Query 032009
Match_columns 149
No_of_seqs 143 out of 897
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 08:21:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032009.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032009hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0944 Ubiquitin-specific pro 99.9 1.9E-25 4E-30 201.2 6.4 109 20-137 145-267 (763)
2 PF02148 zf-UBP: Zn-finger in 99.9 1.2E-23 2.6E-28 139.5 5.8 61 55-115 1-62 (63)
3 COG5207 UBP14 Isopeptidase T [ 99.9 2.2E-22 4.8E-27 178.0 3.5 108 24-137 145-263 (749)
4 KOG0804 Cytoplasmic Zn-finger 99.7 1.1E-18 2.3E-23 152.1 3.3 64 51-114 227-290 (493)
5 cd02669 Peptidase_C19M A subfa 99.6 3.5E-16 7.6E-21 136.7 6.0 69 51-119 15-83 (440)
6 smart00290 ZnF_UBP Ubiquitin C 99.6 4.3E-15 9.4E-20 93.4 4.2 49 54-102 1-49 (50)
7 KOG1873 Ubiquitin-specific pro 99.5 3.6E-15 7.9E-20 136.4 1.8 79 32-110 43-143 (877)
8 KOG2026 Spindle pole body prot 96.2 0.0045 9.8E-08 54.4 3.4 67 51-117 28-95 (442)
9 COG5207 UBP14 Isopeptidase T [ 95.5 0.0023 5E-08 58.2 -1.3 69 32-101 1-76 (749)
10 KOG0944 Ubiquitin-specific pro 94.6 0.025 5.4E-07 52.8 2.7 49 49-101 21-73 (763)
11 KOG1867 Ubiquitin-specific pro 94.5 0.017 3.6E-07 52.2 1.4 70 49-120 40-111 (492)
12 PF09416 UPF1_Zn_bind: RNA hel 93.3 0.2 4.2E-06 38.9 5.1 57 54-110 2-68 (152)
13 PRK14890 putative Zn-ribbon RN 87.0 0.2 4.2E-06 33.1 0.1 23 52-74 36-58 (59)
14 COG2888 Predicted Zn-ribbon RN 84.1 0.31 6.7E-06 32.2 -0.1 24 51-74 37-60 (61)
15 PF14369 zf-RING_3: zinc-finge 74.5 2.2 4.7E-05 25.0 1.5 13 102-114 2-14 (35)
16 KOG1802 RNA helicase nonsense 65.2 10 0.00022 36.4 4.4 59 52-110 60-128 (935)
17 PF08274 PhnA_Zn_Ribbon: PhnA 63.8 6 0.00013 22.5 1.7 21 53-73 3-28 (30)
18 cd00729 rubredoxin_SM Rubredox 63.6 4 8.7E-05 23.6 1.0 14 64-77 2-15 (34)
19 COG1997 RPL43A Ribosomal prote 61.7 6.6 0.00014 27.9 2.0 27 51-77 34-66 (89)
20 PF14803 Nudix_N_2: Nudix N-te 59.9 7.7 0.00017 22.6 1.8 13 62-74 20-32 (34)
21 PF11781 RRN7: RNA polymerase 56.5 9 0.0002 22.5 1.7 21 53-73 9-34 (36)
22 cd00350 rubredoxin_like Rubred 55.5 6.3 0.00014 22.4 0.9 13 64-76 1-13 (33)
23 PF01927 Mut7-C: Mut7-C RNAse 54.9 10 0.00023 28.4 2.3 26 50-75 89-135 (147)
24 KOG0704 ADP-ribosylation facto 50.5 6.9 0.00015 34.3 0.8 41 51-104 18-67 (386)
25 PF01780 Ribosomal_L37ae: Ribo 49.7 13 0.00028 26.4 1.9 26 52-77 35-66 (90)
26 smart00661 RPOL9 RNA polymeras 49.6 14 0.00029 22.5 1.8 11 63-73 19-29 (52)
27 PRK10220 hypothetical protein; 48.8 14 0.00031 27.2 2.0 21 53-73 4-29 (111)
28 TIGR00686 phnA alkylphosphonat 47.9 14 0.00031 27.1 2.0 22 53-74 3-29 (109)
29 PF07754 DUF1610: Domain of un 47.6 14 0.0003 20.0 1.4 11 62-72 14-24 (24)
30 PF08792 A2L_zn_ribbon: A2L zi 46.8 19 0.00042 20.7 2.0 23 52-74 3-31 (33)
31 PF08271 TF_Zn_Ribbon: TFIIB z 46.6 15 0.00032 21.9 1.6 18 95-112 12-29 (43)
32 PF05766 NinG: Bacteriophage L 45.6 8.1 0.00018 30.9 0.4 46 85-135 104-151 (189)
33 PF10571 UPF0547: Uncharacteri 45.4 12 0.00027 20.4 1.0 21 54-74 2-24 (26)
34 COG0777 AccD Acetyl-CoA carbox 44.6 8.1 0.00018 32.9 0.3 24 50-73 26-56 (294)
35 PF15616 TerY-C: TerY-C metal 42.7 18 0.00039 27.4 1.8 24 53-77 78-101 (131)
36 PF01412 ArfGap: Putative GTPa 42.2 36 0.00079 24.5 3.4 50 51-104 12-61 (116)
37 KOG0317 Predicted E3 ubiquitin 41.5 18 0.00039 30.9 1.9 41 47-91 234-274 (293)
38 COG5574 PEX10 RING-finger-cont 39.2 13 0.00029 31.4 0.7 53 50-117 213-266 (271)
39 smart00154 ZnF_AN1 AN1-like Zi 38.6 26 0.00056 20.7 1.8 23 55-77 1-25 (39)
40 PF04810 zf-Sec23_Sec24: Sec23 36.6 24 0.00052 20.8 1.4 12 62-73 22-33 (40)
41 CHL00174 accD acetyl-CoA carbo 36.4 14 0.0003 31.5 0.5 22 51-72 37-65 (296)
42 PHA00626 hypothetical protein 35.7 23 0.00049 23.2 1.3 24 53-76 12-35 (59)
43 TIGR00515 accD acetyl-CoA carb 35.5 15 0.00033 31.0 0.5 23 51-73 25-54 (285)
44 COG1656 Uncharacterized conser 35.4 22 0.00049 27.9 1.4 27 49-75 94-141 (165)
45 PF13923 zf-C3HC4_2: Zinc fing 34.5 33 0.00071 19.6 1.7 31 55-89 1-32 (39)
46 PF07282 OrfB_Zn_ribbon: Putat 33.0 40 0.00086 21.6 2.1 23 51-73 27-55 (69)
47 PRK05654 acetyl-CoA carboxylas 32.9 18 0.00039 30.7 0.6 24 51-74 26-56 (292)
48 PF05715 zf-piccolo: Piccolo Z 31.9 26 0.00056 23.2 1.0 19 54-72 32-57 (61)
49 PHA02942 putative transposase; 31.5 39 0.00084 29.6 2.4 24 51-74 324-352 (383)
50 PF00096 zf-C2H2: Zinc finger, 31.0 17 0.00038 18.1 0.1 11 65-75 1-11 (23)
51 TIGR01031 rpmF_bact ribosomal 30.9 42 0.00091 21.4 1.9 23 51-73 25-48 (55)
52 PF08882 Acetone_carb_G: Aceto 30.1 27 0.00059 25.8 1.0 53 62-114 13-86 (112)
53 PRK12286 rpmF 50S ribosomal pr 29.5 41 0.00089 21.7 1.7 23 51-73 26-49 (57)
54 PHA00616 hypothetical protein 29.4 8.1 0.00018 23.9 -1.5 25 65-89 2-27 (44)
55 smart00105 ArfGap Putative GTP 29.2 80 0.0017 22.5 3.4 49 52-104 3-51 (112)
56 PRK11788 tetratricopeptide rep 27.0 35 0.00075 28.2 1.3 26 51-76 353-380 (389)
57 COG1592 Rubrerythrin [Energy p 26.0 30 0.00064 27.2 0.7 13 64-76 134-146 (166)
58 PF13240 zinc_ribbon_2: zinc-r 25.8 42 0.0009 17.6 1.0 18 55-72 2-21 (23)
59 PF14968 CCDC84: Coiled coil p 25.2 50 0.0011 28.8 2.0 25 91-115 44-71 (336)
60 cd02340 ZZ_NBR1_like Zinc fing 25.0 65 0.0014 19.3 2.0 8 63-70 13-20 (43)
61 PF04438 zf-HIT: HIT zinc fing 24.9 34 0.00075 19.2 0.6 22 54-76 4-25 (30)
62 PF13894 zf-C2H2_4: C2H2-type 24.9 24 0.00052 17.1 -0.0 11 65-75 1-11 (24)
63 PF02207 zf-UBR: Putative zinc 24.2 20 0.00044 23.6 -0.5 40 53-105 14-53 (71)
64 PTZ00255 60S ribosomal protein 24.0 58 0.0013 23.1 1.8 27 51-77 35-67 (90)
65 smart00614 ZnF_BED BED zinc fi 23.8 78 0.0017 19.2 2.2 24 66-89 20-45 (50)
66 COG2023 RPR2 RNase P subunit R 23.8 38 0.00082 24.8 0.8 12 63-74 81-92 (105)
67 cd02249 ZZ Zinc finger, ZZ typ 23.8 60 0.0013 19.5 1.6 17 55-71 3-21 (46)
68 PRK14873 primosome assembly pr 23.8 46 0.00099 31.4 1.6 23 51-73 409-431 (665)
69 PF11261 IRF-2BP1_2: Interfero 23.7 38 0.00082 21.8 0.7 9 101-109 2-10 (54)
70 TIGR00280 L37a ribosomal prote 23.1 60 0.0013 23.1 1.7 27 51-77 34-66 (91)
71 PF14690 zf-ISL3: zinc-finger 22.8 19 0.00041 21.4 -0.8 41 66-108 4-47 (47)
72 PF00643 zf-B_box: B-box zinc 22.7 75 0.0016 18.2 1.9 26 52-77 3-28 (42)
73 cd00730 rubredoxin Rubredoxin; 22.6 40 0.00087 21.2 0.7 11 65-75 2-12 (50)
74 COG0675 Transposase and inacti 22.4 65 0.0014 25.9 2.1 26 51-76 308-334 (364)
75 PRK14704 anaerobic ribonucleos 22.3 52 0.0011 30.8 1.7 25 48-72 555-580 (618)
76 PF14835 zf-RING_6: zf-RING of 22.1 59 0.0013 21.8 1.4 26 52-77 7-33 (65)
77 PF06221 zf-C2HC5: Putative zi 21.1 31 0.00068 22.4 -0.0 13 65-77 19-31 (57)
