Query 035491
Match_columns 292
No_of_seqs 229 out of 1057
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 03:21:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035491.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035491hhsearch_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 7.9E-33 1.7E-37 272.8 15.8 211 2-219 348-604 (846)
2 PF00872 Transposase_mut: Tran 99.5 1.6E-15 3.4E-20 140.7 -0.8 124 2-135 228-353 (381)
3 PF10551 MULE: MULE transposas 99.1 3.9E-11 8.4E-16 89.0 3.2 37 2-38 57-93 (93)
4 COG3328 Transposase and inacti 98.7 3.8E-08 8.3E-13 90.4 8.6 122 4-137 209-334 (379)
5 smart00575 ZnF_PMZ plant mutat 98.7 1.2E-08 2.6E-13 58.0 1.9 25 194-218 1-25 (28)
6 PF04434 SWIM: SWIM zinc finge 97.7 2.2E-05 4.8E-10 48.5 1.7 26 192-217 13-38 (40)
7 PF01610 DDE_Tnp_ISL3: Transpo 96.4 0.0011 2.4E-08 57.9 0.6 40 3-42 58-97 (249)
8 PF06782 UPF0236: Uncharacteri 95.8 0.064 1.4E-06 51.5 9.7 117 4-137 261-383 (470)
9 smart00412 Cu_FIST Copper-Fist 60.3 4.6 0.0001 24.4 0.9 12 265-276 28-39 (39)
10 PF03461 TRCF: TRCF domain; I 60.0 19 0.00041 26.7 4.4 38 55-92 20-57 (101)
11 PF13610 DDE_Tnp_IS240: DDE do 59.3 12 0.00026 29.5 3.4 23 2-24 59-81 (140)
12 PF02178 AT_hook: AT hook moti 54.9 6.2 0.00013 18.0 0.6 8 270-277 2-9 (13)
13 PF00649 Copper-fist: Copper f 42.1 7 0.00015 23.8 -0.3 12 265-276 29-40 (40)
14 COG3464 Transposase and inacti 41.0 33 0.00071 32.4 3.7 33 3-35 206-238 (402)
15 smart00384 AT_hook DNA binding 37.6 20 0.00044 19.6 1.0 8 270-277 2-9 (26)
16 COG3316 Transposase and inacti 37.6 24 0.00052 30.1 2.0 25 2-26 127-151 (215)
17 COG5431 Uncharacterized metal- 34.9 14 0.00031 27.5 0.3 24 194-217 50-78 (117)
18 PF08358 Flexi_CP_N: Carlaviru 34.0 25 0.00055 22.8 1.3 17 272-288 25-41 (52)
19 KOG4844 Mitochondrial ribosoma 33.8 22 0.00048 25.8 1.0 18 268-285 82-100 (102)
20 PHA02687 ORF061 late transcrip 32.1 45 0.00097 27.7 2.7 21 254-277 72-92 (231)
21 COG4279 Uncharacterized conser 31.7 32 0.00069 30.0 1.9 21 194-217 125-145 (266)
22 PF08459 UvrC_HhH_N: UvrC Heli 25.3 56 0.0012 26.4 2.2 25 1-25 79-103 (155)
23 PF09248 DUF1965: Domain of un 24.7 22 0.00047 25.0 -0.3 10 282-291 17-26 (74)
24 PF03050 DDE_Tnp_IS66: Transpo 22.8 24 0.00053 30.9 -0.4 35 3-42 121-155 (271)
25 KOG4825 Component of synaptic 21.5 92 0.002 29.7 3.0 25 268-292 285-309 (666)
26 PF11460 DUF3007: Protein of u 20.9 1.1E+02 0.0025 22.8 2.9 22 231-252 82-103 (104)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=7.9e-33 Score=272.80 Aligned_cols=211 Identities=19% Similarity=0.254 Sum_probs=161.9
Q ss_pred CcEEEecccHHHHHHHHHhCccccchhHHHHHHHHHHHHhhhcccchHHHHHHHHHHH-HHhcCCCHHHHHHHHHHHHhh
Q 035491 2 HFLTLNNRDLALVNTIERVFPNAKHLLCRWHIKKNVIAKCKKLFTIKEIWEKFMMSWN-VLLLSSSEDEFITRLNALQQD 80 (292)
Q Consensus 2 P~viitD~~~al~~Ai~~vfP~a~~~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~~-~l~~a~t~~ef~~~~~~l~~~ 80 (292)
|.+||||+|.||.+||++|||++.|++|.|||.+|+.+++...+.. .+.|...|. +|..+.|++||+..|..|+++
T Consensus 348 P~tIiTDqd~am~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~~~---~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~k 424 (846)
T PLN03097 348 PKVIITDQDKAMKSVISEVFPNAHHCFFLWHILGKVSENLGQVIKQ---HENFMAKFEKCIYRSWTEEEFGKRWWKILDR 424 (846)
