Query 002957
Match_columns 863
No_of_seqs 147 out of 199
Neff 3.9
Searched_HMMs 46136
Date Thu Mar 28 14:10:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002957.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002957hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1356 Putative transcription 100.0 1E-168 2E-173 1429.8 28.3 594 171-842 269-871 (889)
2 PF02373 JmjC: JmjC domain, hy 99.5 1.1E-14 2.3E-19 131.5 6.0 86 704-803 29-114 (114)
3 PF13621 Cupin_8: Cupin-like d 99.0 9.3E-11 2E-15 117.8 1.2 40 768-807 207-249 (251)
4 smart00558 JmjC A domain famil 96.6 0.00071 1.5E-08 55.8 1.0 54 541-612 3-56 (57)
5 KOG2131 Uncharacterized conser 95.9 0.0081 1.8E-07 67.2 4.4 60 764-823 262-322 (427)
6 cd02340 ZZ_NBR1_like Zinc fing 95.8 0.0041 8.9E-08 50.1 1.4 31 259-289 1-32 (43)
7 cd02249 ZZ Zinc finger, ZZ typ 95.4 0.0065 1.4E-07 49.0 1.0 32 260-291 2-34 (46)
8 cd02335 ZZ_ADA2 Zinc finger, Z 95.3 0.0075 1.6E-07 49.5 1.2 30 260-289 2-33 (49)
9 KOG1356 Putative transcription 94.9 0.011 2.4E-07 71.5 1.7 37 254-290 225-261 (889)
10 cd02339 ZZ_Mind_bomb Zinc fing 94.7 0.015 3.3E-07 47.4 1.4 30 259-288 1-32 (45)
11 PF00569 ZZ: Zinc finger, ZZ t 94.6 0.018 4E-07 46.7 1.7 34 257-290 3-38 (46)
12 smart00291 ZnF_ZZ Zinc-binding 93.8 0.028 6.1E-07 45.1 1.3 35 258-292 4-39 (44)
13 cd02344 ZZ_HERC2 Zinc finger, 93.4 0.04 8.6E-07 45.2 1.4 31 259-289 1-33 (45)
14 PF07883 Cupin_2: Cupin domain 93.1 0.041 8.8E-07 45.8 1.1 26 771-796 38-63 (71)
15 cd02341 ZZ_ZZZ3 Zinc finger, Z 92.9 0.052 1.1E-06 45.0 1.5 31 260-290 2-36 (48)
16 COG1917 Uncharacterized conser 92.8 0.048 1E-06 51.6 1.3 58 739-801 56-115 (131)
17 cd02345 ZZ_dah Zinc finger, ZZ 91.7 0.087 1.9E-06 43.5 1.4 33 259-291 1-35 (49)
18 KOG2130 Phosphatidylserine-spe 91.5 0.12 2.6E-06 57.5 2.6 43 768-810 261-303 (407)
19 cd02338 ZZ_PCMF_like Zinc fing 91.3 0.095 2.1E-06 43.2 1.2 31 259-289 1-33 (49)
20 COG0662 {ManC} Mannose-6-phosp 90.4 0.2 4.4E-06 47.9 2.7 43 769-811 74-116 (127)
21 cd02337 ZZ_CBP Zinc finger, ZZ 88.7 0.18 3.8E-06 40.5 0.8 29 260-289 2-31 (41)
22 TIGR03214 ura-cupin putative a 87.6 0.28 6E-06 52.7 1.7 30 765-794 213-242 (260)
23 cd02334 ZZ_dystrophin Zinc fin 87.2 0.39 8.4E-06 40.0 1.9 34 259-292 1-36 (49)
24 PRK09943 DNA-binding transcrip 84.1 0.78 1.7E-05 46.2 2.8 55 748-807 129-183 (185)
25 cd02343 ZZ_EF Zinc finger, ZZ 83.2 0.57 1.2E-05 39.2 1.2 32 259-290 1-33 (48)
26 PRK13290 ectC L-ectoine syntha 81.7 0.99 2.2E-05 43.8 2.3 37 769-807 74-110 (125)
27 PF07649 C1_3: C1-like domain; 81.4 0.61 1.3E-05 34.6 0.6 27 260-286 2-29 (30)
28 cd02342 ZZ_UBA_plant Zinc fing 79.9 0.97 2.1E-05 37.1 1.3 31 259-289 1-33 (43)
29 TIGR00218 manA mannose-6-phosp 79.0 1 2.2E-05 49.2 1.6 15 775-789 156-170 (302)
30 KOG4582 Uncharacterized conser 78.0 1 2.3E-05 49.2 1.3 58 207-290 127-186 (278)
31 PF01050 MannoseP_isomer: Mann 77.7 1.4 2.9E-05 44.3 1.9 22 775-796 107-128 (151)
32 PRK15131 mannose-6-phosphate i 77.0 1.2 2.7E-05 50.7 1.6 17 773-789 240-256 (389)
33 COG4101 Predicted mannose-6-ph 76.3 1.3 2.8E-05 43.7 1.2 26 771-796 89-114 (142)
34 PRK04190 glucose-6-phosphate i 72.2 2.7 5.9E-05 43.8 2.6 42 769-811 119-160 (191)
35 COG1482 ManA Phosphomannose is 70.5 2.2 4.8E-05 47.6 1.6 20 772-791 160-179 (312)
36 PLN02288 mannose-6-phosphate i 68.0 2.6 5.7E-05 48.3 1.5 15 775-789 256-270 (394)
37 PF10571 UPF0547: Uncharacteri 66.2 3.6 7.7E-05 30.4 1.4 23 260-282 2-24 (26)
38 PF13248 zf-ribbon_3: zinc-rib 66.1 2.9 6.3E-05 30.4 0.9 25 258-282 2-26 (26)
39 TIGR01479 GMP_PMI mannose-1-ph 65.1 3.5 7.6E-05 47.8 1.8 42 767-808 412-453 (468)
40 KOG0457 Histone acetyltransfer 64.1 2.7 5.9E-05 48.6 0.6 33 256-288 12-46 (438)
41 PF00190 Cupin_1: Cupin; Inte 63.9 6 0.00013 38.4 2.9 38 771-808 81-125 (144)
42 PF13240 zinc_ribbon_2: zinc-r 63.6 3.5 7.6E-05 29.5 0.9 23 260-282 1-23 (23)
43 cd02336 ZZ_RSC8 Zinc finger, Z 60.1 4.5 9.8E-05 33.4 1.1 35 260-297 2-37 (45)
44 COG5114 Histone acetyltransfer 59.8 2.8 6E-05 47.0 -0.2 31 258-288 5-37 (432)
45 KOG2508 Predicted phospholipas 59.5 9.5 0.00021 43.7 3.8 39 433-471 33-74 (437)
46 PF08007 Cupin_4: Cupin superf 58.6 9.8 0.00021 42.1 3.7 41 770-810 176-216 (319)
47 PRK15460 cpsB mannose-1-phosph 56.8 6.4 0.00014 46.3 2.0 46 766-811 420-465 (478)
48 KOG2583 Ubiquinol cytochrome c 56.4 7.6 0.00017 44.9 2.5 46 402-449 158-206 (429)
49 PTZ00194 60S ribosomal protein 54.5 6.1 0.00013 39.9 1.2 43 743-787 18-60 (143)
50 TIGR03404 bicupin_oxalic bicup 52.9 11 0.00024 42.9 3.0 85 739-825 258-343 (367)
51 PF02041 Auxin_BP: Auxin bindi 52.0 8 0.00017 39.6 1.6 41 749-794 75-115 (167)
52 KOG1280 Uncharacterized conser 52.0 5.7 0.00012 45.1 0.6 35 254-288 4-40 (381)
53 smart00835 Cupin_1 Cupin. This 51.2 12 0.00026 36.4 2.6 58 743-800 47-107 (146)
54 TIGR03214 ura-cupin putative a 50.0 12 0.00025 40.5 2.5 47 744-795 77-123 (260)
55 PF01238 PMI_typeI: Phosphoman 46.0 7.3 0.00016 44.2 0.2 18 773-790 253-270 (373)
56 PF02938 GAD: GAD domain; Int 43.3 8.4 0.00018 35.5 0.2 69 712-792 23-93 (95)
57 PRK01191 rpl24p 50S ribosomal 42.4 12 0.00026 36.8 1.1 42 743-786 17-58 (120)
58 PF03107 C1_2: C1 domain; Int 42.4 15 0.00032 27.5 1.3 27 260-286 2-29 (30)
59 PRK11171 hypothetical protein; 40.3 16 0.00035 39.5 1.8 28 767-794 98-125 (266)
60 KOG4286 Dystrophin-like protei 39.5 14 0.0003 45.7 1.3 36 260-295 605-642 (966)
61 PRK10371 DNA-binding transcrip 39.2 23 0.00049 38.6 2.7 33 765-797 59-91 (302)
62 PRK14892 putative transcriptio 38.9 21 0.00046 34.0 2.1 29 253-281 16-51 (99)
63 PRK14559 putative protein seri 37.6 19 0.00042 44.0 2.0 33 255-289 12-50 (645)
64 PRK12380 hydrogenase nickel in 36.9 19 0.0004 34.6 1.4 23 258-280 70-94 (113)
65 PRK13264 3-hydroxyanthranilate 36.1 27 0.00059 36.5 2.6 45 768-812 74-118 (177)
66 TIGR03037 anthran_nbaC 3-hydro 35.4 28 0.0006 35.8 2.5 46 768-813 68-113 (159)
67 KOG2107 Uncharacterized conser 34.6 28 0.00061 36.3 2.3 56 718-790 80-136 (179)
68 KOG3905 Dynein light intermedi 33.9 18 0.00039 41.4 0.9 24 764-787 289-313 (473)
69 TIGR03404 bicupin_oxalic bicup 32.6 43 0.00094 38.2 3.7 40 768-807 108-152 (367)
70 PF14446 Prok-RING_1: Prokaryo 31.6 22 0.00049 30.7 0.9 24 254-280 17-44 (54)
71 PF08271 TF_Zn_Ribbon: TFIIB z 31.4 27 0.00058 27.9 1.3 23 259-281 1-28 (43)
72 PRK11171 hypothetical protein; 31.1 28 0.00061 37.7 1.8 30 765-794 218-247 (266)
73 PF05899 Cupin_3: Protein of u 29.9 28 0.00061 30.7 1.3 17 771-787 45-61 (74)
74 PF12852 Cupin_6: Cupin 29.8 31 0.00066 34.6 1.7 24 772-795 57-80 (186)
75 PF02311 AraC_binding: AraC-li 29.2 39 0.00085 30.3 2.2 46 765-811 36-83 (136)
76 COG4039 Predicted membrane pro 28.9 31 0.00066 32.0 1.4 17 126-142 70-86 (86)
77 PF09567 RE_MamI: MamI restric 28.8 24 0.00053 38.9 0.8 21 260-280 84-104 (314)
78 PF02944 BESS: BESS motif; In 28.2 65 0.0014 25.2 2.9 24 212-235 6-29 (37)
79 TIGR02297 HpaA 4-hydroxyphenyl 27.2 50 0.0011 34.8 2.8 31 765-795 57-87 (287)
80 TIGR01080 rplX_A_E ribosomal p 26.7 36 0.00078 33.3 1.5 44 743-788 13-56 (114)
81 PRK13503 transcriptional activ 25.4 37 0.0008 35.5 1.4 31 765-795 48-78 (278)
82 PF08990 Docking: Erythronolid 25.1 54 0.0012 24.8 1.8 17 716-732 3-19 (27)
83 PF01783 Ribosomal_L32p: Ribos 24.5 51 0.0011 28.1 1.9 22 258-280 26-47 (56)
84 PRK12286 rpmF 50S ribosomal pr 24.5 44 0.00096 28.9 1.5 23 257-280 26-48 (57)
85 COG2956 Predicted N-acetylgluc 24.1 35 0.00076 39.1 1.0 22 258-279 354-375 (389)
86 TIGR00100 hypA hydrogenase nic 23.7 43 0.00092 32.3 1.4 23 258-280 70-94 (115)
87 PRK15457 ethanolamine utilizat 23.5 45 0.00098 36.3 1.7 75 705-793 142-216 (233)
88 PF10367 Vps39_2: Vacuolar sor 23.3 56 0.0012 29.5 2.1 23 248-270 68-90 (109)
89 smart00647 IBR In Between Ring 22.8 53 0.0012 27.0 1.7 32 257-288 17-56 (64)
90 PRK13501 transcriptional activ 22.4 48 0.001 35.3 1.7 29 765-793 51-79 (290)
91 PF06220 zf-U1: U1 zinc finger 22.4 37 0.00081 27.0 0.6 12 258-269 3-14 (38)
92 PF06249 EutQ: Ethanolamine ut 22.1 66 0.0014 32.9 2.4 21 767-787 110-130 (152)
93 PF14816 FAM178: Family of unk 21.0 56 0.0012 37.8 1.9 28 753-781 63-91 (377)
94 PF12773 DZR: Double zinc ribb 20.3 59 0.0013 26.2 1.4 26 255-280 9-37 (50)
95 PRK13502 transcriptional activ 20.3 1E+02 0.0022 32.6 3.5 30 765-794 51-80 (282)
No 1
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=100.00 E-value=1.1e-168 Score=1429.82 Aligned_cols=594 Identities=42% Similarity=0.692 Sum_probs=524.4
Q ss_pred CCCCcccccccCCCCccccc--cccccccccc----CChhhHHHHHH--HHHHHHhhhhhhcCHHHhhhhhhhhhhcccc
Q 002957 171 SSGSSDSVLKSNSNNNGRCT--ARNVKTSKIN----MTDCEKVEHLR--YLMVSLLPFIRQICEEQTQEIEFEASIQRVH 242 (863)
Q Consensus 171 ~~~ss~~~~~~~~~~~~~C~--~~~~k~~~~e----is~~~k~~~~~--yll~~lLP~Lkqi~~EQ~~E~EiEaki~G~~ 242 (863)
..+-.+.++.+.||+. .|. +....+.+.. .+..+++.++. |+|..++|+|+.++..|-.+.+.||+|||..