78 COG2051 RPS27A Ribosomal prote 21.1 75 0.0016 21.4 1.8 26 52-77 19-51 (67)
79 PRK03976 rpl37ae 50S ribosomal 20.9 71 0.0015 22.7 1.7 27 51-77 35-67 (90)
80 PF01783 Ribosomal_L32p: Ribos 20.7 51 0.0011 20.9 0.9 23 51-73 25-48 (56)
81 TIGR03830 CxxCG_CxxCG_HTH puta 20.7 41 0.00089 23.8 0.5 50 83-134 14-64 (127)
82 PF13920 zf-C3HC4_3: Zinc fing 20.6 88 0.0019 18.7 1.9 24 53-76 3-27 (50)
83 PF13719 zinc_ribbon_5: zinc-r 20.2 25 0.00055 20.4 -0.6 29 32-60 3-33 (37)
No 1
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=99.92 E-value=1.9e-25 Score=201.21 Aligned_cols=109 Identities=30% Similarity=0.608 Sum_probs=93.7
Q ss_pred hhcCccccccCCCC-CcccccccccC--CCCCCCCCCCCCCCCCCCCceeccccCeeeecCC------CChhHHHHhhhc
Q 032009 20 MFGAESGWVEPLTS-CDHLVASLSSD--LAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRF------VNKHMLQHYLET 90 (149)
Q Consensus 20 ~~~~~~~w~~~~~~-CpHl~~~l~~~--~~~i~~~~~~C~~C~~~~~lW~CL~Cg~vgCgr~------~~~Ha~~H~~~t 90 (149)
.+..+.+|+.++.. +.|. ..+.|. .+++++..|+|..|....|||+||+||.|||||. +|+||+.||++|
T Consensus 145 ~k~~~~aWd~Evr~v~k~~-~nl~q~dng~~~~~~gwkCs~CDL~~NLWlcLtcG~v~CGR~qfg~~GgNgHA~~HYr~t 223 (763)
T KOG0944|consen 145 RKDRVNAWDNEVRTVSKHA-NNLSQIDNGKRIPPSGWKCSKCDLTENLWLCLTCGSVGCGRKQFGGSGGNGHALSHYRET 223 (763)
T ss_pred hhhhhhhhhhheeeccCCC-CChhhcccCcccCCCcceecccCcccceEEEeccCceeecceeecCCCCCcchHHhhhhc
Confidence 34467899999855 5555 567664 3577789999999999999999999999999993 599999999999
Q ss_pred CCeeEEECCCC-----cEEEcCCCceecccccCCchhhhHHHHHHhhCCCCC
Q 032009 91 NHSVALSYSDL-----SVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAPP 137 (149)
Q Consensus 91 ~H~l~v~l~t~-----~vwCY~Cd~~V~~~~~~~L~~~~~~~hl~kfg~~~~ 137 (149)
+|||+|+|+|+ +||||.||+ ..++|+| +.||.+|||++.
T Consensus 224 ghPLaVKLgsIs~dg~DvycY~cDd---~v~dPnl-----~~hl~hfGId~~ 267 (763)
T KOG0944|consen 224 GHPLAVKLGSISPDGADVYCYDCDD---EVRDPNL-----ESHLSHFGIDMA 267 (763)
T ss_pred CCceEEEecccCCCccceeeecccc---cccCccH-----HHHHHhcCccHH
Confidence 99999999986 899999994 5577899 899999999984
No 2
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=99.89 E-value=1.2e-23 Score=139.47 Aligned_cols=61 Identities=46% Similarity=1.015 Sum_probs=54.2
Q ss_pred CCCCCCC-CCceeccccCeeeecCCCChhHHHHhhhcCCeeEEECCCCcEEEcCCCceeccc
Q 032009 55 CNRCQHP-SENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNAQ 115 (149)
Q Consensus 55 C~~C~~~-~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~t~H~l~v~l~t~~vwCY~Cd~~V~~~ 115 (149)
|.+|+.. .++|+||+||++||||+.++||++|+++++|+|+|++.+..||||+|++||+++
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~~~~H~l~v~~~~~~i~C~~C~~~v~~~ 62 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGRYSNGHALKHYKETGHPLAVSLSTGSIWCYACDDYVYDP 62 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETTTSTSHHHHHHHHHT--EEEETTTTCEEETTTTEEEEST
T ss_pred CCCCCCcCCceEEeCCCCcccccCCcCcHHHHhhcccCCeEEEECCCCeEEEcCCCcEEeCC
Confidence 7788877 899999999999999998999999999999999999999999999999999864
No 3
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=99.85 E-value=2.2e-22 Score=177.95 Aligned_cols=108 Identities=25% Similarity=0.548 Sum_probs=87.8
Q ss_pred ccccccCCCCCcccccccccCCC-CCCCCCCCCCCCCCCCCceeccccCeeeecC--C---CChhHHHHhhhcCCeeEEE
Q 032009 24 ESGWVEPLTSCDHLVASLSSDLA-HIPTPDTPCNRCQHPSENWLCLCCKEVLCSR--F---VNKHMLQHYLETNHSVALS 97 (149)
Q Consensus 24 ~~~w~~~~~~CpHl~~~l~~~~~-~i~~~~~~C~~C~~~~~lW~CL~Cg~vgCgr--~---~~~Ha~~H~~~t~H~l~v~ 97 (149)
..+|+.++.+|+|. ..+..+.. --+....+|+.|....+||+||+||++|||| | +||||+.||++|+||++|+
T Consensus 145 ~~~w~~E~~tC~H~-~n~~~~s~~~~ni~~~~Cs~CDl~~nLW~Cl~CG~vgCGR~QyG~~GngHAlsHY~~t~Hplavk 223 (749)
T COG5207 145 RVLWRDEEVTCVHG-CNEGPSSIEMGNIGGLKCSLCDLKTNLWVCLSCGYVGCGRMQYGAEGNGHALSHYEETQHPLAVK 223 (749)
T ss_pred hhhhhhhccccccc-CCCCCCcccccccCCceeccccchhceEEEEecCcccccceeecCCCCcchhhhhhccCCceEEE
Confidence 36799999999999 55544321 1234678899999999999999999999999 2 8999999999999999999
Q ss_pred CCCC-----cEEEcCCCceecccccCCchhhhHHHHHHhhCCCCC
Q 032009 98 YSDL-----SVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAPP 137 (149)
Q Consensus 98 l~t~-----~vwCY~Cd~~V~~~~~~~L~~~~~~~hl~kfg~~~~ 137 (149)
+.++ +||||.||+++-.+.-.++ ..|+..|||++.
T Consensus 224 l~Sls~~~~diyCY~CD~e~R~~~n~n~-----~s~~~~fGinIa 263 (749)
T COG5207 224 LPSLSKEDCDIYCYLCDSEIRSRYNSNE-----NSVTIDFGINIA 263 (749)
T ss_pred ccccccccccEEEEecCcccccCCcccc-----cceeeeeccchh
Confidence 9965 8999999987644333345 568888999764
No 4
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=99.73 E-value=1.1e-18 Score=152.09 Aligned_cols=64 Identities=31% Similarity=0.724 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCCCceeccccCeeeecCCCChhHHHHhhhcCCeeEEECCCCcEEEcCCCceecc
Q 032009 51 PDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNA 114 (149)
Q Consensus 51 ~~~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~t~H~l~v~l~t~~vwCY~Cd~~V~~ 114 (149)
....|..|+.+.+||+||.||++|||||..|||++||++|+|.+++.|+|.+||.|+-|+||+.
T Consensus 227 e~~~c~~c~~~~~LwicliCg~vgcgrY~eghA~rHweet~H~yalel~tqrVWDYAGDnYVhR 290 (493)
T KOG0804|consen 227 ESSLCLACGCTEDLWICLICGNVGCGRYKEGHARRHWEETGHCYALELETQRVWDYAGDNYVHR 290 (493)
T ss_pred hhhhhhhhcccccEEEEEEccceecccccchhHHHHHHhhcceEEEeecceeeeecccchhhhh
Confidence 3567999999999999999999999999999999999999999999999999999999999986
No 5
>cd02669 Peptidase_C19M A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.63 E-value=3.5e-16 Score=136.71 Aligned_cols=69 Identities=22% Similarity=0.385 Sum_probs=63.2
Q ss_pred CCCCCCCCCCCCCceeccccCeeeecCCCChhHHHHhhhcCCeeEEECCCCcEEEcCCCceecccccCC
Q 032009 51 PDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNAQVIPQ 119 (149)
Q Consensus 51 ~~~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~t~H~l~v~l~t~~vwCY~Cd~~V~~~~~~~ 119 (149)
....|..|....++|+||+||.++|||++++||..|+.+++|+++|+++|..||||.|++||.+..+.+
T Consensus 15 ~e~~C~~~~~~~n~~~CL~cg~~~~g~~~~~ha~~H~~~~~H~~~v~l~t~~~yc~~~~~~v~d~~l~~ 83 (440)
T cd02669 15 FEKVCSVSLSNLNVYACLVCGKYFQGRGKGSHAYTHSLEDNHHVFLNLETLKFYCLPDNYEIIDSSLDD 83 (440)
T ss_pred ccccccccCCCCcEEEEcccCCeecCCCCCcHHHHHhhccCCCEEEECCCCCEEEeCCCCEEeCccHHH
Confidence 566799999999999999999888888899999999999999999999999999999999998655443
No 6
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=99.55 E-value=4.3e-15 Score=93.44 Aligned_cols=49 Identities=33% Similarity=0.750 Sum_probs=46.1
Q ss_pred CCCCCCCCCCceeccccCeeeecCCCChhHHHHhhhcCCeeEEECCCCc
Q 032009 54 PCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLS 102 (149)
Q Consensus 54 ~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~t~H~l~v~l~t~~ 102 (149)
+|.+|+...++|+||+|+++||+|+..+|++.|+++++|++++++.++.
