Query 035792
Match_columns 856
No_of_seqs 356 out of 1223
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 06:29:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035792.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035792hhsearch_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 4E-129 9E-134 1152.0 61.0 627 42-707 65-722 (846)
2 PF10551 MULE: MULE transposas 99.8 8E-21 1.7E-25 171.2 9.1 90 275-366 1-93 (93)
3 PF03101 FAR1: FAR1 DNA-bindin 99.7 1.6E-16 3.4E-21 142.8 7.6 77 65-141 1-91 (91)
4 PF00872 Transposase_mut: Tran 99.2 2.5E-12 5.5E-17 145.2 0.5 179 269-451 163-350 (381)
5 PF08731 AFT: Transcription fa 98.7 3.3E-08 7.1E-13 89.4 8.4 76 57-139 1-111 (111)
6 smart00575 ZnF_PMZ plant mutat 98.7 5.4E-09 1.2E-13 72.1 0.7 27 557-583 1-27 (28)
7 PF03108 DBD_Tnp_Mut: MuDR fam 98.5 4.2E-07 9E-12 76.8 8.0 65 49-128 2-67 (67)
8 COG3328 Transposase and inacti 98.2 5.8E-06 1.3E-10 92.4 10.0 137 269-410 146-284 (379)
9 cd04757 Commd9 COMM_Domain con 98.1 2.9E-06 6.2E-11 77.2 3.8 63 794-856 31-103 (108)
10 PF04434 SWIM: SWIM zinc finge 98.0 3.1E-06 6.7E-11 63.8 2.3 28 555-582 13-40 (40)
11 cd04757 Commd9 COMM_Domain con 97.9 3.6E-06 7.8E-11 76.6 1.7 75 736-811 24-107 (108)
12 cd04749 Commd1_MURR1 COMM_Doma 94.1 0.064 1.4E-06 53.5 4.6 61 794-856 105-171 (174)
13 PF01610 DDE_Tnp_ISL3: Transpo 93.8 0.092 2E-06 55.9 5.6 81 287-371 15-98 (249)
14 cd04749 Commd1_MURR1 COMM_Doma 90.3 0.28 6.2E-06 49.0 3.7 64 742-808 104-172 (174)
15 PF03106 WRKY: WRKY DNA -bindi 90.1 0.92 2E-05 37.4 5.9 55 75-138 4-59 (60)
16 cd04748 Commd COMM_Domain, a f 89.2 0.44 9.6E-06 42.3 3.8 62 794-856 20-87 (87)
17 PF13610 DDE_Tnp_IS240: DDE do 87.7 0.11 2.4E-06 50.4 -1.2 81 268-352 1-81 (140)
18 PF04684 BAF1_ABF1: BAF1 / ABF 87.4 0.87 1.9E-05 51.5 5.4 56 53-122 24-79 (496)
19 PF04937 DUF659: Protein of un 84.1 9 0.00019 37.9 10.2 109 261-371 26-138 (153)
20 PF00665 rve: Integrase core d 83.3 4 8.6E-05 37.6 7.1 76 268-344 6-82 (120)
21 PF04500 FLYWCH: FLYWCH zinc f 79.8 3.1 6.6E-05 33.7 4.4 49 74-137 14-62 (62)
22 PF06782 UPF0236: Uncharacteri 78.4 31 0.00067 40.6 13.7 92 308-405 235-328 (470)
23 smart00774 WRKY DNA binding do 77.2 4.3 9.4E-05 33.3 4.3 37 94-137 22-59 (59)
24 cd04748 Commd COMM_Domain, a f 71.2 3.1 6.8E-05 36.8 2.4 64 741-806 18-86 (87)
25 PF07258 HCaRG: HCaRG protein; 64.5 2.2 4.7E-05 42.6 0.0 61 794-856 109-175 (178)
26 PF07258 HCaRG: HCaRG protein; 56.0 3.8 8.2E-05 40.9 0.0 66 740-808 106-176 (178)
27 cd04756 Commd8 COMM_Domain con 47.6 26 0.00057 35.4 4.5 45 807-854 127-171 (176)
28 cd04752 Commd4 COMM_Domain con 43.8 32 0.00069 34.7 4.5 45 809-854 125-169 (174)
29 COG5431 Uncharacterized metal- 37.8 26 0.00056 32.0 2.3 31 544-578 41-76 (117)
30 cd04753 Commd5_HCaRG COMM_Doma 37.8 10 0.00022 35.3 -0.1 60 794-853 35-101 (110)
31 cd04756 Commd8 COMM_Domain con 37.4 24 0.00052 35.7 2.4 59 739-801 104-167 (176)
32 COG4279 Uncharacterized conser 35.3 13 0.00029 39.1 0.2 24 556-582 124-147 (266)
33 COG3316 Transposase and inacti 32.0 77 0.0017 33.1 5.0 83 269-356 71-153 (215)
34 cd04758 Commd10 COMM_Domain co 28.8 70 0.0015 32.6 4.2 42 813-856 142-183 (186)
35 PRK14702 insertion element IS2 23.0 2.3E+02 0.0051 30.4 7.2 72 269-341 88-164 (262)
36 PHA02517 putative transposase 22.6 1.8E+02 0.004 31.2 6.3 72 268-341 110-181 (277)
37 PF04800 ETC_C1_NDUFA4: ETC co 22.5 72 0.0016 29.3 2.6 28 52-83 50-77 (101)
38 PRK09409 IS2 transposase TnpB; 21.1 2.9E+02 0.0064 30.4 7.6 72 269-341 127-203 (301)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=4.3e-129 Score=1152.04 Aligned_cols=627 Identities=35% Similarity=0.673 Sum_probs=550.7
Q ss_pred cCCCCCCCCCCCCCeeCCHHHHHHHHHHHhhhcCcEEEEcceeccCCCCCeEEEEeecCcccccc---------------
Q 035792 42 NHDNGESSKPYVGMEFDSEDAAKTFYDAYARRMGFSTHVGPFTRAKPDGPIITWDFACSREVFKR--------------- 106 (856)
Q Consensus 42 ~~~~~~~~~P~vG~~F~S~eea~~fyn~YA~~~GF~vr~~~s~r~k~~g~~~~~~f~CsreG~~R--------------- 106 (856)
+.+++...+|.+||+|+|+|||++||+.||++.||+||++++++++.+|.++.++|+|+|+|++|
T Consensus 65 ~~~~~~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k 144 (846)
T PLN03097 65 EFKEDTNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTK 144 (846)
T ss_pred cccCCCCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccc
Confidence 34567888999999999999999999999999999999999999999999999999999999752
Q ss_pred --------cc---ccCCcceeEEEEecCCcEEEEEeecCccCCCCCCCcccccCCCccCCchhhhhHHhhhccCCceecc
Q 035792 107 --------KN---VESCNAVLRIERKDSEKWTVTKFVEDHNHSMVTPNKVQYLRPRRHFAGATKNVAEALDVSGDVYITT 175 (856)
Q Consensus 107 --------kr---r~gCpa~i~v~~~~~~~W~V~~~~~eHNH~l~~~~~~~~l~~hR~ls~~~k~~i~~l~~~gi~~~~i 175 (856)
+| |+||||+|+|++..+|+|+|+.|+.+|||+|.++..+. ...+.....+..
