Query 006675
Match_columns 636
No_of_seqs 196 out of 341
Neff 5.7
Searched_HMMs 46136
Date Thu Mar 28 12:52:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006675.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006675hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2031 Tyrosyl-DNA phosphodie 100.0 5E-107 1E-111 862.9 28.0 504 62-626 2-518 (519)
2 PF06087 Tyr-DNA_phospho: Tyro 100.0 8.4E-97 2E-101 811.1 11.5 404 161-602 1-443 (443)
3 cd00060 FHA Forkhead associate 97.6 0.00014 2.9E-09 63.2 6.1 94 7-108 2-101 (102)
4 TIGR01663 PNK-3'Pase polynucle 97.0 0.00069 1.5E-08 77.2 5.5 94 3-106 11-106 (526)
5 PF00498 FHA: FHA domain; Int 97.0 0.00089 1.9E-08 54.8 4.5 62 33-98 2-67 (68)
6 PF13091 PLDc_2: PLD-like doma 94.6 0.027 5.9E-07 50.8 3.1 38 482-534 73-110 (126)
7 TIGR03354 VI_FHA type VI secre 91.2 0.41 8.9E-06 53.1 6.4 88 10-100 4-96 (396)
8 PLN02927 antheraxanthin epoxid 90.6 0.68 1.5E-05 54.7 7.8 96 8-106 535-643 (668)
9 smart00240 FHA Forkhead associ 89.0 0.52 1.1E-05 36.0 3.6 38 37-74 10-48 (52)
10 PRK13912 nuclease NucT; Provis 87.7 0.63 1.4E-05 45.7 4.1 38 481-533 117-154 (177)
11 smart00155 PLDc Phospholipase 85.8 0.65 1.4E-05 31.9 2.1 25 482-510 3-27 (28)
12 COG1716 FOG: FHA domain [Signa 84.2 1.4 2.9E-05 43.0 4.5 67 31-103 90-159 (191)
13 PF00614 PLDc: Phospholipase D 83.7 0.98 2.1E-05 31.5 2.3 25 252-279 2-26 (28)
14 COG1502 Cls Phosphatidylserine 80.5 1.2 2.7E-05 49.0 2.9 40 482-536 353-392 (438)
15 smart00155 PLDc Phospholipase 80.3 2.1 4.5E-05 29.4 2.9 25 252-279 2-26 (28)
16 PRK09428 pssA phosphatidylseri 78.8 3.5 7.5E-05 46.7 5.8 42 479-535 351-392 (451)
17 PRK01642 cls cardiolipin synth 78.0 2 4.3E-05 48.9 3.6 38 482-534 398-435 (483)
18 PF09565 RE_NgoFVII: NgoFVII r 77.9 2.3 5E-05 45.5 3.8 42 485-535 82-123 (296)
19 cd00138 PLDc Phospholipase D. 76.0 2.8 6.1E-05 40.0 3.6 38 482-534 112-149 (176)
20 PRK11263 cardiolipin synthase 75.1 2.6 5.6E-05 47.1 3.5 39 482-535 286-324 (411)
21 cd00138 PLDc Phospholipase D. 68.8 5.9 0.00013 37.8 3.9 38 252-292 111-149 (176)
22 PF13091 PLDc_2: PLD-like doma 66.0 8.9 0.00019 34.3 4.3 37 253-292 73-110 (126)
23 PRK12452 cardiolipin synthetas 64.4 5.9 0.00013 45.5 3.5 39 482-535 424-462 (509)
24 PRK13912 nuclease NucT; Provis 55.0 10 0.00022 37.2 2.8 30 251-283 116-145 (177)
25 PF09565 RE_NgoFVII: NgoFVII r 38.4 28 0.0006 37.4 3.2 27 254-280 80-107 (296)
26 PHA02820 phospholipase-D-like 37.7 29 0.00063 39.0 3.3 29 252-286 111-139 (424)
27 PHA02820 phospholipase-D-like 31.9 39 0.00085 38.0 3.2 37 482-533 112-148 (424)
28 TIGR02500 type_III_yscD type I 31.3 62 0.0013 36.1 4.6 37 24-60 14-54 (410)
29 COG3886 Predicted HKD family n 24.9 61 0.0013 32.8 2.8 32 481-513 117-148 (198)
30 PF10382 DUF2439: Protein of u 20.2 2E+02 0.0043 25.0 4.7 61 44-109 10-73 (83)
No 1
>KOG2031 consensus Tyrosyl-DNA phosphodiesterase [Replication, recombination and repair]
Probab=100.00 E-value=5e-107 Score=862.87 Aligned_cols=504 Identities=38% Similarity=0.626 Sum_probs=404.2
Q ss_pred EEEeecCCcEEEee--CCcccccccccccccccCCccccCCCCccceeeeeccccccccCCCCCcccchhhhhhhccccc
Q 006675 62 SLVVDGTNPVVVKS--GDQRKKLSSNEHVSIADGDIIELIPGHHFFKYVTLSRSQKRVSNDGATNGELSSKKMRQQDEQD 139 (636)
Q Consensus 62 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 (636)
++++.++++..++| ..++.+.-...+....+++.++.+++++..+.+.+ .++. .+.+
T Consensus 2 s~ss~~~~~~p~~s~~~~~~s~~~~~~~isa~~~~~~~~~~n~~~~~~~~l-------~g~~--------------~~~~ 60 (519)
T KOG2031|consen 2 SLSSNFNGLKPERSDVAEEKSQRKKSSRISAENDNAAPVTENHHKDDCVIL-------KGSR--------------DIKL 60 (519)
T ss_pred ccccCCCCcccccccccchhcccccCccccccCcccccccccccchhhhhc-------CCCc--------------cccc
Confidence 35667778888888 45566666778888899999999999999875543 1111 1122
Q ss_pred CCCCCCccccccccccCCCCCCCceEEEEecCCCCCCCCCceeecccc---cccHHHhhhhhcccCHHhhhccCCCCCCC
Q 006675 140 NENGKNSEEALCNFHVSRDKLPSTFRLLRVQGLPAWANTSCVSIRDVI---QGDIIVAILSNYMVDIDWLLPACPVLAKI 216 (636)
Q Consensus 140 ~~~~~~~~~~~~~~~~~~~~~~~~FrLtrv~g~~~~~N~~~Itl~DIL---~gdl~~ail~nF~~Dl~WLl~~~p~~~~~ 216 (636)
+...+...|+....+.+......+++..-+.+++. ...+++.+|+ .|++..++|||||+|++||+.+||...+.