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~~~~~~h~~~H~~~t~H~~~~~~~~~~ 49 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCGRYQLGHALEHFEETGHPLVVKLGTQR 49 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccCCCCCcHHHHHhhhhCCCEEEEccccc
Confidence 5999999889999999999999999889999999999999999998864
No 7
>KOG1873 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.51 E-value=3.6e-15 Score=136.39 Aligned_cols=79 Identities=29% Similarity=0.740 Sum_probs=64.7
Q ss_pred CCCcccccccccC-C-CCCC-CCCCCCCCCCCC---------------CCceeccccCeeeecC-CCChhHHHHhhhc--
Q 032009 32 TSCDHLVASLSSD-L-AHIP-TPDTPCNRCQHP---------------SENWLCLCCKEVLCSR-FVNKHMLQHYLET-- 90 (149)
Q Consensus 32 ~~CpHl~~~l~~~-~-~~i~-~~~~~C~~C~~~---------------~~lW~CL~Cg~vgCgr-~~~~Ha~~H~~~t-- 90 (149)
..|.|+.+++.+. + +.+. ..+..|.+|... ..+|+||.||+.|||| ....|+++||+..
T Consensus 43 ~~C~Hi~Kav~l~~lk~~iks~~~~~C~eC~e~~~~k~g~s~~~~~~~~~iWLCLkCG~q~CG~~~~~~halkH~~~~r~ 122 (877)
T KOG1873|consen 43 VECQHIKKAVDLSHLKRAIKSLLWIKCSECNEEVKVKDGGSSDQFEFDNAIWLCLKCGYQGCGRNSESQHALKHFLTPRS 122 (877)
T ss_pred cccchHHhhhcHHHHHHHHHHHHHHHHHHhhhcceeccCCCccccccccceeeecccCCeeeCCCcccchhhhhhcccCC
Confidence 4499998888764 2 1121 256679999862 4699999999999999 6789999999875
Q ss_pred -CCeeEEECCCCcEEEcCCCc
Q 032009 91 -NHSVALSYSDLSVWCFTCDA 110 (149)
Q Consensus 91 -~H~l~v~l~t~~vwCY~Cd~ 110 (149)
.|+|+|++.++.||||.||.
T Consensus 123 ~~Hclvin~~n~~~WCy~Cd~ 143 (877)
T KOG1873|consen 123 EPHCLVINLINWLIWCYSCDA 143 (877)
T ss_pred CCeeEEEEeeeeeeEEEeccc
Confidence 59999999999999999998
No 8
>KOG2026 consensus Spindle pole body protein - Sad1p [Cytoskeleton]
Probab=96.20 E-value=0.0045 Score=54.38 Aligned_cols=67 Identities=22% Similarity=0.403 Sum_probs=58.2
Q ss_pred CCCCCCCCCCCCCceeccccCeeeecCCCChhHHHHhhhcCCeeEEECCC-CcEEEcCCCceeccccc
Q 032009 51 PDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSD-LSVWCFTCDAYLNAQVI 117 (149)
Q Consensus 51 ~~~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~t~H~l~v~l~t-~~vwCY~Cd~~V~~~~~ 117 (149)
....|..-...-+.+.||.||...=||....||..|.-+.||-+.+++.| ...|+..-++.+++...
T Consensus 28 ~ek~c~vslsnLnvyAclvcg~y~qgr~~kS~A~~h~l~~ghhvf~nl~telkfyvlpe~~ei~d~s~ 95 (442)
T KOG2026|consen 28 FEKPCSVSLSNLNVYACLVCGKYFQGRGEKSHAYTHSLEEGHHVFLNLSTELKFYVLPENYEIDDPSL 95 (442)
T ss_pred CCCCCcccccccceeeeeeeCchhhCcCccccchhccccccccceeccccceeEEecchhccccCchh
Confidence 45568888888899999999999999999999999999999999999999 78888887766665443
No 9
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=95.48 E-value=0.0023 Score=58.19 Aligned_cols=69 Identities=22% Similarity=0.387 Sum_probs=50.2
Q ss_pred CCCcccccccccCCCCCC--CCCCCCCCCCCC----CCceeccccCeeeecCCCChhH-HHHhhhcCCeeEEECCCC
Q 032009 32 TSCDHLVASLSSDLAHIP--TPDTPCNRCQHP----SENWLCLCCKEVLCSRFVNKHM-LQHYLETNHSVALSYSDL 101 (149)
Q Consensus 32 ~~CpHl~~~l~~~~~~i~--~~~~~C~~C~~~----~~lW~CL~Cg~vgCgr~~~~Ha-~~H~~~t~H~l~v~l~t~ 101 (149)
+.|+|. ...+..+..++ .+...|..|+.+ ..+-+||.|++.+|++-+--|. +.|+..|=|++.+-+...
T Consensus 1 ~S~~H~-e~ae~vlpn~~av~~reeC~yCf~S~~~e~si~vClnCfqs~C~~h~~~H~~~~~~c~tvh~i~~tia~~ 76 (749)
T COG5207 1 KSFSHS-EMAEMVLPNLPAVRFREECCYCFRSIGDEHSISVCLNCFQSFCEKHRGIHLGTKSGCRTVHDIKETIADL 76 (749)
T ss_pred CCCchh-hhhhhcCCCCchhhhhhhhheeeccCCCCcceehHHHHhHhhhhhccceeecchhhhhhhhhhhhhhhhc
Confidence 478998 32322222222 256679999975 4588999999999999777787 699999999988766543
No 10
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=94.61 E-value=0.025 Score=52.79 Aligned_cols=49 Identities=22% Similarity=0.438 Sum_probs=42.4
Q ss_pred CCCCCCCCCCCCC----CCceeccccCeeeecCCCChhHHHHhhhcCCeeEEECCCC
Q 032009 49 PTPDTPCNRCQHP----SENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDL 101 (149)
Q Consensus 49 ~~~~~~C~~C~~~----~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~t~H~l~v~l~t~ 101 (149)
.+.+..|..|+.+ .+|++||.|....+ ..|...||.+|+|++++.|+..
T Consensus 21 ~i~kdeC~ycf~sp~~e~glyicl~~f~afg----~~~v~~~f~~tg~~~yl~i~r~ 73 (763)
T KOG0944|consen 21 VIYKDECAYCFDSPESEGGLYICLNCFLAFG----REHVEEYFRKTGHSVYLHIARV 73 (763)
T ss_pred ceehhhceeeccCCCCCCCEEeehhhhhhhh----hHHHHHHHhhcCceEEEEeccc
Confidence 3478889999985 67999999998855 5799999999999999999854
No 11
>KOG1867 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=94.54 E-value=0.017 Score=52.16 Aligned_cols=70 Identities=23% Similarity=0.552 Sum_probs=57.5
Q ss_pred CCCCCCCCCCCC-CCCcee-ccccCeeeecCCCChhHHHHhhhcCCeeEEECCCCcEEEcCCCceecccccCCc
Q 032009 49 PTPDTPCNRCQH-PSENWL-CLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNAQVIPQL 120 (149)
Q Consensus 49 ~~~~~~C~~C~~-~~~lW~-CL~Cg~vgCgr~~~~Ha~~H~~~t~H~l~v~l~t~~vwCY~Cd~~V~~~~~~~L 120 (149)
+.....|..|.. ...+.. |+.|+.++|. .+.|...|....+|-+.+++.++-.+||.|++||+.....++
T Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~g~~~~~~c~~~i~~~~~~~~ 111 (492)
T KOG1867|consen 40 PLKTINCGTCGVLQIRLAVPCLICDSLGCL--SNSHKLEHSGNKKHNNTIDVNNGLLYCFACPDFIYDAELLKL 111 (492)
T ss_pred ccccceeEEechhhhhhcccceechhcccc--cccccccccccccccccceeehhhheeccCCcEeeccchhhH
Confidence 335566777775 344555 8999999995 577999999999999999999999999999999988665555
No 12
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=93.32 E-value=0.2 Score=38.88 Aligned_cols=57 Identities=23% Similarity=0.559 Sum_probs=33.8
Q ss_pred CCCCCCC--CCCceeccccCeeeecCC---CChhHHHHhhhcCCeeEEEC-----CCCcEEEcCCCc
Q 032009 54 PCNRCQH--PSENWLCLCCKEVLCSRF---VNKHMLQHYLETNHSVALSY-----SDLSVWCFTCDA 110 (149)
Q Consensus 54 ~C~~C~~--~~~lW~CL~Cg~vgCgr~---~~~Ha~~H~~~t~H~l~v~l-----~t~~vwCY~Cd~ 110 (149)
.|..|+. ...+-.|+.|++-+|-.. ...|+..|...++|.-+.-- ++..+-||.|..