T Consensus 145 ~~~~~~~~rR~~tRtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~~~~~---------~~~r~~~~~~~~-------- 207 (846)
T PLN03097 145 QDPENGTGRRSCAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPAQAVS---------EQTRKMYAAMAR-------- 207 (846)
T ss_pred cCcccccccccccCCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCccccc---------hhhhhhHHHHHh--------
Confidence 11 79999999999977999999999999999999775421 111111111110
Q ss_pred cccccccCCCCCCCCCCCCCCCCCCCCCCcccccccccccccCccHHHHHHHHHHHhhcCCCcEEEEEecCCcceeEEEe
Q 035792 176 DGNHLSYEPNSIRNSLPVDPSRSTRNMGPVNYLRQPSRTRSLGRDAQNLLNYFKKMQAENPGFYYAIQLDDDNRMTNVFW 255 (856)
Q Consensus 176 ~~~~~~~~~g~~~~v~~~~k~r~~~~~Di~N~~~~~~r~~~~~~D~~~ll~~l~~~q~~nP~f~y~v~~d~~~~l~~ifw 255 (856)
+.++..+++++. .|..|+..+..+....++|+++||+||+++|.+||+|||++++|++++|++|||
T Consensus 208 -------~~~~~~~v~~~~-------~d~~~~~~~~r~~~~~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFW 273 (846)
T PLN03097 208 -------QFAEYKNVVGLK-------NDSKSSFDKGRNLGLEAGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFW 273 (846)
T ss_pred -------hhhccccccccc-------hhhcchhhHHHhhhcccchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEe
Confidence 122233444333 255666433323344569999999999999999999999999999999999999
Q ss_pred cchhhhHHhhhcCceEEecccccCCCCCCccccEEEEeeCCcEEEEEEEeecCCchhhHHHHHHHHHHhcCCCCCeEEec
Q 035792 256 ADARSRMAYNHFSDAVIFDTMYRPNQYQVPFAPFTGVNHHGQMVLFGCALLLDESEASFTWLFRTWLSAMNDRPPVSITT 335 (856)
Q Consensus 256 a~~~s~~~y~~f~dVl~~D~Ty~tnky~~pL~~~vgvn~~g~~~~~g~all~~Et~es~~Wll~~f~~~m~~~~P~~iiT 335 (856)
+|++|+.+|.+|||||+||+||+||+|++||++|+|||||+|+++||||||.+|+.+||.|||++|+++|+|++|.+|||
T Consensus 274 aD~~sr~~Y~~FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiT 353 (846)
T PLN03097 274 VDAKSRHDYGNFSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKVIIT 353 (846)
T ss_pred ccHHHHHHHHhcCCEEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccHHHHHHHHhhCCCcccccchhHHHHHHHHhhhhhccCChhHHHHHHHHHhccCCHHHHHHHHHHhhhhccchhhHHH
Q 035792 336 DQDRAIQVAVAQVLPETCHCICKWHILREGQERLAHIYLAHPSFYGELYSCINFCETIEEFESSWCSLLDKYDLQKNEWL 415 (856)
Q Consensus 336 D~d~al~~AI~~vFP~a~h~lC~~HI~kn~~~~l~~~~~~~~~~~~~~~~~v~~s~t~eeFe~~w~~l~~~~~l~~~~wL 415 (856)
|+|.+|++||++|||+|.|++|.|||++|+.++|+.++..++.|..+|++||+.+++++|||..|..|+++|+|++|+||
T Consensus 354 Dqd~am~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL 433 (846)
T PLN03097 354 DQDKAMKSVISEVFPNAHHCFFLWHILGKVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWM 433 (846)
T ss_pred cCCHHHHHHHHHHCCCceehhhHHHHHHHHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHH
Confidence 99999999999999999999999999999999999999889999999999999999999999999999999999999999
Q ss_pred HHHHhcccccccccccCceeeccccccch---hhhhcccccccCCHHHHHHHHHHHHHHHHHhhhhhhhhcccccCcccC
Q 035792 416 HAVYNARRQWAPVYFRGTFFAALSSNQGI---SSFFDGYVHQQTTIPLFFKQYERALENSREKEIELDYDTICTTPVLKT 492 (856)
Q Consensus 416 ~~ly~~r~~Wa~ay~~~~f~~g~~s~~rs---ns~~k~~v~~~~sL~~fv~~~~~~l~~~~~ke~~~d~~s~~~~p~lkt 492 (856)
+.||+.|++|||+|+++.||+||++|+|+ |++|++|++++++|..|+++|+++++.++++|+++|+++.++.|.+++
T Consensus 434 ~~LY~~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t 513 (846)
T PLN03097 434 QSLYEDRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKS 513 (846)
T ss_pred HHHHHhHhhhhHHHhcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCccccc
Confidence 99999999999999999999999999998 999999999999999999999999999999999999999999999999
Q ss_pred CChHHHHHHhhccHHHHHHHHHHHHhhccceEEEeecCceeEEEEEEEeeCCCceEEEEe--cCCceeeecCCcccCccc
Q 035792 493 PSPMEQQAANLYTKKVFAKFQEELVETFVYTANKIEGDGVLSKFRVAKYEQDDKAYIVSF--SEMKASCSCQMFEYSGIL 570 (856)
Q Consensus 493 ~~p~Ekqaa~~yT~~if~kfq~el~~s~~~~v~~~~~~g~~~~y~V~~~~~~~~~~~V~~--~~~~~sCsC~~fe~~Gip 570 (856)
++|||+||+++||++||++||+|+..+..|.+....++|...+|.|...+. .+.|.|.+ .+..++|+|++||+.|||
T Consensus 514 ~~piEkQAs~iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~-~~~~~V~~d~~~~~v~CsC~kFE~~GIL 592 (846)
T PLN03097 514 PSPLEKSVSGVYTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEK-NQDFTVTWNQTKLEVSCICRLFEYKGYL 592 (846)
T ss_pred ccHHHHHHHHHhHHHHHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecC-CCcEEEEEecCCCeEEeeccCeecCccc
Confidence 999999999999999999999999999999988887888889999987654 56899988 567899999999999999
Q ss_pred ccchhhhhhccCcccCCccchhhhhcccccccCCCCCCCCCCCCcccHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHH
Q 035792 571 CRHILTVFTVTNVLTLPSHYILKRWTRNAKSSIGLDEQNTDTQGIETLTLRFNKLCQEAIKYAEVGALAVETYNVAISAL 650 (856)
Q Consensus 571 CrHiL~Vl~~~~v~~IP~~YIlkRWtk~ak~~~~~~~~~~~~~~~~s~~~Ry~~L~~~~~~l~~~g~~s~E~y~~a~~~L 650 (856)
|+|||+||.+.||.+||++|||+||||+||.....+.... ...+.+.||+.||+.+++++++|+.|+|.|..|+++|
T Consensus 593 CrHaLkVL~~~~v~~IP~~YILkRWTKdAK~~~~~~~~~~---~~~~~~~Ryn~L~r~a~kla~~as~S~E~y~~a~~~L 669 (846)
T PLN03097 593 CRHALVVLQMCQLSAIPSQYILKRWTKDAKSRHLLGEESE---QVQSRVQRYNDLCQRALKLSEEASLSQESYNIAFRAL 669 (846)
T ss_pred hhhHHHHHhhcCcccCchhhhhhhchhhhhhcccCccccc---cccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 9999999999999999999999999999998766543221 2345678999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhccCCCCCCCCCcccccccCCCCCCCCCCCCcCCCCCCCcccCCcc
Q 035792 651 KEAGKKVLAVKKNVAKISPPSSQVVLYSQEDSNKKTPPSVPEMIPSLWPWQEAMPHR 707 (856)
Q Consensus 651 ~e~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 (856)
+++.++++.++++...++.+++...+..-. .-.+..+...++.-|+......|
T Consensus 670 ~e~~~~~~~~~n~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~ 722 (846)
T PLN03097 670 EEAFGNCISMNNSNKSLVEAGTSPTHGLLC----IEDDNQSRSMTKTNKKKNPTKKR 722 (846)
T ss_pred HHHHHHHHHhhccCCCccccccccccCCcc----ccccccccccCcCCccccccccc
Confidence 999999999988877777555543321100 11344555666666665444333
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=99.83 E-value=8e-21 Score=171.22 Aligned_cols=90 Identities=32% Similarity=0.599 Sum_probs=86.9
Q ss_pred ccccCCCCCCcccc---EEEEeeCCcEEEEEEEeecCCchhhHHHHHHHHHHhcCCCCCeEEecCccHHHHHHHHhhCCC
Q 035792 275 TMYRPNQYQVPFAP---FTGVNHHGQMVLFGCALLLDESEASFTWLFRTWLSAMNDRPPVSITTDQDRAIQVAVAQVLPE 351 (856)
Q Consensus 275 ~Ty~tnky~~pL~~---~vgvn~~g~~~~~g~all~~Et~es~~Wll~~f~~~m~~~~P~~iiTD~d~al~~AI~~vFP~ 351 (856)
+||+||+| +|++. ++|+|++|+.+|+||+++.+|+.++|.|+|+.+++.++.+ |.+||||++.++.+||+++||+
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 88886 9999999999999999999999999999999999999887 9999999999999999999999
Q ss_pred cccccchhHHHHHHH
Q 035792 352 TCHCICKWHILREGQ 366 (856)
Q Consensus 352 a~h~lC~~HI~kn~~ 366 (856)
+.|++|.||+.+|++
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=99.66 E-value=1.6e-16 Score=142.76 Aligned_cols=77 Identities=36% Similarity=0.699 Sum_probs=70.0
Q ss_pred HHHHHHhhhcCcEEEEcceeccCCCCCeEEEEeecCcccccc-----------cc---ccCCcceeEEEEecCCcEEEEE
Q 035792 65 TFYDAYARRMGFSTHVGPFTRAKPDGPIITWDFACSREVFKR-----------KN---VESCNAVLRIERKDSEKWTVTK 130 (856)
Q Consensus 65 ~fyn~YA~~~GF~vr~~~s~r~k~~g~~~~~~f~CsreG~~R-----------kr---r~gCpa~i~v~~~~~~~W~V~~ 130 (856)
+||+.||..+||+|++.++++.+.+|.++++.|+|+++|.++ ++ ++||||+|.+++..+|+|.|+.
