Query 002828
Match_columns 876
No_of_seqs 447 out of 2011
Neff 8.7
Searched_HMMs 46136
Date Thu Mar 28 11:36:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002828.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002828hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 1.2E-80 2.6E-85 726.1 43.3 511 31-570 69-628 (846)
2 PF10551 MULE: MULE transposas 99.8 4.9E-20 1.1E-24 163.2 9.0 90 260-352 1-93 (93)
3 PF00872 Transposase_mut: Tran 99.7 2E-17 4.4E-22 183.8 4.3 248 152-448 98-352 (381)
4 PF03101 FAR1: FAR1 DNA-bindin 99.6 5.6E-16 1.2E-20 136.3 7.8 90 50-142 1-91 (91)
5 PF02338 OTU: OTU-like cystein 99.6 5.5E-16 1.2E-20 144.5 6.1 109 706-829 1-121 (121)
6 PF08731 AFT: Transcription fa 99.4 9.8E-13 2.1E-17 113.8 10.5 93 42-140 1-111 (111)
7 KOG2606 OTU (ovarian tumor)-li 99.3 1.4E-12 2.9E-17 131.6 6.2 134 690-835 149-298 (302)
8 COG3328 Transposase and inacti 99.1 3E-09 6.4E-14 116.0 15.7 241 154-449 86-332 (379)
9 PF03108 DBD_Tnp_Mut: MuDR fam 98.9 4.3E-09 9.2E-14 86.4 7.5 66 34-129 2-67 (67)
10 KOG2605 OTU (ovarian tumor)-li 98.6 1.2E-08 2.5E-13 110.1 1.4 133 692-835 210-344 (371)
11 smart00575 ZnF_PMZ plant mutat 98.4 1.3E-07 2.9E-12 62.2 1.9 26 522-547 1-26 (28)
12 PF10275 Peptidase_C65: Peptid 97.6 0.00012 2.5E-09 77.0 6.9 52 782-834 190-244 (244)
13 KOG3288 OTU-like cysteine prot 97.6 0.00021 4.5E-09 71.0 7.5 121 703-838 113-236 (307)
14 PF04434 SWIM: SWIM zinc finge 97.5 6E-05 1.3E-09 54.7 2.0 30 517-546 10-39 (40)
15 KOG3991 Uncharacterized conser 96.4 0.011 2.5E-07 58.2 7.7 88 736-835 165-256 (256)
16 PF06782 UPF0236: Uncharacteri 96.1 0.7 1.5E-05 53.3 21.6 246 150-450 115-382 (470)
17 PF03106 WRKY: WRKY DNA -bindi 95.5 0.041 8.8E-07 43.6 5.9 57 59-139 3-59 (60)
18 PF01610 DDE_Tnp_ISL3: Transpo 94.3 0.056 1.2E-06 57.0 5.1 67 289-357 31-98 (249)
19 COG5539 Predicted cysteine pro 94.1 0.025 5.5E-07 58.0 1.8 109 684-799 155-273 (306)
20 PF05412 Peptidase_C33: Equine 93.6 0.14 3E-06 44.5 5.1 85 704-836 3-87 (108)
21 smart00774 WRKY DNA binding do 92.6 0.23 4.9E-06 39.0 4.6 56 60-138 4-59 (59)
22 PF04500 FLYWCH: FLYWCH zinc f 90.3 0.7 1.5E-05 36.6 5.5 49 59-138 14-62 (62)
23 PF13610 DDE_Tnp_IS240: DDE do 88.6 0.31 6.6E-06 46.4 2.5 81 253-338 1-81 (140)
24 PF00665 rve: Integrase core d 78.8 9.5 0.00021 34.5 7.9 76 253-330 6-82 (120)
25 PF04684 BAF1_ABF1: BAF1 / ABF 77.7 3.8 8.3E-05 45.4 5.4 56 37-121 23-78 (496)
26 PF15299 ALS2CR8: Amyotrophic 68.9 32 0.0007 35.5 9.6 98 101-200 69-221 (225)
27 PHA02517 putative transposase 65.3 39 0.00084 36.0 9.9 69 253-326 110-180 (277)
28 COG5539 Predicted cysteine pro 63.3 7 0.00015 40.7 3.4 112 707-834 119-231 (306)
29 KOG4345 NF-kappa B regulator A 56.5 7 0.00015 45.5 2.2 52 780-833 225-290 (774)
30 PF04937 DUF659: Protein of un 56.3 97 0.0021 29.8 9.7 107 248-357 28-138 (153)
31 COG4279 Uncharacterized conser 55.3 8.8 0.00019 39.2 2.4 30 521-553 124-153 (266)
32 COG3464 Transposase and inacti 51.2 92 0.002 35.3 10.0 56 289-349 183-238 (402)
33 COG3316 Transposase and inacti 48.8 40 0.00086 34.2 5.8 81 253-340 70-151 (215)
34 PF03050 DDE_Tnp_IS66: Transpo 44.2 68 0.0015 34.0 7.4 59 285-357 98-156 (271)
35 PRK13907 rnhA ribonuclease H; 42.3 2E+02 0.0043 26.4 9.3 78 255-335 3-81 (128)
36 PF13936 HTH_38: Helix-turn-he 41.4 35 0.00076 25.0 3.2 30 151-180 3-32 (44)
37 PF08069 Ribosomal_S13_N: Ribo 41.3 42 0.0009 26.6 3.7 29 155-183 31-59 (60)
38 PRK09784 hypothetical protein; 40.7 15 0.00033 36.9 1.5 40 697-737 197-236 (417)
39 COG5431 Uncharacterized metal- 34.1 16 0.00034 31.9 0.4 25 521-545 49-78 (117)
40 KOG4825 Component of synaptic 27.4 87 0.0019 34.9 4.6 36 616-651 279-314 (666)
41 PRK08561 rps15p 30S ribosomal 26.2 1.5E+02 0.0031 28.3 5.3 31 154-184 30-60 (151)
42 KOG4027 Uncharacterized conser 24.8 87 0.0019 29.8 3.5 37 258-294 70-109 (187)
43 PF09607 BrkDBD: Brinker DNA-b 24.5 59 0.0013 25.6 2.0 18 707-724 20-39 (58)
44 PF03412 Peptidase_C39: Peptid 22.0 3.2E+02 0.007 24.8 7.1 86 708-837 10-95 (131)
45 KOG0030 Myosin essential light 21.8 31 0.00066 32.2 0.0 86 699-786 16-116 (152)
46 PRK14702 insertion element IS2 21.0 3.2E+02 0.0069 28.9 7.5 72 253-325 87-162 (262)
47 PF05415 Peptidase_C36: Beet n 20.3 1.1E+02 0.0024 26.0 2.9 22 705-726 3-24 (104)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=1.2e-80 Score=726.05 Aligned_cols=511 Identities=19% Similarity=0.269 Sum_probs=411.4
Q ss_pred CCCCCCCCCceecCHHHHHHHHHHHhhccCEEEEEEeecCCC-CCCCceEEEEEecCCccCCCCCCCCCC------C---
Q 002828 31 DFSSAFTTDMVFNSREELVEWIRDTGKRNGLVIVIKKSDVGG-DGRRPRITFACERSGAYRRKYTEGQTP------K--- 100 (876)
Q Consensus 31 ~~~~~~~~g~~F~S~de~~~~~~~ya~~~GF~v~~~~S~~~~-~g~~~~~~~vC~r~G~~r~~~~~~~~~------~--- 100 (876)
+....|.+||+|+|.|||++||+.||...||+||+.++.+++ ++.++.++|+|+|+|+++.+.....+. .
T Consensus 69 ~~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~ 148 (846)
T PLN03097 69 DTNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPE 148 (846)
T ss_pred CCCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCcc
Confidence 444578999999999999999999999999999999998876 677888999999999765432100000 0
Q ss_pred -CCCCCCcceeCCccEEEEeeeCCCCCeEEEEEccccCCCCCCCccccccccCCCHHHHHHHHHHhhCCCChHHHHHHHH
Q 002828 101 -RPKTTGTKKCGCPFLLKGHKLDTDDDWILKVVCGVHNHPVTQHVEGHSYAGRLTEQEANILVDLSRSNISPKEILQTLK 179 (876)
Q Consensus 101 -~rr~~~s~~~gCp~~i~~~~~~~~~~w~V~~~~~~HNH~~~~~~~~~~~~rrl~~~~k~~i~~l~~~~~~p~~I~~~l~ 179 (876)
.+++++.+++||+|+|+++. ..+|+|.|+.+..+|||++.++... +...+.....+.. .+.
T Consensus 149 ~~~~rR~~tRtGC~A~m~Vk~-~~~gkW~V~~fv~eHNH~L~p~~~~-------~~~~r~~~~~~~~----------~~~ 210 (846)
T PLN03097 149 NGTGRRSCAKTDCKASMHVKR-RPDGKWVIHSFVKEHNHELLPAQAV-------SEQTRKMYAAMAR----------QFA 210 (846)
T ss_pred cccccccccCCCCceEEEEEE-cCCCeEEEEEEecCCCCCCCCcccc-------chhhhhhHHHHHh----------hhh
Confidence 01123457899999999965 5689999999999999999976321 1122221111110 000
Q ss_pred hcCCCccchHHHHHHHHHHhhhccccCcchHHHHHHHHH----hcCcEEEEEeecCCCceeeeEecChHHHHHHHhCCce
Q 002828 180 QRDMHNVSTIKAIYNARHKYRVGEQVGQLHMHQLLDKLR----KHGYIEWHRYNEETDCFKDLFWAHPFAVGLLRAFPSV 255 (876)
Q Consensus 180 ~~~~~~~~t~kdi~n~~~~~r~~~~~g~~~~~~ll~~l~----e~~~~~~~~~~d~~~~~~~if~~~~~~~~~~~~~~~v 255 (876)
. +.....+..+..|...+.|..... ..+++.|+++|+ ++|.|+|++++|+++++++|||+++.++..|.+||||
T Consensus 211 ~-~~~v~~~~~d~~~~~~~~r~~~~~-~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y~~FGDv 288 (846)
T PLN03097 211 E-YKNVVGLKNDSKSSFDKGRNLGLE-AGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDYGNFSDV 288 (846)
T ss_pred c-cccccccchhhcchhhHHHhhhcc-cchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHHHHHHHhcCCE
Confidence 0 000112334445554444443332 338999999985 5999999999999999999999999999999999999
Q ss_pred EEEeccccCCCCCCeeEEEEeecCCCCeEEEEEEeeccCccchHHHHHHHHHHhhcCCCCCeEEEeeccHHHHHHHHHhC
Q 002828 256 VMIDCTYKTSMYPFSFLEIVGATSTELTFSIAFAYLESERDDNYIWTLERLRSMMEDDALPRVIVTDKDLALMNSIRAVF 335 (876)
Q Consensus 256 l~iD~T~~tn~~~~~l~~~~g~~~~~~~~~va~al~~~E~~~s~~w~l~~l~~~~~~~~~P~~ivtD~d~al~~Ai~~vf 335 (876)
|+||+||.||+|++||..|+|+|+|++++++|+||+.+|+.++|.|+|++|+++| ++..|++||||+|.+|.+||.+||
T Consensus 289 V~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM-~gk~P~tIiTDqd~am~~AI~~Vf 367 (846)
T PLN03097 289 VSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAM-GGQAPKVIITDQDKAMKSVISEVF 367 (846)
T ss_pred EEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHh-CCCCCceEEecCCHHHHHHHHHHC
Confidence 9999999999999999999999999999999999999999999999999999999 889999999999999999999999
Q ss_pred CCccccchhhhhhhhhHhhhhhhhhchhHHHHHHHhhhhcc-cCcCHHHHHHHHHHhHhhcccchhHHHHHHHhhhhhhH
Q 002828 336 PRATNLLCRWHISKNISVNCKKLFETKERWEAFICSWNVLV-LSVTEQEYMQHLGAMESDFSRYPQAIDYVKQTWLANYK 414 (876)
Q Consensus 336 P~~~~~lC~~Hi~kn~~~~~~~~~~~~~~~~~~~~~~~~l~-~s~t~~~f~~~~~~l~~~~~~~~~~~~y~~~~Wl~~~k 414 (876)
|++.|++|.|||++|+.+++...+.. .+.|...|..++ .+.++++|+..|..|.+.+.-.. .+|+..-| ..|
T Consensus 368 P~t~Hr~C~wHI~~~~~e~L~~~~~~---~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~--n~WL~~LY--~~R 440 (846)
T PLN03097 368 PNAHHCFFLWHILGKVSENLGQVIKQ---HENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKE--DEWMQSLY--EDR 440 (846)
T ss_pred CCceehhhHHHHHHHHHHHhhHHhhh---hhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccc--cHHHHHHH--HhH
Confidence 99999999999999999999877643 346777776654 59999999999999988763211 13333332 479
Q ss_pred HHHHHHhhccccccCcccccccchhhHhHhhhhcCCCCChhhHHHHHHHHHHH-HHHHHHHHhhhccceeecccchhHHH
Q 002828 415 EKFVAAWTDLAMHFGNVTMNRGETTHTKLKRLLAVPQGNFETSWAKVHSLLEQ-QHYEIKASFERSSTIVQHNFKVPIFE 493 (876)
Q Consensus 415 e~w~~~~~~~~~~~g~~Ttn~~Es~n~~LK~~l~~s~~~l~~~~~~i~~~i~~-~~~~i~~~~~~~~~~~~~~~~~~~~~ 493 (876)
++||++|+++.|.+|+.||+++||+|+.||+++.. ..+|..|+.+++.+++. ..+|..++++.....+......|+.+
T Consensus 441 ekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~-~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEk 519 (846)
