Query 004450
Match_columns 753
No_of_seqs 388 out of 1262
Neff 8.1
Searched_HMMs 46136
Date Thu Mar 28 23:38:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004450.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004450hhsearch_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 2E-141 4E-146 1224.6 61.3 612 44-684 62-688 (846)
2 PF10551 MULE: MULE transposas 99.9 4.8E-22 1E-26 174.3 7.4 90 283-374 1-93 (93)
3 PF03101 FAR1: FAR1 DNA-bindin 99.8 1.3E-20 2.9E-25 164.3 9.1 89 70-158 1-91 (91)
4 PF00872 Transposase_mut: Tran 99.7 3.4E-17 7.4E-22 179.8 3.5 255 164-464 92-352 (381)
5 PF08731 AFT: Transcription fa 99.2 8.2E-11 1.8E-15 102.1 10.0 88 62-156 1-111 (111)
6 COG3328 Transposase and inacti 99.0 3.3E-09 7.2E-14 114.6 11.5 262 168-479 82-348 (379)
7 smart00575 ZnF_PMZ plant mutat 98.8 9.7E-10 2.1E-14 72.6 1.0 26 571-596 2-27 (28)
8 PF03108 DBD_Tnp_Mut: MuDR fam 98.8 2.2E-08 4.8E-13 81.7 7.7 65 54-145 2-67 (67)
9 PF04434 SWIM: SWIM zinc finge 98.2 7.4E-07 1.6E-11 64.6 2.6 30 566-595 11-40 (40)
10 PF01610 DDE_Tnp_ISL3: Transpo 96.8 0.00088 1.9E-08 69.7 3.2 95 280-380 2-99 (249)
11 PF06782 UPF0236: Uncharacteri 94.1 1.1 2.4E-05 51.0 15.3 141 316-465 235-381 (470)
12 PF13610 DDE_Tnp_IS240: DDE do 92.7 0.016 3.5E-07 54.6 -2.1 81 276-360 1-81 (140)
13 PF03106 WRKY: WRKY DNA -bindi 92.7 0.82 1.8E-05 36.2 7.9 55 80-155 4-59 (60)
14 PF00665 rve: Integrase core d 89.1 1.4 2.9E-05 39.6 7.1 76 276-352 6-82 (120)
15 PF04500 FLYWCH: FLYWCH zinc f 87.7 0.96 2.1E-05 35.5 4.5 25 127-154 38-62 (62)
16 PF04684 BAF1_ABF1: BAF1 / ABF 84.6 2.2 4.8E-05 46.9 6.6 56 58-139 24-79 (496)
17 smart00774 WRKY DNA binding do 79.7 4.2 9E-05 32.0 4.7 28 127-154 31-59 (59)
18 PF04937 DUF659: Protein of un 74.2 20 0.00043 34.2 8.8 108 270-379 27-138 (153)
19 COG3316 Transposase and inacti 59.3 18 0.00038 36.4 5.3 82 276-363 70-152 (215)
20 PF03050 DDE_Tnp_IS66: Transpo 54.8 12 0.00026 39.2 3.6 40 333-378 116-155 (271)
21 COG3074 Uncharacterized protei 46.5 70 0.0015 25.8 5.6 66 658-735 13-78 (79)
22 PRK08561 rps15p 30S ribosomal 46.1 17 0.00038 34.2 2.7 77 173-249 31-142 (151)
23 PHA02047 phage lambda Rz1-like 42.6 63 0.0014 27.9 5.2 46 700-749 31-76 (101)
24 PF12329 TMF_DNA_bd: TATA elem 42.2 1E+02 0.0023 25.4 6.5 51 699-749 8-61 (74)
25 PF06005 DUF904: Protein of un 34.7 1.4E+02 0.003 24.7 5.9 61 656-735 11-71 (72)
26 PRK14143 heat shock protein Gr 34.2 1.6E+02 0.0036 30.2 7.8 55 695-749 59-113 (238)
27 KOG3517 Transcription factor P 34.1 37 0.0008 34.4 3.0 77 168-248 18-99 (334)
28 COG5431 Uncharacterized metal- 32.6 30 0.00065 30.3 1.8 29 556-590 42-75 (117)
29 COG4279 Uncharacterized conser 31.7 19 0.00042 36.7 0.6 23 570-595 125-147 (266)
30 PRK14702 insertion element IS2 30.5 1.4E+02 0.0031 31.1 7.0 70 277-347 88-162 (262)
31 PF07544 Med9: RNA polymerase 29.7 3.4E+02 0.0074 22.9 7.9 64 651-726 19-82 (83)
32 COG5470 Uncharacterized conser 29.4 27 0.00058 30.2 1.0 40 45-84 43-82 (96)
33 PF04800 ETC_C1_NDUFA4: ETC co 29.1 35 0.00076 30.1 1.8 28 57-88 50-77 (101)
34 PHA02517 putative transposase 29.0 1.3E+02 0.0027 31.5 6.4 70 276-347 110-179 (277)
35 COG4715 Uncharacterized conser 28.8 1.9E+02 0.0041 33.3 7.7 37 557-595 58-96 (587)
36 KOG0963 Transcription factor/C 28.7 3.7E+02 0.0079 31.4 10.0 53 696-748 285-337 (629)
37 PF14201 DUF4318: Domain of un 28.3 1.5E+02 0.0032 24.6 5.1 39 61-99 13-54 (74)
38 KOG4460 Nuclear pore complex, 27.7 4.1E+02 0.0088 30.5 9.9 119 633-752 600-740 (741)
39 PRK09409 IS2 transposase TnpB; 26.8 2E+02 0.0043 30.8 7.4 71 276-347 126-201 (301)
40 PF12491 ApoB100_C: Apolipopro 26.8 2.2E+02 0.0047 22.2 5.3 28 651-678 28-55 (58)
41 PF13936 HTH_38: Helix-turn-he 25.7 25 0.00055 25.7 0.2 29 168-196 2-30 (44)
42 PRK14154 heat shock protein Gr 24.9 2.2E+02 0.0049 28.6 6.8 55 695-749 44-98 (208)
43 KOG3647 Predicted coiled-coil 23.9 6E+02 0.013 26.5 9.4 53 698-750 135-187 (338)
44 PF15299 ALS2CR8: Amyotrophic 22.2 82 0.0018 32.1 3.3 20 118-137 69-88 (225)
45 PF15456 Uds1: Up-regulated Du 21.2 3.4E+02 0.0074 24.9 6.7 30 699-728 84-113 (124)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=1.9e-141 Score=1224.58 Aligned_cols=612 Identities=37% Similarity=0.710 Sum_probs=561.1
Q ss_pred CccccCCCCCCCCCCCCccCCHHHHHHHHHHHhhhcCcEEEEeeeeeccCCCceeEEEEEecCCCcccCCCc--------
Q 004450 44 NFETLNGDPNLEPFEGMEFDSEQAARIFYNSYARRIGFSTRVSVYQRSRRDGSIICRQIVCSREGFRRGSSE-------- 115 (753)
Q Consensus 44 ~~~~~~~~~~~~P~~Gm~F~S~eea~~fy~~YA~~~GF~vr~~~s~r~k~~g~~~~~~f~C~r~G~~~~~~~-------- 115 (753)
..+...++...+|.+||+|+|+|||++||+.||+++||+||+.+++|++.+|.+++++|+|+|+|+++....