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 599999999999999999988878899999999999999761 11 9999999999987799999999
Q ss_pred eecCccCCCCC
Q 035792 131 FVEDHNHSMVT 141 (856)
Q Consensus 131 ~~~eHNH~l~~ 141 (856)
++.+|||+|.|
T Consensus 81 ~~~~HNH~L~P 91 (91)
T PF03101_consen 81 FVLEHNHPLCP 91 (91)
T ss_pred CcCCcCCCCCC
Confidence 99999999864
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=99.20 E-value=2.5e-12 Score=145.22 Aligned_cols=179 Identities=12% Similarity=0.139 Sum_probs=136.0
Q ss_pred ceEEecccccCCCC-----CCccccEEEEeeCCcEEEEEEEeecCCchhhHHHHHHHHHHhcCCCCCeEEecCccHHHHH
Q 035792 269 DAVIFDTMYRPNQY-----QVPFAPFTGVNHHGQMVLFGCALLLDESEASFTWLFRTWLSAMNDRPPVSITTDQDRAIQV 343 (856)
Q Consensus 269 dVl~~D~Ty~tnky-----~~pL~~~vgvn~~g~~~~~g~all~~Et~es~~Wll~~f~~~m~~~~P~~iiTD~d~al~~ 343 (856)
++|++|++|.+-+. +.++++++|+|.+|+..++|+.+...|+.++|.-+|..|++- |-..|..||+|..+++.+
T Consensus 163 ~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R-Gl~~~~lvv~Dg~~gl~~ 241 (381)
T PF00872_consen 163 PYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER-GLKDILLVVSDGHKGLKE 241 (381)
T ss_pred cceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc-cccccceeeccccccccc
Confidence 47899999987553 467899999999999999999999999999999999999766 224589999999999999
Q ss_pred HHHhhCCCcccccchhHHHHHHHHhhhhhccCChhHHHHHHHHHhccCCHHHHHHHHHHhhhhccchhhHHHHHHHhcc-
Q 035792 344 AVAQVLPETCHCICKWHILREGQERLAHIYLAHPSFYGELYSCINFCETIEEFESSWCSLLDKYDLQKNEWLHAVYNAR- 422 (856)
Q Consensus 344 AI~~vFP~a~h~lC~~HI~kn~~~~l~~~~~~~~~~~~~~~~~v~~s~t~eeFe~~w~~l~~~~~l~~~~wL~~ly~~r- 422 (856)
||.++||++.++.|.+|+++|+.+++.. ...+.+..+|+.+ +.+.+.++....+..+.+++..........|-+..
T Consensus 242 ai~~~fp~a~~QrC~vH~~RNv~~~v~~--k~~~~v~~~Lk~I-~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~ 318 (381)
T PF00872_consen 242 AIREVFPGAKWQRCVVHLMRNVLRKVPK--KDRKEVKADLKAI-YQAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWD 318 (381)
T ss_pred cccccccchhhhhheechhhhhcccccc--ccchhhhhhcccc-ccccccchhhhhhhhcccccccccchhhhhhhhccc
Confidence 9999999999999999999999998854 3456777777665 55789999999999998877665444333332111
Q ss_pred cccccccccCceeeccccccch---hhhhccc
Q 035792 423 RQWAPVYFRGTFFAALSSNQGI---SSFFDGY 451 (856)
Q Consensus 423 ~~Wa~ay~~~~f~~g~~s~~rs---ns~~k~~ 451 (856)
+.|.-.-|+...+..+.||+.. |+-+|..
T Consensus 319 ~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr 350 (381)
T PF00872_consen 319 ELLTFLDFPPEHRRSIRTTNAIESLNKEIRRR 350 (381)
T ss_pred cccceeeecchhccccchhhhccccccchhhh
Confidence 1222111334444566677665 4444443
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=98.74 E-value=3.3e-08 Score=89.44 Aligned_cols=76 Identities=22% Similarity=0.416 Sum_probs=64.5
Q ss_pred eCCHHHHHHHHHHHhhhcCcEEEEcceeccCCCCCeEEEEeecCcccccc------------------------------
Q 035792 57 FDSEDAAKTFYDAYARRMGFSTHVGPFTRAKPDGPIITWDFACSREVFKR------------------------------ 106 (856)
Q Consensus 57 F~S~eea~~fyn~YA~~~GF~vr~~~s~r~k~~g~~~~~~f~CsreG~~R------------------------------ 106 (856)
|.+.+|.+.|+...++.+||.|++.+|... .+.|.|--+|.+|
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~-------ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~ 73 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKK-------KIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKK 73 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCc-------eEEEEEecCCCcccccccccccccccccccccccccccccccC
Confidence 889999999999999999999999988643 4778996555320
Q ss_pred c----cccCCcceeEEEEec-CCcEEEEEeecCccCCC
Q 035792 107 K----NVESCNAVLRIERKD-SEKWTVTKFVEDHNHSM 139 (856)
Q Consensus 107 k----rr~gCpa~i~v~~~~-~~~W~V~~~~~eHNH~l 139 (856)
+ +.++||++|++.+.. .+.|.|..++..|||+|
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 1 189999999999864 89999999999999986
No 6
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.67 E-value=5.4e-09 Score=72.11 Aligned_cols=27 Identities=41% Similarity=0.844 Sum_probs=25.2
Q ss_pred eeeecCCcccCcccccchhhhhhccCc
Q 035792 557 ASCSCQMFEYSGILCRHILTVFTVTNV 583 (856)
Q Consensus 557 ~sCsC~~fe~~GipCrHiL~Vl~~~~v 583 (856)
.+|+|++||..||||+|+|+|+...++
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCC
Confidence 379999999999999999999999885
No 7
>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=98.50 E-value=4.2e-07 Score=76.76 Aligned_cols=65 Identities=22% Similarity=0.398 Sum_probs=56.1
Q ss_pred CCCCCCCeeCCHHHHHHHHHHHhhhcCcEEEEcceeccCCCCCeEEEEeecCccccccccccCCcceeEEEEec-CCcEE
Q 035792 49 SKPYVGMEFDSEDAAKTFYDAYARRMGFSTHVGPFTRAKPDGPIITWDFACSREVFKRKNVESCNAVLRIERKD-SEKWT 127 (856)
Q Consensus 49 ~~P~vG~~F~S~eea~~fyn~YA~~~GF~vr~~~s~r~k~~g~~~~~~f~CsreG~~Rkrr~gCpa~i~v~~~~-~~~W~ 127 (856)
+...+||.|.|.+|++.++..||...||.+++.++.+ .++..+|.. .||||+|++.+.. ++.|.
T Consensus 2 ~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~-------~r~~~~C~~--------~~C~Wrv~as~~~~~~~~~ 66 (67)
T PF03108_consen 2 PELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDK-------KRYRAKCKD--------KGCPWRVRASKRKRSDTFQ 66 (67)
T ss_pred CccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCC-------EEEEEEEcC--------CCCCEEEEEEEcCCCCEEE
Confidence 4568999999999999999999999999999976643 378899973 7899999999876 67787
Q ss_pred E
Q 035792 128 V 128 (856)
Q Consensus 128 V 128 (856)
|
T Consensus 67 I 67 (67)
T PF03108_consen 67 I 67 (67)
T ss_pred C
Confidence 5
No 8
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=98.19 E-value=5.8e-06 Score=92.44 Aligned_cols=137 Identities=15% Similarity=0.178 Sum_probs=107.4
Q ss_pred ceEEecccccCCC--CCCccccEEEEeeCCcEEEEEEEeecCCchhhHHHHHHHHHHhcCCCCCeEEecCccHHHHHHHH
Q 035792 269 DAVIFDTMYRPNQ--YQVPFAPFTGVNHHGQMVLFGCALLLDESEASFTWLFRTWLSAMNDRPPVSITTDQDRAIQVAVA 346 (856)
Q Consensus 269 dVl~~D~Ty~tnk--y~~pL~~~vgvn~~g~~~~~g~all~~Et~es~~Wll~~f~~~m~~~~P~~iiTD~d~al~~AI~ 346 (856)
.+|++|++|.+-+ -+..+++++||+.+|+-.++|+.+-..|+ ..|.-+|..|+..- -..-..+++|...++.+||.
