Query 038926
Match_columns 153
No_of_seqs 123 out of 649
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 04:39:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038926.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038926hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 1.3E-27 2.7E-32 207.1 13.4 142 3-152 344-491 (846)
2 PF00872 Transposase_mut: Tran 99.6 7.3E-17 1.6E-21 130.9 -0.2 125 4-134 225-352 (381)
3 PF10551 MULE: MULE transposas 99.4 2.8E-13 6.1E-18 88.8 3.4 37 7-43 57-93 (93)
4 COG3328 Transposase and inacti 98.9 1.3E-08 2.8E-13 82.5 10.4 121 8-135 208-332 (379)
5 PF01610 DDE_Tnp_ISL3: Transpo 97.5 2.6E-05 5.7E-10 59.6 0.3 44 4-47 54-97 (249)
6 PF06782 UPF0236: Uncharacteri 96.7 0.0094 2E-07 50.1 8.2 86 9-102 261-352 (470)
7 PF03461 TRCF: TRCF domain; I 84.6 3.8 8.3E-05 27.0 5.4 39 60-98 20-58 (101)
8 PF13610 DDE_Tnp_IS240: DDE do 84.6 1.2 2.7E-05 31.0 3.2 25 5-29 57-81 (140)
9 PF00888 Cullin: Cullin family 59.4 51 0.0011 28.1 7.4 127 17-150 3-142 (588)
10 COG3316 Transposase and inacti 58.2 7.7 0.00017 29.4 2.0 27 5-31 125-151 (215)
11 PF03050 DDE_Tnp_IS66: Transpo 48.6 8 0.00017 29.7 0.8 38 6-48 119-156 (271)
12 PF13812 PPR_3: Pentatricopept 33.1 64 0.0014 15.5 3.1 29 122-152 1-29 (34)
13 PF08621 RPAP1_N: RPAP1-like, 32.6 1E+02 0.0022 17.6 3.9 30 68-99 13-42 (49)
14 COG1197 Mfd Transcription-repa 31.8 1.1E+02 0.0024 29.1 5.3 39 60-98 1015-1053(1139)
15 PF12762 DDE_Tnp_IS1595: ISXO2 30.7 48 0.001 22.9 2.4 22 114-135 108-129 (151)
16 TIGR00334 5S_RNA_mat_M5 ribonu 29.2 45 0.00097 24.5 2.0 29 5-33 47-78 (174)
17 PF15059 Speriolin_C: Sperioli 25.4 97 0.0021 22.0 3.1 29 19-49 11-39 (146)
18 PF09524 Phg_2220_C: Conserved 24.7 1.8E+02 0.004 18.1 5.6 32 66-97 28-59 (74)
19 PF03474 DMA: DMRTA motif; In 24.5 99 0.0021 16.8 2.3 21 127-147 18-38 (39)
20 PF09039 HTH_Tnp_Mu_2: Mu DNA 24.0 1.4E+02 0.003 20.0 3.5 29 122-150 32-61 (108)
21 COG3464 Transposase and inacti 23.6 41 0.00089 27.9 1.1 36 6-41 204-239 (402)
22 PF13891 zf-C3Hc3H: Potential 21.6 35 0.00075 20.5 0.2 19 24-44 12-30 (65)
23 cd03568 VHS_STAM VHS domain fa 21.5 2.8E+02 0.0061 19.4 4.9 43 27-69 49-91 (144)
24 COG3947 Response regulator con 21.3 75 0.0016 25.7 2.0 24 7-30 1-24 (361)
25 PF04937 DUF659: Protein of un 20.7 85 0.0018 22.3 2.1 40 9-48 96-138 (153)
26 PF03564 DUF1759: Protein of u 20.2 2.9E+02 0.0063 18.7 5.7 18 71-88 52-69 (145)
27 PF00665 rve: Integrase core d 20.0 75 0.0016 20.4 1.7 15 7-21 68-82 (120)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=99.95 E-value=1.3e-27 Score=207.09 Aligned_cols=142 Identities=21% Similarity=0.359 Sum_probs=123.1
Q ss_pred CCCCCcEEEeeccHHHHHHHHhhCccccchhhHHHHhhhhHhhhcccccchhHHHHHHHHHHHHh-hcCCHHHHHHHHHH
Q 038926 3 ENMLASVIVTDRELALMKVIQKIFPSATTFLCRWHISRNVLANCKNLFETNEIWQTFISSWNLLV-LSASEEEFAQRLKG 81 (153)
Q Consensus 3 ~~~~P~~i~TD~d~a~~~Ai~~vFP~~~~~lC~wHi~~n~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~t~~~f~~~~~~ 81 (153)
+|+.|++|+||+|.||.+||+.|||+|.|++|.|||++|+.++++..+.. .+.|...|..++ .+.|++||+.+|..