T PLN03097 441 KQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHK-KTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEK 519 (846)
T ss_pred hhhhHHHhcccccCCcccccccccHHHHHHHHhCc-CCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHH
Confidence 99999999999999999999999999999999975 67899999999999985 66778888877666555556678999
Q ss_pred HhhhhhcHHHHHHhhcccccc---------------------------cccC----CcCCCCCccccccCCccchhHhhH
Q 002828 494 ELRGFVSLNAMNIILGESERA---------------------------DSVG----LNASACGCVFRRTHGLPCAHEIAE 542 (876)
Q Consensus 494 ~l~~~is~~a~~~~~~e~~~~---------------------------~~V~----~~~~~CsC~~~~~~GlPC~H~lav 542 (876)
++.+.+|+.+|+.++.|+..+ +.|. ....+|+|.+|+..||||+|+|+|
T Consensus 520 QAs~iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkV 599 (846)
T PLN03097 520 SVSGVYTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVV 599 (846)
T ss_pred HHHHHhHHHHHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHH
Confidence 999999999999998775321 0111 135699999999999999999999
Q ss_pred HhhcC-CCCCccccccccccccCCCCccc
Q 002828 543 YKHER-RSIPLLAVDRHWKKLDFVPVTQD 570 (876)
Q Consensus 543 ~~~~~-~~lp~~~i~~rW~~~~~~~~~~~ 570 (876)
+.+.+ ..||..||++|||+.+......+
T Consensus 600 L~~~~v~~IP~~YILkRWTKdAK~~~~~~ 628 (846)
T PLN03097 600 LQMCQLSAIPSQYILKRWTKDAKSRHLLG 628 (846)
T ss_pred HhhcCcccCchhhhhhhchhhhhhcccCc
Confidence 99998 89999999999999988765433
No 2
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=99.81 E-value=4.9e-20 Score=163.16 Aligned_cols=90 Identities=43% Similarity=0.743 Sum_probs=85.3
Q ss_pred ccccCCCCCCeeEE---EEeecCCCCeEEEEEEeeccCccchHHHHHHHHHHhhcCCCCCeEEEeeccHHHHHHHHHhCC
Q 002828 260 CTYKTSMYPFSFLE---IVGATSTELTFSIAFAYLESERDDNYIWTLERLRSMMEDDALPRVIVTDKDLALMNSIRAVFP 336 (876)
Q Consensus 260 ~T~~tn~~~~~l~~---~~g~~~~~~~~~va~al~~~E~~~s~~w~l~~l~~~~~~~~~P~~ivtD~d~al~~Ai~~vfP 336 (876)
+||+||+| ++++. ++|+|++|+.+|+||+++.+|+.++|.|+|+.+++.+ ... |.+||+|++.++++||+++||
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~-~~~-p~~ii~D~~~~~~~Ai~~vfP 77 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAM-PQK-PKVIISDFDKALINAIKEVFP 77 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhcc-ccC-ceeeeccccHHHHHHHHHHCC
Confidence 69999999 88885 9999999999999999999999999999999999998 345 999999999999999999999
Q ss_pred CccccchhhhhhhhhH
Q 002828 337 RATNLLCRWHISKNIS 352 (876)
Q Consensus 337 ~~~~~lC~~Hi~kn~~ 352 (876)
+++|++|.||+.||++
T Consensus 78 ~~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 78 DARHQLCLFHILRNIK 93 (93)
T ss_pred CceEehhHHHHHHhhC
Confidence 9999999999999974
No 3
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=99.67 E-value=2e-17 Score=183.81 Aligned_cols=248 Identities=16% Similarity=0.174 Sum_probs=190.1
Q ss_pred CCCHHHHHHHHHHhhCCCChHHHHHHHHhcCCCccchHHHHHHHHHHhhhccccCcchHHHHHHHHHhcCcEEEEEeecC
Q 002828 152 RLTEQEANILVDLSRSNISPKEILQTLKQRDMHNVSTIKAIYNARHKYRVGEQVGQLHMHQLLDKLRKHGYIEWHRYNEE 231 (876)
Q Consensus 152 rl~~~~k~~i~~l~~~~~~p~~I~~~l~~~~~~~~~t~kdi~n~~~~~r~~~~~g~~~~~~ll~~l~e~~~~~~~~~~d~ 231 (876)
+.++.....|..|.-.|++.++|...++.-++..-.+...|.++...+... +..+++-
T Consensus 98 r~~~~l~~~i~~ly~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~-----------~~~w~~R----------- 155 (381)
T PF00872_consen 98 RREDSLEELIISLYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEE-----------VEAWRNR----------- 155 (381)
T ss_pred hhhhhhhhhhhhhhccccccccccchhhhhhcccccCchhhhhhhhhhhhh-----------HHHHhhh-----------
Confidence 345666677888889999999999999888763323444454443333221 1111111
Q ss_pred CCceeeeEecChHHHHHHHhC-CceEEEeccccCCCC-----CCeeEEEEeecCCCCeEEEEEEeeccCccchHHHHHHH
Q 002828 232 TDCFKDLFWAHPFAVGLLRAF-PSVVMIDCTYKTSMY-----PFSFLEIVGATSTELTFSIAFAYLESERDDNYIWTLER 305 (876)
Q Consensus 232 ~~~~~~if~~~~~~~~~~~~~-~~vl~iD~T~~tn~~-----~~~l~~~~g~~~~~~~~~va~al~~~E~~~s~~w~l~~ 305 (876)
-+... -++|++|++|-.-+. +..+++++|++.+|+-.++|+.+...|+..+|.-+|+.
T Consensus 156 ----------------~L~~~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~ 219 (381)
T PF00872_consen 156 ----------------PLESEPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQD 219 (381)
T ss_pred ----------------ccccccccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchh
Confidence 11122 257899999976542 46789999999999999999999999999999999999
Q ss_pred HHHhhcCCCCCeEEEeeccHHHHHHHHHhCCCccccchhhhhhhhhHhhhhhhhhchhHHHHHHHhhhhcccCcCHHHHH
Q 002828 306 LRSMMEDDALPRVIVTDKDLALMNSIRAVFPRATNLLCRWHISKNISVNCKKLFETKERWEAFICSWNVLVLSVTEQEYM 385 (876)
Q Consensus 306 l~~~~~~~~~P~~ivtD~d~al~~Ai~~vfP~~~~~lC~~Hi~kn~~~~~~~~~~~~~~~~~~~~~~~~l~~s~t~~~f~ 385 (876)
|++. |...|..||+|..+||.+||.++||++.++.|.+|+++|+.+++.+. ..+.+...++.+..+.+.++..
T Consensus 220 L~~R--Gl~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~k-----~~~~v~~~Lk~I~~a~~~e~a~ 292 (381)
T PF00872_consen 220 LKER--GLKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPKK-----DRKEVKADLKAIYQAPDKEEAR 292 (381)
T ss_pred hhhc--cccccceeeccccccccccccccccchhhhhheechhhhhccccccc-----cchhhhhhccccccccccchhh
Confidence 9988 67789999999999999999999999999999999999999987542 3467888889999999999999
Q ss_pred HHHHHhHhhc-ccchhHHHHHHHhhhhhhHHHHHHHhhccccccCcccccccchhhHhHhhhhc
Q 002828 386 QHLGAMESDF-SRYPQAIDYVKQTWLANYKEKFVAAWTDLAMHFGNVTMNRGETTHTKLKRLLA 448 (876)
Q Consensus 386 ~~~~~l~~~~-~~~~~~~~y~~~~Wl~~~ke~w~~~~~~~~~~~g~~Ttn~~Es~n~~LK~~l~ 448 (876)
+.++.|.+.| ..+|.+.+++...|-. .|.-.-+....+--+.|||.+|++|+.+|+...
T Consensus 293 ~~l~~f~~~~~~kyp~~~~~l~~~~~~----~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~ 352 (381)
T PF00872_consen 293 EALEEFAEKWEKKYPKAAKSLEENWDE----LLTFLDFPPEHRRSIRTTNAIESLNKEIRRRTK 352 (381)
T ss_pred hhhhhcccccccccchhhhhhhhcccc----ccceeeecchhccccchhhhccccccchhhhcc
Confidence 9999998877 5688888888887731 111111222333457899999999999998665
No 4
>PF03101 FAR1: FAR1 DNA-binding domain; InterPro: IPR004330 Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. It has been found that the proteins governing this response, which include FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), are a pair of homologous proteins sharing significant sequence homology to mutator-like transposases. These proteins appear to be novel transcription factors, which are essential for activating the expression of FHY1 and FHL (for FHY1-like) and related genes, whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses in plants. The FRS (FAR1 Related Sequences) family of proteins share a similar domain structure to mutator-like transposases, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). It seems plausible that the FRS family represent transcription factors derived from mutator-like transposases [, ]. This entry represents a domain found in FAR1 and FRS proteins. It contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.
Probab=99.63 E-value=5.6e-16 Score=136.34 Aligned_cols=90 Identities=27% Similarity=0.539 Sum_probs=77.6
Q ss_pred HHHHHHhhccCEEEEEEeecCC-CCCCCceEEEEEecCCccCCCCCCCCCCCCCCCCCcceeCCccEEEEeeeCCCCCeE
Q 002828 50 EWIRDTGKRNGLVIVIKKSDVG-GDGRRPRITFACERSGAYRRKYTEGQTPKRPKTTGTKKCGCPFLLKGHKLDTDDDWI 128 (876)
Q Consensus 50 ~~~~~ya~~~GF~v~~~~S~~~-~~g~~~~~~~vC~r~G~~r~~~~~~~~~~~rr~~~s~~~gCp~~i~~~~~~~~~~w~ 128 (876)
+||+.||..+||+|++.+|.+. ++|...++.|+|+++|.++.+... ..+.++.+.+.+|||||+|.+.... +|.|.
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~--~~~~~r~~~s~ktgC~a~i~v~~~~-~~~w~ 77 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKN--EEKRRRNRPSKKTGCKARINVKRRK-DGKWR 77 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccc--cccccccccccccCCCEEEEEEEcc-CCEEE
Confidence 4899999999999999999988 477788999999999998865422 2345677889999999999997666 99999
Q ss_pred EEEEccccCCCCCC
Q 002828 129 LKVVCGVHNHPVTQ 142 (876)
Q Consensus 129 V~~~~~~HNH~~~~ 142 (876)
|..+..+|||++.+
T Consensus 78 v~~~~~~HNH~L~P 91 (91)
T PF03101_consen 78 VTSFVLEHNHPLCP 91 (91)
T ss_pred EEECcCCcCCCCCC
Confidence 99999999999864
No 5
>PF02338 OTU: OTU-like cysteine protease; InterPro: IPR003323 This is a group of proteins found primarily in viruses, eukaryotes and in the pathogenic bacterium Chlamydia pneumoniae. In viruses they are annotated as replicase or RNA-dependent RNA polymerase. The eukaryotic sequences are related to the Ovarian Tumour (OTU) gene in Drosophila, cezanne deubiquitinating peptidase and tumor necrosis factor, alpha-induced protein 3 (MEROPS peptidase family C64) and otubain 1 and otubain 2 (MEROPS peptidase family C65). None of these proteins has a known biochemical function but low sequence similarity with the polyprotein regions of arteriviruses, and conserved cysteine and histidine, and possibly the aspartate, residues suggests that those not yet recognised as peptidases could possess cysteine protease activity [].; PDB: 2VFJ_C 3DKB_F 3PHW_A 3PHU_B 3PHX_A 3BY4_A 3C0R_C 3PRM_C 3PRP_C 3ZRH_A ....