T ss_pred CceEEecCCHHHHHHHHHHCCCceehhhHHHHHHHHHHHhhHHhhh---hhHHHHHHHHHHhCCCCHHHHHHHHHHHHHh
Confidence 8999999999999999999999999999999999999999877643 357888886 678899999999999999999
Q ss_pred ccCchhhhHHHhhhhhhhhhhhhhhhhhccccccCCCcCchhhhhhHHhhhhhcchHHHHH--------------HHHHH
Q 035491 81 FISYPQTIEYVTSTWLDKYKENFVSAWTYKIMHFGNLTTNKVESLHSRLKKELGTSQELLH--------------TNIKV 146 (292)
Q Consensus 81 ~~~~p~~~~Y~~~~Wl~~~k~~w~~~~~~~~~~~g~~Ttnr~ES~n~~lK~~l~~~~~lq~--------------~~i~~ 146 (292)
|+... -+||..- ...|++||++|+++.|.+|+.||+|+||+|+.||+|+...++|.. .++++
T Consensus 425 y~L~~--n~WL~~L--Y~~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~a 500 (846)
T PLN03097 425 FELKE--DEWMQSL--YEDRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKA 500 (846)
T ss_pred hcccc--cHHHHHH--HHhHhhhhHHHhcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 86321 1234332 258999999999999999999999999999999999999885421 12333
Q ss_pred HHHhhhhhhcCccchhhhhhhhccccHHHHHHHHHHHHHhhhC--------C-------------------CC----CCC
Q 035491 147 SFEKSLTIVQHPFKLAEFKELRGFISITALQMVLTESKHANSI--------G-------------------ID----VSA 195 (292)
Q Consensus 147 ~~~~~~~~v~~~~~~~~~~~l~g~iS~~al~~~~~q~~~~~~~--------~-------------------~d----~~~ 195 (292)
+++............++.....+..|+.++.++.+|+..+... | .| ..+
T Consensus 501 D~~s~~~~P~l~t~~piEkQAs~iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~ 580 (846)
T PLN03097 501 DSDTWNKQPALKSPSPLEKSVSGVYTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVS 580 (846)
T ss_pred hhhcccCCcccccccHHHHHHHHHhHHHHHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEE
Confidence 3333221110001113444566777888888888887653210 0 01 258
Q ss_pred ccceeccccccchhhHhHHHHHhc
Q 035491 196 CGCTIRSTHGLPCAHEIAEYKKKR 219 (292)
Q Consensus 196 Csc~~~~~~GiPC~H~l~~~~~~~ 219 (292)
|+|..|+..||||+|+|+++...+
T Consensus 581 CsC~kFE~~GILCrHaLkVL~~~~ 604 (846)
T PLN03097 581 CICRLFEYKGYLCRHALVVLQMCQ 604 (846)
T ss_pred eeccCeecCccchhhHHHHHhhcC
Confidence 999999999999999999999854
No 2
>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=99.51 E-value=1.6e-15 Score=140.73 Aligned_cols=124 Identities=20% Similarity=0.323 Sum_probs=101.7
Q ss_pred CcEEEecccHHHHHHHHHhCccccchhHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhhc
Q 035491 2 HFLTLNNRDLALVNTIERVFPNAKHLLCRWHIKKNVIAKCKKLFTIKEIWEKFMMSWNVLLLSSSEDEFITRLNALQQDF 81 (292)
Q Consensus 2 P~viitD~~~al~~Ai~~vfP~a~~~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~~~l~~a~t~~ef~~~~~~l~~~~ 81 (292)
|..||+|..+||..||+++||++.++.|.+|+.+|+.+++.+ .+++.+..+++.++.+.+.+++...++.|.+.+
T Consensus 228 ~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~-----k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~ 302 (381)
T PF00872_consen 228 ILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPK-----KDRKEVKADLKAIYQAPDKEEAREALEEFAEKW 302 (381)
T ss_pred cceeeccccccccccccccccchhhhhheechhhhhcccccc-----ccchhhhhhccccccccccchhhhhhhhccccc
Confidence 678999999999999999999999999999999999998764 345678889999999999999999999999988
Q ss_pred c-CchhhhHHHhhhhhhhhhhhhhhhh-hccccccCCCcCchhhhhhHHhhhhhcc
Q 035491 82 I-SYPQTIEYVTSTWLDKYKENFVSAW-TYKIMHFGNLTTNKVESLHSRLKKELGT 135 (292)
Q Consensus 82 ~-~~p~~~~Y~~~~Wl~~~k~~w~~~~-~~~~~~~g~~Ttnr~ES~n~~lK~~l~~ 135 (292)
. .+|.+.++++++|-. .| .+| +....+--.+|||.+||+|+.||+....