T Consensus 344 ~gk~P~tIiTDqd~am~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~~~---~~~f~~~f~~cv~~s~t~eEFE~~W~~ 420 (846)
T PLN03097 344 GGQAPKVIITDQDKAMKSVISEVFPNAHHCFFLWHILGKVSENLGQVIKQ---HENFMAKFEKCIYRSWTEEEFGKRWWK 420 (846)
T ss_pred CCCCCceEEecCCHHHHHHHHHHCCCceehhhHHHHHHHHHHHhhHHhhh---hhHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence 57899999999999999999999999999999999999999999887653 356778887755 67799999999999
Q ss_pred HHHhccCchHHHHHHHHhhchhhhHHHHHHHhccCCCcch-----hhhhHHHHHhhhhcCCCcHHHHHHHHHhhhc
Q 038926 82 METDFSKYPIVLTYIRNVWLDKCKEKFVSAWTNSVMHFRN-----VESSHSKLKKQLRTSRGTFESSWTKIHTFLE 152 (153)
Q Consensus 82 ~~~~~~~~~~~~~Y~~~~W~~p~~e~w~~~~~~~~~~~~n-----~Es~~~~lK~~l~~~~~~l~~~~~~~~~~l~ 152 (153)
|.++|+. .-..||..-| ..+++||++|.+..+..|. +||+|+.||+|+.. ..+|..|++++..+|+
T Consensus 421 mi~ky~L--~~n~WL~~LY--~~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~-~tsL~~Fv~qye~~l~ 491 (846)
T PLN03097 421 ILDRFEL--KEDEWMQSLY--EDRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHK-KTTVQEFVKQYETILQ 491 (846)
T ss_pred HHHhhcc--cccHHHHHHH--HhHhhhhHHHhcccccCCcccccccccHHHHHHHHhCc-CCCHHHHHHHHHHHHH
Confidence 9999973 2234666666 3799999999998876555 99999999999976 7899999999999875
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=99.61 E-value=7.3e-17 Score=130.90 Aligned_cols=125 Identities=18% Similarity=0.302 Sum_probs=104.4
Q ss_pred CCCCcEEEeeccHHHHHHHHhhCccccchhhHHHHhhhhHhhhcccccchhHHHHHHHHHHHHhhcCCHHHHHHHHHHHH
Q 038926 4 NMLASVIVTDRELALMKVIQKIFPSATTFLCRWHISRNVLANCKNLFETNEIWQTFISSWNLLVLSASEEEFAQRLKGME 83 (153)
Q Consensus 4 ~~~P~~i~TD~d~a~~~Ai~~vFP~~~~~lC~wHi~~n~~~~~~~~~~~~~~~~~~~~~~~~l~~~~t~~~f~~~~~~~~ 83 (153)
-..|..|++|..+++..||+++||++.++.|.+|.++|+.+++.+ ...+.+.+.++.+..+++.++....+++|.
T Consensus 225 l~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~-----k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~ 299 (381)
T PF00872_consen 225 LKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPK-----KDRKEVKADLKAIYQAPDKEEAREALEEFA 299 (381)
T ss_pred ccccceeeccccccccccccccccchhhhhheechhhhhcccccc-----ccchhhhhhccccccccccchhhhhhhhcc
Confidence 346999999999999999999999999999999999999999865 355677888999999999999999999999
Q ss_pred Hhcc-CchHHHHHHHHhhchhhhHHH-HHHHhccCCCcch-hhhhHHHHHhhhh
Q 038926 84 TDFS-KYPIVLTYIRNVWLDKCKEKF-VSAWTNSVMHFRN-VESSHSKLKKQLR 134 (153)
Q Consensus 84 ~~~~-~~~~~~~Y~~~~W~~p~~e~w-~~~~~~~~~~~~n-~Es~~~~lK~~l~ 134 (153)
+++. +||.+.++++++|.. .-..+ .+.-....++++| +||+|+.+|+...
