Query 023654
Match_columns 279
No_of_seqs 254 out of 1439
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 05:39:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023654.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023654hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0944 Ubiquitin-specific pro 100.0 1.7E-33 3.6E-38 278.0 9.1 188 51-273 23-270 (763)
2 COG5207 UBP14 Isopeptidase T [ 100.0 3.3E-31 7.1E-36 255.5 2.7 208 32-273 1-266 (749)
3 PF02148 zf-UBP: Zn-finger in 99.8 5.4E-21 1.2E-25 139.5 5.4 60 188-247 1-61 (63)
4 PF02148 zf-UBP: Zn-finger in 99.8 7.3E-20 1.6E-24 133.5 4.8 61 55-115 1-62 (63)
5 KOG0944 Ubiquitin-specific pro 99.7 1.9E-18 4.1E-23 171.8 5.9 107 25-139 150-269 (763)
6 COG5207 UBP14 Isopeptidase T [ 99.7 4.8E-17 1E-21 158.0 4.1 89 25-114 146-245 (749)
7 KOG0804 Cytoplasmic Zn-finger 99.6 9.1E-17 2E-21 153.9 3.7 66 184-249 227-292 (493)
8 cd02669 Peptidase_C19M A subfa 99.5 4.7E-14 1E-18 138.0 8.7 99 168-268 1-103 (440)
9 cd02669 Peptidase_C19M A subfa 99.5 5.5E-14 1.2E-18 137.6 6.2 85 35-121 1-85 (440)
10 KOG0804 Cytoplasmic Zn-finger 99.4 8E-14 1.7E-18 133.8 3.4 64 52-115 228-291 (493)
11 smart00290 ZnF_UBP Ubiquitin C 99.4 2.4E-13 5.2E-18 94.2 4.5 49 187-235 1-49 (50)
12 KOG1873 Ubiquitin-specific pro 99.4 1.5E-13 3.2E-18 138.5 1.1 90 158-247 36-147 (877)
13 smart00290 ZnF_UBP Ubiquitin C 99.3 4.1E-12 8.9E-17 88.0 4.1 48 54-101 1-48 (50)
14 KOG1873 Ubiquitin-specific pro 99.1 2.8E-11 6.1E-16 122.3 0.8 78 33-110 44-143 (877)
15 KOG2026 Spindle pole body prot 97.0 0.00071 1.5E-08 65.1 4.0 92 29-122 8-100 (442)
16 KOG2026 Spindle pole body prot 96.1 0.0055 1.2E-07 59.1 4.0 83 165-249 11-94 (442)
17 PF09416 UPF1_Zn_bind: RNA hel 86.3 1.1 2.3E-05 38.4 4.1 57 54-110 2-68 (152)
18 KOG1867 Ubiquitin-specific pro 82.4 0.5 1.1E-05 47.5 0.7 69 51-121 42-112 (492)
19 PRK14890 putative Zn-ribbon RN 77.6 0.74 1.6E-05 33.2 0.0 23 185-207 36-58 (59)
20 PF09416 UPF1_Zn_bind: RNA hel 75.3 5.7 0.00012 34.0 4.8 57 187-243 2-68 (152)
21 COG2888 Predicted Zn-ribbon RN 74.1 1 2.2E-05 32.6 -0.0 24 184-207 37-60 (61)
22 KOG1867 Ubiquitin-specific pro 73.5 1.2 2.7E-05 44.8 0.4 67 181-249 39-107 (492)
23 PF14369 zf-RING_3: zinc-finge 60.0 4.6 0.0001 25.9 0.9 13 102-114 2-14 (35)
24 cd00350 rubredoxin_like Rubred 52.6 6.4 0.00014 24.7 0.6 20 186-205 2-25 (33)
25 PRK14890 putative Zn-ribbon RN 52.1 5.2 0.00011 28.9 0.2 23 52-74 36-58 (59)
26 cd00729 rubredoxin_SM Rubredox 49.1 9.8 0.00021 24.2 1.1 14 197-210 2-15 (34)
27 COG2888 Predicted Zn-ribbon RN 47.3 6.4 0.00014 28.5 0.0 23 52-74 38-60 (61)
28 PF08274 PhnA_Zn_Ribbon: PhnA 45.4 16 0.00035 22.8 1.6 21 186-206 3-28 (30)
29 COG1997 RPL43A Ribosomal prote 44.4 16 0.00034 28.5 1.8 26 52-77 35-66 (89)
30 PF14803 Nudix_N_2: Nudix N-te 39.8 22 0.00047 22.8 1.6 13 195-207 20-32 (34)
31 PF13923 zf-C3HC4_2: Zinc fing 36.1 21 0.00046 22.7 1.2 23 188-210 1-24 (39)
32 PF01927 Mut7-C: Mut7-C RNAse 34.9 31 0.00068 28.8 2.4 13 195-207 122-134 (147)
33 PF11781 RRN7: RNA polymerase 33.5 27 0.00059 22.5 1.4 21 53-73 9-34 (36)
34 PF01412 ArfGap: Putative GTPa 32.7 54 0.0012 26.2 3.3 52 183-238 11-62 (116)
35 TIGR00686 phnA alkylphosphonat 31.3 37 0.00079 27.5 2.0 23 186-208 3-30 (109)
36 PF07754 DUF1610: Domain of un 31.0 38 0.00081 20.1 1.5 12 194-205 13-24 (24)
37 PRK10220 hypothetical protein; 30.7 40 0.00088 27.3 2.2 23 186-208 4-31 (111)
38 COG5574 PEX10 RING-finger-cont 30.3 23 0.00049 33.0 0.8 30 181-210 211-240 (271)
39 PF10571 UPF0547: Uncharacteri 30.1 32 0.00068 20.6 1.2 21 187-207 2-24 (26)
40 KOG0317 Predicted E3 ubiquitin 29.3 22 0.00048 33.5 0.6 40 180-223 234-273 (293)
41 smart00661 RPOL9 RNA polymeras 28.9 45 0.00097 22.3 1.9 11 196-206 19-29 (52)
42 COG1997 RPL43A Ribosomal prote 28.8 47 0.001 25.9 2.2 28 184-211 34-67 (89)
43 PF01412 ArfGap: Putative GTPa 28.2 63 0.0014 25.8 3.0 48 51-102 12-59 (116)
44 PF02207 zf-UBR: Putative zinc 27.7 26 0.00055 25.7 0.6 35 53-100 14-48 (71)
45 PF08792 A2L_zn_ribbon: A2L zi 27.2 59 0.0013 20.5 2.1 23 185-207 3-31 (33)
46 COG0777 AccD Acetyl-CoA carbox 25.9 27 0.0006 32.8 0.5 25 183-207 26-57 (294)
47 KOG1802 RNA helicase nonsense 25.8 78 0.0017 33.7 3.8 59 52-110 60-128 (935)
48 KOG1802 RNA helicase nonsense 25.3 95 0.0021 33.1 4.3 60 184-243 59-128 (935)
49 KOG0704 ADP-ribosylation facto 24.9 34 0.00074 33.2 1.0 23 51-73 18-48 (386)
50 PF08271 TF_Zn_Ribbon: TFIIB z 24.8 62 0.0013 21.2 2.0 11 196-206 18-28 (43)
51 TIGR03830 CxxCG_CxxCG_HTH puta 24.1 61 0.0013 25.6 2.2 53 215-269 13-66 (127)
52 PF01780 Ribosomal_L37ae: Ribo 23.4 33 0.00073 26.8 0.5 22 55-76 38-65 (90)
53 PF07282 OrfB_Zn_ribbon: Putat 23.2 71 0.0015 22.8 2.2 23 184-206 27-55 (69)
54 smart00396 ZnF_UBR1 Putative z 23.1 1.1E+02 0.0024 22.5 3.3 40 53-105 14-53 (71)
55 smart00105 ArfGap Putative GTP 23.1 1E+02 0.0023 24.4 3.4 49 185-237 3-51 (112)
56 COG1773 Rubredoxin [Energy pro 22.9 34 0.00074 24.4 0.4 11 195-205 34-44 (55)
57 smart00154 ZnF_AN1 AN1-like Zi 21.7 49 0.0011 21.6 1.0 23 188-210 1-25 (39)
58 PF05715 zf-piccolo: Piccolo Z 21.6 55 0.0012 23.8 1.3 20 186-205 31-57 (61)
59 KOG0317 Predicted E3 ubiquitin 20.8 42 0.0009 31.7 0.7 39 47-89 234-272 (293)
60 COG1592 Rubrerythrin [Energy p 20.7 44 0.00096 29.0 0.8 22 184-205 133-157 (166)
61 PF14835 zf-RING_6: zf-RING of 20.5 59 0.0013 24.0 1.3 28 185-212 7-35 (65)
No 1
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.7e-33 Score=277.97 Aligned_cols=188 Identities=23% Similarity=0.446 Sum_probs=153.2
Q ss_pred CCCCCCCC----CCCCCeeeecccCceeecccccchhhhhhhccCCeEEEEcCCCcEEEcCCCcccchhhhhhccccchh
Q 023654 51 PDTPCNMC----KHPRGNWLCLCCKEVLCSRYVNKHMLRHYREKNHSVALDYSDLSVWCFACHAYLNAQAILQLRPVHET 126 (279)
Q Consensus 51 ~~~~C~~C----~~~~~lwvCL~Cg~~~Cgr~~~~Ha~~H~~~t~H~l~l~l~~~~vwCy~Cd~~V~~~~l~~l~~~~~~ 126 (279)
...+|.+| ...+|+++||.|+..+++. |++.|+.+|+|++++++++. .+...+.
