-+||.. +.||...
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred ccccccccccccccCccCCCCC
Confidence 4699999999987 6899864
No 6
>smart00343 ZnF_C2HC zinc finger.
Probab=94.61 E-value=0.015 Score=29.93 Aligned_cols=18 Identities=39% Similarity=0.866 Sum_probs=16.0
Q ss_pred cccccCccccCCCCCCCC
Q 041240 70 TSFLCGKYGHSKDICPNR 87 (113)
Q Consensus 70 fC~~Cg~iGH~~~~C~~~ 87 (113)
.|+.||..||..++|+..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 599999999999999843
No 7
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=91.00 E-value=0.12 Score=39.17 Aligned_cols=16 Identities=31% Similarity=0.802 Sum_probs=8.7
Q ss_pred ccccccCccccCCCCC
Q 041240 69 NTSFLCGKYGHSKDIC 84 (113)
Q Consensus 69 ~fC~~Cg~iGH~~~~C 84 (113)
..|++||..||..++|
T Consensus 98 ~~C~~Cg~~GH~~~dC 113 (190)
T COG5082 98 KKCYNCGETGHLSRDC 113 (190)
T ss_pred cccccccccCcccccc
Confidence 4455555555555555
No 8
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=90.98 E-value=0.099 Score=39.57 Aligned_cols=22 Identities=32% Similarity=0.679 Sum_probs=18.9
Q ss_pred EccccccccccCccccCCCCCC
Q 041240 64 YEGLPNTSFLCGKYGHSKDICP 85 (113)
Q Consensus 64 YE~Lp~fC~~Cg~iGH~~~~C~ 85 (113)
+-.-..+||+||..||..++||
T Consensus 56 ~~~~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 56 IREENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccccccchhcccCcccccCC
Confidence 3344579999999999999999
No 9
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=89.71 E-value=0.18 Score=29.37 Aligned_cols=19 Identities=37% Similarity=0.639 Sum_probs=17.4
Q ss_pred cccccccCccccCCCCCCC
Q 041240 68 PNTSFLCGKYGHSKDICPN 86 (113)
Q Consensus 68 p~fC~~Cg~iGH~~~~C~~ 86 (113)
...|..|+..||...+|+.
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4689999999999999996
No 10
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=88.95 E-value=0.23 Score=35.17 Aligned_cols=18 Identities=39% Similarity=0.944 Sum_probs=10.5
Q ss_pred ccccccCccccCCCCCCC
Q 041240 69 NTSFLCGKYGHSKDICPN 86 (113)
Q Consensus 69 ~fC~~Cg~iGH~~~~C~~ 86 (113)
.+|++||..||..++||.
T Consensus 130 ~~C~~Cg~~gH~~~dCp~ 147 (148)
T PTZ00368 130 KTCYNCGQTGHLSRDCPD 147 (148)
T ss_pred CccccCCCcCcccccCCC
Confidence 456666666666666654
No 11
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=84.50 E-value=0.45 Score=36.75 Aligned_cols=25 Identities=32% Similarity=0.678 Sum_probs=20.3
Q ss_pred EEEccccccccccCccccCCCCCCCC
Q 041240 62 VEYEGLPNTSFLCGKYGHSKDICPNR 87 (113)
Q Consensus 62 v~YE~Lp~fC~~Cg~iGH~~~~C~~~ 87 (113)
+.+.+- .+||.||..||....|+..
T Consensus 138 ~~~~~~-~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 138 VDGPKP-AKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred ccCCCC-CccCCCCcCCcchhhCCCC
Confidence 344444 7899999999999999964
No 12
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=81.87 E-value=0.54 Score=34.62 Aligned_cols=31 Identities=26% Similarity=0.503 Sum_probs=23.5
Q ss_pred CCCCceeEEEEcCe-EEEEEEccccccccccCc
Q 041240 45 PNKPLISQFFLDGK-LQKVEYEGLPNTSFLCGK 76 (113)
Q Consensus 45 l~kpL~~~v~v~g~-~~~v~YE~Lp~fC~~Cg~ 76 (113)
-+-|++....++|. .+.-.|+ .|.||++||.
T Consensus 45 C~~~IrG~y~v~gv~~~g~~~~-~PsYC~~CGk 76 (158)
T PF10083_consen 45 CSTPIRGDYHVEGVFGLGGHYE-APSYCHNCGK 76 (158)
T ss_pred CCCCCCCceecCCeeeeCCCCC-CChhHHhCCC
Confidence 45566777777775 4557888 9999999996
No 13
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=80.61 E-value=1.2 Score=25.17 Aligned_cols=25 Identities=32% Similarity=0.452 Sum_probs=14.7
Q ss_pred cccccccCccccCCCCCCCCCcccc
Q 041240 68 PNTSFLCGKYGHSKDICPNRTEEDH 92 (113)
Q Consensus 68 p~fC~~Cg~iGH~~~~C~~~~~~~~ 92 (113)
|..|+.||+-.|-.++|......++
T Consensus 2 ~~~CprC~kg~Hwa~~C~sk~d~~G 26 (36)
T PF14787_consen 2 PGLCPRCGKGFHWASECRSKTDVDG 26 (36)
T ss_dssp --C-TTTSSSCS-TTT---TCCCCC
T ss_pred CccCcccCCCcchhhhhhhhhcccC
Confidence 5679999999999999998754443
No 14
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=79.69 E-value=1.2 Score=36.29 Aligned_cols=23 Identities=30% Similarity=0.637 Sum_probs=19.5
Q ss_pred cccccccCccccCCCCCCCCCcc
Q 041240 68 PNTSFLCGKYGHSKDICPNRTEE 90 (113)
Q Consensus 68 p~fC~~Cg~iGH~~~~C~~~~~~ 90 (113)
+.-|+.||+-||-.++||.....