T Consensus 146 ~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~rg-l~~v~l~v~Dg~~gl~~aI~ 223 (379)
T COG3328 146 PYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNRG-LSDVLLVVVDGLKGLPEAIS 223 (379)
T ss_pred eEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhcc-ccceeEEecchhhhhHHHHH
Confidence 4688999999877 56788999999999999999999999999 88886777676551 22345677799999999999
Q ss_pred hhCCCcccccchhHHHHHHHHhhhhhccCChhHHHHHHHHHhccCCHHHHHHHHHHhhhhccch
Q 035792 347 QVLPETCHCICKWHILREGQERLAHIYLAHPSFYGELYSCINFCETIEEFESSWCSLLDKYDLQ 410 (856)
Q Consensus 347 ~vFP~a~h~lC~~HI~kn~~~~l~~~~~~~~~~~~~~~~~v~~s~t~eeFe~~w~~l~~~~~l~ 410 (856)
.+||.+.++.|..|+.+|+..+.... ..+....++ +.++.+.+.++-...|..+.+.+...
T Consensus 224 ~v~p~a~~Q~C~vH~~Rnll~~v~~k--~~d~i~~~~-~~I~~a~~~e~~~~~~~~~~~~w~~~ 284 (379)
T COG3328 224 AVFPQAAVQRCIVHLVRNLLDKVPRK--DQDAVLSDL-RSIYIAPDAEEALLALLAFSELWGKR 284 (379)
T ss_pred HhccHhhhhhhhhHHHhhhhhhhhhh--hhHHHHhhh-hhhhccCCcHHHHHHHHHHHHhhhhh
Confidence 99999999999999999998877532 222233333 34556788888888888877644433
No 9
>cd04757 Commd9 COMM_Domain containing protein 9. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=98.08 E-value=2.9e-06 Score=77.20 Aligned_cols=63 Identities=25% Similarity=0.435 Sum_probs=53.7
Q ss_pred hhhhhhhhh-hhhcc-----CCCccccEEEEeccccccCCCcce----eEEEEeehhhHHHHHHhHhHhhhcC
Q 035792 794 EPMLRSMAY-ISQQL-----SAPANKVAVINLKLQDTKTTSGEA----EVKFQVSRDTLGSMLRSLAYIREQL 856 (856)
Q Consensus 794 ~~~~~~m~~-~~~~~-----~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~ 856 (856)
.|.|..+.| +--+. +....++.+++||++|..+..|+. .|.|+|+|+||+.||.++..||+||
T Consensus 31 lp~l~dldWRldv~isS~sl~r~~~P~vll~lkv~~~~~~~~~~~~~~~v~~ELsKe~l~tml~~L~~i~~QL 103 (108)
T cd04757 31 LPKLVDHDWRVDIKTSSDSLGRMAVPTCLLQMKIQEAPSLCGLLPPLSTLTMELSKETLDTMLDGLGRIRDQL 103 (108)
T ss_pred chhhhCccceehhHHHHHHHHhhhcCeEEEEEEeecCccccccCCCcceEEEEcCHHHHHHHHHHHHHHHHHH
Confidence 689999999 33244 566778999999999966677776 9999999999999999999999996
No 10
>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=98.01 E-value=3.1e-06 Score=63.76 Aligned_cols=28 Identities=43% Similarity=0.899 Sum_probs=25.4
Q ss_pred CceeeecCCcccCcccccchhhhhhccC
Q 035792 555 MKASCSCQMFEYSGILCRHILTVFTVTN 582 (856)
Q Consensus 555 ~~~sCsC~~fe~~GipCrHiL~Vl~~~~ 582 (856)
...+|+|..|+..|.||+|+++|+...+
T Consensus 13 ~~~~CsC~~~~~~~~~CkHi~av~~~~~ 40 (40)
T PF04434_consen 13 EQASCSCPYFQFRGGPCKHIVAVLLALN 40 (40)
T ss_pred cccEeeCCCccccCCcchhHHHHHHhhC
Confidence 4789999999999999999999997654
No 11
>cd04757 Commd9 COMM_Domain containing protein 9. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=97.93 E-value=3.6e-06 Score=76.55 Aligned_cols=75 Identities=27% Similarity=0.412 Sum_probs=64.3
Q ss_pred CCCCceeeccccccchhhccCCC-----CCCCccEEEEEEeccCCCCCCCcc----eEEEEeecccchhhhhhhhhhhhc
Q 035792 736 TPDSTVVLTCFKSMTWVIENKNS-----TSASKVAVINLKLQDYGKKPSGET----EVQFRLTKTTLEPMLRSMAYISQQ 806 (856)
Q Consensus 736 ~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~m~~~~~~ 806 (856)
...++.++|+|..+.|-+.-+=+ ....|+++++||++|.++ ..|+. .|.|+|+|+||+.||.++.-|+||
T Consensus 24 ~~~~~~slp~l~dldWRldv~isS~sl~r~~~P~vll~lkv~~~~~-~~~~~~~~~~v~~ELsKe~l~tml~~L~~i~~Q 102 (108)
T cd04757 24 ASENQISLPKLVDHDWRVDIKTSSDSLGRMAVPTCLLQMKIQEAPS-LCGLLPPLSTLTMELSKETLDTMLDGLGRIRDQ 102 (108)
T ss_pred HHhcCCCchhhhCccceehhHHHHHHHHhhhcCeEEEEEEeecCcc-ccccCCCcceEEEEcCHHHHHHHHHHHHHHHHH
Confidence 34568999999999999988873 455688999999999766 55665 899999999999999999999999
Q ss_pred cCCCc
Q 035792 807 LSAPA 811 (856)
Q Consensus 807 ~~~~~ 811 (856)
+++.|
T Consensus 103 L~~va 107 (108)
T cd04757 103 LSAVA 107 (108)
T ss_pred HHHHh
Confidence 99754
No 12
>cd04749 Commd1_MURR1 COMM_Domain containing protein 1, also called Murr1. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=94.09 E-value=0.064 Score=53.54 Aligned_cols=61 Identities=26% Similarity=0.431 Sum_probs=50.0
Q ss_pred hhhhhhhhh-h-----hhccCCCccccEEEEeccccccCCCcceeEEEEeehhhHHHHHHhHhHhhhcC
Q 035792 794 EPMLRSMAY-I-----SQQLSAPANKVAVINLKLQDTKTTSGEAEVKFQVSRDTLGSMLRSLAYIREQL 856 (856)
Q Consensus 794 ~~~~~~m~~-~-----~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 856 (856)
+|.|++|.| + ++..+...+++|.+.|+++++.. +..-|-|.+++++++.||..|.-|++++
T Consensus 105 ~~~L~~l~WRVD~~tsS~~~~evn~P~~~l~L~v~~~~~--~~~~v~~emd~ek~~~lL~eLk~iq~~m 171 (174)
T cd04749 105 ENSLRGLSWRVDLKTQSRHIAQINSPVAIVELELGKTGQ--ESEFVCLEFDEAKVNRVLKQLAEIQESL 171 (174)
T ss_pred cccccCCCCeeeeecccchhhhccCCeEEEEEeeccCCC--CCceEEEEecHHHHHHHHHHHHHHHHHH
Confidence 799999999 3 23555678899999999988422 2338999999999999999999999863
No 13
>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=93.82 E-value=0.092 Score=55.94 Aligned_cols=81 Identities=12% Similarity=0.211 Sum_probs=62.1
Q ss_pred ccEEEEee--CCcEEEEEEEeecCCchhhHHHHHHHH-HHhcCCCCCeEEecCccHHHHHHHHhhCCCcccccchhHHHH
Q 035792 287 APFTGVNH--HGQMVLFGCALLLDESEASFTWLFRTW-LSAMNDRPPVSITTDQDRAIQVAVAQVLPETCHCICKWHILR 363 (856)
Q Consensus 287 ~~~vgvn~--~g~~~~~g~all~~Et~es~~Wll~~f-~~~m~~~~P~~iiTD~d~al~~AI~~vFP~a~h~lC~~HI~k 363 (856)
+..+.+|. +...++ +++.+-+.+++.-+|..+ -.. .....++|.+|...+...|+++.||+|.+.+-.|||++
T Consensus 15 y~t~~~d~~~~~~~il---~i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~~~P~A~iv~DrFHvvk 90 (249)
T PF01610_consen 15 YVTVVVDLDTDTGRIL---DILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIREYFPNAQIVADRFHVVK 90 (249)
T ss_pred eeEEEEECccCCceEE---EEcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCccccccccccccccccccccchhhh
Confidence 44455555 333332 578888888877777765 222 34567899999999999999999999999999999999
Q ss_pred HHHHhhhh
Q 035792 364 EGQERLAH 371 (856)
Q Consensus 364 n~~~~l~~ 371 (856)
++.+.+..