T Consensus 300 ~~~~~kyp~~~~~l~~~~~~-~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~ 352 (381)
T PF00872_consen 300 EKWEKKYPKAAKSLEENWDE-LLTFLDFPPEHRRSIRTTNAIESLNKEIRRRTK 352 (381)
T ss_pred cccccccchhhhhhhhcccc-ccceeeecchhccccchhhhccccccchhhhcc
Confidence 9987 699999999999863 21111 1112234678888 9999999999765
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=99.38 E-value=2.8e-13 Score=88.83 Aligned_cols=37 Identities=41% Similarity=0.746 Sum_probs=35.9
Q ss_pred CcEEEeeccHHHHHHHHhhCccccchhhHHHHhhhhH
Q 038926 7 ASVIVTDRELALMKVIQKIFPSATTFLCRWHISRNVL 43 (153)
Q Consensus 7 P~~i~TD~d~a~~~Ai~~vFP~~~~~lC~wHi~~n~~ 43 (153)
|++||||++.|+++||+++||++.|++|.||+.||+.
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 9999999999999999999999999999999999974
No 4
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=98.91 E-value=1.3e-08 Score=82.50 Aligned_cols=121 Identities=21% Similarity=0.332 Sum_probs=98.9
Q ss_pred cEEEeeccHHHHHHHHhhCccccchhhHHHHhhhhHhhhcccccchhHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHhcc
Q 038926 8 SVIVTDRELALMKVIQKIFPSATTFLCRWHISRNVLANCKNLFETNEIWQTFISSWNLLVLSASEEEFAQRLKGMETDFS 87 (153)
Q Consensus 8 ~~i~TD~d~a~~~Ai~~vFP~~~~~lC~wHi~~n~~~~~~~~~~~~~~~~~~~~~~~~l~~~~t~~~f~~~~~~~~~~~~ 87 (153)
..+++|.-.++-+||.++||.+.++.|+.|+.+|+.++... .+.+.....++.+..+++.++...+|..+.+.+.
T Consensus 208 ~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~-----k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~ 282 (379)
T COG3328 208 LLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPR-----KDQDAVLSDLRSIYIAPDAEEALLALLAFSELWG 282 (379)
T ss_pred eEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhh-----hhhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhh
Confidence 45678999999999999999999999999999999999865 3566777888889999999999999999988886
Q ss_pred -CchHHHHHHHHhhchhhhH--HHHHHHhccCCCcch-hhhhHHHHHhhhhc
Q 038926 88 -KYPIVLTYIRNVWLDKCKE--KFVSAWTNSVMHFRN-VESSHSKLKKQLRT 135 (153)
Q Consensus 88 -~~~~~~~Y~~~~W~~p~~e--~w~~~~~~~~~~~~n-~Es~~~~lK~~l~~ 135 (153)
.+|.+...+.++|.. ... .+...|. .+.+++| +|++|..+++.+..
T Consensus 283 ~~yP~i~~~~~~~~~~-~~~F~~fp~~~r-~~i~ttN~IE~~n~~ir~~~~~ 332 (379)
T COG3328 283 KRYPAILKSWRNALEE-LLPFFAFPSEIR-KIIYTTNAIESLNKLIRRRTKV 332 (379)
T ss_pred hhcchHHHHHHHHHHH-hcccccCcHHHH-hHhhcchHHHHHHHHHHHHHhh
Confidence 699999999998863 110 1122222 5677888 99999998877664
No 5
>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=97.49 E-value=2.6e-05 Score=59.56 Aligned_cols=44 Identities=18% Similarity=0.237 Sum_probs=40.1
Q ss_pred CCCCcEEEeeccHHHHHHHHhhCccccchhhHHHHhhhhHhhhc
Q 038926 4 NMLASVIVTDRELALMKVIQKIFPSATTFLCRWHISRNVLANCK 47 (153)
Q Consensus 4 ~~~P~~i~TD~d~a~~~Ai~~vFP~~~~~lC~wHi~~n~~~~~~ 47 (153)
....++|.+|...+-..|+++.||+|.+..-.|||+|++.+.+.
T Consensus 54 ~~~v~~V~~Dm~~~y~~~~~~~~P~A~iv~DrFHvvk~~~~al~ 97 (249)
T PF01610_consen 54 RKNVKVVSMDMSPPYRSAIREYFPNAQIVADRFHVVKLANRALD 97 (249)
T ss_pred ccceEEEEcCCCccccccccccccccccccccchhhhhhhhcch
Confidence 45688999999999999999999999999999999999887544
No 6
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=96.71 E-value=0.0094 Score=50.08 Aligned_cols=86 Identities=20% Similarity=0.289 Sum_probs=55.8
Q ss_pred EEEeeccHHHHHHHHhhCccccchhhHHHHhhhhHhhhcccccchhHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHhcc-
Q 038926 9 VIVTDRELALMKVIQKIFPSATTFLCRWHISRNVLANCKNLFETNEIWQTFISSWNLLVLSASEEEFAQRLKGMETDFS- 87 (153)
Q Consensus 9 ~i~TD~d~a~~~Ai~~vFP~~~~~lC~wHi~~n~~~~~~~~~~~~~~~~~~~~~~~~l~~~~t~~~f~~~~~~~~~~~~- 87 (153)
++..|...-+.+++. .||++.+.|..||+.|.+.+.++.. .+..+.+. +.+ .......++..++.+.....
