Query 002886
Match_columns 870
No_of_seqs 222 out of 482
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 12:46:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002886.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002886hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2169 Zn-finger transcriptio 100.0 1.9E-33 4.1E-38 324.2 22.6 188 201-390 183-397 (636)
2 PF02891 zf-MIZ: MIZ/SP-RING z 99.8 1E-20 2.2E-25 154.4 1.7 50 298-347 1-50 (50)
3 PF14324 PINIT: PINIT domain; 99.5 1.2E-13 2.5E-18 134.1 9.0 129 136-264 3-144 (144)
4 PF11789 zf-Nse: Zinc-finger o 98.5 4.2E-08 9.2E-13 82.7 2.3 55 289-345 1-57 (57)
5 smart00504 Ubox Modified RING 97.3 0.00036 7.9E-09 57.8 4.8 61 300-365 2-62 (63)
6 KOG2979 Protein involved in DN 97.0 0.00033 7.2E-09 74.8 2.1 75 289-365 166-244 (262)
7 PF04564 U-box: U-box domain; 96.5 0.0033 7.2E-08 55.0 4.4 63 299-365 4-66 (73)
8 COG5627 MMS21 DNA repair prote 95.3 0.01 2.2E-07 63.2 2.3 73 288-362 178-252 (275)
9 COG5222 Uncharacterized conser 93.0 0.11 2.4E-06 57.2 4.5 82 275-359 249-332 (427)
10 PLN03208 E3 ubiquitin-protein 92.6 0.12 2.7E-06 53.8 4.1 66 288-354 7-84 (193)
11 KOG2164 Predicted E3 ubiquitin 87.5 0.4 8.6E-06 56.1 2.9 56 299-355 186-242 (513)
12 PF14835 zf-RING_6: zf-RING of 86.0 0.94 2E-05 40.2 3.7 59 299-363 7-65 (65)
13 TIGR00599 rad18 DNA repair pro 82.4 1.7 3.7E-05 49.9 4.9 65 296-366 23-88 (397)
14 PF02837 Glyco_hydro_2_N: Glyc 81.4 3.3 7.2E-05 40.2 5.9 69 163-249 67-136 (167)
15 cd00162 RING RING-finger (Real 73.8 2.9 6.2E-05 31.2 2.4 42 302-347 2-44 (45)
16 PF14447 Prok-RING_4: Prokaryo 71.3 2.2 4.8E-05 36.8 1.3 37 306-353 18-54 (55)
17 PF04641 Rtf2: Rtf2 RING-finge 70.5 2.7 5.8E-05 45.2 2.1 55 296-355 110-167 (260)
18 KOG0311 Predicted E3 ubiquitin 68.1 0.64 1.4E-05 52.5 -3.2 77 295-374 39-116 (381)
19 TIGR00570 cdk7 CDK-activating 53.5 9.7 0.00021 42.7 2.6 40 312-359 25-68 (309)
20 PRK10340 ebgA cryptic beta-D-g 51.2 33 0.00071 44.0 7.0 66 164-249 109-176 (1021)
21 PHA02672 ORF110 EEV glycoprote 49.4 7.9 0.00017 39.6 1.1 25 88-112 21-60 (166)
22 KOG2177 Predicted E3 ubiquitin 49.3 7.6 0.00017 38.8 0.9 60 299-365 13-72 (386)
23 PF13923 zf-C3HC4_2: Zinc fing 47.6 11 0.00023 29.2 1.3 39 302-344 1-39 (39)
24 PRK09525 lacZ beta-D-galactosi 45.4 43 0.00094 43.1 6.8 67 164-249 120-188 (1027)
25 PF08531 Bac_rhamnosid_N: Alph 45.0 14 0.00031 37.3 2.1 40 207-249 15-62 (172)
26 COG5243 HRD1 HRD ubiquitin lig 44.3 11 0.00024 43.3 1.4 26 316-348 319-344 (491)
27 KOG0978 E3 ubiquitin ligase in 41.5 9 0.00019 47.0 0.1 54 296-354 640-694 (698)
28 PF13445 zf-RING_UBOX: RING-ty 41.4 15 0.00032 30.0 1.3 39 302-342 1-43 (43)
29 KOG0320 Predicted E3 ubiquitin 41.0 18 0.00038 38.1 2.1 46 300-353 132-182 (187)
30 COG5533 UBP5 Ubiquitin C-termi 39.7 12 0.00025 42.5 0.6 37 312-348 258-294 (415)
31 PF13894 zf-C2H2_4: C2H2-type 39.2 12 0.00025 24.9 0.4 11 339-349 1-11 (24)
32 PF04423 Rad50_zn_hook: Rad50 38.3 18 0.00039 30.1 1.4 26 326-352 9-34 (54)
33 PF02228 Gag_p19: Major core p 36.9 20 0.00044 33.4 1.5 20 325-344 45-64 (92)
34 PRK10150 beta-D-glucuronidase; 36.4 81 0.0018 37.8 6.9 66 166-249 67-133 (604)
35 PF04810 zf-Sec23_Sec24: Sec23 36.1 4.8 0.00011 32.0 -2.2 17 332-348 18-34 (40)
36 smart00748 HEPN Higher Eukaryt 36.1 1.7E+02 0.0036 27.2 7.5 76 47-122 27-113 (113)
37 PF04780 DUF629: Protein of un 35.8 12 0.00026 44.1 -0.1 58 325-386 44-115 (466)
38 KOG0801 Predicted E3 ubiquitin 35.7 19 0.0004 37.5 1.3 54 337-392 137-191 (205)
39 PF00097 zf-C3HC4: Zinc finger 35.5 21 0.00045 27.4 1.2 41 302-344 1-41 (41)
40 PF11793 FANCL_C: FANCL C-term 33.4 28 0.00061 30.8 1.9 32 319-351 32-68 (70)
41 cd00350 rubredoxin_like Rubred 33.0 21 0.00046 27.3 0.9 12 336-347 15-26 (33)
42 PF13920 zf-C3HC4_3: Zinc fing 32.2 30 0.00066 28.0 1.7 44 301-349 4-48 (50)
43 KOG0307 Vesicle coat complex C 29.3 7.9E+02 0.017 32.4 13.7 26 721-746 830-855 (1049)
44 KOG2008 BTK-associated SH3-dom 29.1 42 0.00092 38.1 2.7 47 415-461 259-305 (426)
45 PF15227 zf-C3HC4_4: zinc fing 27.1 27 0.00059 28.0 0.6 42 302-344 1-42 (42)
46 COG4068 Uncharacterized protei 26.4 48 0.001 29.4 2.0 29 337-365 7-35 (64)
47 cd00730 rubredoxin Rubredoxin; 25.7 32 0.00069 29.1 0.8 11 337-347 33-43 (50)
48 PHA02929 N1R/p28-like protein; 24.6 74 0.0016 34.7 3.5 46 299-349 174-227 (238)
49 KOG0287 Postreplication repair 24.2 30 0.00066 39.6 0.6 64 298-367 22-86 (442)
50 smart00734 ZnF_Rad18 Rad18-lik 24.1 26 0.00056 25.8 0.0 10 339-348 2-11 (26)
51 smart00184 RING Ring finger. E 23.7 53 0.0012 23.3 1.6 25 316-344 14-39 (39)
52 PF00096 zf-C2H2: Zinc finger, 23.7 26 0.00056 23.8 -0.1 11 339-349 1-11 (23)
53 PF00301 Rubredoxin: Rubredoxi 22.5 42 0.00091 28.1 0.9 12 336-347 32-43 (47)
54 PLN00162 transport protein sec 22.2 24 0.00051 43.9 -0.8 35 311-349 52-86 (761)
55 COG5574 PEX10 RING-finger-cont 21.9 49 0.0011 36.7 1.6 55 299-356 215-269 (271)
56 PF14683 CBM-like: Polysacchar 21.3 2.7E+02 0.0058 28.6 6.6 75 166-250 63-150 (167)
57 PF12861 zf-Apc11: Anaphase-pr 20.5 72 0.0016 30.0 2.1 30 318-351 52-84 (85)
No 1
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=100.00 E-value=1.9e-33 Score=324.25 Aligned_cols=188 Identities=28% Similarity=0.554 Sum_probs=157.3
Q ss_pred eeeCCCcEEEEEcCceecccc--------ccCCCCCCCCcccccc--cccccc-cEEEE--EeeeCceEEEEEEEEEeec
Q 002886 201 CVISPQHVNFILNGKGIERRT--------NVFMDPGPQLPTNVSP--MLKYGT-NLLQA--VGQFNGHYIIIVAVMSTAS 267 (870)
Q Consensus 201 ci~wP~~I~IkVNGk~Ie~rr--------nvk~kpG~d~PIDIT~--~LK~G~-N~IqI--v~~fn~~YiiaV~lV~v~s 267 (870)
...||..+.++||++.++..+ +++ .+++.+|.|||. +++.-. |.+.+ ..++++.|.+.+++++...