T Consensus 23 ~kdeC~ycf~sp~~e~glyicl~~f~afg~~----~v~~~f~~tg~~~yl~i~r~------------------~k~k~~~ 80 (763)
T KOG0944|consen 23 YKDECAYCFDSPESEGGLYICLNCFLAFGRE----HVEEYFRKTGHSVYLHIARV------------------KKIKEEG 80 (763)
T ss_pred ehhhceeeccCCCCCCCEEeehhhhhhhhhH----HHHHHHhhcCceEEEEeccc------------------cchhhcc
Confidence 46799999 4678999999999998764 99999999999999999822 2222221
Q ss_pred hhhhhhccCCCCCCCCCccccc-cchhhh-----------------------------------------cccccccccc
Q 023654 127 SYVLKFGRALPFNTGQHPKVKE-DDEMML-----------------------------------------GAESGSVRHL 164 (279)
Q Consensus 127 ~~~~~fg~~~~~~~~kl~i~~~-~~e~~~-----------------------------------------~~~~~~~~~~ 164 (279)
.-|..+..|+++|+|+++ .-+|.| ..+.+|+.++
T Consensus 81 ----~~~~~p~~K~tkl~i~~d~e~~d~~~iv~~p~~~~~~i~n~~~~~~i~~~~e~i~a~~sa~~~~~k~~~~aWd~Ev 156 (763)
T KOG0944|consen 81 ----AEGAEPKRKITKLEIGEDLECEDVYDIVVVPDDLEIAIKNIQLLPEIVSATEAIEAMLSAISPSRKDRVNAWDNEV 156 (763)
T ss_pred ----CcCCCccccceeEEeccccccceeEEEEEeccccccccCCccccHHHHHHHHHHHHHHhhcCcchhhhhhhhhhhe
Confidence 112467778999999987 335655 1467899998
Q ss_pred ccchhhhhhhccc--ccCCCCCCCCCCCCCCCCCeeeecccCceecccC------CChHHHHHhhhcCCeeEEeCCCc--
Q 023654 165 TSCDHLVASLSTD--LARIPNPDTPCNRCQHPRGNWLCLCCKEVLCSRY------VNKHMLQHYQETNHSVALGYSDL-- 234 (279)
Q Consensus 165 ~~C~Hl~~~l~~~--~~~~~~~~~~C~~C~~~~~lW~CL~Cg~vgCgr~------~~~Ha~~H~~~~~H~l~v~l~t~-- 234 (279)
..+++-...|.|. ...+++..|+|+.|++..|||+||+||.|||||. +|+||+.||++|+||++|+|+|+
T Consensus 157 r~v~k~~~nl~q~dng~~~~~~gwkCs~CDL~~NLWlcLtcG~v~CGR~qfg~~GgNgHA~~HYr~tghPLaVKLgsIs~ 236 (763)
T KOG0944|consen 157 RTVSKHANNLSQIDNGKRIPPSGWKCSKCDLTENLWLCLTCGSVGCGRKQFGGSGGNGHALSHYRETGHPLAVKLGSISP 236 (763)
T ss_pred eeccCCCCChhhcccCcccCCCcceecccCcccceEEEeccCceeecceeecCCCCCcchHHhhhhcCCceEEEecccCC
Confidence 5544432666665 3567789999999999999999999999999998 59999999999999999999986
Q ss_pred ---cEEECCCCcee-chhHHhhhcchhhHHHHHhhCCCCCCCc
Q 023654 235 ---SVWCFACHAYL-NAQAILQLQPVHETAYVLKFGRALPFLM 273 (279)
Q Consensus 235 ---~v~CY~Cd~~V-~~~~~~~l~~~~~~~h~~~fg~~~~~~~ 273 (279)
+||||.||+.| ||++ ..||.+|||++....
T Consensus 237 dg~DvycY~cDd~v~dPnl---------~~hl~hfGId~~~m~ 270 (763)
T KOG0944|consen 237 DGADVYCYDCDDEVRDPNL---------ESHLSHFGIDMAKMD 270 (763)
T ss_pred CccceeeecccccccCccH---------HHHHHhcCccHHHhc
Confidence 99999999777 8888 899999999987543
No 2
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=3.3e-31 Score=255.49 Aligned_cols=208 Identities=20% Similarity=0.355 Sum_probs=157.2
Q ss_pred CCCcccccccccCcCCCCC--CCCCCCCC----CCCCCeeeecccCceeecccccchh-hhhhhccCCeEEEEcCCCcEE
Q 023654 32 ASCDHLVASLSSDLARIPT--PDTPCNMC----KHPRGNWLCLCCKEVLCSRYVNKHM-LRHYREKNHSVALDYSDLSVW 104 (279)
Q Consensus 32 ~~CpHl~~~l~~~~~~~~~--~~~~C~~C----~~~~~lwvCL~Cg~~~Cgr~~~~Ha-~~H~~~t~H~l~l~l~~~~vw 104 (279)
++|||+..+ .......|. ...+|.+| ....++-+||+|++.+|++..--|. +.|+.+|-|++++.+.
T Consensus 1 ~S~~H~e~a-e~vlpn~~av~~reeC~yCf~S~~~e~si~vClnCfqs~C~~h~~~H~~~~~~c~tvh~i~~tia----- 74 (749)
T COG5207 1 KSFSHSEMA-EMVLPNLPAVRFREECCYCFRSIGDEHSISVCLNCFQSFCEKHRGIHLGTKSGCRTVHDIKETIA----- 74 (749)
T ss_pred CCCchhhhh-hhcCCCCchhhhhhhhheeeccCCCCcceehHHHHhHhhhhhccceeecchhhhhhhhhhhhhhh-----
Confidence 478999443 111111121 35789999 3455799999999999999877888 6888999999998886
Q ss_pred EcCCCcccchhhhhhccccchhhhhhhhccCCCCCCCCCccccccchhhh------------------------------
Q 023654 105 CFACHAYLNAQAILQLRPVHETSYVLKFGRALPFNTGQHPKVKEDDEMML------------------------------ 154 (279)
Q Consensus 105 Cy~Cd~~V~~~~l~~l~~~~~~~~~~~fg~~~~~~~~kl~i~~~~~e~~~------------------------------ 154 (279)
++.|.. +.-++++.|..||.+.+.+|||.|
T Consensus 75 --------------~~~PKQ------e~~eE~~nK~ikl~~~e~seed~~~~~~VPr~vl~k~t~s~~s~~~~~kiE~m~ 134 (749)
T COG5207 75 --------------DLGPKQ------ENVEENNNKKIKLKNAELSEEDVEELRRVPRTVLSKSTDSDISSTALEKIERME 134 (749)
T ss_pred --------------hcCchh------hccccCccceeeeeeeccchhhhHHhhccchhhcccccccccchhhHHHHHHHH
Confidence 232432 223566668889999888888777
Q ss_pred --------ccccccccccccchhhhhhhcccccCC-CCCCCCCCCCCCCCCeeeecccCceecccC-----CChHHHHHh
Q 023654 155 --------GAESGSVRHLTSCDHLVASLSTDLARI-PNPDTPCNRCQHPRGNWLCLCCKEVLCSRY-----VNKHMLQHY 220 (279)
Q Consensus 155 --------~~~~~~~~~~~~C~Hl~~~l~~~~~~~-~~~~~~C~~C~~~~~lW~CL~Cg~vgCgr~-----~~~Ha~~H~ 220 (279)
.+..+|+.++..|+|. ..+....... .....+|+.|++..|+|+||+||++||||- +||||+.||
T Consensus 135 ~a~k~~~ed~~~~w~~E~~tC~H~-~n~~~~s~~~~ni~~~~Cs~CDl~~nLW~Cl~CG~vgCGR~QyG~~GngHAlsHY 213 (749)
T COG5207 135 IAIKPGDEDERVLWRDEEVTCVHG-CNEGPSSIEMGNIGGLKCSLCDLKTNLWVCLSCGYVGCGRMQYGAEGNGHALSHY 213 (749)
T ss_pred HhcCCCchhhhhhhhhhccccccc-CCCCCCcccccccCCceeccccchhceEEEEecCcccccceeecCCCCcchhhhh
Confidence 1567799999999999 5443321111 125689999999999999999999999997 899999999
Q ss_pred hhcCCeeEEeCCCc-----cEEECCCCcee--chhHHhhhcchhhHHHHHhhCCCCCCCc
Q 023654 221 QETNHSVALGYSDL-----SVWCFACHAYL--NAQAILQLQPVHETAYVLKFGRALPFLM 273 (279)
Q Consensus 221 ~~~~H~l~v~l~t~-----~v~CY~Cd~~V--~~~~~~~l~~~~~~~h~~~fg~~~~~~~ 273 (279)
++++||++|+|.++ +||||.||+.+ +++.- ...|+..|||++..-.