T Consensus 261 iingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~---~~~~~~~~---~al-~~~d~~~l~~~L~~~~~~~~~ 332 (470)
T PF06782_consen 261 IINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHD---PELKEKIR---KAL-KKGDKKKLETVLDTAESCAKD 332 (470)
T ss_pred EEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhC---hHHHHHHH---HHH-HhcCHHHHHHHHHHHHHhhhc
Confidence 456777777777766 9999999999999999999887642 22222222 222 23345555555555544332
Q ss_pred -----CchHHHHHHHHhhch
Q 038926 88 -----KYPIVLTYIRNVWLD 102 (153)
Q Consensus 88 -----~~~~~~~Y~~~~W~~ 102 (153)
....+..||.+||-.
T Consensus 333 ~~~~~~i~~~~~Yl~~n~~~ 352 (470)
T PF06782_consen 333 EEERKKIRKLRKYLLNNWDG 352 (470)
T ss_pred hHHHHHHHHHHHHHHHCHHH
Confidence 123678899999863
No 7
>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=84.56 E-value=3.8 Score=27.01 Aligned_cols=39 Identities=18% Similarity=0.254 Sum_probs=28.7
Q ss_pred HHHHHHHhhcCCHHHHHHHHHHHHHhccCchHHHHHHHH
Q 038926 60 ISSWNLLVLSASEEEFAQRLKGMETDFSKYPIVLTYIRN 98 (153)
Q Consensus 60 ~~~~~~l~~~~t~~~f~~~~~~~~~~~~~~~~~~~Y~~~ 98 (153)
+..++.+..+.|.++.+.-.+++.++|+..|.-+..+-.
T Consensus 20 l~~Yrrl~~~~~~~el~~l~~El~DRFG~~P~ev~~L~~ 58 (101)
T PF03461_consen 20 LELYRRLASAESEEELEDLREELIDRFGPLPEEVENLLE 58 (101)
T ss_dssp HHHHHHHHC--SHHHHHHHHHHHHHHH-S--HHHHHHHH
T ss_pred HHHHHHHhhCCCHHHHHHHHHHHHHHcCCCcHHHHHHHH
Confidence 577889999999999999999999999987776665543
No 8
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=84.55 E-value=1.2 Score=30.98 Aligned_cols=25 Identities=32% Similarity=0.319 Sum_probs=23.5
Q ss_pred CCCcEEEeeccHHHHHHHHhhCccc
Q 038926 5 MLASVIVTDRELALMKVIQKIFPSA 29 (153)
Q Consensus 5 ~~P~~i~TD~d~a~~~Ai~~vFP~~ 29 (153)
..|.+|+||+-.+-..|++.++|+.
T Consensus 57 ~~p~~ivtDk~~aY~~A~~~l~~~~ 81 (140)
T PF13610_consen 57 GEPRVIVTDKLPAYPAAIKELNPEG 81 (140)
T ss_pred cccceeecccCCccchhhhhccccc
Confidence 6899999999999999999999984
No 9
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=59.39 E-value=51 Score=28.11 Aligned_cols=127 Identities=13% Similarity=0.243 Sum_probs=67.6
Q ss_pred HHHHHHHhhCccccchhhHHHHhhhhHhhhcccccch--hHHHHHH-HHHHHHh-------hcCCHHHHHHHHHHHHHhc
Q 038926 17 ALMKVIQKIFPSATTFLCRWHISRNVLANCKNLFETN--EIWQTFI-SSWNLLV-------LSASEEEFAQRLKGMETDF 86 (153)
Q Consensus 17 a~~~Ai~~vFP~~~~~lC~wHi~~n~~~~~~~~~~~~--~~~~~~~-~~~~~l~-------~~~t~~~f~~~~~~~~~~~ 86 (153)
.+..||..+|.+.....+.-++.+.|..-+....+.. +..++++ .....+. ....-+.|...|..+....