T Consensus 61 t~~e~~~~~~~~~~~~p~~~~ft~v~~~s~~~~~s---~~s~sl~~il~~i~g~~v~silfsfmvdid~Lv~~y~~~~~~ 137 (519)
T KOG2031|consen 61 TNQEKDDSERILTNDNPKGAVFTTVKGDSVPRYDS---MGSVSLMEILADIFGTPVNSILFSFMVDIDWLVGQYPPSVRI 137 (519)
T ss_pred CccccccHHHHhccCCcccccccccccccccccCc---ccchHHHHHHHHhhCCchhheEEEEEeEHHHHHhhCcchhcc
Confidence 23333344555555544433333333333333333 3555555554 47899999999999999999999865556
Q ss_pred CeEEEEeCCCCchhhhhhhcCCCceEEecCCCCCCCCCccceeEEEEeCCccEEEEeCCCCCccccccccceEEeecccC
Q 006675 217 PHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPL 296 (636)
Q Consensus 217 ~~i~Vv~ge~~~~~~~~~~~~p~n~~l~~p~mp~~fGtHHSKmmLL~y~dglRVVI~TANLi~~DW~~~tQ~vW~qDfP~ 296 (636)
+.|+++||+.++.........+.+++++.+.||++|||||+|||+|+|++|+|||||||||++.||+++||++|++++++
T Consensus 138 ~~i~l~~G~~d~~~~~~~~K~~~l~~~~~~~LpipF~thHtKm~~l~y~~G~rvvv~taNl~~~Dw~~ktQ~~w~sp~~~ 217 (519)
T KOG2031|consen 138 KPITLVHGEPDEARLLAQTKAPILVTVKLASLPIPFGTHHTKMIILFYEEGCRVVVHTANLIHDDWNNKTQGFWCSPLLK 217 (519)
T ss_pred CceEEEecCCchHHHHhhhhccceeeeecccccccccccccceEEEeccCccEEEEecCCcceecccccccceeecCCcc
Confidence 67889999987443333334567999999999999999999999999999999999999999999999999999999888
Q ss_pred CCCCCCCCCCCcHHHHHHHHHhcCCCcccccCCCCCCccccccccccccccccceEEEEccCCCCCCCccccccHHHHHH
Q 006675 297 KDQNNLSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRT 376 (636)
Q Consensus 297 ~~~~s~~~~t~Fk~DLi~YL~ay~~~~~~~~~p~lg~~~I~~~~L~~yDFS~a~v~LVaSVPG~H~g~~~~~~G~~~L~~ 376 (636)
+.......++.|+.||++||++|++|.+. .|++.|++||||.++|+||+||||++.|.....|||+||++
T Consensus 218 ~~~~~g~~~~~Fk~DLi~YL~~Y~~~~l~----------~~i~~lkk~DfS~i~v~fIgStPG~f~gs~~~~WGh~kL~k 287 (519)
T KOG2031|consen 218 IGDKKGVSPTGFKQDLIEYLNSYRLPQLK----------EWIASLKKVDFSAINVRFIGSTPGKFQGSGLLSWGHNKLKK 287 (519)
T ss_pred cccCCCCCCCchHHHHHHHHHHhccchhH----------HHHHHHHhcchhhceEEEEeecCCcccCcccccccHHHHHH
Confidence 76667788999999999999999987543 34689999999999999999999998887777799999999
Q ss_pred HHhhccccCCCcccCeEEEecCCCcCChHHHHHHHhcccCCCCCCCCCCCC--CCceEEccCchhhhcCcccccCCcccc
Q 006675 377 VLQECTFEKGFKKSPLVYQFSSLGSLDEKWMAELSSSMSSGFSEDKTPLGI--GEPLIVWPTVEDVRCSLEGYAAGNAIP 454 (636)
Q Consensus 377 ~L~~~~~~~~~~~~~i~~Q~SSIGsl~~~wL~~f~~sl~~g~~~~~~~~~~--~~~~IIfPT~e~Vr~S~~G~~~Ggsi~ 454 (636)
+|+++......++++++||+||+|+++..|...|...+.....++.++.+. ++++|||||+||||+|.+||++|||||
T Consensus 288 iL~~~~~~~~~~r~~~v~q~sS~gsl~~~~~~~~~~~f~~~l~kdt~~~gk~~~~~yiIfPTveeVrtS~~G~~~Ggsip 367 (519)
T KOG2031|consen 288 ILKEHAASPYLERTPVVGQSSSIGSLGSLWSAWFIGDFVESLAKDTTPPGKLRPPFYIIFPTVEEVRTSLLGYAGGGSLP 367 (519)
T ss_pred HHHhhccCcccccCceeeeeeccccccchhhhhhhhhhccchhhccCCCCCCCCCeeEEcccHHHhhccccccccCceec
Confidence 999987656668899999999999999887776666665555555555443 468999999999999999999999999
Q ss_pred CCCccch-hHhHHHHHhhhcCCCCCCCCCCCcceeEEeec--CCceeEEEEeccccchhhhhccccCCc---eeeeeeee
Q 006675 455 SPQKNVD-KDFLKKYWAKWKASHTGRSRAMPHIKTFARYN--GQKLAWFLLTSANLSKAAWGALQKNNS---QLMIRSYE 528 (636)
Q Consensus 455 ~~~~~~~-~~~l~~~~~kw~~~~s~R~~a~PHiKty~r~~--~~~i~W~lltSaNLSkaAWG~l~k~~s---ql~IrNyE 528 (636)
|..++.+ +.|+++|||||.+.+++|+|||||||||||++ ++.+.|||||||||||||||+++++++ ||||||||
T Consensus 368 y~~~~~~kq~~lk~y~~kW~A~~s~R~ramPHiKtYmr~~~d~q~l~W~LlTSANLSKaAWG~l~kn~sk~~~LmIRsYE 447 (519)
T KOG2031|consen 368 YGKNTNEKQPWLKKYLCKWKAMDSRRSRAMPHIKTYMRFNLDDQKLAWFLLTSANLSKAAWGTLSKNKSKQPQLMIRSYE 447 (519)
T ss_pred ccchhhhhhHHHHHHHHhhhhhhhhccccCCcceeeeeecCCCCEEEEEEEeccccchhhhhhhccCCCCCchheeeecc
Confidence 9877666 47999999999999999999999999999998 789999999999999999999999875 89999999
Q ss_pred eeeEEcCCcccCCCccccccCCCCccccCCCccchhcccceeeeeecCCCCCCCCCCcceeeccccCCCCCCCCCCCCCc