T Consensus 214 ~~t~Hplavkl~Sls~~~~diyCY~CD~e~R~~~n~n-------~~s~~~~fGinIa~~~ 266 (749)
T COG5207 214 EETQHPLAVKLPSLSKEDCDIYCYLCDSEIRSRYNSN-------ENSVTIDFGINIADGK 266 (749)
T ss_pred hccCCceEEEccccccccccEEEEecCcccccCCccc-------ccceeeeeccchhhcc
Confidence 99999999999876 99999999875 34221 0577889999876543
No 3
>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=99.83 E-value=5.4e-21 Score=139.49 Aligned_cols=60 Identities=45% Similarity=1.028 Sum_probs=53.8
Q ss_pred CCCCCCC-CCeeeecccCceecccCCChHHHHHhhhcCCeeEEeCCCccEEECCCCceech
Q 023654 188 CNRCQHP-RGNWLCLCCKEVLCSRYVNKHMLQHYQETNHSVALGYSDLSVWCFACHAYLNA 247 (279)
Q Consensus 188 C~~C~~~-~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~~~H~l~v~l~t~~v~CY~Cd~~V~~ 247 (279)
|++|+.. .++|+||+||++||||+.++||++|+++++|+++|++.+..||||.||+||.+
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~~~~H~l~v~~~~~~i~C~~C~~~v~~ 61 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGRYSNGHALKHYKETGHPLAVSLSTGSIWCYACDDYVYD 61 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETTTSTSHHHHHHHHHT--EEEETTTTCEEETTTTEEEES
T ss_pred CCCCCCcCCceEEeCCCCcccccCCcCcHHHHhhcccCCeEEEECCCCeEEEcCCCcEEeC
Confidence 7889888 99999999999999999999999999999999999999999999999999964
No 4
>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=99.79 E-value=7.3e-20 Score=133.52 Aligned_cols=61 Identities=43% Similarity=1.030 Sum_probs=54.3
Q ss_pred CCCCCCC-CCeeeecccCceeecccccchhhhhhhccCCeEEEEcCCCcEEEcCCCcccchh
Q 023654 55 CNMCKHP-RGNWLCLCCKEVLCSRYVNKHMLRHYREKNHSVALDYSDLSVWCFACHAYLNAQ 115 (279)
Q Consensus 55 C~~C~~~-~~lwvCL~Cg~~~Cgr~~~~Ha~~H~~~t~H~l~l~l~~~~vwCy~Cd~~V~~~ 115 (279)
|..|... .++|+||+||++||+|+.++|++.|+++++|+|+|++.+..||||.|++||+++
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 7788766 899999999999999999999999999999999999999999999999999986
No 5
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=99.73 E-value=1.9e-18 Score=171.76 Aligned_cols=107 Identities=29% Similarity=0.599 Sum_probs=90.1
Q ss_pred ceeeecCCCCccccccccc--CcCCCCCCCCCCCCCCCCCCeeeecccCceeeccc------ccchhhhhhhccCCeEEE
Q 023654 25 LGWVRHLASCDHLVASLSS--DLARIPTPDTPCNMCKHPRGNWLCLCCKEVLCSRY------VNKHMLRHYREKNHSVAL 96 (279)
Q Consensus 25 ~~~~~~~~~CpHl~~~l~~--~~~~~~~~~~~C~~C~~~~~lwvCL~Cg~~~Cgr~------~~~Ha~~H~~~t~H~l~l 96 (279)
.+|+.++..+++-...|.+ +...+|+..++|+.|+...++|+||+||.++|||. +|+||+.||++|+|||+|
T Consensus 150 ~aWd~Evr~v~k~~~nl~q~dng~~~~~~gwkCs~CDL~~NLWlcLtcG~v~CGR~qfg~~GgNgHA~~HYr~tghPLaV 229 (763)
T KOG0944|consen 150 NAWDNEVRTVSKHANNLSQIDNGKRIPPSGWKCSKCDLTENLWLCLTCGSVGCGRKQFGGSGGNGHALSHYRETGHPLAV 229 (763)
T ss_pred hhhhhheeeccCCCCChhhcccCcccCCCcceecccCcccceEEEeccCceeecceeecCCCCCcchHHhhhhcCCceEE
Confidence 4799998555444255554 23567777899999999999999999999999993 599999999999999999
Q ss_pred EcCC-----CcEEEcCCCcccchhhhhhccccchhhhhhhhccCCCCC
Q 023654 97 DYSD-----LSVWCFACHAYLNAQAILQLRPVHETSYVLKFGRALPFN 139 (279)
Q Consensus 97 ~l~~-----~~vwCy~Cd~~V~~~~l~~l~~~~~~~~~~~fg~~~~~~ 139 (279)
++++ .+||||.||+.|.||.|. .|++.||+++...
T Consensus 230 KLgsIs~dg~DvycY~cDd~v~dPnl~--------~hl~hfGId~~~m 269 (763)
T KOG0944|consen 230 KLGSISPDGADVYCYDCDDEVRDPNLE--------SHLSHFGIDMAKM 269 (763)
T ss_pred EecccCCCccceeeecccccccCccHH--------HHHHhcCccHHHh
Confidence 9986 689999999999999776 6889999987643
No 6
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=99.65 E-value=4.8e-17 Score=157.97 Aligned_cols=89 Identities=25% Similarity=0.627 Sum_probs=74.8
Q ss_pred ceeeecCCCCcccccccccCcCCC-CCCCCCCCCCCCCCCeeeecccCceeeccc-----ccchhhhhhhccCCeEEEEc
Q 023654 25 LGWVRHLASCDHLVASLSSDLARI-PTPDTPCNMCKHPRGNWLCLCCKEVLCSRY-----VNKHMLRHYREKNHSVALDY 98 (279)
Q Consensus 25 ~~~~~~~~~CpHl~~~l~~~~~~~-~~~~~~C~~C~~~~~lwvCL~Cg~~~Cgr~-----~~~Ha~~H~~~t~H~l~l~l 98 (279)
+.|+.++.+|+|. ..+.++.... .....+|+.|+...++|+||+||.+||||. +++||+.||++|+|||+|.+
T Consensus 146 ~~w~~E~~tC~H~-~n~~~~s~~~~ni~~~~Cs~CDl~~nLW~Cl~CG~vgCGR~QyG~~GngHAlsHY~~t~Hplavkl 224 (749)
T COG5207 146 VLWRDEEVTCVHG-CNEGPSSIEMGNIGGLKCSLCDLKTNLWVCLSCGYVGCGRMQYGAEGNGHALSHYEETQHPLAVKL 224 (749)
T ss_pred hhhhhhccccccc-CCCCCCcccccccCCceeccccchhceEEEEecCcccccceeecCCCCcchhhhhhccCCceEEEc
Confidence 5899999999999 5554433211 113579999999999999999999999993 69999999999999999999
Q ss_pred CC-----CcEEEcCCCcccch
Q 023654 99 SD-----LSVWCFACHAYLNA 114 (279)
Q Consensus 99 ~~-----~~vwCy~Cd~~V~~ 114 (279)
.+ .++|||.||+.+..
T Consensus 225 ~Sls~~~~diyCY~CD~e~R~ 245 (749)
T COG5207 225 PSLSKEDCDIYCYLCDSEIRS 245 (749)
T ss_pred cccccccccEEEEecCccccc
Confidence 75 58999999998653
No 7
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=99.64 E-value=9.1e-17 Score=153.85 Aligned_cols=66 Identities=32% Similarity=0.702 Sum_probs=62.9
Q ss_pred CCCCCCCCCCCCCeeeecccCceecccCCChHHHHHhhhcCCeeEEeCCCccEEECCCCceechhH
Q 023654 184 PDTPCNRCQHPRGNWLCLCCKEVLCSRYVNKHMLQHYQETNHSVALGYSDLSVWCFACHAYLNAQA 249 (279)
Q Consensus 184 ~~~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~~~H~l~v~l~t~~v~CY~Cd~~V~~~~ 249 (279)
....|..|+...++|+||.||+||||||..+||++||++|+|+++++|+|.+||.|+-|+||++-.
T Consensus 227 e~~~c~~c~~~~~LwicliCg~vgcgrY~eghA~rHweet~H~yalel~tqrVWDYAGDnYVhRl~ 292 (493)
T KOG0804|consen 227 ESSLCLACGCTEDLWICLICGNVGCGRYKEGHARRHWEETGHCYALELETQRVWDYAGDNYVHRLP 292 (493)
T ss_pred hhhhhhhhcccccEEEEEEccceecccccchhHHHHHHhhcceEEEeecceeeeecccchhhhhcc
Confidence 467899999999999999999999999999999999999999999999999999999999999744
No 8
>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=99.50 E-value=4.7e-14 Score=138.04 Aligned_cols=99 Identities=18% Similarity=0.283 Sum_probs=76.8
Q ss_pred hhhhhhhcccccCCCCCCCCCCCCCCCCCeeeecccCceecccCCChHHHHHhhhcCCeeEEeCCCccEEECCCCceech
Q 023654 168 DHLVASLSTDLARIPNPDTPCNRCQHPRGNWLCLCCKEVLCSRYVNKHMLQHYQETNHSVALGYSDLSVWCFACHAYLNA 247 (279)
Q Consensus 168 ~Hl~~~l~~~~~~~~~~~~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~~~H~l~v~l~t~~v~CY~Cd~~V~~ 247 (279)
|++ +++.+.. ..+..+..|+.|+...|+|+||+||++++||.+++||..|+.+++|+++|+++|.+||||.|+++|..