T Consensus 3 ~l~~~i~~i~~~~~~~~~~~~lY~~vy~l~~~~~~~~LY~~l~~~i~~~~~~~~~~l~~~~~~~~l~~~~~~w~~~~~~~ 82 (588)
T PF00888_consen 3 ILEEAIDQIFKKSISKLSYMELYTCVYNLCDNKYGEQLYDKLKEFISEYLKNIIESLLSSSDEDLLEEYVQEWEKYKKAI 82 (588)
T ss_dssp HHHHHHHHHHTT-GCCSHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTCHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCChhHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHHhcChhHHHHHHHHHHHHHHHHH
Confidence 3677899999888888888888888876544332210 1112111 1122221 1123345667777766655
Q ss_pred cCchHHHHHHHHhhchhhhHHHHHHHhccCCCc-ch--hhhhHHHHHhhhhcCCCcHHHHHHHHHhh
Q 038926 87 SKYPIVLTYIRNVWLDKCKEKFVSAWTNSVMHF-RN--VESSHSKLKKQLRTSRGTFESSWTKIHTF 150 (153)
Q Consensus 87 ~~~~~~~~Y~~~~W~~p~~e~w~~~~~~~~~~~-~n--~Es~~~~lK~~l~~~~~~l~~~~~~~~~~ 150 (153)
.--..+..|+.+.|+.+. .|...+... .. ...+-..+++.-.+...+ ..+++.+-.+
T Consensus 83 ~~i~~if~yLdr~yv~~~------~f~~~v~~~~~~~i~~~ll~~I~~~R~g~~~~-~~~l~~~~~~ 142 (588)
T PF00888_consen 83 KYISDIFSYLDRNYVKRN------LFREQVFKPLKDKIINALLNLIKNEREGEKID-RSLLKNVIEM 142 (588)
T ss_dssp HHHHHHTHHHHHTSTTTT------HHHHHTTTSHHHHHHHHHHHHHHHHHTTTTSH-HHHHHHHHHH
T ss_pred HHHHHHHHHHhHhhhhhh------hHHHHHHHHHHHHHHHHHHHHHHHHhcCCccc-HHHHHHHHHH
Confidence 434578899999998522 555544322 11 555555555443332223 4444444443
No 10
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=58.23 E-value=7.7 Score=29.39 Aligned_cols=27 Identities=19% Similarity=0.185 Sum_probs=24.2
Q ss_pred CCCcEEEeeccHHHHHHHHhhCccccc
Q 038926 5 MLASVIVTDRELALMKVIQKIFPSATT 31 (153)
Q Consensus 5 ~~P~~i~TD~d~a~~~Ai~~vFP~~~~ 31 (153)
..|.+|+||+..+...|++.+-++..|
T Consensus 125 g~p~v~vtDka~s~~~A~~~l~~~~eh 151 (215)
T COG3316 125 GEPRVFVTDKAPSYTAALRKLGSEVEH 151 (215)
T ss_pred CCCceEEecCccchHHHHHhcCcchhe
Confidence 579999999999999999999996655
No 11
>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=48.65 E-value=8 Score=29.75 Aligned_cols=38 Identities=24% Similarity=0.391 Sum_probs=28.9
Q ss_pred CCcEEEeeccHHHHHHHHhhCccccchhhHHHHhhhhHhhhcc
Q 038926 6 LASVIVTDRELALMKVIQKIFPSATTFLCRWHISRNVLANCKN 48 (153)
Q Consensus 6 ~P~~i~TD~d~a~~~Ai~~vFP~~~~~lC~wHi~~n~~~~~~~ 48 (153)
.+.+++||+-.+=.. +.+..|+.|+-|+.|.+..-...
T Consensus 119 ~~GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 119 FSGILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred cceeeeccccccccc-----ccccccccccccccccccccccc
Confidence 456888998877544 23889999999999888865543
No 12
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=33.09 E-value=64 Score=15.51 Aligned_cols=29 Identities=14% Similarity=0.219 Sum_probs=20.6
Q ss_pred hhhhHHHHHhhhhcCCCcHHHHHHHHHhhhc
Q 038926 122 VESSHSKLKKQLRTSRGTFESSWTKIHTFLE 152 (153)
Q Consensus 122 ~Es~~~~lK~~l~~~~~~l~~~~~~~~~~l~ 152 (153)
++++|..++-+... ++....++-+++|.+
T Consensus 1 v~ty~~ll~a~~~~--g~~~~a~~~~~~M~~ 29 (34)
T PF13812_consen 1 VHTYNALLRACAKA--GDPDAALQLFDEMKE 29 (34)
T ss_pred CcHHHHHHHHHHHC--CCHHHHHHHHHHHHH
Confidence 35677788888764 677777777777754
No 13
>PF08621 RPAP1_N: RPAP1-like, N-terminal; InterPro: IPR013930 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.