T Consensus 303 ~~kyp~~~~~l~~~~~~----~~-tf~~fP~~~~~~i~TTN~iEsln~~irrr~~~ 353 (381)
T PF00872_consen 303 EKKYPKAAKSLEENWDE----LL-TFLDFPPEHRRSIRTTNAIESLNKEIRRRTKV 353 (381)
T ss_pred ccccchhhhhhhhcccc----cc-ceeeecchhccccchhhhccccccchhhhccc
Confidence 6 689999999988742 11 111 1111122468999999999999986543
No 3
>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=99.12 E-value=3.9e-11 Score=88.99 Aligned_cols=37 Identities=41% Similarity=0.753 Sum_probs=35.6
Q ss_pred CcEEEecccHHHHHHHHHhCccccchhHHHHHHHHHH
Q 035491 2 HFLTLNNRDLALVNTIERVFPNAKHLLCRWHIKKNVI 38 (292)
Q Consensus 2 P~viitD~~~al~~Ai~~vfP~a~~~lC~~Hi~~n~~ 38 (292)
|.+||||++.|+++||++|||++.|++|.||+.||++
T Consensus 57 p~~ii~D~~~~~~~Ai~~vfP~~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 57 PKVIISDFDKALINAIKEVFPDARHQLCLFHILRNIK 93 (93)
T ss_pred ceeeeccccHHHHHHHHHHCCCceEehhHHHHHHhhC
Confidence 8899999999999999999999999999999999973
No 4
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=98.73 E-value=3.8e-08 Score=90.45 Aligned_cols=122 Identities=18% Similarity=0.239 Sum_probs=97.2
Q ss_pred EEEecccHHHHHHHHHhCccccchhHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhhcc-
Q 035491 4 LTLNNRDLALVNTIERVFPNAKHLLCRWHIKKNVIAKCKKLFTIKEIWEKFMMSWNVLLLSSSEDEFITRLNALQQDFI- 82 (292)
Q Consensus 4 viitD~~~al~~Ai~~vfP~a~~~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~~~l~~a~t~~ef~~~~~~l~~~~~- 82 (292)
.+++|...++-+||..+||.+.++.|..|+.+|+.++... .+++.....+..+..+++.++....|..+.+.+.
T Consensus 209 l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~-----k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~ 283 (379)
T COG3328 209 LVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPR-----KDQDAVLSDLRSIYIAPDAEEALLALLAFSELWGK 283 (379)
T ss_pred EEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhh-----hhhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhh
Confidence 4677999999999999999999999999999999988764 4567788888889999999999999999988776
Q ss_pred CchhhhHHHhhhhhhhhhhhhhhhhhccccc---cCCCcCchhhhhhHHhhhhhcchH
Q 035491 83 SYPQTIEYVTSTWLDKYKENFVSAWTYKIMH---FGNLTTNKVESLHSRLKKELGTSQ 137 (292)
Q Consensus 83 ~~p~~~~Y~~~~Wl~~~k~~w~~~~~~~~~~---~g~~Ttnr~ES~n~~lK~~l~~~~ 137 (292)
.+|.....+.++|.. .+ ++..++. --..|||.+|++|..++.......