T Consensus 183 e~~~p~~~~~~vn~~~~~l~~~~~~~n~~~~~-~~~~~~P~n~t~~~~~~~~~~~~~~~~~~~~~~~~ysl~~~~v~~~t 261 (636)
T KOG2169|consen 183 EDHFPPNVQVKVNNSPCQLPFGYMPNNKHGLE-PKRPSRPGNITSLSRLSVTTPNQITVLWTAQGGKSYSLSVYFVEGLT 261 (636)
T ss_pred ccccCceeEEEecCCcceeeccccCCCCcccc-cCCCCCCCcCcccccccccccccceEEEEeccCcccceEEEEecccC
Confidence 346999999999988766441 122 368999999999 554433 45443 4478889999999987654
Q ss_pred ccc-----------hh--hH-HHhhhcccCCCCCCCCeeeccceecccCCCcccccccCCCCCCcCcccccchHHHHHHH
Q 002886 268 SLE-----------SS--KL-QDYVQSGITMQDSDSDLIEGPSRISLNCPISYKRINTPVKGHSCRHHQCFDFSNYVHIN 333 (870)
Q Consensus 268 ~~e-----------~~--~L-qd~Iq~~lss~D~DDDIv~~s~~VSL~CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n 333 (870)
... .. .. .++|++++ ..++|.||+++.++|||+|||+++||++|+|+..|+|+||||+.+||++|
T Consensus 262 ~~~llq~~~~~~~~~~~~~~s~~~~~~~l-~~~~d~~i~tt~~~vSL~CPl~~~Rm~~P~r~~~CkHlQcFD~~~~lq~n 340 (636)
T KOG2169|consen 262 SKDLLQRLKQNGKINRNLSQSDALIKKKL-TAGPDSEIATTSLRVSLNCPLSKMRMSLPARGHTCKHLQCFDALSYLQMN 340 (636)
T ss_pred HHHHHHHHhccCCccCchhHhHHHhhccc-ccCCcccceeccceeEecCCcccceeecCCcccccccceecchhhhHHhc
Confidence 221 11 11 34566666 77888899999999999999999999999999999999999999999999
Q ss_pred cCCCcccccCCCCccCcCCeeecHHHHHHHHHhCCCccEEEEccCCceEeeccCCcc
Q 002886 334 SRRPSWRCPHCNQHVCYTDIRVDQNMVKVLREVGENVADVIISADGSWKAIMEADDN 390 (870)
Q Consensus 334 ~qkptW~CPIC~k~~~~~dL~ID~y~~eILk~~~enveeV~V~~DGsW~pv~E~ddd 390 (870)
+++|+|+||+|++.+.|++|+||+||.+||..+..++++|++..||+|+++.+++++
T Consensus 341 ~~~pTW~CPVC~~~~~~e~l~iD~~~~~iL~~~~~~~~ev~~~~dGsw~pi~~~~~~ 397 (636)
T KOG2169|consen 341 EQKPTWRCPVCQKAAPFEGLIIDGYFLNILQSCQANVEEVEVSEDGSWKPIPEEAEA 397 (636)
T ss_pred cCCCeeeCccCCccccccchhhhHHHHHHHhhccCCCcceEecCCCceecCcccccc
Confidence 999999999999999999999999999999999999999999999999999998863
No 2
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=99.80 E-value=1e-20 Score=154.38 Aligned_cols=50 Identities=48% Similarity=1.258 Sum_probs=36.5
Q ss_pred ecccCCCcccccccCCCCCCcCcccccchHHHHHHHcCCCcccccCCCCc
Q 002886 298 ISLNCPISYKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHCNQH 347 (870)
Q Consensus 298 VSL~CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC~k~ 347 (870)
|||+||||++||++|+||+.|+|+|||||++||+++.+++.|+||+|+++
T Consensus 1 vsL~CPls~~~i~~P~Rg~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 1 VSLRCPLSFQRIRIPVRGKNCKHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp EESB-TTTSSB-SSEEEETT--SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred CeeeCCCCCCEEEeCccCCcCcccceECHHHHHHHhhccCCeECcCCcCc
Confidence 79999999999999999999999999999999999999999999999974
No 3
>PF14324 PINIT: PINIT domain; PDB: 3I2D_A.
Probab=99.47 E-value=1.2e-13 Score=134.11 Aligned_cols=129 Identities=19% Similarity=0.310 Sum_probs=77.7
Q ss_pred cccceeecccccccchhceeeccee-ecCCCceeeEEEEeecccc----c-CCCceEEEEEEecCCCCCc--ceeeCCCc
Q 002886 136 VSTVSTIMTRFYPLLKMGQILASLE-VEPGYGAFMIDFHISKNMI----Q-STEEKIRLFVAQTDKTETS--ACVISPQH 207 (870)
Q Consensus 136 ~~~vs~imsrFYP~~kl~~Il~slE-v~pG~g~~~idF~IsKs~~----~-~sq~kLrLfc~q~d~~~~s--~ci~wP~~ 207 (870)
++.+.+.-+|||..+++.+-..-+. ...+++.+.+.|+++.++. . ...++++|||+..+..+.+ ..+.||..
T Consensus 3 ~~~~~Fk~sPFY~~~~~i~~~~~~~~~~~~r~~~~~~F~L~~~~~~~l~~~~~~~~v~L~c~~~~~~~~~~~q~i~FP~~ 82 (144)
T PF14324_consen 3 HPDLRFKPSPFYKVLRLIHPTPLLPASSSGRQTCSFSFKLSPDQVELLKSSNPSYQVYLFCGKFCLSESSGNQPIEFPPP 82 (144)
T ss_dssp -----B--BTTEEEEEEEEEEEEEE--EEEEEEEEEEE---HHHHHHHHSTT--EEEEEEEEESS-SS-GGGB-----SS
T ss_pred CCccEeccCCCcceeEEcCCccccccccCCCCeEEEEEEECHHHHHHHhcCCCCeEEEEEEeccccCCCCCccccccCCC
Confidence 3556677899999997655543222 2347889999999998752 2 4688999999976655543 56889999
Q ss_pred EEEEEcCceeccc-cccCCCCCCCCccccccccccc---ccEEEEEeee-CceEEEEEEEEE
Q 002886 208 VNFILNGKGIERR-TNVFMDPGPQLPTNVSPMLKYG---TNLLQAVGQF-NGHYIIIVAVMS 264 (870)
Q Consensus 208 I~IkVNGk~Ie~r-rnvk~kpG~d~PIDIT~~LK~G---~N~IqIv~~f-n~~YiiaV~lV~ 264 (870)
++|+|||+.++.. +++++|+|+.+|+|||++|+.. .|.|++.|.+ ++.|+++|++|+
T Consensus 83 ~evkvN~~~v~~~~~glknKpGt~rPvdIT~~l~~~~~~~N~i~v~y~~~~~~Y~~~vylVk 144 (144)
T PF14324_consen 83 CEVKVNGKQVKLNNRGLKNKPGTARPVDITPYLRLSPPQTNRIEVTYANTKKKYYVYVYLVK 144 (144)
T ss_dssp EEEEETTEE--S--SS-TTS-GGGS-EE-GGG---S-SS-EEEEEEEEEESS-EEEEEEEEE
T ss_pred eEEEEeCEEcccCccCCCCCCCCCCCcccchhhcccCCCCeEEEEEEeCCCCeEEEEEEEEC
Confidence 9999999999864 6788899999999999999876 6999999865 468999999984
No 4
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=98.52 E-value=4.2e-08 Score=82.73 Aligned_cols=55 Identities=36% Similarity=0.728 Sum_probs=38.6
Q ss_pred CCeeeccceecccCCCcccccccCCCCCCcCcccccchHHHHHHHcCCCcccccC--CC
Q 002886 289 SDLIEGPSRISLNCPISYKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPH--CN 345 (870)
Q Consensus 289 DDIv~~s~~VSL~CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPI--C~ 345 (870)
|||+.+...++++||||++.|+-|+++..|.| .||.++++++-.+...-+||+ |+
T Consensus 1 ddi~i~~~~~~~~CPiT~~~~~~PV~s~~C~H--~fek~aI~~~i~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 1 DDIVIEGGTISLKCPITLQPFEDPVKSKKCGH--TFEKEAILQYIQRNGSKRCPVAGCN 57 (57)
T ss_dssp S-----SSB--SB-TTTSSB-SSEEEESSS----EEEHHHHHHHCTTTS-EE-SCCC-S
T ss_pred CceEEeccEeccCCCCcCChhhCCcCcCCCCC--eecHHHHHHHHHhcCCCCCCCCCCC
Confidence 67888889999999999999999999999999 899999999998889999999 64
No 5
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=97.30 E-value=0.00036 Score=57.81 Aligned_cols=61 Identities=16% Similarity=0.208 Sum_probs=52.1
Q ss_pred ccCCCcccccccCCCCCCcCcccccchHHHHHHHcCCCcccccCCCCccCcCCeeecHHHHHHHHH
Q 002886 300 LNCPISYKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHCNQHVCYTDIRVDQNMVKVLRE 365 (870)
Q Consensus 300 L~CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC~k~~~~~dL~ID~y~~eILk~ 365 (870)
|.|||++..|+.|+.. .|.| .||.+.+...-.+ ...||+|++.+..++|+-+..+.+.+++
T Consensus 2 ~~Cpi~~~~~~~Pv~~-~~G~--v~~~~~i~~~~~~--~~~cP~~~~~~~~~~l~~~~~l~~~i~~ 62 (63)
T smart00504 2 FLCPISLEVMKDPVIL-PSGQ--TYERRAIEKWLLS--HGTDPVTGQPLTHEDLIPNLALKSAIQE 62 (63)
T ss_pred cCCcCCCCcCCCCEEC-CCCC--EEeHHHHHHHHHH--CCCCCCCcCCCChhhceeCHHHHHHHHh
Confidence 7899999999999986 5667 7999888887655 4589999999999999999888877653
No 6
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=96.99 E-value=0.00033 Score=74.78 Aligned_cols=75 Identities=25% Similarity=0.437 Sum_probs=58.9
Q ss_pred CCeeeccceecccCCCcccccccCCCCCCcCcccccchHHHHHHHcCCCcccccC--CCCcc--CcCCeeecHHHHHHHH
Q 002886 289 SDLIEGPSRISLNCPISYKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPH--CNQHV--CYTDIRVDQNMVKVLR 364 (870)
Q Consensus 289 DDIv~~s~~VSL~CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPI--C~k~~--~~~dL~ID~y~~eILk 364 (870)
+++......+|++||+|+..|..|++++.|.| -||-++.+++-....+-+||+ |.... ....|.-|.-++.-|+