T Consensus 269 e~a~k~~~~~~~C~~~-q~h~~~~Lm~Tq~i~~~al~~~~~~~h~~r~k~~I~~~cpcl~~~~~~~~~~~~~e~~vq~~~ 347 (889)
T KOG1356|consen 269 EVAEKCEFSWLKCNKG-QCHALSELMPTQIIPGSALLDLSDRVHAVREKFGIKAHCPCLKKQNKQQPLDAETEASVQGTE 347 (889)
T ss_pred HhhhhhhHHHHhcCCc-cccchhhcccccccchhhhhhHHHHHHHHHHHhhHHhhChhHHhhhhhccccHHHHHHHhcCC
Confidence 3455678888888874 554 4445666666 77889999999 9999999999999999999999999999999
Q ss_pred CCcccccccccCCCCceecCCCCcccccccccCCCCCcccchhchHHHhcCcCCCccccceeeeccCCccccCCCCCCCc
Q 002957 243 SSKVGVSETLCGNDERVYCNHCATSIIDLHRSCPKCSYELCLTCCKEICEGRLSGRAEMKFQYVNRGYGYMQGGDPLPES 322 (863)
Q Consensus 243 ~~e~~i~~a~~~~DERv~CD~CkTSI~D~HRsC~~CsyDLCL~CC~ELR~G~l~g~~~~~~~~~~rg~~y~~g~~~~~~~ 322 (863)
+++ +++.+.++++|++|||+|.|||.|+||+||+|+|++||.||.+||+|.+.-..+..+.|.+||..|.||.++...+
T Consensus 348 ~~~-~~~~~~~~~~e~~~~~~~~~si~~l~r~cP~~s~~~~l~~~~~i~~g~l~~~~e~~~~~~~r~~~~~~g~~~~~~~ 426 (889)
T KOG1356|consen 348 PTS-KPPVTQANPEEPLYCDHCATSIGDLKRSCPDSSYAICLPWLADLRRGDLKEKEECELMLRSRGVKYEHGPDPIEPS 426 (889)
T ss_pred CCC-CccccccCcCCCccccccccchhhccccCCCccccccchHHHHhhcCCcccchhHHHHHHHHHHHhhcCccccccc
Confidence 988 7777888889999999999999999999999999999999999999988777666888999999999998875433
Q ss_pred cCCCCCCCCCCCCcccccCCCCCccCCCCCCCCCCCccccccccCcchhHHHHHHHHHHHHHHhcccccccccC-ccccC
Q 002957 323 CLHQTPDVHVEPSVMWSADDNGTISCPPTEMGGCGDCVLELTRILPDRWISDLEKEARDLVLILDNKLTNLRQN-RAETG 401 (863)
Q Consensus 323 ~~~~~~~~~~~~~~~W~a~~dGSIpCpPke~GgCg~s~L~Lrrifp~nwis~L~~~aee~~~~~~~~~~~~~~C-s~~~~ 401 (863)
-.....+. +.+ ++++|+|.|-|...+||+...|+|+|++|.-|.+.++..||.-+..+-+.... .-| +...+
T Consensus 427 ~~s~~~~~---~~~---~~~ng~~r~l~~~~~g~~~~~l~lkr~lpn~~~s~i~~~vE~k~~~~~~~~~l-~~~~~~~~~ 499 (889)
T KOG1356|consen 427 LSSVSVDE---PSS---ANENGSLRDLLLSLAGCLDRGLKLKRILPNILDSIIASVVENKLTSKLSKPPL-RLCRSSQDG 499 (889)
T ss_pred cCCCCCCC---Ccc---cccccchhhcccccCccchhhhhhhhcCchHHHHHHHHHHHhhcccccCCchh-hcCcccccc
Confidence 22111111 112 88999999999999999999999999999999999999999887775554432 223 22345
Q ss_pred cccchhccccCCCCCCeeecCCCCCCCchhhHHHHHHHhhcCCCEEEEccccccCCCCCChhHHHHHHhhhccccccccc
Q 002957 402 TDMLCKAASREGSDDNLLYCPDSTKIQEDEELFRFQKHWIKGEPVIVRNVLDKVTGLSWEPMVMWRALCENVDSEVSSKM 481 (863)
Q Consensus 402 ~~~lrkAA~Re~S~DN~LYcP~~~di~~~d~l~hFQ~HW~kGePVIVr~Vl~~~s~lsWeP~~mwra~~e~~~~~~~d~~ 481 (863)
.+.++++|.|+.+.|||||||.+.+.+. +||.|||+||++|||||||||++++++++|+||+|||+|+++.+.-..-.+
T Consensus 500 ~~~~~s~~~~~~~cdn~Ll~l~~d~~~~-~n~~~FQEhWkqGqPViVs~V~~~l~g~lW~P~a~~~~~g~q~~~l~n~~~ 578 (889)
T KOG1356|consen 500 SGLLLSAASHSWLCDNRLLSLKVDPLNQ-NNLKHFQEHWKQGQPVIVSGVHKKLNGLLWKPEALSRAFGDQVVDLSNCNN 578 (889)
T ss_pred ccCccccCCCCcCCCCceecCccCccch-hHHHHHHHHHhcCCcEEehHhhhhccccccchHHHHHHhccchhhhhcCCC
Confidence 6778899999999999999999944555 999999999999999999999999999999999999999998766666667
Q ss_pred CceeEeecCCCceeecchhhhhccccCCccCCCCCcceeeccCCCCCCchhhhcccchHHHHhCCCccccCCCCCccccc
Q 002957 482 SEVKAIDCLASCEVEISTRQFFKGYTQGRTYDNFWPEMLKLKDWPPSDKFEDLMPRHCDEFISALPFQEYSDPRAGILNL 561 (863)
Q Consensus 482 ~~vkaIDCld~~eVei~v~qFF~Gy~~gr~~~ngwp~mLKLKDWPps~~Fee~LPrh~~EFi~aLP~pEYT~Pr~G~LNL 561 (863)
.++.++||++ ++.+||.||++|+++++|||+|||||||||+++|+++||+||+|||++|||||||| ++|+|||
T Consensus 579 ~~i~s~d~~~------~fwegFe~~~kr~~~~~g~p~vLKLKDWpp~~~Fkd~lP~r~eell~sLPlpEYt~-r~G~LNl 651 (889)
T KOG1356|consen 579 SQIISNDCVD------NFWEGFEGYSKRLKSENGWPEVLKLKDWPPGEDFKDMLPRRFEELLASLPLPEYTD-RDGKLNL 651 (889)
T ss_pred CCccccchhh------hHHHhhcccccCcccccCCeeEEeecCCCchHhHhhhhhHHHHHHHHcCCchhhhc-CCCccch
Confidence 7788888888 78999999999999999999999999999999999999999999999999999999 8999999
Q ss_pred cccCCCCCCCCCCCcchhhccccccccCCCCCcccccccccchhhhhhcccccccchhhHHHHHHHHHHHHHhhhhhhhc
Q 002957 562 AVKLPSGVLKPDLGPKTYIAYGVAEELGRGDSVTKLHCDMSDAVNILTHTEEVLLTEEQHSAVERLKKEHRAQDLKENLV 641 (863)
Q Consensus 562 AskLP~~~lkPDLGPK~YIAYG~~eelGrGDSVTkLHcDmSDAVNIL~HtaeV~~~~~q~~~I~kLk~k~~~q~~~e~~~ 641 (863)
|++||.+|++||||||||||||+++++|||||||||||||||||||||||++++. +...|+++++++.+++..|+.-
T Consensus 652 As~LP~~fv~PDLGPk~y~AYG~~~e~gr~~gtTnLH~dvSDaVNILvyv~e~~~---~~~~~~~~~k~~~~~~~de~~~ 728 (889)
T KOG1356|consen 652 ASKLPEGFVRPDLGPKLYNAYGVSTELGRGDGTTNLHLDVSDAVNILVYVGEPPG---QIEQIAKVLKKIQEGDLDEITR 728 (889)
T ss_pred HhhCcccccCCCCCchhhhhccccccccCCCCceeeceehhhhhhheeeeccCCc---hHHhHHHHHHhhhhcchhhhhh
Confidence 9999999999999999999999999999999999999999999999999998776 4455666666655443322210
Q ss_pred cCCCCccccCCCCCCCCCCCccccccccCCCCCCcccccccccccccCCccccCCCCCCcCCCCceEEEeecCCChhHHH
Q 002957 642 QDGMDESIEEPNSDNNKEDTDVSEINDSELLPSGIRGEFKMSRDEMQGTAFTCPHSEGTMVESGGALWDIFRRQDVPKLE 721 (863)
Q Consensus 642 ~~~~~~~~~e~~~d~~~~d~~~~~~~~~e~~~s~~~~~~~~~~~~~~g~~~~~~~~~g~~~~~~GALWDIFRreDvpKLr 721 (863)
. ++ . +..+.+||||||||||||||||
T Consensus 729 ~----------------------~~------------------------------~--~~~e~~GALWhIF~~~Dv~Kir 754 (889)
T KOG1356|consen 729 S----------------------RI------------------------------S--SVSETPGALWHIFRAQDVPKIR 754 (889)
T ss_pred h----------------------hc------------------------------c--ccccCCcchhhhhhhcchHHHH
Confidence 0 00 0 0136899999999999999999
Q ss_pred HHHHHHHHhhccccCCCCCcccCCcccCccccCHHHHHHHHHHhCccceEEEeecCceEEecCCCccccccccccceeec
Q 002957 722 AYLRKHFKEFRHVYCSPVEQVIHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAV 801 (863)
Q Consensus 722 eYL~kh~~EFrh~~~~pv~~v~dPIHDQsfYLd~ehk~rLkEEyGVEpWTF~Q~lGEAVFIPAGCPHQVRNLkSCIKVAl 801 (863)
|||+||.+||+| ++.+|+||||||+||||.+||+|||||||||||||+|+||||||||||||||||||+||||||+
T Consensus 755 eyL~k~~~E~~~----~~~~v~hPIhDQS~YLd~~lr~RLkeEyGVe~WtfvQ~LGdAVfIPAGaPHQVrNLkSCikVa~ 830 (889)
T KOG1356|consen 755 EYLRKVCKEQGH----EVPKVHHPIHDQSWYLDRYLRRRLKEEYGVEPWTFVQFLGDAVFIPAGAPHQVRNLKSCIKVAE 830 (889)
T ss_pred HHHHHhhHHhcC----CCCcccCCCcccceeccHHHHHHHHHHhCCCccchhhcccceEEecCCCcHHhhhhhhHHHHHH
Confidence 999999999998 7899999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCcccHHHHHHHHHHhhcCChhhhcccchhcccceehhh
Q 002957 802 DFVSPENVDECLRLTKEFRLLPKNHRAREDKLEVYLVFIKR 842 (863)
Q Consensus 802 DFVSPEnV~eC~rLTeEfR~LP~~H~akEDKLEVKkm~lh~ 842 (863)
||||||||.||+|||+|||+||++|.|||||||||||+||+
T Consensus 831 DFVSPE~v~ec~rLT~EfR~Lp~~h~~~eDKLqvK~mi~hA 871 (889)
T KOG1356|consen 831 DFVSPEHVSECFRLTQEFRQLPQNHKNHEDKLQVKNMIYHA 871 (889)
T ss_pred hhCChhhHHHHHHHHHHHhhCCCcccchHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999998
No 2
>PF02373 JmjC: JmjC domain, hydroxylase; InterPro: IPR013129 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with jmjN (see IPR003349 from INTERPRO) and belongs to the Cupin superfamily [].; PDB: 2YU2_A 2YU1_A 3AVR_A 3AVS_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=99.52 E-value=1.1e-14 Score=131.46 Aligned_cols=86 Identities=33% Similarity=0.447 Sum_probs=64.6
Q ss_pred CCceEEEeecCCChhHHHHHHHHHHHhhccccCCCCCcccCCcccCccccCHHHHHHHHHHhCccceEEEeecCceEEec
Q 002957 704 SGGALWDIFRRQDVPKLEAYLRKHFKEFRHVYCSPVEQVIHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIP 783 (863)
Q Consensus 704 ~~GALWDIFRreDvpKLreYL~kh~~EFrh~~~~pv~~v~dPIHDQsfYLd~ehk~rLkEEyGVEpWTF~Q~lGEAVFIP 783 (863)
.+..+|-+++++|.+|++++++++... .+|+| +..+.+.-.+.. ..+.||+.|+|+|++||+||||
T Consensus 29 g~~k~W~~v~~~~~~~~~~~~~~~~~~------------~~~~~-~~~~~~~~~p~~-l~~~gi~~~~~~Q~~Ge~V~i~ 94 (114)
T PF02373_consen 29 GGSKVWYIVPPEDADKFEKFLRSKESQ------------NCPQF-LDHKNIFVSPEQ-LKKAGIPVYRFVQKPGEFVFIP 94 (114)
T ss_dssp ESEEEEEEE-GGGHHHHHHHHHHHHHH------------HSTTG-GCTGGEEEGHHH-HHHTTS--EEEEEETT-EEEE-
T ss_pred CcceEeEEechhhhhhHHHHHhhcccc------------ccccc-ccccccccceee-eeccCcccccceECCCCEEEEC
Confidence 357899999999999999999987221 34454 444444444443 6779999999999999999999
Q ss_pred CCCccccccccccceeeccc
Q 002957 784 AGCPHQVRNLKSCTKVAVDF 803 (863)
Q Consensus 784 AGCPHQVRNLkSCIKVAlDF 803 (863)
+|++|||.|+-.||++|.+|
T Consensus 95 pg~~H~v~n~g~~i~~a~Nf 114 (114)
T PF02373_consen 95 PGAYHQVFNLGDNISEAVNF 114 (114)
T ss_dssp TT-EEEEEESSSEEEEEEEE
T ss_pred CCceEEEEeCCceEEEEecC
Confidence 99999999999999999988
No 3
>PF13621 Cupin_8: Cupin-like domain; PDB: 3AL6_C 3AL5_C 2XUM_A 2Y0I_A 1MZE_A 3KCY_A 1MZF_A 1YCI_A 2ILM_A 1H2L_A ....
Probab=99.00 E-value=9.3e-11 Score=117.76 Aligned_cols=40 Identities=35% Similarity=0.544 Sum_probs=33.2
Q ss_pred cceEEEeecCceEEecCCCccccccc--cc-cceeeccccCcc
Q 002957 768 EPWTFEQKLGEAVFIPAGCPHQVRNL--KS-CTKVAVDFVSPE 807 (863)
Q Consensus 768 EpWTF~Q~lGEAVFIPAGCPHQVRNL--kS-CIKVAlDFVSPE 807 (863)
.+|.+++.+||++|||+|-.|||+|| .. ||.|...|..|.
T Consensus 207 ~~~~~~l~pGD~LfiP~gWwH~V~~~~~~~~sisvn~w~~~~~ 249 (251)
T PF13621_consen 207 PPYEVVLEPGDVLFIPPGWWHQVENLSDDDLSISVNYWFRTPF 249 (251)
T ss_dssp -EEEEEEETT-EEEE-TT-EEEEEESTTSSCEEEEEEEEESS-
T ss_pred ceeEEEECCCeEEEECCCCeEEEEEcCCCCeEEEEEEEecccc
Confidence 89999999999999999999999999 76 999999998764
No 4
>smart00558 JmjC A domain family that is part of the cupin metalloenzyme superfamily. Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).