T Consensus 284 ~yP~i~~~~~~~~~~----~~---~F~~fp~~~r~~i~ttN~IE~~n~~ir~~~~~~~ 334 (379)
T COG3328 284 RYPAILKSWRNALEE----LL---PFFAFPSEIRKIIYTTNAIESLNKLIRRRTKVVG 334 (379)
T ss_pred hcchHHHHHHHHHHH----hc---ccccCcHHHHhHhhcchHHHHHHHHHHHHHhhhc
Confidence 589998888887753 11 0111111 126899999999998887655543
No 5
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.66 E-value=1.2e-08 Score=57.96 Aligned_cols=25 Identities=28% Similarity=0.675 Sum_probs=22.5
Q ss_pred CCccceeccccccchhhHhHHHHHh
Q 035491 194 SACGCTIRSTHGLPCAHEIAEYKKK 218 (292)
Q Consensus 194 ~~Csc~~~~~~GiPC~H~l~~~~~~ 218 (292)
.+|||+.|+..||||+|+|+++...
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~ 25 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHI 25 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHh
Confidence 3799999999999999999998754
No 6
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=97.68 E-value=2.2e-05 Score=48.50 Aligned_cols=26 Identities=27% Similarity=0.602 Sum_probs=23.5
Q ss_pred CCCCccceeccccccchhhHhHHHHH
Q 035491 192 DVSACGCTIRSTHGLPCAHEIAEYKK 217 (292)
Q Consensus 192 d~~~Csc~~~~~~GiPC~H~l~~~~~ 217 (292)
....|+|..|+..|.||+|++|+++.
T Consensus 13 ~~~~CsC~~~~~~~~~CkHi~av~~~ 38 (40)
T PF04434_consen 13 EQASCSCPYFQFRGGPCKHIVAVLLA 38 (40)
T ss_pred cccEeeCCCccccCCcchhHHHHHHh
Confidence 35799999999999999999999874
No 7
>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=96.37 E-value=0.0011 Score=57.92 Aligned_cols=40 Identities=20% Similarity=0.211 Sum_probs=36.9
Q ss_pred cEEEecccHHHHHHHHHhCccccchhHHHHHHHHHHHHhh
Q 035491 3 FLTLNNRDLALVNTIERVFPNAKHLLCRWHIKKNVIAKCK 42 (292)
Q Consensus 3 ~viitD~~~al~~Ai~~vfP~a~~~lC~~Hi~~n~~~~~~ 42 (292)
++|++|...+-..||++.||+|.+..-.|||.+++...+.
T Consensus 58 ~~V~~Dm~~~y~~~~~~~~P~A~iv~DrFHvvk~~~~al~ 97 (249)
T PF01610_consen 58 KVVSMDMSPPYRSAIREYFPNAQIVADRFHVVKLANRALD 97 (249)
T ss_pred EEEEcCCCccccccccccccccccccccchhhhhhhhcch
Confidence 6899999999999999999999999999999999877543
No 8
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=95.80 E-value=0.064 Score=51.46 Aligned_cols=117 Identities=17% Similarity=0.217 Sum_probs=75.6
Q ss_pred EEEecccHHHHHHHHHhCccccchhHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhhccC
Q 035491 4 LTLNNRDLALVNTIERVFPNAKHLLCRWHIKKNVIAKCKKLFTIKEIWEKFMMSWNVLLLSSSEDEFITRLNALQQDFIS 83 (292)
Q Consensus 4 viitD~~~al~~Ai~~vfP~a~~~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~~~l~~a~t~~ef~~~~~~l~~~~~~ 83 (292)
++..|+...+.++++ .||++.+.|..||+.+.+...++.. .+..+.+ +++ ....+..++...++.+......
T Consensus 261 iingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~---~~~~~~~---~~a-l~~~d~~~l~~~L~~~~~~~~~ 332 (470)
T PF06782_consen 261 IINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHD---PELKEKI---RKA-LKKGDKKKLETVLDTAESCAKD 332 (470)
T ss_pred EEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhC---hHHHHHH---HHH-HHhcCHHHHHHHHHHHHHhhhc
Confidence 567899999988776 9999999999999999998776532 1222222 222 2345566666666666543321
Q ss_pred ------chhhhHHHhhhhhhhhhhhhhhhhhccccccCCCcCchhhhhhHHhhhhhcchH
Q 035491 84 ------YPQTIEYVTSTWLDKYKENFVSAWTYKIMHFGNLTTNKVESLHSRLKKELGTSQ 137 (292)
Q Consensus 84 ------~p~~~~Y~~~~Wl~~~k~~w~~~~~~~~~~~g~~Ttnr~ES~n~~lK~~l~~~~ 137 (292)
...+..|+.++|=. . ..|... .|....+..||.|..+...++...