T Consensus 1 ~yl-~ti~r~~-ldfd~e~~C~~~~~~~n~~~CL~cg~~~~g~~~~~ha~~H~~~~~H~~~v~l~t~~~yc~~~~~~v~d 78 (440)
T cd02669 1 PYL-DTINRSV-LDFDFEKVCSVSLSNLNVYACLVCGKYFQGRGKGSHAYTHSLEDNHHVFLNLETLKFYCLPDNYEIID 78 (440)
T ss_pred Cch-hhhhhhh-ccccccccccccCCCCcEEEEcccCCeecCCCCCcHHHHHhhccCCCEEEECCCCCEEEeCCCCEEeC
Confidence 345 4554431 23467888999999999999999999999999999999999999999999999999999999999954
Q ss_pred h----HHhhhcchhhHHHHHhhCCC
Q 023654 248 Q----AILQLQPVHETAYVLKFGRA 268 (279)
Q Consensus 248 ~----~~~~l~~~~~~~h~~~fg~~ 268 (279)
. ++..+.+.++..-+..+..+
T Consensus 79 ~~l~~i~~~~~~~~~~~~i~~~~~~ 103 (440)
T cd02669 79 SSLDDIKYVLNPTYTKEQISDLDRD 103 (440)
T ss_pred ccHHHHHHHhcCCCCHHHHHHhhhc
Confidence 3 33334444554444444443
No 9
>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=99.46 E-value=5.5e-14 Score=137.56 Aligned_cols=85 Identities=18% Similarity=0.350 Sum_probs=75.2
Q ss_pred cccccccccCcCCCCCCCCCCCCCCCCCCeeeecccCceeecccccchhhhhhhccCCeEEEEcCCCcEEEcCCCcccch
Q 023654 35 DHLVASLSSDLARIPTPDTPCNMCKHPRGNWLCLCCKEVLCSRYVNKHMLRHYREKNHSVALDYSDLSVWCFACHAYLNA 114 (279)
Q Consensus 35 pHl~~~l~~~~~~~~~~~~~C~~C~~~~~lwvCL~Cg~~~Cgr~~~~Ha~~H~~~t~H~l~l~l~~~~vwCy~Cd~~V~~ 114 (279)
|.| +++++..+.++ ....|+.|.+..++|+||+||.+++|+..++||..|+.+++|+++|+++++.||||.|+++|.|
T Consensus 1 ~yl-~ti~r~~ldfd-~e~~C~~~~~~~n~~~CL~cg~~~~g~~~~~ha~~H~~~~~H~~~v~l~t~~~yc~~~~~~v~d 78 (440)
T cd02669 1 PYL-DTINRSVLDFD-FEKVCSVSLSNLNVYACLVCGKYFQGRGKGSHAYTHSLEDNHHVFLNLETLKFYCLPDNYEIID 78 (440)
T ss_pred Cch-hhhhhhhcccc-ccccccccCCCCcEEEEcccCCeecCCCCCcHHHHHhhccCCCEEEECCCCCEEEeCCCCEEeC
Confidence 456 66666555555 5678999999999999999999999998999999999999999999999999999999999999
Q ss_pred hhhhhcc
Q 023654 115 QAILQLR 121 (279)
Q Consensus 115 ~~l~~l~ 121 (279)
+.|..++
T Consensus 79 ~~l~~i~ 85 (440)
T cd02669 79 SSLDDIK 85 (440)
T ss_pred ccHHHHH
Confidence 9888665
No 10
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=99.41 E-value=8e-14 Score=133.80 Aligned_cols=64 Identities=33% Similarity=0.739 Sum_probs=60.0
Q ss_pred CCCCCCCCCCCCeeeecccCceeecccccchhhhhhhccCCeEEEEcCCCcEEEcCCCcccchh
Q 023654 52 DTPCNMCKHPRGNWLCLCCKEVLCSRYVNKHMLRHYREKNHSVALDYSDLSVWCFACHAYLNAQ 115 (279)
Q Consensus 52 ~~~C~~C~~~~~lwvCL~Cg~~~Cgr~~~~Ha~~H~~~t~H~l~l~l~~~~vwCy~Cd~~V~~~ 115 (279)
...|..|....++|+||.||++|||||..+||++|+++|+|.+++.+++.+||.|+-|+||+.-
T Consensus 228 ~~~c~~c~~~~~LwicliCg~vgcgrY~eghA~rHweet~H~yalel~tqrVWDYAGDnYVhRl 291 (493)
T KOG0804|consen 228 SSLCLACGCTEDLWICLICGNVGCGRYKEGHARRHWEETGHCYALELETQRVWDYAGDNYVHRL 291 (493)
T ss_pred hhhhhhhcccccEEEEEEccceecccccchhHHHHHHhhcceEEEeecceeeeecccchhhhhc
Confidence 3468888889999999999999999999999999999999999999999999999999999853
No 11
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=99.41 E-value=2.4e-13 Score=94.18 Aligned_cols=49 Identities=35% Similarity=0.788 Sum_probs=46.5
Q ss_pred CCCCCCCCCCeeeecccCceecccCCChHHHHHhhhcCCeeEEeCCCcc
Q 023654 187 PCNRCQHPRGNWLCLCCKEVLCSRYVNKHMLQHYQETNHSVALGYSDLS 235 (279)
Q Consensus 187 ~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~~~H~l~v~l~t~~ 235 (279)
+|.+|+...++|+||+|+++||+|+.++|++.||++++|++++++.++.
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 5999999999999999999999999999999999999999999998864
No 12
>KOG1873 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.35 E-value=1.5e-13 Score=138.48 Aligned_cols=90 Identities=24% Similarity=0.600 Sum_probs=70.9
Q ss_pred cccccccccchhhhhhhccc-c-cCCC-CCCCCCCCCCCC---------------CCeeeecccCceeccc-CCChHHHH
Q 023654 158 SGSVRHLTSCDHLVASLSTD-L-ARIP-NPDTPCNRCQHP---------------RGNWLCLCCKEVLCSR-YVNKHMLQ 218 (279)
Q Consensus 158 ~~~~~~~~~C~Hl~~~l~~~-~-~~~~-~~~~~C~~C~~~---------------~~lW~CL~Cg~vgCgr-~~~~Ha~~ 218 (279)
++..++...|.|+.+.+.+. + +.|. .....|++|... ..+|+||.||+.|||| ....||+.
T Consensus 36 ~t~t~~~~~C~Hi~Kav~l~~lk~~iks~~~~~C~eC~e~~~~k~g~s~~~~~~~~~iWLCLkCG~q~CG~~~~~~halk 115 (877)
T KOG1873|consen 36 KTPTETPVECQHIKKAVDLSHLKRAIKSLLWIKCSECNEEVKVKDGGSSDQFEFDNAIWLCLKCGYQGCGRNSESQHALK 115 (877)
T ss_pred cCCCCCccccchHHhhhcHHHHHHHHHHHHHHHHHHhhhcceeccCCCccccccccceeeecccCCeeeCCCcccchhhh
Confidence 44444445599998888865 2 2222 255689999864 4699999999999999 57899999
Q ss_pred Hhhhc---CCeeEEeCCCccEEECCCCceech
Q 023654 219 HYQET---NHSVALGYSDLSVWCFACHAYLNA 247 (279)
Q Consensus 219 H~~~~---~H~l~v~l~t~~v~CY~Cd~~V~~ 247 (279)
||+.. .|+++|++.++.||||.||..+-+
T Consensus 116 H~~~~r~~~Hclvin~~n~~~WCy~Cd~kl~~ 147 (877)
T KOG1873|consen 116 HFLTPRSEPHCLVINLINWLIWCYSCDAKLVP 147 (877)
T ss_pred hhcccCCCCeeEEEEeeeeeeEEEeccchhcc
Confidence 99864 699999999999999999985443
No 13
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=99.27 E-value=4.1e-12 Score=87.95 Aligned_cols=48 Identities=33% Similarity=0.807 Sum_probs=45.0
Q ss_pred CCCCCCCCCCeeeecccCceeecccccchhhhhhhccCCeEEEEcCCC
Q 023654 54 PCNMCKHPRGNWLCLCCKEVLCSRYVNKHMLRHYREKNHSVALDYSDL 101 (279)
Q Consensus 54 ~C~~C~~~~~lwvCL~Cg~~~Cgr~~~~Ha~~H~~~t~H~l~l~l~~~ 101 (279)
+|..|....++|+||+|++++|+++.++|++.|+++++|++++++++.
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~~~~~~h~~~H~~~t~H~~~~~~~~~ 48 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCGRYQLGHALEHFEETGHPLVVKLGTQ 48 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccCCCCCcHHHHHhhhhCCCEEEEcccc
Confidence 589998888999999999999999988999999999999999999865
No 14
>KOG1873 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.07 E-value=2.8e-11 Score=122.27 Aligned_cols=78 Identities=26% Similarity=0.684 Sum_probs=63.4
Q ss_pred CCcccccccccCcC--CCC-CCCCCCCCCC------C---------CCCeeeecccCceeecc-cccchhhhhhhc---c
Q 023654 33 SCDHLVASLSSDLA--RIP-TPDTPCNMCK------H---------PRGNWLCLCCKEVLCSR-YVNKHMLRHYRE---K 90 (279)
Q Consensus 33 ~CpHl~~~l~~~~~--~~~-~~~~~C~~C~------~---------~~~lwvCL~Cg~~~Cgr-~~~~Ha~~H~~~---t 90 (279)
.|.|+.++|++..+ .+. ..+..|..|. . ...+|+||.||+.|||| ....|++.||.. +
T Consensus 44 ~C~Hi~Kav~l~~lk~~iks~~~~~C~eC~e~~~~k~g~s~~~~~~~~~iWLCLkCG~q~CG~~~~~~halkH~~~~r~~ 123 (877)
T KOG1873|consen 44 ECQHIKKAVDLSHLKRAIKSLLWIKCSECNEEVKVKDGGSSDQFEFDNAIWLCLKCGYQGCGRNSESQHALKHFLTPRSE 123 (877)
T ss_pred ccchHHhhhcHHHHHHHHHHHHHHHHHHhhhcceeccCCCccccccccceeeecccCCeeeCCCcccchhhhhhcccCCC
Confidence 49999888876432 111 1356899992 1 45799999999999999 577899999986 5
Q ss_pred CCeEEEEcCCCcEEEcCCCc
Q 023654 91 NHSVALDYSDLSVWCFACHA 110 (279)
Q Consensus 91 ~H~l~l~l~~~~vwCy~Cd~ 110 (279)
.|+|+|++.++.+|||.||.