T Consensus 62 ~~~~~~~~~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~ 141 (846)
T PLN03097 62 ELVEFKEDTNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRAR 141 (846)
T ss_pred ccccccCCCCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCccccccccccccc
Confidence 334445567899999999999999999999999999999999999999999999999999999998752110
Q ss_pred ------ccccccCcccccCCceEEEEEEeCCCcEEEEEeeccccCCCCCCCCcccccccccCCcchhhHHHHHHhcCCCC
Q 004450 116 ------NRSKRQRTITRVGCKAQMTVKKQGSGKWAVSKLIKEHNHELVPPDKVHCLRSHRHVSGPARSLIDTLQAAGMGP 189 (753)
Q Consensus 116 ------~~~~r~r~s~r~gCpa~i~v~~~~~~~W~V~~~~~~HNH~l~~~~~~~~l~shr~is~~~k~~i~~l~~~gi~~ 189 (753)
...+++|+.+||||||+|+|++..+|+|+|+.|+.+|||+|.|+..+. +.+
T Consensus 142 ~~k~~~~~~~~rR~~tRtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~~~~~-----------------------~~~ 198 (846)
T PLN03097 142 QTKQDPENGTGRRSCAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPAQAVS-----------------------EQT 198 (846)
T ss_pred ccccCcccccccccccCCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCccccc-----------------------hhh
Confidence 011235667999999999999977899999999999999999874321 123
Q ss_pred cchhhhHhhhcCCcccccccccccchhhhhhhhhcc-CcChHHHHHHHHHhhhcCCccEEEEecCCCCCeeEEEecCcch
Q 004450 190 SGVMSVLIKESGGVNNVGFTKVDCQNYMSSSRQRTL-GSGGQVVIDNLKQMQAEDPSFFCAFQGDFENTTGNIFWADANS 268 (753)
Q Consensus 190 ~~I~~~l~~~~g~~~~~~~t~~Di~N~~~~~r~~~~-~gd~~~ll~~l~~~~~~np~f~y~~~~d~~~~~~~ifw~~~~~ 268 (753)
+.++..+....++..+++++..|..|...+.|+..+ .||+++||+||+++|.+||+|||++++|++|++++|||+|++|
T Consensus 199 r~~~~~~~~~~~~~~~v~~~~~d~~~~~~~~r~~~~~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~s 278 (846)
T PLN03097 199 RKMYAAMARQFAEYKNVVGLKNDSKSSFDKGRNLGLEAGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKS 278 (846)
T ss_pred hhhHHHHHhhhhccccccccchhhcchhhHHHhhhcccchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHH
Confidence 445555556666677888888888888877776555 4999999999999999999999999999999999999999999
Q ss_pred HHHhhhcCcEEEecccccccccCCcccceEEeecCCceEEEEEEeecccchhHHHHHHHHHHHHhCCCCCceecchhhHH
Q 004450 269 RMNYSYFGDTVTFDTTYRMNRYRIPFAPFTGLNHHGQPVLFGCALLLNESEASFIWLFEAWLAAMSGRSPNSITTDQDRI 348 (753)
Q Consensus 269 ~~~~~~f~dvv~~D~Ty~tn~y~~pl~~~~gvn~~~~~~~~g~al~~~Et~es~~W~~~~~~~~m~~~~p~~iitD~~~~ 348 (753)
+.+|.+|||||+|||||+||+|++||++|+|||||+|+++||||||.+|+.+||.|||++|+++|+|++|.+||||+|.+
T Consensus 279 r~~Y~~FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiTDqd~a 358 (846)
T PLN03097 279 RHDYGNFSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKVIITDQDKA 358 (846)
T ss_pred HHHHHhcCCEEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEecCCHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhCCCCccccCCCchHHHHHHhhhhhccCCccHHHHHHHhhcCCCCHHHHHHHHHHHHHhhccCcChHHHHHHH
Q 004450 349 IRAAVAQVFPGTRHRFCKWNVFREAQERLSDVYQSHPHFEAEFQRCINMTETVDEFESCWESLIRRYNLVGNEWLQSMYN 428 (753)
Q Consensus 349 l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~l~~~~~~~~~~~~~~~~~v~~~~~~eeFe~~w~~l~~~~~l~~~~wL~~l~~ 428 (753)
|.+||++|||+|.||+|.|||++|+.++|++++..++.|..+|.+||+.+++++|||..|..|+++|+|++|+||+.||+
T Consensus 359 m~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~ 438 (846)
T PLN03097 359 MKSVISEVFPNAHHCFFLWHILGKVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYE 438 (846)
T ss_pred HHHHHHHHCCCceehhhHHHHHHHHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHH
Confidence 99999999999999999999999999999999998999999999999999999999999999999999999999999999
Q ss_pred HhccchhhhccccccccccccCCccchhhhhhcccCcCCCHHHHHHHHHHHHHHHHHHhhhhcccccccccccCCCChHH
Q 004450 429 VRQQWVPVYLRDTFFGEMSMTQASDNINSYFDGYINASTNIQALIKQYEKAIASRHEKEVKADYDTVNTEPVLKTPSPME 508 (753)
Q Consensus 429 ~r~~W~~~y~~~~f~~g~~tt~r~Es~n~~~k~~v~~~~~l~~f~~~~~~~~~~~~~~e~~~d~~~~~~~p~l~~~~~~e 508 (753)
.|++|||+|+++.|++||.||+|+||+|++|++||++.++|..|+++|+++++.++++|+++|+++.++.|.+++++|||
T Consensus 439 ~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piE 518 (846)
T PLN03097 439 DRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLE 518 (846)
T ss_pred hHhhhhHHHhcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhccHHHHHHHHHHHHHhcCcceEEEccCCceEEEEEeeecCccceEEEEEEecCceEEeeccccccCCceeeehh
Q 004450 509 KQVANLYTRKIFMKFQEELVETLAYPATIVNDTGSEIIYRVAKFGEEQKAHFVRYNIFEKKASCSCQLFEFSGIICRHIL 588 (753)
Q Consensus 509 ~qa~~~yT~~~f~~fq~e~~~s~~~~~~~~~~~~~~~~y~V~~~~~~~~~~~V~~~~~~~~~~CsC~~fe~~GipC~Hil 588 (753)
+||+++|||+||++||+|+..+..|.+....++|...+|.|..... .+.|.|.+|...+.++|+|++||+.||||+|||
T Consensus 519 kQAs~iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~-~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaL 597 (846)
T PLN03097 519 KSVSGVYTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEK-NQDFTVTWNQTKLEVSCICRLFEYKGYLCRHAL 597 (846)
T ss_pred HHHHHHhHHHHHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecC-CCcEEEEEecCCCeEEeeccCeecCccchhhHH
Confidence 9999999999999999999999999998888889999999987654 478999999999999999999999999999999
Q ss_pred HHHhhhcccccCCcchhccccccccCCccccCcccCCCCcccCChHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHH
Q 004450 589 AVFRVTNILTLPSHYILKRWTRNAKSGVLLNGHVLGLASSRQESSAARYDNLCREVIKYVEEGAESAHIYNMAMDVLREA 668 (753)
Q Consensus 589 ~Vl~~~~v~~iP~~yil~RWtk~ak~~~~~~~~~~~~~~~~~~s~~~Ry~~L~~~~~~~~~~~~~s~e~~~~a~~~l~e~ 668 (753)
+||.++||.+||++|||+||||+||...+.+... ....+.+.||+.||++++++|++|+.|.|.|..||++|+|+
T Consensus 598 kVL~~~~v~~IP~~YILkRWTKdAK~~~~~~~~~-----~~~~~~~~Ryn~L~r~a~kla~~as~S~E~y~~a~~~L~e~ 672 (846)
T PLN03097 598 VVLQMCQLSAIPSQYILKRWTKDAKSRHLLGEES-----EQVQSRVQRYNDLCQRALKLSEEASLSQESYNIAFRALEEA 672 (846)
T ss_pred HHHhhcCcccCchhhhhhhchhhhhhcccCcccc-----ccccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 9999999999999999999999999876554322 11235578999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCccc
Q 004450 669 AKKVAAAKKYGPGVTQ 684 (753)
Q Consensus 669 ~~~~~~~~~~~~~~~~ 684 (753)
.++++.+++.+...+.
T Consensus 673 ~~~~~~~~n~~~~~~~ 688 (846)
T PLN03097 673 FGNCISMNNSNKSLVE 688 (846)
T ss_pred HHHHHHhhccCCCccc
Confidence 9999988887666653
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=99.86 E-value=4.8e-22 Score=174.27 Aligned_cols=90 Identities=32% Similarity=0.646 Sum_probs=87.0
Q ss_pred ccccccccCCcccc---eEEeecCCceEEEEEEeecccchhHHHHHHHHHHHHhCCCCCceecchhhHHHHHHHHhhCCC
Q 004450 283 TTYRMNRYRIPFAP---FTGLNHHGQPVLFGCALLLNESEASFIWLFEAWLAAMSGRSPNSITTDQDRIIRAAVAQVFPG 359 (753)
Q Consensus 283 ~Ty~tn~y~~pl~~---~~gvn~~~~~~~~g~al~~~Et~es~~W~~~~~~~~m~~~~p~~iitD~~~~l~~Ai~~vfP~ 359 (753)
+||+||+| +|++. ++|+|++|+.+|+||+++.+|+.++|.|+|+.|++.++.. |.+||||++.++.+||+++||+
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~-p~~ii~D~~~~~~~Ai~~vfP~ 78 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQK-PKVIISDFDKALINAIKEVFPD 78 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccC-ceeeeccccHHHHHHHHHHCCC
Confidence 69999999 98886 9999999999999999999999999999999999999987 9999999999999999999999
Q ss_pred CccccCCCchHHHHH
Q 004450 360 TRHRFCKWNVFREAQ 374 (753)
Q Consensus 360 a~h~~C~~Hi~~n~~ 374 (753)
+.|++|.||+.+|++
T Consensus 79 ~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 79 ARHQLCLFHILRNIK 93 (93)
T ss_pred ceEehhHHHHHHhhC
Confidence 999999999999974
No 3
>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=99.83 E-value=1.3e-20 Score=164.33 Aligned_cols=89 Identities=44% Similarity=0.811 Sum_probs=80.9
Q ss_pred HHHHHHhhhcCcEEEEeeeeeccCCCceeEEEEEecCCCcccCCCc--ccccccCcccccCCceEEEEEEeCCCcEEEEE
Q 004450 70 IFYNSYARRIGFSTRVSVYQRSRRDGSIICRQIVCSREGFRRGSSE--NRSKRQRTITRVGCKAQMTVKKQGSGKWAVSK 147 (753)
Q Consensus 70 ~fy~~YA~~~GF~vr~~~s~r~k~~g~~~~~~f~C~r~G~~~~~~~--~~~~r~r~s~r~gCpa~i~v~~~~~~~W~V~~ 147 (753)
+||+.||..+||+||+.++++++.+|.++++.|+|+++|.++.... ...++++++++|||||+|.|++..+|.|.|+.