Probab=96.63 E-value=0.00071 Score=55.81 Aligned_cols=54 Identities=41% Similarity=0.632 Sum_probs=42.8
Q ss_pred HHHhCCCccccCCCCCccccccccCCCCCCCCCCCcchhhccccccccCCCCCcccccccccchhhhhhccc
Q 002957 541 EFISALPFQEYSDPRAGILNLAVKLPSGVLKPDLGPKTYIAYGVAEELGRGDSVTKLHCDMSDAVNILTHTE 612 (863)
Q Consensus 541 EFi~aLP~pEYT~Pr~G~LNLAskLP~~~lkPDLGPK~YIAYG~~eelGrGDSVTkLHcDmSDAVNIL~Hta 612 (863)
..+..||+ .+||+.+++.....|+. +|+.+|. .+|+|.+|.|..|.+|++.+.+
T Consensus 3 ~~l~~lP~---------~~~ll~~~~~~~~~~~~---~~~~~G~------~~s~t~~H~d~~~~~n~~~~~~ 56 (57)
T smart00558 3 NNLAKLPF---------KLNLLSDLPEDILGPDV---PYLYMGM------AGSVTPWHIDDYDLVNYLHQGA 56 (57)
T ss_pred chhhhCCC---------cchHHHHCCcccCCCCc---ceEEEeC------CCCccceeEcCCCeEEEEEecC
Confidence 34567776 78999999988887877 6666664 4789999999999999887643
No 5
>KOG2131 consensus Uncharacterized conserved protein, contains JmjC domain [Chromatin structure and dynamics; Signal transduction mechanisms]
Probab=95.88 E-value=0.0081 Score=67.24 Aligned_cols=60 Identities=27% Similarity=0.394 Sum_probs=49.2
Q ss_pred HhCccceEEEeecCceEEecCCCccccccccccceeeccccCcccHHHHHH-HHHHhhcCC
Q 002957 764 EFGVEPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVDECLR-LTKEFRLLP 823 (863)
Q Consensus 764 EyGVEpWTF~Q~lGEAVFIPAGCPHQVRNLkSCIKVAlDFVSPEnV~eC~r-LTeEfR~LP 823 (863)
++.+.+.++-|.+||+||+|.|==|||-||-..|.|--.++--=|+..=.+ |-+++-.++
T Consensus 262 ~~~~~~lei~Qepge~VFvPsGW~hQV~NL~dTISINHNW~N~~nl~~~w~~Lk~~y~a~~ 322 (427)
T KOG2131|consen 262 LFRGPLLEIFQEPGETVFVPSGWHHQVLNLGDTISINHNWCNATNLAWMWDALKEDYPALA 322 (427)
T ss_pred ccccchhhhhccCCceeeccCccccccccccceeeecccccccccHHHHHHHHHhhhhhhh
Confidence 345677899999999999999999999999999999999998888877655 344454443
No 6
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=95.82 E-value=0.0041 Score=50.07 Aligned_cols=31 Identities=32% Similarity=0.935 Sum_probs=28.7
Q ss_pred eecCCCCcccccccccCCCC-CcccchhchHH
Q 002957 259 VYCNHCATSIIDLHRSCPKC-SYELCLTCCKE 289 (863)
Q Consensus 259 v~CD~CkTSI~D~HRsC~~C-syDLCL~CC~E 289 (863)
+.||.|+.+|..+...|..| .||||..|...
T Consensus 1 v~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~ 32 (43)
T cd02340 1 VICDGCQGPIVGVRYKCLVCPDYDLCESCEAK 32 (43)
T ss_pred CCCCCCCCcCcCCeEECCCCCCccchHHhhCc
Confidence 57999999999999999999 79999999873
No 7
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=95.37 E-value=0.0065 Score=49.04 Aligned_cols=32 Identities=25% Similarity=0.783 Sum_probs=29.4
Q ss_pred ecCCCCcccccccccCCCCC-cccchhchHHHh
Q 002957 260 YCNHCATSIIDLHRSCPKCS-YELCLTCCKEIC 291 (863)
Q Consensus 260 ~CD~CkTSI~D~HRsC~~Cs-yDLCL~CC~ELR 291 (863)
.||.|..+|...+..|..|. ||||..|..+-.
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc
Confidence 59999999999999999999 999999998543
No 8
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=95.29 E-value=0.0075 Score=49.49 Aligned_cols=30 Identities=30% Similarity=1.000 Sum_probs=28.2
Q ss_pred ecCCCCccccc-ccccCCCC-CcccchhchHH
Q 002957 260 YCNHCATSIID-LHRSCPKC-SYELCLTCCKE 289 (863)
Q Consensus 260 ~CD~CkTSI~D-~HRsC~~C-syDLCL~CC~E 289 (863)
.||+|...|.. ++-.|..| .||||+.|...
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~ 33 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSA 33 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhC
Confidence 59999999999 99999999 99999999984
No 9
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=94.95 E-value=0.011 Score=71.53 Aligned_cols=37 Identities=30% Similarity=0.978 Sum_probs=34.0
Q ss_pred CCCCceecCCCCcccccccccCCCCCcccchhchHHH
Q 002957 254 GNDERVYCNHCATSIIDLHRSCPKCSYELCLTCCKEI 290 (863)
Q Consensus 254 ~~DERv~CD~CkTSI~D~HRsC~~CsyDLCL~CC~EL 290 (863)
....|-+||.|.|++|+||+.|++|++.+|+.|.+.-
T Consensus 225 ~~g~~~mC~~C~~tlfn~hw~C~~C~~~~Cl~C~r~~ 261 (889)
T KOG1356|consen 225 VKGIREMCDRCETTLFNIHWRCPRCGFGVCLDCYRKW 261 (889)
T ss_pred ccCcchhhhhhcccccceeEEccccCCeeeecchhhc
Confidence 4677889999999999999999999999999998865
No 10
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=94.67 E-value=0.015 Score=47.40 Aligned_cols=30 Identities=37% Similarity=1.124 Sum_probs=28.0
Q ss_pred eecCCCC-cccccccccCCCC-CcccchhchH
Q 002957 259 VYCNHCA-TSIIDLHRSCPKC-SYELCLTCCK 288 (863)
Q Consensus 259 v~CD~Ck-TSI~D~HRsC~~C-syDLCL~CC~ 288 (863)
+.||.|+ .+|.-....|..| .||||..|..
T Consensus 1 i~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~ 32 (45)
T cd02339 1 IICDTCRKQGIIGIRWKCAECPNYDLCTTCYH 32 (45)
T ss_pred CCCCCCCCCCcccCeEECCCCCCccchHHHhC
Confidence 4799999 7899999999999 7999999998
No 11
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=94.60 E-value=0.018 Score=46.66 Aligned_cols=34 Identities=32% Similarity=0.806 Sum_probs=27.3
Q ss_pred CceecCCCCc-ccccccccCCCCC-cccchhchHHH
Q 002957 257 ERVYCNHCAT-SIIDLHRSCPKCS-YELCLTCCKEI 290 (863)
Q Consensus 257 ERv~CD~CkT-SI~D~HRsC~~Cs-yDLCL~CC~EL 290 (863)
..+.||.|++ +|.-....|..|. ||||..|..+-
T Consensus 3 ~~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~g 38 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSKG 38 (46)
T ss_dssp SSCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH-
T ss_pred CCeECcCCCCCcCcCCeEECCCCCCCchhhHHHhCc
Confidence 3578999999 9999999999998 99999999863
No 12
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=93.85 E-value=0.028 Score=45.13 Aligned_cols=35 Identities=26% Similarity=0.788 Sum_probs=30.8
Q ss_pred ceecCCCCcccccccccCCCC-CcccchhchHHHhc
Q 002957 258 RVYCNHCATSIIDLHRSCPKC-SYELCLTCCKEICE 292 (863)
Q Consensus 258 Rv~CD~CkTSI~D~HRsC~~C-syDLCL~CC~ELR~ 292 (863)
.+.||.|..+|......|..| .||||..|..+-+.
T Consensus 4 ~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~~~~ 39 (44)
T smart00291 4 SYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKGSA 39 (44)
T ss_pred CcCCCCCCCCCcCCEEECCCCCCccchHHHHhCcCc
Confidence 357999999999999999999 89999999986543
No 13
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=93.36 E-value=0.04 Score=45.20 Aligned_cols=31 Identities=29% Similarity=0.834 Sum_probs=28.2
Q ss_pred eecCCCCc-ccccccccCCCCC-cccchhchHH
Q 002957 259 VYCNHCAT-SIIDLHRSCPKCS-YELCLTCCKE 289 (863)
Q Consensus 259 v~CD~CkT-SI~D~HRsC~~Cs-yDLCL~CC~E 289 (863)
|.||.|.+ +|+-....|..|. ||||..|...
T Consensus 1 V~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~ 33 (45)
T cd02344 1 VTCDGCQMFPINGPRFKCRNCDDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCCCCCccCeEECCCCCCccchHHhhCC
Confidence 56999985 8999999999998 9999999976
No 14
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=93.07 E-value=0.041 Score=45.82 Aligned_cols=26 Identities=50% Similarity=0.814 Sum_probs=22.4
Q ss_pred EEEeecCceEEecCCCcccccccccc
Q 002957 771 TFEQKLGEAVFIPAGCPHQVRNLKSC 796 (863)
Q Consensus 771 TF~Q~lGEAVFIPAGCPHQVRNLkSC 796 (863)
++.=..||+++||||++|+++|..+.
T Consensus 38 ~~~l~~Gd~~~i~~~~~H~~~n~~~~ 63 (71)
T PF07883_consen 38 RVELKPGDAIYIPPGVPHQVRNPGDE 63 (71)
T ss_dssp EEEEETTEEEEEETTSEEEEEEESSS
T ss_pred EeEccCCEEEEECCCCeEEEEECCCC
Confidence 55557899999999999999998754
No 15
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=92.93 E-value=0.052 Score=44.96 Aligned_cols=31 Identities=26% Similarity=0.809 Sum_probs=28.5
Q ss_pred ecCCCCc-ccccccccCCCCC---cccchhchHHH
Q 002957 260 YCNHCAT-SIIDLHRSCPKCS---YELCLTCCKEI 290 (863)
Q Consensus 260 ~CD~CkT-SI~D~HRsC~~Cs---yDLCL~CC~EL 290 (863)
.||+|.. +|.-+...|..|. ||||..|...-
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~ 36 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKG 36 (48)
T ss_pred CCCCCCCCccccceEECCCCCCCCCccCHHHHhCc
Confidence 4999998 9999999999999 99999999843
No 16
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=92.81 E-value=0.048 Score=51.61 Aligned_cols=58 Identities=22% Similarity=0.379 Sum_probs=45.8
Q ss_pred CCcccCCcccCccccCHHHHHHHHHHhCccceEEEeecCceEEecCCCcccccccccc--ceeec
Q 002957 739 VEQVIHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQVRNLKSC--TKVAV 801 (863)
Q Consensus 739 v~~v~dPIHDQsfYLd~ehk~rLkEEyGVEpWTF~Q~lGEAVFIPAGCPHQVRNLkSC--IKVAl 801 (863)
+....||-++|.+|..+-.-+ |.++.=+++=+.||.|+||||.+|-+.|..+. +.+++
T Consensus 56 ~~~H~hp~~~~~~~Vl~G~~~-----~~~~g~~~~l~~Gd~i~ip~g~~H~~~a~~~~~~~~l~v 115 (131)
T COG1917 56 IPWHTHPLGEQTIYVLEGEGT-----VQLEGEKKELKAGDVIIIPPGVVHGLKAVEDEPMVLLLV 115 (131)
T ss_pred cccccCCCcceEEEEEecEEE-----EEecCCceEecCCCEEEECCCCeeeeccCCCCceeEEEE
Confidence 345689989999998776443 55556666778999999999999999999999 55543
No 17
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=91.70 E-value=0.087 Score=43.52 Aligned_cols=33 Identities=30% Similarity=0.803 Sum_probs=28.7
Q ss_pred eecCCCCc-ccccccccCCCC-CcccchhchHHHh
Q 002957 259 VYCNHCAT-SIIDLHRSCPKC-SYELCLTCCKEIC 291 (863)
Q Consensus 259 v~CD~CkT-SI~D~HRsC~~C-syDLCL~CC~ELR 291 (863)
+.||+|+. +|.-++..|..| .||||+.|...-+
T Consensus 1 ~~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~~ 35 (49)
T cd02345 1 LSCSACRKQDISGIRFPCQVCRDYSLCLGCYTKGR 35 (49)
T ss_pred CcCCCCCCCCceEeeEECCCCCCcCchHHHHhCCC
Confidence 36999998 999999999999 4999999998443
No 18
>KOG2130 consensus Phosphatidylserine-specific receptor PtdSerR, contains JmjC domain [Chromatin structure and dynamics; Signal transduction mechanisms]
Probab=91.54 E-value=0.12 Score=57.46 Aligned_cols=43 Identities=37% Similarity=0.560 Sum_probs=40.5
Q ss_pred cceEEEeecCceEEecCCCccccccccccceeeccccCcccHH
Q 002957 768 EPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVD 810 (863)
Q Consensus 768 EpWTF~Q~lGEAVFIPAGCPHQVRNLkSCIKVAlDFVSPEnV~ 810 (863)
+|-...|.+||.||||.|-=|=|-||.-.|-|++.|+|=||.+
T Consensus 261 kPIEc~q~pGEt~fVP~GWWHvVlNle~TIAiTqNf~s~eNf~ 303 (407)
T KOG2130|consen 261 KPIECLQKPGETMFVPSGWWHVVLNLEPTIAITQNFASKENFP 303 (407)
T ss_pred CCceeeecCCceEEecCCeEEEEeccCceeeeeeccccccCCc
Confidence 4667899999999999999999999999999999999999975
No 19
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=91.31 E-value=0.095 Score=43.25 Aligned_cols=31 Identities=29% Similarity=0.870 Sum_probs=27.9
Q ss_pred eecCCCC-cccccccccCCCC-CcccchhchHH
Q 002957 259 VYCNHCA-TSIIDLHRSCPKC-SYELCLTCCKE 289 (863)
Q Consensus 259 v~CD~Ck-TSI~D~HRsC~~C-syDLCL~CC~E 289 (863)
+.||+|+ .+|.-....|..| .||||..|...
T Consensus 1 i~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~ 33 (49)
T cd02338 1 VSCDGCGKSNFTGRRYKCLICYDYDLCADCYDS 33 (49)
T ss_pred CCCCCCcCCCcEEeeEEeCCCCCCccchhHHhC
Confidence 5799999 8999999999999 79999999983
No 20
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=90.37 E-value=0.2 Score=47.92 Aligned_cols=43 Identities=40% Similarity=0.611 Sum_probs=32.5
Q ss_pred ceEEEeecCceEEecCCCccccccccccceeeccccCcccHHH
Q 002957 769 PWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVDE 811 (863)
Q Consensus 769 pWTF~Q~lGEAVFIPAGCPHQVRNLkSCIKVAlDFVSPEnV~e 811 (863)
.=.++=+.||+|+||||.||.++|.-+.-=+.++=-+|+..++
T Consensus 74 ~~~~~v~~gd~~~iP~g~~H~~~N~G~~~L~liei~~p~~~~e 116 (127)
T COG0662 74 GEEVEVKAGDSVYIPAGTPHRVRNTGKIPLVLIEVQSPPYLGE 116 (127)
T ss_pred CEEEEecCCCEEEECCCCcEEEEcCCCcceEEEEEecCCcCCC
Confidence 5567778999999999999999999984444444446655443
No 21
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=88.74 E-value=0.18 Score=40.53 Aligned_cols=29 Identities=34% Similarity=1.040 Sum_probs=25.7
Q ss_pred ecCCCCcccccccccCCCC-CcccchhchHH
Q 002957 260 YCNHCATSIIDLHRSCPKC-SYELCLTCCKE 289 (863)
Q Consensus 260 ~CD~CkTSI~D~HRsC~~C-syDLCL~CC~E 289 (863)
.||.|.. |+-..+.|..| .||||..|...