T Consensus 124 ~Hclvin~~n~~~WCy~Cd~ 143 (877)
T KOG1873|consen 124 PHCLVINLINWLIWCYSCDA 143 (877)
T ss_pred CeeEEEEeeeeeeEEEeccc
Confidence 89999999999999999998
No 15
>KOG2026 consensus Spindle pole body protein - Sad1p [Cytoskeleton]
Probab=96.98 E-value=0.00071 Score=65.12 Aligned_cols=92 Identities=16% Similarity=0.322 Sum_probs=73.2
Q ss_pred ecCCCCcccccccccCcCCCCCCCCCCCCCCCCCCeeeecccCceeecccccchhhhhhhccCCeEEEEcCC-CcEEEcC
Q 023654 29 RHLASCDHLVASLSSDLARIPTPDTPCNMCKHPRGNWLCLCCKEVLCSRYVNKHMLRHYREKNHSVALDYSD-LSVWCFA 107 (279)
Q Consensus 29 ~~~~~CpHl~~~l~~~~~~~~~~~~~C~~C~~~~~lwvCL~Cg~~~Cgr~~~~Ha~~H~~~t~H~l~l~l~~-~~vwCy~ 107 (279)
.....|+.+ +++......+. ....|+...+.-+.+.||.||..+=||..++||..|.-++||.+++++.+ ...++..
T Consensus 8 ~~~~~~~yl-dtv~r~vldfd-~ek~c~vslsnLnvyAclvcg~y~qgr~~kS~A~~h~l~~ghhvf~nl~telkfyvlp 85 (442)
T KOG2026|consen 8 KQEPNYAYL-ETVVRRVLDFD-FEKPCSVSLSNLNVYACLVCGKYFQGRGEKSHAYTHSLEEGHHVFLNLSTELKFYVLP 85 (442)
T ss_pred ccCcchHhh-hhhhhhhcccc-CCCCCcccccccceeeeeeeCchhhCcCccccchhccccccccceeccccceeEEecc
Confidence 344567777 55443223322 45679999888999999999999999999999999999999999999999 7777777
Q ss_pred CCcccchhhhhhccc
Q 023654 108 CHAYLNAQAILQLRP 122 (279)
Q Consensus 108 Cd~~V~~~~l~~l~~ 122 (279)
-++.+.|+.+.+++-
T Consensus 86 e~~ei~d~s~~~ikh 100 (442)
T KOG2026|consen 86 ENYEIDDPSLGDIKH 100 (442)
T ss_pred hhccccCchhhhhhc
Confidence 778899888776543
No 16
>KOG2026 consensus Spindle pole body protein - Sad1p [Cytoskeleton]
Probab=96.13 E-value=0.0055 Score=59.14 Aligned_cols=83 Identities=18% Similarity=0.289 Sum_probs=67.6
Q ss_pred ccchhhhhhhcccccCCCCCCCCCCCCCCCCCeeeecccCceecccCCChHHHHHhhhcCCeeEEeCCC-ccEEECCCCc
Q 023654 165 TSCDHLVASLSTDLARIPNPDTPCNRCQHPRGNWLCLCCKEVLCSRYVNKHMLQHYQETNHSVALGYSD-LSVWCFACHA 243 (279)
Q Consensus 165 ~~C~Hl~~~l~~~~~~~~~~~~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~~~H~l~v~l~t-~~v~CY~Cd~ 243 (279)
..|+++ +++.... .-+..+..|+.....-+...||.||...-||..+.||+.|.-+.+|.+++++.| ...|+...++
T Consensus 11 ~~~~yl-dtv~r~v-ldfd~ek~c~vslsnLnvyAclvcg~y~qgr~~kS~A~~h~l~~ghhvf~nl~telkfyvlpe~~ 88 (442)
T KOG2026|consen 11 PNYAYL-ETVVRRV-LDFDFEKPCSVSLSNLNVYACLVCGKYFQGRGEKSHAYTHSLEEGHHVFLNLSTELKFYVLPENY 88 (442)
T ss_pred cchHhh-hhhhhhh-ccccCCCCCcccccccceeeeeeeCchhhCcCccccchhccccccccceeccccceeEEecchhc
Confidence 456777 5544321 123577889999999999999999999999999999999999999999999999 8888888777
Q ss_pred eechhH
Q 023654 244 YLNAQA 249 (279)
Q Consensus 244 ~V~~~~ 249 (279)
.|+.+.
T Consensus 89 ei~d~s 94 (442)
T KOG2026|consen 89 EIDDPS 94 (442)
T ss_pred cccCch
Confidence 775543
No 17
>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=86.27 E-value=1.1 Score=38.42 Aligned_cols=57 Identities=25% Similarity=0.619 Sum_probs=34.6
Q ss_pred CCCCCC--CCCCeeeecccCceeeccc---ccchhhhhhhccCCe-EEEEc----CCCcEEEcCCCc
Q 023654 54 PCNMCK--HPRGNWLCLCCKEVLCSRY---VNKHMLRHYREKNHS-VALDY----SDLSVWCFACHA 110 (279)
Q Consensus 54 ~C~~C~--~~~~lwvCL~Cg~~~Cgr~---~~~Ha~~H~~~t~H~-l~l~l----~~~~vwCy~Cd~ 110 (279)
.|.+|+ ....+-.|++|+.-+|-.. ..+|...|...+.|- +.+.- ++..+-||.|..
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 599996 6779999999999999643 468999999988876 55543 346799999984
No 18
>KOG1867 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=82.44 E-value=0.5 Score=47.55 Aligned_cols=69 Identities=28% Similarity=0.607 Sum_probs=56.3
Q ss_pred CCCCCCCCC-CCCCeee-ecccCceeecccccchhhhhhhccCCeEEEEcCCCcEEEcCCCcccchhhhhhcc
Q 023654 51 PDTPCNMCK-HPRGNWL-CLCCKEVLCSRYVNKHMLRHYREKNHSVALDYSDLSVWCFACHAYLNAQAILQLR 121 (279)
Q Consensus 51 ~~~~C~~C~-~~~~lwv-CL~Cg~~~Cgr~~~~Ha~~H~~~t~H~l~l~l~~~~vwCy~Cd~~V~~~~l~~l~ 121 (279)
....|.+|. ......+ |+.|..++|. .+.|...|....+|-+.+++.++..+|+.|++||++.++.++.
T Consensus 42 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~g~~~~~~c~~~i~~~~~~~~~ 112 (492)
T KOG1867|consen 42 KTINCGTCGVLQIRLAVPCLICDSLGCL--SNSHKLEHSGNKKHNNTIDVNNGLLYCFACPDFIYDAELLKLA 112 (492)
T ss_pred ccceeEEechhhhhhcccceechhcccc--cccccccccccccccccceeehhhheeccCCcEeeccchhhHH
Confidence 456788883 3456666 8999999995 4678999999999999999999999999999999977655443
No 19
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=77.61 E-value=0.74 Score=33.23 Aligned_cols=23 Identities=17% Similarity=0.444 Sum_probs=21.3
Q ss_pred CCCCCCCCCCCCeeeecccCcee
Q 023654 185 DTPCNRCQHPRGNWLCLCCKEVL 207 (279)
Q Consensus 185 ~~~C~~C~~~~~lW~CL~Cg~vg 207 (279)
.++|..|....+.+.|..||+.|
T Consensus 36 I~RC~~CRk~~~~Y~CP~CGF~G 58 (59)
T PRK14890 36 IYRCEKCRKQSNPYTCPKCGFEG 58 (59)
T ss_pred EeechhHHhcCCceECCCCCCcC
Confidence 58999999999999999999986
No 20
>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=75.34 E-value=5.7 Score=33.99 Aligned_cols=57 Identities=21% Similarity=0.526 Sum_probs=32.7
Q ss_pred CCCCCCC--CCCeeeecccCceecccC---CChHHHHHhhhcCCeeEEe-----CCCccEEECCCCc
Q 023654 187 PCNRCQH--PRGNWLCLCCKEVLCSRY---VNKHMLQHYQETNHSVALG-----YSDLSVWCFACHA 243 (279)
Q Consensus 187 ~C~~C~~--~~~lW~CL~Cg~vgCgr~---~~~Ha~~H~~~~~H~l~v~-----l~t~~v~CY~Cd~ 243 (279)
.|.-|+. ..-+-.|++|++-+|-.. ...|...|...+.|--+.- |++..+-||.|..
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 5888884 478888999999999755 4589999998887764322 2345899999973
No 21
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=74.09 E-value=1 Score=32.58 Aligned_cols=24 Identities=17% Similarity=0.350 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCCCeeeecccCcee
Q 023654 184 PDTPCNRCQHPRGNWLCLCCKEVL 207 (279)
Q Consensus 184 ~~~~C~~C~~~~~lW~CL~Cg~vg 207 (279)
..++|..|....+.+.|..||+.|
T Consensus 37 ~I~Rc~~CRk~g~~Y~Cp~CGF~G 60 (61)
T COG2888 37 EIYRCAKCRKLGNPYRCPKCGFEG 60 (61)
T ss_pred eeehhhhHHHcCCceECCCcCccC
Confidence 358999999999999999999986
No 22
>KOG1867 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=73.52 E-value=1.2 Score=44.77 Aligned_cols=67 Identities=24% Similarity=0.567 Sum_probs=53.9
Q ss_pred CCCCCCCCCCCCCC-CCeee-ecccCceecccCCChHHHHHhhhcCCeeEEeCCCccEEECCCCceechhH
Q 023654 181 IPNPDTPCNRCQHP-RGNWL-CLCCKEVLCSRYVNKHMLQHYQETNHSVALGYSDLSVWCFACHAYLNAQA 249 (279)
Q Consensus 181 ~~~~~~~C~~C~~~-~~lW~-CL~Cg~vgCgr~~~~Ha~~H~~~~~H~l~v~l~t~~v~CY~Cd~~V~~~~ 249 (279)
.+...+.|..|... ...-+ |+.|+.++|.. +.|...|....+|-+.+++.++-.+|+.|++||....
T Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~g~~~~~~c~~~i~~~~ 107 (492)
T KOG1867|consen 39 LPLKTINCGTCGVLQIRLAVPCLICDSLGCLS--NSHKLEHSGNKKHNNTIDVNNGLLYCFACPDFIYDAE 107 (492)
T ss_pred cccccceeEEechhhhhhcccceechhccccc--ccccccccccccccccceeehhhheeccCCcEeeccc
Confidence 33456777777764 33334 89999999954 7899999999999999999999999999999996543
No 23
>PF14369 zf-RING_3: zinc-finger
Probab=60.00 E-value=4.6 Score=25.93 Aligned_cols=13 Identities=23% Similarity=1.091 Sum_probs=11.2
Q ss_pred cEEEcCCCcccch
Q 023654 102 SVWCFACHAYLNA 114 (279)
Q Consensus 102 ~vwCy~Cd~~V~~ 114 (279)
+.|||.|+..|.-
T Consensus 2 ~ywCh~C~~~V~~ 14 (35)
T PF14369_consen 2 RYWCHQCNRFVRI 14 (35)
T ss_pred CEeCccCCCEeEe
Confidence 5799999999874
No 24
>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=52.60 E-value=6.4 Score=24.70 Aligned_cols=20 Identities=25% Similarity=0.770 Sum_probs=12.6
Q ss_pred CCCCCCCCC----CCeeeecccCc
Q 023654 186 TPCNRCQHP----RGNWLCLCCKE 205 (279)
Q Consensus 186 ~~C~~C~~~----~~lW~CL~Cg~ 205 (279)
++|..|+.. ...|.|..||.
T Consensus 2 ~~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCcCCCcCcCCCC
Confidence 456666664 35677777764
No 25
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=52.08 E-value=5.2 Score=28.91 Aligned_cols=23 Identities=17% Similarity=0.403 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCCeeeecccCcee
Q 023654 52 DTPCNMCKHPRGNWLCLCCKEVL 74 (279)
Q Consensus 52 ~~~C~~C~~~~~lwvCL~Cg~~~ 74 (279)
.++|..|....+.|.|..||+.|
T Consensus 36 I~RC~~CRk~~~~Y~CP~CGF~G 58 (59)
T PRK14890 36 IYRCEKCRKQSNPYTCPKCGFEG 58 (59)
T ss_pred EeechhHHhcCCceECCCCCCcC
Confidence 46899999999999999999875
No 26
>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=49.09 E-value=9.8 Score=24.16 Aligned_cols=14 Identities=21% Similarity=0.707 Sum_probs=12.1
Q ss_pred eeeecccCceeccc
Q 023654 197 NWLCLCCKEVLCSR 210 (279)
Q Consensus 197 lW~CL~Cg~vgCgr 210 (279)
.|+|..||++.=|+
T Consensus 2 ~~~C~~CG~i~~g~ 15 (34)
T cd00729 2 VWVCPVCGYIHEGE 15 (34)
T ss_pred eEECCCCCCEeECC
Confidence 69999999997665
No 27
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=47.35 E-value=6.4 Score=28.52 Aligned_cols=23 Identities=17% Similarity=0.330 Sum_probs=20.4
Q ss_pred CCCCCCCCCCCCeeeecccCcee
Q 023654 52 DTPCNMCKHPRGNWLCLCCKEVL 74 (279)
Q Consensus 52 ~~~C~~C~~~~~lwvCL~Cg~~~ 74 (279)
..+|..|...++.|.|..||+.|
T Consensus 38 I~Rc~~CRk~g~~Y~Cp~CGF~G 60 (61)
T COG2888 38 IYRCAKCRKLGNPYRCPKCGFEG 60 (61)
T ss_pred eehhhhHHHcCCceECCCcCccC
Confidence 46899999999999999999875
No 28
>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=45.38 E-value=16 Score=22.76 Aligned_cols=21 Identities=19% Similarity=0.463 Sum_probs=12.8
Q ss_pred CCCCCCCCC-----CCeeeecccCce
Q 023654 186 TPCNRCQHP-----RGNWLCLCCKEV 206 (279)
Q Consensus 186 ~~C~~C~~~-----~~lW~CL~Cg~v 206 (279)
.+|..|+.. ..+++|-+||+.
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 468888875 789999999974
No 29
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=44.36 E-value=16 Score=28.52 Aligned_cols=26 Identities=23% Similarity=0.714 Sum_probs=21.1
Q ss_pred CCCCCCC------CCCCCeeeecccCceeecc
Q 023654 52 DTPCNMC------KHPRGNWLCLCCKEVLCSR 77 (279)
Q Consensus 52 ~~~C~~C------~~~~~lwvCL~Cg~~~Cgr 77 (279)
.-.|..| ....++|.|-.||..+-|-
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCeeccc
Confidence 3478999 3577999999999988764
No 30
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=39.76 E-value=22 Score=22.76 Aligned_cols=13 Identities=23% Similarity=0.583 Sum_probs=9.5
Q ss_pred CCeeeecccCcee
Q 023654 195 RGNWLCLCCKEVL 207 (279)
Q Consensus 195 ~~lW~CL~Cg~vg 207 (279)
+.-++|..||.|.
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 5678899998874
No 31
>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=36.09 E-value=21 Score=22.67 Aligned_cols=23 Identities=22% Similarity=0.587 Sum_probs=16.8
Q ss_pred CCCCCCC-CCeeeecccCceeccc
Q 023654 188 CNRCQHP-RGNWLCLCCKEVLCSR 210 (279)
Q Consensus 188 C~~C~~~-~~lW~CL~Cg~vgCgr 210 (279)
|..|... .+.++-+.||+++|.+
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~ 24 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKE 24 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHH
T ss_pred CCCCCCcccCcCEECCCCCchhHH
Confidence 3445543 5677899999999965
No 32
>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=34.93 E-value=31 Score=28.80 Aligned_cols=13 Identities=23% Similarity=0.762 Sum_probs=11.2
Q ss_pred CCeeeecccCcee
Q 023654 195 RGNWLCLCCKEVL 207 (279)
Q Consensus 195 ~~lW~CL~Cg~vg 207 (279)
...|.|..||.++
T Consensus 122 ~~f~~C~~C~kiy 134 (147)
T PF01927_consen 122 DEFWRCPGCGKIY 134 (147)
T ss_pred CeEEECCCCCCEe
Confidence 4589999999987
No 33
>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=33.55 E-value=27 Score=22.50 Aligned_cols=21 Identities=29% Similarity=0.811 Sum_probs=16.2
Q ss_pred CCCCCCC-----CCCCeeeecccCce
Q 023654 53 TPCNMCK-----HPRGNWLCLCCKEV 73 (279)
Q Consensus 53 ~~C~~C~-----~~~~lwvCL~Cg~~ 73 (279)
..|..|. ...|.+.|-+||++
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceE
Confidence 4588883 56788899888875
No 34
>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=32.67 E-value=54 Score=26.25 Aligned_cols=52 Identities=19% Similarity=0.356 Sum_probs=33.3
Q ss_pred CCCCCCCCCCCCCCeeeecccCceecccCCChHHHHHhhhcCCeeEEeCCCccEEE
Q 023654 183 NPDTPCNRCQHPRGNWLCLCCKEVLCSRYVNKHMLQHYQETNHSVALGYSDLSVWC 238 (279)
Q Consensus 183 ~~~~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~~~H~l~v~l~t~~v~C 238 (279)
+....|.+|+.....|+++.=|..-|.+ .|-.|-.-..|--.|+.-+++-|-
T Consensus 11 ~~N~~CaDCg~~~p~w~s~~~GiflC~~----Cag~HR~lg~~is~VkSi~~d~w~ 62 (116)
T PF01412_consen 11 PGNKVCADCGAPNPTWASLNYGIFLCLE----CAGIHRSLGVHISRVKSITMDNWS 62 (116)
T ss_dssp TTCTB-TTT-SBS--EEETTTTEEE-HH----HHHHHHHHTTTT--EEETTTS---
T ss_pred cCcCcCCCCCCCCCCEEEeecChhhhHH----HHHHHHHhcccchhccccccCCCC
Confidence 4568999999999999999999999965 777786654576677777777663
No 35
>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=31.30 E-value=37 Score=27.52 Aligned_cols=23 Identities=22% Similarity=0.650 Sum_probs=18.4
Q ss_pred CCCCCCCCC-----CCeeeecccCceec
Q 023654 186 TPCNRCQHP-----RGNWLCLCCKEVLC 208 (279)
Q Consensus 186 ~~C~~C~~~-----~~lW~CL~Cg~vgC 208 (279)
..|-.|... .++|+|..||+.--
T Consensus 3 p~CP~C~seytY~dg~~~iCpeC~~EW~ 30 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQLICPSCLYEWN 30 (109)
T ss_pred CcCCcCCCcceEecCCeeECcccccccc
Confidence 468888875 79999999998654
No 36
>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=30.97 E-value=38 Score=20.09 Aligned_cols=12 Identities=17% Similarity=0.285 Sum_probs=8.2
Q ss_pred CCCeeeecccCc
Q 023654 194 PRGNWLCLCCKE 205 (279)
Q Consensus 194 ~~~lW~CL~Cg~ 205 (279)
....+.|..||+
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 356777887774
No 37
>PRK10220 hypothetical protein; Provisional
Probab=30.72 E-value=40 Score=27.33 Aligned_cols=23 Identities=22% Similarity=0.706 Sum_probs=18.3
Q ss_pred CCCCCCCCC-----CCeeeecccCceec
Q 023654 186 TPCNRCQHP-----RGNWLCLCCKEVLC 208 (279)
Q Consensus 186 ~~C~~C~~~-----~~lW~CL~Cg~vgC 208 (279)
..|-.|... .++|+|..|++--=
T Consensus 4 P~CP~C~seytY~d~~~~vCpeC~hEW~ 31 (111)
T PRK10220 4 PHCPKCNSEYTYEDNGMYICPECAHEWN 31 (111)
T ss_pred CcCCCCCCcceEcCCCeEECCcccCcCC
Confidence 468888775 79999999998643
No 38
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.25 E-value=23 Score=33.02 Aligned_cols=30 Identities=27% Similarity=0.523 Sum_probs=26.0
Q ss_pred CCCCCCCCCCCCCCCCeeeecccCceeccc
Q 023654 181 IPNPDTPCNRCQHPRGNWLCLCCKEVLCSR 210 (279)
Q Consensus 181 ~~~~~~~C~~C~~~~~lW~CL~Cg~vgCgr 210 (279)
++....+|.-|....+.-.|..||+++|.-
T Consensus 211 ip~~d~kC~lC~e~~~~ps~t~CgHlFC~~ 240 (271)
T COG5574 211 IPLADYKCFLCLEEPEVPSCTPCGHLFCLS 240 (271)
T ss_pred ccccccceeeeecccCCcccccccchhhHH
Confidence 344678899999999999999999999953
No 39
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=30.13 E-value=32 Score=20.63 Aligned_cols=21 Identities=19% Similarity=0.540 Sum_probs=12.3
Q ss_pred CCCCCCCC--CCeeeecccCcee
Q 023654 187 PCNRCQHP--RGNWLCLCCKEVL 207 (279)
Q Consensus 187 ~C~~C~~~--~~lW~CL~Cg~vg 207 (279)
.|-+|+.. ...-.|..||+.+
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 35566554 4455677777654
No 40
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=29.28 E-value=22 Score=33.49 Aligned_cols=40 Identities=25% Similarity=0.523 Sum_probs=32.2
Q ss_pred CCCCCCCCCCCCCCCCCeeeecccCceecccCCChHHHHHhhhc
Q 023654 180 RIPNPDTPCNRCQHPRGNWLCLCCKEVLCSRYVNKHMLQHYQET 223 (279)
Q Consensus 180 ~~~~~~~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~~ 223 (279)
.++....+|.-|......--|.-|||++|.. ..+.+..+.