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~~~~w~v~~ 80 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRKDGKWRVTS 80 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEccCCEEEEEE
Confidence 5999999999999999999988889999999999999999884433 35678889999999999999998789999999
Q ss_pred eeccccCCCCC
Q 004450 148 LIKEHNHELVP 158 (753)
Q Consensus 148 ~~~~HNH~l~~ 158 (753)
+..+|||+|.|
T Consensus 81 ~~~~HNH~L~P 91 (91)
T PF03101_consen 81 FVLEHNHPLCP 91 (91)
T ss_pred CcCCcCCCCCC
Confidence 99999999976
No 4
>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=99.65 E-value=3.4e-17 Score=179.83 Aligned_cols=255 Identities=15% Similarity=0.172 Sum_probs=185.6
Q ss_pred cccccccCCcchhhHHHHHHhcCCCCcchhhhHhhhcCCcccccccccccchhhhhhhhhccCcChHHHHHHHHHhhhcC
Q 004450 164 CLRSHRHVSGPARSLIDTLQAAGMGPSGVMSVLIKESGGVNNVGFTKVDCQNYMSSSRQRTLGSGGQVVIDNLKQMQAED 243 (753)
Q Consensus 164 ~l~shr~is~~~k~~i~~l~~~gi~~~~I~~~l~~~~g~~~~~~~t~~Di~N~~~~~r~~~~~gd~~~ll~~l~~~~~~n 243 (753)
.++.+++.+......|..|-..|+++++|...+...+|+. ++.+..|.++..... .-+.-++.....+
T Consensus 92 ll~~y~r~~~~l~~~i~~ly~~G~Str~i~~~l~~l~g~~---~~S~s~vSri~~~~~---------~~~~~w~~R~L~~ 159 (381)
T PF00872_consen 92 LLPKYQRREDSLEELIISLYLKGVSTRDIEEALEELYGEV---AVSKSTVSRITKQLD---------EEVEAWRNRPLES 159 (381)
T ss_pred ccchhhhhhhhhhhhhhhhhccccccccccchhhhhhccc---ccCchhhhhhhhhhh---------hhHHHHhhhcccc
Confidence 3455666666777778888889999999999999988833 245555555443221 1111122111111
Q ss_pred CccEEEEecCCCCCeeEEEecCcchHHHhhhcCcEEEeccccccccc-----CCcccceEEeecCCceEEEEEEeecccc
Q 004450 244 PSFFCAFQGDFENTTGNIFWADANSRMNYSYFGDTVTFDTTYRMNRY-----RIPFAPFTGLNHHGQPVLFGCALLLNES 318 (753)
Q Consensus 244 p~f~y~~~~d~~~~~~~ifw~~~~~~~~~~~f~dvv~~D~Ty~tn~y-----~~pl~~~~gvn~~~~~~~~g~al~~~Et 318 (753)
.. -++|.+|++|.+-+. +.++++++|+|.+|+..++|+.+...|+
T Consensus 160 ~~------------------------------y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es 209 (381)
T PF00872_consen 160 EP------------------------------YPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRES 209 (381)
T ss_pred cc------------------------------ccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCc
Confidence 10 147899999987552 5678999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHhCCCCCceecchhhHHHHHHHHhhCCCCccccCCCchHHHHHHhhhhhccCCccHHHHHHHhhcCC
Q 004450 319 EASFIWLFEAWLAAMSGRSPNSITTDQDRIIRAAVAQVFPGTRHRFCKWNVFREAQERLSDVYQSHPHFEAEFQRCINMT 398 (753)
Q Consensus 319 ~es~~W~~~~~~~~m~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~l~~~~~~~~~~~~~~~~~v~~~ 398 (753)
.++|.-+|..|++- |-..|..||+|..+|+..||.++||++.++.|.+|+++|+..++.. +..+.+..+|+. |+.+
T Consensus 210 ~~~W~~~l~~L~~R-Gl~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~--k~~~~v~~~Lk~-I~~a 285 (381)
T PF00872_consen 210 AASWREFLQDLKER-GLKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPK--KDRKEVKADLKA-IYQA 285 (381)
T ss_pred cCEeeecchhhhhc-cccccceeeccccccccccccccccchhhhhheechhhhhcccccc--ccchhhhhhccc-cccc
Confidence 99999999998665 4457999999999999999999999999999999999999988854 234567777755 4667
Q ss_pred CCHHHHHHHHHHHHHhhccCcChHHHHHHHHh-ccchhhhccccccccccccCCccchhhhhhcccC
Q 004450 399 ETVDEFESCWESLIRRYNLVGNEWLQSMYNVR-QQWVPVYLRDTFFGEMSMTQASDNINSYFDGYIN 464 (753)
Q Consensus 399 ~~~eeFe~~w~~l~~~~~l~~~~wL~~l~~~r-~~W~~~y~~~~f~~g~~tt~r~Es~n~~~k~~v~ 464 (753)
.+.++....|.++++++........+.|-... +.|.-.-++...+.-+.|||.+|++|+.+|+..+
T Consensus 286 ~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~ 352 (381)
T PF00872_consen 286 PDKEEAREALEEFAEKWEKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRRTK 352 (381)
T ss_pred cccchhhhhhhhcccccccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhhhcc
Confidence 89999999999998887664443333332211 2222222344445678899999999999987554
No 5
>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=99.21 E-value=8.2e-11 Score=102.05 Aligned_cols=88 Identities=16% Similarity=0.323 Sum_probs=71.1
Q ss_pred cCCHHHHHHHHHHHhhhcCcEEEEeeeeeccCCCceeEEEEEecCCCcccCCCc---------------------ccccc
Q 004450 62 FDSEQAARIFYNSYARRIGFSTRVSVYQRSRRDGSIICRQIVCSREGFRRGSSE---------------------NRSKR 120 (753)
Q Consensus 62 F~S~eea~~fy~~YA~~~GF~vr~~~s~r~k~~g~~~~~~f~C~r~G~~~~~~~---------------------~~~~r 120 (753)
|.+.+|.+.|+...+...||+|++.+|...+ +.|.|--+|.++.... ...+.
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~k-------i~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~ 73 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKKK-------IVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKK 73 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCce-------EEEEEecCCCcccccccccccccccccccccccccccccccC
Confidence 8899999999999999999999999998764 8999987776652111 11112
Q ss_pred c-CcccccCCceEEEEEEeC-CCcEEEEEeeccccCCC
Q 004450 121 Q-RTITRVGCKAQMTVKKQG-SGKWAVSKLIKEHNHEL 156 (753)
Q Consensus 121 ~-r~s~r~gCpa~i~v~~~~-~~~W~V~~~~~~HNH~l 156 (753)
+ ..+.+++|||+|++.... .+.|.|..++..|||+|
T Consensus 74 k~t~srk~~CPFriRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 74 KRTKSRKNTCPFRIRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred CcccccccCCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence 2 335569999999999876 89999999999999986
No 6
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=98.96 E-value=3.3e-09 Score=114.63 Aligned_cols=262 Identities=12% Similarity=0.070 Sum_probs=167.7
Q ss_pred cccCCcchhhHHHHHHhcCCCCcchhhhHhhhcCCcccccccccccchhhhhhhhhccCcChHHHHHHHHHhhhcCCccE
Q 004450 168 HRHVSGPARSLIDTLQAAGMGPSGVMSVLIKESGGVNNVGFTKVDCQNYMSSSRQRTLGSGGQVVIDNLKQMQAEDPSFF 247 (753)
Q Consensus 168 hr~is~~~k~~i~~l~~~gi~~~~I~~~l~~~~g~~~~~~~t~~Di~N~~~~~r~~~~~gd~~~ll~~l~~~~~~np~f~ 247 (753)
+++........|-.|...|++++.+-..+...++. ++.+.-+..+ ...+...+...+..-.+
T Consensus 82 ~~r~~~~~~~~v~~~y~~gv~Tr~i~~~~~~~~~~----~~s~~~iS~~------------~~~~~e~v~~~~~r~l~-- 143 (379)
T COG3328 82 YQRRERALDLPVLSMYAKGVTTREIEALLEELYGH----KVSPSVISVV------------TDRLDEKVKAWQNRPLG-- 143 (379)
T ss_pred hHhhhhhHHHHHHHHHHcCCcHHHHHHHHHHhhCc----ccCHHHhhhH------------HHHHHHHHHHHHhcccc--
Confidence 44444455566778888999999999988887663 1211111111 12333334333322110
Q ss_pred EEEecCCCCCeeEEEecCcchHHHhhhcCcEEEecccccccc--cCCcccceEEeecCCceEEEEEEeecccchhHHHHH
Q 004450 248 CAFQGDFENTTGNIFWADANSRMNYSYFGDTVTFDTTYRMNR--YRIPFAPFTGLNHHGQPVLFGCALLLNESEASFIWL 325 (753)
Q Consensus 248 y~~~~d~~~~~~~ifw~~~~~~~~~~~f~dvv~~D~Ty~tn~--y~~pl~~~~gvn~~~~~~~~g~al~~~Et~es~~W~ 325 (753)
--.+|.+|++|.+-+ -+..+++++||+.+|+..++|+.+-..|+ ..|.-+
T Consensus 144 ---------------------------~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~ 195 (379)
T COG3328 144 ---------------------------DYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSF 195 (379)
T ss_pred ---------------------------CceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHH
Confidence 014689999998876 56889999999999999999999999999 888855
Q ss_pred HHHHHHHhCCCCCceecchhhHHHHHHHHhhCCCCccccCCCchHHHHHHhhhhhccCCccHHHHHHHhhcCCCCHHHHH
Q 004450 326 FEAWLAAMSGRSPNSITTDQDRIIRAAVAQVFPGTRHRFCKWNVFREAQERLSDVYQSHPHFEAEFQRCINMTETVDEFE 405 (753)
Q Consensus 326 ~~~~~~~m~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~l~~~~~~~~~~~~~~~~~v~~~~~~eeFe 405 (753)
|..|+.- |-..-..+++|..+++.+||..+||.+.++.|..|+.+|+..+.... ..+....++ +.++.+.+.++-.
T Consensus 196 l~~l~~r-gl~~v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~k--~~d~i~~~~-~~I~~a~~~e~~~ 271 (379)
T COG3328 196 LLDLKNR-GLSDVLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPRK--DQDAVLSDL-RSIYIAPDAEEAL 271 (379)
T ss_pred HHHHHhc-cccceeEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhhh--hhHHHHhhh-hhhhccCCcHHHH
Confidence 5555543 22334466779999999999999999999999999999998876542 112222233 4566678888888
Q ss_pred HHHHHHHHhhccCcChHHHHHHHHh-ccchhhhccccccccccccCCccchhhhhhcccCc--CCCHHHHHHHHHHH
Q 004450 406 SCWESLIRRYNLVGNEWLQSMYNVR-QQWVPVYLRDTFFGEMSMTQASDNINSYFDGYINA--STNIQALIKQYEKA 479 (753)
Q Consensus 406 ~~w~~l~~~~~l~~~~wL~~l~~~r-~~W~~~y~~~~f~~g~~tt~r~Es~n~~~k~~v~~--~~~l~~f~~~~~~~ 479 (753)
..|..+.+.+......-++.+.... +.|.-.-|......-+.|||-+|++|+.++..+.. ..+-.+++..+...