Probab=32.65 E-value=1e+02 Score=17.60 Aligned_cols=30 Identities=17% Similarity=0.366 Sum_probs=24.3
Q ss_pred hcCCHHHHHHHHHHHHHhccCchHHHHHHHHh
Q 038926 68 LSASEEEFAQRLKGMETDFSKYPIVLTYIRNV 99 (153)
Q Consensus 68 ~~~t~~~f~~~~~~~~~~~~~~~~~~~Y~~~~ 99 (153)
..=|+++.+..-.++.+.++ |.+++.|.+.
T Consensus 13 ~~MS~eEI~~er~eL~~~Ld--P~li~~L~~R 42 (49)
T PF08621_consen 13 ASMSPEEIEEEREELLESLD--PKLIEFLKKR 42 (49)
T ss_pred HhCCHHHHHHHHHHHHHhCC--HHHHHHHHHh
Confidence 34578898998899999886 8999988764
No 14
>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]
Probab=31.78 E-value=1.1e+02 Score=29.09 Aligned_cols=39 Identities=18% Similarity=0.260 Sum_probs=35.0
Q ss_pred HHHHHHHhhcCCHHHHHHHHHHHHHhccCchHHHHHHHH
Q 038926 60 ISSWNLLVLSASEEEFAQRLKGMETDFSKYPIVLTYIRN 98 (153)
Q Consensus 60 ~~~~~~l~~~~t~~~f~~~~~~~~~~~~~~~~~~~Y~~~ 98 (153)
+..++++..+.|+++.++--+++.++|+..|.-+.++-+
T Consensus 1015 l~~YkRi~~~~s~~el~~i~~EliDRFG~lP~ev~~Ll~ 1053 (1139)
T COG1197 1015 LELYKRLANAESEEELEEIKEELIDRFGPLPDEVKNLLD 1053 (1139)
T ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHhcCCCCHHHHHHHH
Confidence 577889999999999999999999999999988887765
No 15
>PF12762 DDE_Tnp_IS1595: ISXO2-like transposase domain; InterPro: IPR024445 This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.
Probab=30.68 E-value=48 Score=22.88 Aligned_cols=22 Identities=32% Similarity=0.371 Sum_probs=17.4
Q ss_pred ccCCCcchhhhhHHHHHhhhhc
Q 038926 114 NSVMHFRNVESSHSKLKKQLRT 135 (153)
Q Consensus 114 ~~~~~~~n~Es~~~~lK~~l~~ 135 (153)
+...|+..+|++++.+|+.+.+
T Consensus 108 ~~~~h~n~ie~~~s~~K~~l~g 129 (151)
T PF12762_consen 108 DGGVHTNWIESFWSRLKRWLKG 129 (151)
T ss_pred ccccccchhhhHHHHHHHHhhh
Confidence 3445666699999999999974
No 16
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=29.16 E-value=45 Score=24.46 Aligned_cols=29 Identities=21% Similarity=0.389 Sum_probs=23.7
Q ss_pred CCCcEEEeeccHH---HHHHHHhhCccccchh
Q 038926 5 MLASVIVTDRELA---LMKVIQKIFPSATTFL 33 (153)
Q Consensus 5 ~~P~~i~TD~d~a---~~~Ai~~vFP~~~~~l 33 (153)
...-.|+||-|.+ +++-|...+|++.|.+
T Consensus 47 ~rgVIIfTDpD~~GekIRk~i~~~vp~~khaf 78 (174)
T TIGR00334 47 KQGVIILTDPDFPGEKIRKKIEQHLPGYENCF 78 (174)
T ss_pred cCCEEEEeCCCCchHHHHHHHHHHCCCCeEEe
Confidence 3566799999976 7889999999999943
No 17
>PF15059 Speriolin_C: Speriolin C-terminus
Probab=25.44 E-value=97 Score=21.98 Aligned_cols=29 Identities=21% Similarity=0.383 Sum_probs=23.0
Q ss_pred HHHHHhhCccccchhhHHHHhhhhHhhhccc
Q 038926 19 MKVIQKIFPSATTFLCRWHISRNVLANCKNL 49 (153)
Q Consensus 19 ~~Ai~~vFP~~~~~lC~wHi~~n~~~~~~~~ 49 (153)
+..+..|||+ ..++--|++. |+.+++.+.