T Consensus 234 ~i~~a~~kC~LCLe~~~~pSaTpCGHiFCWs----CI~~w~~ek 273 (293)
T KOG0317|consen 234 SIPEATRKCSLCLENRSNPSATPCGHIFCWS----CILEWCSEK 273 (293)
T ss_pred cCCCCCCceEEEecCCCCCCcCcCcchHHHH----HHHHHHccc
Confidence 3556778999999999999999999999965 666665544
No 41
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=28.93 E-value=45 Score=22.34 Aligned_cols=11 Identities=18% Similarity=0.516 Sum_probs=8.6
Q ss_pred CeeeecccCce
Q 023654 196 GNWLCLCCKEV 206 (279)
Q Consensus 196 ~lW~CL~Cg~v 206 (279)
+.|+|-.||+.
T Consensus 19 ~~~vC~~Cg~~ 29 (52)
T smart00661 19 RRFVCRKCGYE 29 (52)
T ss_pred CEEECCcCCCe
Confidence 47889888865
No 42
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=28.81 E-value=47 Score=25.94 Aligned_cols=28 Identities=21% Similarity=0.571 Sum_probs=22.1
Q ss_pred CCCCCCCCCCC------CCeeeecccCceecccC
Q 023654 184 PDTPCNRCQHP------RGNWLCLCCKEVLCSRY 211 (279)
Q Consensus 184 ~~~~C~~C~~~------~~lW~CL~Cg~vgCgr~ 211 (279)
....|..|+.. ..+|.|-.||+.+-|-.
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGga 67 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGGA 67 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCeecccc
Confidence 34668888764 68999999999988754
No 43
>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=28.24 E-value=63 Score=25.84 Aligned_cols=48 Identities=19% Similarity=0.293 Sum_probs=29.2
Q ss_pred CCCCCCCCCCCCCeeeecccCceeecccccchhhhhhhccCCeEEEEcCCCc
Q 023654 51 PDTPCNMCKHPRGNWLCLCCKEVLCSRYVNKHMLRHYREKNHSVALDYSDLS 102 (279)
Q Consensus 51 ~~~~C~~C~~~~~lwvCL~Cg~~~Cgr~~~~Ha~~H~~~t~H~l~l~l~~~~ 102 (279)
.+..|.+|....-.|+++.=|.+.|.+ -+-.|-.-..|.-.|..-+++
T Consensus 12 ~N~~CaDCg~~~p~w~s~~~GiflC~~----Cag~HR~lg~~is~VkSi~~d 59 (116)
T PF01412_consen 12 GNKVCADCGAPNPTWASLNYGIFLCLE----CAGIHRSLGVHISRVKSITMD 59 (116)
T ss_dssp TCTB-TTT-SBS--EEETTTTEEE-HH----HHHHHHHHTTTT--EEETTTS
T ss_pred CcCcCCCCCCCCCCEEEeecChhhhHH----HHHHHHHhcccchhccccccC
Confidence 567999999888899999988888875 667775544455555554444
No 44
>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=27.67 E-value=26 Score=25.69 Aligned_cols=35 Identities=26% Similarity=0.453 Sum_probs=25.2
Q ss_pred CCCCCCCCCCCeeeecccCceeecccccchhhhhhhccCCeEEEEcCC
Q 023654 53 TPCNMCKHPRGNWLCLCCKEVLCSRYVNKHMLRHYREKNHSVALDYSD 100 (279)
Q Consensus 53 ~~C~~C~~~~~lwvCL~Cg~~~Cgr~~~~Ha~~H~~~t~H~l~l~l~~ 100 (279)
-+|.+|......-+|+.|+..+| |. ||-+.+-..+
T Consensus 14 y~C~tC~~~~~~~iC~~CF~~~~------H~-------gH~~~~~~~~ 48 (71)
T PF02207_consen 14 YRCLTCSLDESSGICEECFANSC------HE-------GHRVVYYRSS 48 (71)
T ss_dssp EEETTTBSSTT-BBEHHHHCTSG------GG-------GSSEEEEE--
T ss_pred EECccCCCCCCEEEchhhCCCCC------cC-------CCcEEEEEeC
Confidence 47889988888999999988877 33 7777776665
No 45
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=27.16 E-value=59 Score=20.53 Aligned_cols=23 Identities=17% Similarity=0.577 Sum_probs=15.9
Q ss_pred CCCCCCCCCC------CCeeeecccCcee
Q 023654 185 DTPCNRCQHP------RGNWLCLCCKEVL 207 (279)
Q Consensus 185 ~~~C~~C~~~------~~lW~CL~Cg~vg 207 (279)
.+.|+.|+.. .+..+|..||.+.
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 3678888765 4556788888764
No 46
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=25.90 E-value=27 Score=32.80 Aligned_cols=25 Identities=20% Similarity=0.364 Sum_probs=19.0
Q ss_pred CCCCCCCCCCCC-------CCeeeecccCcee
Q 023654 183 NPDTPCNRCQHP-------RGNWLCLCCKEVL 207 (279)
Q Consensus 183 ~~~~~C~~C~~~-------~~lW~CL~Cg~vg 207 (279)
+.+.+|..|+.. .|+|+|+.|++-.
T Consensus 26 ~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 26 GLWTKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred CceeECCCccceeeHHHHHhhhhcccccCccc
Confidence 355678888764 7899999998743
No 47
>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]
Probab=25.84 E-value=78 Score=33.69 Aligned_cols=59 Identities=17% Similarity=0.455 Sum_probs=45.1
Q ss_pred CCCCCCCCCCC--CeeeecccCceeeccc---ccchhhhhhhccCCeEEEEcC-----CCcEEEcCCCc
Q 023654 52 DTPCNMCKHPR--GNWLCLCCKEVLCSRY---VNKHMLRHYREKNHSVALDYS-----DLSVWCFACHA 110 (279)
Q Consensus 52 ~~~C~~C~~~~--~lwvCL~Cg~~~Cgr~---~~~Ha~~H~~~t~H~l~l~l~-----~~~vwCy~Cd~ 110 (279)
...|.+|+... .+--|.+|+.-+|... ..+|...|-.++.|.-+--.. +..+-||.|..
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 34699997655 7778999999999642 457999999888887655443 36789999984
No 48
>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]
Probab=25.28 E-value=95 Score=33.07 Aligned_cols=60 Identities=20% Similarity=0.501 Sum_probs=45.8
Q ss_pred CCCCCCCCCCCC--CeeeecccCceecccC---CChHHHHHhhhcCCeeEEeCCC-----ccEEECCCCc
Q 023654 184 PDTPCNRCQHPR--GNWLCLCCKEVLCSRY---VNKHMLQHYQETNHSVALGYSD-----LSVWCFACHA 243 (279)
Q Consensus 184 ~~~~C~~C~~~~--~lW~CL~Cg~vgCgr~---~~~Ha~~H~~~~~H~l~v~l~t-----~~v~CY~Cd~ 243 (279)
....|.-|+... ..--|.+||+-+|... ...|...|...+.|.-+--..+ -.+=||.|..
T Consensus 59 ~~~~c~Ycgi~~p~~v~kc~~c~Kwfcn~r~gtsgshIv~hlvra~hk~v~lh~ds~lget~lecyncg~ 128 (935)
T KOG1802|consen 59 PEHACAYCGISEPACVIKCNTCGKWFCNSRGGTSGSHIVNHLVRAKHKEVSLHKDSPLGETVLECYNCGS 128 (935)
T ss_pred chhhhhhccCCCchheeeccccCceeecCCCCCchhHHHHHHHHhhhheeEeccCCCCCcceEEeeccCc
Confidence 356799999986 7778999999999755 4589999998888765544332 3688998874
No 49
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=24.87 E-value=34 Score=33.18 Aligned_cols=23 Identities=26% Similarity=0.673 Sum_probs=17.1
Q ss_pred CCCCCCCCC--------CCCCeeeecccCce
Q 023654 51 PDTPCNMCK--------HPRGNWLCLCCKEV 73 (279)
Q Consensus 51 ~~~~C~~C~--------~~~~lwvCL~Cg~~ 73 (279)
....|.+|. ..=|+||||.|--.