T Consensus 166 ~e~~i~~e~fs~rdPis~~~I~nPviSkkC~H--vydrDsI~~~l~~~~~i~CPv~gC~~~~~~~~~~l~~d~el~~kIr 243 (262)
T KOG2979|consen 166 DEELIGQEVFSNRDPISKKPIVNPVISKKCGH--VYDRDSIMQILCDEITIRCPVLGCENPYYIQPGHLDEDKELQQKIR 243 (262)
T ss_pred HHHHhhhhhhcccCchhhhhhhchhhhcCcCc--chhhhhHHHHhccCceeecccccCCccccccccccCchHHHHHHHH
Confidence 45777889999999999999999999999999 699999999988888999998 77334 3444455533333344
Q ss_pred H
Q 002886 365 E 365 (870)
Q Consensus 365 ~ 365 (870)
+
T Consensus 244 ~ 244 (262)
T KOG2979|consen 244 Q 244 (262)
T ss_pred H
Confidence 3
No 7
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.51 E-value=0.0033 Score=55.01 Aligned_cols=63 Identities=19% Similarity=0.259 Sum_probs=49.5
Q ss_pred cccCCCcccccccCCCCCCcCcccccchHHHHHHHcCCCcccccCCCCccCcCCeeecHHHHHHHHH
Q 002886 299 SLNCPISYKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHCNQHVCYTDIRVDQNMVKVLRE 365 (870)
Q Consensus 299 SL~CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC~k~~~~~dL~ID~y~~eILk~ 365 (870)
.|.||||+..|+-||..-.| | .||-..+.....+ ..-.||+|++++...+|+-+.-++..+++
T Consensus 4 ~f~CpIt~~lM~dPVi~~~G-~--tyer~~I~~~l~~-~~~~~P~t~~~l~~~~l~pn~~Lk~~I~~ 66 (73)
T PF04564_consen 4 EFLCPITGELMRDPVILPSG-H--TYERSAIERWLEQ-NGGTDPFTRQPLSESDLIPNRALKSAIEE 66 (73)
T ss_dssp GGB-TTTSSB-SSEEEETTS-E--EEEHHHHHHHHCT-TSSB-TTT-SB-SGGGSEE-HHHHHHHHH
T ss_pred ccCCcCcCcHhhCceeCCcC-C--EEcHHHHHHHHHc-CCCCCCCCCCcCCcccceECHHHHHHHHH
Confidence 48999999999999999877 5 7999998887766 56689999999999999999998887765
No 8
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=95.26 E-value=0.01 Score=63.22 Aligned_cols=73 Identities=18% Similarity=0.251 Sum_probs=61.8
Q ss_pred CCCeeeccceecccCCCcccccccCCCCCCcCcccccchHHHHHHHcCCCccccc--CCCCccCcCCeeecHHHHHH
Q 002886 288 DSDLIEGPSRISLNCPISYKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCP--HCNQHVCYTDIRVDQNMVKV 362 (870)
Q Consensus 288 DDDIv~~s~~VSL~CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CP--IC~k~~~~~dL~ID~y~~eI 362 (870)
-|||+.....++++|||+...+.+|.-+..|.| -||.+..+..-.--++--|| +|.+.....+++-|..+.+-
T Consensus 178 ~d~i~I~~~~~~nrCpitl~p~~~pils~kcnh--~~e~D~I~~~lq~~~trvcp~~~Csq~~~~~~~v~d~IlE~R 252 (275)
T COG5627 178 VDKILIHQELLSNRCPITLNPDFYPILSSKCNH--KPEMDLINKKLQVECTRVCPRLICSQKEVVDPYVCDHILEKR 252 (275)
T ss_pred hhhhhhhhhhhcccCCcccCcchhHHHHhhhcc--cccHHHHHHHhcCCceeecchhhcchheeccchhhhHHHHHH
Confidence 367888889999999999999999999999999 59998888777777888999 59988877777777666543
No 9
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.04 E-value=0.11 Score=57.23 Aligned_cols=82 Identities=22% Similarity=0.511 Sum_probs=52.0
Q ss_pred HHhhhcccCCCCCCCCeeec-cceecccCCCcccccccCCCCCCcCcccccchHHHHHHHcCCCcccccCCCC-ccCcCC
Q 002886 275 QDYVQSGITMQDSDSDLIEG-PSRISLNCPISYKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHCNQ-HVCYTD 352 (870)
Q Consensus 275 qd~Iq~~lss~D~DDDIv~~-s~~VSL~CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC~k-~~~~~d 352 (870)
++|-+++.+....-|+|... .-.|||+||+....++.|+|..-|.|+=|=+ -|....--..+.||.|.. ++-++.
T Consensus 249 e~Yq~r~~a~~~~~Dqv~k~~~~~i~LkCplc~~Llrnp~kT~cC~~~fc~e---ci~~al~dsDf~CpnC~rkdvlld~ 325 (427)
T COG5222 249 EKYQQRTKAVAEIPDQVYKMQPPNISLKCPLCHCLLRNPMKTPCCGHTFCDE---CIGTALLDSDFKCPNCSRKDVLLDG 325 (427)
T ss_pred HHHHHHHHhhhhCchhhhccCCCCccccCcchhhhhhCcccCccccchHHHH---HHhhhhhhccccCCCcccccchhhc
Confidence 45555443222222335433 3578999999999999999999999975532 233333346789999985 444555
Q ss_pred eeecHHH
Q 002886 353 IRVDQNM 359 (870)
Q Consensus 353 L~ID~y~ 359 (870)
|.-|.-.
T Consensus 326 l~pD~dk 332 (427)
T COG5222 326 LTPDIDK 332 (427)
T ss_pred cCccHHH
Confidence 5554433
No 10
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=92.64 E-value=0.12 Score=53.81 Aligned_cols=66 Identities=21% Similarity=0.458 Sum_probs=45.8
Q ss_pred CCCeeeccceecccCCCcccccccCCCCCCcCcccccchH-HHHHHH-----------cCCCcccccCCCCccCcCCee
Q 002886 288 DSDLIEGPSRISLNCPISYKRINTPVKGHSCRHHQCFDFS-NYVHIN-----------SRRPSWRCPHCNQHVCYTDIR 354 (870)
Q Consensus 288 DDDIv~~s~~VSL~CPIS~~RIkiPvRG~~CkHLQCFDL~-sFL~~n-----------~qkptW~CPIC~k~~~~~dL~ 354 (870)
+||.......=.+.|||-+..++.|+-. .|.|+=|.+-- .|+... ..+...+||+|...+...+|+
T Consensus 7 ~~~~~~~~~~~~~~CpICld~~~dPVvT-~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~Lv 84 (193)
T PLN03208 7 EDDTTLVDSGGDFDCNICLDQVRDPVVT-LCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLV 84 (193)
T ss_pred cccceeccCCCccCCccCCCcCCCcEEc-CCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEE
Confidence 3343333333468999999999999884 69999777744 466532 134568999999998765553
No 11
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.46 E-value=0.4 Score=56.07 Aligned_cols=56 Identities=23% Similarity=0.577 Sum_probs=46.4
Q ss_pred cccCCCcccccccCCCCCCcCcccccc-hHHHHHHHcCCCcccccCCCCccCcCCeee
Q 002886 299 SLNCPISYKRINTPVKGHSCRHHQCFD-FSNYVHINSRRPSWRCPHCNQHVCYTDIRV 355 (870)
Q Consensus 299 SL~CPIS~~RIkiPvRG~~CkHLQCFD-L~sFL~~n~qkptW~CPIC~k~~~~~dL~I 355 (870)
...|||-+---..|+|.. |.|+=||- +..|+.+-..+.--.||+|...+.+.||.-
T Consensus 186 ~~~CPICL~~~~~p~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~p 242 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLP 242 (513)
T ss_pred CCcCCcccCCCCcccccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccccceee
Confidence 899999999999999999 99999985 556777664444445999999999988854
No 12
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=85.99 E-value=0.94 Score=40.20 Aligned_cols=59 Identities=22% Similarity=0.500 Sum_probs=26.9
Q ss_pred cccCCCcccccccCCCCCCcCcccccchHHHHHHHcCCCcccccCCCCccCcCCeeecHHHHHHH
Q 002886 299 SLNCPISYKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHCNQHVCYTDIRVDQNMVKVL 363 (870)
Q Consensus 299 SL~CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC~k~~~~~dL~ID~y~~eIL 363 (870)
.|+|++-+..|+.|+--..|.|.=|=.-- ..... -.||+|+.++-..|++|..-+..++
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci-----~~~~~-~~CPvC~~Paw~qD~~~NrqLd~~i 65 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSCI-----RDCIG-SECPVCHTPAWIQDIQINRQLDSMI 65 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTTG-----GGGTT-TB-SSS--B-S-SS----HHHHHHH
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHHh-----HHhcC-CCCCCcCChHHHHHHHhhhhhhccC
Confidence 58999999999999999999996443111 11112 3599999999999999988877653
No 13
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=82.36 E-value=1.7 Score=49.93 Aligned_cols=65 Identities=22% Similarity=0.380 Sum_probs=50.5
Q ss_pred ceecccCCCcccccccCCCCCCcCcccccchHH-HHHHHcCCCcccccCCCCccCcCCeeecHHHHHHHHHh
Q 002886 296 SRISLNCPISYKRINTPVKGHSCRHHQCFDFSN-YVHINSRRPSWRCPHCNQHVCYTDIRVDQNMVKVLREV 366 (870)
Q Consensus 296 ~~VSL~CPIS~~RIkiPvRG~~CkHLQCFDL~s-FL~~n~qkptW~CPIC~k~~~~~dL~ID~y~~eILk~~ 366 (870)
+.-.|.|||-+..++.|+- ..|.|.=|.+--. |+.. ...||+|...+....|+.+..+.+|++..