T Consensus 11 rrIL~~iFp~-~~rlyGft~s-NipeKi~Q~ 39 (146)
T PF15059_consen 11 RRILSYIFPG-RRRLYGFTVS-NIPEKIIQA 39 (146)
T ss_pred HHHHHHhccc-ceeeeccccc-ccHHHHHhh
Confidence 3568899999 7778888887 888887654
No 18
>PF09524 Phg_2220_C: Conserved phage C-terminus (Phg_2220_C); InterPro: IPR011741 This entry is represented by the C-terminal domain of Bacteriophage r1t, Orf11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
Probab=24.68 E-value=1.8e+02 Score=18.08 Aligned_cols=32 Identities=19% Similarity=0.330 Sum_probs=22.7
Q ss_pred HhhcCCHHHHHHHHHHHHHhccCchHHHHHHH
Q 038926 66 LVLSASEEEFAQRLKGMETDFSKYPIVLTYIR 97 (153)
Q Consensus 66 l~~~~t~~~f~~~~~~~~~~~~~~~~~~~Y~~ 97 (153)
+-...|.++|....+.....+...+....|++
T Consensus 28 l~eG~t~edf~~VID~k~~~W~~~~~m~~YLR 59 (74)
T PF09524_consen 28 LNEGYTLEDFKKVIDNKVAEWKGDPKMEKYLR 59 (74)
T ss_pred HHCCCCHHHHHHHHHHHHHHHCCCHHHHHhcC
Confidence 44677899988877777777765566666655
No 19
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=24.47 E-value=99 Score=16.84 Aligned_cols=21 Identities=19% Similarity=0.226 Sum_probs=15.3
Q ss_pred HHHHhhhhcCCCcHHHHHHHH
Q 038926 127 SKLKKQLRTSRGTFESSWTKI 147 (153)
Q Consensus 127 ~~lK~~l~~~~~~l~~~~~~~ 147 (153)
+.|...|++.+||+...++++
T Consensus 18 ~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 18 SVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred HHHHHHHHHcCCcHHHHHHHh
Confidence 456667777888888777764
No 20
>PF09039 HTH_Tnp_Mu_2: Mu DNA binding, I gamma subdomain; InterPro: IPR015126 This domain is responsible for binding the DNA attachment sites at each end of the Mu genome. They adopt a secondary structure comprising a four helix bundle tightly packed around a hydrophobic core consisting of aliphatic and aromatic amino acid residues. Helices 1 and 2 are oriented antiparallel to each other. Helix 3 crosses helices 1 and 2 at angles of 60 and 120 degrees, respectively. Excluding the C-terminal helix 4, the fold of the I-gamma subdomain is remarkably similar to that of the homeodomain family of helix-turn-helix DNA-binding proteins, although their amino acid sequences are completely unrelated []. ; PDB: 2EZL_A 2EZH_A 2EZI_A 2EZK_A.
Probab=23.99 E-value=1.4e+02 Score=19.99 Aligned_cols=29 Identities=17% Similarity=0.337 Sum_probs=20.5
Q ss_pred hhhhHHHHHh-hhhcCCCcHHHHHHHHHhh
Q 038926 122 VESSHSKLKK-QLRTSRGTFESSWTKIHTF 150 (153)
Q Consensus 122 ~Es~~~~lK~-~l~~~~~~l~~~~~~~~~~ 150 (153)
.|.+...||. ||...+.+|-.|.+++..+
T Consensus 32 ~~eaw~~fksdYLr~e~Ps~~~cyrr~~~~ 61 (108)
T PF09039_consen 32 DEEAWEFFKSDYLRPEKPSFSACYRRLKRA 61 (108)
T ss_dssp -HHHHHHHHHHHTSTT---HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHcCccCCCHHHHHHHHHHH
Confidence 6777788885 8888889999999988765
No 21
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.61 E-value=41 Score=27.86 Aligned_cols=36 Identities=19% Similarity=0.302 Sum_probs=33.0
Q ss_pred CCcEEEeeccHHHHHHHHhhCccccchhhHHHHhhh
Q 038926 6 LASVIVTDRELALMKVIQKIFPSATTFLCRWHISRN 41 (153)
Q Consensus 6 ~P~~i~TD~d~a~~~Ai~~vFP~~~~~lC~wHi~~n 41 (153)
+-+.+..|-..+-.+++++.||++.+..=.||+.+.
T Consensus 204 ~v~~V~~D~~~~y~~~v~e~~pna~i~~d~fh~~~~ 239 (402)
T COG3464 204 QVKSVSMDMFGPYASAVQELFPNALIIADRFHVVQY 239 (402)
T ss_pred ceeEEEccccHHHHHHHHHhCCChheeeeeeeeeee
Confidence 567899999999999999999999999999999873
No 22
>PF13891 zf-C3Hc3H: Potential DNA-binding domain
Probab=21.59 E-value=35 Score=20.53 Aligned_cols=19 Identities=21% Similarity=0.368 Sum_probs=13.2
Q ss_pred hhCccccchhhHHHHhhhhHh
Q 038926 24 KIFPSATTFLCRWHISRNVLA 44 (153)
Q Consensus 24 ~vFP~~~~~lC~wHi~~n~~~ 44 (153)
...|.+.+ |+.||+.+-..