T Consensus 2 ~C~~C~~-~~~~r~~C~~C~dfDLC~~C~~~ 31 (41)
T cd02337 2 TCNECKH-HVETRWHCTVCEDYDLCITCYNT 31 (41)
T ss_pred cCCCCCC-cCCCceECCCCcchhhHHHHhCC
Confidence 4999988 66799999999 89999999875
No 22
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=87.63 E-value=0.28 Score=52.69 Aligned_cols=30 Identities=13% Similarity=0.287 Sum_probs=24.5
Q ss_pred hCccceEEEeecCceEEecCCCcccccccc
Q 002957 765 FGVEPWTFEQKLGEAVFIPAGCPHQVRNLK 794 (863)
Q Consensus 765 yGVEpWTF~Q~lGEAVFIPAGCPHQVRNLk 794 (863)
|.+..=...=..||+|||||||||+..|.=
T Consensus 213 ~~~~g~~~~V~~GD~i~i~~~~~h~~~~~G 242 (260)
T TIGR03214 213 YNLDNNWVPVEAGDYIWMGAYCPQACYAGG 242 (260)
T ss_pred EEECCEEEEecCCCEEEECCCCCEEEEecC
Confidence 455555666778999999999999999964
No 23
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=87.20 E-value=0.39 Score=40.04 Aligned_cols=34 Identities=32% Similarity=0.766 Sum_probs=28.6
Q ss_pred eecCCCCc-ccccccccCCCC-CcccchhchHHHhc
Q 002957 259 VYCNHCAT-SIIDLHRSCPKC-SYELCLTCCKEICE 292 (863)
Q Consensus 259 v~CD~CkT-SI~D~HRsC~~C-syDLCL~CC~ELR~ 292 (863)
+-||.|+. +|.-+...|..| .||||..|+..-+.
T Consensus 1 ~~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~ 36 (49)
T cd02334 1 AKCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRT 36 (49)
T ss_pred CCCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCc
Confidence 46999995 799999999988 49999999975443
No 24
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=84.12 E-value=0.78 Score=46.23 Aligned_cols=55 Identities=13% Similarity=0.160 Sum_probs=41.5
Q ss_pred cCccccCHHHHHHHHHHhCccceEEEeecCceEEecCCCccccccccccceeeccccCcc
Q 002957 748 DQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPE 807 (863)
Q Consensus 748 DQsfYLd~ehk~rLkEEyGVEpWTF~Q~lGEAVFIPAGCPHQVRNLkSCIKVAlDFVSPE 807 (863)
++.+|+-.-.- ++-|..=++.-..||.++||||.||..+|..++-=+++-+++|-
T Consensus 129 ~E~~~Vl~G~~-----~~~~~~~~~~l~~Gd~~~~~~~~~H~~~n~~~~~~~~l~~~~p~ 183 (185)
T PRK09943 129 EEIGTVLEGEI-----VLTINGQDYHLVAGQSYAINTGIPHSFSNTSAGICRIISAHTPT 183 (185)
T ss_pred cEEEEEEEeEE-----EEEECCEEEEecCCCEEEEcCCCCeeeeCCCCCCeEEEEEeCCC
Confidence 45555543322 25566778889999999999999999999887766777777774
No 25
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=83.23 E-value=0.57 Score=39.16 Aligned_cols=32 Identities=25% Similarity=0.587 Sum_probs=26.5
Q ss_pred eecCCCCcccccccccCCCCC-cccchhchHHH
Q 002957 259 VYCNHCATSIIDLHRSCPKCS-YELCLTCCKEI 290 (863)
Q Consensus 259 v~CD~CkTSI~D~HRsC~~Cs-yDLCL~CC~EL 290 (863)
+.||.|...|.-+.-.|-.|. ||||..|...=
T Consensus 1 i~CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g 33 (48)
T cd02343 1 ISCDGCDEIAPWHRYRCLQCTDMDLCKTCFLGG 33 (48)
T ss_pred CCCCCCCCcCCCceEECCCCCCchhHHHHHhCC
Confidence 359999998888887888884 99999998743
No 26
>PRK13290 ectC L-ectoine synthase; Reviewed
Probab=81.67 E-value=0.99 Score=43.84 Aligned_cols=37 Identities=16% Similarity=0.098 Sum_probs=27.5
Q ss_pred ceEEEeecCceEEecCCCccccccccccceeeccccCcc
Q 002957 769 PWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPE 807 (863)
Q Consensus 769 pWTF~Q~lGEAVFIPAGCPHQVRNLkSCIKVAlDFVSPE 807 (863)
.=++.=..||+++||||-||+.+|...|.=++. ++|.
T Consensus 74 g~~~~L~aGD~i~~~~~~~H~~~N~e~~~~l~v--~tP~ 110 (125)
T PRK13290 74 GEVHPIRPGTMYALDKHDRHYLRAGEDMRLVCV--FNPP 110 (125)
T ss_pred CEEEEeCCCeEEEECCCCcEEEEcCCCEEEEEE--ECCC
Confidence 334555789999999999999999866554443 5554
No 27
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=81.43 E-value=0.61 Score=34.62 Aligned_cols=27 Identities=26% Similarity=0.806 Sum_probs=12.9
Q ss_pred ecCCCCccccc-ccccCCCCCcccchhc
Q 002957 260 YCNHCATSIID-LHRSCPKCSYELCLTC 286 (863)
Q Consensus 260 ~CD~CkTSI~D-~HRsC~~CsyDLCL~C 286 (863)
.|+.|+.+|.. +.-+|+.|.|.|.+.|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhc
Confidence 59999999998 8888999999999887
No 28
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=79.89 E-value=0.97 Score=37.15 Aligned_cols=31 Identities=23% Similarity=0.599 Sum_probs=27.1
Q ss_pred eecCCCC-cccccccccCCCC-CcccchhchHH
Q 002957 259 VYCNHCA-TSIIDLHRSCPKC-SYELCLTCCKE 289 (863)
Q Consensus 259 v~CD~Ck-TSI~D~HRsC~~C-syDLCL~CC~E 289 (863)
+.||.|. .||+-+-..|..| .||||-.|..+
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~ 33 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSR 33 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhh
Confidence 3699999 5999999999977 69999999875
No 29
>TIGR00218 manA mannose-6-phosphate isomerase, class I. The names phosphomannose isomerase and mannose-6-phosphate isomerase are synonomous. This family contains two rather deeply branched groups. One group contains an experimentally determined phosphomannose isomerase of Streptococcus mutans as well as three uncharacterized paralogous proteins of Bacillus subtilis, all at more than 50 % identity to each other, plus a more distant homolog from Archaeoglobus fulgidus. The other group contains members from E. coli, budding yeast, Borrelia burgdorferi, etc.
Probab=79.03 E-value=1 Score=49.22 Aligned_cols=15 Identities=40% Similarity=0.986 Sum_probs=13.7
Q ss_pred ecCceEEecCCCccc
Q 002957 775 KLGEAVFIPAGCPHQ 789 (863)
Q Consensus 775 ~lGEAVFIPAGCPHQ 789 (863)
++||+||||||.||=
T Consensus 156 ~~Gd~i~ipaGt~HA 170 (302)
T TIGR00218 156 KPGDFFYVPSGTPHA 170 (302)
T ss_pred CCCCEEEeCCCCccc
Confidence 479999999999995
No 30
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=78.00 E-value=1 Score=49.17 Aligned_cols=58 Identities=24% Similarity=0.615 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHhhhhhhcCHHHhhhhhhhhhhccccCCcccccccccCCCCceecCCCCc-ccccccccCCCCC-cccch
Q 002957 207 VEHLRYLMVSLLPFIRQICEEQTQEIEFEASIQRVHSSKVGVSETLCGNDERVYCNHCAT-SIIDLHRSCPKCS-YELCL 284 (863)
Q Consensus 207 ~~~~~yll~~lLP~Lkqi~~EQ~~E~EiEaki~G~~~~e~~i~~a~~~~DERv~CD~CkT-SI~D~HRsC~~Cs-yDLCL 284 (863)
.+-+++++..+-|.+-.+|..--+- -+-||+|.+ .|+-.-..|.-|. ||||-
T Consensus 127 ~~~~~~~~~~~~~~~~~~H~~~~~~--------------------------~v~CD~C~~~~IvG~RyKC~~C~dYDLCe 180 (278)
T KOG4582|consen 127 YQKLASLVITLNPVVGEMHPNISKL--------------------------SVPCDNCGKPGIVGARYKCTVCPDYDLCE 180 (278)
T ss_pred HhhhhhhhhhcCCCccccCCCcccc--------------------------cccCCCccCCccccceeeecCCCccchhH
Confidence 7778888888888766665431110 467999999 9999999999995 99999
Q ss_pred hchHHH
Q 002957 285 TCCKEI 290 (863)
Q Consensus 285 ~CC~EL 290 (863)
.|-...
T Consensus 181 ~Ce~~~ 186 (278)
T KOG4582|consen 181 RCEAGN 186 (278)
T ss_pred HhhcCC
Confidence 998753
No 31
>PF01050 MannoseP_isomer: Mannose-6-phosphate isomerase; InterPro: IPR001538 Mannose-6-phosphate isomerase or phosphomannose isomerase (5.3.1.8 from EC) (PMI) is the enzyme that catalyses the interconversion of mannose-6-phosphate and fructose-6-phosphate. In eukaryotes PMI is involved in the synthesis of GDP-mannose, a constituent of N- and O-linked glycans and GPI anchors and in prokaryotes it participates in a variety of pathways, including capsular polysaccharide biosynthesis and D-mannose metabolism. PMI's belong to the cupin superfamily whose functions range from isomerase and epimerase activities involved in the modification of cell wall carbohydrates in bacteria and plants, to non-enzymatic storage proteins in plant seeds, and transcription factors linked to congenital baldness in mammals []. Three classes of PMI have been defined []. The type II phosphomannose isomerases are bifunctional enzymes 5.3.1.8 from EC. This entry covers the isomerase region of the protein []. The guanosine diphospho-D-mannose pyrophosphorylase region is described in another InterPro entry (see IPR005836 from INTERPRO).; GO: 0016779 nucleotidyltransferase activity, 0005976 polysaccharide metabolic process
Probab=77.65 E-value=1.4 Score=44.34 Aligned_cols=22 Identities=36% Similarity=0.724 Sum_probs=19.5
Q ss_pred ecCceEEecCCCcccccccccc
Q 002957 775 KLGEAVFIPAGCPHQVRNLKSC 796 (863)
Q Consensus 775 ~lGEAVFIPAGCPHQVRNLkSC 796 (863)
..||.|+||+|+.|++.|.-+.
T Consensus 107 ~~g~sv~Ip~g~~H~i~n~g~~ 128 (151)
T PF01050_consen 107 KEGDSVYIPRGAKHRIENPGKT 128 (151)
T ss_pred cCCCEEEECCCCEEEEECCCCc
Confidence 5799999999999999998654
No 32
>PRK15131 mannose-6-phosphate isomerase; Provisional
Probab=76.99 E-value=1.2 Score=50.68 Aligned_cols=17 Identities=41% Similarity=0.643 Sum_probs=14.9
Q ss_pred EeecCceEEecCCCccc
Q 002957 773 EQKLGEAVFIPAGCPHQ 789 (863)
Q Consensus 773 ~Q~lGEAVFIPAGCPHQ 789 (863)
.=++|||+|||||.||=
T Consensus 240 ~l~pGeaifipAg~~HA 256 (389)
T PRK15131 240 KLNPGEAMFLFAETPHA 256 (389)
T ss_pred EeCCCCEEEeCCCCCeE
Confidence 34689999999999996
No 33
>COG4101 Predicted mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=76.28 E-value=1.3 Score=43.71 Aligned_cols=26 Identities=38% Similarity=0.604 Sum_probs=23.0
Q ss_pred EEEeecCceEEecCCCcccccccccc
Q 002957 771 TFEQKLGEAVFIPAGCPHQVRNLKSC 796 (863)
Q Consensus 771 TF~Q~lGEAVFIPAGCPHQVRNLkSC 796 (863)
+.+-.+||...||+|.|||--||.+-
T Consensus 89 ha~~~pGDf~YiPpgVPHqp~N~S~e 114 (142)
T COG4101 89 HAEVGPGDFFYIPPGVPHQPANLSTE 114 (142)
T ss_pred eEEecCCCeEEcCCCCCCcccccCCC
Confidence 56778999999999999999999753
No 34
>PRK04190 glucose-6-phosphate isomerase; Provisional
Probab=72.23 E-value=2.7 Score=43.79 Aligned_cols=42 Identities=19% Similarity=0.253 Sum_probs=31.3
Q ss_pred ceEEEeecCceEEecCCCccccccccccceeeccccCcccHHH
Q 002957 769 PWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVDE 811 (863)
Q Consensus 769 pWTF~Q~lGEAVFIPAGCPHQVRNLkSCIKVAlDFVSPEnV~e 811 (863)
.+.+.=..||+|+||+|..|++.|.-+.-=+.+- +.|...++
T Consensus 119 ~~~~~v~pGd~v~IPpg~~H~~iN~G~epl~fl~-v~p~~~~~ 160 (191)
T PRK04190 119 ARWIEMEPGTVVYVPPYWAHRSVNTGDEPLVFLA-CYPADAGH 160 (191)
T ss_pred EEEEEECCCCEEEECCCCcEEeEECCCCCEEEEE-EEcCCccc
Confidence 7889999999999999999999998754433332 44444443
No 35
>COG1482 ManA Phosphomannose isomerase [Carbohydrate transport and metabolism]
Probab=70.53 E-value=2.2 Score=47.65 Aligned_cols=20 Identities=50% Similarity=0.821 Sum_probs=16.9
Q ss_pred EEeecCceEEecCCCccccc
Q 002957 772 FEQKLGEAVFIPAGCPHQVR 791 (863)
Q Consensus 772 F~Q~lGEAVFIPAGCPHQVR 791 (863)
+.=++|||+|||||.||=.-
T Consensus 160 v~lkpGe~~fl~Agt~HA~~ 179 (312)
T COG1482 160 VKLKPGEAFFLPAGTPHAYL 179 (312)
T ss_pred EecCCCCEEEecCCCceeec
Confidence 55678999999999999743
No 36
>PLN02288 mannose-6-phosphate isomerase
Probab=67.99 E-value=2.6 Score=48.32 Aligned_cols=15 Identities=40% Similarity=0.720 Sum_probs=13.9
Q ss_pred ecCceEEecCCCccc
Q 002957 775 KLGEAVFIPAGCPHQ 789 (863)
Q Consensus 775 ~lGEAVFIPAGCPHQ 789 (863)
.+|||||||||.||=
T Consensus 256 ~PGeaifl~ag~~HA 270 (394)
T PLN02288 256 NPGEALYLGANEPHA 270 (394)
T ss_pred CCCCEEEecCCCCce
Confidence 589999999999995
No 37
>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=66.19 E-value=3.6 Score=30.41 Aligned_cols=23 Identities=26% Similarity=0.959 Sum_probs=20.8
Q ss_pred ecCCCCcccccccccCCCCCccc
Q 002957 260 YCNHCATSIIDLHRSCPKCSYEL 282 (863)
Q Consensus 260 ~CD~CkTSI~D~HRsC~~CsyDL 282 (863)
.|..|..-|-.--+.||.|+|++
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 48899999999999999999985
No 38
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=66.09 E-value=2.9 Score=30.39 Aligned_cols=25 Identities=28% Similarity=0.814 Sum_probs=22.1
Q ss_pred ceecCCCCcccccccccCCCCCccc
Q 002957 258 RVYCNHCATSIIDLHRSCPKCSYEL 282 (863)
Q Consensus 258 Rv~CD~CkTSI~D~HRsC~~CsyDL 282 (863)
.++|.+|.+.|-+=.+-|++|+..|
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 3689999999999999999999765
No 39
>TIGR01479 GMP_PMI mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase. This enzyme is known to be bifunctional, as both mannose-6-phosphate isomerase (EC 5.3.1.8) (PMI) and mannose-1-phosphate guanylyltransferase (EC 2.7.7.22) in Pseudomonas aeruginosa, Xanthomonas campestris, and Gluconacetobacter xylinus. The literature on the enzyme from E. coli attributes mannose-6-phosphate isomerase activity to an adjacent gene, but the present sequence has not been shown to lack the activity. The PMI domain is C-terminal.