Probab=99.61 E-value=5.5e-16 Score=144.48 Aligned_cols=109 Identities=19% Similarity=0.275 Sum_probs=86.6
Q ss_pred cCCCCcchhhHHhhhc----cCCchHHHHHHHHHHHHH-hhhhhhhhhhcCHHHHHHHHhhcCCCCCCCCcccccccCCc
Q 002828 706 IADGHCGFRVVAELMD----IGEDNWAQVRRDLVDELQ-SHYDDYIQLYGDAEIARELLHSLSYSESNPGIEHRMIMPDT 780 (876)
Q Consensus 706 ~~dg~Cgfraia~~l~----~~~~~~~~vR~~l~~el~-~~~~~y~~~~~~~~~~~~~~~~l~~~~~~~~~~~w~~~~~~ 780 (876)
+|||||+|||||.+|+ .+++.|..||++++++|+ .+++.|.+++.+. .|. ..+.|++.+++
T Consensus 1 pgDGnClF~Avs~~l~~~~~~~~~~~~~lR~~~~~~l~~~~~~~~~~~~~~~--------~~~------~~~~Wg~~~el 66 (121)
T PF02338_consen 1 PGDGNCLFRAVSDQLYGDGGGSEDNHQELRKAVVDYLRDKNRDKFEEFLEGD--------KMS------KPGTWGGEIEL 66 (121)
T ss_dssp -SSTTHHHHHHHHHHCTT-SSSTTTHHHHHHHHHHHHHTHTTTHHHHHHHHH--------HHT------STTSHEEHHHH
T ss_pred CCCccHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhccchhhhhhhhh--------hhc------cccccCcHHHH
Confidence 6999999999999999 999999999999999999 9999999887443 333 67899999988
Q ss_pred hhhhhcccceeEEEEccCcc--eeeccCccCCCCCCCCceEEEEEec-----CCce
Q 002828 781 GHLIASRYNIVLMHLSQQQC--FTFLPLRSVPLPRTSRKIVTIGFVN-----ECQF 829 (876)
Q Consensus 781 g~~iA~~~~~~v~~~~~~~~--~~~~p~~~~p~~~~~~~~i~l~~~~-----~~Hf 829 (876)
+++|+.|+|+|++|+.... ..+++..+.-.+....++|+|+|.. .+||
T Consensus 67 -~a~a~~~~~~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~~~~~l~~~~~Hy 121 (121)
T PF02338_consen 67 -QALANVLNRPIIVYSSSDGDNVVFIKFTGKYPPLESPPPICLCYHGHLYYTGNHY 121 (121)
T ss_dssp -HHHHHHHTSEEEEECETTTBEEEEEEESCEESTTTTTTSEEEEEETEEEEETTEE
T ss_pred -HHHHHHhCCeEEEEEcCCCCccceeeecCccccCCCCCeEEEEEcCCccCCCCCC
Confidence 6999999999999887433 3343333210122336789999998 8998
No 6
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=99.43 E-value=9.8e-13 Score=113.82 Aligned_cols=93 Identities=32% Similarity=0.661 Sum_probs=78.9
Q ss_pred ecCHHHHHHHHHHHhhccCEEEEEEeecCCCCCCCceEEEEEecCCccCCCCCCC------------------CCCCCCC
Q 002828 42 FNSREELVEWIRDTGKRNGLVIVIKKSDVGGDGRRPRITFACERSGAYRRKYTEG------------------QTPKRPK 103 (876)
Q Consensus 42 F~S~de~~~~~~~ya~~~GF~v~~~~S~~~~~g~~~~~~~vC~r~G~~r~~~~~~------------------~~~~~rr 103 (876)
|.+.+|+..|++..+..+||.|++.||+.. .++|.|--+|.++...... ....+.+
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~------ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~k 74 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKK------KIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKKK 74 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCc------eEEEEEecCCCcccccccccccccccccccccccccccccccCC
Confidence 889999999999999999999999999987 7999999988877544310 1122235
Q ss_pred CCCcceeCCccEEEEeeeCCCCCeEEEEEccccCCCC
Q 002828 104 TTGTKKCGCPFLLKGHKLDTDDDWILKVVCGVHNHPV 140 (876)
Q Consensus 104 ~~~s~~~gCp~~i~~~~~~~~~~w~V~~~~~~HNH~~ 140 (876)
.+.+++++|||+|++......+.|.|..+++.|||++
T Consensus 75 ~t~srk~~CPFriRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 75 RTKSRKNTCPFRIRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred cccccccCCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence 6678899999999999888999999999999999986
No 7
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.33 E-value=1.4e-12 Score=131.58 Aligned_cols=134 Identities=11% Similarity=0.104 Sum_probs=111.4
Q ss_pred cccccccccccccccccCCCCcchhhHHhhhccCC---chHHHHHHHHHHHHHhhhhhhhhhhc--------CHHHHHHH
Q 002828 690 SFPAGLRPYIHDVQDVIADGHCGFRVVAELMDIGE---DNWAQVRRDLVDELQSHYDDYIQLYG--------DAEIAREL 758 (876)
Q Consensus 690 ~~~~~l~~~~~~~~~v~~dg~Cgfraia~~l~~~~---~~~~~vR~~l~~el~~~~~~y~~~~~--------~~~~~~~~ 758 (876)
.+-+.|.+-.+.++|+++||||.|+||++||.... -+-..+|++..+++++|.+++.+++- ++++|+.|
T Consensus 149 k~~~il~~~~l~~~~Ip~DG~ClY~aI~hQL~~~~~~~~~v~kLR~~~a~Ymr~H~~df~pf~~~eet~d~~~~~~f~~Y 228 (302)
T KOG2606|consen 149 KLAQILEERGLKMFDIPADGHCLYAAISHQLKLRSGKLLSVQKLREETADYMREHVEDFLPFLLDEETGDSLGPEDFDKY 228 (302)
T ss_pred HHHHHHHhccCccccCCCCchhhHHHHHHHHHhccCCCCcHHHHHHHHHHHHHHHHHHhhhHhcCccccccCCHHHHHHH
Confidence 56778889999999999999999999999998864 46889999999999999999999882 24579999
Q ss_pred HhhcCCCCCCCCcccccccCCchhhhhcccceeEEEEccCcceeeccCccCCCCCCCCceEEEEEec-----CCceEEee
Q 002828 759 LHSLSYSESNPGIEHRMIMPDTGHLIASRYNIVLMHLSQQQCFTFLPLRSVPLPRTSRKIVTIGFVN-----ECQFVKVF 833 (876)
Q Consensus 759 ~~~l~~~~~~~~~~~w~~~~~~g~~iA~~~~~~v~~~~~~~~~~~~p~~~~p~~~~~~~~i~l~~~~-----~~Hf~~~~ 833 (876)
+..+. .+..|++.++.+ +|+++|.+||.+|....+ ++..++...+ .+||+|.|+- +-||+|+.
T Consensus 229 c~eI~------~t~~WGgelEL~-AlShvL~~PI~Vy~~~~p----~~~~geey~k-d~pL~lvY~rH~y~LGeHYNS~~ 296 (302)
T KOG2606|consen 229 CREIR------NTAAWGGELELK-ALSHVLQVPIEVYQADGP----ILEYGEEYGK-DKPLILVYHRHAYGLGEHYNSVT 296 (302)
T ss_pred HHHhh------hhccccchHHHH-HHHHhhccCeEEeecCCC----ceeechhhCC-CCCeeeehHHhHHHHHhhhcccc
Confidence 99996 678999999995 999999999999998765 4444544443 4789998862 37888876
Q ss_pred cc
Q 002828 834 MH 835 (876)
Q Consensus 834 ~~ 835 (876)
+.
T Consensus 297 ~~ 298 (302)
T KOG2606|consen 297 PL 298 (302)
T ss_pred cc
Confidence 53
No 8
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.05 E-value=3e-09 Score=115.97 Aligned_cols=241 Identities=15% Similarity=0.124 Sum_probs=174.3
Q ss_pred CHHHHHHHHHHhhCCCChHHHHHHHHhcCCCccchHHHHHHHHHHhhhccccCcchHHHHHHHHHhcCcEEEEEeecCCC
Q 002828 154 TEQEANILVDLSRSNISPKEILQTLKQRDMHNVSTIKAIYNARHKYRVGEQVGQLHMHQLLDKLRKHGYIEWHRYNEETD 233 (876)
Q Consensus 154 ~~~~k~~i~~l~~~~~~p~~I~~~l~~~~~~~~~t~kdi~n~~~~~r~~~~~g~~~~~~ll~~l~e~~~~~~~~~~d~~~ 233 (876)
....-..|..|...|++++++-..++..+...+ ..+.++.... .+..-+..+++.+.
T Consensus 86 ~~~~~~~v~~~y~~gv~Tr~i~~~~~~~~~~~~--s~~~iS~~~~----------~~~e~v~~~~~r~l----------- 142 (379)
T COG3328 86 ERALDLPVLSMYAKGVTTREIEALLEELYGHKV--SPSVISVVTD----------RLDEKVKAWQNRPL----------- 142 (379)
T ss_pred hhhHHHHHHHHHHcCCcHHHHHHHHHHhhCccc--CHHHhhhHHH----------HHHHHHHHHHhccc-----------
Confidence 334445677788899999999999998765422 2222111100 11111111221111
Q ss_pred ceeeeEecChHHHHHHHhCCceEEEeccccCCC--CCCeeEEEEeecCCCCeEEEEEEeeccCccchHHHHHHHHHHhhc
Q 002828 234 CFKDLFWAHPFAVGLLRAFPSVVMIDCTYKTSM--YPFSFLEIVGATSTELTFSIAFAYLESERDDNYIWTLERLRSMME 311 (876)
Q Consensus 234 ~~~~if~~~~~~~~~~~~~~~vl~iD~T~~tn~--~~~~l~~~~g~~~~~~~~~va~al~~~E~~~s~~w~l~~l~~~~~ 311 (876)
..-.++++|++|..-+ -+..++.++|++.+|.-..+|+-+-..|+ ..|.-+|..|+..
T Consensus 143 -----------------~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~r-- 202 (379)
T COG3328 143 -----------------GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNR-- 202 (379)
T ss_pred -----------------cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhc--
Confidence 1235788999998776 56789999999999999999999999999 8888888888887
Q ss_pred CCCCCeEEEeeccHHHHHHHHHhCCCccccchhhhhhhhhHhhhhhhhhchhHHHHHHHhhhhcccCcCHHHHHHHHHHh
Q 002828 312 DDALPRVIVTDKDLALMNSIRAVFPRATNLLCRWHISKNISVNCKKLFETKERWEAFICSWNVLVLSVTEQEYMQHLGAM 391 (876)
Q Consensus 312 ~~~~P~~ivtD~d~al~~Ai~~vfP~~~~~lC~~Hi~kn~~~~~~~~~~~~~~~~~~~~~~~~l~~s~t~~~f~~~~~~l 391 (876)
+......+|+|...++-+||.++||.+.++.|..|+.+|+..+.... ..+.+...++.+..+++.++....|..+
T Consensus 203 gl~~v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~k-----~~d~i~~~~~~I~~a~~~e~~~~~~~~~ 277 (379)
T COG3328 203 GLSDVLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPRK-----DQDAVLSDLRSIYIAPDAEEALLALLAF 277 (379)
T ss_pred cccceeEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhhh-----hhHHHHhhhhhhhccCCcHHHHHHHHHH
Confidence 45666778889999999999999999999999999999999886543 4567777888888899999999999998
Q ss_pred Hhhcc-cchhHHHHHHHhhhhhhHHHHHHHhhccccc---cCcccccccchhhHhHhhhhcC
Q 002828 392 ESDFS-RYPQAIDYVKQTWLANYKEKFVAAWTDLAMH---FGNVTMNRGETTHTKLKRLLAV 449 (876)
Q Consensus 392 ~~~~~-~~~~~~~y~~~~Wl~~~ke~w~~~~~~~~~~---~g~~Ttn~~Es~n~~LK~~l~~ 449 (876)
.+.|. .+|.....+.+.|.. .|. +..++. --..|||.+|++|..++.....
T Consensus 278 ~~~w~~~yP~i~~~~~~~~~~----~~~---F~~fp~~~r~~i~ttN~IE~~n~~ir~~~~~ 332 (379)
T COG3328 278 SELWGKRYPAILKSWRNALEE----LLP---FFAFPSEIRKIIYTTNAIESLNKLIRRRTKV 332 (379)
T ss_pred HHhhhhhcchHHHHHHHHHHH----hcc---cccCcHHHHhHhhcchHHHHHHHHHHHHHhh
Confidence 77664 567777766666642 111 111111 1368999999999988866553
No 9
>PF03108 DBD_Tnp_Mut: MuDR family transposase; InterPro: IPR004332 The plant MuDR transposase domain is present in plant proteins that are presumed to be the transposases for Mutator transposable elements [, ]. The function of these proteins is unknown. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=98.90 E-value=4.3e-09 Score=86.37 Aligned_cols=66 Identities=29% Similarity=0.543 Sum_probs=59.0
Q ss_pred CCCCCCceecCHHHHHHHHHHHhhccCEEEEEEeecCCCCCCCceEEEEEecCCccCCCCCCCCCCCCCCCCCcceeCCc
Q 002828 34 SAFTTDMVFNSREELVEWIRDTGKRNGLVIVIKKSDVGGDGRRPRITFACERSGAYRRKYTEGQTPKRPKTTGTKKCGCP 113 (876)
Q Consensus 34 ~~~~~g~~F~S~de~~~~~~~ya~~~GF~v~~~~S~~~~~g~~~~~~~vC~r~G~~r~~~~~~~~~~~rr~~~s~~~gCp 113 (876)
+.+.+||+|+|.+|++.++..||..+||.+++.+|++. ++.++|. ..|||
T Consensus 2 ~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~------r~~~~C~------------------------~~~C~ 51 (67)
T PF03108_consen 2 PELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKK------RYRAKCK------------------------DKGCP 51 (67)
T ss_pred CccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCE------EEEEEEc------------------------CCCCC
Confidence 46899999999999999999999999999999999876 8999993 24799
Q ss_pred cEEEEeeeCCCCCeEE
Q 002828 114 FLLKGHKLDTDDDWIL 129 (876)
Q Consensus 114 ~~i~~~~~~~~~~w~V 129 (876)
|+|++.....++.|.|
T Consensus 52 Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 52 WRVRASKRKRSDTFQI 67 (67)
T ss_pred EEEEEEEcCCCCEEEC
Confidence 9999998888888875
No 10
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=98.60 E-value=1.2e-08 Score=110.10 Aligned_cols=133 Identities=16% Similarity=0.177 Sum_probs=109.1
Q ss_pred cccccccccccccccCCCCcchhhHHhhhccCCchHHHHHHHHHHHHHhhhhhhhhhhcCHHHHHHHHhhcCCCCCCCCc
Q 002828 692 PAGLRPYIHDVQDVIADGHCGFRVVAELMDIGEDNWAQVRRDLVDELQSHYDDYIQLYGDAEIARELLHSLSYSESNPGI 771 (876)
Q Consensus 692 ~~~l~~~~~~~~~v~~dg~Cgfraia~~l~~~~~~~~~vR~~l~~el~~~~~~y~~~~~~~~~~~~~~~~l~~~~~~~~~ 771 (876)
...+..|+.-+..|.+||+|.|||+|++++++.|.|..||++..++++..++.|..++ ++.|..+++... ..