T Consensus 2 aC~YCG~~~p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~ 68 (152)
T PF09416_consen 2 ACAYCGIHDPSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGS 68 (152)
T ss_dssp S-TTT----CCCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT--
T ss_pred CccccCCCCcccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCC
Confidence 5899994 577899999999999752 56899999999998744332 234799999984
No 13
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=87.01 E-value=0.2 Score=33.05 Aligned_cols=23 Identities=22% Similarity=0.486 Sum_probs=20.8
Q ss_pred CCCCCCCCCCCCceeccccCeee
Q 032009 52 DTPCNRCQHPSENWLCLCCKEVL 74 (149)
Q Consensus 52 ~~~C~~C~~~~~lW~CL~Cg~vg 74 (149)
.++|..|....+.+.|..|||.|
T Consensus 36 I~RC~~CRk~~~~Y~CP~CGF~G 58 (59)
T PRK14890 36 IYRCEKCRKQSNPYTCPKCGFEG 58 (59)
T ss_pred EeechhHHhcCCceECCCCCCcC
Confidence 57899999999999999999986
No 14
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=84.11 E-value=0.31 Score=32.24 Aligned_cols=24 Identities=17% Similarity=0.376 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCCCceeccccCeee
Q 032009 51 PDTPCNRCQHPSENWLCLCCKEVL 74 (149)
Q Consensus 51 ~~~~C~~C~~~~~lW~CL~Cg~vg 74 (149)
..++|..|....+.+.|..|||.|
T Consensus 37 ~I~Rc~~CRk~g~~Y~Cp~CGF~G 60 (61)
T COG2888 37 EIYRCAKCRKLGNPYRCPKCGFEG 60 (61)
T ss_pred eeehhhhHHHcCCceECCCcCccC
Confidence 457888888899999999999986
No 15
>PF14369 zf-RING_3: zinc-finger
Probab=74.54 E-value=2.2 Score=24.99 Aligned_cols=13 Identities=23% Similarity=1.122 Sum_probs=11.2
Q ss_pred cEEEcCCCceecc
Q 032009 102 SVWCFTCDAYLNA 114 (149)
Q Consensus 102 ~vwCY~Cd~~V~~ 114 (149)
..|||.|+..|..
T Consensus 2 ~ywCh~C~~~V~~ 14 (35)
T PF14369_consen 2 RYWCHQCNRFVRI 14 (35)
T ss_pred CEeCccCCCEeEe
Confidence 5799999999875
No 16
>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]
Probab=65.24 E-value=10 Score=36.41 Aligned_cols=59 Identities=19% Similarity=0.496 Sum_probs=46.7
Q ss_pred CCCCCCCCCCC--CceeccccCeeeecCC---CChhHHHHhhhcCCeeEEECCC-----CcEEEcCCCc
Q 032009 52 DTPCNRCQHPS--ENWLCLCCKEVLCSRF---VNKHMLQHYLETNHSVALSYSD-----LSVWCFTCDA 110 (149)
Q Consensus 52 ~~~C~~C~~~~--~lW~CL~Cg~vgCgr~---~~~Ha~~H~~~t~H~l~v~l~t-----~~vwCY~Cd~ 110 (149)
.-.|..|+... .+--|.+||.-+|-.. ..+|+..|...+.|.-+--..+ ..+=||.|..
T Consensus 60 ~~~c~Ycgi~~p~~v~kc~~c~Kwfcn~r~gtsgshIv~hlvra~hk~v~lh~ds~lget~lecyncg~ 128 (935)
T KOG1802|consen 60 EHACAYCGISEPACVIKCNTCGKWFCNSRGGTSGSHIVNHLVRAKHKEVSLHKDSPLGETVLECYNCGS 128 (935)
T ss_pred hhhhhhccCCCchheeeccccCceeecCCCCCchhHHHHHHHHhhhheeEeccCCCCCcceEEeeccCc
Confidence 34599999876 6778999999999642 5689999999999887665554 3688999983
No 17
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=63.78 E-value=6 Score=22.50 Aligned_cols=21 Identities=24% Similarity=0.555 Sum_probs=12.8
Q ss_pred CCCCCCCCC-----CCceeccccCee
Q 032009 53 TPCNRCQHP-----SENWLCLCCKEV 73 (149)
Q Consensus 53 ~~C~~C~~~-----~~lW~CL~Cg~v 73 (149)
.+|..|+.. ..+++|-.||+.
T Consensus 3 p~Cp~C~se~~y~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGELLVCPECGHE 28 (30)
T ss_dssp ---TTT-----EE-SSSEEETTTTEE
T ss_pred CCCCCCCCcceeccCCEEeCCccccc
Confidence 468888874 678999999974
No 18
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=63.62 E-value=4 Score=23.58 Aligned_cols=14 Identities=21% Similarity=0.707 Sum_probs=11.6
Q ss_pred ceeccccCeeeecC
Q 032009 64 NWLCLCCKEVLCSR 77 (149)
Q Consensus 64 lW~CL~Cg~vgCgr 77 (149)
.|+|..||++.=|+
T Consensus 2 ~~~C~~CG~i~~g~ 15 (34)
T cd00729 2 VWVCPVCGYIHEGE 15 (34)
T ss_pred eEECCCCCCEeECC
Confidence 69999999996554
No 19
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=61.66 E-value=6.6 Score=27.86 Aligned_cols=27 Identities=19% Similarity=0.549 Sum_probs=22.3
Q ss_pred CCCCCCCCCCC------CCceeccccCeeeecC
Q 032009 51 PDTPCNRCQHP------SENWLCLCCKEVLCSR 77 (149)
Q Consensus 51 ~~~~C~~C~~~------~~lW~CL~Cg~vgCgr 77 (149)
..-.|..|+.. ..+|.|-.||+.+-|-
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCeeccc
Confidence 34569999974 6899999999998875
No 20
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=59.93 E-value=7.7 Score=22.60 Aligned_cols=13 Identities=23% Similarity=0.570 Sum_probs=9.9
Q ss_pred CCceeccccCeee
Q 032009 62 SENWLCLCCKEVL 74 (149)
Q Consensus 62 ~~lW~CL~Cg~vg 74 (149)
..-++|..||+|.
T Consensus 20 r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 20 RERLVCPACGFIH 32 (34)
T ss_dssp S-EEEETTTTEEE
T ss_pred ccceECCCCCCEE
Confidence 5568999999884
No 21
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=56.50 E-value=9 Score=22.49 Aligned_cols=21 Identities=24% Similarity=0.648 Sum_probs=15.5
Q ss_pred CCCCCCCCC-----CCceeccccCee
Q 032009 53 TPCNRCQHP-----SENWLCLCCKEV 73 (149)
Q Consensus 53 ~~C~~C~~~-----~~lW~CL~Cg~v 73 (149)
.+|.+|+.. .+.+.|-.||++
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceE
Confidence 459999874 567788888875
No 22
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=55.48 E-value=6.3 Score=22.43 Aligned_cols=13 Identities=15% Similarity=0.613 Sum_probs=10.3
Q ss_pred ceeccccCeeeec
Q 032009 64 NWLCLCCKEVLCS 76 (149)
Q Consensus 64 lW~CL~Cg~vgCg 76 (149)
.|+|..||++.=+
T Consensus 1 ~~~C~~CGy~y~~ 13 (33)
T cd00350 1 KYVCPVCGYIYDG 13 (33)
T ss_pred CEECCCCCCEECC
Confidence 4899999998544
No 23
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=54.88 E-value=10 Score=28.45 Aligned_cols=26 Identities=27% Similarity=0.759 Sum_probs=20.3
Q ss_pred CCCCCCCCCCCC---------------------CCceeccccCeeee
Q 032009 50 TPDTPCNRCQHP---------------------SENWLCLCCKEVLC 75 (149)
Q Consensus 50 ~~~~~C~~C~~~---------------------~~lW~CL~Cg~vgC 75 (149)
+..++|..|+.. ...|.|..||.+.=
T Consensus 89 ~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW 135 (147)
T PF01927_consen 89 PIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYW 135 (147)
T ss_pred CCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEec
Confidence 356899999972 35899999999853
No 24
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=50.53 E-value=6.9 Score=34.35 Aligned_cols=41 Identities=20% Similarity=0.484 Sum_probs=27.0
Q ss_pred CCCCCCCCCCC--------CCceeccccCeeeecCCCChhHHHHhhhcC-CeeEEECCCCcEE
Q 032009 51 PDTPCNRCQHP--------SENWLCLCCKEVLCSRFVNKHMLQHYLETN-HSVALSYSDLSVW 104 (149)
Q Consensus 51 ~~~~C~~C~~~--------~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~t~-H~l~v~l~t~~vw 104 (149)
....|.+|+.. -++||||.|.-+. +-.| |--+|..-|++=|
T Consensus 18 eNk~CfeC~a~NPQWvSvsyGIfICLECSG~H-------------RgLGVhiSFVRSVTMD~w 67 (386)
T KOG0704|consen 18 ENKKCFECGAPNPQWVSVSYGIFICLECSGKH-------------RGLGVHISFVRSVTMDKW 67 (386)
T ss_pred cCCceeecCCCCCCeEeecccEEEEEecCCcc-------------cccceeeEEEEeeecccc
Confidence 45679999984 4678999996331 1222 6666666666666
No 25
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=49.73 E-value=13 Score=26.44 Aligned_cols=26 Identities=19% Similarity=0.586 Sum_probs=20.8
Q ss_pred CCCCCCCCCC------CCceeccccCeeeecC
Q 032009 52 DTPCNRCQHP------SENWLCLCCKEVLCSR 77 (149)
Q Consensus 52 ~~~C~~C~~~------~~lW~CL~Cg~vgCgr 77 (149)
.-.|..|+.. .++|-|-.||+..-|-
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AGG 66 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKKCGKKFAGG 66 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETTTTEEEE-B
T ss_pred CCcCCCCCCceeEEeeeEEeecCCCCCEEeCC
Confidence 3459999974 7899999999999886
No 26
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=49.60 E-value=14 Score=22.45 Aligned_cols=11 Identities=18% Similarity=0.558 Sum_probs=8.7
Q ss_pred CceeccccCee
Q 032009 63 ENWLCLCCKEV 73 (149)
Q Consensus 63 ~lW~CL~Cg~v 73 (149)
+.|+|-.||+.