T Consensus 91 ~~~~al~~ 98 (249)
T PF01610_consen 91 LANRALDK 98 (249)
T ss_pred hhhhcchh
Confidence 99876654
No 14
>cd04749 Commd1_MURR1 COMM_Domain containing protein 1, also called Murr1. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=90.25 E-value=0.28 Score=49.04 Aligned_cols=64 Identities=19% Similarity=0.393 Sum_probs=52.4
Q ss_pred eeccccccchhh-----ccCCCCCCCccEEEEEEeccCCCCCCCcceEEEEeecccchhhhhhhhhhhhccC
Q 035792 742 VLTCFKSMTWVI-----ENKNSTSASKVAVINLKLQDYGKKPSGETEVQFRLTKTTLEPMLRSMAYISQQLS 808 (856)
Q Consensus 742 ~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~ 808 (856)
-+|+|++|.|-. ++.-+...+|+|++.|++++.++.+. -|.|.++++++.-||+.|.=|.++.+
T Consensus 104 ~~~~L~~l~WRVD~~tsS~~~~evn~P~~~l~L~v~~~~~~~~---~v~~emd~ek~~~lL~eLk~iq~~m~ 172 (174)
T cd04749 104 WENSLRGLSWRVDLKTQSRHIAQINSPVAIVELELGKTGQESE---FVCLEFDEAKVNRVLKQLAEIQESLD 172 (174)
T ss_pred hcccccCCCCeeeeecccchhhhccCCeEEEEEeeccCCCCCc---eEEEEecHHHHHHHHHHHHHHHHHHh
Confidence 568888899976 44556678899999999999766543 79999999999999999987776644
No 15
>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=90.09 E-value=0.92 Score=37.39 Aligned_cols=55 Identities=18% Similarity=0.374 Sum_probs=36.3
Q ss_pred CcEEEEcceeccCCCCCeEEEEeecCccccccccccCCcceeEEEEec-CCcEEEEEeecCccCC
Q 035792 75 GFSTHVGPFTRAKPDGPIITWDFACSREVFKRKNVESCNAVLRIERKD-SEKWTVTKFVEDHNHS 138 (856)
Q Consensus 75 GF~vr~~~s~r~k~~g~~~~~~f~CsreG~~Rkrr~gCpa~i~v~~~~-~~~W~V~~~~~eHNH~ 138 (856)
||..|+=-....+ +...-+..|.|+- .+|||+=.|.+.. ++.-+++....+|||+
T Consensus 4 gy~WRKYGqK~i~-g~~~pRsYYrCt~--------~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 4 GYRWRKYGQKNIK-GSPYPRSYYRCTH--------PGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp SS-EEEEEEEEET-TTTCEEEEEEEEC--------TTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CCchhhccCcccC-CCceeeEeeeccc--------cChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 6777662222222 1223467899985 5999999999876 7778899999999996
No 16
>cd04748 Commd COMM_Domain, a family of domains found at the C-terminus of HCarG, the copper metabolism gene MURR1 product, and related proteins. Presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. HCaRG, a nuclear protein that might be involved in cell proliferation, is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals.
Probab=89.23 E-value=0.44 Score=42.27 Aligned_cols=62 Identities=24% Similarity=0.425 Sum_probs=48.3
Q ss_pred hhhhhhhhh-hhhccC-----CCccccEEEEeccccccCCCcceeEEEEeehhhHHHHHHhHhHhhhcC
Q 035792 794 EPMLRSMAY-ISQQLS-----APANKVAVINLKLQDTKTTSGEAEVKFQVSRDTLGSMLRSLAYIREQL 856 (856)
Q Consensus 794 ~~~~~~m~~-~~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 856 (856)
.|.|++|.| +.-+.+ ...++++++.|++.+.... ....|-|+++.+.|..++..|.-|.+||
T Consensus 20 ~~~L~d~~Wrld~~~sS~~~~~~~~P~~~~~L~l~~~~~~-~~~~v~~E~~~~~l~~l~~~L~~a~~~l 87 (87)
T cd04748 20 LPQLVDFDWRLDVQISSSSLAKVKQPTILVQLKLQVGDNN-SSEKICFEMTKEELQNFLNKLKKIKAQL 87 (87)
T ss_pred CCeeeeeeeEEEEEEchhHHHHhhCCeEEEEEEEecCCCC-ccceEEEEeCHHHHHHHHHHHHHHHhcC
Confidence 577888888 322333 4556899999999985433 3458999999999999999999999886
No 17
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=87.68 E-value=0.11 Score=50.43 Aligned_cols=81 Identities=19% Similarity=0.188 Sum_probs=66.4
Q ss_pred CceEEecccccCCCCCCccccEEEEeeCCcEEEEEEEeecCCchhhHHHHHHHHHHhcCCCCCeEEecCccHHHHHHHHh
Q 035792 268 SDAVIFDTMYRPNQYQVPFAPFTGVNHHGQMVLFGCALLLDESEASFTWLFRTWLSAMNDRPPVSITTDQDRAIQVAVAQ 347 (856)
Q Consensus 268 ~dVl~~D~Ty~tnky~~pL~~~vgvn~~g~~~~~g~all~~Et~es~~Wll~~f~~~m~~~~P~~iiTD~d~al~~AI~~ 347 (856)
|+.+.+|=||.+-+- ---+....||.+|+ ++.+-|-..-+..+=..||+..++..+ ..|..|+||+..+...|+++
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 GDSWHVDETYIKIKG-KWHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-GEPRVIVTDKLPAYPAAIKE 76 (140)
T ss_pred CCEEEEeeEEEEECC-EEEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-cccceeecccCCccchhhhh
Confidence 578889999976543 34556888999999 788888888888887788777777665 68999999999999999999
Q ss_pred hCCCc
Q 035792 348 VLPET 352 (856)
Q Consensus 348 vFP~a 352 (856)
.+|..
T Consensus 77 l~~~~ 81 (140)
T PF13610_consen 77 LNPEG 81 (140)
T ss_pred ccccc
Confidence 99974
No 18
>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=87.43 E-value=0.87 Score=51.53 Aligned_cols=56 Identities=16% Similarity=0.234 Sum_probs=48.6
Q ss_pred CCCeeCCHHHHHHHHHHHhhhcCcEEEEcceeccCCCCCeEEEEeecCccccccccccCCcceeEEEEec
Q 035792 53 VGMEFDSEDAAKTFYDAYARRMGFSTHVGPFTRAKPDGPIITWDFACSREVFKRKNVESCNAVLRIERKD 122 (856)
Q Consensus 53 vG~~F~S~eea~~fyn~YA~~~GF~vr~~~s~r~k~~g~~~~~~f~CsreG~~Rkrr~gCpa~i~v~~~~ 122 (856)
.+..|+|.++.|..+|.|.....+-|....|.|.| -++|.|.. ..|||+|.+.+.+
T Consensus 24 ~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nk------hftfachl--------k~c~fkillsy~g 79 (496)
T PF04684_consen 24 QARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNK------HFTFACHL--------KNCPFKILLSYCG 79 (496)
T ss_pred cccCCCcHHHHHHHHhhhhhhhcCceeeccccccc------ceEEEeec--------cCCCceeeeeecc
Confidence 36689999999999999999999999998876543 58999995 7899999999864
No 19
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=84.14 E-value=9 Score=37.88 Aligned_cols=109 Identities=12% Similarity=0.139 Sum_probs=77.8
Q ss_pred hHHhhhcCceEEecccccCCCCCCccccEEEEeeCCcEEEEEEEeec-CCchhhHHHHHHHHHHhcCCCCCeEEecCccH
Q 035792 261 RMAYNHFSDAVIFDTMYRPNQYQVPFAPFTGVNHHGQMVLFGCALLL-DESEASFTWLFRTWLSAMNDRPPVSITTDQDR 339 (856)
Q Consensus 261 ~~~y~~f~dVl~~D~Ty~tnky~~pL~~~vgvn~~g~~~~~g~all~-~Et~es~~Wll~~f~~~m~~~~P~~iiTD~d~ 339 (856)
+..+..+|=.|..|+= ++..+.+|+.|+.....|..|+-..-.-. ..+.+.+.-+|+...+.+|...-..||||-..