T Consensus 210 ~~~~~~~g~e~~Kv~edGsC~fra~aDQvy~d~e~~~~~~~~~~dq~~~e~~~~~~~v--t~~~~~y~k~kr------~~ 281 (371)
T KOG2605|consen 210 AKRKKHFGFEYKKVVEDGSCLFRALADQVYGDDEQHDHNRRECVDQLKKERDFYEDYV--TEDFTSYIKRKR------AD 281 (371)
T ss_pred HHHHHHhhhhhhhcccCCchhhhccHHHhhcCHHHHHHHHHHHHHHHhhccccccccc--ccchhhcccccc------cC
Confidence 4455788899999999999999999999999999999999999999999999999888 567888777775 66
Q ss_pred ccccccCCchhhhhc--ccceeEEEEccCcceeeccCccCCCCCCCCceEEEEEecCCceEEeecc
Q 002828 772 EHRMIMPDTGHLIAS--RYNIVLMHLSQQQCFTFLPLRSVPLPRTSRKIVTIGFVNECQFVKVFMH 835 (876)
Q Consensus 772 ~~w~~~~~~g~~iA~--~~~~~v~~~~~~~~~~~~p~~~~p~~~~~~~~i~l~~~~~~Hf~~~~~~ 835 (876)
+.|++..++ |++|. -+-.+.+++++.....|.-.. |....+...+++.+|...||..+...
T Consensus 282 ~~~gnhie~-Qa~a~~~~~~~~~~~~~~~~~t~~~~~~--~~~~~~~~~~~~n~~~~~h~~~~~~~ 344 (371)
T KOG2605|consen 282 GEPGNHIEQ-QAAADIYEEIEKPLNITSFKDTCYIQTP--PAIEESVKMEKYNFWVEVHYNTARHS 344 (371)
T ss_pred CCCcchHHH-hhhhhhhhhccccceeecccccceeccC--cccccchhhhhhcccchhhhhhcccc
Confidence 789999988 68887 555666677776666665544 44555566799999999999998763
No 11
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.40 E-value=1.3e-07 Score=62.15 Aligned_cols=26 Identities=31% Similarity=0.676 Sum_probs=23.9
Q ss_pred CCCCccccccCCccchhHhhHHhhcC
Q 002828 522 SACGCVFRRTHGLPCAHEIAEYKHER 547 (876)
Q Consensus 522 ~~CsC~~~~~~GlPC~H~lav~~~~~ 547 (876)
.+|||+.|+..||||+|+|+|+...+
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~ 26 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIG 26 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhC
Confidence 37999999999999999999998875
No 12
>PF10275 Peptidase_C65: Peptidase C65 Otubain; InterPro: IPR019400 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This family of proteins is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryotes, as it is a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localisation signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif. ; PDB: 4DDG_C 3VON_O 2ZFY_A 4DHZ_A 4DDI_C 1TFF_A 4DHJ_I 4DHI_B.
Probab=97.59 E-value=0.00012 Score=76.97 Aligned_cols=52 Identities=6% Similarity=-0.017 Sum_probs=29.4
Q ss_pred hhhhcccceeEEEEccCcc---eeeccCccCCCCCCCCceEEEEEecCCceEEeec
Q 002828 782 HLIASRYNIVLMHLSQQQC---FTFLPLRSVPLPRTSRKIVTIGFVNECQFVKVFM 834 (876)
Q Consensus 782 ~~iA~~~~~~v~~~~~~~~---~~~~p~~~~p~~~~~~~~i~l~~~~~~Hf~~~~~ 834 (876)
-+||+++++||-++-...+ ..+=....+|.+....+.|.|-|- +.||..|+.
T Consensus 190 ~ALa~aL~v~i~v~yld~~~~~~~~~~~~~~~~~~~~~~~i~LLyr-pgHYdIly~ 244 (244)
T PF10275_consen 190 IALAQALGVPIRVEYLDRSVEGDEVNRHEFPPDNESQEPQITLLYR-PGHYDILYP 244 (244)
T ss_dssp HHHHHHHT--EEEEESSSSGCSTTSEEEEES-SSTTSS-SEEEEEE-TBEEEEEEE
T ss_pred HHHHHHhCCeEEEEEecCCCCCCccccccCCCccCCCCCEEEEEEc-CCccccccC
Confidence 3689999999988754332 111111112223334677999987 679998873
No 13
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=97.56 E-value=0.00021 Score=70.99 Aligned_cols=121 Identities=13% Similarity=0.118 Sum_probs=85.4
Q ss_pred ccccCCCCcchhhHHhhhccCCchH-HHHHHHHHHHHHhhhhhhhhhh-cCH-HHHHHHHhhcCCCCCCCCcccccccCC
Q 002828 703 QDVIADGHCGFRVVAELMDIGEDNW-AQVRRDLVDELQSHYDDYIQLY-GDA-EIARELLHSLSYSESNPGIEHRMIMPD 779 (876)
Q Consensus 703 ~~v~~dg~Cgfraia~~l~~~~~~~-~~vR~~l~~el~~~~~~y~~~~-~~~-~~~~~~~~~l~~~~~~~~~~~w~~~~~ 779 (876)
.=|+.|--|+|+||+.-+...-+.- ..+|+-+.+|+-++++.|..-+ |.+ .+|-.+|.+ ++.|++-.+
T Consensus 113 ~vvp~DNSCLF~ai~yv~~k~~~~~~~elR~iiA~~Vasnp~~yn~AiLgK~n~eYc~WI~k---------~dsWGGaIE 183 (307)
T KOG3288|consen 113 RVVPDDNSCLFTAIAYVIFKQVSNRPYELREIIAQEVASNPDKYNDAILGKPNKEYCAWILK---------MDSWGGAIE 183 (307)
T ss_pred EeccCCcchhhhhhhhhhcCccCCCcHHHHHHHHHHHhcChhhhhHHHhCCCcHHHHHHHcc---------ccccCceEE
Confidence 3489999999999988776644222 6899999999999999997644 433 445555443 478998888
Q ss_pred chhhhhcccceeEEEEccCcceeeccCccCCCCCCCCceEEEEEecCCceEEeeccCCC
Q 002828 780 TGHLIASRYNIVLMHLSQQQCFTFLPLRSVPLPRTSRKIVTIGFVNECQFVKVFMHPGA 838 (876)
Q Consensus 780 ~g~~iA~~~~~~v~~~~~~~~~~~~p~~~~p~~~~~~~~i~l~~~~~~Hf~~~~~~~~~ 838 (876)
.+ ||++.|++-|++++.+.... ...+ +..+. ..-++|-| ++-||.+|.+..-.
T Consensus 184 ls-ILS~~ygveI~vvDiqt~ri--d~fg-ed~~~-~~rv~lly-dGIHYD~l~m~~~~ 236 (307)
T KOG3288|consen 184 LS-ILSDYYGVEICVVDIQTVRI--DRFG-EDKNF-DNRVLLLY-DGIHYDPLAMNEFK 236 (307)
T ss_pred ee-eehhhhceeEEEEecceeee--hhcC-CCCCC-CceEEEEe-cccccChhhhccCC
Confidence 87 99999999999998753311 1121 11122 23466666 58999999886543
No 14
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=97.48 E-value=6e-05 Score=54.67 Aligned_cols=30 Identities=27% Similarity=0.612 Sum_probs=26.2
Q ss_pred cCCcCCCCCccccccCCccchhHhhHHhhc
Q 002828 517 VGLNASACGCVFRRTHGLPCAHEIAEYKHE 546 (876)
Q Consensus 517 V~~~~~~CsC~~~~~~GlPC~H~lav~~~~ 546 (876)
+++...+|+|..|+..|.||+|+++++...
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhh
Confidence 355688999999999999999999998754
No 15
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.39 E-value=0.011 Score=58.20 Aligned_cols=88 Identities=11% Similarity=0.084 Sum_probs=51.0
Q ss_pred HHHHhhhhhhhhhhcCHHHHHHHHhhcCCCCCCCCcccccccCCchh--hhhcccce--eEEEEccCcceeeccCccCCC
Q 002828 736 DELQSHYDDYIQLYGDAEIARELLHSLSYSESNPGIEHRMIMPDTGH--LIASRYNI--VLMHLSQQQCFTFLPLRSVPL 811 (876)
Q Consensus 736 ~el~~~~~~y~~~~~~~~~~~~~~~~l~~~~~~~~~~~w~~~~~~g~--~iA~~~~~--~v~~~~~~~~~~~~p~~~~p~ 811 (876)
.+|+++.+.|.+++.+++..+.++..= ++.+. .-.+|-+ +|+++.+. -|.+++-+...++=+.. -
T Consensus 165 ~~ik~~adfy~pFI~e~~tV~~fC~~e--VEPm~------kesdhi~I~ALs~Al~i~irVey~dr~~~~~~~hH~---f 233 (256)
T KOG3991|consen 165 GFIKSNADFYQPFIDEGMTVKAFCTQE--VEPMY------KESDHIHITALSQALGIRIRVEYVDRGSGDTVNHHD---F 233 (256)
T ss_pred HHHhhChhhhhccCCCCCcHHHHHHhh--cchhh------hccCceeHHHHHhhhCceEEEEEecCCCCCCCCCCc---C
Confidence 456677778888777767777766553 12211 1123334 36788875 45566654443322222 1
Q ss_pred CCCCCceEEEEEecCCceEEeecc
Q 002828 812 PRTSRKIVTIGFVNECQFVKVFMH 835 (876)
Q Consensus 812 ~~~~~~~i~l~~~~~~Hf~~~~~~ 835 (876)
+.-+.|-|+|.|- +-||..||.+
T Consensus 234 pe~s~P~I~LLYr-pGHYdilY~~ 256 (256)
T KOG3991|consen 234 PEASAPEIYLLYR-PGHYDILYKK 256 (256)
T ss_pred ccccCceEEEEec-CCccccccCC
Confidence 1233567999996 6899988753
No 16
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=96.08 E-value=0.7 Score=53.34 Aligned_cols=246 Identities=13% Similarity=0.130 Sum_probs=133.4
Q ss_pred ccCCCHHHHHHHHHHhhCCCChHHHHHHHHhcCCCccchHHHHHHHHHHhhhccccCcchHHHHHHHHHhcCcEEEEEee
Q 002828 150 AGRLTEQEANILVDLSRSNISPKEILQTLKQRDMHNVSTIKAIYNARHKYRVGEQVGQLHMHQLLDKLRKHGYIEWHRYN 229 (876)
Q Consensus 150 ~rrl~~~~k~~i~~l~~~~~~p~~I~~~l~~~~~~~~~t~kdi~n~~~~~r~~~~~g~~~~~~ll~~l~e~~~~~~~~~~ 229 (876)
..++++..+..+..++.. ++-+...+.+....+....+...|.|..+..-..... .+ .
T Consensus 115 ~~R~S~~~~~~i~~~a~~-~sYr~aa~~l~~~~~~~~iS~~tV~~~v~~~g~~~~~------------~~---------~ 172 (470)
T PF06782_consen 115 YQRISPELKEKIVELATE-MSYRKAAEILEELLGNVSISKQTVWNIVKEAGFEEIK------------EE---------E 172 (470)
T ss_pred ccchhHHHHHHHHHHHhh-cCHHHHHHHHhhccCCCccCHHHHHHHHHhccchhhh------------cc---------c
Confidence 358999999888877644 8888888888776654445777788887665411100 00 0
Q ss_pred cCCCceeeeEecChHHHHHHHhCCceEEEeccccC----CCC--CCee-EEEEe---e-cCCCCeEEEEE-Eeec---cC
Q 002828 230 EETDCFKDLFWAHPFAVGLLRAFPSVVMIDCTYKT----SMY--PFSF-LEIVG---A-TSTELTFSIAF-AYLE---SE 294 (876)
Q Consensus 230 d~~~~~~~if~~~~~~~~~~~~~~~vl~iD~T~~t----n~~--~~~l-~~~~g---~-~~~~~~~~va~-al~~---~E 294 (876)
.+......+| |-.|++|-. ++. ...+ ++-.| . .+.+......- .++. ..