T Consensus 333 ~~~~~~i~~~~~Yl~~n~~~-i-----~~y~~~---~~~~g~g~ee~~~~~~s~RmK~rg 383 (470)
T PF06782_consen 333 EEERKKIRKLRKYLLNNWDG-I-----KPYRER---EGLRGIGAEESVSHVLSYRMKSRG 383 (470)
T ss_pred hHHHHHHHHHHHHHHHCHHH-h-----hhhhhc---cCCCccchhhhhhhHHHHHhcCCC
Confidence 23678899998842 1 112111 345556668999998877666653
No 9
>smart00412 Cu_FIST Copper-Fist. binds DNA only in present of copper or silver
Probab=60.30 E-value=4.6 Score=24.44 Aligned_cols=12 Identities=42% Similarity=0.739 Sum_probs=10.2
Q ss_pred CcccCCCCCCCC
Q 035491 265 PEAKKNTRGRPN 276 (292)
Q Consensus 265 pp~k~~~kGrPk 276 (292)
|...++.||||.
T Consensus 28 pL~~i~kkGRP~ 39 (39)
T smart00412 28 PLIPVRPRGRPS 39 (39)
T ss_pred cceeecCCCCCC
Confidence 677899999994
No 10
>PF03461 TRCF: TRCF domain; InterPro: IPR005118 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by the transcription-repair-coupling factor (TRCF) which releases RNAP and the truncated transcript.; GO: 0003684 damaged DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0006281 DNA repair; PDB: 2QSR_A 2EYQ_A.
Probab=59.97 E-value=19 Score=26.73 Aligned_cols=38 Identities=21% Similarity=0.279 Sum_probs=27.4
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHhhccCchhhhHHHh
Q 035491 55 MMSWNVLLLSSSEDEFITRLNALQQDFISYPQTIEYVT 92 (292)
Q Consensus 55 ~~~~~~l~~a~t~~ef~~~~~~l~~~~~~~p~~~~Y~~ 92 (292)
+..++.+..+.|+++.+...++|.+.|+..|.-++.+-
T Consensus 20 l~~Yrrl~~~~~~~el~~l~~El~DRFG~~P~ev~~L~ 57 (101)
T PF03461_consen 20 LELYRRLASAESEEELEDLREELIDRFGPLPEEVENLL 57 (101)
T ss_dssp HHHHHHHHC--SHHHHHHHHHHHHHHH-S--HHHHHHH
T ss_pred HHHHHHHhhCCCHHHHHHHHHHHHHHcCCCcHHHHHHH
Confidence 45677899999999999999999999998887665543
No 11
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=59.26 E-value=12 Score=29.46 Aligned_cols=23 Identities=13% Similarity=0.176 Sum_probs=21.8
Q ss_pred CcEEEecccHHHHHHHHHhCccc
Q 035491 2 HFLTLNNRDLALVNTIERVFPNA 24 (292)
Q Consensus 2 P~viitD~~~al~~Ai~~vfP~a 24 (292)
|.+|+||+..+...|+++++++.
T Consensus 59 p~~ivtDk~~aY~~A~~~l~~~~ 81 (140)
T PF13610_consen 59 PRVIVTDKLPAYPAAIKELNPEG 81 (140)
T ss_pred cceeecccCCccchhhhhccccc
Confidence 88999999999999999999984
No 12
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=54.90 E-value=6.2 Score=17.96 Aligned_cols=8 Identities=50% Similarity=1.016 Sum_probs=3.3
Q ss_pred CCCCCCCC
Q 035491 270 NTRGRPNS 277 (292)
Q Consensus 270 ~~kGrPk~ 277 (292)
+.+|||++
T Consensus 2 r~RGRP~k 9 (13)
T PF02178_consen 2 RKRGRPRK 9 (13)
T ss_dssp --SS--TT
T ss_pred CcCCCCcc
Confidence 46899986
No 13
>PF00649 Copper-fist: Copper fist DNA binding domain; InterPro: IPR001083 Some fungal transcription factors contain an N-terminal domain, the copper fist, which seems to be involved in copper-dependent DNA-binding [, ]. These proteins activate the transcription of the metallothionein gene in response to copper. Metallothionein maintains copper levels in yeast [, ]. The copper fist domain, which is similar in structure to metallothionein itself, undergoes a large conformational change on copper-binding that allows DNA-binding. The domain contains a conserved array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) and forms a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet []. Conserved residues form a basic patch that may be important for DNA binding. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0005507 copper ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1CO4_A.