T Consensus 18 eNk~CfeC~a~NPQWvSvsyGIfICLECSG~ 48 (386)
T KOG0704|consen 18 ENKKCFECGAPNPQWVSVSYGIFICLECSGK 48 (386)
T ss_pred cCCceeecCCCCCCeEeecccEEEEEecCCc
Confidence 356899994 34599999999543
No 50
>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=24.82 E-value=62 Score=21.20 Aligned_cols=11 Identities=36% Similarity=0.818 Sum_probs=4.8
Q ss_pred CeeeecccCce
Q 023654 196 GNWLCLCCKEV 206 (279)
Q Consensus 196 ~lW~CL~Cg~v 206 (279)
...+|-.||.|
T Consensus 18 g~~vC~~CG~V 28 (43)
T PF08271_consen 18 GELVCPNCGLV 28 (43)
T ss_dssp TEEEETTT-BB
T ss_pred CeEECCCCCCE
Confidence 33455555544
No 51
>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=24.05 E-value=61 Score=25.60 Aligned_cols=53 Identities=17% Similarity=0.219 Sum_probs=34.6
Q ss_pred HHHHHhhhcCCeeEEeCCCccEEECCCC-ceechhHHhhhcchhhHHHHHhhCCCC
Q 023654 215 HMLQHYQETNHSVALGYSDLSVWCFACH-AYLNAQAILQLQPVHETAYVLKFGRAL 269 (279)
Q Consensus 215 Ha~~H~~~~~H~l~v~l~t~~v~CY~Cd-~~V~~~~~~~l~~~~~~~h~~~fg~~~ 269 (279)
-...||.-.|+.+.+.+. -.+|-.|. .+++++....+......++.++-|...
T Consensus 13 ~~~~~~~~~G~~~~v~~~--~~~C~~CGe~~~~~e~~~~~~~~i~~~~~~~~~~~~ 66 (127)
T TIGR03830 13 VKDEPYTYKGESITIGVP--GWYCPACGEELLDPEESKRNSAALADFYRKVDGLLT 66 (127)
T ss_pred eecceEEEcCEEEEEeee--eeECCCCCCEEEcHHHHHHHHHHHHHHHHHccCCcC
Confidence 334456677888888333 44788898 455777777776666666666655443
No 52
>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=23.39 E-value=33 Score=26.83 Aligned_cols=22 Identities=27% Similarity=0.906 Sum_probs=0.0
Q ss_pred CCCC------CCCCCeeeecccCceeec
Q 023654 55 CNMC------KHPRGNWLCLCCKEVLCS 76 (279)
Q Consensus 55 C~~C------~~~~~lwvCL~Cg~~~Cg 76 (279)
|..| ....|+|.|-.|+..+-|
T Consensus 38 Cp~Cgk~~vkR~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 38 CPFCGKTSVKRVATGIWKCKKCGKKFAG 65 (90)
T ss_dssp ESSSSSSEEEEEETTEEEETTTTEEEE-
T ss_pred CCCCCCceeEEeeeEEeecCCCCCEEeC
No 53
>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=23.16 E-value=71 Score=22.76 Aligned_cols=23 Identities=26% Similarity=0.605 Sum_probs=16.3
Q ss_pred CCCCCCCCCCC------CCeeeecccCce
Q 023654 184 PDTPCNRCQHP------RGNWLCLCCKEV 206 (279)
Q Consensus 184 ~~~~C~~C~~~------~~lW~CL~Cg~v 206 (279)
.+..|..|+.. ...|.|..||..
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 45567777653 567888888887
No 54
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=23.10 E-value=1.1e+02 Score=22.46 Aligned_cols=40 Identities=33% Similarity=0.512 Sum_probs=28.8
Q ss_pred CCCCCCCCCCCeeeecccCceeecccccchhhhhhhccCCeEEEEcCCCcEEE
Q 023654 53 TPCNMCKHPRGNWLCLCCKEVLCSRYVNKHMLRHYREKNHSVALDYSDLSVWC 105 (279)
Q Consensus 53 ~~C~~C~~~~~lwvCL~Cg~~~Cgr~~~~Ha~~H~~~t~H~l~l~l~~~~vwC 105 (279)
-+|..|......-+|+.|+...| | .||.+.+.......+|
T Consensus 14 y~C~tC~~~~~~~iC~~Cf~~~~------H-------~gH~~~~~~~~~~~~C 53 (71)
T smart00396 14 YRCKTCGLDPTCVLCSDCFRSNC------H-------KGHDYSLKTSRGSGIC 53 (71)
T ss_pred EECcCCCCCCCEeEChHHCCCCC------C-------CCCCEEEEEecCCEEE
Confidence 57999988888889999988776 3 5777766665443333
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=23.07 E-value=1e+02 Score=24.44 Aligned_cols=49 Identities=20% Similarity=0.387 Sum_probs=34.5
Q ss_pred CCCCCCCCCCCCeeeecccCceecccCCChHHHHHhhhcCCeeEEeCCCccEE
Q 023654 185 DTPCNRCQHPRGNWLCLCCKEVLCSRYVNKHMLQHYQETNHSVALGYSDLSVW 237 (279)
Q Consensus 185 ~~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~~~H~l~v~l~t~~v~ 237 (279)
...|.+|+...-.|+++.=|.+-|.+ .+-.|-.-..|--.|+.-+++-|
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 46799999999999999999999976 55555443345444555555544
No 56
>COG1773 Rubredoxin [Energy production and conversion]
Probab=22.92 E-value=34 Score=24.37 Aligned_cols=11 Identities=27% Similarity=0.972 Sum_probs=7.7
Q ss_pred CCeeeecccCc
Q 023654 195 RGNWLCLCCKE 205 (279)
Q Consensus 195 ~~lW~CL~Cg~ 205 (279)
.+.|.|..||.
T Consensus 34 Pd~w~CP~Cg~ 44 (55)
T COG1773 34 PDDWVCPECGV 44 (55)
T ss_pred CCccCCCCCCC
Confidence 56777777774
No 57
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=21.72 E-value=49 Score=21.56 Aligned_cols=23 Identities=26% Similarity=0.933 Sum_probs=16.9
Q ss_pred CCCCCCCCC--eeeecccCceeccc
Q 023654 188 CNRCQHPRG--NWLCLCCKEVLCSR 210 (279)
Q Consensus 188 C~~C~~~~~--lW~CL~Cg~vgCgr 210 (279)
|..|..... ...|-.|+.++|++
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCcccccCeECCccCCccccc
Confidence 555666544 36799999999986
No 58
>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=21.59 E-value=55 Score=23.76 Aligned_cols=20 Identities=40% Similarity=1.024 Sum_probs=13.6
Q ss_pred CCCCCCCCC-------CCeeeecccCc
Q 023654 186 TPCNRCQHP-------RGNWLCLCCKE 205 (279)
Q Consensus 186 ~~C~~C~~~-------~~lW~CL~Cg~ 205 (279)
.-|..||.. ..-|+||.|..
T Consensus 31 ~VCnlCGFNP~Phl~E~~eWLCLnCQ~ 57 (61)
T PF05715_consen 31 QVCNLCGFNPTPHLTEVKEWLCLNCQM 57 (61)
T ss_pred hhhcccCCCCCccccccceeeeecchh
Confidence 345566654 57899999864
No 59
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=20.77 E-value=42 Score=31.70 Aligned_cols=39 Identities=26% Similarity=0.551 Sum_probs=30.4
Q ss_pred CCCCCCCCCCCCCCCCCeeeecccCceeecccccchhhhhhhc
Q 023654 47 RIPTPDTPCNMCKHPRGNWLCLCCKEVLCSRYVNKHMLRHYRE 89 (279)
Q Consensus 47 ~~~~~~~~C~~C~~~~~lwvCL~Cg~~~Cgr~~~~Ha~~H~~~ 89 (279)
.++...-+|.-|......-.|.-||+++|+. -...+..+
T Consensus 234 ~i~~a~~kC~LCLe~~~~pSaTpCGHiFCWs----CI~~w~~e 272 (293)
T KOG0317|consen 234 SIPEATRKCSLCLENRSNPSATPCGHIFCWS----CILEWCSE 272 (293)
T ss_pred cCCCCCCceEEEecCCCCCCcCcCcchHHHH----HHHHHHcc
Confidence 3444567999999999889999999999985 55666443
No 60
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=20.72 E-value=44 Score=29.02 Aligned_cols=22 Identities=18% Similarity=0.368 Sum_probs=15.0
Q ss_pred CCCCCCCCCCC---CCeeeecccCc
Q 023654 184 PDTPCNRCQHP---RGNWLCLCCKE 205 (279)
Q Consensus 184 ~~~~C~~C~~~---~~lW~CL~Cg~ 205 (279)
..|.|.+||.+ ...+.|..||.
T Consensus 133 ~~~vC~vCGy~~~ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGYTHEGEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCCcccCCCCCcCCCCCC
Confidence 35777777765 66777777774
No 61
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=20.46 E-value=59 Score=23.96 Aligned_cols=28 Identities=25% Similarity=0.628 Sum_probs=13.5
Q ss_pred CCCCCCCCCCCCeeeecc-cCceecccCC
Q 023654 185 DTPCNRCQHPRGNWLCLC-CKEVLCSRYV 212 (279)
Q Consensus 185 ~~~C~~C~~~~~lW~CL~-Cg~vgCgr~~ 212 (279)
..+|+.|...-+.=+||. |.|++|+--.
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci 35 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSCI 35 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTTG
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHHh
Confidence 378999999988888975 9999997643
Done!