Probab=65.12 E-value=3.5 Score=47.85 Aligned_cols=42 Identities=19% Similarity=0.217 Sum_probs=29.1
Q ss_pred ccceEEEeecCceEEecCCCccccccccccceeeccccCccc
Q 002957 767 VEPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPEN 808 (863)
Q Consensus 767 VEpWTF~Q~lGEAVFIPAGCPHQVRNLkSCIKVAlDFVSPEn 808 (863)
+..=++.=..||.|+||+|.||+.+|.-+.-=+.+--.+|+-
T Consensus 412 ~dg~~~~l~~GDsi~ip~~~~H~~~N~g~~~~~~i~v~~~~~ 453 (468)
T TIGR01479 412 IGDETLLLTENESTYIPLGVIHRLENPGKIPLELIEVQSGSY 453 (468)
T ss_pred ECCEEEEecCCCEEEECCCCcEEEEcCCCCCEEEEEEEcCCC
Confidence 334456678999999999999999998764333333344543
No 40
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=64.05 E-value=2.7 Score=48.62 Aligned_cols=33 Identities=30% Similarity=0.896 Sum_probs=29.4
Q ss_pred CCceecCCCCccccccc-ccCCCCC-cccchhchH
Q 002957 256 DERVYCNHCATSIIDLH-RSCPKCS-YELCLTCCK 288 (863)
Q Consensus 256 DERv~CD~CkTSI~D~H-RsC~~Cs-yDLCL~CC~ 288 (863)
.+...||+|.--|-+.- -.|..|- |||||-|+.
T Consensus 12 g~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs 46 (438)
T KOG0457|consen 12 GGKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFS 46 (438)
T ss_pred CCCCCCccHhHHhccceEEEeecCCCcchhHHHHh
Confidence 46788999999999865 8999999 999999986
No 41
>PF00190 Cupin_1: Cupin; InterPro: IPR006045 This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant. ; GO: 0045735 nutrient reservoir activity; PDB: 2E9Q_A 2EVX_A 1OD5_A 1UCX_A 1UD1_C 1FXZ_C 3KGL_C 3KSC_D 1UIJ_F 1IPK_B ....
Probab=63.89 E-value=6 Score=38.39 Aligned_cols=38 Identities=32% Similarity=0.496 Sum_probs=26.6
Q ss_pred EEEee----cCceEEecCCCccccccc--cccceeecccc-Cccc
Q 002957 771 TFEQK----LGEAVFIPAGCPHQVRNL--KSCTKVAVDFV-SPEN 808 (863)
Q Consensus 771 TF~Q~----lGEAVFIPAGCPHQVRNL--kSCIKVAlDFV-SPEn 808 (863)
.+.|. .||.++||+|.||=+.|. .+.+.++.=+. +|++
T Consensus 81 ~~~~~v~l~~Gdv~~vP~G~~h~~~n~~~~~~~~~~~f~~~~~~~ 125 (144)
T PF00190_consen 81 DFSQKVRLKAGDVFVVPAGHPHWIINDGDDEALVLIIFDTNNPPN 125 (144)
T ss_dssp EEEEEEEEETTEEEEE-TT-EEEEEECSSSSEEEEEEEEESSTTG
T ss_pred eeeceeeeecccceeeccceeEEEEcCCCCCCEEEEEEECCCCcc
Confidence 45565 999999999999999999 56666655444 4444
No 42
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=63.64 E-value=3.5 Score=29.52 Aligned_cols=23 Identities=39% Similarity=0.969 Sum_probs=20.6
Q ss_pred ecCCCCcccccccccCCCCCccc
Q 002957 260 YCNHCATSIIDLHRSCPKCSYEL 282 (863)
Q Consensus 260 ~CD~CkTSI~D~HRsC~~CsyDL 282 (863)
||-+|...|-|=.+-|++|+..|
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCcC
Confidence 68999999999999999999865
No 43
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=60.11 E-value=4.5 Score=33.36 Aligned_cols=35 Identities=29% Similarity=0.690 Sum_probs=27.7
Q ss_pred ecCCCCcccccccccCCCCC-cccchhchHHHhcCcCCC
Q 002957 260 YCNHCATSIIDLHRSCPKCS-YELCLTCCKEICEGRLSG 297 (863)
Q Consensus 260 ~CD~CkTSI~D~HRsC~~Cs-yDLCL~CC~ELR~G~l~g 297 (863)
.||.|..-+..-+-+|.++. ||||..|+.+ |+.++
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~---G~f~~ 37 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE---GRFPS 37 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC---cCCCC
Confidence 58888888877777788887 9999999985 55543
No 44
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=59.79 E-value=2.8 Score=47.04 Aligned_cols=31 Identities=32% Similarity=0.929 Sum_probs=27.3
Q ss_pred ceecCCCCcccccc-cccCCCC-CcccchhchH
Q 002957 258 RVYCNHCATSIIDL-HRSCPKC-SYELCLTCCK 288 (863)
Q Consensus 258 Rv~CD~CkTSI~D~-HRsC~~C-syDLCL~CC~ 288 (863)
...||+|..-|.|. |-+|..| -||||+-|+-
T Consensus 5 k~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~ 37 (432)
T COG5114 5 KIHCDVCFLDMTDLTFIKCNECPAVDLCLPCFV 37 (432)
T ss_pred eeeehHHHHhhhcceeeeeecccccceehhhhh
Confidence 46799999999986 5689999 9999999985
No 45
>KOG2508 consensus Predicted phospholipase [Lipid transport and metabolism]
Probab=59.53 E-value=9.5 Score=43.71 Aligned_cols=39 Identities=26% Similarity=0.491 Sum_probs=31.7
Q ss_pred HHHHHHHh-hcCCCEEEEccccccCCC-CCChh-HHHHHHhh
Q 002957 433 LFRFQKHW-IKGEPVIVRNVLDKVTGL-SWEPM-VMWRALCE 471 (863)
Q Consensus 433 l~hFQ~HW-~kGePVIVr~Vl~~~s~l-sWeP~-~mwra~~e 471 (863)
-.+|-+-| .+..|||+|+.+..-.++ .|.+. ++..|++.
T Consensus 33 pl~Fyr~fvs~n~PvIIrkAL~hWpal~lWs~p~Yl~~algd 74 (437)
T KOG2508|consen 33 PLDFYRKFVSTNTPVIIRKALPHWPALKLWSQPDYLLSALGD 74 (437)
T ss_pred hHHHHHhhhcCCCcEEEecccccCchhhccCchHHHHHhccC
Confidence 46788888 789999999999977777 89888 77766654
No 46
>PF08007 Cupin_4: Cupin superfamily protein; InterPro: IPR022777 This signature represents primarily the cupin fold found in JmjC transcription factors. The fold is also found in lysine-specific demethylase NO66.; PDB: 2XDV_A 1VRB_B 4DIQ_B.
Probab=58.60 E-value=9.8 Score=42.08 Aligned_cols=41 Identities=22% Similarity=0.366 Sum_probs=31.2
Q ss_pred eEEEeecCceEEecCCCccccccccccceeeccccCcccHH
Q 002957 770 WTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVD 810 (863)
Q Consensus 770 WTF~Q~lGEAVFIPAGCPHQVRNLkSCIKVAlDFVSPEnV~ 810 (863)
..|+=.+||..+||.|++|++.....|+.+++-|..|--..
T Consensus 176 ~~~~L~pGD~LYlPrG~~H~~~~~~~S~hltv~~~~~t~~d 216 (319)
T PF08007_consen 176 EEVVLEPGDVLYLPRGWWHQAVTTDPSLHLTVGFRAPTWAD 216 (319)
T ss_dssp EEEEE-TT-EEEE-TT-EEEEEESS-EEEEEEEECCEBHHH
T ss_pred EEEEECCCCEEEECCCccCCCCCCCCceEEEEeeeCCchhh
Confidence 35777899999999999999999999999999999985444
No 47
>PRK15460 cpsB mannose-1-phosphate guanyltransferase; Provisional
Probab=56.77 E-value=6.4 Score=46.26 Aligned_cols=46 Identities=17% Similarity=0.198 Sum_probs=30.4
Q ss_pred CccceEEEeecCceEEecCCCccccccccccceeeccccCcccHHH
Q 002957 766 GVEPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVDE 811 (863)
Q Consensus 766 GVEpWTF~Q~lGEAVFIPAGCPHQVRNLkSCIKVAlDFVSPEnV~e 811 (863)
.|..=++.=..||.|+||+|.||+.+|.-.=-=+.+--.+|+-++|
T Consensus 420 ~idg~~~~L~~GDSi~ip~g~~H~~~N~g~~~l~iI~V~~g~yl~e 465 (478)
T PRK15460 420 TIDGDIKLLGENESIYIPLGATHCLENPGKIPLDLIEVRSGSYLEE 465 (478)
T ss_pred EECCEEEEecCCCEEEECCCCcEEEEcCCCCCEEEEEEEcCCCCCC
Confidence 3444456668999999999999999998542222222355554444
No 48
>KOG2583 consensus Ubiquinol cytochrome c reductase, subunit QCR2 [Energy production and conversion]
Probab=56.43 E-value=7.6 Score=44.90 Aligned_cols=46 Identities=37% Similarity=0.557 Sum_probs=39.5
Q ss_pred cccchhccccCCCCCCeeecCC--CCCCCchhhHHHH-HHHhhcCCCEEEE
Q 002957 402 TDMLCKAASREGSDDNLLYCPD--STKIQEDEELFRF-QKHWIKGEPVIVR 449 (863)
Q Consensus 402 ~~~lrkAA~Re~S~DN~LYcP~--~~di~~~d~l~hF-Q~HW~kGePVIVr 449 (863)
-++|.+||+|. +-.|-||||. ...+.. .++.+| ++|..+|.-|+|-
T Consensus 158 ~e~lH~aAfRn-gLgnslY~p~~~vg~vss-~eL~~Fa~k~fv~gn~~lvg 206 (429)
T KOG2583|consen 158 IEQLHAAAFRN-GLGNSLYSPGYQVGSVSS-SELKDFAAKHFVKGNAVLVG 206 (429)
T ss_pred HHHHHHHHHhc-ccCCcccCCcccccCccH-HHHHHHHHHHhhccceEEEe
Confidence 46789999998 7899999996 666777 889999 6899999999885
No 49
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=54.50 E-value=6.1 Score=39.91 Aligned_cols=43 Identities=19% Similarity=0.317 Sum_probs=39.1
Q ss_pred cCCcccCccccCHHHHHHHHHHhCccceEEEeecCceEEecCCCc
Q 002957 743 IHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCP 787 (863)
Q Consensus 743 ~dPIHDQsfYLd~ehk~rLkEEyGVEpWTF~Q~lGEAVFIPAGCP 787 (863)
.-|+|...-.+.+.+=+.|+++|||..|.| +-||-|.|=+|=.
T Consensus 18 ~Ap~h~r~k~msa~LSkeLr~k~~~Rs~~I--kkGD~V~Vi~Gk~ 60 (143)
T PTZ00194 18 TAPSHLRRKLMSAPLSKELRAKYNVRSMPV--RKDDEVMVVRGHH 60 (143)
T ss_pred cCcHHHHHHHhcCccCHHHHHHhCCcccee--ecCCEEEEecCCC
Confidence 578999999999999999999999999987 7799999988864
No 50
>TIGR03404 bicupin_oxalic bicupin, oxalate decarboxylase family. Members of this protein family are defined as bicupins as they have two copies of the cupin domain (pfam00190). Two different known activities for members of this family are oxalate decarboxylase (EC 4.1.1.2) and oxalate oxidase (EC 1.2.3.4), although the latter activity has more often been found in distantly related monocupin (germin) proteins.
Probab=52.89 E-value=11 Score=42.88 Aligned_cols=85 Identities=21% Similarity=0.311 Sum_probs=48.5
Q ss_pred CCcccCCcccCccccCHH-HHHHHHHHhCccceEEEeecCceEEecCCCccccccccccceeeccccCcccHHHHHHHHH
Q 002957 739 VEQVIHPIHDQCFYLSSE-HKKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVDECLRLTK 817 (863)
Q Consensus 739 v~~v~dPIHDQsfYLd~e-hk~rLkEEyGVEpWTF~Q~lGEAVFIPAGCPHQVRNLkSCIKVAlDFVSPEnV~eC~rLTe 817 (863)
.....||--+..+|+-.- -+..+-..-| ...++.=..||++|||+|.+|.++|.-+--=+-+-+.+....+.- .|++
T Consensus 258 ~~~H~H~~~~E~~yvl~G~~~~~v~d~~g-~~~~~~l~~GD~~~iP~g~~H~i~N~G~e~l~fL~if~s~~~~~i-~l~~ 335 (367)
T TIGR03404 258 RELHWHPNADEWQYFIQGQARMTVFAAGG-NARTFDYQAGDVGYVPRNMGHYVENTGDETLVFLEVFKADRFADV-SLNQ 335 (367)
T ss_pred cCCeeCcCCCeEEEEEEEEEEEEEEecCC-cEEEEEECCCCEEEECCCCeEEEEECCCCCEEEEEEECCCCCcee-EHHH
Confidence 345678876775665433 2221111111 356677789999999999999999997543333333333322221 2455
Q ss_pred HhhcCChh
Q 002957 818 EFRLLPKN 825 (863)
Q Consensus 818 EfR~LP~~ 825 (863)
=+..+|.+
T Consensus 336 ~l~~~p~~ 343 (367)
T TIGR03404 336 WLALTPPQ 343 (367)
T ss_pred HHhhCCHH
Confidence 55555544
No 51
>PF02041 Auxin_BP: Auxin binding protein; InterPro: IPR000526 Auxin binding protein is located in the lumen of the endoplasmic reticulum (ER). The primary structure contains an N-terminal hydrophobic leader sequence of 30-40 amino acids, which could represent a signal for translocation of the protein to the ER [, ]. The mature protein comprises around 165 residues, and contains a number of potential N-glycosylation sites. In vitro transport studies have demonstrated co-translational glycosylation []. Retention within the lumen of the ER correlates with an additional signal located at the C terminus, represented by the sequence Lys-Asp-Glu-Leu, known to be responsible for preventing secretion of proteins from the lumen of the ER in eukaryotic cells [, ].; GO: 0004872 receptor activity, 0005788 endoplasmic reticulum lumen; PDB: 1LR5_D 1LRH_D.