T Consensus 19 ~~~vC~~Cg~~ 29 (52)
T smart00661 19 RRFVCRKCGYE 29 (52)
T ss_pred CEEECCcCCCe
Confidence 47889988876
No 27
>PRK10220 hypothetical protein; Provisional
Probab=48.81 E-value=14 Score=27.21 Aligned_cols=21 Identities=19% Similarity=0.705 Sum_probs=17.1
Q ss_pred CCCCCCCCC-----CCceeccccCee
Q 032009 53 TPCNRCQHP-----SENWLCLCCKEV 73 (149)
Q Consensus 53 ~~C~~C~~~-----~~lW~CL~Cg~v 73 (149)
..|..|... .++|+|..|++-
T Consensus 4 P~CP~C~seytY~d~~~~vCpeC~hE 29 (111)
T PRK10220 4 PHCPKCNSEYTYEDNGMYICPECAHE 29 (111)
T ss_pred CcCCCCCCcceEcCCCeEECCcccCc
Confidence 468888863 789999999976
No 28
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=47.86 E-value=14 Score=27.11 Aligned_cols=22 Identities=23% Similarity=0.742 Sum_probs=17.4
Q ss_pred CCCCCCCCC-----CCceeccccCeee
Q 032009 53 TPCNRCQHP-----SENWLCLCCKEVL 74 (149)
Q Consensus 53 ~~C~~C~~~-----~~lW~CL~Cg~vg 74 (149)
..|..|... .++|+|..|++.-
T Consensus 3 p~CP~C~seytY~dg~~~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQLICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcceEecCCeeECccccccc
Confidence 358888863 7899999999863
No 29
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=47.56 E-value=14 Score=20.02 Aligned_cols=11 Identities=18% Similarity=0.410 Sum_probs=7.5
Q ss_pred CCceeccccCe
Q 032009 62 SENWLCLCCKE 72 (149)
Q Consensus 62 ~~lW~CL~Cg~ 72 (149)
...+.|..||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 45677777774
No 30
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=46.82 E-value=19 Score=20.70 Aligned_cols=23 Identities=17% Similarity=0.627 Sum_probs=15.7
Q ss_pred CCCCCCCCCC------CCceeccccCeee
Q 032009 52 DTPCNRCQHP------SENWLCLCCKEVL 74 (149)
Q Consensus 52 ~~~C~~C~~~------~~lW~CL~Cg~vg 74 (149)
.+.|..|+.. .+..+|..||.+.
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 3568888764 4556888888763
No 31
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=46.64 E-value=15 Score=21.89 Aligned_cols=18 Identities=17% Similarity=0.296 Sum_probs=7.4
Q ss_pred EEECCCCcEEEcCCCcee
Q 032009 95 ALSYSDLSVWCFTCDAYL 112 (149)
Q Consensus 95 ~v~l~t~~vwCY~Cd~~V 112 (149)
..+-.++.+-|-.|..-|
T Consensus 12 ~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 12 VFDPERGELVCPNCGLVL 29 (43)
T ss_dssp EEETTTTEEEETTT-BBE
T ss_pred EEcCCCCeEECCCCCCEe
Confidence 334444444444444333
No 32
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=45.64 E-value=8.1 Score=30.94 Aligned_cols=46 Identities=22% Similarity=0.530 Sum_probs=31.1
Q ss_pred HHhhhcCCeeEEECCC--CcEEEcCCCceecccccCCchhhhHHHHHHhhCCC
Q 032009 85 QHYLETNHSVALSYSD--LSVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEA 135 (149)
Q Consensus 85 ~H~~~t~H~l~v~l~t--~~vwCY~Cd~~V~~~~~~~L~~~~~~~hl~kfg~~ 135 (149)
.||...+....+-+.. ..-=|-.|+.+....+. .|+...+.++|+.
T Consensus 104 gHy~s~g~~~~lRF~~~N~~~qC~~CN~~~sgn~~-----~Yr~~Li~kiG~~ 151 (189)
T PF05766_consen 104 GHYRSRGAAPELRFNEDNIHAQCKHCNRHLSGNIV-----EYRIGLIEKIGQE 151 (189)
T ss_pred ccccccccCcccccChhhHhHcCCccccccccCHH-----HHHHHHHHHHhHH
Confidence 3777777655565654 45569999988765333 3667778888864
No 33
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=45.40 E-value=12 Score=20.42 Aligned_cols=21 Identities=19% Similarity=0.534 Sum_probs=13.7
Q ss_pred CCCCCCCC--CCceeccccCeee
Q 032009 54 PCNRCQHP--SENWLCLCCKEVL 74 (149)
Q Consensus 54 ~C~~C~~~--~~lW~CL~Cg~vg 74 (149)
.|.+|+.. ...-.|-.||+.+
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 47777754 4455788888753
No 34
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=44.57 E-value=8.1 Score=32.91 Aligned_cols=24 Identities=25% Similarity=0.386 Sum_probs=19.5
Q ss_pred CCCCCCCCCCC-------CCCceeccccCee
Q 032009 50 TPDTPCNRCQH-------PSENWLCLCCKEV 73 (149)
Q Consensus 50 ~~~~~C~~C~~-------~~~lW~CL~Cg~v 73 (149)
..+.+|..|+. ..|+|+|+.|++-
T Consensus 26 ~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h 56 (294)
T COG0777 26 GLWTKCPSCGEMLYRKELESNLKVCPKCGHH 56 (294)
T ss_pred CceeECCCccceeeHHHHHhhhhcccccCcc
Confidence 36678999997 3789999999864
No 35
>PF15616 TerY-C: TerY-C metal binding domain
Probab=42.70 E-value=18 Score=27.38 Aligned_cols=24 Identities=21% Similarity=0.677 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCceeccccCeeeecC
Q 032009 53 TPCNRCQHPSENWLCLCCKEVLCSR 77 (149)
Q Consensus 53 ~~C~~C~~~~~lW~CL~Cg~vgCgr 77 (149)
..|.-|+.....-+| .||++.|-.
T Consensus 78 PgCP~CGn~~~fa~C-~CGkl~Ci~ 101 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC-GCGKLFCID 101 (131)
T ss_pred CCCCCCcChhcEEEe-cCCCEEEeC
Confidence 569999999899999 899999953
No 36
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=42.23 E-value=36 Score=24.47 Aligned_cols=50 Identities=20% Similarity=0.385 Sum_probs=30.9
Q ss_pred CCCCCCCCCCCCCceeccccCeeeecCCCChhHHHHhhhcCCeeEEECCCCcEE
Q 032009 51 PDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVW 104 (149)
Q Consensus 51 ~~~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~t~H~l~v~l~t~~vw 104 (149)
....|.+|+.....|+++.=|.+-|. ..+-.|-.-..|---|+.-+++-|
T Consensus 12 ~N~~CaDCg~~~p~w~s~~~GiflC~----~Cag~HR~lg~~is~VkSi~~d~w 61 (116)
T PF01412_consen 12 GNKVCADCGAPNPTWASLNYGIFLCL----ECAGIHRSLGVHISRVKSITMDNW 61 (116)
T ss_dssp TCTB-TTT-SBS--EEETTTTEEE-H----HHHHHHHHHTTTT--EEETTTS--
T ss_pred CcCcCCCCCCCCCCEEEeecChhhhH----HHHHHHHHhcccchhccccccCCC
Confidence 55789999999999999998888885 567777554446666666666655
No 37
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=41.53 E-value=18 Score=30.88 Aligned_cols=41 Identities=22% Similarity=0.440 Sum_probs=32.7
Q ss_pred CCCCCCCCCCCCCCCCCceeccccCeeeecCCCChhHHHHhhhcC
Q 032009 47 HIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETN 91 (149)
Q Consensus 47 ~i~~~~~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~t~ 91 (149)
.++...-+|.-|......-.|.-||+++| ....+.+..+..
T Consensus 234 ~i~~a~~kC~LCLe~~~~pSaTpCGHiFC----WsCI~~w~~ek~ 274 (293)
T KOG0317|consen 234 SIPEATRKCSLCLENRSNPSATPCGHIFC----WSCILEWCSEKA 274 (293)
T ss_pred cCCCCCCceEEEecCCCCCCcCcCcchHH----HHHHHHHHcccc
Confidence 34445678999999999999999999999 467778766543
No 38
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.21 E-value=13 Score=31.36 Aligned_cols=53 Identities=21% Similarity=0.465 Sum_probs=35.9
Q ss_pred CCCCCCCCCCCCCCceeccccCeeeecCCCChhHHHHhhhcCCeeEEECCCC-cEEEcCCCceeccccc
Q 032009 50 TPDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDL-SVWCFTCDAYLNAQVI 117 (149)
Q Consensus 50 ~~~~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~t~H~l~v~l~t~-~vwCY~Cd~~V~~~~~ 117 (149)
...-+|.-|....+.-.|..||+++|- |++.+..... .-+|-.|...|+.+.+
T Consensus 213 ~~d~kC~lC~e~~~~ps~t~CgHlFC~---------------~Cl~~~~t~~k~~~CplCRak~~pk~v 266 (271)
T COG5574 213 LADYKCFLCLEEPEVPSCTPCGHLFCL---------------SCLLISWTKKKYEFCPLCRAKVYPKKV 266 (271)
T ss_pred ccccceeeeecccCCcccccccchhhH---------------HHHHHHHHhhccccCchhhhhccchhh
Confidence 345679999999999999999999995 2222222222 2347777777665443
No 39
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=38.57 E-value=26 Score=20.75 Aligned_cols=23 Identities=22% Similarity=0.791 Sum_probs=17.0
Q ss_pred CCCCCCCCCc--eeccccCeeeecC
Q 032009 55 CNRCQHPSEN--WLCLCCKEVLCSR 77 (149)
Q Consensus 55 C~~C~~~~~l--W~CL~Cg~vgCgr 77 (149)
|..|+....| ..|-.|+.++|.+
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCcccccCeECCccCCccccc
Confidence 5667765444 6799999999974
No 40
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=36.58 E-value=24 Score=20.84 Aligned_cols=12 Identities=25% Similarity=0.983 Sum_probs=7.9
Q ss_pred CCceeccccCee
Q 032009 62 SENWLCLCCKEV 73 (149)
Q Consensus 62 ~~lW~CL~Cg~v 73 (149)
...|.|-.|+..