Probab=42.12 E-value=7 Score=23.77 Aligned_cols=12 Identities=33% Similarity=0.672 Sum_probs=4.0
Q ss_pred CcccCCCCCCCC
Q 035491 265 PEAKKNTRGRPN 276 (292)
Q Consensus 265 pp~k~~~kGrPk 276 (292)
|...++.||||.
T Consensus 29 ~L~~v~~kGRP~ 40 (40)
T PF00649_consen 29 PLVEVRKKGRPV 40 (40)
T ss_dssp -EEEE-S-----
T ss_pred cceeecCCCCCC
Confidence 567899999994
No 14
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=41.04 E-value=33 Score=32.35 Aligned_cols=33 Identities=18% Similarity=0.233 Sum_probs=30.2
Q ss_pred cEEEecccHHHHHHHHHhCccccchhHHHHHHH
Q 035491 3 FLTLNNRDLALVNTIERVFPNAKHLLCRWHIKK 35 (292)
Q Consensus 3 ~viitD~~~al~~Ai~~vfP~a~~~lC~~Hi~~ 35 (292)
+.+..|...+..+++.+.||++.+..=.||+.+
T Consensus 206 ~~V~~D~~~~y~~~v~e~~pna~i~~d~fh~~~ 238 (402)
T COG3464 206 KSVSMDMFGPYASAVQELFPNALIIADRFHVVQ 238 (402)
T ss_pred eEEEccccHHHHHHHHHhCCChheeeeeeeeee
Confidence 468889999999999999999999999999876
No 15
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=37.60 E-value=20 Score=19.60 Aligned_cols=8 Identities=50% Similarity=1.016 Sum_probs=6.8
Q ss_pred CCCCCCCC
Q 035491 270 NTRGRPNS 277 (292)
Q Consensus 270 ~~kGrPk~ 277 (292)
+.+|||++
T Consensus 2 RkRGRPrK 9 (26)
T smart00384 2 RKRGRPRK 9 (26)
T ss_pred CCCCCCCC
Confidence 57899997
No 16
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.55 E-value=24 Score=30.11 Aligned_cols=25 Identities=4% Similarity=0.167 Sum_probs=22.5
Q ss_pred CcEEEecccHHHHHHHHHhCccccc
Q 035491 2 HFLTLNNRDLALVNTIERVFPNAKH 26 (292)
Q Consensus 2 P~viitD~~~al~~Ai~~vfP~a~~ 26 (292)
|.+|+||+......|+.++-++..|
T Consensus 127 p~v~vtDka~s~~~A~~~l~~~~eh 151 (215)
T COG3316 127 PRVFVTDKAPSYTAALRKLGSEVEH 151 (215)
T ss_pred CceEEecCccchHHHHHhcCcchhe
Confidence 8899999999999999999986654
No 17
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=34.94 E-value=14 Score=27.53 Aligned_cols=24 Identities=29% Similarity=0.422 Sum_probs=17.2
Q ss_pred CCccceecccc-----ccchhhHhHHHHH
Q 035491 194 SACGCTIRSTH-----GLPCAHEIAEYKK 217 (292)
Q Consensus 194 ~~Csc~~~~~~-----GiPC~H~l~~~~~ 217 (292)
.-|||.++... --||.|++..-..
T Consensus 50 gfCSCp~~~~svvl~Gk~~C~Hi~glk~A 78 (117)
T COG5431 50 GFCSCPDFLGSVVLKGKSPCAHIIGLKVA 78 (117)
T ss_pred CcccCHHHHhHhhhcCcccchhhhheeee
Confidence 47999988732 2479999975444
No 18
>PF08358 Flexi_CP_N: Carlavirus coat; InterPro: IPR013569 This domain is found together with the viral coat protein domain (IPR000052 from INTERPRO) in coat/capsid proteins of the plant infecting Carlavirus. It is required for genome encapsidation by forming ribonucleoprotein complexes along with TGB1 helicase and viral RNA. The N- and the C terminus of this coat protein can be exposed on the surface of the virus particle. The central core sequence may be important in maintaining correct tertiary structure of the coat protein and/or play a role in the interaction with the viral RNA. Coat proteins are often used to distinguish between Carlavirus isolates. In the coat protein amino acid sequences of definitive and tentative species of carlaviruses, there is a region of seven amino acids (GLGVPTE) that are conserved []. The complete coat protein (CP) sequences of 29 Indian Chrysanthemum virus B (CVB) isolates were highly heterogeneous, sharing nucleotide sequence identities of 74-98% [, ].