Q 006675 529 LGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVPW 608 (636)
Q Consensus 529 lGVL~~P~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~pvPy~LP~~~Y~~~D~PW 608 (636)
+||||+|.++.+..++ |++..+|..+.. ....+.|||||||||+||++.|+||
T Consensus 448 aGVLf~p~~~~~~kt~------------------------k~~~~tf~~~~~---~~~v~~vpvpydlPp~pY~~~d~~~ 500 (519)
T KOG2031|consen 448 AGVLFLPRFFANLKTF------------------------KVVEDTFPRDNN---GDGVIAVPVPYDLPPVPYSPKDEPF 500 (519)
T ss_pred cceEecchhhhccccc------------------------cccceecccccC---CCCcceeccccCCCCcCCCccCCce
Confidence 9999999976532122 122223434332 2335789999999999999999999
Q ss_pred eecCCCCCcccCCCCccc
Q 006675 609 SWDKRYTKKDVYGQVWPR 626 (636)
Q Consensus 609 ~~~~~y~~pD~~G~~w~~ 626 (636)
++++.+.++||+|.+|++
T Consensus 501 ~~~~~~~~~d~lG~vW~p 518 (519)
T KOG2031|consen 501 FTDIYRQGPDWLGCVWTP 518 (519)
T ss_pred eecccccCCcceeeccCC
Confidence 999777789999999986
No 2
>PF06087 Tyr-DNA_phospho: Tyrosyl-DNA phosphodiesterase; InterPro: IPR010347 Covalent intermediates between topoisomerase I and DNA can become dead-end complexes that lead to cell death. Tyrosyl-DNA phosphodiesterase can hydrolyse the bond between topoisomerase I and DNA [].; GO: 0008081 phosphoric diester hydrolase activity, 0006281 DNA repair, 0005634 nucleus; PDB: 3SQ8_A 3SQ5_B 3SQ3_A 1Q32_D 3SQ7_A 1QZQ_A 1RGU_B 1RG2_B 1MU9_B 1RFI_B ....
Probab=100.00 E-value=8.4e-97 Score=811.13 Aligned_cols=404 Identities=42% Similarity=0.703 Sum_probs=289.4
Q ss_pred CCceEEEEecCCCCC--CCCCceeecccccc-cHHHhhhhhcccCHHhhhccCCCC-CCCCeEEEEeCCCCc-hhhhhhh
Q 006675 161 PSTFRLLRVQGLPAW--ANTSCVSIRDVIQG-DIIVAILSNYMVDIDWLLPACPVL-AKIPHVLVIHGESDG-TLEHMKR 235 (636)
Q Consensus 161 ~~~FrLtrv~g~~~~--~N~~~Itl~DIL~g-dl~~ail~nF~~Dl~WLl~~~p~~-~~~~~i~Vv~ge~~~-~~~~~~~ 235 (636)
|+.|.++++.++++. .|.++|||+|||++ +|++|++||||+|++|||++|+.. ++...|++++|+... ....++.
T Consensus 1 P~~~~~~~i~~~~~~~~~~~~~itl~dil~~~~l~~~~~~nf~~D~~wll~~~~~~~~~~~~i~~v~g~~~~~~~~~~~~ 80 (443)
T PF06087_consen 1 PFKLYLTTIYDLPPRSNNNPDTITLEDILGDPDLEEALLFNFMIDLDWLLSQFPPSTRKNIPITIVHGTKDPPDKREIRQ 80 (443)
T ss_dssp SCEEEEBTTTTS-GG--GTTTEE-HHHHCSGTTEEEEEEE-SSEEHHHHHCCS-CCGTTCEEEEEECTSEEHHHHHHHHH
T ss_pred CcceEEeeecCCCccccCCCCcEeHHHHcCCccHHHHHhhhheeeHHHHHHhCCHhhcccceEEEEeCCCcchhhhhhhh
Confidence 567889999998876 68899999999986 799999999999999999999863 322368888985432 2223332
Q ss_pred --cCCCceEEecCCCCCCCCCccceeEEEEeCCc-cEEEEeCCCCCccccccccceEEeecc-cCCCC---CCCCCCCCc
Q 006675 236 --NKPANWILHKPPLPISFGTHHSKAMLLIYPRG-VRIIVHTANLIHVDWNNKSQGLWMQDF-PLKDQ---NNLSEECGF 308 (636)
Q Consensus 236 --~~p~n~~l~~p~mp~~fGtHHSKmmLL~y~dg-lRVVI~TANLi~~DW~~~tQ~vW~qDf-P~~~~---~s~~~~t~F 308 (636)
...+|+++|.|+||.+|||||||||||+|+|| ||||||||||+++||+++||+||+||| |++.. .....+++|
T Consensus 81 ~~~~~~nv~~~~~~mp~~~g~hHsKm~ll~y~~~~lRVvI~TaNl~~~Dw~~~~q~vw~~d~lP~~~~~~~~~~~~~~~F 160 (443)
T PF06087_consen 81 QAAIYPNVKLIFPPMPIPFGTHHSKMMLLFYEDGSLRVVIPTANLTPYDWNNKTQGVWIQDFLPRLPSSKSSSEESGSRF 160 (443)
T ss_dssp HHCCHTTEEEEEE---STT--B--EEEEEEETTCEEEEEEESS-BSHHHHCSSB-EEEE---E-B-ECTS-S--SSTTHH
T ss_pred hcccCCCeEEEccCCCcccccccceeEEEEeCCccEEEEEECCCCCHHHHCCcceeEEEecccCcccccccccCCCCCch
Confidence 35679999999999999999999999999999 999999999999999999999999998 98754 234578999
Q ss_pred HHHHHHHHHhcCCCcccccCCCCCCccccccccccccccccceEEEEccCCCCCCCccccccHHHHHHHHhhccccC---
Q 006675 309 ENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEK--- 385 (636)
Q Consensus 309 k~DLi~YL~ay~~~~~~~~~p~lg~~~I~~~~L~~yDFS~a~v~LVaSVPG~H~g~~~~~~G~~~L~~~L~~~~~~~--- 385 (636)
++||++||++|+.+.... +++.|++||||.++|+||+||||+|. .+..+|||++|+++|+++....