T Consensus 22 ~~~w~C~~C~~~ 33 (40)
T PF04810_consen 22 GKTWICNFCGTK 33 (40)
T ss_dssp TTEEEETTT--E
T ss_pred CCEEECcCCCCc
Confidence 468999988865
No 41
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=36.36 E-value=14 Score=31.54 Aligned_cols=22 Identities=23% Similarity=0.388 Sum_probs=18.5
Q ss_pred CCCCCCCCCCC-------CCceeccccCe
Q 032009 51 PDTPCNRCQHP-------SENWLCLCCKE 72 (149)
Q Consensus 51 ~~~~C~~C~~~-------~~lW~CL~Cg~ 72 (149)
.+.+|..|+.. .++++|..||+
T Consensus 37 lw~kc~~C~~~~~~~~l~~~~~vcp~c~~ 65 (296)
T CHL00174 37 LWVQCENCYGLNYKKFLKSKMNICEQCGY 65 (296)
T ss_pred CeeECCCccchhhHHHHHHcCCCCCCCCC
Confidence 46789999974 67899999997
No 42
>PHA00626 hypothetical protein
Probab=35.68 E-value=23 Score=23.25 Aligned_cols=24 Identities=13% Similarity=0.186 Sum_probs=19.9
Q ss_pred CCCCCCCCCCCceeccccCeeeec
Q 032009 53 TPCNRCQHPSENWLCLCCKEVLCS 76 (149)
Q Consensus 53 ~~C~~C~~~~~lW~CL~Cg~vgCg 76 (149)
.+|..|...++.+.|-.||+..--
T Consensus 12 vrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 12 AKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred eeeceecccCcceEcCCCCCeech
Confidence 368888888999999999998653
No 43
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=35.46 E-value=15 Score=31.01 Aligned_cols=23 Identities=22% Similarity=0.437 Sum_probs=18.4
Q ss_pred CCCCCCCCCCC-------CCceeccccCee
Q 032009 51 PDTPCNRCQHP-------SENWLCLCCKEV 73 (149)
Q Consensus 51 ~~~~C~~C~~~-------~~lW~CL~Cg~v 73 (149)
.+.+|..|+.. .++++|..||+-
T Consensus 25 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h 54 (285)
T TIGR00515 25 VWTKCPKCGQVLYTKELERNLEVCPKCDHH 54 (285)
T ss_pred CeeECCCCcchhhHHHHHhhCCCCCCCCCc
Confidence 46789999973 678899999873
No 44
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=35.39 E-value=22 Score=27.92 Aligned_cols=27 Identities=19% Similarity=0.444 Sum_probs=20.4
Q ss_pred CCCCCCCCCCCCC---------------------CCceeccccCeeee
Q 032009 49 PTPDTPCNRCQHP---------------------SENWLCLCCKEVLC 75 (149)
Q Consensus 49 ~~~~~~C~~C~~~---------------------~~lW~CL~Cg~vgC 75 (149)
.+..++|..|+.. ...|.|-.||.++=
T Consensus 94 ~~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW 141 (165)
T COG1656 94 FPEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYW 141 (165)
T ss_pred ccccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccccc
Confidence 3467889999862 35789999998853
No 45
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=34.47 E-value=33 Score=19.63 Aligned_cols=31 Identities=13% Similarity=0.379 Sum_probs=19.6
Q ss_pred CCCCCCC-CCceeccccCeeeecCCCChhHHHHhhh
Q 032009 55 CNRCQHP-SENWLCLCCKEVLCSRFVNKHMLQHYLE 89 (149)
Q Consensus 55 C~~C~~~-~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~ 89 (149)
|..|... .+.++-+.||+++|. .-+.++.+.
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~----~C~~~~~~~ 32 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCK----ECIEKYLEK 32 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEH----HHHHHHHHC
T ss_pred CCCCCCcccCcCEECCCCCchhH----HHHHHHHHC
Confidence 4456543 456688999999995 344444433
No 46
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=33.01 E-value=40 Score=21.63 Aligned_cols=23 Identities=26% Similarity=0.645 Sum_probs=17.1
Q ss_pred CCCCCCCCCCC------CCceeccccCee
Q 032009 51 PDTPCNRCQHP------SENWLCLCCKEV 73 (149)
Q Consensus 51 ~~~~C~~C~~~------~~lW~CL~Cg~v 73 (149)
....|..|+.. ...|.|..||+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 34458888863 467899999987
No 47
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=32.94 E-value=18 Score=30.65 Aligned_cols=24 Identities=21% Similarity=0.416 Sum_probs=18.9
Q ss_pred CCCCCCCCCCC-------CCceeccccCeee
Q 032009 51 PDTPCNRCQHP-------SENWLCLCCKEVL 74 (149)
Q Consensus 51 ~~~~C~~C~~~-------~~lW~CL~Cg~vg 74 (149)
.+.+|..|+.. .++++|..||+-.
T Consensus 26 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 26 LWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 46789999973 6788999998743
No 48
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=31.93 E-value=26 Score=23.21 Aligned_cols=19 Identities=42% Similarity=1.135 Sum_probs=12.6
Q ss_pred CCCCCCCC-------CCceeccccCe
Q 032009 54 PCNRCQHP-------SENWLCLCCKE 72 (149)
Q Consensus 54 ~C~~C~~~-------~~lW~CL~Cg~ 72 (149)
.|..|+.. ..-|+||.|-.
T Consensus 32 VCnlCGFNP~Phl~E~~eWLCLnCQ~ 57 (61)
T PF05715_consen 32 VCNLCGFNPTPHLTEVKEWLCLNCQM 57 (61)
T ss_pred hhcccCCCCCccccccceeeeecchh
Confidence 46666653 46799998853
No 49
>PHA02942 putative transposase; Provisional
Probab=31.48 E-value=39 Score=29.57 Aligned_cols=24 Identities=21% Similarity=0.599 Sum_probs=17.6
Q ss_pred CCCCCCCCCCC-----CCceeccccCeee
Q 032009 51 PDTPCNRCQHP-----SENWLCLCCKEVL 74 (149)
Q Consensus 51 ~~~~C~~C~~~-----~~lW~CL~Cg~vg 74 (149)
....|..|+.. ...|.|..||+..
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFHCPSCGYEN 352 (383)
T ss_pred CCccCCCCCCccCcCCCCEEECCCCCCEe
Confidence 34459999853 3578999999874
No 50
>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=30.97 E-value=17 Score=18.12 Aligned_cols=11 Identities=18% Similarity=0.691 Sum_probs=7.7
Q ss_pred eeccccCeeee
Q 032009 65 WLCLCCKEVLC 75 (149)
Q Consensus 65 W~CL~Cg~vgC 75 (149)
|.|..||..+=
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 46777887754
No 51
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=30.94 E-value=42 Score=21.43 Aligned_cols=23 Identities=17% Similarity=0.392 Sum_probs=18.4
Q ss_pred CCCCCCCCCCC-CCceeccccCee
Q 032009 51 PDTPCNRCQHP-SENWLCLCCKEV 73 (149)
Q Consensus 51 ~~~~C~~C~~~-~~lW~CL~Cg~v 73 (149)
....|..|+.. ..--+|..||+.
T Consensus 25 ~l~~C~~cG~~~~~H~vc~~cG~Y 48 (55)
T TIGR01031 25 TLVVCPNCGEFKLPHRVCPSCGYY 48 (55)
T ss_pred cceECCCCCCcccCeeECCccCeE
Confidence 55679999975 567799999976
No 52
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=30.06 E-value=27 Score=25.80 Aligned_cols=53 Identities=15% Similarity=0.343 Sum_probs=34.3
Q ss_pred CCceeccc--------cCeeeecCC--CChhHHHHhhhcC--C----eeEEECCCC-----cEEEcCCCceecc
Q 032009 62 SENWLCLC--------CKEVLCSRF--VNKHMLQHYLETN--H----SVALSYSDL-----SVWCFTCDAYLNA 114 (149)
Q Consensus 62 ~~lW~CL~--------Cg~vgCgr~--~~~Ha~~H~~~t~--H----~l~v~l~t~-----~vwCY~Cd~~V~~ 114 (149)
..+|+|-. ||+.+|.-. =..|++.|-+++. | |..+.-... ..||=.|...++.
T Consensus 13 ~~l~i~~~~~k~vkc~CGh~f~d~r~NwK~~alv~vRd~~E~~~~iYp~~~aPdp~w~~irEyyCP~Cgt~lev 86 (112)
T PF08882_consen 13 PHLWIVQKKDKVVKCDCGHEFCDARENWKLGALVYVRDPEEIHPEIYPFTMAPDPEWQVIREYYCPGCGTQLEV 86 (112)
T ss_pred CcEEEEEecCceeeccCCCeecChhcChhhCcEEEecChHHhhhhhcccccCCCCCcEEEEEEECCCCcceeEE
Confidence 56777777 999999852 3367777766554 3 233332222 6899999987765
No 53
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=29.54 E-value=41 Score=21.70 Aligned_cols=23 Identities=22% Similarity=0.551 Sum_probs=18.1
Q ss_pred CCCCCCCCCCC-CCceeccccCee
Q 032009 51 PDTPCNRCQHP-SENWLCLCCKEV 73 (149)
Q Consensus 51 ~~~~C~~C~~~-~~lW~CL~Cg~v 73 (149)
....|..|+.. ..--+|..||+.