Probab=34.03 E-value=25 Score=22.81 Aligned_cols=17 Identities=35% Similarity=0.673 Sum_probs=13.8
Q ss_pred CCCCCCCCCCCcCCCCC
Q 035491 272 RGRPNSKANASTRHDPS 288 (292)
Q Consensus 272 kGrPk~~~~~stkr~ps 288 (292)
.|||+.+..-+.|+|||
T Consensus 25 ~GRP~l~~~~~mr~d~t 41 (52)
T PF08358_consen 25 IGRPKLEPSDDMRGDPT 41 (52)
T ss_pred cCCcCCcCchhhCCCcC
Confidence 39999877778888886
No 19
>KOG4844 consensus Mitochondrial ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=33.76 E-value=22 Score=25.80 Aligned_cols=18 Identities=22% Similarity=0.562 Sum_probs=12.2
Q ss_pred cCCCCCCCCC-CCCCCcCC
Q 035491 268 KKNTRGRPNS-KANASTRH 285 (292)
Q Consensus 268 k~~~kGrPk~-~~~~stkr 285 (292)
+.+.||+||+ ++.+..+|
T Consensus 82 kRrgKGapKk~kk~~aa~~ 100 (102)
T KOG4844|consen 82 KRRGKGAPKKGKKKRAAKR 100 (102)
T ss_pred HHccCCCCcccchhhhhhc
Confidence 6789999998 44444443
No 20
>PHA02687 ORF061 late transcription factor VLTF-4; Provisional
Probab=32.05 E-value=45 Score=27.67 Aligned_cols=21 Identities=19% Similarity=0.332 Sum_probs=12.5
Q ss_pred hcCCCCccccCCcccCCCCCCCCC
Q 035491 254 IANPQSTSLIEPEAKKNTRGRPNS 277 (292)
Q Consensus 254 ~~~~~~~~~~~pp~k~~~kGrPk~ 277 (292)
|+-|. ...+||+|.+ |-||++
T Consensus 72 lpvpe--~vp~~p~ktp-krr~~k 92 (231)
T PHA02687 72 LPVPE--SVPPAPVKTP-KRRTKK 92 (231)
T ss_pred CCCCC--CCCCCCcCCc-ccccch
Confidence 44455 3344565554 888877
No 21
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=31.69 E-value=32 Score=30.02 Aligned_cols=21 Identities=33% Similarity=0.719 Sum_probs=17.4
Q ss_pred CCccceeccccccchhhHhHHHHH
Q 035491 194 SACGCTIRSTHGLPCAHEIAEYKK 217 (292)
Q Consensus 194 ~~Csc~~~~~~GiPC~H~l~~~~~ 217 (292)
..|||. -+-.||.|+-|++..
T Consensus 125 ~dCSCP---D~anPCKHi~AvyY~ 145 (266)
T COG4279 125 TDCSCP---DYANPCKHIAAVYYL 145 (266)
T ss_pred cccCCC---CcccchHHHHHHHHH
Confidence 579996 456799999999886
No 22
>PF08459 UvrC_HhH_N: UvrC Helix-hairpin-helix N-terminal; InterPro: IPR001162 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. Proteins that contain the UvrC homology region 1, IPR000305 from INTERPRO, are listed below: Prokaryotic UvrC proteins. Bacteriophage T4 END2 protein. Small subunit of ribonucleotide reductase enzyme. T4 TEV1 protein. Endonuclease specific to the thymidylate synthase (td) gene splice junction. Found in putative intron-homing endonucleases encoded by group I introns of fungi and phage. Mycobacterium hypothetical protein Y002. Exonuclease by similarity. Bacillus subtilis hypothetical protein YURQ. ; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3C65_A 2NRZ_A 2NRR_A 2NRX_A 2NRV_A 2NRT_A 2NRW_A.