T Consensus 12 ~~lp~~~y--C~~HIl~D~~Q 30 (65)
T PF13891_consen 12 PALPGSKY--CIRHILEDPNQ 30 (65)
T ss_pred ccCchhhH--HHHHhccCCCC
Confidence 35666766 99999865443
No 23
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=21.50 E-value=2.8e+02 Score=19.37 Aligned_cols=43 Identities=14% Similarity=0.182 Sum_probs=21.2
Q ss_pred ccccchhhHHHHhhhhHhhhcccccchhHHHHHHHHHHHHhhc
Q 038926 27 PSATTFLCRWHISRNVLANCKNLFETNEIWQTFISSWNLLVLS 69 (153)
Q Consensus 27 P~~~~~lC~wHi~~n~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 69 (153)
++...++=-..+...+.++|+..|...-.-++|++.+..++..
T Consensus 49 ~n~~v~l~AL~LLe~~vkNCG~~fh~evask~Fl~eL~kl~~~ 91 (144)
T cd03568 49 KDPNVQLRALTLLDACAENCGKRFHQEVASRDFTQELKKLIND 91 (144)
T ss_pred CCHHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHhcc
Confidence 3444444455555666666665543222234455555555544
No 24
>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]
Probab=21.26 E-value=75 Score=25.67 Aligned_cols=24 Identities=25% Similarity=0.512 Sum_probs=19.8
Q ss_pred CcEEEeeccHHHHHHHHhhCcccc
Q 038926 7 ASVIVTDRELALMKVIQKIFPSAT 30 (153)
Q Consensus 7 P~~i~TD~d~a~~~Ai~~vFP~~~ 30 (153)
|++|+.|.|.|+.+-|..+...+.
T Consensus 1 ~~~iiVDdd~a~~~~l~~iLs~~~ 24 (361)
T COG3947 1 PRIIIVDDDAAIVKLLSVILSRAG 24 (361)
T ss_pred CcEEEEcchHHHHHHHHHHHHhcc
Confidence 788899999998888888777665
No 25
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=20.71 E-value=85 Score=22.28 Aligned_cols=40 Identities=20% Similarity=0.262 Sum_probs=33.1
Q ss_pred EEEeeccHHHHHH---HHhhCccccchhhHHHHhhhhHhhhcc
Q 038926 9 VIVTDRELALMKV---IQKIFPSATTFLCRWHISRNVLANCKN 48 (153)
Q Consensus 9 ~i~TD~d~a~~~A---i~~vFP~~~~~lC~wHi~~n~~~~~~~ 48 (153)
.|+||-...+++| |.+-+|...-..|.-|-+.-+.+.+.+
T Consensus 96 qVVTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 96 QVVTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred HHhccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 4789999888887 566789998899999998888877764
No 26
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=20.24 E-value=2.9e+02 Score=18.69 Aligned_cols=18 Identities=22% Similarity=0.462 Sum_probs=14.4
Q ss_pred CHHHHHHHHHHHHHhccC
Q 038926 71 SEEEFAQRLKGMETDFSK 88 (153)
Q Consensus 71 t~~~f~~~~~~~~~~~~~ 88 (153)
+++.|+.+|..+.+.|+.
T Consensus 52 ~~~~Y~~a~~~L~~~yg~ 69 (145)
T PF03564_consen 52 SEENYEEAWELLEERYGN 69 (145)
T ss_pred cchhhHHHHHHHHHHhCC
Confidence 667788888888888874
No 27
>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=20.01 E-value=75 Score=20.41 Aligned_cols=15 Identities=27% Similarity=0.215 Sum_probs=12.2
Q ss_pred CcEEEeeccHHHHHH
Q 038926 7 ASVIVTDRELALMKV 21 (153)
Q Consensus 7 P~~i~TD~d~a~~~A 21 (153)
|++|.||+..+..+.
T Consensus 68 p~~i~tD~g~~f~~~ 82 (120)
T PF00665_consen 68 PRVIRTDNGSEFTSH 82 (120)
T ss_dssp -SEEEEESCHHHHSH
T ss_pred ceecccccccccccc
Confidence 999999999997754
Done!