Probab=52.04 E-value=8 Score=39.61 Aligned_cols=41 Identities=32% Similarity=0.456 Sum_probs=24.2
Q ss_pred CccccCHHHHHHHHHHhCccceEEEeecCceEEecCCCcccccccc
Q 002957 749 QCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQVRNLK 794 (863)
Q Consensus 749 QsfYLd~ehk~rLkEEyGVEpWTF~Q~lGEAVFIPAGCPHQVRNLk 794 (863)
++.||...+ ++|.-+|=.|.=.++.-.-||.+|+|||.|-.
T Consensus 75 GTl~l~~~~-----~~~pG~pqef~~~pnSTf~IPvn~~HQv~NT~ 115 (167)
T PF02041_consen 75 GTLYLASSH-----EKYPGKPQEFPIFPNSTFHIPVNDAHQVWNTN 115 (167)
T ss_dssp EEEEE--SS-----SSS--S-EEEEE-TTEEEEE-TT--EEEE---
T ss_pred eEEEEeccc-----ccCCCCceEEEecCCCeEEeCCCCcceeecCC
Confidence 356776433 26999999999999999999999999999954
No 52
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=52.00 E-value=5.7 Score=45.09 Aligned_cols=35 Identities=34% Similarity=1.009 Sum_probs=28.8
Q ss_pred CCCCceecCCCCcccccccc-cCCCCC-cccchhchH
Q 002957 254 GNDERVYCNHCATSIIDLHR-SCPKCS-YELCLTCCK 288 (863)
Q Consensus 254 ~~DERv~CD~CkTSI~D~HR-sC~~Cs-yDLCL~CC~ 288 (863)
+--|+|-||.|..-=|-|.| -|-.|+ ||||-+|+.
T Consensus 4 ~rHe~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCye 40 (381)
T KOG1280|consen 4 SRHEGVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYE 40 (381)
T ss_pred CCcCCceeccccccceeeeeeEeeeecchhHHHHHhh
Confidence 34589999999887777766 488886 999999986
No 53
>smart00835 Cupin_1 Cupin. This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant.
Probab=51.19 E-value=12 Score=36.38 Aligned_cols=58 Identities=21% Similarity=0.338 Sum_probs=35.8
Q ss_pred cCCcccCccccCHHH-HHHHHHHhCccceEEEeecCceEEecCCCcccccccc--ccceee
Q 002957 743 IHPIHDQCFYLSSEH-KKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQVRNLK--SCTKVA 800 (863)
Q Consensus 743 ~dPIHDQsfYLd~eh-k~rLkEEyGVEpWTF~Q~lGEAVFIPAGCPHQVRNLk--SCIKVA 800 (863)
.||-.++-+|+-.-. +-.+-++.|=+-+++.-..||+++||+|-+|+..|.- .+.-++
T Consensus 47 ~H~~~~e~~~Vl~G~~~~~~~~~~~~~~~~~~l~~GD~~~ip~g~~H~~~n~~~~~~~~l~ 107 (146)
T smart00835 47 YHPRATELLYVVRGEGRVGVVDPNGNKVYDARLREGDVFVVPQGHPHFQVNSGDENLEFVA 107 (146)
T ss_pred eCCCCCEEEEEEeCeEEEEEEeCCCCeEEEEEecCCCEEEECCCCEEEEEcCCCCCEEEEE
Confidence 455445555643321 2111122222557888999999999999999999974 344443
No 54
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=49.95 E-value=12 Score=40.51 Aligned_cols=47 Identities=17% Similarity=0.240 Sum_probs=32.4
Q ss_pred CCcccCccccCHHHHHHHHHHhCccceEEEeecCceEEecCCCccccccccc
Q 002957 744 HPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQVRNLKS 795 (863)
Q Consensus 744 dPIHDQsfYLd~ehk~rLkEEyGVEpWTF~Q~lGEAVFIPAGCPHQVRNLkS 795 (863)
|+-.++-+|+-.---. .-+..-+++=..||+++||||+||..+|...
T Consensus 77 ~~g~ee~iyVl~G~l~-----v~~~g~~~~L~~Gd~~y~pa~~~H~~~N~~~ 123 (260)
T TIGR03214 77 GEGIETFLFVISGEVN-----VTAEGETHELREGGYAYLPPGSKWTLANAQA 123 (260)
T ss_pred CCceEEEEEEEeCEEE-----EEECCEEEEECCCCEEEECCCCCEEEEECCC
Confidence 3444455665433221 2345667788889999999999999999863
No 55
>PF01238 PMI_typeI: Phosphomannose isomerase type I; InterPro: IPR001250 Mannose-6-phosphate isomerase or phosphomannose isomerase (5.3.1.8 from EC) (PMI) is the enzyme that catalyses the interconversion of mannose-6-phosphate and fructose-6-phosphate. In eukaryotes PMI is involved in the synthesis of GDP-mannose, a constituent of N- and O-linked glycans and GPI anchors and in prokaryotes it participates in a variety of pathways, including capsular polysaccharide biosynthesis and D-mannose metabolism. PMI's belong to the cupin superfamily whose functions range from isomerase and epimerase activities involved in the modification of cell wall carbohydrates in bacteria and plants, to non-enzymatic storage proteins in plant seeds, and transcription factors linked to congenital baldness in mammals []. Three classes of PMI have been defined []. Type I includes eukaryotic PMI and the enzyme encoded by the manA gene in enterobacteria. PMI has a bound zinc ion, which is essential for activity. A crystal structure of PMI from Candida albicans shows that the enzyme has three distinct domains []. The active site lies in the central domain, contains a single essential zinc atom, and forms a deep, open cavity of suitable dimensions to contain M6P or F6P The central domain is flanked by a helical domain on one side and a jelly-roll like domain on the other.; GO: 0004476 mannose-6-phosphate isomerase activity, 0008270 zinc ion binding, 0005975 carbohydrate metabolic process; PDB: 1PMI_A 1QWR_B 1ZX5_A 3H1Y_A 2WFP_A 3H1M_A 3H1W_A.
Probab=45.98 E-value=7.3 Score=44.21 Aligned_cols=18 Identities=56% Similarity=0.973 Sum_probs=13.9
Q ss_pred EeecCceEEecCCCcccc
Q 002957 773 EQKLGEAVFIPAGCPHQV 790 (863)
Q Consensus 773 ~Q~lGEAVFIPAGCPHQV 790 (863)
.=.+|||+|+|||.||-.
T Consensus 253 ~L~pGeaifl~a~~~HAY 270 (373)
T PF01238_consen 253 ELQPGEAIFLPAGEPHAY 270 (373)
T ss_dssp EE-TT-EEEEHTTHHEEE
T ss_pred EecCCceEEecCCCcccc
Confidence 335999999999999984
No 56
>PF02938 GAD: GAD domain; InterPro: IPR004115 This entry represetns an 2 layer alpha/beta insertion domain found in some glutamyl-tRNA amidotransferases and aspartyl tRNA synthetases [, ]. The function of this domain is not yet known.; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0005737 cytoplasm; PDB: 1ZQ1_D 1EQR_B 1IL2_B 1C0A_A 1L0W_A 1G51_B 1EFW_B 2D6F_D.
Probab=43.33 E-value=8.4 Score=35.47 Aligned_cols=69 Identities=29% Similarity=0.468 Sum_probs=42.9
Q ss_pred ecCCChhHHHHHHHHHHHhhccccCCCC--CcccCCcccCccccCHHHHHHHHHHhCccceEEEeecCceEEecCCCccc
Q 002957 712 FRRQDVPKLEAYLRKHFKEFRHVYCSPV--EQVIHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQ 789 (863)
Q Consensus 712 FRreDvpKLreYL~kh~~EFrh~~~~pv--~~v~dPIHDQsfYLd~ehk~rLkEEyGVEpWTF~Q~lGEAVFIPAGCPHQ 789 (863)
|.|...++|.+|.++.-.. ...-..+ .....||-. ||+++.+++|.+.+|.++ ||+||+=||-.+.
T Consensus 23 ~srk~id~l~~~ak~~ga~--gL~~ikv~~~~~~s~i~k---fl~e~~~~~l~~~~~a~~-------GD~ll~~Ag~~~~ 90 (95)
T PF02938_consen 23 LSRKQIDKLEEFAKKFGAK--GLAWIKVEEGELKSPIAK---FLSEEELKALIERLGAKP-------GDLLLFVAGKKEI 90 (95)
T ss_dssp TTHCCCCCCCCHHHHCCHC--HCCCEEESTCEEECTTCC---CCHHHHHHHHHHHTT--T-------TEEEEEEEESHHH
T ss_pred CCHHHHHHHHHHHHHhCCC--CceeeeEcCCcccCcccc---cCCHHHHHHHHHHhCCCC-------CCEEEEECCCHHH
Confidence 4556666666666532111 0000000 233455543 599999999999999985 9999999999888
Q ss_pred ccc
Q 002957 790 VRN 792 (863)
Q Consensus 790 VRN 792 (863)
|++
T Consensus 91 v~~ 93 (95)
T PF02938_consen 91 VNK 93 (95)
T ss_dssp HHH
T ss_pred HHh
Confidence 764
No 57
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=42.42 E-value=12 Score=36.83 Aligned_cols=42 Identities=24% Similarity=0.426 Sum_probs=37.3
Q ss_pred cCCcccCccccCHHHHHHHHHHhCccceEEEeecCceEEecCCC
Q 002957 743 IHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGC 786 (863)
Q Consensus 743 ~dPIHDQsfYLd~ehk~rLkEEyGVEpWTF~Q~lGEAVFIPAGC 786 (863)
.-|.|...-.+.+.+=+.|+++|||..|.+ +.||-|.|=||-
T Consensus 17 ~a~~~~r~k~msa~LSkeLr~~y~ir~~~I--kkGD~V~VisG~ 58 (120)
T PRK01191 17 NAPLHLRQKLMSAPLSKELREKYGIRSLPV--RKGDTVKVMRGD 58 (120)
T ss_pred cCCHHHHHHHhcCccCHHHHHHhCCccceE--eCCCEEEEeecC
Confidence 467888888899999999999999999977 589999999985
No 58
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=42.38 E-value=15 Score=27.55 Aligned_cols=27 Identities=26% Similarity=0.892 Sum_probs=22.6
Q ss_pred ecCCCCcccccc-cccCCCCCcccchhc
Q 002957 260 YCNHCATSIIDL-HRSCPKCSYELCLTC 286 (863)
Q Consensus 260 ~CD~CkTSI~D~-HRsC~~CsyDLCL~C 286 (863)
-|+.|...+-.+ --+|..|.|.|-+.|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCFTLHVRC 29 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCCeEcCcc
Confidence 388888888888 888899889888876
No 59
>PRK11171 hypothetical protein; Provisional
Probab=40.26 E-value=16 Score=39.55 Aligned_cols=28 Identities=25% Similarity=0.372 Sum_probs=23.4
Q ss_pred ccceEEEeecCceEEecCCCcccccccc
Q 002957 767 VEPWTFEQKLGEAVFIPAGCPHQVRNLK 794 (863)
Q Consensus 767 VEpWTF~Q~lGEAVFIPAGCPHQVRNLk 794 (863)
+..=++.=..||.|+||+|.||+.+|.-
T Consensus 98 ~~g~~~~L~~GDsi~~p~~~~H~~~N~g 125 (266)
T PRK11171 98 LEGKTHALSEGGYAYLPPGSDWTLRNAG 125 (266)
T ss_pred ECCEEEEECCCCEEEECCCCCEEEEECC
Confidence 3444667788999999999999999975
No 60
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=39.52 E-value=14 Score=45.66 Aligned_cols=36 Identities=25% Similarity=0.482 Sum_probs=30.4
Q ss_pred ecCCCC-cccccccccCCCCC-cccchhchHHHhcCcC
Q 002957 260 YCNHCA-TSIIDLHRSCPKCS-YELCLTCCKEICEGRL 295 (863)
Q Consensus 260 ~CD~Ck-TSI~D~HRsC~~Cs-yDLCL~CC~ELR~G~l 295 (863)
-|+.|+ .+|+-|...|-+|. ||||++|+--=|.|.-
T Consensus 605 kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak~ 642 (966)
T KOG4286|consen 605 KCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAKG 642 (966)
T ss_pred hcchhhhCccceeeeeehhhcChhHHhhHhhhcccccC
Confidence 499997 59999999999995 8999999987666543
No 61
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=39.20 E-value=23 Score=38.65 Aligned_cols=33 Identities=18% Similarity=0.322 Sum_probs=28.0
Q ss_pred hCccceEEEeecCceEEecCCCccccccccccc
Q 002957 765 FGVEPWTFEQKLGEAVFIPAGCPHQVRNLKSCT 797 (863)
Q Consensus 765 yGVEpWTF~Q~lGEAVFIPAGCPHQVRNLkSCI 797 (863)
|-|.+-++.-.+||+||||+|.||+......|-
T Consensus 59 ~~i~g~~~~l~~Gd~ili~s~~~H~~~~~~~~~ 91 (302)
T PRK10371 59 YLINNEKVQINQGHITLFWACTPHQLTDPGNCR 91 (302)
T ss_pred EEECCEEEEEcCCcEEEEecCCcccccccCCCc
Confidence 667888899999999999999999987666554
No 62
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=38.88 E-value=21 Score=34.04 Aligned_cols=29 Identities=17% Similarity=0.334 Sum_probs=23.1
Q ss_pred cCCCCceecCCCCccccc-------ccccCCCCCcc
Q 002957 253 CGNDERVYCNHCATSIID-------LHRSCPKCSYE 281 (863)
Q Consensus 253 ~~~DERv~CD~CkTSI~D-------~HRsC~~CsyD 281 (863)
...+-.+.|.+|....+. .|+.|++|+|-
T Consensus 16 ~klpt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 16 PKLPKIFECPRCGKVSISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred cCCCcEeECCCCCCeEeeeecCCCcceEECCCCCCc
Confidence 334456789999987777 79999999983
No 63
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=37.63 E-value=19 Score=44.00 Aligned_cols=33 Identities=36% Similarity=1.020 Sum_probs=24.4
Q ss_pred CCCceecCCCCcccccccccCCCCCcc------cchhchHH
Q 002957 255 NDERVYCNHCATSIIDLHRSCPKCSYE------LCLTCCKE 289 (863)
Q Consensus 255 ~DERv~CD~CkTSI~D~HRsC~~CsyD------LCL~CC~E 289 (863)
.+.--||..|.+++. +..||+|+.. +|..|=..