T Consensus 272 ~~~~~~~~~w~~~yP~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~~~~~~~~fpn~~sv~k~~y~ 348 (379)
T COG3328 272 LALLAFSELWGKRYPAILKSWRNALEELLPFFAFPSEIRKIIYTTNAIESLNKLIRRRTKVVGIFPNEESVEKLVYL 348 (379)
T ss_pred HHHHHHHHhhhhhcchHHHHHHHHHHHhcccccCcHHHHhHhhcchHHHHHHHHHHHHHhhhccCCCHHHHHHHHHH
Confidence 8898887755433332222222211 12211111111113467999999999988765443 34445555544333
No 7
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.83 E-value=9.7e-10 Score=72.58 Aligned_cols=26 Identities=46% Similarity=0.907 Sum_probs=24.7
Q ss_pred EeeccccccCCceeeehhHHHhhhcc
Q 004450 571 SCSCQLFEFSGIICRHILAVFRVTNI 596 (753)
Q Consensus 571 ~CsC~~fe~~GipC~Hil~Vl~~~~v 596 (753)
+|+|++||..||||+|+|+|+...|+
T Consensus 2 ~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 2 TCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred cccCCCcccCCccHHHHHHHHHHhCC
Confidence 79999999999999999999998876
No 8
>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=98.78 E-value=2.2e-08 Score=81.71 Aligned_cols=65 Identities=22% Similarity=0.333 Sum_probs=56.6
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhhcCcEEEEeeeeeccCCCceeEEEEEecCCCcccCCCcccccccCcccccCCceEE
Q 004450 54 LEPFEGMEFDSEQAARIFYNSYARRIGFSTRVSVYQRSRRDGSIICRQIVCSREGFRRGSSENRSKRQRTITRVGCKAQM 133 (753)
Q Consensus 54 ~~P~~Gm~F~S~eea~~fy~~YA~~~GF~vr~~~s~r~k~~g~~~~~~f~C~r~G~~~~~~~~~~~r~r~s~r~gCpa~i 133 (753)
+...+||.|+|.+|++.++..||..+||.+++.+|.+. ++.++|.. .||||+|
T Consensus 2 ~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~-------r~~~~C~~--------------------~~C~Wrv 54 (67)
T PF03108_consen 2 PELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKK-------RYRAKCKD--------------------KGCPWRV 54 (67)
T ss_pred CccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCE-------EEEEEEcC--------------------CCCCEEE
Confidence 46789999999999999999999999999999888654 48889963 3899999
Q ss_pred EEEEeC-CCcEEE
Q 004450 134 TVKKQG-SGKWAV 145 (753)
Q Consensus 134 ~v~~~~-~~~W~V 145 (753)
++++.+ ++.|.|
T Consensus 55 ~as~~~~~~~~~I 67 (67)
T PF03108_consen 55 RASKRKRSDTFQI 67 (67)
T ss_pred EEEEcCCCCEEEC
Confidence 999987 688875
No 9
>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=98.22 E-value=7.4e-07 Score=64.60 Aligned_cols=30 Identities=47% Similarity=0.844 Sum_probs=26.2
Q ss_pred cCceEEeeccccccCCceeeehhHHHhhhc
Q 004450 566 FEKKASCSCQLFEFSGIICRHILAVFRVTN 595 (753)
Q Consensus 566 ~~~~~~CsC~~fe~~GipC~Hil~Vl~~~~ 595 (753)
.....+|+|..|+..|.||+|+++|+...+
T Consensus 11 ~~~~~~CsC~~~~~~~~~CkHi~av~~~~~ 40 (40)
T PF04434_consen 11 SIEQASCSCPYFQFRGGPCKHIVAVLLALN 40 (40)
T ss_pred cccccEeeCCCccccCCcchhHHHHHHhhC
Confidence 356789999999999999999999997653
No 10
>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=96.78 E-value=0.00088 Score=69.68 Aligned_cols=95 Identities=15% Similarity=0.174 Sum_probs=66.8
Q ss_pred EecccccccccCCcccceEEeec--CCceEEEEEEeecccchhHHHHHHHHH-HHHhCCCCCceecchhhHHHHHHHHhh
Q 004450 280 TFDTTYRMNRYRIPFAPFTGLNH--HGQPVLFGCALLLNESEASFIWLFEAW-LAAMSGRSPNSITTDQDRIIRAAVAQV 356 (753)
Q Consensus 280 ~~D~Ty~tn~y~~pl~~~~gvn~--~~~~~~~g~al~~~Et~es~~W~~~~~-~~~m~~~~p~~iitD~~~~l~~Ai~~v 356 (753)
+||=+.....++. +..+-+|. .+..++ .++.+-+.+++.-+|..+ -.. ......+|.+|...+...||++.
T Consensus 2 giDE~~~~~g~~~--y~t~~~d~~~~~~~il---~i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~~ 75 (249)
T PF01610_consen 2 GIDEFAFRKGHRS--YVTVVVDLDTDTGRIL---DILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIREY 75 (249)
T ss_pred eEeeeeeecCCcc--eeEEEEECccCCceEE---EEcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCcccccccccc
Confidence 4554444333322 34445555 444433 478888888877766655 222 33466799999999999999999
Q ss_pred CCCCccccCCCchHHHHHHhhhhh
Q 004450 357 FPGTRHRFCKWNVFREAQERLSDV 380 (753)
Q Consensus 357 fP~a~h~~C~~Hi~~n~~~~l~~~ 380 (753)
||+|.+.+-.|||++++.+.+..+
T Consensus 76 ~P~A~iv~DrFHvvk~~~~al~~v 99 (249)
T PF01610_consen 76 FPNAQIVADRFHVVKLANRALDKV 99 (249)
T ss_pred ccccccccccchhhhhhhhcchhh
Confidence 999999999999999987766544
No 11
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=94.12 E-value=1.1 Score=51.02 Aligned_cols=141 Identities=9% Similarity=0.175 Sum_probs=84.6
Q ss_pred ccchhHHHHHHHHHHHHhCCCCC--ceecchhhHHHHHHHHhhCCCCccccCCCchHHHHHHhhhhhccCCccHHHHHHH
Q 004450 316 NESEASFIWLFEAWLAAMSGRSP--NSITTDQDRIIRAAVAQVFPGTRHRFCKWNVFREAQERLSDVYQSHPHFEAEFQR 393 (753)
Q Consensus 316 ~Et~es~~W~~~~~~~~m~~~~p--~~iitD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~l~~~~~~~~~~~~~~~~ 393 (753)
..+.+-|.-+.+.+-........ .++..|....+..++. .||++.|.+..||+.+.+.+.++. .+...+.+.+
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~----~~~~~~~~~~ 309 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSH----DPELKEKIRK 309 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhh----ChHHHHHHHH
Confidence 44456676666655555443322 3677999999988776 999999999999999999988865 3556666777
Q ss_pred hhcCCCCHHHHHHHHHHHHHhhccCcC-hHHHHHHH-Hhccch--hhhccccccccccccCCccchhhhhhcccCc
Q 004450 394 CINMTETVDEFESCWESLIRRYNLVGN-EWLQSMYN-VRQQWV--PVYLRDTFFGEMSMTQASDNINSYFDGYINA 465 (753)
Q Consensus 394 ~v~~~~~~eeFe~~w~~l~~~~~l~~~-~wL~~l~~-~r~~W~--~~y~~~~f~~g~~tt~r~Es~n~~~k~~v~~ 465 (753)
++.. .+...++...+.+...-..... +-+..+.. ....|- .+|... .|+....-.|+.+..+...++.
T Consensus 310 al~~-~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~i~~y~~~---~~~~g~g~ee~~~~~~s~RmK~ 381 (470)
T PF06782_consen 310 ALKK-GDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDGIKPYRER---EGLRGIGAEESVSHVLSYRMKS 381 (470)
T ss_pred HHHh-cCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHHhhhhhhc---cCCCccchhhhhhhHHHHHhcC
Confidence 7764 5667777777665543222111 11111111 123342 233221 2333333467888877655543
No 12
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=92.72 E-value=0.016 Score=54.62 Aligned_cols=81 Identities=20% Similarity=0.216 Sum_probs=66.3
Q ss_pred CcEEEecccccccccCCcccceEEeecCCceEEEEEEeecccchhHHHHHHHHHHHHhCCCCCceecchhhHHHHHHHHh
Q 004450 276 GDTVTFDTTYRMNRYRIPFAPFTGLNHHGQPVLFGCALLLNESEASFIWLFEAWLAAMSGRSPNSITTDQDRIIRAAVAQ 355 (753)
Q Consensus 276 ~dvv~~D~Ty~tn~y~~pl~~~~gvn~~~~~~~~g~al~~~Et~es~~W~~~~~~~~m~~~~p~~iitD~~~~l~~Ai~~ 355 (753)
|+.+.+|=||.+-+ |---+.+..||.+|+ ++++-|-..-+...=..||+..++..+ ..|..|+||..++...|+++
T Consensus 1 ~~~w~~DEt~iki~-G~~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~-~~p~~ivtDk~~aY~~A~~~ 76 (140)
T PF13610_consen 1 GDSWHVDETYIKIK-GKWHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-GEPRVIVTDKLPAYPAAIKE 76 (140)
T ss_pred CCEEEEeeEEEEEC-CEEEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-cccceeecccCCccchhhhh
Confidence 68899999997743 234556788999999 777888888888887888877777665 68899999999999999999
Q ss_pred hCCCC
Q 004450 356 VFPGT 360 (753)
Q Consensus 356 vfP~a 360 (753)
.+|..