T Consensus 23 Le~~l~C~IC~d~~~~Pvi-tpCgH~FCs~CI~~~l~~-----~~~CP~Cr~~~~~~~Lr~N~~L~~iVe~~ 88 (397)
T TIGR00599 23 LDTSLRCHICKDFFDVPVL-TSCSHTFCSLCIRRCLSN-----QPKCPLCRAEDQESKLRSNWLVSEIVESF 88 (397)
T ss_pred cccccCCCcCchhhhCccC-CCCCCchhHHHHHHHHhC-----CCCCCCCCCccccccCccchHHHHHHHHH
Confidence 4457899999999999985 6899987765433 3321 23899999999988999888888887754
No 14
>PF02837 Glyco_hydro_2_N: Glycosyl hydrolases family 2, sugar binding domain; InterPro: IPR006104 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities; beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. This domain has a jelly-roll fold [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3DEC_A 3OB8_A 3OBA_A 3CMG_A 3FN9_C 2VZU_A 2X09_A 2VZO_A 2X05_A 2VZV_B ....
Probab=81.44 E-value=3.3 Score=40.23 Aligned_cols=69 Identities=19% Similarity=0.269 Sum_probs=45.0
Q ss_pred CCCceeeEEEEeecccccCCCceEEEEEEecCCCCCcceeeCCCcEEEEEcCceeccccccCCCCCCCCccccccccccc
Q 002886 163 PGYGAFMIDFHISKNMIQSTEEKIRLFVAQTDKTETSACVISPQHVNFILNGKGIERRTNVFMDPGPQLPTNVSPMLKYG 242 (870)
Q Consensus 163 pG~g~~~idF~IsKs~~~~sq~kLrLfc~q~d~~~~s~ci~wP~~I~IkVNGk~Ie~rrnvk~kpG~d~PIDIT~~LK~G 242 (870)
-|...+.-.|.|...+ ..+++.|.....+. ...|.|||+.|-...+. -...=+|||++|+.|
T Consensus 67 ~~~~wYr~~f~lp~~~---~~~~~~L~f~gv~~-----------~a~v~vNG~~vg~~~~~----~~~~~~dIt~~l~~g 128 (167)
T PF02837_consen 67 SGYAWYRRTFTLPADW---KGKRVFLRFEGVDY-----------AAEVYVNGKLVGSHEGG----YTPFEFDITDYLKPG 128 (167)
T ss_dssp CSEEEEEEEEEESGGG---TTSEEEEEESEEES-----------EEEEEETTEEEEEEEST----TS-EEEECGGGSSSE
T ss_pred CceEEEEEEEEeCchh---cCceEEEEeccceE-----------eeEEEeCCeEEeeeCCC----cCCeEEeChhhccCC
Confidence 3455666678887654 35667777643322 35789999988643211 122338999999999
Q ss_pred c-cEEEEE
Q 002886 243 T-NLLQAV 249 (870)
Q Consensus 243 ~-N~IqIv 249 (870)
. |.|.|.
T Consensus 129 ~~N~l~V~ 136 (167)
T PF02837_consen 129 EENTLAVR 136 (167)
T ss_dssp EEEEEEEE
T ss_pred CCEEEEEE
Confidence 8 999875
No 15
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=73.79 E-value=2.9 Score=31.21 Aligned_cols=42 Identities=26% Similarity=0.619 Sum_probs=27.6
Q ss_pred CCCcccccccCCCCCCcCcccccch-HHHHHHHcCCCcccccCCCCc
Q 002886 302 CPISYKRINTPVKGHSCRHHQCFDF-SNYVHINSRRPSWRCPHCNQH 347 (870)
Q Consensus 302 CPIS~~RIkiPvRG~~CkHLQCFDL-~sFL~~n~qkptW~CPIC~k~ 347 (870)
|+|-...+..+..-..|.|.-|.+- +.|+.. ...+||+|++.
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~----~~~~Cp~C~~~ 44 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKS----GKNTCPLCRTP 44 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHHh----CcCCCCCCCCc
Confidence 5565666666666667998766553 234432 56789999875
No 16
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=71.30 E-value=2.2 Score=36.83 Aligned_cols=37 Identities=27% Similarity=0.557 Sum_probs=28.7
Q ss_pred ccccccCCCCCCcCcccccchHHHHHHHcCCCcccccCCCCccCcCCe
Q 002886 306 YKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHCNQHVCYTDI 353 (870)
Q Consensus 306 ~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC~k~~~~~dL 353 (870)
.+.+..|+--.-|.+ |||++.|= -||+|++++.+.+.
T Consensus 18 ~~~~~~pCgH~I~~~--~f~~~rYn---------gCPfC~~~~~~~~~ 54 (55)
T PF14447_consen 18 TKGTVLPCGHLICDN--CFPGERYN---------GCPFCGTPFEFDDP 54 (55)
T ss_pred cccccccccceeecc--ccChhhcc---------CCCCCCCcccCCCC
Confidence 456677877777877 99998763 59999999877653
No 17
>PF04641 Rtf2: Rtf2 RING-finger
Probab=70.50 E-value=2.7 Score=45.23 Aligned_cols=55 Identities=25% Similarity=0.405 Sum_probs=38.5
Q ss_pred ceecccCCCcccccc--cC-CCCCCcCcccccchHHHHHHHcCCCcccccCCCCccCcCCeee
Q 002886 296 SRISLNCPISYKRIN--TP-VKGHSCRHHQCFDFSNYVHINSRRPSWRCPHCNQHVCYTDIRV 355 (870)
Q Consensus 296 ~~VSL~CPIS~~RIk--iP-vRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC~k~~~~~dL~I 355 (870)
....+.||||...|. ++ |=-..|.|. |-.+.+=++. ..|.||+|++++.-.|+++
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V--~s~~alke~k---~~~~Cp~c~~~f~~~DiI~ 167 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCV--FSEKALKELK---KSKKCPVCGKPFTEEDIIP 167 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCE--eeHHHHHhhc---ccccccccCCccccCCEEE
Confidence 345679999998882 22 222478884 4444444442 6899999999999888875
No 18
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.09 E-value=0.64 Score=52.48 Aligned_cols=77 Identities=21% Similarity=0.466 Sum_probs=60.8
Q ss_pred cceecccCCCcccccccCCCCCCcCcccccchHHHHHHHcCCCcccccCCCCcc-CcCCeeecHHHHHHHHHhCCCccEE
Q 002886 295 PSRISLNCPISYKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHCNQHV-CYTDIRVDQNMVKVLREVGENVADV 373 (870)
Q Consensus 295 s~~VSL~CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC~k~~-~~~dL~ID~y~~eILk~~~enveeV 373 (870)
.+.+.+.|||-+..|+-----..|-|-=|||+-+ .+.+..--.||-|.|.+ .--.|++|.-|..++.++-.+++.+
T Consensus 39 ~~~~~v~c~icl~llk~tmttkeClhrfc~~ci~---~a~r~gn~ecptcRk~l~SkrsLr~Dp~fdaLis~i~~sie~~ 115 (381)
T KOG0311|consen 39 MFDIQVICPICLSLLKKTMTTKECLHRFCFDCIW---KALRSGNNECPTCRKKLVSKRSLRIDPNFDALISKIYPSIEEY 115 (381)
T ss_pred HhhhhhccHHHHHHHHhhcccHHHHHHHHHHHHH---HHHHhcCCCCchHHhhccccccCCCCccHHHHHHHHhccHHHH
Confidence 4678999999999999888889999999998633 33444556799999876 4678999999999998886655444
Q ss_pred E
Q 002886 374 I 374 (870)
Q Consensus 374 ~ 374 (870)
+
T Consensus 116 e 116 (381)
T KOG0311|consen 116 E 116 (381)
T ss_pred h
Confidence 3
No 19
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=53.47 E-value=9.7 Score=42.73 Aligned_cols=40 Identities=23% Similarity=0.452 Sum_probs=25.6
Q ss_pred CCCCCCcCcccccchHHHHHHHcCCCcccccCCCCccCcCC----eeecHHH
Q 002886 312 PVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHCNQHVCYTD----IRVDQNM 359 (870)
Q Consensus 312 PvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC~k~~~~~d----L~ID~y~ 359 (870)
+|-..+|.+ |.|.. -..+.-.||+|++.++..+ +..|..+
T Consensus 25 ~CGH~~C~s--Cv~~l------~~~~~~~CP~C~~~lrk~~fr~q~F~D~~v 68 (309)
T TIGR00570 25 VCGHTLCES--CVDLL------FVRGSGSCPECDTPLRKNNFRVQLFEDPTV 68 (309)
T ss_pred CCCCcccHH--HHHHH------hcCCCCCCCCCCCccchhhccccccccHHH
Confidence 455555554 55544 2345569999999998888 4555444
No 20
>PRK10340 ebgA cryptic beta-D-galactosidase subunit alpha; Reviewed
Probab=51.17 E-value=33 Score=44.04 Aligned_cols=66 Identities=24% Similarity=0.336 Sum_probs=45.4
Q ss_pred CCceeeEEEEeecccccCCCceEEEEEEecCCCCCcceeeCCCcEEEEEcCceeccccccCCCCCCCCc--ccccccccc
Q 002886 164 GYGAFMIDFHISKNMIQSTEEKIRLFVAQTDKTETSACVISPQHVNFILNGKGIERRTNVFMDPGPQLP--TNVSPMLKY 241 (870)
Q Consensus 164 G~g~~~idF~IsKs~~~~sq~kLrLfc~q~d~~~~s~ci~wP~~I~IkVNGk~Ie~rrnvk~kpG~d~P--IDIT~~LK~ 241 (870)
|.|.+.-.|.|.+.+ ..++++|...-. . ...++.|||+.|-. +.|--.| +|||++|+.