T Consensus 26 ~l~~C~~CG~~~~~H~vC~~CG~Y 49 (57)
T PRK12286 26 GLVECPNCGEPKLPHRVCPSCGYY 49 (57)
T ss_pred cceECCCCCCccCCeEECCCCCcC
Confidence 55679999975 467799999965
No 54
>PHA00616 hypothetical protein
Probab=29.44 E-value=8.1 Score=23.93 Aligned_cols=25 Identities=24% Similarity=0.507 Sum_probs=15.5
Q ss_pred eeccccCeeeecCC-CChhHHHHhhh
Q 032009 65 WLCLCCKEVLCSRF-VNKHMLQHYLE 89 (149)
Q Consensus 65 W~CL~Cg~vgCgr~-~~~Ha~~H~~~ 89 (149)
..|+.||.++.-.. -..|.+.|..+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCC
Confidence 46999999988542 33455555443
No 55
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=29.22 E-value=80 Score=22.54 Aligned_cols=49 Identities=20% Similarity=0.388 Sum_probs=31.9
Q ss_pred CCCCCCCCCCCCceeccccCeeeecCCCChhHHHHhhhcCCeeEEECCCCcEE
Q 032009 52 DTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVW 104 (149)
Q Consensus 52 ~~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~t~H~l~v~l~t~~vw 104 (149)
...|.+|+.....|+++.=|-+-|.+ .+-.|-.-..|--.|..-+++.|
T Consensus 3 N~~CaDC~~~~p~w~s~~~GifvC~~----CsgiHR~lg~his~VkSl~md~w 51 (112)
T smart00105 3 NKKCFDCGAPNPTWASVNLGVFLCIE----CSGIHRSLGVHISKVRSLTLDTW 51 (112)
T ss_pred CCcccCCCCCCCCcEEeccceeEhHH----hHHHHHhcCCCcCeeeecccCCC
Confidence 35799999988899999999998864 44455433335333444444433
No 56
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=26.99 E-value=35 Score=28.17 Aligned_cols=26 Identities=23% Similarity=0.549 Sum_probs=20.0
Q ss_pred CCCCCCCCCCCCCce--eccccCeeeec
Q 032009 51 PDTPCNRCQHPSENW--LCLCCKEVLCS 76 (149)
Q Consensus 51 ~~~~C~~C~~~~~lW--~CL~Cg~vgCg 76 (149)
-.+.|..|+.....| .|..||..+--
T Consensus 353 p~~~c~~cg~~~~~~~~~c~~c~~~~~~ 380 (389)
T PRK11788 353 PRYRCRNCGFTARTLYWHCPSCKAWETI 380 (389)
T ss_pred CCEECCCCCCCCccceeECcCCCCccCc
Confidence 346799999887755 89999987643
No 57
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=26.02 E-value=30 Score=27.18 Aligned_cols=13 Identities=23% Similarity=0.672 Sum_probs=11.1
Q ss_pred ceeccccCeeeec
Q 032009 64 NWLCLCCKEVLCS 76 (149)
Q Consensus 64 lW~CL~Cg~vgCg 76 (149)
.|+|..||++.=|
T Consensus 134 ~~vC~vCGy~~~g 146 (166)
T COG1592 134 VWVCPVCGYTHEG 146 (166)
T ss_pred EEEcCCCCCcccC
Confidence 8999999998554
No 58
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=25.77 E-value=42 Score=17.64 Aligned_cols=18 Identities=22% Similarity=0.726 Sum_probs=8.2
Q ss_pred CCCCCCC--CCceeccccCe
Q 032009 55 CNRCQHP--SENWLCLCCKE 72 (149)
Q Consensus 55 C~~C~~~--~~lW~CL~Cg~ 72 (149)
|..|+.. .+.-.|..||.
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CcccCCCCCCcCcchhhhCC
Confidence 4455532 23334555553
No 59
>PF14968 CCDC84: Coiled coil protein 84
Probab=25.21 E-value=50 Score=28.76 Aligned_cols=25 Identities=24% Similarity=0.668 Sum_probs=19.6
Q ss_pred CCeeEEECCC---CcEEEcCCCceeccc
Q 032009 91 NHSVALSYSD---LSVWCFTCDAYLNAQ 115 (149)
Q Consensus 91 ~H~l~v~l~t---~~vwCY~Cd~~V~~~ 115 (149)
.+|.+++... ..+|||-|+..|...
T Consensus 44 k~p~v~~~~~~~~~~fWC~fC~~ev~~~ 71 (336)
T PF14968_consen 44 KKPSVLRYDPEHRNRFWCVFCDCEVREH 71 (336)
T ss_pred hCCccCCCCccccceeEeeCccchhhhc
Confidence 5888877653 589999999888643
No 60
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=25.02 E-value=65 Score=19.34 Aligned_cols=8 Identities=38% Similarity=1.140 Sum_probs=4.0
Q ss_pred Cceecccc
Q 032009 63 ENWLCLCC 70 (149)
Q Consensus 63 ~lW~CL~C 70 (149)
.-|-|+.|
T Consensus 13 ~ry~C~~C 20 (43)
T cd02340 13 VRYKCLVC 20 (43)
T ss_pred CeEECCCC
Confidence 34455555
No 61
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=24.89 E-value=34 Score=19.17 Aligned_cols=22 Identities=27% Similarity=0.788 Sum_probs=15.7
Q ss_pred CCCCCCCCCCceeccccCeeeec
Q 032009 54 PCNRCQHPSENWLCLCCKEVLCS 76 (149)
Q Consensus 54 ~C~~C~~~~~lW~CL~Cg~vgCg 76 (149)
.|..|+. ...+.|..|+.-.|+
T Consensus 4 ~C~vC~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 4 LCSVCGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp EETSSSS-EESEE-TTT--EESS
T ss_pred CCccCcC-CCEEECCCcCCceeC
Confidence 4888888 788899999988885
No 62
>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=24.88 E-value=24 Score=17.10 Aligned_cols=11 Identities=18% Similarity=0.622 Sum_probs=6.1
Q ss_pred eeccccCeeee
Q 032009 65 WLCLCCKEVLC 75 (149)
Q Consensus 65 W~CL~Cg~vgC 75 (149)
|.|-.|++..=
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 56777777754
No 63
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 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 N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=24.20 E-value=20 Score=23.62 Aligned_cols=40 Identities=25% Similarity=0.451 Sum_probs=25.8
Q ss_pred CCCCCCCCCCCceeccccCeeeecCCCChhHHHHhhhcCCeeEEECCCCcEEE
Q 032009 53 TPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWC 105 (149)
Q Consensus 53 ~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~t~H~l~v~l~t~~vwC 105 (149)
-+|.+|......-+|+.|...+| |. ||-+.+-..+...+|
T Consensus 14 y~C~tC~~~~~~~iC~~CF~~~~------H~-------gH~~~~~~~~~~~~C 53 (71)
T PF02207_consen 14 YRCLTCSLDESSGICEECFANSC------HE-------GHRVVYYRSSSGGCC 53 (71)
T ss_dssp EEETTTBSSTT-BBEHHHHCTSG------GG-------GSSEEEEE--SCEBB
T ss_pred EECccCCCCCCEEEchhhCCCCC------cC-------CCcEEEEEeCCCeEE
Confidence 46888988888889999876656 33 677776666633333
No 64
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=23.95 E-value=58 Score=23.13 Aligned_cols=27 Identities=22% Similarity=0.555 Sum_probs=21.6
Q ss_pred CCCCCCCCCCC------CCceeccccCeeeecC
Q 032009 51 PDTPCNRCQHP------SENWLCLCCKEVLCSR 77 (149)
Q Consensus 51 ~~~~C~~C~~~------~~lW~CL~Cg~vgCgr 77 (149)
..-.|..|+.. .++|.|-.||+..-|.
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 35 AKYFCPFCGKHAVKRQAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred CCccCCCCCCCceeeeeeEEEEcCCCCCEEeCC
Confidence 34569999763 5799999999998875
No 65
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=23.84 E-value=78 Score=19.21 Aligned_cols=24 Identities=17% Similarity=0.279 Sum_probs=16.7
Q ss_pred eccccCeeeecC--CCChhHHHHhhh
Q 032009 66 LCLCCKEVLCSR--FVNKHMLQHYLE 89 (149)
Q Consensus 66 ~CL~Cg~vgCgr--~~~~Ha~~H~~~ 89 (149)
.|-.|+.+.-.. .+.+|..+|...
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 566666665544 577899999875
No 66
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=23.84 E-value=38 Score=24.76 Aligned_cols=12 Identities=25% Similarity=0.437 Sum_probs=10.0
Q ss_pred CceeccccCeee
Q 032009 63 ENWLCLCCKEVL 74 (149)
Q Consensus 63 ~lW~CL~Cg~vg 74 (149)
-.|.||.||++-
T Consensus 81 v~vtC~~CG~~~ 92 (105)
T COG2023 81 VVVTCLECGTIR 92 (105)
T ss_pred EEEEecCCCcEE
Confidence 478999999873
No 67
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=23.83 E-value=60 Score=19.46 Aligned_cols=17 Identities=29% Similarity=0.991 Sum_probs=8.1
Q ss_pred CCCCCC--CCCceeccccC
Q 032009 55 CNRCQH--PSENWLCLCCK 71 (149)
Q Consensus 55 C~~C~~--~~~lW~CL~Cg 71 (149)
|..|+. .+..|.|+.|.
T Consensus 3 C~~C~~~i~g~r~~C~~C~ 21 (46)
T cd02249 3 CDGCLKPIVGVRYHCLVCE 21 (46)
T ss_pred CcCCCCCCcCCEEECCCCC
Confidence 444443 23445555554
No 68
>PRK14873 primosome assembly protein PriA; Provisional
Probab=23.77 E-value=46 Score=31.38 Aligned_cols=23 Identities=22% Similarity=0.706 Sum_probs=18.2
Q ss_pred CCCCCCCCCCCCCceeccccCee
Q 032009 51 PDTPCNRCQHPSENWLCLCCKEV 73 (149)
Q Consensus 51 ~~~~C~~C~~~~~lW~CL~Cg~v 73 (149)
...+|..|+.....|.|..||.-
T Consensus 409 ~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 409 GTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred CeeECCCCcCCCcCccCCCCcCC
Confidence 34679999987778999999864
No 69
>PF11261 IRF-2BP1_2: Interferon regulatory factor 2-binding protein zinc finger; InterPro: IPR022750 IRF-2BP1 and IRF-2BP2 are nuclear transcriptional repressor proteins and can inhibit both enhancer-activated and basal transcription. They both contain N-terminal zinc finger and C-terminal RING finger domains []. This entry represents the N-terminal zinc finger domain of IRF-2BP1 and IRF-2BP2.