T Consensus 77 l~~~~ 81 (140)
T PF13610_consen 77 LNPEG 81 (140)
T ss_pred ccccc
Confidence 99984
No 13
>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=92.66 E-value=0.82 Score=36.16 Aligned_cols=55 Identities=20% Similarity=0.330 Sum_probs=35.3
Q ss_pred CcEEEEeeeeeccCCCceeEEEEEecCCCcccCCCcccccccCcccccCCceEEEEEEeC-CCcEEEEEeeccccCC
Q 004450 80 GFSTRVSVYQRSRRDGSIICRQIVCSREGFRRGSSENRSKRQRTITRVGCKAQMTVKKQG-SGKWAVSKLIKEHNHE 155 (753)
Q Consensus 80 GF~vr~~~s~r~k~~g~~~~~~f~C~r~G~~~~~~~~~~~r~r~s~r~gCpa~i~v~~~~-~~~W~V~~~~~~HNH~ 155 (753)
||..|+--.+.- .....-+..|.|+.. ||||+=.|.+.. ++.-.++....+|||+
T Consensus 4 gy~WRKYGqK~i-~g~~~pRsYYrCt~~--------------------~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 4 GYRWRKYGQKNI-KGSPYPRSYYRCTHP--------------------GCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp SS-EEEEEEEEE-TTTTCEEEEEEEECT--------------------TEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CCchhhccCccc-CCCceeeEeeecccc--------------------ChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 666665433322 122234567888652 899999999886 7788888999999996
No 14
>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=89.06 E-value=1.4 Score=39.64 Aligned_cols=76 Identities=13% Similarity=0.127 Sum_probs=56.8
Q ss_pred CcEEEecccccc-cccCCcccceEEeecCCceEEEEEEeecccchhHHHHHHHHHHHHhCCCCCceecchhhHHHHHH
Q 004450 276 GDTVTFDTTYRM-NRYRIPFAPFTGLNHHGQPVLFGCALLLNESEASFIWLFEAWLAAMSGRSPNSITTDQDRIIRAA 352 (753)
Q Consensus 276 ~dvv~~D~Ty~t-n~y~~pl~~~~gvn~~~~~~~~g~al~~~Et~es~~W~~~~~~~~m~~~~p~~iitD~~~~l~~A 352 (753)
+.++.+|.+... ...++..+.++.+|.+-..+ +++.+-..++.+.+..+|.......++..|.+|+||+..+..+.
T Consensus 6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~~~ 82 (120)
T PF00665_consen 6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSRFI-YAFPVSSKETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFTSH 82 (120)
T ss_dssp TTEEEEEEEEETGGCTT-CEEEEEEEETTTTEE-EEEEESSSSHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHHSH
T ss_pred CCEEEEeeEEEecCCCCccEEEEEEEECCCCcE-EEEEeecccccccccccccccccccccccceecccccccccccc
Confidence 467888988544 34555788888888877654 46777777788898888888888877777999999999987753
No 15
>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=87.68 E-value=0.96 Score=35.48 Aligned_cols=25 Identities=36% Similarity=0.627 Sum_probs=10.4
Q ss_pred cCCceEEEEEEeCCCcEEEEEeeccccC
Q 004450 127 VGCKAQMTVKKQGSGKWAVSKLIKEHNH 154 (753)
Q Consensus 127 ~gCpa~i~v~~~~~~~W~V~~~~~~HNH 154 (753)
.+|+|++.+. . +.-.|.....+|||
T Consensus 38 ~~C~a~~~~~-~--~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 38 HGCRARLITD-A--GDGRVVRTNGEHNH 62 (62)
T ss_dssp S----EEEEE-----TTEEEE-S---SS
T ss_pred CCCeEEEEEE-C--CCCEEEECCCccCC
Confidence 5899999998 2 23345555688999
No 16
>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=84.65 E-value=2.2 Score=46.90 Aligned_cols=56 Identities=14% Similarity=0.217 Sum_probs=48.5
Q ss_pred CCCccCCHHHHHHHHHHHhhhcCcEEEEeeeeeccCCCceeEEEEEecCCCcccCCCcccccccCcccccCCceEEEEEE
Q 004450 58 EGMEFDSEQAARIFYNSYARRIGFSTRVSVYQRSRRDGSIICRQIVCSREGFRRGSSENRSKRQRTITRVGCKAQMTVKK 137 (753)
Q Consensus 58 ~Gm~F~S~eea~~fy~~YA~~~GF~vr~~~s~r~k~~g~~~~~~f~C~r~G~~~~~~~~~~~r~r~s~r~gCpa~i~v~~ 137 (753)
.+..|+|+++-|..+|.|-....--|....|.|.| -.+|.|..- +|||+|.+..
T Consensus 24 ~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nk------hftfachlk--------------------~c~fkillsy 77 (496)
T PF04684_consen 24 QARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNK------HFTFACHLK--------------------NCPFKILLSY 77 (496)
T ss_pred cccCCCcHHHHHHHHhhhhhhhcCceeeccccccc------ceEEEeecc--------------------CCCceeeeee
Confidence 46789999999999999999999999988887754 389999863 8999999997
Q ss_pred eC
Q 004450 138 QG 139 (753)
Q Consensus 138 ~~ 139 (753)
.+
T Consensus 78 ~g 79 (496)
T PF04684_consen 78 CG 79 (496)
T ss_pred cc
Confidence 65
No 17
>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=79.72 E-value=4.2 Score=32.03 Aligned_cols=28 Identities=25% Similarity=0.387 Sum_probs=23.8
Q ss_pred cCCceEEEEEEeC-CCcEEEEEeeccccC
Q 004450 127 VGCKAQMTVKKQG-SGKWAVSKLIKEHNH 154 (753)
Q Consensus 127 ~gCpa~i~v~~~~-~~~W~V~~~~~~HNH 154 (753)
.||||+=.|.+.. ++.-.++.+..+|||
T Consensus 31 ~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 31 QGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred CCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 3899998888775 778888889999998
No 18
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=74.21 E-value=20 Score=34.24 Aligned_cols=108 Identities=12% Similarity=0.130 Sum_probs=74.6
Q ss_pred HHhhhcCcEEEecccccccccCCcccceEEeecCCceEEEEEEe-ecccchhHHHHHHHHHHHHhCCCCCceecchhhHH
Q 004450 270 MNYSYFGDTVTFDTTYRMNRYRIPFAPFTGLNHHGQPVLFGCAL-LLNESEASFIWLFEAWLAAMSGRSPNSITTDQDRI 348 (753)
Q Consensus 270 ~~~~~f~dvv~~D~Ty~tn~y~~pl~~~~gvn~~~~~~~~g~al-~~~Et~es~~W~~~~~~~~m~~~~p~~iitD~~~~ 348 (753)
..+...|=.|..|+= ++..+.+|+.|+.....|-.|+-..-. -...+.+.+.-+|+...+.+|...-..||||-...
T Consensus 27 ~~w~~~Gcsi~~DgW--td~~~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ll~~vIeeVG~~nVvqVVTDn~~~ 104 (153)
T PF04937_consen 27 KSWKRTGCSIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFELLDEVIEEVGEENVVQVVTDNASN 104 (153)
T ss_pred HHHHhcCEEEEEecC--cCCCCCeEEEEEEEcccccEEEEEEecccccccHHHHHHHHHHHHHHhhhhhhhHHhccCchh
Confidence 344555656667765 456667777777666666555433211 12246667777777777777766777899999999
Q ss_pred HHHHH---HhhCCCCccccCCCchHHHHHHhhhh
Q 004450 349 IRAAV---AQVFPGTRHRFCKWNVFREAQERLSD 379 (753)
Q Consensus 349 l~~Ai---~~vfP~a~h~~C~~Hi~~n~~~~l~~ 379 (753)
+++|- .+-+|......|.-|-+.-+.+.+..
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 98884 44578888889999999888877764
No 19
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=59.34 E-value=18 Score=36.39 Aligned_cols=82 Identities=18% Similarity=0.207 Sum_probs=57.0
Q ss_pred CcEEEecccccccc-cCCcccceEEeecCCceEEEEEEeecccchhHHHHHHHHHHHHhCCCCCceecchhhHHHHHHHH
Q 004450 276 GDTVTFDTTYRMNR-YRIPFAPFTGLNHHGQPVLFGCALLLNESEASFIWLFEAWLAAMSGRSPNSITTDQDRIIRAAVA 354 (753)
Q Consensus 276 ~dvv~~D~Ty~tn~-y~~pl~~~~gvn~~~~~~~~g~al~~~Et~es~~W~~~~~~~~m~~~~p~~iitD~~~~l~~Ai~ 354 (753)
++.+-+|=||.+-+ -..=| .-.||..|+ ++.+-|...-+...=.-||..+++.. ..|.+|+||+.+....|+.
T Consensus 70 ~~~w~vDEt~ikv~gkw~yl--yrAid~~g~--~Ld~~L~~rRn~~aAk~Fl~kllk~~--g~p~v~vtDka~s~~~A~~ 143 (215)
T COG3316 70 GDSWRVDETYIKVNGKWHYL--YRAIDADGL--TLDVWLSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAALR 143 (215)
T ss_pred ccceeeeeeEEeeccEeeeh--hhhhccCCC--eEEEEEEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHHH
Confidence 46777888886632 12222 334565555 44555666656666667777777776 6788999999999999999
Q ss_pred hhCCCCccc
Q 004450 355 QVFPGTRHR 363 (753)
Q Consensus 355 ~vfP~a~h~ 363 (753)
++-+.+.|+
T Consensus 144 ~l~~~~ehr 152 (215)
T COG3316 144 KLGSEVEHR 152 (215)
T ss_pred hcCcchhee
Confidence 999977666
No 20
>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=54.77 E-value=12 Score=39.24 Aligned_cols=40 Identities=15% Similarity=0.282 Sum_probs=29.8
Q ss_pred hCCCCCceecchhhHHHHHHHHhhCCCCccccCCCchHHHHHHhhh
Q 004450 333 MSGRSPNSITTDQDRIIRAAVAQVFPGTRHRFCKWNVFREAQERLS 378 (753)
Q Consensus 333 m~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~l~ 378 (753)
+++ .+-+++||+-.+-.. +..+.|+.|.-|+.|.+.+-..