T Consensus 161 ~~dL~~yL~~y~~~~~~~----------~~~~l~~yDFS~~~v~lV~SvPG~h~-~~~~~~G~~~L~~~L~~~~~~~~~~ 229 (443)
T PF06087_consen 161 KKDLVAYLNSYGKSPLDK----------LIERLRKYDFSSARVHLVASVPGKHK-EDKDKWGHMRLRKVLKRLGLPSNKD 229 (443)
T ss_dssp HHHHHHHHHTT--HHHHH----------CHHHHHTEE-CCGTSEEEEE-SECCC-GGGGGSHHHHHHHHHHHCCTT---T
T ss_pred HHHHHHHHHHhCCcchhH----------HHHHHHhcCCccCceEEEeccCcccc-CCCcchhHHHHHHHHHhccccccCC
Confidence 999999999998543211 14789999999999999999999999 5566899999999999987754
Q ss_pred CCcccCeEEEecCCCcCC---hHHH-HHHHhcccCCCCC-C----------CCCCCCCCceEEccCchhhhcCcccccCC
Q 006675 386 GFKKSPLVYQFSSLGSLD---EKWM-AELSSSMSSGFSE-D----------KTPLGIGEPLIVWPTVEDVRCSLEGYAAG 450 (636)
Q Consensus 386 ~~~~~~i~~Q~SSIGsl~---~~wL-~~f~~sl~~g~~~-~----------~~~~~~~~~~IIfPT~e~Vr~S~~G~~~G 450 (636)
.....+|+||+||||+++ ..|| .+|+.+|...... . ......++++|||||+||||+|.+||.+|
T Consensus 230 ~~~~~~~~~Q~SSIGs~~~~~~~Wl~~~f~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvfPT~e~Vr~S~~G~~~g 309 (443)
T PF06087_consen 230 KDKESDIVCQFSSIGSLGSSPKDWLTSEFLTSLYPASFSSPSTPSSKSSSSQQENNRPPLKIVFPTVEEVRNSPEGYNGG 309 (443)
T ss_dssp TCCCCEEEEE-SBB---SSSTTTTTTTHHHHHCCHHCCT------HHHHHHHCCHHTEEEEEE--BCHHHCTSTTGGGGG
T ss_pred cCCCCeEEEEcccccccCcchhhhHHHHHHHHHhhccccccccccccccccccccCCCCceEECCCHHHHhhCccCCcCc
Confidence 346789999999999994 4588 4788877654320 0 01112356899999999999999999999
Q ss_pred ccccCCCc----cchhHhHHHHHhhhcCC--CCCCCCCCCcceeEEeec---CCceeEEEEeccccchhhhhccccCCce
Q 006675 451 NAIPSPQK----NVDKDFLKKYWAKWKAS--HTGRSRAMPHIKTFARYN---GQKLAWFLLTSANLSKAAWGALQKNNSQ 521 (636)
Q Consensus 451 gsi~~~~~----~~~~~~l~~~~~kw~~~--~s~R~~a~PHiKty~r~~---~~~i~W~lltSaNLSkaAWG~l~k~~sq 521 (636)
||||++.+ +..+.||+++||+|.+. .++|++++||+|+|+|++ .+.++|+|+||||||+||||+.+++++|
T Consensus 310 gsi~~~~~~~~~~~~~~~l~~~~~~w~~~~~~~~R~~~~pH~K~y~~~~~~~~~~~~W~~lgShNLS~aAWG~~~~~~~~ 389 (443)
T PF06087_consen 310 GSIPFKYKWWEPNFPQEWLRPYFHKWYASDDPSGRSRAPPHIKTYMRFSKNDFKSLGWFYLGSHNLSKAAWGKRSKNGSQ 389 (443)
T ss_dssp GGSB--HC--GHHCCHHHHHHCCE-EEEC-TGCTTTTS-B--EEEEEEE-TTTSEECEEEEES--BSHHHH-EEETTTTC
T ss_pred eeEEecchhccccchHHHHHHHHhhhccccccCCCCCcCcceEEEEEecCCCCCccceEEeCcccCCHHHhcccccCCce
Confidence 99999865 34467999999999998 899999999999999997 5789999999999999999999999999
Q ss_pred eeeeeeeeeeEEcCCcccCCCccccccCCCCccccCCCccchhcccceeeeeecCCCCCCCCCCcceeeccccCCCCCCC
Q 006675 522 LMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRY 601 (636)
Q Consensus 522 l~IrNyElGVL~~P~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~pvPy~LP~~~Y 601 (636)
++||||||||||+|..... ...|.+....... .......+.|||||+||++||
T Consensus 390 l~i~nyElGVl~~P~~~~~--~~~~~~~~~~~~~-------------------------~~~~~~~~~v~vPf~lP~~~Y 442 (443)
T PF06087_consen 390 LSIRNYELGVLFLPSSFGV--MLPVFSLDDPVYR-------------------------SISSTNTVPVPVPFDLPPTPY 442 (443)
T ss_dssp CEESSBEEEEEEEGGGCTS--SSSCEEEECCG--------------------------------GGGCEEESS-SSEEE-
T ss_pred eeecceEEEEEEecCcccc--ccccccccccccc-------------------------ccccCCCceEEecCCCCCcCc
Confidence 9999999999999986541 1222221111000 112344678999999999999
Q ss_pred C
Q 006675 602 S 602 (636)
Q Consensus 602 ~ 602 (636)
+
T Consensus 443 ~ 443 (443)
T PF06087_consen 443 G 443 (443)
T ss_dssp -
T ss_pred C
Confidence 6
No 3
>cd00060 FHA Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
Probab=97.59 E-value=0.00014 Score=63.20 Aligned_cols=94 Identities=29% Similarity=0.426 Sum_probs=76.3
Q ss_pred eeEeeCCCCccCCCCCCcccCCC-CCccccCC----CccccccccccceeEEEecC-CcceEEEeecCCcEEEeeCCccc
Q 006675 7 GYLVPLDNNLREDNSLPKLPLSQ-GPNVIGRT----NIPVSDKRLSRKHITLTASA-DGSASLVVDGTNPVVVKSGDQRK 80 (636)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~----~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 80 (636)
.+|.+++.+ .....++|.. +.-+|||+ ++.+.|+.+||+|.+|.... ++..-+...+.|++.|+. +
T Consensus 2 ~~L~~~~~~----~~~~~~~l~~~~~~~iGr~~~~~~i~l~~~~iS~~H~~i~~~~~~~~~~~~~~s~~g~~vn~----~ 73 (102)
T cd00060 2 PRLVVLSGD----ASGRRYYLDPGGTYTIGRDSDNCDIVLDDPSVSRRHAVIRYDGDGGVVLIDLGSTNGTFVNG----Q 73 (102)
T ss_pred eEEEEecCC----CceeEEEECCCCeEEECcCCCcCCEEcCCCCeeCcceEEEEcCCCCEEEEECCCCCCeEECC----E
Confidence 356666554 4477889999 99999998 88899999999999999998 788888999999999865 2
Q ss_pred ccccccccccccCCccccCCCCccceee
Q 006675 81 KLSSNEHVSIADGDIIELIPGHHFFKYV 108 (636)
Q Consensus 81 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~ 108 (636)
++.......+.+||++++-++.+.|++.