T Consensus 160 q~~cyrcGkeghwskEcP~~~~~ 182 (346)
T KOG0109|consen 160 QSGCYRCGKEGHWSKECPVDRTG 182 (346)
T ss_pred HHHheeccccccccccCCccCCC
Confidence 45799999999999999987543
No 15
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=78.53 E-value=1.1 Score=31.65 Aligned_cols=16 Identities=38% Similarity=0.976 Sum_probs=8.1
Q ss_pred ccccCccccCCCCCCC
Q 041240 71 SFLCGKYGHSKDICPN 86 (113)
Q Consensus 71 C~~Cg~iGH~~~~C~~ 86 (113)
||.|+..||...+||.
T Consensus 30 C~~Cg~~GH~~~~Cp~ 45 (148)
T PTZ00368 30 CYKCGEPGHLSRECPS 45 (148)
T ss_pred CccCCCCCcCcccCcC
Confidence 4445555555555544
No 16
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.30 E-value=1.1 Score=32.32 Aligned_cols=30 Identities=20% Similarity=0.502 Sum_probs=20.3
Q ss_pred CCCceeEEEEcCe-EEEEEEccccccccccCc
Q 041240 46 NKPLISQFFLDGK-LQKVEYEGLPNTSFLCGK 76 (113)
Q Consensus 46 ~kpL~~~v~v~g~-~~~v~YE~Lp~fC~~Cg~ 76 (113)
+-|++....|+|. .+-=+|| .|.||.+||.
T Consensus 46 sasirgd~~vegvlglg~dye-~psfchncgs 76 (160)
T COG4306 46 SASIRGDYYVEGVLGLGGDYE-PPSFCHNCGS 76 (160)
T ss_pred CCcccccceeeeeeccCCCCC-CcchhhcCCC
Confidence 3455555666664 3455777 7999999995
No 17
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=72.77 E-value=1.5 Score=28.23 Aligned_cols=15 Identities=40% Similarity=0.862 Sum_probs=11.4
Q ss_pred ccccccccCc-cccCC
Q 041240 67 LPNTSFLCGK-YGHSK 81 (113)
Q Consensus 67 Lp~fC~~Cg~-iGH~~ 81 (113)
+|..||.||+ +||.-
T Consensus 3 iPVRCFTCGkvig~~w 18 (71)
T PLN00032 3 IPVRCFTCGKVIGNKW 18 (71)
T ss_pred CceeecCCCCCcHHHH
Confidence 5889999997 45543
No 18
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=71.95 E-value=1.8 Score=27.08 Aligned_cols=14 Identities=43% Similarity=0.997 Sum_probs=9.2
Q ss_pred ccccccccCcc-ccC
Q 041240 67 LPNTSFLCGKY-GHS 80 (113)
Q Consensus 67 Lp~fC~~Cg~i-GH~ 80 (113)
.|..||.||++ ||.
T Consensus 3 iPVRCFTCGkvi~~~ 17 (60)
T PF01194_consen 3 IPVRCFTCGKVIGNK 17 (60)
T ss_dssp -SSS-STTTSBTCGH
T ss_pred CceecCCCCCChhHh
Confidence 58899999974 544
No 19
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=71.11 E-value=1.8 Score=27.24 Aligned_cols=13 Identities=38% Similarity=0.904 Sum_probs=10.5
Q ss_pred ccccccccCc-ccc
Q 041240 67 LPNTSFLCGK-YGH 79 (113)
Q Consensus 67 Lp~fC~~Cg~-iGH 79 (113)
+|..||.||+ +||
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 5889999997 455
No 20
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=69.82 E-value=2.2 Score=34.96 Aligned_cols=20 Identities=30% Similarity=0.738 Sum_probs=18.1
Q ss_pred ccccccCccccCCCCCCCCC
Q 041240 69 NTSFLCGKYGHSKDICPNRT 88 (113)
Q Consensus 69 ~fC~~Cg~iGH~~~~C~~~~ 88 (113)
..||.||--||-...||...
T Consensus 177 Y~CyRCGqkgHwIqnCpTN~ 196 (427)
T COG5222 177 YVCYRCGQKGHWIQNCPTNQ 196 (427)
T ss_pred eeEEecCCCCchhhcCCCCC
Confidence 48999999999999999764
No 21
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=68.90 E-value=3.8 Score=31.58 Aligned_cols=25 Identities=36% Similarity=0.772 Sum_probs=22.1
Q ss_pred ccccccccCccccCCCCCCCCCccc
Q 041240 67 LPNTSFLCGKYGHSKDICPNRTEED 91 (113)
Q Consensus 67 Lp~fC~~Cg~iGH~~~~C~~~~~~~ 91 (113)
.+..|+.|+..||...+|+.....+
T Consensus 163 ~~~~c~~c~~~~h~~~~C~~~~~~~ 187 (261)
T KOG4400|consen 163 KGGTCFRCGKVGHGSRDCPSKQKSK 187 (261)
T ss_pred CCCccccCCCcceecccCCcccccc
Confidence 5889999999999999999886653
No 22
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=67.73 E-value=2.2 Score=26.84 Aligned_cols=16 Identities=44% Similarity=0.947 Sum_probs=12.0
Q ss_pred ccccccccCc-cccCCC
Q 041240 67 LPNTSFLCGK-YGHSKD 82 (113)
Q Consensus 67 Lp~fC~~Cg~-iGH~~~ 82 (113)
.|..||.||+ +||.-.