T Consensus 173 ~~k~~~~~Ly----------------IEaDg~~v~~qg~~~~~~e~k~~~vheG~~~~~~~~~R~~L~n~~~f~~~~~~~ 236 (470)
T PF06782_consen 173 KEKKKVPVLY----------------IEADGVHVKLQGKKKKKKEVKLFVVHEGWEKEKPGGKRNKLKNKRHFVSGVGES 236 (470)
T ss_pred cccCCCCeEE----------------EecCcceecccccccccceeeEEEEEeeeeeeeccCCcceeecchheecccccc
Confidence 0001111111 112333321 111 1122 22224 1 11122222222 2332 34
Q ss_pred ccchHHHHHHHHHHhhcCCCC-CeEEEeeccHHHHHHHHHhCCCccccchhhhhhhhhHhhhhhhhhchhHHHHHHHhhh
Q 002828 295 RDDNYIWTLERLRSMMEDDAL-PRVIVTDKDLALMNSIRAVFPRATNLLCRWHISKNISVNCKKLFETKERWEAFICSWN 373 (876)
Q Consensus 295 ~~~s~~w~l~~l~~~~~~~~~-P~~ivtD~d~al~~Ai~~vfP~~~~~lC~~Hi~kn~~~~~~~~~~~~~~~~~~~~~~~ 373 (876)
..+-|..+.+.+-+....... -.++..|...-+.+++. .||.+.+.+..||+.|.+.+.+... ++..+.+..++
T Consensus 237 ~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~---~~~~~~~~~al- 311 (470)
T PF06782_consen 237 AEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHD---PELKEKIRKAL- 311 (470)
T ss_pred hHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhC---hHHHHHHHHHH-
Confidence 455666667766666522222 34566788888887776 9999999999999999999877542 12222222222
Q ss_pred hcccCcCHHHHHHHHHHhHhhcc------cchhHHHHHHHhhhhhhHHHHHHHhhccccccCcccccccchhhHhHhhhh
Q 002828 374 VLVLSVTEQEYMQHLGAMESDFS------RYPQAIDYVKQTWLANYKEKFVAAWTDLAMHFGNVTMNRGETTHTKLKRLL 447 (876)
Q Consensus 374 ~l~~s~t~~~f~~~~~~l~~~~~------~~~~~~~y~~~~Wl~~~ke~w~~~~~~~~~~~g~~Ttn~~Es~n~~LK~~l 447 (876)
...+...+...++.+..... ....+..|+.++|=. . ..|... .|.......|+.|..+...+
T Consensus 312 ---~~~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~-i-----~~y~~~---~~~~g~g~ee~~~~~~s~Rm 379 (470)
T PF06782_consen 312 ---KKGDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDG-I-----KPYRER---EGLRGIGAEESVSHVLSYRM 379 (470)
T ss_pred ---HhcCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHH-h-----hhhhhc---cCCCccchhhhhhhHHHHHh
Confidence 24455666666666654332 233567888888831 1 112111 34444555789998887766
Q ss_pred cCC
Q 002828 448 AVP 450 (876)
Q Consensus 448 ~~s 450 (876)
+.+
T Consensus 380 K~r 382 (470)
T PF06782_consen 380 KSR 382 (470)
T ss_pred cCC
Confidence 653
No 17
>PF03106 WRKY: WRKY DNA -binding domain; InterPro: IPR003657 The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding []. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure []. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2AYD_A 1WJ2_A 2LEX_A.
Probab=95.51 E-value=0.041 Score=43.57 Aligned_cols=57 Identities=23% Similarity=0.363 Sum_probs=41.6
Q ss_pred cCEEEEEEeecCCCCCCCceEEEEEecCCccCCCCCCCCCCCCCCCCCcceeCCccEEEEeeeCCCCCeEEEEEccccCC
Q 002828 59 NGLVIVIKKSDVGGDGRRPRITFACERSGAYRRKYTEGQTPKRPKTTGTKKCGCPFLLKGHKLDTDDDWILKVVCGVHNH 138 (876)
Q Consensus 59 ~GF~v~~~~S~~~~~g~~~~~~~vC~r~G~~r~~~~~~~~~~~rr~~~s~~~gCp~~i~~~~~~~~~~w~V~~~~~~HNH 138 (876)
=||..|+--....++....|.+|.|+. .+||++=.+.+...++...++.+.++|||
T Consensus 3 Dgy~WRKYGqK~i~g~~~pRsYYrCt~------------------------~~C~akK~Vqr~~~d~~~~~vtY~G~H~h 58 (60)
T PF03106_consen 3 DGYRWRKYGQKNIKGSPYPRSYYRCTH------------------------PGCPAKKQVQRSADDPNIVIVTYEGEHNH 58 (60)
T ss_dssp SSS-EEEEEEEEETTTTCEEEEEEEEC------------------------TTEEEEEEEEEETTCCCEEEEEEES--SS
T ss_pred CCCchhhccCcccCCCceeeEeeeccc------------------------cChhheeeEEEecCCCCEEEEEEeeeeCC
Confidence 377888776666555556678899944 28999988888777888899999999999
Q ss_pred C
Q 002828 139 P 139 (876)
Q Consensus 139 ~ 139 (876)
+
T Consensus 59 ~ 59 (60)
T PF03106_consen 59 P 59 (60)
T ss_dssp -
T ss_pred C
Confidence 6
No 18
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=94.29 E-value=0.056 Score=56.99 Aligned_cols=67 Identities=19% Similarity=0.219 Sum_probs=57.0
Q ss_pred EeeccCccchHHHHHHHH-HHhhcCCCCCeEEEeeccHHHHHHHHHhCCCccccchhhhhhhhhHhhhhh
Q 002828 289 AYLESERDDNYIWTLERL-RSMMEDDALPRVIVTDKDLALMNSIRAVFPRATNLLCRWHISKNISVNCKK 357 (876)
Q Consensus 289 al~~~E~~~s~~w~l~~l-~~~~~~~~~P~~ivtD~d~al~~Ai~~vfP~~~~~lC~~Hi~kn~~~~~~~ 357 (876)
.++++-+.+++.-+|..+ -.. .....++|++|...+...|+++.||+|.+..-.|||++++.+.+.+
T Consensus 31 ~i~~~r~~~~l~~~~~~~~~~~--~~~~v~~V~~Dm~~~y~~~~~~~~P~A~iv~DrFHvvk~~~~al~~ 98 (249)
T PF01610_consen 31 DILPGRDKETLKDFFRSLYPEE--ERKNVKVVSMDMSPPYRSAIREYFPNAQIVADRFHVVKLANRALDK 98 (249)
T ss_pred EEcCCccHHHHHHHHHHhCccc--cccceEEEEcCCCccccccccccccccccccccchhhhhhhhcchh
Confidence 478888999888888876 333 3567889999999999999999999999999999999998875543
No 19
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=94.10 E-value=0.025 Score=58.04 Aligned_cols=109 Identities=9% Similarity=-0.097 Sum_probs=70.7
Q ss_pred CccccccccccccccccccccccCCCCcchhhHHhhhccCCc-----hHHHHHHHHHHHHHhhhhhhhhhhcCH-----H
Q 002828 684 PLCFIDSFPAGLRPYIHDVQDVIADGHCGFRVVAELMDIGED-----NWAQVRRDLVDELQSHYDDYIQLYGDA-----E 753 (876)
Q Consensus 684 ~~~~~~~~~~~l~~~~~~~~~v~~dg~Cgfraia~~l~~~~~-----~~~~vR~~l~~el~~~~~~y~~~~~~~-----~ 753 (876)
..+++-.+|.....--..-.|..|||||.|-+|+++|+..-. -=...|..=......+...|.++.-++ .
T Consensus 155 ~n~~i~~~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~~dr~~~~~~~q~~~i~f~g~hfD~~t~~m~ 234 (306)
T COG5539 155 YNPAILEIDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDSEDRYNSHPYVQRISILFTGIHFDEETLAMV 234 (306)
T ss_pred cchhhcCcchHHHHHhhhccccCCCceEEEeEeccccceeeeeeecchhHHhhccCChhhhhhhhhhcccccchhhhhcc
Confidence 345555666655555555567899999999999999998421 012222222233334445565554333 3
Q ss_pred HHHHHHhhcCCCCCCCCcccccccCCchhhhhcccceeEEEEccCc
Q 002828 754 IARELLHSLSYSESNPGIEHRMIMPDTGHLIASRYNIVLMHLSQQQ 799 (876)
Q Consensus 754 ~~~~~~~~l~~~~~~~~~~~w~~~~~~g~~iA~~~~~~v~~~~~~~ 799 (876)
.|+.+.+.+. ....|+..+.. +.||+.+..|+-++....
T Consensus 235 ~~dt~~ne~~------~~a~~g~~~ei-~qLas~lk~~~~~~nT~~ 273 (306)
T COG5539 235 LWDTYVNEVL------FDASDGITIEI-QQLASLLKNPHYYTNTAS 273 (306)
T ss_pred hHHHHHhhhc------ccccccchHHH-HHHHHHhcCceEEeecCC
Confidence 5788877776 56788866655 689999999998887643
No 20
>PF05412 Peptidase_C33: Equine arterivirus Nsp2-type cysteine proteinase; InterPro: IPR008743 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases corresponds to MEROPS peptidase family C33 (clan CA). The type example is equine arteritis virus Nsp2-type cysteine proteinase, which is involved in viral polyprotein processing [].; GO: 0016032 viral reproduction, 0019082 viral protein processing
Probab=93.62 E-value=0.14 Score=44.46 Aligned_cols=85 Identities=13% Similarity=0.126 Sum_probs=51.1
Q ss_pred cccCCCCcchhhHHhhhccCCchHHHHHHHHHHHHHhhhhhhhhhhcCHHHHHHHHhhcCCCCCCCCcccccccCCchhh
Q 002828 704 DVIADGHCGFRVVAELMDIGEDNWAQVRRDLVDELQSHYDDYIQLYGDAEIARELLHSLSYSESNPGIEHRMIMPDTGHL 783 (876)
Q Consensus 704 ~v~~dg~Cgfraia~~l~~~~~~~~~vR~~l~~el~~~~~~y~~~~~~~~~~~~~~~~l~~~~~~~~~~~w~~~~~~g~~ 783 (876)
.+++||+||+|+||.-+.. ++++. |. .. .+.-+-+.+.|++.-+++++
T Consensus 3 sPP~DG~CG~H~i~aI~n~-------------------------m~~~~--~t---~~--l~~~~r~~d~W~~dedl~~~ 50 (108)
T PF05412_consen 3 SPPGDGSCGWHCIAAIMNH-------------------------MMGGE--FT---TP--LPQRNRPSDDWADDEDLYQV 50 (108)
T ss_pred CCCCCCchHHHHHHHHHHH-------------------------hhccC--CC---cc--ccccCCChHHccChHHHHHH
Confidence 4899999999999976632 11110 00 00 12234578999999999998
Q ss_pred hhcccceeEEEEccCcceeeccCccCCCCCCCCceEEEEEecCCceEEeeccC
Q 002828 784 IASRYNIVLMHLSQQQCFTFLPLRSVPLPRTSRKIVTIGFVNECQFVKVFMHP 836 (876)
Q Consensus 784 iA~~~~~~v~~~~~~~~~~~~p~~~~p~~~~~~~~i~l~~~~~~Hf~~~~~~~ 836 (876)
|-.. +.|+-+.- |..-+.-.++-=..+.||..-.-++
T Consensus 51 iq~l-~lPat~~~---------------~~~Cp~ArYv~~l~~qHW~V~~~~g 87 (108)
T PF05412_consen 51 IQSL-RLPATLDR---------------NGACPHARYVLKLDGQHWEVSVRKG 87 (108)
T ss_pred HHHc-cCceeccC---------------CCCCCCCEEEEEecCceEEEEEcCC
Confidence 8554 55554422 2222233455444679997655554
No 21
>smart00774 WRKY DNA binding domain. The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding.
Probab=92.63 E-value=0.23 Score=39.02 Aligned_cols=56 Identities=23% Similarity=0.292 Sum_probs=40.0
Q ss_pred CEEEEEEeecCCCCCCCceEEEEEecCCccCCCCCCCCCCCCCCCCCcceeCCccEEEEeeeCCCCCeEEEEEccccCC
Q 002828 60 GLVIVIKKSDVGGDGRRPRITFACERSGAYRRKYTEGQTPKRPKTTGTKKCGCPFLLKGHKLDTDDDWILKVVCGVHNH 138 (876)
Q Consensus 60 GF~v~~~~S~~~~~g~~~~~~~vC~r~G~~r~~~~~~~~~~~rr~~~s~~~gCp~~i~~~~~~~~~~w~V~~~~~~HNH 138 (876)
||..|+--.+..++....|.+|.|+. ..||+++=.|.+...++.-.++.+.++|||
T Consensus 4 Gy~WRKYGQK~ikgs~~pRsYYrCt~-----------------------~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 4 GYQWRKYGQKVIKGSPFPRSYYRCTY-----------------------SQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cccccccCcEecCCCcCcceEEeccc-----------------------cCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 66666655555444455577888844 148999876766666788888899999998
No 22
>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 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 potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.