T Consensus 74 ~~~~~~~~~l~~gd~i~ig~~~~~~~~~ 101 (102)
T cd00060 74 RVSPGEPVRLRDGDVIRLGNTSISFRFE 101 (102)
T ss_pred ECCCCCcEECCCCCEEEECCeEEEEEEe
Confidence 3343566779999999999877777643
No 4
>TIGR01663 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase. Note that the EC number for the kinase function is: 2.7.1.78
Probab=97.05 E-value=0.00069 Score=77.18 Aligned_cols=94 Identities=24% Similarity=0.408 Sum_probs=80.4
Q ss_pred ccceeeEeeCCCCccCCCCCCcccCCCCCccccCC-CccccccccccceeEEEecCC-cceEEEeecCCcEEEeeCCccc
Q 006675 3 ATKIGYLVPLDNNLREDNSLPKLPLSQGPNVIGRT-NIPVSDKRLSRKHITLTASAD-GSASLVVDGTNPVVVKSGDQRK 80 (636)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 80 (636)
..+|.+|+|.. ++-|.|+|..|.++|||. .--|.|++-||+.+.|.|..+ |.+.+.+-|.||-.|.. .
T Consensus 11 ~~~~c~l~~~~------~~~~~~~~~~~~~~~gr~pet~i~d~~cs~~qv~l~a~~~~~~v~~k~lg~np~~~~~----~ 80 (526)
T TIGR01663 11 AARICTLKPGE------AEHHFIHLDAGALFLGRGPETGIRDRKCSKRQIELQADLEKATVALKQLGVNPCGTGG----L 80 (526)
T ss_pred ceeeeEecCCC------CCCCeeccCCCceEEccCcccccchhhhchhhheeeecccCceEEEEEccCCCcccCc----e
Confidence 35788999864 445999999999999998 456889999999999999865 67889999999988865 4
Q ss_pred ccccccccccccCCccccCCCCccce
Q 006675 81 KLSSNEHVSIADGDIIELIPGHHFFK 106 (636)
Q Consensus 81 ~~~~~~~~~i~~~~~~~~~~~~~~~~ 106 (636)
.|..++..+..+||++||.+|.|.|.
T Consensus 81 ~~~~~~~~~l~~g~~l~~v~~~~~~~ 106 (526)
T TIGR01663 81 ELKPGGEGELGHGDLLEIVNGLHPLT 106 (526)
T ss_pred EecCCCeeeecCCCEEEEecccccee
Confidence 57778888899999999999999884
No 5
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=97.02 E-value=0.00089 Score=54.77 Aligned_cols=62 Identities=34% Similarity=0.544 Sum_probs=50.9
Q ss_pred cccCC---CccccccccccceeEEEecCCcceEEEee-cCCcEEEeeCCcccccccccccccccCCcccc
Q 006675 33 VIGRT---NIPVSDKRLSRKHITLTASADGSASLVVD-GTNPVVVKSGDQRKKLSSNEHVSIADGDIIEL 98 (636)
Q Consensus 33 ~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~ 98 (636)
+|||+ +|++.|+.+||.|..|....++.+.|.-- ++|++.|+ .+++.+.+...+.+||+|++
T Consensus 2 ~iGR~~~~di~l~~~~iSr~Ha~i~~~~~~~~~i~d~~s~ngt~vn----g~~l~~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 2 TIGRSPDCDIVLPDPSISRRHARISFDDDGQFYIEDLGSTNGTFVN----GQRLGPGEPVPLKDGDIIRF 67 (68)
T ss_dssp EEESSTTSSEEETSTTSSTTSEEEEEETTEEEEEEESSSSS-EEET----TEEESSTSEEEE-TTEEEEE
T ss_pred EEcCCCCCCEEECCHheeeeeeEEEEeceeeEEEEeCCCCCcEEEC----CEEcCCCCEEECCCCCEEEc
Confidence 47776 79999999999999999999978888874 59999883 27788888889999999875
No 6
>PF13091 PLDc_2: PLD-like domain; PDB: 2ZE4_A 2ZE9_A 1BYS_A 1BYR_A 1V0T_A 1V0U_A 1V0V_A 1V0S_A 1V0R_A 1V0W_A ....
Probab=94.64 E-value=0.027 Score=50.77 Aligned_cols=38 Identities=34% Similarity=0.500 Sum_probs=26.8
Q ss_pred CCCcceeEEeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEc
Q 006675 482 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLIL 534 (636)
Q Consensus 482 a~PHiKty~r~~~~~i~W~lltSaNLSkaAWG~l~k~~sql~IrNyElGVL~~ 534 (636)
...|.|+|+-.+ + .+++||+|||..||. +|+|+||++.
T Consensus 73 ~~~H~K~~i~d~-~---~~iiGS~N~t~~~~~-----------~n~E~~~~~~ 110 (126)
T PF13091_consen 73 NRLHAKFYIIDD-K---VAIIGSANLTSSSFR-----------RNYELGVIID 110 (126)
T ss_dssp S-B--EEEEETT-T---EEEEES--CSCCCSC-----------TSEEEEEEEE
T ss_pred cCCCcceEEecC-c---cEEEcCCCCCcchhc-----------CCcceEEEEE
Confidence 477999998742 2 799999999999992 5999999984
No 7
>TIGR03354 VI_FHA type VI secretion system FHA domain protein. Members of this protein family are FHA (forkhead-associated) domain-containing proteins that are part of type VI secretion loci in a considerable number of bacteria, most of which are known pathogens. Species include Pseudomonas aeruginosa PAO1, Aeromonas hydrophila, Yersinia pestis, Burkholderia mallei, etc.