T Consensus 109 ~~g~Yrr~F~lp~~~---~gkrv~L~FeGV---~--------s~a~VwvNG~~VG~------~~g~~~pfefDIT~~l~~ 168 (1021)
T PRK10340 109 PTGAYQRTFTLSDGW---QGKQTIIKFDGV---E--------TYFEVYVNGQYVGF------SKGSRLTAEFDISAMVKT 168 (1021)
T ss_pred CeEEEEEEEEeCccc---ccCcEEEEECcc---c--------eEEEEEECCEEecc------ccCCCccEEEEcchhhCC
Confidence 567888889997764 345676665322 1 13578899998853 2333333 899999999
Q ss_pred cccEEEEE
Q 002886 242 GTNLLQAV 249 (870)
Q Consensus 242 G~N~IqIv 249 (870)
|.|.|.|.
T Consensus 169 G~N~LaV~ 176 (1021)
T PRK10340 169 GDNLLCVR 176 (1021)
T ss_pred CccEEEEE
Confidence 99999874
No 21
>PHA02672 ORF110 EEV glycoprotein; Provisional
Probab=49.42 E-value=7.9 Score=39.56 Aligned_cols=25 Identities=28% Similarity=0.651 Sum_probs=19.4
Q ss_pred HHHHHHHhhhh---------------ccccccCCCChhhH
Q 002886 88 QAAIMVLMFSV---------------KSACRIEWFSVEEA 112 (870)
Q Consensus 88 ~~avmvlmisv---------------KnAc~~gwF~~~~~ 112 (870)
-+|++|+++++ |+||+.||.+.++.
T Consensus 21 PaAi~v~ilTivssIGailkYk~~f~~~AC~~GWvp~dd~ 60 (166)
T PHA02672 21 PVATLVTVLSLFTSLGAIIKYTDFFLKEACENGWVPIKDL 60 (166)
T ss_pred cHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhcCCeeccCE
Confidence 36677777665 99999999998753
No 22
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.26 E-value=7.6 Score=38.81 Aligned_cols=60 Identities=20% Similarity=0.434 Sum_probs=41.6
Q ss_pred cccCCCcccccccCCCCCCcCcccccchHHHHHHHcCCCcccccCCCCccCcCCeeecHHHHHHHHH
Q 002886 299 SLNCPISYKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHCNQHVCYTDIRVDQNMVKVLRE 365 (870)
Q Consensus 299 SL~CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC~k~~~~~dL~ID~y~~eILk~ 365 (870)
-|.|||-+..++.| +...|.|.-|++-..=+.- ....||.|.. ...+|.-...+..+++.
T Consensus 13 ~~~C~iC~~~~~~p-~~l~C~H~~c~~C~~~~~~----~~~~Cp~cr~--~~~~~~~n~~l~~~~~~ 72 (386)
T KOG2177|consen 13 ELTCPICLEYFREP-VLLPCGHNFCRACLTRSWE----GPLSCPVCRP--PSRNLRPNVLLANLVER 72 (386)
T ss_pred cccChhhHHHhhcC-ccccccchHhHHHHHHhcC----CCcCCcccCC--chhccCccHHHHHHHHH
Confidence 47899999999999 8888999888865543333 5689999995 22245433334444443
No 23
>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=47.57 E-value=11 Score=29.22 Aligned_cols=39 Identities=28% Similarity=0.688 Sum_probs=26.7
Q ss_pred CCCcccccccCCCCCCcCcccccchHHHHHHHcCCCcccccCC
Q 002886 302 CPISYKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHC 344 (870)
Q Consensus 302 CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC 344 (870)
|||=+..++.|+....|.|+=|++ =+.+..++ ..+||+|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~--C~~~~~~~--~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKE--CIEKYLEK--NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHH--HHHHHHHC--TSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHH--HHHHHHHC--cCCCcCC
Confidence 567777888898999999986664 34444444 3799998
No 24
>PRK09525 lacZ beta-D-galactosidase; Reviewed
Probab=45.36 E-value=43 Score=43.06 Aligned_cols=67 Identities=21% Similarity=0.454 Sum_probs=45.1
Q ss_pred CCceeeEEEEeecccccCCCceEEEEEEecCCCCCcceeeCCCcEEEEEcCceeccccccCCCCCCCCc--ccccccccc
Q 002886 164 GYGAFMIDFHISKNMIQSTEEKIRLFVAQTDKTETSACVISPQHVNFILNGKGIERRTNVFMDPGPQLP--TNVSPMLKY 241 (870)
Q Consensus 164 G~g~~~idF~IsKs~~~~sq~kLrLfc~q~d~~~~s~ci~wP~~I~IkVNGk~Ie~rrnvk~kpG~d~P--IDIT~~LK~ 241 (870)
|-|.+.-.|.+.+.+.. ..+++|...-.+ ...++.|||+.|-. +.|.-.| +|||++|+.
T Consensus 120 ~~gwYrr~F~vp~~w~~--~~rv~L~FeGV~-----------~~a~VwvNG~~VG~------~~g~~~pfefDIT~~l~~ 180 (1027)
T PRK09525 120 PTGCYSLTFTVDESWLQ--SGQTRIIFDGVN-----------SAFHLWCNGRWVGY------SQDSRLPAEFDLSPFLRA 180 (1027)
T ss_pred CeEEEEEEEEeChhhcC--CCeEEEEECeec-----------cEEEEEECCEEEEe------ecCCCceEEEEChhhhcC
Confidence 56778888999876422 225666653221 13578899998853 3333445 899999999
Q ss_pred cccEEEEE
Q 002886 242 GTNLLQAV 249 (870)
Q Consensus 242 G~N~IqIv 249 (870)
|.|.|.|.
T Consensus 181 G~N~L~V~ 188 (1027)
T PRK09525 181 GENRLAVM 188 (1027)
T ss_pred CccEEEEE
Confidence 99998764
No 25
>PF08531 Bac_rhamnosid_N: Alpha-L-rhamnosidase N-terminal domain; InterPro: IPR013737 This domain is found in bacterial rhamnosidase A and B enzymes and is probably involved in substrate recognition. ; PDB: 2OKX_B.
Probab=45.01 E-value=14 Score=37.32 Aligned_cols=40 Identities=23% Similarity=0.451 Sum_probs=24.1
Q ss_pred cEEEEEcCceeccccccCCCCC--------CCCcccccccccccccEEEEE
Q 002886 207 HVNFILNGKGIERRTNVFMDPG--------PQLPTNVSPMLKYGTNLLQAV 249 (870)
Q Consensus 207 ~I~IkVNGk~Ie~rrnvk~kpG--------~d~PIDIT~~LK~G~N~IqIv 249 (870)
..++.|||+.|-.-. +.|| .-.-.|||++|+.|.|.|-+.
T Consensus 15 ~Y~l~vNG~~V~~~~---l~P~~t~y~~~~~Y~tyDVt~~L~~G~N~iav~ 62 (172)
T PF08531_consen 15 RYELYVNGERVGDGP---LAPGWTDYDKRVYYQTYDVTPYLRPGENVIAVW 62 (172)
T ss_dssp EEEEEETTEEEEEE-----------BTTEEEEEEEE-TTT--TTEEEEEEE
T ss_pred eEEEEECCEEeeCCc---cccccccCCCceEEEEEeChHHhCCCCCEEEEE
Confidence 467899999886311 1122 123589999999999999874
No 26
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=44.27 E-value=11 Score=43.30 Aligned_cols=26 Identities=27% Similarity=0.704 Sum_probs=19.8
Q ss_pred CCcCcccccchHHHHHHHcCCCcccccCCCCcc
Q 002886 316 HSCRHHQCFDFSNYVHINSRRPSWRCPHCNQHV 348 (870)
Q Consensus 316 ~~CkHLQCFDL~sFL~~n~qkptW~CPIC~k~~ 348 (870)
-+|-|+.| |++|++.+. .||||..++
T Consensus 319 GHilHl~C--LknW~ERqQ-----TCPICr~p~ 344 (491)
T COG5243 319 GHILHLHC--LKNWLERQQ-----TCPICRRPV 344 (491)
T ss_pred cceeeHHH--HHHHHHhcc-----CCCcccCcc
Confidence 35677777 689988543 599999886
No 27
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=41.48 E-value=9 Score=47.04 Aligned_cols=54 Identities=22% Similarity=0.474 Sum_probs=39.9
Q ss_pred ceecccCCCcccccccCCCCCCcCcccccch-HHHHHHHcCCCcccccCCCCccCcCCee
Q 002886 296 SRISLNCPISYKRINTPVKGHSCRHHQCFDF-SNYVHINSRRPSWRCPHCNQHVCYTDIR 354 (870)
Q Consensus 296 ~~VSL~CPIS~~RIkiPvRG~~CkHLQCFDL-~sFL~~n~qkptW~CPIC~k~~~~~dL~ 354 (870)
.+=-|+||.-.+|.+-=| -..|-|+=||+. ..++.++ .-+||.|+..+...|+.