T Consensus 3 iPiRCFsCGkvi~~~w~ 19 (63)
T COG1644 3 IPVRCFSCGKVIGHKWE 19 (63)
T ss_pred CceEeecCCCCHHHHHH
Confidence 5889999997 566543
No 23
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=64.02 E-value=3 Score=35.57 Aligned_cols=21 Identities=29% Similarity=0.605 Sum_probs=18.5
Q ss_pred cccccccCccccCCCCCCCCC
Q 041240 68 PNTSFLCGKYGHSKDICPNRT 88 (113)
Q Consensus 68 p~fC~~Cg~iGH~~~~C~~~~ 88 (113)
-.-|..||-+||...+||+..
T Consensus 570 ~kGCayCgGLGHRItdCPKle 590 (610)
T KOG0341|consen 570 EKGCAYCGGLGHRITDCPKLE 590 (610)
T ss_pred ccccccccCCCcccccCchhh
Confidence 357999999999999999874
No 24
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=63.88 E-value=2.5 Score=26.68 Aligned_cols=11 Identities=45% Similarity=1.011 Sum_probs=9.3
Q ss_pred ccccccccCcc
Q 041240 67 LPNTSFLCGKY 77 (113)
Q Consensus 67 Lp~fC~~Cg~i 77 (113)
+|..||.||++
T Consensus 3 iPiRCFtCGKv 13 (69)
T KOG3497|consen 3 IPIRCFTCGKV 13 (69)
T ss_pred eeeEeeecccc
Confidence 58899999974
No 25
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=63.40 E-value=4.2 Score=23.96 Aligned_cols=18 Identities=28% Similarity=0.213 Sum_probs=15.1
Q ss_pred ccccccccCccccCCCCC
Q 041240 67 LPNTSFLCGKYGHSKDIC 84 (113)
Q Consensus 67 Lp~fC~~Cg~iGH~~~~C 84 (113)
-..||+.|+...|....|
T Consensus 47 ~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 47 GFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred CCeECCCCCCcCCCCCCC
Confidence 367999999999987766
No 26
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=63.08 E-value=11 Score=24.34 Aligned_cols=40 Identities=25% Similarity=0.203 Sum_probs=29.1
Q ss_pred CCcccccHHHHHHHhhccCceEEEecCCCcccccceeEEE
Q 041240 1 MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLA 40 (113)
Q Consensus 1 LP~~y~~~~~l~~I~~~iG~~l~vD~~t~~~~~g~faRV~ 40 (113)
||.-.-++-+.+.+|..-|.++++...+......-+-|+.
T Consensus 34 LP~I~~~DPv~r~~g~k~GdVvkI~R~S~taG~~v~YR~V 73 (74)
T PF01191_consen 34 LPKILSSDPVARYLGAKPGDVVKIIRKSETAGEYVTYRLV 73 (74)
T ss_dssp SSEEETTSHHHHHTT--TTSEEEEEEEETTTSEEEEEEEE
T ss_pred CCcccccChhhhhcCCCCCCEEEEEecCCCCCCcEEEEEe
Confidence 6777888899999999999999999887654444444544
No 27
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=61.70 E-value=14 Score=24.33 Aligned_cols=40 Identities=20% Similarity=0.223 Sum_probs=30.6
Q ss_pred CCcccccHHHHHHHhhccCceEEEecCCCcccccceeEEE
Q 041240 1 MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLA 40 (113)
Q Consensus 1 LP~~y~~~~~l~~I~~~iG~~l~vD~~t~~~~~g~faRV~ 40 (113)
||-...++-+.+.|+.+.|.++++=........--|-|++
T Consensus 40 LPkI~~~DPva~~lgak~GdvVkIvRkS~TaGe~v~YR~V 79 (80)
T COG2012 40 LPKIKASDPVAKALGAKPGDVVKIVRKSPTAGESVYYRLV 79 (80)
T ss_pred CCcccccChhHHHccCCCCcEEEEEecCCCCCceEEEEEe
Confidence 6777888889999999999999998876554444444543
No 28
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=59.66 E-value=5.5 Score=36.33 Aligned_cols=28 Identities=29% Similarity=0.682 Sum_probs=23.9
Q ss_pred EEEccccccccccCccccCCCCCCCCCc
Q 041240 62 VEYEGLPNTSFLCGKYGHSKDICPNRTE 89 (113)
Q Consensus 62 v~YE~Lp~fC~~Cg~iGH~~~~C~~~~~ 89 (113)
+-+.+-|..||.||..||..++|.-...