Probab=91.22 E-value=0.41 Score=53.13 Aligned_cols=88 Identities=20% Similarity=0.264 Sum_probs=67.3
Q ss_pred eeCCCCccCCCCCCcccCCCCCccccC---CCccccccc--cccceeEEEecCCcceEEEeecCCcEEEeeCCccccccc
Q 006675 10 VPLDNNLREDNSLPKLPLSQGPNVIGR---TNIPVSDKR--LSRKHITLTASADGSASLVVDGTNPVVVKSGDQRKKLSS 84 (636)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (636)
+=+|...-+.+....+++..+..+||| +++++.|.. +||.|.+|+.. +|...|.--.+|.+.|+..+.| +..
T Consensus 4 ~v~n~~~l~~g~~~~~~f~~~~~~IGR~~~~d~~l~d~~~~VS~~Ha~I~~~-~g~~~l~DlStNGT~VN~sg~~--l~~ 80 (396)
T TIGR03354 4 TVLNAHQLTPGIAAQKTFGTNGGTIGRSEDCDWVLPDPERHVSGRHARIRYR-DGAYLLTDLSTNGVFLNGSGSP--LGR 80 (396)
T ss_pred EEeccccCCCCcceEEEECCCCEEEecCCCCCEEeCCCCCCcchhhcEEEEE-CCEEEEEECCCCCeEECCCCCC--CCC
Confidence 334555557777889999999999999 578888887 99999999987 5666666668899999754433 445
Q ss_pred ccccccccCCccccCC
Q 006675 85 NEHVSIADGDIIELIP 100 (636)
Q Consensus 85 ~~~~~i~~~~~~~~~~ 100 (636)
+..+.+.+||+|.+=+
T Consensus 81 ~~~~~L~~GD~I~iG~ 96 (396)
T TIGR03354 81 GNPVRLEQGDRLRLGD 96 (396)
T ss_pred CCceEcCCCCEEEECC
Confidence 5567799999988844
No 8
>PLN02927 antheraxanthin epoxidase/zeaxanthin epoxidase
Probab=90.64 E-value=0.68 Score=54.70 Aligned_cols=96 Identities=19% Similarity=0.296 Sum_probs=72.9
Q ss_pred eEeeCCCCccCCCCCCcccC---CCCCccccCCC--------ccccccccccceeEEEecCCcceEEEeecCCcEEEee-
Q 006675 8 YLVPLDNNLREDNSLPKLPL---SQGPNVIGRTN--------IPVSDKRLSRKHITLTASADGSASLVVDGTNPVVVKS- 75 (636)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 75 (636)
||+|..... .....|+| -..|=+|||+. |++.|..+|+.|.+++...+.-.---..-||--.|+.
T Consensus 535 ~l~~~~~~~---~~~~~~~l~~~~~~p~~iG~~~~~~~~~~~i~i~~~~vS~~Ha~i~~~~~~~~~~Dl~S~nGT~v~~~ 611 (668)
T PLN02927 535 YLIPHGDDC---CVSETLCLTKDEDQPCIVGSEPDQDFPGMRIVIPSSQVSKMHARVIYKDGAFFLMDLRSEHGTYVTDN 611 (668)
T ss_pred EEEecCCCC---cccceeeeecCCCCCeEecCCCCcCCCCceEEecCCccChhHeEEEEECCEEEEEECCCCCccEEeCC
Confidence 788975443 33567888 78888999973 3889999999999999984433322344567677776
Q ss_pred CCcccccccccccccccCCccccCCCCcc-ce
Q 006675 76 GDQRKKLSSNEHVSIADGDIIELIPGHHF-FK 106 (636)
Q Consensus 76 ~~~~~~~~~~~~~~i~~~~~~~~~~~~~~-~~ 106 (636)
+++|=++.++..+.+..||+|++=..++. |+
T Consensus 612 ~~~r~~~~p~~~~~l~~~d~I~~g~~~~~~fr 643 (668)
T PLN02927 612 EGRRYRATPNFPARFRSSDIIEFGSDKKAAFR 643 (668)
T ss_pred CCceEecCCCCceEeCCCCEEEeCCCcceeEE
Confidence 45566788999999999999999888766 75
No 9
>smart00240 FHA Forkhead associated domain. Found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain.
Probab=89.02 E-value=0.52 Score=36.00 Aligned_cols=38 Identities=26% Similarity=0.389 Sum_probs=31.1
Q ss_pred CCccccccccccceeEEEecCCcceEEEeec-CCcEEEe
Q 006675 37 TNIPVSDKRLSRKHITLTASADGSASLVVDG-TNPVVVK 74 (636)
Q Consensus 37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ 74 (636)
.++.+.|..+||+|..|..+.++.+.+.--+ +|.+.|+
T Consensus 10 ~~i~~~~~~vs~~H~~i~~~~~~~~~i~d~~s~~gt~vn 48 (52)
T smart00240 10 CDIQLPGPSISRRHAEIVYDGGGRFYLIDLGSTNGTFVN 48 (52)
T ss_pred CCEEeCCCCcchhHcEEEECCCCeEEEEECCCCCCeeEC
Confidence 4599999999999999999999866666655 7877664
No 10
>PRK13912 nuclease NucT; Provisional
Probab=87.67 E-value=0.63 Score=45.70 Aligned_cols=38 Identities=29% Similarity=0.305 Sum_probs=30.5
Q ss_pred CCCCcceeEEeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEE
Q 006675 481 RAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLI 533 (636)
Q Consensus 481 ~a~PHiKty~r~~~~~i~W~lltSaNLSkaAWG~l~k~~sql~IrNyElGVL~ 533 (636)
...+|.|+++-.. .|+++||+|++..++. .|+|+||++
T Consensus 117 ~~~~H~K~~viD~----~~~~iGS~N~t~~s~~-----------~N~E~~lii 154 (177)
T PRK13912 117 YGIMHQKVAIIDD----KIVVLGSANWSKNAFE-----------NNYEVLLIT 154 (177)
T ss_pred ccccceeEEEEcC----CEEEEeCCCCChhHhc-----------cCCceEEEE
Confidence 3468999987532 4899999999987774 399999987
No 11
>smart00155 PLDc Phospholipase D. Active site motifs. Phosphatidylcholine-hydrolyzing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, aspartic acid, and/or asparagine residues which may contribute to the active site. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not be
Probab=85.75 E-value=0.65 Score=31.90 Aligned_cols=25 Identities=24% Similarity=0.190 Sum_probs=19.6
Q ss_pred CCCcceeEEeecCCceeEEEEeccccchh
Q 006675 482 AMPHIKTFARYNGQKLAWFLLTSANLSKA 510 (636)
Q Consensus 482 a~PHiKty~r~~~~~i~W~lltSaNLSka 510 (636)
...|.|+++-.. .|+++||+||+..