Probab=25.32 E-value=56 Score=26.44 Aligned_cols=25 Identities=16% Similarity=0.139 Sum_probs=20.4
Q ss_pred CCcEEEecccHHHHHHHHHhCcccc
Q 035491 1 MHFLTLNNRDLALVNTIERVFPNAK 25 (292)
Q Consensus 1 ~P~viitD~~~al~~Ai~~vfP~a~ 25 (292)
+|..|+.|+..+..+|+.+++-+..
T Consensus 79 lPDLilIDGG~gQl~aa~~~l~~lg 103 (155)
T PF08459_consen 79 LPDLILIDGGKGQLNAAKEVLKELG 103 (155)
T ss_dssp --SEEEESSSHHHHHHHHHHHHCTT
T ss_pred CCCEEEEcCCHHHHHHHHHHHHHcC
Confidence 5899999999999999999886554
No 23
>PF09248 DUF1965: Domain of unknown function (DUF1965); InterPro: IPR015328 Members of this family of fungal domains adopt a structure that consists of an alpha/beta motif. Their exact function has not, as yet, been determined []. ; PDB: 1N9E_A 1RKY_A 1W7C_A 3PGB_A.
Probab=24.69 E-value=22 Score=24.95 Aligned_cols=10 Identities=40% Similarity=0.640 Sum_probs=5.0
Q ss_pred CcCCCCCCCC
Q 035491 282 STRHDPSAFE 291 (292)
Q Consensus 282 stkr~ps~~e 291 (292)
-|.||||.|-
T Consensus 17 iTGrDpS~Wk 26 (74)
T PF09248_consen 17 ITGRDPSKWK 26 (74)
T ss_dssp --SS-GGG-E
T ss_pred eccCChHHcE
Confidence 4789999884
No 24
>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=22.81 E-value=24 Score=30.89 Aligned_cols=35 Identities=14% Similarity=0.274 Sum_probs=26.7
Q ss_pred cEEEecccHHHHHHHHHhCccccchhHHHHHHHHHHHHhh
Q 035491 3 FLTLNNRDLALVNTIERVFPNAKHLLCRWHIKKNVIAKCK 42 (292)
Q Consensus 3 ~viitD~~~al~~Ai~~vfP~a~~~lC~~Hi~~n~~~~~~ 42 (292)
-+++||+-.+-.. +.++.|+.|+-|+.+.+..-..
T Consensus 121 GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~ 155 (271)
T PF03050_consen 121 GILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAE 155 (271)
T ss_pred eeeeccccccccc-----cccccccccccccccccccccc
Confidence 4788888776643 3388999999999999876443
No 25
>KOG4825 consensus Component of synaptic membrane glycine-, glutamate- and thienylcyclohexylpiperidine-binding glycoprotein (43kDa) [Signal transduction mechanisms]
Probab=21.51 E-value=92 Score=29.74 Aligned_cols=25 Identities=28% Similarity=0.449 Sum_probs=18.5
Q ss_pred cCCCCCCCCCCCCCCcCCCCCCCCC
Q 035491 268 KKNTRGRPNSKANASTRHDPSAFEI 292 (292)
Q Consensus 268 k~~~kGrPk~~~~~stkr~ps~~e~ 292 (292)
..-++|||...-.-+|+|-||.||+
T Consensus 285 qleepgrenqfaepflqekpsswel 309 (666)
T KOG4825|consen 285 QLEEPGRENQFAEPFLQEKPSSWEL 309 (666)
T ss_pred cccCCCCccccccchhhcCCCccee
Confidence 4457777776456788999999984
No 26
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=20.87 E-value=1.1e+02 Score=22.85 Aligned_cols=22 Identities=14% Similarity=0.197 Sum_probs=18.2
Q ss_pred HHHHHhhcCChHHHHHHHHHHh
Q 035491 231 LIAKRFNENDDDAKLHILQKLT 252 (292)
Q Consensus 231 ~~~~~~~~~~~~~k~~~~~~l~ 252 (292)
.+++||.+++++.+..+..++.
T Consensus 82 ~lqkRle~l~~eE~~~L~~eie 103 (104)
T PF11460_consen 82 ELQKRLEELSPEELEALQAEIE 103 (104)
T ss_pred HHHHHHHhCCHHHHHHHHHHhc
Confidence 5789999999999888877654
Done!