T Consensus 254 ~~~P~~~~~C~~cgq~gh~~~dc~g~~~ 281 (931)
T KOG2044|consen 254 EFFPNKPRRCFLCGQTGHEAKDCEGKPR 281 (931)
T ss_pred eecCCCcccchhhcccCCcHhhcCCcCC
Confidence 4458888999999999999999997744
No 29
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=56.72 E-value=6.7 Score=23.70 Aligned_cols=17 Identities=18% Similarity=0.204 Sum_probs=13.3
Q ss_pred EEEEEE---ccccccccccC
Q 041240 59 LQKVEY---EGLPNTSFLCG 75 (113)
Q Consensus 59 ~~~v~Y---E~Lp~fC~~Cg 75 (113)
+|+|+. .++..||..||
T Consensus 7 yY~v~~~kv~rk~~~CPrCG 26 (51)
T COG1998 7 YYEVDDEKVKRKNRFCPRCG 26 (51)
T ss_pred EEEEcCCcEEEccccCCCCC
Confidence 566666 56788999999
No 30
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=56.16 E-value=14 Score=28.62 Aligned_cols=82 Identities=20% Similarity=0.257 Sum_probs=53.6
Q ss_pred ccccc-HHHHHHHhhccCceEEEecCCCcccccce-------eEEEEEecCCCCceeEEEEcCeEE-------------E
Q 041240 3 LHYYN-KKILRMLGQIFGRVFKTDYNTESASRDKF-------GRLAVEIDPNKPLISQFFLDGKLQ-------------K 61 (113)
Q Consensus 3 ~~y~~-~~~l~~I~~~iG~~l~vD~~t~~~~~g~f-------aRV~VeiDl~kpL~~~v~v~g~~~-------------~ 61 (113)
+.+|+ .++...|...+|.|+.++.+......+.. .+..+-+.+..-+=..+.++|+.+ .
T Consensus 90 ~~~~~~~~l~~~L~~~~~~Pv~veNDan~aalaE~~~g~~~~~~~~~~i~~gtGIG~giv~~g~l~~G~~g~age~Gh~~ 169 (314)
T COG1940 90 LGWWNGVDLAEELEARLGLPVFVENDANAAALAEAWFGAGRGIDDVVYITLGTGIGGGIIVNGKLLRGANGNAGEIGHMV 169 (314)
T ss_pred CCccccccHHHHHHHHHCCCEEEecHHHHHHHHHHHhCCCCCCCCEEEEEEccceeEEEEECCEEeecCCCccccccceE
Confidence 34555 45788999999999999987764333222 223444556666666677776533 2
Q ss_pred EEEccccccccccCccccCCCCCCCCC
Q 041240 62 VEYEGLPNTSFLCGKYGHSKDICPNRT 88 (113)
Q Consensus 62 v~YE~Lp~fC~~Cg~iGH~~~~C~~~~ 88 (113)
+...+- | .||..|+....+....
T Consensus 170 v~~~g~---c-~cG~~GclE~~as~~a 192 (314)
T COG1940 170 VDPDGE---C-GCGRRGCLETYASGRA 192 (314)
T ss_pred ECCCCc---c-CCCCCCchHHhccHHH
Confidence 333333 9 9999999888777553
No 31
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=55.19 E-value=23 Score=23.19 Aligned_cols=41 Identities=20% Similarity=0.261 Sum_probs=30.5
Q ss_pred CCcccccHHHHHHHhhccCceEEEecCCCcccccceeEEEE
Q 041240 1 MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAV 41 (113)
Q Consensus 1 LP~~y~~~~~l~~I~~~iG~~l~vD~~t~~~~~g~faRV~V 41 (113)
||.-+-++-+.+.+|..-|.++++-..+......-+-|+.|
T Consensus 37 LP~I~~~DPv~r~~g~k~GdVvkI~R~S~taG~~v~YR~Vv 77 (79)
T PRK09570 37 LPKIKASDPVVKAIGAKPGDVIKIVRKSPTAGEAVYYRLVV 77 (79)
T ss_pred CCceeccChhhhhcCCCCCCEEEEEECCCCCCccEEEEEEe
Confidence 67778888899999999999999998865443333344443
No 32
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=50.76 E-value=5.5 Score=34.17 Aligned_cols=20 Identities=25% Similarity=0.443 Sum_probs=17.9
Q ss_pred ccccccCccccCCCCCCCCC
Q 041240 69 NTSFLCGKYGHSKDICPNRT 88 (113)
Q Consensus 69 ~fC~~Cg~iGH~~~~C~~~~ 88 (113)
.+|-+||-.||..+.|-...
T Consensus 113 GACeNCGAmtHk~KDCmERP 132 (529)
T KOG2560|consen 113 GACENCGAMTHKVKDCMERP 132 (529)
T ss_pred hhhhhhhhhhcchHHHhhcc
Confidence 58999999999999998654
No 33
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=45.50 E-value=37 Score=21.55 Aligned_cols=46 Identities=24% Similarity=0.528 Sum_probs=30.2
Q ss_pred ccceeEEEEEecCCCCceeEEEEc-CeEEEEE----------EccccccccccCccc
Q 041240 33 RDKFGRLAVEIDPNKPLISQFFLD-GKLQKVE----------YEGLPNTSFLCGKYG 78 (113)
Q Consensus 33 ~g~faRV~VeiDl~kpL~~~v~v~-g~~~~v~----------YE~Lp~fC~~Cg~iG 78 (113)
-+.|-|+.|..+.......-..|+ |....|. +..+|..++.|.+-|
T Consensus 65 ~~~w~Ra~I~~~~~~~~~~V~~iD~G~~~~v~~~~l~~l~~~~~~~P~~a~~~~L~g 121 (121)
T PF00567_consen 65 DGRWYRAVITVDIDENQYKVFLIDYGNTEKVSASDLRPLPPEFASLPPQAIKCKLAG 121 (121)
T ss_dssp TSEEEEEEEEEEECTTEEEEEETTTTEEEEEEGGGEEE--HHHCSSSSSCEEEEET-
T ss_pred CCceeeEEEEEecccceeEEEEEecCceEEEcHHHhhhhCHHHhhCChhhEEEEEcC
Confidence 468999999667777666655555 5544343 455688888887655
No 34
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=40.81 E-value=15 Score=33.16 Aligned_cols=25 Identities=36% Similarity=0.705 Sum_probs=19.0
Q ss_pred cccccccCccccCC--CCCCCCCcccc
Q 041240 68 PNTSFLCGKYGHSK--DICPNRTEEDH 92 (113)
Q Consensus 68 p~fC~~Cg~iGH~~--~~C~~~~~~~~ 92 (113)
-..|.+||-+||.. +.||.-...+.