T Consensus 26 k~~w~~~Gcsi~~DgW--td~~~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ll~~vIeeVG~~nVvqVVTDn~~ 103 (153)
T PF04937_consen 26 KKSWKRTGCSIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFELLDEVIEEVGEENVVQVVTDNAS 103 (153)
T ss_pred HHHHHhcCEEEEEecC--cCCCCCeEEEEEEEcccccEEEEEEecccccccHHHHHHHHHHHHHHhhhhhhhHHhccCch
Confidence 3445556656777766 66677788888877776665544332222 24666677777777777777777789999999
Q ss_pred HHHHHH---HhhCCCcccccchhHHHHHHHHhhhh
Q 035792 340 AIQVAV---AQVLPETCHCICKWHILREGQERLAH 371 (856)
Q Consensus 340 al~~AI---~~vFP~a~h~lC~~HI~kn~~~~l~~ 371 (856)
.+++|- .+-+|.....-|.-|-+..+.+.++.
T Consensus 104 ~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 104 NMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred hHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 999884 45588888889999999888877764
No 20
>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=83.28 E-value=4 Score=37.61 Aligned_cols=76 Identities=12% Similarity=0.142 Sum_probs=55.3
Q ss_pred CceEEecccccC-CCCCCccccEEEEeeCCcEEEEEEEeecCCchhhHHHHHHHHHHhcCCCCCeEEecCccHHHHHH
Q 035792 268 SDAVIFDTMYRP-NQYQVPFAPFTGVNHHGQMVLFGCALLLDESEASFTWLFRTWLSAMNDRPPVSITTDQDRAIQVA 344 (856)
Q Consensus 268 ~dVl~~D~Ty~t-nky~~pL~~~vgvn~~g~~~~~g~all~~Et~es~~Wll~~f~~~m~~~~P~~iiTD~d~al~~A 344 (856)
++.+.+|.+... ...++..+.++.+|..-..+ +++.+-..++.+.+..+|.......++..|.+|+||+..+..+.
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 367788877554 34455788888888877654 56777777788888888887777777666999999999988744
No 21
>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=79.76 E-value=3.1 Score=33.69 Aligned_cols=49 Identities=27% Similarity=0.397 Sum_probs=21.8
Q ss_pred cCcEEEEcceeccCCCCCeEEEEeecCccccccccccCCcceeEEEEecCCcEEEEEeecCccC
Q 035792 74 MGFSTHVGPFTRAKPDGPIITWDFACSREVFKRKNVESCNAVLRIERKDSEKWTVTKFVEDHNH 137 (856)
Q Consensus 74 ~GF~vr~~~s~r~k~~g~~~~~~f~CsreG~~Rkrr~gCpa~i~v~~~~~~~W~V~~~~~eHNH 137 (856)
.||.....+.. +| ...+.|++-. ..+|+|++.+. .+.-.|.....+|||
T Consensus 14 ~Gy~y~~~~~~----~~---~~~WrC~~~~-----~~~C~a~~~~~---~~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRN----DG---KTYWRCSRRR-----SHGCRARLITD---AGDGRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-----SS----EEEEEGGGT-----TS----EEEEE-----TTEEEE-S---SS
T ss_pred CCeEEECcCCC----CC---cEEEEeCCCC-----CCCCeEEEEEE---CCCCEEEECCCccCC
Confidence 36666654432 33 3456787531 35899999998 233345555689999
No 22
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=78.36 E-value=31 Score=40.60 Aligned_cols=92 Identities=11% Similarity=0.182 Sum_probs=66.6
Q ss_pred CCchhhHHHHHHHHHHhcCCCC--CeEEecCccHHHHHHHHhhCCCcccccchhHHHHHHHHhhhhhccCChhHHHHHHH
Q 035792 308 DESEASFTWLFRTWLSAMNDRP--PVSITTDQDRAIQVAVAQVLPETCHCICKWHILREGQERLAHIYLAHPSFYGELYS 385 (856)
Q Consensus 308 ~Et~es~~Wll~~f~~~m~~~~--P~~iiTD~d~al~~AI~~vFP~a~h~lC~~HI~kn~~~~l~~~~~~~~~~~~~~~~ 385 (856)
....+-|.-+.+.+-..-.... -.++..|....+..++. .||++.|.|..||+.+.+.+.++. .+.....+++
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 4445667766666655543222 34778899999988776 999999999999999999988864 3556666777
Q ss_pred HHhccCCHHHHHHHHHHhhh
Q 035792 386 CINFCETIEEFESSWCSLLD 405 (856)
Q Consensus 386 ~v~~s~t~eeFe~~w~~l~~ 405 (856)
++. ......++...+.+..
T Consensus 310 al~-~~d~~~l~~~L~~~~~ 328 (470)
T PF06782_consen 310 ALK-KGDKKKLETVLDTAES 328 (470)
T ss_pred HHH-hcCHHHHHHHHHHHHH
Confidence 776 3566777777776654
No 23
>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=77.15 E-value=4.3 Score=33.32 Aligned_cols=37 Identities=19% Similarity=0.441 Sum_probs=30.4
Q ss_pred EEEeecCccccccccccCCcceeEEEEec-CCcEEEEEeecCccC
Q 035792 94 TWDFACSREVFKRKNVESCNAVLRIERKD-SEKWTVTKFVEDHNH 137 (856)
Q Consensus 94 ~~~f~CsreG~~Rkrr~gCpa~i~v~~~~-~~~W~V~~~~~eHNH 137 (856)
+..|.|+. ..||||+=.|.+.. ++.-.++....+|||
T Consensus 22 RsYYrCt~-------~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 22 RSYYRCTY-------SQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred ceEEeccc-------cCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 56789984 15899998888875 778888899999998
No 24
>cd04748 Commd COMM_Domain, a family of domains found at the C-terminus of HCarG, the copper metabolism gene MURR1 product, and related proteins. Presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. HCaRG, a nuclear protein that might be involved in cell proliferation, is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals.
Probab=71.16 E-value=3.1 Score=36.83 Aligned_cols=64 Identities=22% Similarity=0.360 Sum_probs=49.1
Q ss_pred eeeccccccchhhccCCC-----CCCCccEEEEEEeccCCCCCCCcceEEEEeecccchhhhhhhhhhhhc
Q 035792 741 VVLTCFKSMTWVIENKNS-----TSASKVAVINLKLQDYGKKPSGETEVQFRLTKTTLEPMLRSMAYISQQ 806 (856)
Q Consensus 741 ~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~ 806 (856)
...|.|..|.|-..-+=+ ...+|+|++.|++.++... ....|-|+++...|.-+++.|.=+.+|
T Consensus 18 ~~~~~L~d~~Wrld~~~sS~~~~~~~~P~~~~~L~l~~~~~~--~~~~v~~E~~~~~l~~l~~~L~~a~~~ 86 (87)
T cd04748 18 LSLPQLVDFDWRLDVQISSSSLAKVKQPTILVQLKLQVGDNN--SSEKICFEMTKEELQNFLNKLKKIKAQ 86 (87)
T ss_pred cCCCeeeeeeeEEEEEEchhHHHHhhCCeEEEEEEEecCCCC--ccceEEEEeCHHHHHHHHHHHHHHHhc
Confidence 368999999997643332 3457899999999997654 245799999999999988888766654
No 25
>PF07258 HCaRG: HCaRG protein; InterPro: IPR009886 This family consists of several mammalian HCaRG(hypertension-related, calcium-regulated gene) proteins. HCaRG is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals. HCaRG is a nuclear protein potentially involved in the control of cell proliferation [].; PDB: 2H2M_A.