T Consensus 640 yK~~LkCs~Cn~R~Kd~v-I~kC~H~FC~~Cvq~r~etR----qRKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 640 YKELLKCSVCNTRWKDAV-ITKCGHVFCEECVQTRYETR----QRKCPKCNAAFGANDVH 694 (698)
T ss_pred HHhceeCCCccCchhhHH-HHhcchHHHHHHHHHHHHHh----cCCCCCCCCCCCccccc
Confidence 456799999888876533 357999888763 3455554 45899999999998874
No 28
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=41.39 E-value=15 Score=30.01 Aligned_cols=39 Identities=33% Similarity=0.687 Sum_probs=22.1
Q ss_pred CCCccccccc----CCCCCCcCcccccchHHHHHHHcCCCccccc
Q 002886 302 CPISYKRINT----PVKGHSCRHHQCFDFSNYVHINSRRPSWRCP 342 (870)
Q Consensus 302 CPIS~~RIki----PvRG~~CkHLQCFDL~sFL~~n~qkptW~CP 342 (870)
|||++. +.. |..-. |.|.=|.|...=|..+......+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence 788888 766 77644 9999999988887776667888998
No 29
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.05 E-value=18 Score=38.07 Aligned_cols=46 Identities=20% Similarity=0.571 Sum_probs=32.1
Q ss_pred ccCCCccccc--ccCCCCCCcCcccccchHHHHHHH---cCCCcccccCCCCccCcCCe
Q 002886 300 LNCPISYKRI--NTPVKGHSCRHHQCFDFSNYVHIN---SRRPSWRCPHCNQHVCYTDI 353 (870)
Q Consensus 300 L~CPIS~~RI--kiPvRG~~CkHLQCFDL~sFL~~n---~qkptW~CPIC~k~~~~~dL 353 (870)
.+|||-+... +.| =+..|.|+= ...+ ..+.+-+||+|+|++.-.++
T Consensus 132 ~~CPiCl~~~sek~~-vsTkCGHvF-------C~~Cik~alk~~~~CP~C~kkIt~k~~ 182 (187)
T KOG0320|consen 132 YKCPICLDSVSEKVP-VSTKCGHVF-------CSQCIKDALKNTNKCPTCRKKITHKQF 182 (187)
T ss_pred cCCCceecchhhccc-cccccchhH-------HHHHHHHHHHhCCCCCCcccccchhhh
Confidence 7999987766 344 457899963 3332 23578899999998765543
No 30
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=39.68 E-value=12 Score=42.46 Aligned_cols=37 Identities=22% Similarity=0.493 Sum_probs=29.1
Q ss_pred CCCCCCcCcccccchHHHHHHHcCCCcccccCCCCcc
Q 002886 312 PVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHCNQHV 348 (870)
Q Consensus 312 PvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC~k~~ 348 (870)
|-+-+.|.-++|||--.=-+.-+.+..|.||.|+++-
T Consensus 258 ~~~v~~~~l~eC~~~f~~~e~L~g~d~W~CpkC~~k~ 294 (415)
T COG5533 258 PYEVVQLGLQECIDRFYEEEKLEGKDAWRCPKCGRKE 294 (415)
T ss_pred cchheeecHHHHHHHhhhHHhhcCcccccCchhcccc
Confidence 3467889988999876666666778999999999753
No 31
>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=39.20 E-value=12 Score=24.86 Aligned_cols=11 Identities=27% Similarity=1.002 Sum_probs=7.3
Q ss_pred ccccCCCCccC
Q 002886 339 WRCPHCNQHVC 349 (870)
Q Consensus 339 W~CPIC~k~~~ 349 (870)
|.|++|++.++
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 78999998764
No 32
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=38.29 E-value=18 Score=30.14 Aligned_cols=26 Identities=15% Similarity=0.407 Sum_probs=13.0
Q ss_pred hHHHHHHHcCCCcccccCCCCccCcCC
Q 002886 326 FSNYVHINSRRPSWRCPHCNQHVCYTD 352 (870)
Q Consensus 326 L~sFL~~n~qkptW~CPIC~k~~~~~d 352 (870)
+.-+|..-..... .||+|+.++.-+.
T Consensus 9 ~~k~i~~l~~~~~-~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 9 LKKYIEELKEAKG-CCPLCGRPLDEEH 34 (54)
T ss_dssp HHHHHHHHTT-SE-E-TTT--EE-HHH
T ss_pred HHHHHHHHhcCCC-cCCCCCCCCCHHH
Confidence 3445555445444 9999999986543
No 33
>PF02228 Gag_p19: Major core protein p19; InterPro: IPR003139 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from delta-retroviruses such as Human T-lymphotropic virus 1 and Human T-cell leukemia virus 2 (HTLV-2), both members of the human oncovirus subclass of retroviruses [, ].; GO: 0005198 structural molecule activity, 0019013 viral nucleocapsid; PDB: 1JVR_A.
Probab=36.86 E-value=20 Score=33.37 Aligned_cols=20 Identities=20% Similarity=0.622 Sum_probs=16.9
Q ss_pred chHHHHHHHcCCCcccccCC
Q 002886 325 DFSNYVHINSRRPSWRCPHC 344 (870)
Q Consensus 325 DL~sFL~~n~qkptW~CPIC 344 (870)
||+.||.+.-+.+.|.|||-
T Consensus 45 qLr~flk~alkTpvwl~pi~ 64 (92)
T PF02228_consen 45 QLRNFLKLALKTPVWLNPIN 64 (92)
T ss_dssp HHHHHHHHHHT-TTSTTTT-
T ss_pred HHHHHHHHHHcCCeeecccc
Confidence 68999999999999999984
No 34
>PRK10150 beta-D-glucuronidase; Provisional
Probab=36.41 E-value=81 Score=37.79 Aligned_cols=66 Identities=12% Similarity=0.204 Sum_probs=40.8
Q ss_pred ceeeEEEEeecccccCCCceEEEEEEecCCCCCcceeeCCCcEEEEEcCceeccccccCCCCCCCCccccccccccccc-
Q 002886 166 GAFMIDFHISKNMIQSTEEKIRLFVAQTDKTETSACVISPQHVNFILNGKGIERRTNVFMDPGPQLPTNVSPMLKYGTN- 244 (870)
Q Consensus 166 g~~~idF~IsKs~~~~sq~kLrLfc~q~d~~~~s~ci~wP~~I~IkVNGk~Ie~rrnvk~kpG~d~PIDIT~~LK~G~N- 244 (870)
.-+.-.|.|.+.+ ..+++.|...-.+. ..+|.|||+.|-.-.+- -+..=+|||++|+.|.|
T Consensus 67 ~WYrr~f~lp~~~---~gk~v~L~Fegv~~-----------~a~V~lNG~~vg~~~~~----~~~f~~DIT~~l~~G~~n 128 (604)
T PRK10150 67 VWYQREVFIPKGW---AGQRIVLRFGSVTH-----------YAKVWVNGQEVMEHKGG----YTPFEADITPYVYAGKSV 128 (604)
T ss_pred EEEEEEEECCccc---CCCEEEEEECcccc-----------eEEEEECCEEeeeEcCC----ccceEEeCchhccCCCce
Confidence 3366778886542 34567666643222 35688999987542211 02234899999999865
Q ss_pred EEEEE
Q 002886 245 LLQAV 249 (870)
Q Consensus 245 ~IqIv 249 (870)
.|.|.
T Consensus 129 ~L~V~ 133 (604)
T PRK10150 129 RITVC 133 (604)
T ss_pred EEEEE
Confidence 77664
No 35
>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=36.14 E-value=4.8 Score=32.01 Aligned_cols=17 Identities=18% Similarity=0.690 Sum_probs=11.1
Q ss_pred HHcCCCcccccCCCCcc
Q 002886 332 INSRRPSWRCPHCNQHV 348 (870)
Q Consensus 332 ~n~qkptW~CPIC~k~~ 348 (870)
+.....+|.|++|+..-
T Consensus 18 ~~~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 18 FDDGGKTWICNFCGTKN 34 (40)
T ss_dssp EETTTTEEEETTT--EE
T ss_pred EcCCCCEEECcCCCCcC
Confidence 33456799999999753
No 36
>smart00748 HEPN Higher Eukarytoes and Prokaryotes Nucleotide-binding domain.