T Consensus 12 ~~~akFC~~CG~~l~--~~~Cp~CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 12 PNNNRFCQKCGTSLT--HKPCPQCGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CCCCccccccCCCCC--CCcCCCCCCCCCcccccccccCCc
Confidence 455568888888874 4678888887 78888544
No 64
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=36.90 E-value=19 Score=34.65 Aligned_cols=23 Identities=26% Similarity=0.791 Sum_probs=18.3
Q ss_pred ceecCCCCc--ccccccccCCCCCc
Q 002957 258 RVYCNHCAT--SIIDLHRSCPKCSY 280 (863)
Q Consensus 258 Rv~CD~CkT--SI~D~HRsC~~Csy 280 (863)
+.+|..|.. ++-+++..||+|+-
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQHDAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCCcCccCcCCCC
Confidence 679999975 55567788999983
No 65
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=36.10 E-value=27 Score=36.48 Aligned_cols=45 Identities=16% Similarity=0.265 Sum_probs=38.6
Q ss_pred cceEEEeecCceEEecCCCccccccccccceeeccccCcccHHHH
Q 002957 768 EPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVDEC 812 (863)
Q Consensus 768 EpWTF~Q~lGEAVFIPAGCPHQVRNLkSCIKVAlDFVSPEnV~eC 812 (863)
+..++.=+.||..+||+|.||..+.-..||-+.+.=..|+..-.+
T Consensus 74 ~~~~v~L~eGd~fllP~gvpHsP~r~~~tv~LviE~~r~~~~~d~ 118 (177)
T PRK13264 74 KRRDVPIREGEMFLLPPHVPHSPQREAGSIGLVIERKRPEGELDG 118 (177)
T ss_pred ceeeEEECCCCEEEeCCCCCcCCccCCCeEEEEEEeCCCCCCccc
Confidence 346788899999999999999998899999999888888866553
No 66
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=35.43 E-value=28 Score=35.84 Aligned_cols=46 Identities=11% Similarity=0.237 Sum_probs=40.2
Q ss_pred cceEEEeecCceEEecCCCccccccccccceeeccccCcccHHHHH
Q 002957 768 EPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVDECL 813 (863)
Q Consensus 768 EpWTF~Q~lGEAVFIPAGCPHQVRNLkSCIKVAlDFVSPEnV~eC~ 813 (863)
+..++.=..||..+||+|.||..+--..||=+.+.=..|++...++
T Consensus 68 ~~~~v~L~eGd~flvP~gvpHsP~r~~~t~~LvIE~~r~~~~~d~~ 113 (159)
T TIGR03037 68 KREDVPIREGDIFLLPPHVPHSPQRPAGSIGLVIERKRPQGELDGF 113 (159)
T ss_pred cEEEEEECCCCEEEeCCCCCcccccCCCcEEEEEEeCCCCCCCcce
Confidence 3567888899999999999999888999999999999999877643
No 67
>KOG2107 consensus Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=34.58 E-value=28 Score=36.29 Aligned_cols=56 Identities=23% Similarity=0.453 Sum_probs=41.8
Q ss_pred hHHHHHHHHHHHhhccccCCCCCcccCCcccCccccCHHHHHHHHHHhCccceEEEe-ecCceEEecCCCcccc
Q 002957 718 PKLEAYLRKHFKEFRHVYCSPVEQVIHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQ-KLGEAVFIPAGCPHQV 790 (863)
Q Consensus 718 pKLreYL~kh~~EFrh~~~~pv~~v~dPIHDQsfYLd~ehk~rLkEEyGVEpWTF~Q-~lGEAVFIPAGCPHQV 790 (863)
+||..|...|..++. .+-=|-+++-|.|.+-+. +-|-=.+ .-||-|+||||.=|--
T Consensus 80 eKvk~FfEEhlh~de---------eiR~il~GtgYfDVrd~d--------d~WIRi~vekGDlivlPaGiyHRF 136 (179)
T KOG2107|consen 80 EKVKSFFEEHLHEDE---------EIRYILEGTGYFDVRDKD--------DQWIRIFVEKGDLIVLPAGIYHRF 136 (179)
T ss_pred HHHHHHHHHhcCchh---------heEEEeecceEEeeccCC--------CCEEEEEEecCCEEEecCcceeee
Confidence 688888887766542 344577888999888775 6776555 4699999999998863
No 68
>KOG3905 consensus Dynein light intermediate chain [Cell motility]
Probab=33.89 E-value=18 Score=41.42 Aligned_cols=24 Identities=38% Similarity=0.419 Sum_probs=15.0
Q ss_pred HhCccceEEEe-ecCceEEecCCCc
Q 002957 764 EFGVEPWTFEQ-KLGEAVFIPAGCP 787 (863)
Q Consensus 764 EyGVEpWTF~Q-~lGEAVFIPAGCP 787 (863)
-||.---|=-| -.-||||||||--
T Consensus 289 ~yG~~fttpAlVVEkdaVfIPAGWD 313 (473)
T KOG3905|consen 289 SYGFPFTTPALVVEKDAVFIPAGWD 313 (473)
T ss_pred hcCcccCCcceEeecceeEeccCCC
Confidence 36654333333 3469999999963
No 69
>TIGR03404 bicupin_oxalic bicupin, oxalate decarboxylase family. Members of this protein family are defined as bicupins as they have two copies of the cupin domain (pfam00190). Two different known activities for members of this family are oxalate decarboxylase (EC 4.1.1.2) and oxalate oxidase (EC 1.2.3.4), although the latter activity has more often been found in distantly related monocupin (germin) proteins.
Probab=32.56 E-value=43 Score=38.20 Aligned_cols=40 Identities=18% Similarity=0.425 Sum_probs=28.5
Q ss_pred cceEEEeecCceEEecCCCccccccccccceeec-----cccCcc
Q 002957 768 EPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAV-----DFVSPE 807 (863)
Q Consensus 768 EpWTF~Q~lGEAVFIPAGCPHQVRNLkSCIKVAl-----DFVSPE 807 (863)
+-+++.=..||.++||+|.+|-.+|...=..+.+ .|-+|.
T Consensus 108 ~~~~~~L~~GD~~~fP~g~~H~~~n~~~~~~~l~vf~~~~f~~~~ 152 (367)
T TIGR03404 108 RNYIDDVGAGDLWYFPPGIPHSLQGLDEGCEFLLVFDDGNFSEDG 152 (367)
T ss_pred cEEEeEECCCCEEEECCCCeEEEEECCCCeEEEEEeCCcccCCcc
Confidence 3455567899999999999999999854323333 355565
No 70
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=31.61 E-value=22 Score=30.69 Aligned_cols=24 Identities=33% Similarity=0.787 Sum_probs=19.8
Q ss_pred CCCCceecCCCCcccccccccCC----CCCc
Q 002957 254 GNDERVYCNHCATSIIDLHRSCP----KCSY 280 (863)
Q Consensus 254 ~~DERv~CD~CkTSI~D~HRsC~----~Csy 280 (863)
+.|..|.|.-|.++ |||.|- .|.+
T Consensus 17 ~~dDiVvCp~Cgap---yHR~C~~~~g~C~~ 44 (54)
T PF14446_consen 17 DGDDIVVCPECGAP---YHRDCWEKAGGCIN 44 (54)
T ss_pred CCCCEEECCCCCCc---ccHHHHhhCCceEe
Confidence 47888999999998 899996 5554
No 71
>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=31.37 E-value=27 Score=27.93 Aligned_cols=23 Identities=30% Similarity=0.947 Sum_probs=16.0
Q ss_pred eecCCCCcc--cccccc---cCCCCCcc
Q 002957 259 VYCNHCATS--IIDLHR---SCPKCSYE 281 (863)
Q Consensus 259 v~CD~CkTS--I~D~HR---sC~~CsyD 281 (863)
|.|.+|..+ ++|+.+ .|++|++-
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLV 28 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BB
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCE
Confidence 578889886 678664 67777763
No 72
>PRK11171 hypothetical protein; Provisional
Probab=31.10 E-value=28 Score=37.72 Aligned_cols=30 Identities=17% Similarity=0.286 Sum_probs=26.9
Q ss_pred hCccceEEEeecCceEEecCCCcccccccc
Q 002957 765 FGVEPWTFEQKLGEAVFIPAGCPHQVRNLK 794 (863)
Q Consensus 765 yGVEpWTF~Q~lGEAVFIPAGCPHQVRNLk 794 (863)
+.+..-++.=..||++++|+++||+.+|.-
T Consensus 218 ~~~~~~~~~l~~GD~i~~~~~~~h~~~N~g 247 (266)
T PRK11171 218 YRLNNDWVEVEAGDFIWMRAYCPQACYAGG 247 (266)
T ss_pred EEECCEEEEeCCCCEEEECCCCCEEEECCC
Confidence 677888888899999999999999999963
No 73
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=29.94 E-value=28 Score=30.71 Aligned_cols=17 Identities=41% Similarity=0.714 Sum_probs=12.7
Q ss_pred EEEeecCceEEecCCCc
Q 002957 771 TFEQKLGEAVFIPAGCP 787 (863)
Q Consensus 771 TF~Q~lGEAVFIPAGCP 787 (863)
+..=..||+||||+|..
T Consensus 45 ~~~~~aGD~~~~p~G~~ 61 (74)
T PF05899_consen 45 TVTFKAGDAFFLPKGWT 61 (74)
T ss_dssp EEEEETTEEEEE-TTEE
T ss_pred EEEEcCCcEEEECCCCE
Confidence 34457999999999984
No 74
>PF12852 Cupin_6: Cupin
Probab=29.81 E-value=31 Score=34.59 Aligned_cols=24 Identities=21% Similarity=0.457 Sum_probs=18.8
Q ss_pred EEeecCceEEecCCCccccccccc
Q 002957 772 FEQKLGEAVFIPAGCPHQVRNLKS 795 (863)
Q Consensus 772 F~Q~lGEAVFIPAGCPHQVRNLkS 795 (863)
+.=..||.||+|.|.||...--..
T Consensus 57 ~~L~~GDivllp~g~~H~l~~~~~ 80 (186)
T PF12852_consen 57 IRLEAGDIVLLPRGTAHVLSSDPD 80 (186)
T ss_pred EEecCCCEEEEcCCCCeEeCCCCC
Confidence 444679999999999999854433
No 75
>PF02311 AraC_binding: AraC-like ligand binding domain; InterPro: IPR003313 This entry defines the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The crystal structure of the arabinose-binding and dimerization domain of the Escherichia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1XJA_B 2ARA_A 2AAC_B 2ARC_A.
Probab=29.15 E-value=39 Score=30.31 Aligned_cols=46 Identities=24% Similarity=0.404 Sum_probs=28.4
Q ss_pred hCccceEEEeecCceEEecCCCcccccccc--ccceeeccccCcccHHH
Q 002957 765 FGVEPWTFEQKLGEAVFIPAGCPHQVRNLK--SCTKVAVDFVSPENVDE 811 (863)
Q Consensus 765 yGVEpWTF~Q~lGEAVFIPAGCPHQVRNLk--SCIKVAlDFVSPEnV~e 811 (863)
+.|..=++.=.+||++|||.|.+|...--. .+....+.| +|+-+.+
T Consensus 36 ~~~~~~~~~l~~g~~~li~p~~~H~~~~~~~~~~~~~~i~~-~~~~~~~ 83 (136)
T PF02311_consen 36 LHIDGQEYPLKPGDLFLIPPGQPHSYYPDSNEPWEYYWIYF-SPDFLEE 83 (136)
T ss_dssp EEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE----GGGG
T ss_pred EEECCEEEEEECCEEEEecCCccEEEecCCCCCEEEEEEEE-CHHHHHH
Confidence 345566677789999999999999987777 677777766 5554444
No 76
>COG4039 Predicted membrane protein [Function unknown]
Probab=28.88 E-value=31 Score=32.04 Aligned_cols=17 Identities=59% Similarity=0.685 Sum_probs=15.0
Q ss_pred HHHHHhhhhhcccCCCC
Q 002957 126 ALIRIRERRRSRRLEPD 142 (863)
Q Consensus 126 ~~~~~~~~~~~~~~~~~ 142 (863)
.||||+++||+++|+|.
T Consensus 70 yl~ri~~~rrs~~~~~~ 86 (86)
T COG4039 70 YLIRIEEKRRSARNLPI 86 (86)
T ss_pred HHHhHHHHHhhcccCCC
Confidence 38999999999999973
No 77
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=28.85 E-value=24 Score=38.85 Aligned_cols=21 Identities=38% Similarity=1.043 Sum_probs=19.8
Q ss_pred ecCCCCcccccccccCCCCCc
Q 002957 260 YCNHCATSIIDLHRSCPKCSY 280 (863)
Q Consensus 260 ~CD~CkTSI~D~HRsC~~Csy 280 (863)
-|++|.+-+.-|.-+||+|+.
T Consensus 84 ~C~~CGa~V~~~e~~Cp~C~S 104 (314)
T PF09567_consen 84 KCNNCGANVSRLEESCPNCGS 104 (314)
T ss_pred hhccccceeeehhhcCCCCCc
Confidence 699999999999999999975
No 78
>PF02944 BESS: BESS motif; InterPro: IPR004210 The BESS domain has been named after the three proteins that originally defined the domain: BEAF (Boundary element associated factor 32) [], Suvar(3)7 [] and Stonewall []). The BESS domain is 40 amino acid residues long and is predicted to be composed of three alpha helices, as such it might be related to the myb/SANT HTH domain. The BESS domain directs a variety of protein-protein interactions, including interactions with itself, with Dorsal, and with a TBP-associated factor. It is found in a single copy in Drosophila proteins and is often associated with the MADF domain [, , ]. Proteins known to contain a BESS domain include: Drosophila Boundary element associated factor 32 (BEAF-32). Drosophila Suppressor of variegation protein 3-7 (Su(var)3-7), which could play a role in chromosome condensation. Drosophila Ravus, which is homologous to the C-terminal part of Su(var)3-7 []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation. Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3). It functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. ; GO: 0003677 DNA binding
Probab=28.15 E-value=65 Score=25.18 Aligned_cols=24 Identities=21% Similarity=0.539 Sum_probs=20.3
Q ss_pred HHHHHHhhhhhhcCHHHhhhhhhh
Q 002957 212 YLMVSLLPFIRQICEEQTQEIEFE 235 (863)
Q Consensus 212 yll~~lLP~Lkqi~~EQ~~E~EiE 235 (863)
+.|-+++|.+|++...|..+.+++
T Consensus 6 ~Fl~Sl~p~~k~L~~~~k~~~k~~ 29 (37)
T PF02944_consen 6 LFLLSLLPHMKRLPPKQKLKFKMK 29 (37)
T ss_pred HHHHHhHHHHHhCCHHHHHHHHHH
Confidence 567789999999999999886655
No 79
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=27.17 E-value=50 Score=34.79 Aligned_cols=31 Identities=10% Similarity=0.177 Sum_probs=24.9
Q ss_pred hCccceEEEeecCceEEecCCCccccccccc
Q 002957 765 FGVEPWTFEQKLGEAVFIPAGCPHQVRNLKS 795 (863)
Q Consensus 765 yGVEpWTF~Q~lGEAVFIPAGCPHQVRNLkS 795 (863)
+.|..=++.=..||+||||+|.+|+++.-.+
T Consensus 57 ~~~~~~~~~l~~g~~~ii~~~~~H~~~~~~~ 87 (287)
T TIGR02297 57 LQLDEHEYSEYAPCFFLTPPSVPHGFVTDLD 87 (287)
T ss_pred EEECCEEEEecCCeEEEeCCCCccccccCCC
Confidence 5566667777799999999999999875444
No 80
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=26.68 E-value=36 Score=33.28 Aligned_cols=44 Identities=25% Similarity=0.372 Sum_probs=39.2
Q ss_pred cCCcccCccccCHHHHHHHHHHhCccceEEEeecCceEEecCCCcc
Q 002957 743 IHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCPH 788 (863)
Q Consensus 743 ~dPIHDQsfYLd~ehk~rLkEEyGVEpWTF~Q~lGEAVFIPAGCPH 788 (863)
.-|+|...-++...+=+.|.++||++.+.| +-||-|-|=+|-=.