T Consensus 3 ~~~H~K~~v~D~----~~~~iGs~N~~~~ 27 (28)
T smart00155 3 GVLHTKLMIVDD----EIAYIGSANLDGR 27 (28)
T ss_pred CcEEeEEEEEcC----CEEEEeCccCCCC
Confidence 457999887544 3899999999864
No 12
>COG1716 FOG: FHA domain [Signal transduction mechanisms]
Probab=84.18 E-value=1.4 Score=42.97 Aligned_cols=67 Identities=28% Similarity=0.360 Sum_probs=52.7
Q ss_pred CccccC---CCccccccccccceeEEEecCCcceEEEeecCCcEEEeeCCcccccccccccccccCCccccCCCCc
Q 006675 31 PNVIGR---TNIPVSDKRLSRKHITLTASADGSASLVVDGTNPVVVKSGDQRKKLSSNEHVSIADGDIIELIPGHH 103 (636)
Q Consensus 31 ~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~ 103 (636)
...||| +++.+.|+.+||+|..|+...+...-.-+..+|-+.|....-+. +..+.+||++.+.....
T Consensus 90 ~~tigr~~~~~i~~~~~~vSR~Ha~l~~~~~~~~~~d~~S~nGt~vn~~~v~~------~~~l~~gd~i~i~~~~~ 159 (191)
T COG1716 90 VTTIGRDPDNDIVLDDDVVSRRHAELRREGNEVFLEDLGSTNGTYVNGEKVRQ------RVLLQDGDVIRLGGTLA 159 (191)
T ss_pred eEEeccCCCCCEEcCCCccccceEEEEEeCCceEEEECCCCcceEECCeEccC------cEEcCCCCEEEECccce
Confidence 778999 68899999999999999999888777777778877776533322 56688888888866555
No 13
>PF00614 PLDc: Phospholipase D Active site motif; InterPro: IPR001736 Phosphatidylcholine-hydrolysing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, and/or asparagine residues which may contribute to the active site aspartic acid. An Escherichia coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs [, , , ].; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3HSI_C.
Probab=83.73 E-value=0.98 Score=31.52 Aligned_cols=25 Identities=32% Similarity=0.369 Sum_probs=14.9
Q ss_pred CCCccceeEEEEeCCccEEEEeCCCCCc
Q 006675 252 FGTHHSKAMLLIYPRGVRIIVHTANLIH 279 (636)
Q Consensus 252 fGtHHSKmmLL~y~dglRVVI~TANLi~ 279 (636)
+++||+|++++ |+-+.+|.++||..
T Consensus 2 ~~~~H~K~~vv---D~~~a~vGg~nl~~ 26 (28)
T PF00614_consen 2 GGSHHQKFVVV---DDRVAFVGGANLCD 26 (28)
T ss_dssp TBEE---EEEE---TTTEEEEE---SSH
T ss_pred CcceeeEEEEE---cCCEEEECceecCC
Confidence 57899999997 45589999999863
No 14
>COG1502 Cls Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthases and related enzymes [Lipid metabolism]
Probab=80.48 E-value=1.2 Score=48.98 Aligned_cols=40 Identities=28% Similarity=0.335 Sum_probs=33.6
Q ss_pred CCCcceeEEeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEcCC
Q 006675 482 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPS 536 (636)
Q Consensus 482 a~PHiKty~r~~~~~i~W~lltSaNLSkaAWG~l~k~~sql~IrNyElGVL~~P~ 536 (636)
+..|.|+++-.+ .|+++||+||+..++.. |+|++|++...
T Consensus 353 ~~lH~K~~iiD~----~~~~vGS~N~~~rS~~l-----------N~E~~~~i~d~ 392 (438)
T COG1502 353 AFLHSKVMIIDD----RTVLVGSANLDPRSLRL-----------NFEVGLVIEDP 392 (438)
T ss_pred CcceeeEEEEcC----CEEEEeCCcCCHhHHHH-----------hhhheeEEeCH
Confidence 578999988654 47999999999999865 89999999543
No 15
>smart00155 PLDc Phospholipase D. Active site motifs. Phosphatidylcholine-hydrolyzing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, aspartic acid, and/or asparagine residues which may contribute to the active site. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not be
Probab=80.34 E-value=2.1 Score=29.37 Aligned_cols=25 Identities=28% Similarity=0.279 Sum_probs=20.6
Q ss_pred CCCccceeEEEEeCCccEEEEeCCCCCc
Q 006675 252 FGTHHSKAMLLIYPRGVRIIVHTANLIH 279 (636)
Q Consensus 252 fGtHHSKmmLL~y~dglRVVI~TANLi~ 279 (636)
.+.+|+|+|+. |+-.++|.|+||..