T Consensus 116 L~~-~~GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~ 155 (271)
T PF03050_consen 116 LGD-FSGILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAE 155 (271)
T ss_pred hcc-cceeeeccccccccc-----cccccccccccccccccccccc
Confidence 344 345999999876554 3389999999999999876543
No 21
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.49 E-value=70 Score=25.82 Aligned_cols=66 Identities=20% Similarity=0.260 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcccCCCCccCccCCCCCCchhhhHHHHHHHHHhhhhchHHHHHHHHHHHHhHHH
Q 004450 658 YNMAMDVLREAAKKVAAAKKYGPGVTQNSLFSGCQQHHSCSVDQDKKIQELTVELENASQRCEAYRTKLLAVLKDMEE 735 (753)
Q Consensus 658 ~~~a~~~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~ 735 (753)
-..|.+.+.=+.-+|+.++.+...-+. ..-+-..-++.|..|-+.-++-...|+++|.++|-.||+
T Consensus 13 iqqAvdTI~LLQmEieELKEknn~l~~------------e~q~~q~~reaL~~eneqlk~e~~~WQerlrsLLGkme~ 78 (79)
T COG3074 13 VQQAIDTITLLQMEIEELKEKNNSLSQ------------EVQNAQHQREALERENEQLKEEQNGWQERLRALLGKMEE 78 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhHhHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 355666666666777777665443321 111234456677777777788899999999999988875
No 22
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=46.05 E-value=17 Score=34.17 Aligned_cols=77 Identities=14% Similarity=0.086 Sum_probs=53.0
Q ss_pred cchhhHHHHHHhcCCCCcchhhhHhhhcCCccccc-----------------ccccccchhhhhhhh--hc---cC----
Q 004450 173 GPARSLIDTLQAAGMGPSGVMSVLIKESGGVNNVG-----------------FTKVDCQNYMSSSRQ--RT---LG---- 226 (753)
Q Consensus 173 ~~~k~~i~~l~~~gi~~~~I~~~l~~~~g~~~~~~-----------------~t~~Di~N~~~~~r~--~~---~~---- 226 (753)
++..++|..|...|++|++|--+|++++|-..--. -.+.|++|+..++.. +- ..
T Consensus 31 eeve~~I~~lakkG~~pSqIG~~LRD~~gip~Vk~vtG~ki~~iLk~~gl~p~iPEDL~~L~~ri~~L~~HL~~nkKD~~ 110 (151)
T PRK08561 31 EEIEELVVELAKQGYSPSMIGIILRDQYGIPDVKLITGKKITEILEENGLAPEIPEDLRNLIKKAVNLRKHLEENPKDLH 110 (151)
T ss_pred HHHHHHHHHHHHCCCCHHHhhhhHhhccCCCceeeeccchHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHhCCCcch
Confidence 44567788999999999999999999997432111 224677777765431 11 11
Q ss_pred ---------cChHHHHHHHHHhhhcCCccEEE
Q 004450 227 ---------SGGQVVIDNLKQMQAEDPSFFCA 249 (753)
Q Consensus 227 ---------gd~~~ll~~l~~~~~~np~f~y~ 249 (753)
+....|++|++....-.|+|.|.
T Consensus 111 skRgL~~~~skrrRLl~Yyk~~~~LP~~WkY~ 142 (151)
T PRK08561 111 NKRGLQLIESKIRRLVKYYKRTGVLPADWRYS 142 (151)
T ss_pred hHHHHHHHHHHHHHHHHHHHhcCCCCCCCcCC
Confidence 23467889998877778888775
No 23
>PHA02047 phage lambda Rz1-like protein
Probab=42.60 E-value=63 Score=27.88 Aligned_cols=46 Identities=15% Similarity=0.095 Sum_probs=33.5
Q ss_pred chhhhHHHHHHHHHhhhhchHHHHHHHHHHHHhHHHHHhhhhHHHHHHHh
Q 004450 700 DQDKKIQELTVELENASQRCEAYRTKLLAVLKDMEEEKTKMLVKVENVRL 749 (753)
Q Consensus 700 ~~~~~i~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 749 (753)
--.++++.|+.+|++.+.|.++|+++...+=.. .+.-+.-|.+..+
T Consensus 31 ~~h~~a~~la~qLE~a~~r~~~~Q~~V~~l~~k----ae~~t~Ei~~aL~ 76 (101)
T PHA02047 31 IAHEEAKRQTARLEALEVRYATLQRHVQAVEAR----TNTQRQEVDRALD 76 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence 357889999999999999999999997655444 4444444444433
No 24
>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.
Probab=42.22 E-value=1e+02 Score=25.44 Aligned_cols=51 Identities=24% Similarity=0.326 Sum_probs=39.8
Q ss_pred CchhhhHHHHHHHHHh---hhhchHHHHHHHHHHHHhHHHHHhhhhHHHHHHHh
Q 004450 699 VDQDKKIQELTVELEN---ASQRCEAYRTKLLAVLKDMEEEKTKMLVKVENVRL 749 (753)
Q Consensus 699 ~~~~~~i~~l~~~l~~---~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 749 (753)
.+||..|..|..|.+. +.-....=-..|..-+++.|+....|+.+++....
T Consensus 8 ~EKDe~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~ 61 (74)
T PF12329_consen 8 AEKDEQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEK 61 (74)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6899999999976554 44466666677888889999999999888887644
No 25
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=34.72 E-value=1.4e+02 Score=24.66 Aligned_cols=61 Identities=20% Similarity=0.237 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCcccCCCCccCccCCCCCCchhhhHHHHHHHHHhhhhchHHHHHHHHHHHHhHHH
Q 004450 656 HIYNMAMDVLREAAKKVAAAKKYGPGVTQNSLFSGCQQHHSCSVDQDKKIQELTVELENASQRCEAYRTKLLAVLKDMEE 735 (753)
Q Consensus 656 e~~~~a~~~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~ 735 (753)
..+..|++.+.-+..++...+.....- .....+|..|.+.-++-..+++++|.++|.-|++
T Consensus 11 ~ki~~aveti~~Lq~e~eeLke~n~~L-------------------~~e~~~L~~en~~L~~e~~~~~~rl~~LL~kl~~ 71 (72)
T PF06005_consen 11 EKIQQAVETIALLQMENEELKEKNNEL-------------------KEENEELKEENEQLKQERNAWQERLRSLLGKLEE 71 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhH-------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 346667777777777777766543221 1667788888888888889999999999988875
No 26
>PRK14143 heat shock protein GrpE; Provisional
Probab=34.19 E-value=1.6e+02 Score=30.24 Aligned_cols=55 Identities=20% Similarity=0.370 Sum_probs=47.1
Q ss_pred CCCCCchhhhHHHHHHHHHhhhhchHHHHHHHHHHHHhHHHHHhhhhHHHHHHHh
Q 004450 695 HSCSVDQDKKIQELTVELENASQRCEAYRTKLLAVLKDMEEEKTKMLVKVENVRL 749 (753)
Q Consensus 695 ~~~~~~~~~~i~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 749 (753)
.....+.++++.+|..+|+..++..+.++.+++...-++|+....+.+-+++++.
T Consensus 59 ~~~~~~~~~~~~~l~~el~~l~~e~~elkd~~lR~~AdfeN~RKR~~kE~e~~~~ 113 (238)
T PRK14143 59 SETAADNAARLAQLEQELESLKQELEELNSQYMRIAADFDNFRKRTSREQEDLRL 113 (238)
T ss_pred CCccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455667888999999999999999999999999999999999988887777654
No 27
>KOG3517 consensus Transcription factor PAX1/9 [Transcription]
Probab=34.05 E-value=37 Score=34.37 Aligned_cols=77 Identities=21% Similarity=0.298 Sum_probs=52.0
Q ss_pred cccCCcchhhHHHHHHhcCCCCcchhhhHhhhcCCcccccccccccchhhhhhhhhccCcC-----hHHHHHHHHHhhhc
Q 004450 168 HRHVSGPARSLIDTLQAAGMGPSGVMSVLIKESGGVNNVGFTKVDCQNYMSSSRQRTLGSG-----GQVVIDNLKQMQAE 242 (753)
Q Consensus 168 hr~is~~~k~~i~~l~~~gi~~~~I~~~l~~~~g~~~~~~~t~~Di~N~~~~~r~~~~~gd-----~~~ll~~l~~~~~~ 242 (753)
-|.+..+.+-.|..|...|++|..|-..|+-.+|-...|.- -+|.-..+-...++|. ...+.+|.++++..