Probab=64.48 E-value=2.2 Score=42.65 Aligned_cols=61 Identities=28% Similarity=0.412 Sum_probs=0.0
Q ss_pred hhhhhhhhhhhh-ccC-----CCccccEEEEeccccccCCCcceeEEEEeehhhHHHHHHhHhHhhhcC
Q 035792 794 EPMLRSMAYISQ-QLS-----APANKVAVINLKLQDTKTTSGEAEVKFQVSRDTLGSMLRSLAYIREQL 856 (856)
Q Consensus 794 ~~~~~~m~~~~~-~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 856 (856)
.|.|.++.|=.+ +.+ ....++++++|++++. ...+..+.|+++++.|..|+..|..|..|+
T Consensus 109 ~~~l~d~~Wrl~~~~~s~~~~~~~~p~~~l~L~~~~~--~~~~~~~~~e~~~~~l~~l~~~L~~a~~~l 175 (178)
T PF07258_consen 109 FPHLVDVDWRLDVQVSSSSLAKINEPVVILQLKTQNG--NGKEETVTFELSKEELQDLLNELKDAQKQL 175 (178)
T ss_dssp ---------------------------------------------------------------------
T ss_pred ccccCCCcEEEEeeecccHhhhccCcEEEEEEEecCC--CCcCceEEEEECHHHHHHHHHHHHHHHHHH
Confidence 467888888222 222 2345788899999876 445678999999999999999999998764
No 26
>PF07258 HCaRG: HCaRG protein; InterPro: IPR009886 This family consists of several mammalian HCaRG(hypertension-related, calcium-regulated gene) proteins. HCaRG is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals. HCaRG is a nuclear protein potentially involved in the control of cell proliferation [].; PDB: 2H2M_A.
Probab=55.98 E-value=3.8 Score=40.91 Aligned_cols=66 Identities=21% Similarity=0.384 Sum_probs=0.0
Q ss_pred ceeeccccccch----hhccCCCC-CCCccEEEEEEeccCCCCCCCcceEEEEeecccchhhhhhhhhhhhccC
Q 035792 740 TVVLTCFKSMTW----VIENKNST-SASKVAVINLKLQDYGKKPSGETEVQFRLTKTTLEPMLRSMAYISQQLS 808 (856)
Q Consensus 740 ~~~~~~~~~~~~----~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~ 808 (856)
...+|+++.+.| .+.+.... ...|+++++|++++. ...+..+.|.++++.|.-++..+.-+.++..
T Consensus 106 ~~~~~~l~d~~Wrl~~~~~s~~~~~~~~p~~~l~L~~~~~---~~~~~~~~~e~~~~~l~~l~~~L~~a~~~l~ 176 (178)
T PF07258_consen 106 SFSFPHLVDVDWRLDVQVSSSSLAKINEPVVILQLKTQNG---NGKEETVTFELSKEELQDLLNELKDAQKQLD 176 (178)
T ss_dssp --------------------------------------------------------------------------
T ss_pred cccccccCCCcEEEEeeecccHhhhccCcEEEEEEEecCC---CCcCceEEEEECHHHHHHHHHHHHHHHHHHh
Confidence 455899999999 34444332 345788899999997 3335579999999999999998888777654
No 27
>cd04756 Commd8 COMM_Domain containing protein 8. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=47.58 E-value=26 Score=35.45 Aligned_cols=45 Identities=16% Similarity=0.304 Sum_probs=34.1
Q ss_pred cCCCccccEEEEeccccccCCCcceeEEEEeehhhHHHHHHhHhHhhh
Q 035792 807 LSAPANKVAVINLKLQDTKTTSGEAEVKFQVSRDTLGSMLRSLAYIRE 854 (856)
Q Consensus 807 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 854 (856)
.+....+.++++|++++ .+. .+.|-|.+++++|..|+..+.-.+.
T Consensus 127 ~~~l~~P~~~L~L~v~~--~~~-~~~v~~Ems~eel~~li~~Le~a~~ 171 (176)
T cd04756 127 LSSLQEPLLNLDLDVKE--NGI-LKPVSIEMNKEELQNLISSLEAANK 171 (176)
T ss_pred HHHhcCCeEEEEEEecC--CCC-eeEEEEEEcHHHHHHHHHHHHHHHH
Confidence 34456688899999983 222 3589999999999999998876543
No 28
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=43.82 E-value=32 Score=34.74 Aligned_cols=45 Identities=20% Similarity=0.268 Sum_probs=35.0
Q ss_pred CCccccEEEEeccccccCCCcceeEEEEeehhhHHHHHHhHhHhhh
Q 035792 809 APANKVAVINLKLQDTKTTSGEAEVKFQVSRDTLGSMLRSLAYIRE 854 (856)
Q Consensus 809 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 854 (856)
...++.+.++|++.++..+.. +.+.|+++.+.|-.++..|.-.+.
T Consensus 125 ~~~~P~~~l~L~v~~~~~~~~-~~v~~e~s~~ql~~L~~eLe~A~~ 169 (174)
T cd04752 125 EVNEPLVQLRLKVRNADTGEI-TPHPFSVSADKFRVLLAELKQAQT 169 (174)
T ss_pred hcCCCeEEEEEeeecCCCCCc-ceEEEEecHHHHHHHHHHHHHHHH
Confidence 345678889999987655443 489999999999999998876654
No 29
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=37.82 E-value=26 Score=31.96 Aligned_cols=31 Identities=32% Similarity=0.562 Sum_probs=21.7
Q ss_pred CCceEEEEecCCceeeecCCcccC-----cccccchhhhh
Q 035792 544 DDKAYIVSFSEMKASCSCQMFEYS-----GILCRHILTVF 578 (856)
Q Consensus 544 ~~~~~~V~~~~~~~sCsC~~fe~~-----GipCrHiL~Vl 578 (856)
.++.|++.. ..|||.+|-.. .-||.|++.+=
T Consensus 41 ~~rdYIl~~----gfCSCp~~~~svvl~Gk~~C~Hi~glk 76 (117)
T COG5431 41 KERDYILEG----GFCSCPDFLGSVVLKGKSPCAHIIGLK 76 (117)
T ss_pred cccceEEEc----CcccCHHHHhHhhhcCcccchhhhhee
Confidence 345788764 48999998732 45699997643
No 30
>cd04753 Commd5_HCaRG COMM_Domain containing protein 5, also called HCaRG (hypertension-related, calcium-regulated gene). HCaRG is a nuclear protein that might be involved in cell proliferation; it is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=37.76 E-value=10 Score=35.29 Aligned_cols=60 Identities=22% Similarity=0.328 Sum_probs=36.1
Q ss_pred hhhhhhhhhhhh-ccCC-----CccccEEEEeccccccCCCcceeE-EEEeehhhHHHHHHhHhHhh
Q 035792 794 EPMLRSMAYISQ-QLSA-----PANKVAVINLKLQDTKTTSGEAEV-KFQVSRDTLGSMLRSLAYIR 853 (856)
Q Consensus 794 ~~~~~~m~~~~~-~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 853 (856)
.|+|.++.|=-| +.|+ ..++.-+..||++|++....|.-+ |||.=+-.+-.||+.|..+-
T Consensus 35 lp~l~~l~WRVDv~lSSs~l~~~~~PtI~LkLkl~dg~~~~fe~~~~kF~~Lry~~a~~l~em~~le 101 (110)
T cd04753 35 LPHLEDFKWRVDVAISTSSLSRVLQPSILMEMKLSDGKSHRFEVPVAKFHELRYNVALILKEMNDLE 101 (110)
T ss_pred CcccccCcceEEEEEchhhhhcccCCeEEEEEEecCCCeEEEEeeHHHHHHHHHHHHHHHHHHHHHH
Confidence 689999999333 4433 455666677788776544322221 34444445677888887654
No 31
>cd04756 Commd8 COMM_Domain containing protein 8. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=37.38 E-value=24 Score=35.74 Aligned_cols=59 Identities=14% Similarity=0.327 Sum_probs=43.5
Q ss_pred Cceeeccccccchhh-----ccCCCCCCCccEEEEEEeccCCCCCCCcceEEEEeecccchhhhhhhh
Q 035792 739 STVVLTCFKSMTWVI-----ENKNSTSASKVAVINLKLQDYGKKPSGETEVQFRLTKTTLEPMLRSMA 801 (856)
Q Consensus 739 ~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~ 801 (856)
++.++|+|..+.|-+ ++.-+....|.+.++|++++. +. .+.|-|.+++.+|..++....