Probab=90.29 E-value=0.7 Score=36.62 Aligned_cols=49 Identities=27% Similarity=0.421 Sum_probs=24.6
Q ss_pred cCEEEEEEeecCCCCCCCceEEEEEecCCccCCCCCCCCCCCCCCCCCcceeCCccEEEEeeeCCCCCeEEEEEccccCC
Q 002828 59 NGLVIVIKKSDVGGDGRRPRITFACERSGAYRRKYTEGQTPKRPKTTGTKKCGCPFLLKGHKLDTDDDWILKVVCGVHNH 138 (876)
Q Consensus 59 ~GF~v~~~~S~~~~~g~~~~~~~vC~r~G~~r~~~~~~~~~~~rr~~~s~~~gCp~~i~~~~~~~~~~w~V~~~~~~HNH 138 (876)
.||.+...+...+ ...+.|++.. ..+|+++|... .+.-.+.....+|||
T Consensus 14 ~Gy~y~~~~~~~~------~~~WrC~~~~---------------------~~~C~a~~~~~----~~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDG------KTYWRCSRRR---------------------SHGCRARLITD----AGDGRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-------EEEEEGGGT---------------------TS----EEEEE------TTEEEE-S---SS
T ss_pred CCeEEECcCCCCC------cEEEEeCCCC---------------------CCCCeEEEEEE----CCCCEEEECCCccCC
Confidence 5777777666532 6788896531 25899999864 344566667789999
No 23
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=88.56 E-value=0.31 Score=46.37 Aligned_cols=81 Identities=21% Similarity=0.103 Sum_probs=65.1
Q ss_pred CceEEEeccccCCCCCCeeEEEEeecCCCCeEEEEEEeeccCccchHHHHHHHHHHhhcCCCCCeEEEeeccHHHHHHHH
Q 002828 253 PSVVMIDCTYKTSMYPFSFLEIVGATSTELTFSIAFAYLESERDDNYIWTLERLRSMMEDDALPRVIVTDKDLALMNSIR 332 (876)
Q Consensus 253 ~~vl~iD~T~~tn~~~~~l~~~~g~~~~~~~~~va~al~~~E~~~s~~w~l~~l~~~~~~~~~P~~ivtD~d~al~~Ai~ 332 (876)
|+.+.+|-||..-+ +--.+....+|..+. ++.+-|...-+...=..||..+++.. ...|.+|+||+..+...|++
T Consensus 1 ~~~w~~DEt~iki~-G~~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~--~~~p~~ivtDk~~aY~~A~~ 75 (140)
T PF13610_consen 1 GDSWHVDETYIKIK-GKWHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRH--RGEPRVIVTDKLPAYPAAIK 75 (140)
T ss_pred CCEEEEeeEEEEEC-CEEEEEEEeeccccc--chhhhhhhhcccccceeeccccceee--ccccceeecccCCccchhhh
Confidence 57899999996533 235566778899888 77888888888877777777776664 38999999999999999999
Q ss_pred HhCCCc
Q 002828 333 AVFPRA 338 (876)
Q Consensus 333 ~vfP~~ 338 (876)
++++..
T Consensus 76 ~l~~~~ 81 (140)
T PF13610_consen 76 ELNPEG 81 (140)
T ss_pred hccccc
Confidence 999874
No 24
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=78.85 E-value=9.5 Score=34.51 Aligned_cols=76 Identities=21% Similarity=0.109 Sum_probs=48.6
Q ss_pred CceEEEeccccC-CCCCCeeEEEEeecCCCCeEEEEEEeeccCccchHHHHHHHHHHhhcCCCCCeEEEeeccHHHHHH
Q 002828 253 PSVVMIDCTYKT-SMYPFSFLEIVGATSTELTFSIAFAYLESERDDNYIWTLERLRSMMEDDALPRVIVTDKDLALMNS 330 (876)
Q Consensus 253 ~~vl~iD~T~~t-n~~~~~l~~~~g~~~~~~~~~va~al~~~E~~~s~~w~l~~l~~~~~~~~~P~~ivtD~d~al~~A 330 (876)
+.++.+|.+... ...+...+.++.+|..-. +.+++.+...++.+.+..+|....... +...|.+|++|++.+..+.
T Consensus 6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~-~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~p~~i~tD~g~~f~~~ 82 (120)
T PF00665_consen 6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSR-FIYAFPVSSKETAEAALRALKRAIEKR-GGRPPRVIRTDNGSEFTSH 82 (120)
T ss_dssp TTEEEEEEEEETGGCTT-CEEEEEEEETTTT-EEEEEEESSSSHHHHHHHHHHHHHHHH-S-SE-SEEEEESCHHHHSH
T ss_pred CCEEEEeeEEEecCCCCccEEEEEEEECCCC-cEEEEEeeccccccccccccccccccc-ccccceecccccccccccc
Confidence 468899988544 334447777777776555 445666666656666666666544443 2333999999999987643
No 25
>PF04684 BAF1_ABF1: BAF1 / ABF1 chromatin reorganising factor; InterPro: IPR006774 ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture []. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 Saccharomyces cerevisiae (P14164 from SWISSPROT)) []. The N-terminal two thirds of the protein are necessary for DNA binding, and the N terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilise the protein structure [].; GO: 0003677 DNA binding, 0006338 chromatin remodeling, 0005634 nucleus
Probab=77.70 E-value=3.8 Score=45.42 Aligned_cols=56 Identities=25% Similarity=0.326 Sum_probs=47.5
Q ss_pred CCCceecCHHHHHHHHHHHhhccCEEEEEEeecCCCCCCCceEEEEEecCCccCCCCCCCCCCCCCCCCCcceeCCccEE
Q 002828 37 TTDMVFNSREELVEWIRDTGKRNGLVIVIKKSDVGGDGRRPRITFACERSGAYRRKYTEGQTPKRPKTTGTKKCGCPFLL 116 (876)
Q Consensus 37 ~~g~~F~S~de~~~~~~~ya~~~GF~v~~~~S~~~~~g~~~~~~~vC~r~G~~r~~~~~~~~~~~rr~~~s~~~gCp~~i 116 (876)
..+..|++.++-|..+++|.-+..+-|+...|-+.+ .++|.|.. -.|||+|
T Consensus 23 ~~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nk-----hftfachl------------------------k~c~fki 73 (496)
T PF04684_consen 23 AQARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNK-----HFTFACHL------------------------KNCPFKI 73 (496)
T ss_pred ccccCCCcHHHHHHHHhhhhhhhcCceeeccccccc-----ceEEEeec------------------------cCCCcee
Confidence 457889999999999999999999999988887764 79999954 3799999
Q ss_pred EEeee
Q 002828 117 KGHKL 121 (876)
Q Consensus 117 ~~~~~ 121 (876)
.....
T Consensus 74 llsy~ 78 (496)
T PF04684_consen 74 LLSYC 78 (496)
T ss_pred eeeec
Confidence 87543
No 26
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=68.93 E-value=32 Score=35.47 Aligned_cols=98 Identities=19% Similarity=0.265 Sum_probs=58.6
Q ss_pred CCCCCCcceeCCccEEEEeeeCC-----------------------------------CC--CeEEEEE-cccc-CCCCC
Q 002828 101 RPKTTGTKKCGCPFLLKGHKLDT-----------------------------------DD--DWILKVV-CGVH-NHPVT 141 (876)
Q Consensus 101 ~rr~~~s~~~gCp~~i~~~~~~~-----------------------------------~~--~w~V~~~-~~~H-NH~~~ 141 (876)
+++...+.+.+|||+|.++.... .+ .|.|..- ..+| +|+..
T Consensus 69 ~~~~~~skK~~CPA~I~Ik~I~~FPdykv~~~~~~~~~~~r~~~~~~lk~~l~~~~~~~~~~r~yv~lP~~~~H~~H~~~ 148 (225)
T PF15299_consen 69 RRRSKPSKKRDCPARIYIKEIIKFPDYKVPTNSQKDTRRERRKASKKLKKALLSGKSIEGERRFYVQLPSPEEHSGHPIG 148 (225)
T ss_pred ccccccccCCCCCeEEEEEEEEEcCCcccccchhhhhHHHHHHHHHHHHHHHhcCCCCCceEEEEEECCChHhcCCCccc
Confidence 34566788999999999864311 01 1222211 2356 77776
Q ss_pred CCccccccccCCCHHHHHHHHHHhhCCCCh-HHHHHHHHhc-----CC----------CccchHHHHHHHHHHhh
Q 002828 142 QHVEGHSYAGRLTEQEANILVDLSRSNISP-KEILQTLKQR-----DM----------HNVSTIKAIYNARHKYR 200 (876)
Q Consensus 142 ~~~~~~~~~rrl~~~~k~~i~~l~~~~~~p-~~I~~~l~~~-----~~----------~~~~t~kdi~n~~~~~r 200 (876)
....+ ....+.++....|..|...|+.. .+|...|+.. +. .-.+|.+||.|...+..
T Consensus 149 ~~~~~--~~q~~~~~v~~ki~eLv~~gv~~v~e~k~~l~~fV~~~lf~~~~~p~~~n~~y~Pt~~di~n~~~~~~ 221 (225)
T PF15299_consen 149 QEAAG--LKQPLDPRVVEKIHELVAQGVTSVPEMKRHLKKFVEEELFKDQEPPPPTNRRYFPTDKDIRNHMYSAK 221 (225)
T ss_pred ccccc--ccccCCHHHHHHHHHHHHcccccHHHHHHHHHHHhhhhccCCCCCCCCCccccCCchHHHHHHHHHHH
Confidence 53221 22467888889999999999765 5565555321 10 01257788888776554
No 27
>PHA02517 putative transposase OrfB; Reviewed
Probab=65.33 E-value=39 Score=35.99 Aligned_cols=69 Identities=13% Similarity=-0.012 Sum_probs=41.5
Q ss_pred CceEEEeccccCCCCCCeeEEEEeecCCCCeEEEEEEeeccCccchHHHHHHHHHHhhc--CCCCCeEEEeeccHH
Q 002828 253 PSVVMIDCTYKTSMYPFSFLEIVGATSTELTFSIAFAYLESERDDNYIWTLERLRSMME--DDALPRVIVTDKDLA 326 (876)
Q Consensus 253 ~~vl~iD~T~~tn~~~~~l~~~~g~~~~~~~~~va~al~~~E~~~s~~w~l~~l~~~~~--~~~~P~~ivtD~d~a 326 (876)
..++..|.||..... +-.++++.+|.... .++|+.+....+.+. +++.|..++. +...+.+|.||....
T Consensus 110 n~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~---~~~~l~~a~~~~~~~~~~i~~sD~G~~ 180 (277)
T PHA02517 110 NQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDF---VLDALEQALWARGRPGGLIHHSDKGSQ 180 (277)
T ss_pred CCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHH---HHHHHHHHHHhcCCCcCcEeecccccc
Confidence 478999999964433 34566666665544 566777776666664 4455555541 222334667888653
No 28
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=63.33 E-value=7 Score=40.74 Aligned_cols=112 Identities=13% Similarity=0.059 Sum_probs=71.9
Q ss_pred CCCCcchhhHHhhhccCCchHHHHHHHHHHHHHhhhhhhhhhhcCHHHHHHHHhhcCCCCCCCCccccc-ccCCchhhhh
Q 002828 707 ADGHCGFRVVAELMDIGEDNWAQVRRDLVDELQSHYDDYIQLYGDAEIARELLHSLSYSESNPGIEHRM-IMPDTGHLIA 785 (876)
Q Consensus 707 ~dg~Cgfraia~~l~~~~~~~~~vR~~l~~el~~~~~~y~~~~~~~~~~~~~~~~l~~~~~~~~~~~w~-~~~~~g~~iA 785 (876)
.|--|.|+|++..++-- +=..+|+.+..|+.+++|.|....-+-... .++..|. .++-|. +--..+ +|.