T Consensus 937 tr~C~nCGQvGHmkTNK~CP~f~s~~~ 963 (968)
T COG5179 937 TRTCGNCGQVGHMKTNKACPKFSSKDN 963 (968)
T ss_pred ceecccccccccccccccCccccCCCC
Confidence 45899999999976 47998655443
No 35
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=40.65 E-value=11 Score=22.01 Aligned_cols=18 Identities=28% Similarity=0.458 Sum_probs=12.8
Q ss_pred ccccccccCccccCCCCC
Q 041240 67 LPNTSFLCGKYGHSKDIC 84 (113)
Q Consensus 67 Lp~fC~~Cg~iGH~~~~C 84 (113)
-..||+.|+.--|....|
T Consensus 47 ~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 47 GTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp CSEECSSSTSESCTTS-H
T ss_pred CCcCccccCcccCCCCCC
Confidence 356889999888876554
No 36
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=36.87 E-value=16 Score=31.68 Aligned_cols=18 Identities=28% Similarity=0.545 Sum_probs=17.2
Q ss_pred cccccCccccCCCCCCCC
Q 041240 70 TSFLCGKYGHSKDICPNR 87 (113)
Q Consensus 70 fC~~Cg~iGH~~~~C~~~ 87 (113)
.|+.||-+||....|+..
T Consensus 287 ~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 287 VCKICGPLGHISIDCKVN 304 (554)
T ss_pred cccccCCcccccccCCCc
Confidence 899999999999999987
No 37
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=33.72 E-value=22 Score=30.51 Aligned_cols=18 Identities=39% Similarity=0.665 Sum_probs=16.7
Q ss_pred ccccCccccCCCCCCCCC
Q 041240 71 SFLCGKYGHSKDICPNRT 88 (113)
Q Consensus 71 C~~Cg~iGH~~~~C~~~~ 88 (113)
||+||-.-|+..+|+...
T Consensus 131 CFNC~g~~hsLrdC~rp~ 148 (485)
T KOG2673|consen 131 CFNCGGTPHSLRDCPRPF 148 (485)
T ss_pred ccccCCCCCccccCCCcc
Confidence 799999999999999875
No 38
>PF01188 MR_MLE: Mandelate racemase / muconate lactonizing enzyme, C-terminal domain; InterPro: IPR013342 Mandelate racemase 5.1.2.2 from EC (MR) and muconate lactonising enzyme 5.5.1.1 from EC (MLE) are two bacterial enzymes involved in aromatic acid catabolism. They catalyse mechanistically distinct reactions yet they are related at the level of their primary, quaternary (homooctamer) and tertiary structures [, ]. A number of other proteins also seem to be evolutionary related to these two enzymes. These include, various plasmid-encoded chloromuconate cycloisomerases 5.5.1.7 from EC, Escherichia coli protein rspA [], E. coli bifunctional DGOA protein, E. coli hypothetical proteins ycjG, yfaW and yidU and a hypothetical protein from Streptomyces ambofaciens []. This entry represents the C-terminal region of these proteins.; PDB: 3QLD_B 3CYJ_C 2QDD_B 3FVD_A 3H7V_A 2OZT_A 3NXL_A 1JDF_D 1JCT_B 1EC9_C ....
Probab=32.70 E-value=53 Score=19.76 Aligned_cols=24 Identities=21% Similarity=-0.013 Sum_probs=20.0
Q ss_pred CcccccHHHHHHHhhccCceEEEe
Q 041240 2 ALHYYNKKILRMLGQIFGRVFKTD 25 (113)
Q Consensus 2 P~~y~~~~~l~~I~~~iG~~l~vD 25 (113)
|+..++-..+..+...++.||.+|
T Consensus 44 P~~~~d~~~~~~l~~~~~~pia~d 67 (67)
T PF01188_consen 44 PLPPDDLDGLAELRQQTSVPIAAD 67 (67)
T ss_dssp SSSTTSHHHHHHHHHHCSSEEEES
T ss_pred CCCCCCHHHHHHHHHhCCCCEEeC
Confidence 566677788999999999999876
No 39
>KOG2985 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.96 E-value=11 Score=30.06 Aligned_cols=29 Identities=24% Similarity=0.363 Sum_probs=22.4
Q ss_pred ccccccccccCccccCCCCCCCCCccccc
Q 041240 65 EGLPNTSFLCGKYGHSKDICPNRTEEDHA 93 (113)
Q Consensus 65 E~Lp~fC~~Cg~iGH~~~~C~~~~~~~~~ 93 (113)
|....-|..||..||..-+|.+-...+.+
T Consensus 78 ~arsg~ckRcg~~ghl~fqcRn~~~vke~ 106 (306)
T KOG2985|consen 78 EARSGSCKRCGRVGHLTFQCRNFLSVKED 106 (306)
T ss_pred hhcccchhhccccchhhHHHhhhhhcccc
Confidence 44456799999999999999977544443
No 40
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=30.02 E-value=24 Score=21.67 Aligned_cols=15 Identities=13% Similarity=0.235 Sum_probs=12.0
Q ss_pred EEEccccccccccCc
Q 041240 62 VEYEGLPNTSFLCGK 76 (113)
Q Consensus 62 v~YE~Lp~fC~~Cg~ 76 (113)
-+-+.+|.||..|..