T Consensus 104 ~~is~~~L~d~dWrv~l~lSSd~~~~l~~P~~~L~L~v~~~---~~-~~~v~~Ems~eel~~li~~Le 167 (176)
T cd04756 104 NSISSAQLQDFDWQLKLALSSDKLSSLQEPLLNLDLDVKEN---GI-LKPVSIEMNKEELQNLISSLE 167 (176)
T ss_pred hccCchhhccccCeeeeeechhhHHHhcCCeEEEEEEecCC---CC-eeEEEEEEcHHHHHHHHHHHH
Confidence 456788888888865 234445678999999999942 22 247999999999998887654
No 32
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=35.31 E-value=13 Score=39.11 Aligned_cols=24 Identities=29% Similarity=0.744 Sum_probs=20.4
Q ss_pred ceeeecCCcccCcccccchhhhhhccC
Q 035792 556 KASCSCQMFEYSGILCRHILTVFTVTN 582 (856)
Q Consensus 556 ~~sCsC~~fe~~GipCrHiL~Vl~~~~ 582 (856)
...|||.-+. .||.||-+|..++.
T Consensus 124 ~~dCSCPD~a---nPCKHi~AvyY~la 147 (266)
T COG4279 124 STDCSCPDYA---NPCKHIAAVYYLLA 147 (266)
T ss_pred ccccCCCCcc---cchHHHHHHHHHHH
Confidence 4679999876 59999999998876
No 33
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.97 E-value=77 Score=33.10 Aligned_cols=83 Identities=14% Similarity=0.131 Sum_probs=53.8
Q ss_pred ceEEecccccCCCCCCccccEEEEeeCCcEEEEEEEeecCCchhhHHHHHHHHHHhcCCCCCeEEecCccHHHHHHHHhh
Q 035792 269 DAVIFDTMYRPNQYQVPFAPFTGVNHHGQMVLFGCALLLDESEASFTWLFRTWLSAMNDRPPVSITTDQDRAIQVAVAQV 348 (856)
Q Consensus 269 dVl~~D~Ty~tnky~~pL~~~vgvn~~g~~~~~g~all~~Et~es~~Wll~~f~~~m~~~~P~~iiTD~d~al~~AI~~v 348 (856)
+++-+|=||.+-+-+.. +.-..||..|+ ++.+-|...-+...=.-||..+++.. ..|.+|+||+.+....|++++
T Consensus 71 ~~w~vDEt~ikv~gkw~-ylyrAid~~g~--~Ld~~L~~rRn~~aAk~Fl~kllk~~--g~p~v~vtDka~s~~~A~~~l 145 (215)
T COG3316 71 DSWRVDETYIKVNGKWH-YLYRAIDADGL--TLDVWLSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAALRKL 145 (215)
T ss_pred cceeeeeeEEeeccEee-ehhhhhccCCC--eEEEEEEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHHHhc
Confidence 45556666654332211 12233455543 45556666656666666777777665 578999999999999999999
Q ss_pred CCCccccc
Q 035792 349 LPETCHCI 356 (856)
Q Consensus 349 FP~a~h~l 356 (856)
-+.+.|+-
T Consensus 146 ~~~~ehr~ 153 (215)
T COG3316 146 GSEVEHRT 153 (215)
T ss_pred Ccchheec
Confidence 99776654
No 34
>cd04758 Commd10 COMM_Domain containing protein 10. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=28.78 E-value=70 Score=32.63 Aligned_cols=42 Identities=21% Similarity=0.363 Sum_probs=34.8
Q ss_pred ccEEEEeccccccCCCcceeEEEEeehhhHHHHHHhHhHhhhcC
Q 035792 813 KVAVINLKLQDTKTTSGEAEVKFQVSRDTLGSMLRSLAYIREQL 856 (856)
Q Consensus 813 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 856 (856)
+.+.+.||+.+... ....|.|.+|++-|-..+..|.-|..||
T Consensus 142 P~~~L~L~~~~~~g--~~e~v~~E~t~~el~~l~~~le~~q~~l 183 (186)
T cd04758 142 PLAVLELGVTSEDG--NLEKINLEFNHEELLEFYNQLESIQEQL 183 (186)
T ss_pred CcEEEEeecCCCCC--CccceEEEEcHHHHHHHHHHHHHHHHHh
Confidence 67788998887443 2458999999999999999999998875
No 35
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=23.03 E-value=2.3e+02 Score=30.44 Aligned_cols=72 Identities=8% Similarity=-0.061 Sum_probs=48.8
Q ss_pred ceEEecccccCCCCCCccccEEEEeeCCcEEEEEEEeecC-CchhhHHHHHHHHHHhc-C---CCCCeEEecCccHHH
Q 035792 269 DAVIFDTMYRPNQYQVPFAPFTGVNHHGQMVLFGCALLLD-ESEASFTWLFRTWLSAM-N---DRPPVSITTDQDRAI 341 (856)
Q Consensus 269 dVl~~D~Ty~tnky~~pL~~~vgvn~~g~~~~~g~all~~-Et~es~~Wll~~f~~~m-~---~~~P~~iiTD~d~al 341 (856)
.+.+.|-||.....+.-++..+.+|.+.. .++|+++-.. -+.+...-+|+..++.. + ...|..|.||+...-
T Consensus 88 ~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gsqy 164 (262)
T PRK14702 88 QRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSCY 164 (262)
T ss_pred CEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCccc
Confidence 67888988876544556788888888776 6788998874 56666555555443332 2 235789999997653
No 36
>PHA02517 putative transposase OrfB; Reviewed
Probab=22.56 E-value=1.8e+02 Score=31.17 Aligned_cols=72 Identities=8% Similarity=-0.094 Sum_probs=44.9
Q ss_pred CceEEecccccCCCCCCccccEEEEeeCCcEEEEEEEeecCCchhhHHHHHHHHHHhcCCCCCeEEecCccHHH
Q 035792 268 SDAVIFDTMYRPNQYQVPFAPFTGVNHHGQMVLFGCALLLDESEASFTWLFRTWLSAMNDRPPVSITTDQDRAI 341 (856)
Q Consensus 268 ~dVl~~D~Ty~tnky~~pL~~~vgvn~~g~~~~~g~all~~Et~es~~Wll~~f~~~m~~~~P~~iiTD~d~al 341 (856)
.+++..|.||..... +-.+.++.+|.+.. .++|+.+...++.+...-.|+......+...+..|.||+....
T Consensus 110 n~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~~l~~a~~~~~~~~~~i~~sD~G~~y 181 (277)
T PHA02517 110 NQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLDALEQALWARGRPGGLIHHSDKGSQY 181 (277)
T ss_pred CCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHHHHHHHHHHHhcCCCcCcEeeccccccc
Confidence 367888988865443 34566666766655 5567888777777755544444444434333346779997754
No 37
>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=22.50 E-value=72 Score=29.28 Aligned_cols=28 Identities=36% Similarity=0.519 Sum_probs=21.1
Q ss_pred CCCCeeCCHHHHHHHHHHHhhhcCcEEEEcce
Q 035792 52 YVGMEFDSEDAAKTFYDAYARRMGFSTHVGPF 83 (856)
Q Consensus 52 ~vG~~F~S~eea~~fyn~YA~~~GF~vr~~~s 83 (856)
.+.+.|+|.|+|.. ||.++|....+...
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 78899998887543
No 38
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=21.11 E-value=2.9e+02 Score=30.36 Aligned_cols=72 Identities=8% Similarity=-0.034 Sum_probs=49.6
Q ss_pred ceEEecccccCCCCCCccccEEEEeeCCcEEEEEEEeecC-CchhhHHHHHHHHH-HhcCC---CCCeEEecCccHHH
Q 035792 269 DAVIFDTMYRPNQYQVPFAPFTGVNHHGQMVLFGCALLLD-ESEASFTWLFRTWL-SAMND---RPPVSITTDQDRAI 341 (856)
Q Consensus 269 dVl~~D~Ty~tnky~~pL~~~vgvn~~g~~~~~g~all~~-Et~es~~Wll~~f~-~~m~~---~~P~~iiTD~d~al 341 (856)
.+.+.|-||....-+.-++..+.+|.+.. .++|+++-.. .+.+...-+|+.-+ ...+. ..|..|.||+...-
T Consensus 127 ~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGsqy 203 (301)
T PRK09409 127 QRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSCY 203 (301)
T ss_pred CEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCccc
Confidence 68888989865544445778888888876 6789999875 56666666666433 33222 24678999986653
Done!