T Consensus 18 GRPLPna~RlrIVELarlGiRPCDISRQLrvSHGCVSKILa----Ry~EtGsIlPGaIGGSkPRVTTP~VV~~IR~~Kq~ 93 (334)
T KOG3517|consen 18 GRPLPNAIRLRIVELARLGIRPCDISRQLRVSHGCVSKILA----RYNETGSILPGAIGGSKPRVTTPKVVKYIRSLKQR 93 (334)
T ss_pred CccCcchhhhhHHHHHHcCCCccchhhhhhhccchHHHHHH----HhccCCcccccccCCCCCccCChhHHHHHHHhhcc
Confidence 46677778888999999999999999988877774322110 0111111112233442 57899999999999
Q ss_pred CCccEE
Q 004450 243 DPSFFC 248 (753)
Q Consensus 243 np~f~y 248 (753)
||+.|-
T Consensus 94 DPGIFA 99 (334)
T KOG3517|consen 94 DPGIFA 99 (334)
T ss_pred CCceee
Confidence 999763
No 28
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=32.62 E-value=30 Score=30.29 Aligned_cols=29 Identities=28% Similarity=0.478 Sum_probs=20.3
Q ss_pred cceEEEEEEecCceEEeeccccccC-----CceeeehhHH
Q 004450 556 QKAHFVRYNIFEKKASCSCQLFEFS-----GIICRHILAV 590 (753)
Q Consensus 556 ~~~~~V~~~~~~~~~~CsC~~fe~~-----GipC~Hil~V 590 (753)
+++|++.. ..|||..|-.+ .-||.|++.+
T Consensus 42 ~rdYIl~~------gfCSCp~~~~svvl~Gk~~C~Hi~gl 75 (117)
T COG5431 42 ERDYILEG------GFCSCPDFLGSVVLKGKSPCAHIIGL 75 (117)
T ss_pred ccceEEEc------CcccCHHHHhHhhhcCcccchhhhhe
Confidence 45677753 27999988732 3469999864
No 29
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=31.67 E-value=19 Score=36.68 Aligned_cols=23 Identities=35% Similarity=0.784 Sum_probs=19.0
Q ss_pred EEeeccccccCCceeeehhHHHhhhc
Q 004450 570 ASCSCQLFEFSGIICRHILAVFRVTN 595 (753)
Q Consensus 570 ~~CsC~~fe~~GipC~Hil~Vl~~~~ 595 (753)
.-|||.-+. .||.||-+|.-++.
T Consensus 125 ~dCSCPD~a---nPCKHi~AvyY~la 147 (266)
T COG4279 125 TDCSCPDYA---NPCKHIAAVYYLLA 147 (266)
T ss_pred cccCCCCcc---cchHHHHHHHHHHH
Confidence 459999875 59999999987765
No 30
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=30.46 E-value=1.4e+02 Score=31.11 Aligned_cols=70 Identities=10% Similarity=-0.090 Sum_probs=46.3
Q ss_pred cEEEecccccccccCCcccceEEeecCCceEEEEEEeecc-cchhHHHHHHHHHHHHh-C---CCCCceecchhhH
Q 004450 277 DTVTFDTTYRMNRYRIPFAPFTGLNHHGQPVLFGCALLLN-ESEASFIWLFEAWLAAM-S---GRSPNSITTDQDR 347 (753)
Q Consensus 277 dvv~~D~Ty~tn~y~~pl~~~~gvn~~~~~~~~g~al~~~-Et~es~~W~~~~~~~~m-~---~~~p~~iitD~~~ 347 (753)
.+++.|-||....-+.-++..+-+|.+.. .++|+++-.. .+.+...-+|+..+... + ...|..|.||+-.
T Consensus 88 ~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gs 162 (262)
T PRK14702 88 QRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGS 162 (262)
T ss_pred CEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCc
Confidence 78899988866544446777787887776 6678988764 55555555555433332 2 2356788899854
No 31
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=29.69 E-value=3.4e+02 Score=22.86 Aligned_cols=64 Identities=19% Similarity=0.311 Sum_probs=49.0
Q ss_pred hccCHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCCCccCccCCCCCCchhhhHHHHHHHHHhhhhchHHHHHHH
Q 004450 651 GAESAHIYNMAMDVLREAAKKVAAAKKYGPGVTQNSLFSGCQQHHSCSVDQDKKIQELTVELENASQRCEAYRTKL 726 (753)
Q Consensus 651 ~~~s~e~~~~a~~~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~l~~~~~~~~~~~~~l 726 (753)
+..+..-+..+...|+--+.+...+..+-.++. .+.++...+|++|..+++..+..-+-|+++.
T Consensus 19 ~~~~~kd~~~~~~~lk~Klq~ar~~i~~lpgi~------------~s~eeq~~~i~~Le~~i~~k~~~L~~~~~~~ 82 (83)
T PF07544_consen 19 PPLSSKDLDTATGSLKHKLQKARAAIRELPGID------------RSVEEQEEEIEELEEQIRKKREVLQKFKERV 82 (83)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHhCCCcc------------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 667777777777777776666666666555432 5668899999999999999999988888763
No 32
>COG5470 Uncharacterized conserved protein [Function unknown]
Probab=29.37 E-value=27 Score=30.19 Aligned_cols=40 Identities=35% Similarity=0.297 Sum_probs=27.8
Q ss_pred ccccCCCCCCCCCCCCccCCHHHHHHHHHHHhhhcCcEEE
Q 004450 45 FETLNGDPNLEPFEGMEFDSEQAARIFYNSYARRIGFSTR 84 (753)
Q Consensus 45 ~~~~~~~~~~~P~~Gm~F~S~eea~~fy~~YA~~~GF~vr 84 (753)
.-.++|+..+.+-+=++|+|++.|.++||.=+...=-++|
T Consensus 43 v~~lEG~w~ptr~vviEFps~~~ar~~y~SpeYq~a~~~R 82 (96)
T COG5470 43 VETLEGEWRPTRNVVIEFPSLEAARDCYNSPEYQAAAAIR 82 (96)
T ss_pred eeeccCCCCcccEEEEEcCCHHHHHHHhcCHHHHHHHHHH
Confidence 3344566666777889999999999999975443333333
No 33
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=29.14 E-value=35 Score=30.08 Aligned_cols=28 Identities=32% Similarity=0.409 Sum_probs=21.1
Q ss_pred CCCCccCCHHHHHHHHHHHhhhcCcEEEEeee
Q 004450 57 FEGMEFDSEQAARIFYNSYARRIGFSTRVSVY 88 (753)
Q Consensus 57 ~~Gm~F~S~eea~~fy~~YA~~~GF~vr~~~s 88 (753)
.+.+.|+|.|+|.. ||.++|....+..-
T Consensus 50 ~v~l~F~skE~Ai~----yaer~G~~Y~V~~p 77 (101)
T PF04800_consen 50 SVRLKFDSKEDAIA----YAERNGWDYEVEEP 77 (101)
T ss_dssp -CEEEESSHHHHHH----HHHHCT-EEEEE-S
T ss_pred eeEeeeCCHHHHHH----HHHHcCCeEEEeCC
Confidence 47889999999975 79999988876544
No 34
>PHA02517 putative transposase OrfB; Reviewed
Probab=29.03 E-value=1.3e+02 Score=31.55 Aligned_cols=70 Identities=11% Similarity=-0.071 Sum_probs=42.3
Q ss_pred CcEEEecccccccccCCcccceEEeecCCceEEEEEEeecccchhHHHHHHHHHHHHhCCCCCceecchhhH
Q 004450 276 GDTVTFDTTYRMNRYRIPFAPFTGLNHHGQPVLFGCALLLNESEASFIWLFEAWLAAMSGRSPNSITTDQDR 347 (753)
Q Consensus 276 ~dvv~~D~Ty~tn~y~~pl~~~~gvn~~~~~~~~g~al~~~Et~es~~W~~~~~~~~m~~~~p~~iitD~~~ 347 (753)
+.+++.|.||....-+ -.+.++-+|.+.+ .++|+.+-...+.+...-.|+......+...+..|.||+..
T Consensus 110 n~~w~~D~t~~~~~~g-~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~~l~~a~~~~~~~~~~i~~sD~G~ 179 (277)
T PHA02517 110 NQLWVADFTYVSTWQG-WVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLDALEQALWARGRPGGLIHHSDKGS 179 (277)
T ss_pred CCeEEeceeEEEeCCC-CEEEEEecccCCC-eeeecccCCCCChHHHHHHHHHHHHhcCCCcCcEeeccccc
Confidence 4789999999754433 3456666666655 45678887777766544444443333332233466788855
No 35
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=28.84 E-value=1.9e+02 Score=33.30 Aligned_cols=37 Identities=27% Similarity=0.376 Sum_probs=25.4
Q ss_pred ceEEEE--EEecCceEEeeccccccCCceeeehhHHHhhhc
Q 004450 557 KAHFVR--YNIFEKKASCSCQLFEFSGIICRHILAVFRVTN 595 (753)
Q Consensus 557 ~~~~V~--~~~~~~~~~CsC~~fe~~GipC~Hil~Vl~~~~ 595 (753)
+.|.|. ........+|+|.. ...| -|.|+.+|+....
T Consensus 58 ~~y~v~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~~ 96 (587)
T COG4715 58 RRYRVRVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEYL 96 (587)
T ss_pred ceeeEEEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHHh
Confidence 445544 44344578999998 5555 6999999986543
No 36
>KOG0963 consensus Transcription factor/CCAAT displacement protein CDP1 [Transcription]
Probab=28.69 E-value=3.7e+02 Score=31.44 Aligned_cols=53 Identities=21% Similarity=0.288 Sum_probs=36.1
Q ss_pred CCCCchhhhHHHHHHHHHhhhhchHHHHHHHHHHHHhHHHHHhhhhHHHHHHH
Q 004450 696 SCSVDQDKKIQELTVELENASQRCEAYRTKLLAVLKDMEEEKTKMLVKVENVR 748 (753)
Q Consensus 696 ~~~~~~~~~i~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 748 (753)
+...-||+.|..|+.++++...=..--++....=+..+|.+......-++.+.
T Consensus 285 ~~L~~kd~~i~~L~~di~~~~~S~~~e~e~~~~qI~~le~~l~~~~~~leel~ 337 (629)
T KOG0963|consen 285 SVLNQKDSEIAQLSNDIERLEASLVEEREKHKAQISALEKELKAKISELEELK 337 (629)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44466999999999999988776665666666666666666555555444443
No 37
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=28.30 E-value=1.5e+02 Score=24.63 Aligned_cols=39 Identities=15% Similarity=0.163 Sum_probs=29.5
Q ss_pred ccCCHHHHHHHHHHHhhhcCcEEEEeeeee---ccCCCceeE
Q 004450 61 EFDSEQAARIFYNSYARRIGFSTRVSVYQR---SRRDGSIIC 99 (753)
Q Consensus 61 ~F~S~eea~~fy~~YA~~~GF~vr~~~s~r---~k~~g~~~~ 99 (753)
.|+|.++...++..||.++|-.+..-+... -.-+|....