T Consensus 22 T~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 22 TVLKNFPLYCPKCKQ 36 (55)
T ss_pred ceeccccccCCCCCc
Confidence 346789999999975
No 41
>PF05515 Viral_NABP: Viral nucleic acid binding ; InterPro: IPR008891 This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding proteins (NABP).
Probab=29.97 E-value=32 Score=24.44 Aligned_cols=19 Identities=37% Similarity=0.859 Sum_probs=16.4
Q ss_pred ccccccCccccCCCCCCCC
Q 041240 69 NTSFLCGKYGHSKDICPNR 87 (113)
Q Consensus 69 ~fC~~Cg~iGH~~~~C~~~ 87 (113)
..|+.||.+=|....|+..
T Consensus 63 ~~C~~CG~~l~~~~~C~~~ 81 (124)
T PF05515_consen 63 NRCFKCGRYLHNNGNCRRN 81 (124)
T ss_pred CccccccceeecCCcCCCc
Confidence 4799999999988899954
No 42
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=29.92 E-value=25 Score=28.35 Aligned_cols=20 Identities=35% Similarity=0.966 Sum_probs=18.0
Q ss_pred cccccccCccccCCCCCCCC
Q 041240 68 PNTSFLCGKYGHSKDICPNR 87 (113)
Q Consensus 68 p~fC~~Cg~iGH~~~~C~~~ 87 (113)
-.||+.||.+-|....|+.-
T Consensus 261 ~~~C~iC~~~~~~R~~C~~~ 280 (325)
T KOG4399|consen 261 KHGCFICGELDHKRSTCPNI 280 (325)
T ss_pred hcceeeccccccccccCccH
Confidence 46999999999999999975
No 43
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=28.82 E-value=20 Score=18.16 Aligned_cols=9 Identities=22% Similarity=0.368 Sum_probs=6.7
Q ss_pred cccccccCc
Q 041240 68 PNTSFLCGK 76 (113)
Q Consensus 68 p~fC~~Cg~ 76 (113)
-.||.+||.
T Consensus 16 ~~fC~~CG~ 24 (26)
T PF13248_consen 16 AKFCPNCGA 24 (26)
T ss_pred cccChhhCC
Confidence 468888874
No 44
>PRK09698 D-allose kinase; Provisional
Probab=27.98 E-value=1.1e+02 Score=23.47 Aligned_cols=78 Identities=9% Similarity=0.085 Sum_probs=44.4
Q ss_pred HHHHHHHhhccCceEEEecCCCccccccee------EEEEEecCCCCceeEEEEcCeEE-----------EEEEcccccc
Q 041240 8 KKILRMLGQIFGRVFKTDYNTESASRDKFG------RLAVEIDPNKPLISQFFLDGKLQ-----------KVEYEGLPNT 70 (113)
Q Consensus 8 ~~~l~~I~~~iG~~l~vD~~t~~~~~g~fa------RV~VeiDl~kpL~~~v~v~g~~~-----------~v~YE~Lp~f 70 (113)
-.+.+.+.+.+|.|+.++.+......+.+. +-.+-+.+..=+=..+.++|+.+ .+-+..-...
T Consensus 94 ~~l~~~l~~~~~~pv~v~NDa~aaa~~E~~~~~~~~~~~~~v~lgtGIG~giv~~G~~~~G~~g~agEiGh~~v~~~~~~ 173 (302)
T PRK09698 94 YDLADKLENTLNCPVFFSRDVNLQLLWDVKENNLTQQLVLGAYLGTGMGFAVWMNGAPWTGAHGVAGELGHIPLGDMTQH 173 (302)
T ss_pred CCHHHHHHHHhCCCEEEcchHhHHHHHHHHhcCCCCceEEEEEecCceEEEEEECCEEeeCCCCCccccCceEeeCCCcc
Confidence 356677888999999999876654433221 12233344444444555665432 1222222346
Q ss_pred ccccCccccCCCCCCC
Q 041240 71 SFLCGKYGHSKDICPN 86 (113)
Q Consensus 71 C~~Cg~iGH~~~~C~~ 86 (113)
|. ||..|+....|..
T Consensus 174 C~-CG~~gclE~~~S~ 188 (302)
T PRK09698 174 CG-CGNPGCLETNCSG 188 (302)
T ss_pred cC-CCCccchHhhcCH
Confidence 64 8888888777753
No 45
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=27.59 E-value=26 Score=18.40 Aligned_cols=13 Identities=15% Similarity=0.110 Sum_probs=6.8
Q ss_pred cccccccCccccC
Q 041240 68 PNTSFLCGKYGHS 80 (113)
Q Consensus 68 p~fC~~Cg~iGH~ 80 (113)
+.||..||-.-+.