T Consensus 119 ~d~srl~q~~~~~l~~a--sv~~lrE~vs~Ev~snPDl~n~~i~~~~~i-~y~~~i~------k~d~~~dG~ieia-~iS 188 (306)
T COG5539 119 DDNSRLFQAERYSLRDA--SVAKLREVVSLEVLSNPDLYNPAILEIDVI-AYATWIV------KPDSQGDGCIEIA-IIS 188 (306)
T ss_pred CchHHHHHHHHhhhhhh--hHHHHHHHHHHHHhhCccccchhhcCcchH-HHHHhhh------ccccCCCceEEEe-Eec
Confidence 46789999999988753 678899999999999999998765332211 1222222 345555 444444 789
Q ss_pred cccceeEEEEccCcceeeccCccCCCCCCCCceEEEEEecCCceEEeec
Q 002828 786 SRYNIVLMHLSQQQCFTFLPLRSVPLPRTSRKIVTIGFVNECQFVKVFM 834 (876)
Q Consensus 786 ~~~~~~v~~~~~~~~~~~~p~~~~p~~~~~~~~i~l~~~~~~Hf~~~~~ 834 (876)
+.+++-|.++....+. -++..+-+. ..-|++-|. +-||.++++
T Consensus 189 ~~l~v~i~~Vdv~~~~---~dr~~~~~~--~q~~~i~f~-g~hfD~~t~ 231 (306)
T COG5539 189 DQLPVRIHVVDVDKDS---EDRYNSHPY--VQRISILFT-GIHFDEETL 231 (306)
T ss_pred cccceeeeeeecchhH---HhhccCChh--hhhhhhhhc-ccccchhhh
Confidence 9999999887754321 122222221 123677775 689988765
No 29
>KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms]
Probab=56.47 E-value=7 Score=45.49 Aligned_cols=52 Identities=13% Similarity=0.180 Sum_probs=36.8
Q ss_pred chhhhhcccceeEEEEcc--------------CcceeeccCccCCCCCCCCceEEEEEecCCceEEee
Q 002828 780 TGHLIASRYNIVLMHLSQ--------------QQCFTFLPLRSVPLPRTSRKIVTIGFVNECQFVKVF 833 (876)
Q Consensus 780 ~g~~iA~~~~~~v~~~~~--------------~~~~~~~p~~~~p~~~~~~~~i~l~~~~~~Hf~~~~ 833 (876)
+-.++|+...||||+++. ..-..|+||..++...+ --||.|+|- ..||+.++
T Consensus 225 hifvl~~ilRrpivvvsd~mlR~s~~~sfap~~~ggiylpLe~p~~~c~-r~pLvl~yd-~~hf~~lv 290 (774)
T KOG4345|consen 225 HIFVLAHILRRPIVVVSDTMLRDSGGESFAPIPVGGIYLPLEVPAQECH-RSPLVLAYD-QAHFSALV 290 (774)
T ss_pred HHHHHHHHhhCCeeEecccccccCCCcccccCccCceEEeccCchhhcc-cchhhhhhH-hhhhhhhh
Confidence 456789999999999972 12345777776654443 357999985 58998874
No 30
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=56.30 E-value=97 Score=29.81 Aligned_cols=107 Identities=12% Similarity=0.056 Sum_probs=68.2
Q ss_pred HHHhCCceEEEeccccCCCCCCeeEEEEeecCCCCeEEEEEEeec-cCccchHHHHHHHHHHhhcCCCCCeEEEeeccHH
Q 002828 248 LLRAFPSVVMIDCTYKTSMYPFSFLEIVGATSTELTFSIAFAYLE-SERDDNYIWTLERLRSMMEDDALPRVIVTDKDLA 326 (876)
Q Consensus 248 ~~~~~~~vl~iD~T~~tn~~~~~l~~~~g~~~~~~~~~va~al~~-~E~~~s~~w~l~~l~~~~~~~~~P~~ivtD~d~a 326 (876)
.+...|-.|..|+= ++..+.+++.|+.....|..|.-..-.-. ..+.+.+.-+|+...+.+ +......||||-...
T Consensus 28 ~w~~~Gcsi~~DgW--td~~~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ll~~vIeeV-G~~nVvqVVTDn~~~ 104 (153)
T PF04937_consen 28 SWKRTGCSIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFELLDEVIEEV-GEENVVQVVTDNASN 104 (153)
T ss_pred HHHhcCEEEEEecC--cCCCCCeEEEEEEEcccccEEEEEEecccccccHHHHHHHHHHHHHHh-hhhhhhHHhccCchh
Confidence 33445556666764 44556677887777777666644432211 134455555555555555 455666799999999
Q ss_pred HHHHHH---HhCCCccccchhhhhhhhhHhhhhh
Q 002828 327 LMNSIR---AVFPRATNLLCRWHISKNISVNCKK 357 (876)
Q Consensus 327 l~~Ai~---~vfP~~~~~lC~~Hi~kn~~~~~~~ 357 (876)
++.|-+ +-+|..--..|.-|-+.-+.+.+.+
T Consensus 105 ~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 105 MKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred HHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 888844 4477777778999988777766554
No 31
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=55.32 E-value=8.8 Score=39.23 Aligned_cols=30 Identities=23% Similarity=0.348 Sum_probs=23.4
Q ss_pred CCCCCccccccCCccchhHhhHHhhcCCCCCcc
Q 002828 521 ASACGCVFRRTHGLPCAHEIAEYKHERRSIPLL 553 (876)
Q Consensus 521 ~~~CsC~~~~~~GlPC~H~lav~~~~~~~lp~~ 553 (876)
...|||..+ ..||+|+-+|+.+.+..+..+
T Consensus 124 ~~dCSCPD~---anPCKHi~AvyY~lae~f~~d 153 (266)
T COG4279 124 STDCSCPDY---ANPCKHIAAVYYLLAEKFDED 153 (266)
T ss_pred ccccCCCCc---ccchHHHHHHHHHHHHHhccC
Confidence 468999875 589999999999887544443
No 32
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=51.20 E-value=92 Score=35.29 Aligned_cols=56 Identities=18% Similarity=0.214 Sum_probs=43.6
Q ss_pred EeeccCccchHHHHHHHHHHhhcCCCCCeEEEeeccHHHHHHHHHhCCCccccchhhhhhh
Q 002828 289 AYLESERDDNYIWTLERLRSMMEDDALPRVIVTDKDLALMNSIRAVFPRATNLLCRWHISK 349 (876)
Q Consensus 289 al~~~E~~~s~~w~l~~l~~~~~~~~~P~~ivtD~d~al~~Ai~~vfP~~~~~lC~~Hi~k 349 (876)
.++++-+.+++...|..+ +..+.+.+..|......+++++.||++.+.+=.||+.+
T Consensus 183 ~i~~~r~~~ti~~~l~~~-----g~~~v~~V~~D~~~~y~~~v~e~~pna~i~~d~fh~~~ 238 (402)
T COG3464 183 DILEGRSVRTLRRYLRRG-----GSEQVKSVSMDMFGPYASAVQELFPNALIIADRFHVVQ 238 (402)
T ss_pred eecCCccHHHHHHHHHhC-----CCcceeEEEccccHHHHHHHHHhCCChheeeeeeeeee
Confidence 355666666655554443 22277889999999999999999999999999999987
No 33
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=48.81 E-value=40 Score=34.18 Aligned_cols=81 Identities=17% Similarity=0.096 Sum_probs=55.3
Q ss_pred CceEEEeccccCCC-CCCeeEEEEeecCCCCeEEEEEEeeccCccchHHHHHHHHHHhhcCCCCCeEEEeeccHHHHHHH
Q 002828 253 PSVVMIDCTYKTSM-YPFSFLEIVGATSTELTFSIAFAYLESERDDNYIWTLERLRSMMEDDALPRVIVTDKDLALMNSI 331 (876)
Q Consensus 253 ~~vl~iD~T~~tn~-~~~~l~~~~g~~~~~~~~~va~al~~~E~~~s~~w~l~~l~~~~~~~~~P~~ivtD~d~al~~Ai 331 (876)
++++.||-||.+-+ ...-| --.+|..|. ++.+-|...-+...=..||..+++.. ..|.+|+||+.+....|+
T Consensus 70 ~~~w~vDEt~ikv~gkw~yl--yrAid~~g~--~Ld~~L~~rRn~~aAk~Fl~kllk~~---g~p~v~vtDka~s~~~A~ 142 (215)
T COG3316 70 GDSWRVDETYIKVNGKWHYL--YRAIDADGL--TLDVWLSKRRNALAAKAFLKKLLKKH---GEPRVFVTDKAPSYTAAL 142 (215)
T ss_pred ccceeeeeeEEeeccEeeeh--hhhhccCCC--eEEEEEEcccCcHHHHHHHHHHHHhc---CCCceEEecCccchHHHH
Confidence 46788888886432 22223 334555544 45555666666666666777776664 789999999999999999
Q ss_pred HHhCCCccc
Q 002828 332 RAVFPRATN 340 (876)
Q Consensus 332 ~~vfP~~~~ 340 (876)
.++-++..|
T Consensus 143 ~~l~~~~eh 151 (215)
T COG3316 143 RKLGSEVEH 151 (215)
T ss_pred HhcCcchhe
Confidence 999875544
No 34
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=44.23 E-value=68 Score=34.01 Aligned_cols=59 Identities=19% Similarity=0.254 Sum_probs=40.2
Q ss_pred EEEEEeeccCccchHHHHHHHHHHhhcCCCCCeEEEeeccHHHHHHHHHhCCCccccchhhhhhhhhHhhhhh
Q 002828 285 SIAFAYLESERDDNYIWTLERLRSMMEDDALPRVIVTDKDLALMNSIRAVFPRATNLLCRWHISKNISVNCKK 357 (876)
Q Consensus 285 ~va~al~~~E~~~s~~w~l~~l~~~~~~~~~P~~ivtD~d~al~~Ai~~vfP~~~~~lC~~Hi~kn~~~~~~~ 357 (876)
.+.|.+.++-..+...-+|.. ...+++||.-.+... +..+.|+.|+-|+.|.+..-...
T Consensus 98 ~v~f~~~~sR~~~~~~~~L~~---------~~GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 98 VVLFFYAPSRSSKVIKEFLGD---------FSGILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred eeeeeecccccccchhhhhcc---------cceeeeccccccccc-----ccccccccccccccccccccccc
Confidence 555556666555554444322 335999999887654 22789999999999998876543
No 35
>PRK13907 rnhA ribonuclease H; Provisional
Probab=42.32 E-value=2e+02 Score=26.40 Aligned_cols=78 Identities=15% Similarity=0.086 Sum_probs=43.3
Q ss_pred eEEEeccccCCCCCCeeEEEEeecCCCCeEEEEEE-eeccCccchHHHHHHHHHHhhcCCCCCeEEEeeccHHHHHHHHH
Q 002828 255 VVMIDCTYKTSMYPFSFLEIVGATSTELTFSIAFA-YLESERDDNYIWTLERLRSMMEDDALPRVIVTDKDLALMNSIRA 333 (876)
Q Consensus 255 vl~iD~T~~tn~~~~~l~~~~g~~~~~~~~~va~a-l~~~E~~~s~~w~l~~l~~~~~~~~~P~~ivtD~d~al~~Ai~~ 333 (876)
.|.+|+.++.|.-..-...++ .+..+.. ...+. -..+....-|.-++..|+.+...+..+..|.||. +.+.+++..
T Consensus 3 ~iy~DGa~~~~~g~~G~G~vi-~~~~~~~-~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS-~~vi~~~~~ 79 (128)
T PRK13907 3 EVYIDGASKGNPGPSGAGVFI-KGVQPAV-QLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDS-QLVERAVEK 79 (128)
T ss_pred EEEEeeCCCCCCCccEEEEEE-EECCeeE-EEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEech-HHHHHHHhH
Confidence 378999998876443333333 3443432 22221 1123334456666777777664455667778877 556666666
Q ss_pred hC
Q 002828 334 VF 335 (876)
Q Consensus 334 vf 335 (876)
.+
T Consensus 80 ~~ 81 (128)
T PRK13907 80 EY 81 (128)
T ss_pred HH
Confidence 54
No 36
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=41.35 E-value=35 Score=25.04 Aligned_cols=30 Identities=30% Similarity=0.362 Sum_probs=15.0
Q ss_pred cCCCHHHHHHHHHHhhCCCChHHHHHHHHh
Q 002828 151 GRLTEQEANILVDLSRSNISPKEILQTLKQ 180 (876)
Q Consensus 151 rrl~~~~k~~i~~l~~~~~~p~~I~~~l~~ 180 (876)
++|+.+++..|..|.+.|.+.++|...|..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~s~~~IA~~lg~ 32 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGMSIREIAKRLGR 32 (44)
T ss_dssp ---------HHHHHHCS---HHHHHHHTT-
T ss_pred cchhhhHHHHHHHHHHcCCCHHHHHHHHCc
Confidence 468999999999999999999999876643
No 37
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=41.33 E-value=42 Score=26.59 Aligned_cols=29 Identities=21% Similarity=0.416 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhhCCCChHHHHHHHHhcCC
Q 002828 155 EQEANILVDLSRSNISPKEILQTLKQRDM 183 (876)
Q Consensus 155 ~~~k~~i~~l~~~~~~p~~I~~~l~~~~~ 183 (876)
++..+.|..|.+.|++|.+|-..|+++++
T Consensus 31 ~eVe~~I~klakkG~tpSqIG~iLRD~~G 59 (60)
T PF08069_consen 31 EEVEELIVKLAKKGLTPSQIGVILRDQYG 59 (60)
T ss_dssp HHHHHHHHHHCCTTHCHHHHHHHHHHSCT
T ss_pred HHHHHHHHHHHHcCCCHHHhhhhhhhccC
Confidence 56678889999999999999999999875
No 38
>PRK09784 hypothetical protein; Provisional
Probab=40.69 E-value=15 Score=36.91 Aligned_cols=40 Identities=25% Similarity=0.311 Sum_probs=27.1
Q ss_pred ccccccccccCCCCcchhhHHhhhccCCchHHHHHHHHHHH
Q 002828 697 PYIHDVQDVIADGHCGFRVVAELMDIGEDNWAQVRRDLVDE 737 (876)
Q Consensus 697 ~~~~~~~~v~~dg~Cgfraia~~l~~~~~~~~~vR~~l~~e 737 (876)
.|.++---|+|||-|..|||-+.- ..+-+|..+-..-.+|
T Consensus 197 ~~glkyapvdgdgycllrailvlk-~h~yswal~s~ktqk~ 236 (417)
T PRK09784 197 TYGLKYAPVDGDGYCLLRAILVLK-QHDYSWALGSHKTQKE 236 (417)
T ss_pred hhCceecccCCCchhHHHHHHHhh-hcccchhhccchhHHH
Confidence 455566669999999999997643 3446777665443333
No 39
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=34.12 E-value=16 Score=31.95 Aligned_cols=25 Identities=28% Similarity=0.371 Sum_probs=18.1
Q ss_pred CCCCCccccc-----cCCccchhHhhHHhh
Q 002828 521 ASACGCVFRR-----THGLPCAHEIAEYKH 545 (876)
Q Consensus 521 ~~~CsC~~~~-----~~GlPC~H~lav~~~ 545 (876)
..-|||.++. .-.-||.|++.+-..