Probab=23.72 E-value=38 Score=21.80 Aligned_cols=9 Identities=33% Similarity=0.922 Sum_probs=7.1
Q ss_pred CcEEEcCCC
Q 032009 101 LSVWCFTCD 109 (149)
Q Consensus 101 ~~vwCY~Cd 109 (149)
.+.|||.||
T Consensus 2 ~Rq~CyLCd 10 (54)
T PF11261_consen 2 RRQQCYLCD 10 (54)
T ss_pred CceeEEecc
Confidence 467899888
No 70
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=23.10 E-value=60 Score=23.09 Aligned_cols=27 Identities=19% Similarity=0.530 Sum_probs=21.7
Q ss_pred CCCCCCCCCCC------CCceeccccCeeeecC
Q 032009 51 PDTPCNRCQHP------SENWLCLCCKEVLCSR 77 (149)
Q Consensus 51 ~~~~C~~C~~~------~~lW~CL~Cg~vgCgr 77 (149)
..-.|.-|+.. .++|.|-.||+..-|-
T Consensus 34 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRGSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred cCccCCCCCCCceEEEeeEEEEcCCCCCEEeCC
Confidence 34569999763 6799999999998875
No 71
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=22.77 E-value=19 Score=21.36 Aligned_cols=41 Identities=17% Similarity=0.244 Sum_probs=25.5
Q ss_pred eccccCeeeecCCCChh---HHHHhhhcCCeeEEECCCCcEEEcCC
Q 032009 66 LCLCCKEVLCSRFVNKH---MLQHYLETNHSVALSYSDLSVWCFTC 108 (149)
Q Consensus 66 ~CL~Cg~vgCgr~~~~H---a~~H~~~t~H~l~v~l~t~~vwCY~C 108 (149)
.|..||... ...+|. ...|..-.+.++.|.+.-..+.|-.|
T Consensus 4 ~Cp~Cg~~~--~~~~g~~~r~i~~l~~~~~~~~L~i~~~R~~C~~C 47 (47)
T PF14690_consen 4 RCPHCGSPS--VHRHGYKTRRIRHLPIGGRPVYLRIRKRRYRCKNC 47 (47)
T ss_pred cCCCcCCCc--eECCceEEEEEeecccCCEEEEEEEEeEEEECcCC
Confidence 356666554 112222 23355556789999999888888766
No 72
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=22.67 E-value=75 Score=18.19 Aligned_cols=26 Identities=27% Similarity=0.630 Sum_probs=20.2
Q ss_pred CCCCCCCCCCCCceeccccCeeeecC
Q 032009 52 DTPCNRCQHPSENWLCLCCKEVLCSR 77 (149)
Q Consensus 52 ~~~C~~C~~~~~lW~CL~Cg~vgCgr 77 (149)
...|..+....-.+.|..|+..-|..
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~ 28 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSE 28 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHH
T ss_pred CccCccCCccceEEEecCCCCccCcc
Confidence 34688888776788999999999975
No 73
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=22.64 E-value=40 Score=21.19 Aligned_cols=11 Identities=18% Similarity=0.519 Sum_probs=8.1
Q ss_pred eeccccCeeee
Q 032009 65 WLCLCCKEVLC 75 (149)
Q Consensus 65 W~CL~Cg~vgC 75 (149)
|+|..||++.=
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 77888888744
No 74
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.41 E-value=65 Score=25.91 Aligned_cols=26 Identities=23% Similarity=0.441 Sum_probs=19.0
Q ss_pred CCCCCCCCCCC-CCceeccccCeeeec
Q 032009 51 PDTPCNRCQHP-SENWLCLCCKEVLCS 76 (149)
Q Consensus 51 ~~~~C~~C~~~-~~lW~CL~Cg~vgCg 76 (149)
....|..|+.. ...|.|..||+..=-
T Consensus 308 tS~~C~~cg~~~~r~~~C~~cg~~~~r 334 (364)
T COG0675 308 TSKTCPCCGHLSGRLFKCPRCGFVHDR 334 (364)
T ss_pred CcccccccCCccceeEECCCCCCeehh
Confidence 44569999863 467889999887543
No 75
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.34 E-value=52 Score=30.77 Aligned_cols=25 Identities=24% Similarity=0.468 Sum_probs=19.6
Q ss_pred CCCCCCCCCCCCCCCCc-eeccccCe
Q 032009 48 IPTPDTPCNRCQHPSEN-WLCLCCKE 72 (149)
Q Consensus 48 i~~~~~~C~~C~~~~~l-W~CL~Cg~ 72 (149)
+++..+.|..|+....+ |.|..||.
T Consensus 555 in~~~~~C~~CGy~g~~~~~CP~CG~ 580 (618)
T PRK14704 555 INHPVDRCKCCSYHGVIGNECPSCGN 580 (618)
T ss_pred eCCCCeecCCCCCCCCcCccCcCCCC
Confidence 34467789999976565 99999995
No 76
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=22.09 E-value=59 Score=21.80 Aligned_cols=26 Identities=27% Similarity=0.673 Sum_probs=11.6
Q ss_pred CCCCCCCCCCCCceeccc-cCeeeecC
Q 032009 52 DTPCNRCQHPSENWLCLC-CKEVLCSR 77 (149)
Q Consensus 52 ~~~C~~C~~~~~lW~CL~-Cg~vgCgr 77 (149)
..+|+.|+..-+.-+||. |.+++|.-
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~ 33 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSS 33 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TT
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHH
Confidence 457999998877777865 99999964
No 77
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=21.13 E-value=31 Score=22.39 Aligned_cols=13 Identities=31% Similarity=0.933 Sum_probs=11.0
Q ss_pred eeccccCeeeecC
Q 032009 65 WLCLCCKEVLCSR 77 (149)
Q Consensus 65 W~CL~Cg~vgCgr 77 (149)
-.||.||.|-|..
T Consensus 19 ~NCl~CGkIiC~~ 31 (57)
T PF06221_consen 19 PNCLNCGKIICEQ 31 (57)
T ss_pred ccccccChhhccc
Confidence 4699999999964
No 78
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=21.09 E-value=75 Score=21.42 Aligned_cols=26 Identities=27% Similarity=0.579 Sum_probs=19.7
Q ss_pred CCCCCCCCCC-------CCceeccccCeeeecC
Q 032009 52 DTPCNRCQHP-------SENWLCLCCKEVLCSR 77 (149)
Q Consensus 52 ~~~C~~C~~~-------~~lW~CL~Cg~vgCgr 77 (149)
..+|.+|+.. .-.-.|+.||.+-+-.
T Consensus 19 ~VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 19 RVKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EEECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 4579999974 3455899999998854
No 79
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=20.89 E-value=71 Score=22.68 Aligned_cols=27 Identities=22% Similarity=0.647 Sum_probs=21.7
Q ss_pred CCCCCCCCCCC------CCceeccccCeeeecC
Q 032009 51 PDTPCNRCQHP------SENWLCLCCKEVLCSR 77 (149)
Q Consensus 51 ~~~~C~~C~~~------~~lW~CL~Cg~vgCgr 77 (149)
..-.|.-|+.. ..+|-|-.||+..-|.
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 35 AKHVCPVCGRPKVKRVGTGIWECRKCGAKFAGG 67 (90)
T ss_pred cCccCCCCCCCceEEEEEEEEEcCCCCCEEeCC
Confidence 44569999753 6799999999998875
No 80
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=20.72 E-value=51 Score=20.92 Aligned_cols=23 Identities=22% Similarity=0.560 Sum_probs=16.3
Q ss_pred CCCCCCCCCCC-CCceeccccCee
Q 032009 51 PDTPCNRCQHP-SENWLCLCCKEV 73 (149)
Q Consensus 51 ~~~~C~~C~~~-~~lW~CL~Cg~v 73 (149)
....|..|+.. ..--+|..||+.
T Consensus 25 ~l~~c~~cg~~~~~H~vc~~cG~y 48 (56)
T PF01783_consen 25 NLVKCPNCGEPKLPHRVCPSCGYY 48 (56)
T ss_dssp SEEESSSSSSEESTTSBCTTTBBS
T ss_pred ceeeeccCCCEecccEeeCCCCeE
Confidence 44568888864 456789999854
No 81
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=20.70 E-value=41 Score=23.78 Aligned_cols=50 Identities=14% Similarity=0.140 Sum_probs=27.7
Q ss_pred HHHHhhhcCCeeEEECCCCcEEEcCCCceec-ccccCCchhhhHHHHHHhhCC
Q 032009 83 MLQHYLETNHSVALSYSDLSVWCFTCDAYLN-AQVIPQLRPVYETAYILKFGE 134 (149)
Q Consensus 83 a~~H~~~t~H~l~v~l~t~~vwCY~Cd~~V~-~~~~~~L~~~~~~~hl~kfg~ 134 (149)
...|+.-.|+.+.+++ --.+|-.|+..+. ......+.+.+..+++++-|.
T Consensus 14 ~~~~~~~~G~~~~v~~--~~~~C~~CGe~~~~~e~~~~~~~~i~~~~~~~~~~ 64 (127)
T TIGR03830 14 KDEPYTYKGESITIGV--PGWYCPACGEELLDPEESKRNSAALADFYRKVDGL 64 (127)
T ss_pred ecceEEEcCEEEEEee--eeeECCCCCCEEEcHHHHHHHHHHHHHHHHHccCC
Confidence 3445667778888822 2337888886654 334444444444444444443
No 82
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=20.59 E-value=88 Score=18.72 Aligned_cols=24 Identities=21% Similarity=0.610 Sum_probs=19.4
Q ss_pred CCCCCCCCCCCceeccccCee-eec
Q 032009 53 TPCNRCQHPSENWLCLCCKEV-LCS 76 (149)
Q Consensus 53 ~~C~~C~~~~~lW~CL~Cg~v-gCg 76 (149)
..|..|.......+-+-||+. .|.
T Consensus 3 ~~C~iC~~~~~~~~~~pCgH~~~C~ 27 (50)
T PF13920_consen 3 EECPICFENPRDVVLLPCGHLCFCE 27 (50)
T ss_dssp SB-TTTSSSBSSEEEETTCEEEEEH
T ss_pred CCCccCCccCCceEEeCCCChHHHH
Confidence 468899988888888999999 885
No 83
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=20.19 E-value=25 Score=20.41 Aligned_cols=29 Identities=17% Similarity=0.512 Sum_probs=16.1
Q ss_pred CCCcccccccccCCCCCC--CCCCCCCCCCC
Q 032009 32 TSCDHLVASLSSDLAHIP--TPDTPCNRCQH 60 (149)
Q Consensus 32 ~~CpHl~~~l~~~~~~i~--~~~~~C~~C~~ 60 (149)
..||+-...++.+...++ ....+|..|+.
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGH 33 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCc
Confidence 468887444444332232 35567888863
Done!