T Consensus 3 ~rfC~~CG~~t~~ 15 (32)
T PF09297_consen 3 HRFCGRCGAPTKP 15 (32)
T ss_dssp TSB-TTT--BEEE
T ss_pred CcccCcCCccccC
Confidence 5789999865443
No 46
>PF10741 T2SM_b: Type II secretion system (T2SS), protein M subtype b; InterPro: IPR007690 General secretion pathway (GSP) protein M is a membrane protein involved in the export of proteins in bacteria. It consists of a short cytosolic N-terminal domain, a transmembrane domain, and a C-terminal periplasmic domain. The precise function of this protein is unknown, though in Vibrio cholerae, the EpsM protein interacts with the EpsL protein, and also forms homodimers [],; GO: 0006858 extracellular transport
Probab=26.55 E-value=1.2e+02 Score=20.14 Aligned_cols=42 Identities=17% Similarity=0.199 Sum_probs=31.6
Q ss_pred HHHHHHhhccCceEEEecCCCcccccceeEEEEEecCCCCce
Q 041240 9 KILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLI 50 (113)
Q Consensus 9 ~~l~~I~~~iG~~l~vD~~t~~~~~g~faRV~VeiDl~kpL~ 50 (113)
+.++++++.-|-.+...........+.|-||.|.++++-++.
T Consensus 20 ~~l~~~v~~aG~~v~s~q~~p~~~~~~~~~i~v~~~~~g~~~ 61 (110)
T PF10741_consen 20 QRLRALVAAAGGQVSSSQVLPPRPDGNFRRISVRVSLEGDIE 61 (110)
T ss_pred HHHHHHHHHcCCEEEEEEecCCCCCCcceEEEEEEEEEeCHH
Confidence 346777777787777776666777888999999988776653
No 47
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=25.92 E-value=41 Score=20.84 Aligned_cols=20 Identities=25% Similarity=0.454 Sum_probs=9.5
Q ss_pred eEEEEEEccccccccccCcc
Q 041240 58 KLQKVEYEGLPNTSFLCGKY 77 (113)
Q Consensus 58 ~~~~v~YE~Lp~fC~~Cg~i 77 (113)
..-.+.|-.|-..|.+||.+
T Consensus 38 ~~s~v~fH~lg~KC~~C~SY 57 (61)
T PF14599_consen 38 AKSEVPFHFLGHKCSHCGSY 57 (61)
T ss_dssp -EEEEE--TT----TTTS--
T ss_pred CccceeeeHhhhcCCCCCCc
Confidence 35589999999999999976
No 48
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=25.43 E-value=40 Score=20.32 Aligned_cols=25 Identities=36% Similarity=0.635 Sum_probs=16.6
Q ss_pred ccccccccCccccCC----CCCCCCCccc
Q 041240 67 LPNTSFLCGKYGHSK----DICPNRTEED 91 (113)
Q Consensus 67 Lp~fC~~Cg~iGH~~----~~C~~~~~~~ 91 (113)
-..+|+-||.-=-.. +.||-....+
T Consensus 26 ~~~YC~~Cg~~Y~d~~dL~~~CPG~t~~d 54 (55)
T PF13821_consen 26 EHNYCFWCGTKYDDEEDLERNCPGPTEDD 54 (55)
T ss_pred hCceeeeeCCccCCHHHHHhCCCCCCccc
Confidence 367999999854444 5687665443
No 49
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=25.13 E-value=29 Score=20.47 Aligned_cols=11 Identities=18% Similarity=0.111 Sum_probs=8.3
Q ss_pred ccccccccCcc
Q 041240 67 LPNTSFLCGKY 77 (113)
Q Consensus 67 Lp~fC~~Cg~i 77 (113)
--.+|.+||+|
T Consensus 45 ~i~~Cp~CgRi 55 (56)
T PF02591_consen 45 EIVFCPNCGRI 55 (56)
T ss_pred CeEECcCCCcc
Confidence 35689999875
No 50
>smart00769 WHy Water Stress and Hypersensitive response.
Probab=24.14 E-value=93 Score=20.15 Aligned_cols=33 Identities=9% Similarity=0.092 Sum_probs=27.2
Q ss_pred ceeEEEEEecCCCCceeEEEEcCeEEEEEEccc
Q 041240 35 KFGRLAVEIDPNKPLISQFFLDGKLQKVEYEGL 67 (113)
Q Consensus 35 ~faRV~VeiDl~kpL~~~v~v~g~~~~v~YE~L 67 (113)
.=+++.+.+.+..|-...+.+++..|.+.|.+.
T Consensus 13 ~~~~~~l~l~v~NPN~~~l~~~~~~y~l~~~g~ 45 (100)
T smart00769 13 LEIEIVLKVKVQNPNPFPIPVNGLSYDLYLNGV 45 (100)
T ss_pred eEEEEEEEEEEECCCCCccccccEEEEEEECCE
Confidence 346778888899999988889888888888764
No 51
>PRK15329 chaperone protein SicP; Provisional
Probab=23.98 E-value=71 Score=23.09 Aligned_cols=22 Identities=27% Similarity=0.372 Sum_probs=19.4
Q ss_pred HHHHHHHhhccCceEEEecCCC
Q 041240 8 KKILRMLGQIFGRVFKTDYNTE 29 (113)
Q Consensus 8 ~~~l~~I~~~iG~~l~vD~~t~ 29 (113)
.+.|.++|++.|-||..|.+..