T Consensus 13 ~yPs~e~i~~aIE~YC~~~~~~l~Fisr~~Pi~~~idg~lYe 54 (74)
T PF14201_consen 13 KYPSKEEICEAIEKYCIKNGESLEFISRDKPITFKIDGVLYE 54 (74)
T ss_pred CCCCHHHHHHHHHHHHHHcCCceEEEecCCcEEEEECCeEEE
Confidence 478999999999999999999988765443 234565444
No 38
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.75 E-value=4.1e+02 Score=30.54 Aligned_cols=119 Identities=13% Similarity=0.087 Sum_probs=69.6
Q ss_pred hHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCCCccCccCCCCCCchhhhHHHHHHHH
Q 004450 633 SAARYDNLCREVIKYVEEGAESAHIYNMAMDVLREAAKKVAAAKKYGPGVTQNSLFSGCQQHHSCSVDQDKKIQELTVEL 712 (753)
Q Consensus 633 ~~~Ry~~L~~~~~~~~~~~~~s~e~~~~a~~~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~l 712 (753)
+..|...+..+-..+-+.|..-.+.|+.|.+-=+.+..++..+..... ..++.++-.+-.=.+..--..+..+-|..-+
T Consensus 600 QlQ~l~~~~eer~~i~e~a~~La~R~eea~e~qe~L~~~~~~L~~~~~-~~lp~l~~AErdFk~Elq~~~~~~~~L~~~i 678 (741)
T KOG4460|consen 600 QLQDLSYCREERKSLREMAERLADRYEEAKEKQEDLMNRMKKLLHSFH-SELPVLSDAERDFKKELQLIPDQLRHLGNAI 678 (741)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhccc-ccCCcchhHHHHHHHHHHHhHHHHHHHHHHH
Confidence 345666666666667777777788888887776666666666554322 2221111111000000011222333333333
Q ss_pred Hhhhh----------------------chHHHHHHHHHHHHhHHHHHhhhhHHHHHHHhhcc
Q 004450 713 ENASQ----------------------RCEAYRTKLLAVLKDMEEEKTKMLVKVENVRLDLK 752 (753)
Q Consensus 713 ~~~~~----------------------~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 752 (753)
|-.+. +.++-+.+|.++|+.+-+|....+++|..|-+-|+
T Consensus 679 ET~~~~~~KQ~~H~~~v~~al~K~~Y~l~~~Q~~~iqsiL~~L~~~i~~~~k~VK~i~~~v~ 740 (741)
T KOG4460|consen 679 ETVTMKKDKQQQHMEKVLSALPKPTYILSAYQRKCIQSILKELGEHIREMVKQVKDIRNHVN 740 (741)
T ss_pred HHHHHHHHHHHHHHHHHHhhccCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 22211 44566789999999999999999999998876654
No 39
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=26.84 E-value=2e+02 Score=30.76 Aligned_cols=71 Identities=10% Similarity=-0.065 Sum_probs=46.8
Q ss_pred CcEEEecccccccccCCcccceEEeecCCceEEEEEEeecc-cchhHHHHHHHHHH-HHhCC---CCCceecchhhH
Q 004450 276 GDTVTFDTTYRMNRYRIPFAPFTGLNHHGQPVLFGCALLLN-ESEASFIWLFEAWL-AAMSG---RSPNSITTDQDR 347 (753)
Q Consensus 276 ~dvv~~D~Ty~tn~y~~pl~~~~gvn~~~~~~~~g~al~~~-Et~es~~W~~~~~~-~~m~~---~~p~~iitD~~~ 347 (753)
..+++.|-||....-+.-++..+-+|.+.. .++||++-.. .+.+...-+|+.-+ ...++ ..|..|.||+-.
T Consensus 126 N~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGs 201 (301)
T PRK09409 126 NQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGS 201 (301)
T ss_pred CCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCc
Confidence 378999999965443445677777887776 6779999875 56666555665433 33332 246688899844
No 40
>PF12491 ApoB100_C: Apolipoprotein B100 C terminal; InterPro: IPR022176 This domain family is found in eukaryotes, and is approximately 60 amino acids in length. There are two conserved sequence motifs: QLS and LIDL. ApoB100 has an essential role in the assembly and secretion of triglyceride-rich lipoproteins and lipids transport.
Probab=26.78 E-value=2.2e+02 Score=22.21 Aligned_cols=28 Identities=21% Similarity=0.195 Sum_probs=24.4
Q ss_pred hccCHHHHHHHHHHHHHHHHHHHHHHhc
Q 004450 651 GAESAHIYNMAMDVLREAAKKVAAAKKY 678 (753)
Q Consensus 651 ~~~s~e~~~~a~~~l~e~~~~~~~~~~~ 678 (753)
...|.|.|.+.+..+.|+++++..+.-+
T Consensus 28 IDLsIqnY~~Fl~yi~eLL~~lq~ata~ 55 (58)
T PF12491_consen 28 IDLSIQNYHMFLRYITELLKELQSATAN 55 (58)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 4779999999999999999999887654
No 41
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=25.74 E-value=25 Score=25.70 Aligned_cols=29 Identities=24% Similarity=0.385 Sum_probs=13.6
Q ss_pred cccCCcchhhHHHHHHhcCCCCcchhhhH
Q 004450 168 HRHVSGPARSLIDTLQAAGMGPSGVMSVL 196 (753)
Q Consensus 168 hr~is~~~k~~i~~l~~~gi~~~~I~~~l 196 (753)
+++|+.+++..|..+.+.|++.++|...|
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~s~~~IA~~l 30 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGMSIREIAKRL 30 (44)
T ss_dssp ----------HHHHHHCS---HHHHHHHT
T ss_pred ccchhhhHHHHHHHHHHcCCCHHHHHHHH
Confidence 46789999999999999999998887654
No 42
>PRK14154 heat shock protein GrpE; Provisional
Probab=24.88 E-value=2.2e+02 Score=28.60 Aligned_cols=55 Identities=11% Similarity=0.164 Sum_probs=39.2
Q ss_pred CCCCCchhhhHHHHHHHHHhhhhchHHHHHHHHHHHHhHHHHHhhhhHHHHHHHh
Q 004450 695 HSCSVDQDKKIQELTVELENASQRCEAYRTKLLAVLKDMEEEKTKMLVKVENVRL 749 (753)
Q Consensus 695 ~~~~~~~~~~i~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 749 (753)
|.-++...-+|.+|..+|+..++..+.++.+++....+.|+......+.++.+..
T Consensus 44 ~~~~~~~~~~~~~l~~el~~le~e~~elkd~~lRl~ADfeNyRKR~~kE~e~~~~ 98 (208)
T PRK14154 44 PHREGLEFPSREKLEGQLTRMERKVDEYKTQYLRAQAEMDNLRKRIEREKADIIK 98 (208)
T ss_pred cccccccCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555556667777777777777788888888888888888777777766543
No 43
>KOG3647 consensus Predicted coiled-coil protein [General function prediction only]
Probab=23.89 E-value=6e+02 Score=26.46 Aligned_cols=53 Identities=21% Similarity=0.218 Sum_probs=41.6
Q ss_pred CCchhhhHHHHHHHHHhhhhchHHHHHHHHHHHHhHHHHHhhhhHHHHHHHhh
Q 004450 698 SVDQDKKIQELTVELENASQRCEAYRTKLLAVLKDMEEEKTKMLVKVENVRLD 750 (753)
Q Consensus 698 ~~~~~~~i~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 750 (753)
+.+-+.||+.-..||++.++|-++.+.-==.+|.+-|.--++|-+--|.-+.+
T Consensus 135 ea~L~~Kierrk~ElEr~rkRle~LqsiRP~~MdEyE~~EeeLqkly~~Y~l~ 187 (338)
T KOG3647|consen 135 EAALGSKIERRKAELERTRKRLEALQSIRPAHMDEYEDCEEELQKLYQRYFLR 187 (338)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35688999999999999999999988777777777777777776655554443
No 44
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=22.24 E-value=82 Score=32.13 Aligned_cols=20 Identities=20% Similarity=0.537 Sum_probs=16.2
Q ss_pred ccccCcccccCCceEEEEEE
Q 004450 118 SKRQRTITRVGCKAQMTVKK 137 (753)
Q Consensus 118 ~~r~r~s~r~gCpa~i~v~~ 137 (753)
.++...+.+.+|||.|.++.
T Consensus 69 ~~~~~~skK~~CPA~I~Ik~ 88 (225)
T PF15299_consen 69 RRRSKPSKKRDCPARIYIKE 88 (225)
T ss_pred ccccccccCCCCCeEEEEEE
Confidence 45566788999999999984
No 45
>PF15456 Uds1: Up-regulated During Septation
Probab=21.18 E-value=3.4e+02 Score=24.91 Aligned_cols=30 Identities=33% Similarity=0.470 Sum_probs=26.0
Q ss_pred CchhhhHHHHHHHHHhhhhchHHHHHHHHH
Q 004450 699 VDQDKKIQELTVELENASQRCEAYRTKLLA 728 (753)
Q Consensus 699 ~~~~~~i~~l~~~l~~~~~~~~~~~~~l~~ 728 (753)
..-+++|.|+..||.+...|-..-|++|+.
T Consensus 84 ~~~~rk~ee~~~eL~~le~R~~~~~~rLLe 113 (124)
T PF15456_consen 84 AESDRKCEELAQELWKLENRLAEVRQRLLE 113 (124)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 667899999999999999988888888874
Done!