T Consensus 13 ~a~~~~r~~~~~a~ls~elr~~y~~r~~~I--kkGD~V~Vi~Gk~K 56 (114)
T TIGR01080 13 TAPLHVRRKLMSAPLSKELREKYGKRALPV--RKGDKVRIMRGDFK 56 (114)
T ss_pred cCcHhhhhheeecccCHHHHHHcCccccee--ecCCEEEEecCCCC
Confidence 468999999999999999999999999966 78999999998643
No 81
>PRK13503 transcriptional activator RhaS; Provisional
Probab=25.39 E-value=37 Score=35.54 Aligned_cols=31 Identities=10% Similarity=0.083 Sum_probs=23.2
Q ss_pred hCccceEEEeecCceEEecCCCccccccccc
Q 002957 765 FGVEPWTFEQKLGEAVFIPAGCPHQVRNLKS 795 (863)
Q Consensus 765 yGVEpWTF~Q~lGEAVFIPAGCPHQVRNLkS 795 (863)
+.|..=++.=..||++|||+|.+|...+...
T Consensus 48 ~~i~~~~~~l~~g~~~~i~~~~~h~~~~~~~ 78 (278)
T PRK13503 48 HVFNGQPYTLSGGTVCFVRDHDRHLYEHTDN 78 (278)
T ss_pred eEecCCcccccCCcEEEECCCccchhhhccC
Confidence 3344444555789999999999999877665
No 82
>PF08990 Docking: Erythronolide synthase docking; InterPro: IPR015083 The N-terminal docking domain found in modular polyketide synthase assumes an alpha-helical structure, wherein two alpha-helices are connected by a short loop. Two such N-terminal domains dimerise to form amphipathic parallel alpha-helical coiled coils: dimerisation is essential for protein function []. ; GO: 0016740 transferase activity, 0048037 cofactor binding; PDB: 2HG4_E.
Probab=25.11 E-value=54 Score=24.78 Aligned_cols=17 Identities=35% Similarity=0.585 Sum_probs=13.9
Q ss_pred ChhHHHHHHHHHHHhhc
Q 002957 716 DVPKLEAYLRKHFKEFR 732 (863)
Q Consensus 716 DvpKLreYL~kh~~EFr 732 (863)
+-+||++||++...|.+
T Consensus 3 ~e~kLr~YLkr~t~eL~ 19 (27)
T PF08990_consen 3 NEDKLRDYLKRVTAELR 19 (27)
T ss_dssp -HCHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHH
Confidence 45799999999998864
No 83
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=24.51 E-value=51 Score=28.13 Aligned_cols=22 Identities=41% Similarity=0.919 Sum_probs=18.4
Q ss_pred ceecCCCCcccccccccCCCCCc
Q 002957 258 RVYCNHCATSIIDLHRSCPKCSY 280 (863)
Q Consensus 258 Rv~CD~CkTSI~D~HRsC~~Csy 280 (863)
-+.|.+|. .+.=-|+-|++|+|
T Consensus 26 l~~c~~cg-~~~~~H~vc~~cG~ 47 (56)
T PF01783_consen 26 LVKCPNCG-EPKLPHRVCPSCGY 47 (56)
T ss_dssp EEESSSSS-SEESTTSBCTTTBB
T ss_pred eeeeccCC-CEecccEeeCCCCe
Confidence 37899999 56678999999976
No 84
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=24.45 E-value=44 Score=28.93 Aligned_cols=23 Identities=39% Similarity=1.019 Sum_probs=19.3
Q ss_pred CceecCCCCcccccccccCCCCCc
Q 002957 257 ERVYCNHCATSIIDLHRSCPKCSY 280 (863)
Q Consensus 257 ERv~CD~CkTSI~D~HRsC~~Csy 280 (863)
.-+.|-+|...+.- |+-|++|+|
T Consensus 26 ~l~~C~~CG~~~~~-H~vC~~CG~ 48 (57)
T PRK12286 26 GLVECPNCGEPKLP-HRVCPSCGY 48 (57)
T ss_pred cceECCCCCCccCC-eEECCCCCc
Confidence 33679999988775 999999998
No 85
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=24.11 E-value=35 Score=39.10 Aligned_cols=22 Identities=32% Similarity=0.818 Sum_probs=20.2
Q ss_pred ceecCCCCcccccccccCCCCC
Q 002957 258 RVYCNHCATSIIDLHRSCPKCS 279 (863)
Q Consensus 258 Rv~CD~CkTSI~D~HRsC~~Cs 279 (863)
++-|-+|....--+|++||.|.
T Consensus 354 ~YRC~~CGF~a~~l~W~CPsC~ 375 (389)
T COG2956 354 RYRCQNCGFTAHTLYWHCPSCR 375 (389)
T ss_pred CceecccCCcceeeeeeCCCcc
Confidence 5579999999999999999995
No 86
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=23.68 E-value=43 Score=32.29 Aligned_cols=23 Identities=30% Similarity=0.548 Sum_probs=17.4
Q ss_pred ceecCCCCc--ccccccccCCCCCc
Q 002957 258 RVYCNHCAT--SIIDLHRSCPKCSY 280 (863)
Q Consensus 258 Rv~CD~CkT--SI~D~HRsC~~Csy 280 (863)
+.+|.+|.. ++-+++..||+|+-
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECEDCSEEVSPEIDLYRCPKCHG 94 (115)
T ss_pred EEEcccCCCEEecCCcCccCcCCcC
Confidence 579999974 33467788999985
No 87
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=23.54 E-value=45 Score=36.30 Aligned_cols=75 Identities=19% Similarity=0.099 Sum_probs=52.7
Q ss_pred CceEEEeecCCChhHHHHHHHHHHHhhccccCCCCCcccCCcccCccccCHHHHHHHHHHhCccceEEEeecCceEEecC
Q 002957 705 GGALWDIFRRQDVPKLEAYLRKHFKEFRHVYCSPVEQVIHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPA 784 (863)
Q Consensus 705 ~GALWDIFRreDvpKLreYL~kh~~EFrh~~~~pv~~v~dPIHDQsfYLd~ehk~rLkEEyGVEpWTF~Q~lGEAVFIPA 784 (863)
.=.+-|+|-.+|-+.|-- -|-.+... ....+-=|||.+|+-.-.-. +-|.+=++.=.+||.+|||.
T Consensus 142 ~v~~~d~~~~~d~s~m~a-------Gf~~~~~~--sf~wtl~~dEi~YVLEGe~~-----l~IdG~t~~l~pGDvlfIPk 207 (233)
T PRK15457 142 CVGLTDLVTGDDGSSMAA-------GFMQWENA--FFPWTLNYDEIDMVLEGELH-----VRHEGETMIAKAGDVMFIPK 207 (233)
T ss_pred cEEeeeeeccCCCCceee-------EEEEEecC--ccceeccceEEEEEEEeEEE-----EEECCEEEEeCCCcEEEECC
Confidence 456678888888887721 12111222 23477788998887655443 67889999999999999999
Q ss_pred CCccccccc
Q 002957 785 GCPHQVRNL 793 (863)
Q Consensus 785 GCPHQVRNL 793 (863)
|++|.-.+-
T Consensus 208 Gs~~hf~tp 216 (233)
T PRK15457 208 GSSIEFGTP 216 (233)
T ss_pred CCeEEecCC
Confidence 999876544
No 88
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=23.32 E-value=56 Score=29.49 Aligned_cols=23 Identities=13% Similarity=0.264 Sum_probs=15.0
Q ss_pred ccccccCCCCceecCCCCccccc
Q 002957 248 VSETLCGNDERVYCNHCATSIID 270 (863)
Q Consensus 248 i~~a~~~~DERv~CD~CkTSI~D 270 (863)
..+..+.-++-..|..|..+|.+
T Consensus 68 ~~~~~v~i~~~~~C~vC~k~l~~ 90 (109)
T PF10367_consen 68 LRSRSVVITESTKCSVCGKPLGN 90 (109)
T ss_pred hcCceEEECCCCCccCcCCcCCC
Confidence 33344444555569999999885
No 89
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=22.82 E-value=53 Score=27.03 Aligned_cols=32 Identities=31% Similarity=0.956 Sum_probs=23.7
Q ss_pred CceecC--CCCcccc------cccccCCCCCcccchhchH
Q 002957 257 ERVYCN--HCATSII------DLHRSCPKCSYELCLTCCK 288 (863)
Q Consensus 257 ERv~CD--~CkTSI~------D~HRsC~~CsyDLCL~CC~ 288 (863)
...+|- .|...|. +.+-.|++|++..|..|-.
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~ 56 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKV 56 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCC
Confidence 345677 7766554 4588999999999999943
No 90
>PRK13501 transcriptional activator RhaR; Provisional
Probab=22.45 E-value=48 Score=35.34 Aligned_cols=29 Identities=14% Similarity=0.292 Sum_probs=23.9
Q ss_pred hCccceEEEeecCceEEecCCCccccccc
Q 002957 765 FGVEPWTFEQKLGEAVFIPAGCPHQVRNL 793 (863)
Q Consensus 765 yGVEpWTF~Q~lGEAVFIPAGCPHQVRNL 793 (863)
+-|.+-++.=..||.||||+|.+|+++.-
T Consensus 51 ~~i~~~~~~l~~g~~~~I~p~~~H~~~~~ 79 (290)
T PRK13501 51 HVLNDHPYRITCGDVFYIQAADHHSYESV 79 (290)
T ss_pred EEECCeeeeecCCeEEEEcCCCccccccc
Confidence 55677777778999999999999997643
No 91
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=22.42 E-value=37 Score=27.04 Aligned_cols=12 Identities=33% Similarity=0.955 Sum_probs=5.8
Q ss_pred ceecCCCCcccc
Q 002957 258 RVYCNHCATSII 269 (863)
Q Consensus 258 Rv~CD~CkTSI~ 269 (863)
|.|||.|++.|.
T Consensus 3 ryyCdyC~~~~~ 14 (38)
T PF06220_consen 3 RYYCDYCKKYLT 14 (38)
T ss_dssp S-B-TTT--B-S
T ss_pred Ceecccccceec
Confidence 679999999884
No 92
>PF06249 EutQ: Ethanolamine utilisation protein EutQ; InterPro: IPR010424 The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear [].; PDB: 2PYT_B 3LWC_A.
Probab=22.07 E-value=66 Score=32.93 Aligned_cols=21 Identities=33% Similarity=0.670 Sum_probs=16.0
Q ss_pred ccceEEEeecCceEEecCCCc
Q 002957 767 VEPWTFEQKLGEAVFIPAGCP 787 (863)
Q Consensus 767 VEpWTF~Q~lGEAVFIPAGCP 787 (863)
+++=++.=++||+||||.|.-
T Consensus 110 ~~G~~~~A~~GDvi~iPkGs~ 130 (152)
T PF06249_consen 110 IDGQTVTAKPGDVIFIPKGST 130 (152)
T ss_dssp ETTEEEEEETT-EEEE-TT-E
T ss_pred ECCEEEEEcCCcEEEECCCCE
Confidence 568899999999999999963
No 93
>PF14816 FAM178: Family of unknown function, FAM178
Probab=21.03 E-value=56 Score=37.82 Aligned_cols=28 Identities=32% Similarity=0.576 Sum_probs=23.5
Q ss_pred cCHHHHHHHHHHhCccceEEE-eecCceEE
Q 002957 753 LSSEHKKKLKEEFGVEPWTFE-QKLGEAVF 781 (863)
Q Consensus 753 Ld~ehk~rLkEEyGVEpWTF~-Q~lGEAVF 781 (863)
|++|||. +.|.|+|..-.|- +|+||.||
T Consensus 63 l~~Ehr~-~lekfsv~~~~Ip~~HPGE~IF 91 (377)
T PF14816_consen 63 LTPEHRE-FLEKFSVSLQAIPDVHPGEEIF 91 (377)
T ss_pred CCHHHHH-HHHHhchhhccCCCCCCchhhc
Confidence 5688886 7778999988885 78899999
No 94
>PF12773 DZR: Double zinc ribbon
Probab=20.35 E-value=59 Score=26.25 Aligned_cols=26 Identities=31% Similarity=0.908 Sum_probs=17.4
Q ss_pred CCCceecCCCCcccc---cccccCCCCCc
Q 002957 255 NDERVYCNHCATSII---DLHRSCPKCSY 280 (863)
Q Consensus 255 ~DERv~CD~CkTSI~---D~HRsC~~Csy 280 (863)
.++..||.+|.+.+. ..-..|++|+.
T Consensus 9 ~~~~~fC~~CG~~l~~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLPPPDQSKKICPNCGA 37 (50)
T ss_pred CccccCChhhcCChhhccCCCCCCcCCcC
Confidence 445667788887777 33456777766
No 95
>PRK13502 transcriptional activator RhaR; Provisional
Probab=20.31 E-value=1e+02 Score=32.57 Aligned_cols=30 Identities=13% Similarity=0.239 Sum_probs=24.2
Q ss_pred hCccceEEEeecCceEEecCCCcccccccc
Q 002957 765 FGVEPWTFEQKLGEAVFIPAGCPHQVRNLK 794 (863)
Q Consensus 765 yGVEpWTF~Q~lGEAVFIPAGCPHQVRNLk 794 (863)
+-|++=++.-..||++|||+|.+|......
T Consensus 51 ~~i~~~~~~l~~g~l~li~~~~~H~~~~~~ 80 (282)
T PRK13502 51 HVLNERPYRITRGDLFYIRAEDKHSYTSVN 80 (282)
T ss_pred EEECCEEEeecCCcEEEECCCCcccccccC
Confidence 446667788889999999999999876433
Done!