T Consensus 5 ~~lL~~~~~~lGLpL~fDd~gq 26 (138)
T PRK15329 5 TEWLAALGEALGLPLTFDDNGQ 26 (138)
T ss_pred HHHHHHHHHHhCCceEEcCCCc
Confidence 5789999999999999998753
No 52
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=23.39 E-value=40 Score=28.16 Aligned_cols=39 Identities=23% Similarity=0.255 Sum_probs=22.1
Q ss_pred ccccHHHHHHHhhcc-------CceEEEecCCCcccccceeEEEEEecC
Q 041240 4 HYYNKKILRMLGQIF-------GRVFKTDYNTESASRDKFGRLAVEIDP 45 (113)
Q Consensus 4 ~y~~~~~l~~I~~~i-------G~~l~vD~~t~~~~~g~faRV~VeiDl 45 (113)
+|.+|-.|+.|-+.| ++-++-= .+....||.||.|+++=
T Consensus 180 ~~~hE~glR~Lig~vaR~AAkyd~~i~Pl---ls~~~dhY~Rvfv~v~r 225 (380)
T COG1867 180 EFCHEVGLRILIGYVARTAAKYDKAIEPL---LSLSIDHYVRVFVEVRR 225 (380)
T ss_pred cchhHHHHHHHHHHHHHHHHhhcccceeE---EEeeeceEEEEEEEEcc
Confidence 456666666554433 3322222 23456799999998753
No 53
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=22.59 E-value=40 Score=28.58 Aligned_cols=22 Identities=27% Similarity=0.541 Sum_probs=17.8
Q ss_pred cccccccCccccCC--CCCCCCCc
Q 041240 68 PNTSFLCGKYGHSK--DICPNRTE 89 (113)
Q Consensus 68 p~fC~~Cg~iGH~~--~~C~~~~~ 89 (113)
...|-.|+.+||.. ++||....
T Consensus 124 NVrC~kChkwGH~n~DreCplf~~ 147 (453)
T KOG3794|consen 124 NVRCLKCHKWGHINTDRECPLFGK 147 (453)
T ss_pred eeeEEeecccccccCCccCcchhh
Confidence 56899999999975 58997643
No 54
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=22.59 E-value=33 Score=18.76 Aligned_cols=8 Identities=25% Similarity=0.430 Sum_probs=3.0
Q ss_pred ccccccCc
Q 041240 69 NTSFLCGK 76 (113)
Q Consensus 69 ~fC~~Cg~ 76 (113)
.||..||.
T Consensus 1 kfC~~CG~ 8 (34)
T PF14803_consen 1 KFCPQCGG 8 (34)
T ss_dssp -B-TTT--
T ss_pred CccccccC
Confidence 36777764
No 55
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=22.23 E-value=2.5e+02 Score=19.18 Aligned_cols=26 Identities=19% Similarity=0.323 Sum_probs=15.8
Q ss_pred EcCeEEEEEEccccccccccCccccCCCCCC
Q 041240 55 LDGKLQKVEYEGLPNTSFLCGKYGHSKDICP 85 (113)
Q Consensus 55 v~g~~~~v~YE~Lp~fC~~Cg~iGH~~~~C~ 85 (113)
+++....|+-++-.. |..|. ....|.
T Consensus 4 v~~~~~~V~~~r~sa-C~~C~----~~~~Cg 29 (135)
T PF04246_consen 4 VEGGIAWVEVQRSSA-CGSCS----ASGGCG 29 (135)
T ss_pred EeCCEEEEEEccCCc-CcccC----CCCCCC
Confidence 445555566554444 99997 445677
No 56
>PF05037 DUF669: Protein of unknown function (DUF669); InterPro: IPR007731 This entry is represented by Streptococcus phage Sfi11, Gp151. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.33 E-value=51 Score=23.06 Aligned_cols=39 Identities=23% Similarity=0.219 Sum_probs=27.6
Q ss_pred ccHHHHHHHhhccCceEEEecCCCc----ccccceeEEEEEec
Q 041240 6 YNKKILRMLGQIFGRVFKTDYNTES----ASRDKFGRLAVEID 44 (113)
Q Consensus 6 ~~~~~l~~I~~~iG~~l~vD~~t~~----~~~g~faRV~VeiD 44 (113)
|+.+.|..|+.++|.|-..|..+.. ...|+.+||.|..+
T Consensus 71 ~~~~~l~~i~~a~G~~~~~~~~sl~~~~~~l~gk~l~V~v~~~ 113 (141)
T PF05037_consen 71 YSIKRLNAIAKAAGIPEGTDFESLEQFLNQLLGKPLRVTVKWE 113 (141)
T ss_pred hhHHHHHHHHHHhCCCCCCCcccHHHHHHHHcCCeeEEEeccc
Confidence 5667788999999977766665532 44577777777665
No 57
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.09 E-value=60 Score=19.14 Aligned_cols=11 Identities=18% Similarity=0.211 Sum_probs=8.7
Q ss_pred cccccccccCc
Q 041240 66 GLPNTSFLCGK 76 (113)
Q Consensus 66 ~Lp~fC~~Cg~ 76 (113)
.+..||..||.
T Consensus 18 ~~~~fCP~Cg~ 28 (50)
T PRK00432 18 RKNKFCPRCGS 28 (50)
T ss_pred EccCcCcCCCc
Confidence 45679999986
No 58
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=20.06 E-value=1.5e+02 Score=19.32 Aligned_cols=15 Identities=20% Similarity=0.084 Sum_probs=12.4
Q ss_pred ccccccccCccccCC
Q 041240 67 LPNTSFLCGKYGHSK 81 (113)
Q Consensus 67 Lp~fC~~Cg~iGH~~ 81 (113)
.+.+|..||.+-+..
T Consensus 72 ~H~~C~~Cg~i~~~~ 86 (116)
T cd07153 72 HHLICTKCGKVIDFE 86 (116)
T ss_pred CceEeCCCCCEEEec
Confidence 468999999998864
Done!