Probab=36.10 E-value=1.7e+02 Score=27.18 Aligned_cols=76 Identities=21% Similarity=0.337 Sum_probs=44.3
Q ss_pred HHHHHhhchhhhhh-cCCCCccccchHHHHHHHHhhcCC----hhhHHHHHHH---hhhhcc-cc--ccCCCChhhHHHH
Q 002886 47 LCLFLSRGIDYAVA-NNEVPPKAQELPSLLKQICQRKND----PVLQAAIMVL---MFSVKS-AC--RIEWFSVEEAQEL 115 (870)
Q Consensus 47 lc~sl~rgId~ava-n~~~p~~~~~lp~llkqv~~~~~D----~~~~~avmvl---misvKn-Ac--~~gwF~~~~~~el 115 (870)
+-.+.=+.++..+. .|..+++.|+|..|++.+-..... ....-.+-.| .+..+= .. ...||...+++++
T Consensus 27 aqqavEk~lKA~l~~~~~~~p~tH~l~~L~~~l~~~~~~~~~~~~~~~~l~~L~~~~i~~RYp~~~~~~~~~~~~~a~~~ 106 (113)
T smart00748 27 SQQAAELALKALLLALGGEPPKTHSLRELLSELEKLLRLPEFIDEIRECLNLLEEAYIKSRYPDAGEPLEWYTKEDAEEL 106 (113)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHhcccCCCCCCchhhCCHHHHHHH
Confidence 33344444555444 777889999999999966653322 2221111111 121111 11 3458899999999
Q ss_pred HHHHHHh
Q 002886 116 IALADEI 122 (870)
Q Consensus 116 l~la~ei 122 (870)
+.+|++|
T Consensus 107 ~~~a~~v 113 (113)
T smart00748 107 LKCAEEI 113 (113)
T ss_pred HHHHHhC
Confidence 9999865
No 37
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=35.78 E-value=12 Score=44.15 Aligned_cols=58 Identities=19% Similarity=0.477 Sum_probs=36.0
Q ss_pred chHHHHHHHcCCCcccccCCCCccCcCCeeecHHHHHHHHHh------------CCCccE--EEEccCCceEeecc
Q 002886 325 DFSNYVHINSRRPSWRCPHCNQHVCYTDIRVDQNMVKVLREV------------GENVAD--VIISADGSWKAIME 386 (870)
Q Consensus 325 DL~sFL~~n~qkptW~CPIC~k~~~~~dL~ID~y~~eILk~~------------~envee--V~V~~DGsW~pv~E 386 (870)
|+..|..-+..-.-|.||.|.+.+. --+.|...+.++. ++.+++ ++.-..|.|+|+.-
T Consensus 44 eal~fak~n~sWrFWiCp~CskkF~----d~~~~~~H~~~eH~~~l~P~lqs~lPqrId~~w~e~I~~~~WkPvD~ 115 (466)
T PF04780_consen 44 EALSFAKENKSWRFWICPRCSKKFS----DAESCLSHMEQEHPAGLKPKLQSVLPQRIDDDWAEMISVGSWKPVDA 115 (466)
T ss_pred HHHHHHHhcCceeEeeCCcccceeC----CHHHHHHHHHHhhhhhcChhhhhhcCcccCHHHHHHHhcCCCccccH
Confidence 4567777777778899999997642 2344555554432 222322 23337899999864
No 38
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.73 E-value=19 Score=37.54 Aligned_cols=54 Identities=22% Similarity=0.320 Sum_probs=31.5
Q ss_pred CcccccCCCCccCcCCeeecHHHHHHHHHhCC-CccEEEEccCCceEeeccCCcccc
Q 002886 337 PSWRCPHCNQHVCYTDIRVDQNMVKVLREVGE-NVADVIISADGSWKAIMEADDNVD 392 (870)
Q Consensus 337 ptW~CPIC~k~~~~~dL~ID~y~~eILk~~~e-nveeV~V~~DGsW~pv~E~ddd~d 392 (870)
.-.+||||+|.+..+|+.|--.|- |.+-.- --++|.-+.-|.-...+|+-+..|
T Consensus 137 ~g~KCPvC~K~V~sDd~e~HlvMC--LtkPrlsYNdDVL~ddkGECvICLEdL~~Gd 191 (205)
T KOG0801|consen 137 SGMKCPVCHKVVPSDDAEIHLVMC--LTKPRLSYNDDVLKDDKGECVICLEDLEAGD 191 (205)
T ss_pred CCccCCccccccCCCcceEEEEEE--ecccccccccchhcccCCcEEEEhhhccCCC
Confidence 357899999999999887643331 111000 124455555566666666554433
No 39
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=35.48 E-value=21 Score=27.45 Aligned_cols=41 Identities=32% Similarity=0.625 Sum_probs=27.6
Q ss_pred CCCcccccccCCCCCCcCcccccchHHHHHHHcCCCcccccCC
Q 002886 302 CPISYKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHC 344 (870)
Q Consensus 302 CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC 344 (870)
|||=...+..|.+-..|.|.=|.+ =+..+......-+||+|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~--C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRD--CLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHH--HHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCcchHH--HHHHHHHhcCCccCCcC
Confidence 456666777777889999975554 33333333667779988
No 40
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=33.36 E-value=28 Score=30.77 Aligned_cols=32 Identities=19% Similarity=0.519 Sum_probs=19.2
Q ss_pred CcccccchHHHHHHHcCC-----CcccccCCCCccCcC
Q 002886 319 RHHQCFDFSNYVHINSRR-----PSWRCPHCNQHVCYT 351 (870)
Q Consensus 319 kHLQCFDL~sFL~~n~qk-----ptW~CPIC~k~~~~~ 351 (870)
-|+.|. .++|+.....+ -.++||.|.+++..+
T Consensus 32 fH~~CL-~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 32 FHLLCL-SEWFLSLEKSRQSFIPIFGECPYCSSPISWS 68 (70)
T ss_dssp B-SGGG-HHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred HHHHHH-HHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence 488887 56666654432 257899999987653
No 41
>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=33.01 E-value=21 Score=27.32 Aligned_cols=12 Identities=33% Similarity=1.138 Sum_probs=10.1
Q ss_pred CCcccccCCCCc
Q 002886 336 RPSWRCPHCNQH 347 (870)
Q Consensus 336 kptW~CPIC~k~ 347 (870)
.+.|.||+|+.+
T Consensus 15 ~~~~~CP~Cg~~ 26 (33)
T cd00350 15 EAPWVCPVCGAP 26 (33)
T ss_pred cCCCcCcCCCCc
Confidence 488999999864
No 42
>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=32.15 E-value=30 Score=28.02 Aligned_cols=44 Identities=23% Similarity=0.499 Sum_probs=23.7
Q ss_pred cCCCcccccccCCCCCCcCcc-cccchHHHHHHHcCCCcccccCCCCccC
Q 002886 301 NCPISYKRINTPVKGHSCRHH-QCFDFSNYVHINSRRPSWRCPHCNQHVC 349 (870)
Q Consensus 301 ~CPIS~~RIkiPvRG~~CkHL-QCFDL~sFL~~n~qkptW~CPIC~k~~~ 349 (870)
.|+|=+...+.+ --.-|.|+ =|++= +..+.. ...+||+|.+++.
T Consensus 4 ~C~iC~~~~~~~-~~~pCgH~~~C~~C--~~~~~~--~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPRDV-VLLPCGHLCFCEEC--AERLLK--RKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBSSE-EEETTCEEEEEHHH--HHHHHH--TTSBBTTTTBB-S
T ss_pred CCccCCccCCce-EEeCCCChHHHHHH--hHHhcc--cCCCCCcCChhhc
Confidence 455544444332 23358887 44442 222222 7789999998863
No 43
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.26 E-value=7.9e+02 Score=32.42 Aligned_cols=26 Identities=23% Similarity=0.447 Sum_probs=20.7
Q ss_pred CcccCCCCccceeecCCCCCCCcccc
Q 002886 721 PQMTRQPPTVPVQVQTPSAGPRYPTT 746 (870)
Q Consensus 721 ~~~~r~~~s~~vq~~~~~~g~~~~~~ 746 (870)
.+++++|+|-|+-..+-.+|+.+++.
T Consensus 830 ~~~~~~~~S~p~~~~pv~sgs~~P~~ 855 (1049)
T KOG0307|consen 830 SQPPAAPPSFPYAPNPVTSGSVNPAP 855 (1049)
T ss_pred CCCCCCCccCCCCCCCCCCCCCCCCC
Confidence 68889999988877777778777665
No 44
>KOG2008 consensus BTK-associated SH3-domain binding protein SAB [Signal transduction mechanisms]
Probab=29.10 E-value=42 Score=38.13 Aligned_cols=47 Identities=23% Similarity=0.211 Sum_probs=37.5
Q ss_pred CCCCCeEEeCCCCCcccccCCCCCcCCCCCCCCCCCCccCCCCCccc
Q 002886 415 ANSNPVILDLTKNDDEIDAMSTGEIEDVKPDLHSQPVSTNLTMPSEL 461 (870)
Q Consensus 415 ~~~~p~VIDLt~DDDE~D~~~~~~~eD~kP~~qs~~vs~~l~m~~~~ 461 (870)
++..|.-||..+.|-|||+-.+++.||......+.+.++..+.|+++
T Consensus 259 ~~p~p~~~~~~~~~~~dds~~~~~~e~~~e~~~~~s~~sg~~~~s~~ 305 (426)
T KOG2008|consen 259 SKPEPDAISVASEAFEDDSCSNFVSEDDSETQSVSSFSSGPTSPSEM 305 (426)
T ss_pred CCCCCchhhhhhhhcccchhhcccccccccccccccccCCCCCHHhc
Confidence 34577899999999999988889999988877777877777666654
No 45
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=27.11 E-value=27 Score=28.01 Aligned_cols=42 Identities=26% Similarity=0.681 Sum_probs=23.2
Q ss_pred CCCcccccccCCCCCCcCcccccchHHHHHHHcCCCcccccCC
Q 002886 302 CPISYKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHC 344 (870)
Q Consensus 302 CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC 344 (870)
|||=...++-|+. ..|.|.=|++-..=+........+.||+|
T Consensus 1 CpiC~~~~~~Pv~-l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVS-LPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE--SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccc-cCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 6777777788876 68999877664333322233334899998
No 46
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=26.41 E-value=48 Score=29.45 Aligned_cols=29 Identities=14% Similarity=0.359 Sum_probs=23.8
Q ss_pred CcccccCCCCccCcCCeeecHHHHHHHHH
Q 002886 337 PSWRCPHCNQHVCYTDIRVDQNMVKVLRE 365 (870)
Q Consensus 337 ptW~CPIC~k~~~~~dL~ID~y~~eILk~ 365 (870)
|.--|++|++.+++++-.-.+--.|||+.
T Consensus 7 PH~HC~VCg~aIp~de~~CSe~C~eil~k 35 (64)
T COG4068 7 PHRHCVVCGKAIPPDEQVCSEECGEILNK 35 (64)
T ss_pred CCccccccCCcCCCccchHHHHHHHHHHH
Confidence 56679999999999888777777777764
No 47
>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=25.73 E-value=32 Score=29.12 Aligned_cols=11 Identities=36% Similarity=1.192 Sum_probs=9.2
Q ss_pred CcccccCCCCc
Q 002886 337 PSWRCPHCNQH 347 (870)
Q Consensus 337 ptW~CPIC~k~ 347 (870)
..|.||+|+..
T Consensus 33 ~~w~CP~C~a~ 43 (50)
T cd00730 33 DDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCc
Confidence 58999999854
No 48
>PHA02929 N1R/p28-like protein; Provisional
Probab=24.64 E-value=74 Score=34.71 Aligned_cols=46 Identities=20% Similarity=0.530 Sum_probs=27.0
Q ss_pred cccCCCcccccccC-CC------CCCcCcccccc-hHHHHHHHcCCCcccccCCCCccC
Q 002886 299 SLNCPISYKRINTP-VK------GHSCRHHQCFD-FSNYVHINSRRPSWRCPHCNQHVC 349 (870)
Q Consensus 299 SL~CPIS~~RIkiP-vR------G~~CkHLQCFD-L~sFL~~n~qkptW~CPIC~k~~~ 349 (870)
...|||-...+.-+ ++ -..|.|.=|.+ +..|+.. .-.||+|...+.