T Consensus 49 ~gfCSCp~~~~svvl~Gk~~C~Hi~glk~A 78 (117)
T COG5431 49 GGFCSCPDFLGSVVLKGKSPCAHIIGLKVA 78 (117)
T ss_pred cCcccCHHHHhHhhhcCcccchhhhheeee
Confidence 4489999887 224679999976443
No 40
>KOG4825 consensus Component of synaptic membrane glycine-, glutamate- and thienylcyclohexylpiperidine-binding glycoprotein (43kDa) [Signal transduction mechanisms]
Probab=27.35 E-value=87 Score=34.92 Aligned_cols=36 Identities=22% Similarity=0.133 Sum_probs=30.2
Q ss_pred CCCCcccccCCCCCCCCCCCCcccCCCccceecccc
Q 002828 616 ASTSLVELEVDGFPLSKLGTSTYQDPSELQYVLSVQ 651 (876)
Q Consensus 616 ~~~~~~k~~~Kg~p~~~~~~st~~~ps~~e~~~~~~ 651 (876)
.++.+.+..+.|+|..-..-++++.||.||..+++|
T Consensus 279 pmpSlpqleepgrenqfaepflqekpsswelpIrPq 314 (666)
T KOG4825|consen 279 PMPSLPQLEEPGRENQFAEPFLQEKPSSWELPIRPQ 314 (666)
T ss_pred CCCccccccCCCCccccccchhhcCCCcceeecccc
Confidence 344457888899998878889999999999988888
No 41
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=26.24 E-value=1.5e+02 Score=28.33 Aligned_cols=31 Identities=23% Similarity=0.298 Sum_probs=26.7
Q ss_pred CHHHHHHHHHHhhCCCChHHHHHHHHhcCCC
Q 002828 154 TEQEANILVDLSRSNISPKEILQTLKQRDMH 184 (876)
Q Consensus 154 ~~~~k~~i~~l~~~~~~p~~I~~~l~~~~~~ 184 (876)
.++..+.|..|...|++|.+|-..|++++|.
T Consensus 30 ~eeve~~I~~lakkG~~pSqIG~~LRD~~gi 60 (151)
T PRK08561 30 PEEIEELVVELAKQGYSPSMIGIILRDQYGI 60 (151)
T ss_pred HHHHHHHHHHHHHCCCCHHHhhhhHhhccCC
Confidence 4566788899999999999999999999853
No 42
>KOG4027 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.83 E-value=87 Score=29.83 Aligned_cols=37 Identities=22% Similarity=0.331 Sum_probs=30.1
Q ss_pred Eecccc-CCCCCCeeEE--EEeecCCCCeEEEEEEeeccC
Q 002828 258 IDCTYK-TSMYPFSFLE--IVGATSTELTFSIAFAYLESE 294 (876)
Q Consensus 258 iD~T~~-tn~~~~~l~~--~~g~~~~~~~~~va~al~~~E 294 (876)
||.||+ |+.|+-|.++ +.|.|+.|+-...||+.+.--
T Consensus 70 ievt~KstsPygWPqivl~vfg~d~~G~d~v~GYg~~hiP 109 (187)
T KOG4027|consen 70 IEVTLKSTSPYGWPQIVLNVFGKDHSGKDCVTGYGMLHIP 109 (187)
T ss_pred eEEEeccCCCCCCceEEEEEecCCcCCcceeeeeeeEecC
Confidence 788997 7889988654 558899999999999977643
No 43
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=24.45 E-value=59 Score=25.55 Aligned_cols=18 Identities=22% Similarity=0.501 Sum_probs=14.7
Q ss_pred CCCCcc--hhhHHhhhccCC
Q 002828 707 ADGHCG--FRVVAELMDIGE 724 (876)
Q Consensus 707 ~dg~Cg--fraia~~l~~~~ 724 (876)
-||||- +||.|...|.++
T Consensus 20 ~~~nc~~~~RAaarkf~V~r 39 (58)
T PF09607_consen 20 KDNNCKGNQRAAARKFNVSR 39 (58)
T ss_dssp H-TTTTT-HHHHHHHTTS-H
T ss_pred HccchhhhHHHHHHHhCccH
Confidence 789998 999999999975
No 44
>PF03412 Peptidase_C39: Peptidase C39 family This is family C39 in the peptidase classification. ; InterPro: IPR005074 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of sequences defined by this cysteine peptidase domain belong to the MEROPS peptidase family C39 (clan CA). It is found in a wide range of ABC transporters, which are maturation proteases for peptide bacteriocins, the proteolytic domain residing in the N-terminal region of the protein []. A number of the proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. Lantibiotic and non-lantibiotic bacteriocins are synthesised as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. ; GO: 0005524 ATP binding, 0008233 peptidase activity, 0006508 proteolysis, 0016021 integral to membrane; PDB: 3K8U_A 3B79_A.
Probab=22.02 E-value=3.2e+02 Score=24.81 Aligned_cols=86 Identities=20% Similarity=0.277 Sum_probs=44.3
Q ss_pred CCCcchhhHHhhhccCCchHHHHHHHHHHHHHhhhhhhhhhhcCHHHHHHHHhhcCCCCCCCCcccccccCCchhhhhcc
Q 002828 708 DGHCGFRVVAELMDIGEDNWAQVRRDLVDELQSHYDDYIQLYGDAEIARELLHSLSYSESNPGIEHRMIMPDTGHLIASR 787 (876)
Q Consensus 708 dg~Cgfraia~~l~~~~~~~~~vR~~l~~el~~~~~~y~~~~~~~~~~~~~~~~l~~~~~~~~~~~w~~~~~~g~~iA~~ 787 (876)
+-.||..|+|..+.. ++-....+++...+. ....-.++.++. .+|..
T Consensus 10 ~~dcg~acl~~l~~~--------------------------~g~~~s~~~l~~~~~------~~~~g~s~~~L~-~~~~~ 56 (131)
T PF03412_consen 10 SNDCGLACLAMLLKY--------------------------YGIPVSEEELRRQLG------TSEEGTSLADLK-RAARK 56 (131)
T ss_dssp TT-HHHHHHHHHHHH--------------------------TT----HHHHHCCTT-------BTTB--CCCHH-HHHHH
T ss_pred CCCHHHHHHHHHHHH--------------------------hCCCchHHHHHHHhc------CCccCCCHHHHH-HHHHh
Confidence 457999999877733 222334445555553 122334566664 57899
Q ss_pred cceeEEEEccCcceeeccCccCCCCCCCCceEEEEEecCCceEEeeccCC
Q 002828 788 YNIVLMHLSQQQCFTFLPLRSVPLPRTSRKIVTIGFVNECQFVKVFMHPG 837 (876)
Q Consensus 788 ~~~~v~~~~~~~~~~~~p~~~~p~~~~~~~~i~l~~~~~~Hf~~~~~~~~ 837 (876)
||...-.+..... . |. .. +-| +|.++...||+.|...++
T Consensus 57 ~gl~~~~~~~~~~-~-l~------~~--~~P-~I~~~~~~h~vVi~~~~~ 95 (131)
T PF03412_consen 57 YGLKAKAVKLNFE-K-LK------RL--PLP-AIAHLKDGHFVVIYKIDD 95 (131)
T ss_dssp TTEEEEEEE--GG-G-CT------CG--GSS-EEEEECCCEEEEEEEECC
T ss_pred cccceeeeecchh-h-hh------hc--ccc-EEEEecCcceEEEEeEcC
Confidence 9987777654333 1 11 11 111 444447899999976543
No 45
>KOG0030 consensus Myosin essential light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=21.84 E-value=31 Score=32.23 Aligned_cols=86 Identities=12% Similarity=0.164 Sum_probs=48.6
Q ss_pred ccccccccCCCCcchhhH---HhhhccCC---chHHHHHHHHHHHHHhhhhh---hhhhhc------CHHHHHHHHhhcC
Q 002828 699 IHDVQDVIADGHCGFRVV---AELMDIGE---DNWAQVRRDLVDELQSHYDD---YIQLYG------DAEIARELLHSLS 763 (876)
Q Consensus 699 ~~~~~~v~~dg~Cgfrai---a~~l~~~~---~~~~~vR~~l~~el~~~~~~---y~~~~~------~~~~~~~~~~~l~ 763 (876)
|...+|..|||-=+++-+ .++||.++ +-+..+++.--.|+...+-. +.+++. +...|++++.+|+
T Consensus 16 ~F~lfD~~gD~ki~~~q~gdvlRalG~nPT~aeV~k~l~~~~~~~~~~~rl~FE~fLpm~q~vaknk~q~t~edfvegLr 95 (152)
T KOG0030|consen 16 AFLLFDRTGDGKISGSQVGDVLRALGQNPTNAEVLKVLGQPKRREMNVKRLDFEEFLPMYQQVAKNKDQGTYEDFVEGLR 95 (152)
T ss_pred HHHHHhccCcccccHHHHHHHHHHhcCCCcHHHHHHHHcCcccchhhhhhhhHHHHHHHHHHHHhccccCcHHHHHHHHH
Confidence 345677889986665554 56778877 33444444444444445533 344441 2235999999998
Q ss_pred CCCCCCCcccccccCCchhhhhc
Q 002828 764 YSESNPGIEHRMIMPDTGHLIAS 786 (876)
Q Consensus 764 ~~~~~~~~~~w~~~~~~g~~iA~ 786 (876)
..++ ...-|+.-.+.-|+|++
T Consensus 96 vFDk--eg~G~i~~aeLRhvLtt 116 (152)
T KOG0030|consen 96 VFDK--EGNGTIMGAELRHVLTT 116 (152)
T ss_pred hhcc--cCCcceeHHHHHHHHHH
Confidence 7665 23334444444455543
No 46
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=21.02 E-value=3.2e+02 Score=28.90 Aligned_cols=72 Identities=7% Similarity=-0.127 Sum_probs=46.8
Q ss_pred CceEEEeccccCCCCCCeeEEEEeecCCCCeEEEEEEeecc-CccchHHHHHHH-HHHhhc--CCCCCeEEEeeccH
Q 002828 253 PSVVMIDCTYKTSMYPFSFLEIVGATSTELTFSIAFAYLES-ERDDNYIWTLER-LRSMME--DDALPRVIVTDKDL 325 (876)
Q Consensus 253 ~~vl~iD~T~~tn~~~~~l~~~~g~~~~~~~~~va~al~~~-E~~~s~~w~l~~-l~~~~~--~~~~P~~ivtD~d~ 325 (876)
..++..|-||.....+.-++..+.+|.... .++|+++... .+.+...-+|+. +..... ....|.+|.||+..
T Consensus 87 n~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gs 162 (262)
T PRK14702 87 NQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGS 162 (262)
T ss_pred CCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCc
Confidence 378999999865544446777777887666 6788888764 455554455543 332221 23457889999875
No 47
>PF05415 Peptidase_C36: Beet necrotic yellow vein furovirus-type papain-like endopeptidase; InterPro: IPR008746 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases correspond to MEROPS peptidase family C36 (clan CA). The type example is beet necrotic yellow vein furovirus-type papain-like endopeptidase (beet necrotic yellow vein virus), which is involved in processing the viral polyprotein.
Probab=20.29 E-value=1.1e+02 Score=25.99 Aligned_cols=22 Identities=9% Similarity=0.241 Sum_probs=18.2
Q ss_pred ccCCCCcchhhHHhhhccCCch
Q 002828 705 VIADGHCGFRVVAELMDIGEDN 726 (876)
Q Consensus 705 v~~dg~Cgfraia~~l~~~~~~ 726 (876)
+..|.||..-|||.+||-+=|-
T Consensus 3 ~sR~NNCLVVAis~~L~~T~e~ 24 (104)
T PF05415_consen 3 ASRPNNCLVVAISECLGVTLEK 24 (104)
T ss_pred ccCCCCeEeehHHHHhcchHHH
Confidence 4568999999999999988443
Done!