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-----~~tCPlCR~~~~ 227 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-----KNTCPVCRTPFI 227 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-----CCCCCCCCCEee
Confidence 46899988876543 21 23677743333 1245542 237999998753
No 49
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=24.20 E-value=30 Score=39.58 Aligned_cols=64 Identities=22% Similarity=0.537 Sum_probs=50.5
Q ss_pred ecccCCCcccccccCCCCCCcCcccc-cchHHHHHHHcCCCcccccCCCCccCcCCeeecHHHHHHHHHhC
Q 002886 298 ISLNCPISYKRINTPVKGHSCRHHQC-FDFSNYVHINSRRPSWRCPHCNQHVCYTDIRVDQNMVKVLREVG 367 (870)
Q Consensus 298 VSL~CPIS~~RIkiPvRG~~CkHLQC-FDL~sFL~~n~qkptW~CPIC~k~~~~~dL~ID~y~~eILk~~~ 367 (870)
-.|+|-|-+.-+++|+-.- |.|.=| |-...||. ..-+||.|-..++-.+|+=...+.||++.+.
T Consensus 22 ~lLRC~IC~eyf~ip~itp-CsHtfCSlCIR~~L~-----~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~~ 86 (442)
T KOG0287|consen 22 DLLRCGICFEYFNIPMITP-CSHTFCSLCIRKFLS-----YKPQCPTCCVTVTESDLRNNRILDEIVKSLN 86 (442)
T ss_pred HHHHHhHHHHHhcCceecc-ccchHHHHHHHHHhc-----cCCCCCceecccchhhhhhhhHHHHHHHHHH
Confidence 4689999999899988777 999544 34444444 4557999999999999999999999988753
No 50
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=24.05 E-value=26 Score=25.84 Aligned_cols=10 Identities=40% Similarity=0.989 Sum_probs=8.4
Q ss_pred ccccCCCCcc
Q 002886 339 WRCPHCNQHV 348 (870)
Q Consensus 339 W~CPIC~k~~ 348 (870)
-.||||++.+
T Consensus 2 v~CPiC~~~v 11 (26)
T smart00734 2 VQCPVCFREV 11 (26)
T ss_pred CcCCCCcCcc
Confidence 3699999987
No 51
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=23.71 E-value=53 Score=23.32 Aligned_cols=25 Identities=24% Similarity=0.703 Sum_probs=14.8
Q ss_pred CCcCcccccc-hHHHHHHHcCCCcccccCC
Q 002886 316 HSCRHHQCFD-FSNYVHINSRRPSWRCPHC 344 (870)
Q Consensus 316 ~~CkHLQCFD-L~sFL~~n~qkptW~CPIC 344 (870)
..|.|.-|++ ++.|+. ....+||+|
T Consensus 14 ~~C~H~~c~~C~~~~~~----~~~~~CP~C 39 (39)
T smart00184 14 LPCGHTFCRSCIRKWLK----SGNNTCPIC 39 (39)
T ss_pred ecCCChHHHHHHHHHHH----hCcCCCCCC
Confidence 3588875554 234444 345679987
No 52
>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=23.65 E-value=26 Score=23.82 Aligned_cols=11 Identities=27% Similarity=1.123 Sum_probs=9.0
Q ss_pred ccccCCCCccC
Q 002886 339 WRCPHCNQHVC 349 (870)
Q Consensus 339 W~CPIC~k~~~ 349 (870)
|.||+|++.++
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 68999998764
No 53
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=22.52 E-value=42 Score=28.13 Aligned_cols=12 Identities=33% Similarity=1.077 Sum_probs=7.3
Q ss_pred CCcccccCCCCc
Q 002886 336 RPSWRCPHCNQH 347 (870)
Q Consensus 336 kptW~CPIC~k~ 347 (870)
...|.||+|+..
T Consensus 32 p~~w~CP~C~a~ 43 (47)
T PF00301_consen 32 PDDWVCPVCGAP 43 (47)
T ss_dssp -TT-B-TTTSSB
T ss_pred CCCCcCcCCCCc
Confidence 358999999864
No 54
>PLN00162 transport protein sec23; Provisional
Probab=22.18 E-value=24 Score=43.90 Aligned_cols=35 Identities=26% Similarity=0.724 Sum_probs=21.2
Q ss_pred cCCCCCCcCcccccchHHHHHHHcCCCcccccCCCCccC
Q 002886 311 TPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHCNQHVC 349 (870)
Q Consensus 311 iPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC~k~~~ 349 (870)
-|+|...|+-. +.-|..+......|.||+|+..-.
T Consensus 52 ~pvRC~~Cray----lNPf~~~d~~~~~W~C~~C~~~N~ 86 (761)
T PLN00162 52 DPLRCRTCRAV----LNPYCRVDFQAKIWICPFCFQRNH 86 (761)
T ss_pred CCCccCCCcCE----ECCceEEecCCCEEEccCCCCCCC
Confidence 36666666531 122233445678999999997643
No 55
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.86 E-value=49 Score=36.71 Aligned_cols=55 Identities=18% Similarity=0.348 Sum_probs=40.4
Q ss_pred cccCCCcccccccCCCCCCcCcccccchHHHHHHHcCCCcccccCCCCccCcCCeeec
Q 002886 299 SLNCPISYKRINTPVKGHSCRHHQCFDFSNYVHINSRRPSWRCPHCNQHVCYTDIRVD 356 (870)
Q Consensus 299 SL~CPIS~~RIkiPvRG~~CkHLQCFDL~sFL~~n~qkptW~CPIC~k~~~~~dL~ID 356 (870)
+-+|+|-..-+..|++ .-|.|+ |=+.-.|.+-..+..-.||.|..+..++++.|+
T Consensus 215 d~kC~lC~e~~~~ps~-t~CgHl--FC~~Cl~~~~t~~k~~~CplCRak~~pk~viil 269 (271)
T COG5574 215 DYKCFLCLEEPEVPSC-TPCGHL--FCLSCLLISWTKKKYEFCPLCRAKVYPKKVIIL 269 (271)
T ss_pred ccceeeeecccCCccc-ccccch--hhHHHHHHHHHhhccccCchhhhhccchhhhee
Confidence 6789999999988876 468886 434444554445555669999999988888665
No 56
>PF14683 CBM-like: Polysaccharide lyase family 4, domain III; PDB: 1NKG_A 2XHN_B 3NJX_A 3NJV_A.
Probab=21.31 E-value=2.7e+02 Score=28.62 Aligned_cols=75 Identities=16% Similarity=0.216 Sum_probs=35.9
Q ss_pred ceeeEEEEeecccccCCCceEEEEEEecCCCCCcceeeCCCcEEEEEcCceecccc-c-------cC--CCCCCCCc--c
Q 002886 166 GAFMIDFHISKNMIQSTEEKIRLFVAQTDKTETSACVISPQHVNFILNGKGIERRT-N-------VF--MDPGPQLP--T 233 (870)
Q Consensus 166 g~~~idF~IsKs~~~~sq~kLrLfc~q~d~~~~s~ci~wP~~I~IkVNGk~Ie~rr-n-------vk--~kpG~d~P--I 233 (870)
+...|.|.+.+.... ..++|+|....... -....+.|||...+... . ++ .+.|...- +
T Consensus 63 ~~w~I~F~l~~~~~~-~~~tL~i~la~a~~---------~~~~~V~vNg~~~~~~~~~~~~d~~~~r~g~~~G~~~~~~~ 132 (167)
T PF14683_consen 63 GTWTIKFDLDAVQLA-GTYTLRIALAGASA---------GGRLQVSVNGWSGPFPSAPFGNDNAIYRSGIHRGNYRLYEF 132 (167)
T ss_dssp --EEEEEEE-GGG-S---EEEEEEEEEEET---------T-EEEEEETTEE-----------S--GGGT---S---EEEE
T ss_pred CCEEEEEECCCCccC-CcEEEEEEeccccC---------CCCEEEEEcCccCCccccccCCCCceeeCceecccEEEEEE
Confidence 788999999887544 56778777754321 12468899995433110 0 11 12232222 3
Q ss_pred ccc-ccccccccEEEEEe
Q 002886 234 NVS-PMLKYGTNLLQAVG 250 (870)
Q Consensus 234 DIT-~~LK~G~N~IqIv~ 250 (870)
+|. ..|+.|.|+|.+..
T Consensus 133 ~ipa~~L~~G~Nti~lt~ 150 (167)
T PF14683_consen 133 DIPASLLKAGENTITLTV 150 (167)
T ss_dssp EE-TTSS-SEEEEEEEEE
T ss_pred EEcHHHEEeccEEEEEEE
Confidence 333 56788999988753
No 57
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=20.53 E-value=72 Score=29.98 Aligned_cols=30 Identities=23% Similarity=0.642 Sum_probs=19.3
Q ss_pred cCcccccch---HHHHHHHcCCCcccccCCCCccCcC
Q 002886 318 CRHHQCFDF---SNYVHINSRRPSWRCPHCNQHVCYT 351 (870)
Q Consensus 318 CkHLQCFDL---~sFL~~n~qkptW~CPIC~k~~~~~ 351 (870)
|.| +|=+ ..||+.. ...-.||.|.+...++
T Consensus 52 C~H--~FH~hCI~kWl~~~--~~~~~CPmCR~~w~~k 84 (85)
T PF12861_consen 52 CSH--NFHMHCILKWLSTQ--SSKGQCPMCRQPWKFK 84 (85)
T ss_pred Ccc--HHHHHHHHHHHccc--cCCCCCCCcCCeeeeC
Confidence 666 5544 3455543 3345999999987664
Done!