T Consensus 2 ~~~~H~K~~v~---D~~~~~iGs~N~~~ 26 (28)
T smart00155 2 DGVLHTKLMIV---DDEIAYIGSANLDG 26 (28)
T ss_pred CCcEEeEEEEE---cCCEEEEeCccCCC
Confidence 36899999887 45589999999975
No 16
>PRK09428 pssA phosphatidylserine synthase; Provisional
Probab=78.83 E-value=3.5 Score=46.69 Aligned_cols=42 Identities=31% Similarity=0.455 Sum_probs=34.0
Q ss_pred CCCCCCcceeEEeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEcC
Q 006675 479 RSRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILP 535 (636)
Q Consensus 479 R~~a~PHiKty~r~~~~~i~W~lltSaNLSkaAWG~l~k~~sql~IrNyElGVL~~P 535 (636)
+...+-|.|+.+-.. .|+++||+||-.-+|.- |+|+|+++.-
T Consensus 351 ~~~~~~HaK~i~vD~----~~~~iGS~Nld~RS~~l-----------n~E~~l~i~d 392 (451)
T PRK09428 351 DGDNSYHLKGIWVDD----RWMLLTGNNLNPRAWRL-----------DLENALLIHD 392 (451)
T ss_pred cCCCcceEEEEEEeC----CEEEEcCCCCChhHhhh-----------cccceEEEEC
Confidence 346678999977432 49999999999999975 9999999853
No 17
>PRK01642 cls cardiolipin synthetase; Reviewed
Probab=77.96 E-value=2 Score=48.89 Aligned_cols=38 Identities=18% Similarity=0.268 Sum_probs=31.2
Q ss_pred CCCcceeEEeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEc
Q 006675 482 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLIL 534 (636)
Q Consensus 482 a~PHiKty~r~~~~~i~W~lltSaNLSkaAWG~l~k~~sql~IrNyElGVL~~ 534 (636)
.+.|.|+++-.+ .|+++||+||+..+|. .|+|+||++.
T Consensus 398 ~~~HaK~~ivD~----~~~~vGS~N~d~rS~~-----------~N~E~~~~i~ 435 (483)
T PRK01642 398 GLLHTKSVLVDD----ELALVGTVNLDMRSFW-----------LNFEITLVID 435 (483)
T ss_pred CceEeEEEEECC----CEEEeeCCcCCHhHHh-----------hhhcceEEEE
Confidence 467999987543 4899999999988773 4999999984
No 18
>PF09565 RE_NgoFVII: NgoFVII restriction endonuclease; InterPro: IPR019065 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This domain is found in NgoFVII restriction endonuclease, which recognises GCSGC but cleavage site is unknown. It is also found as the C-terminal domain of the res subunit of some type III restriction endonucleases.
Probab=77.91 E-value=2.3 Score=45.54 Aligned_cols=42 Identities=31% Similarity=0.237 Sum_probs=30.4
Q ss_pred cceeEEeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEcC
Q 006675 485 HIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILP 535 (636)
Q Consensus 485 HiKty~r~~~~~i~W~lltSaNLSkaAWG~l~k~~sql~IrNyElGVL~~P 535 (636)
|.|+|.-..+...-=+|+||||||.- ||..+ +.||..|+.-+
T Consensus 82 HgKlY~f~k~g~~~~a~IGSANfS~~-~~~~~--------~~~E~~v~~D~ 123 (296)
T PF09565_consen 82 HGKLYIFSKNGKPFRAYIGSANFSQI-NGFTR--------RQYEAMVTCDP 123 (296)
T ss_pred ccEEEEEecCCCceEEEEeecccccc-ccccc--------cceeEEEecCh
Confidence 99999976554444599999999975 55433 57887776644
No 19
>cd00138 PLDc Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of phospholipids to phosphatidic acid and a hydrophilic constituent. Phosphatidic acid is a compound that is heavily involved in signal transduction. The common features of the family members are that they can bind to a phosphodiester moiety, and that most of these enzymes are active as bi-lobed monomers or dimers.
Probab=75.98 E-value=2.8 Score=39.96 Aligned_cols=38 Identities=26% Similarity=0.260 Sum_probs=31.3
Q ss_pred CCCcceeEEeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEc
Q 006675 482 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLIL 534 (636)
Q Consensus 482 a~PHiKty~r~~~~~i~W~lltSaNLSkaAWG~l~k~~sql~IrNyElGVL~~ 534 (636)
...|.|+++-.. + -+++||+|++..+|. .|.|+||++.
T Consensus 112 ~~~H~K~~iiD~--~--~~~vGS~N~~~~~~~-----------~~~e~~~~~~ 149 (176)
T cd00138 112 GVLHTKLVIVDD--E--TAYIGSANLDGRSLT-----------LNSEVGVVIY 149 (176)
T ss_pred cceeeeEEEEcC--C--EEEEECCcCChhhhh-----------hhcceEEEEe
Confidence 578999987643 2 599999999999998 4889999874
No 20
>PRK11263 cardiolipin synthase 2; Provisional
Probab=75.07 E-value=2.6 Score=47.06 Aligned_cols=39 Identities=21% Similarity=0.189 Sum_probs=31.5
Q ss_pred CCCcceeEEeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEcC
Q 006675 482 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILP 535 (636)
Q Consensus 482 a~PHiKty~r~~~~~i~W~lltSaNLSkaAWG~l~k~~sql~IrNyElGVL~~P 535 (636)
.+.|.|+++-.. .|+++||+||...++. .|+|++|++.-
T Consensus 286 ~~lHaK~~viD~----~~~~vGS~Nld~rS~~-----------lN~E~~~~i~d 324 (411)
T PRK11263 286 RPLHGKVALMDD----HWATVGSSNLDPLSLS-----------LNLEANLIIRD 324 (411)
T ss_pred CCceeEEEEECC----CEEEEeCCcCCHHHhh-----------hhhhcCEEEeC
Confidence 468999987644 4999999999887753 49999999853
No 21
>cd00138 PLDc Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of phospholipids to phosphatidic acid and a hydrophilic constituent. Phosphatidic acid is a compound that is heavily involved in signal transduction. The common features of the family members are that they can bind to a phosphodiester moiety, and that most of these enzymes are active as bi-lobed monomers or dimers.
Probab=68.82 E-value=5.9 Score=37.75 Aligned_cols=38 Identities=21% Similarity=0.239 Sum_probs=29.4
Q ss_pred CCCccceeEEEEeCCccEEEEeCCCCCccccc-cccceEEee
Q 006675 252 FGTHHSKAMLLIYPRGVRIIVHTANLIHVDWN-NKSQGLWMQ 292 (636)
Q Consensus 252 fGtHHSKmmLL~y~dglRVVI~TANLi~~DW~-~~tQ~vW~q 292 (636)
.+++|+|+||. |+=.++|.|+|+....|. +...++.+.
T Consensus 111 ~~~~H~K~~ii---D~~~~~vGS~N~~~~~~~~~~e~~~~~~ 149 (176)
T cd00138 111 GGVLHTKLVIV---DDETAYIGSANLDGRSLTLNSEVGVVIY 149 (176)
T ss_pred ccceeeeEEEE---cCCEEEEECCcCChhhhhhhcceEEEEe
Confidence 58999999998 566899999999998885 333445444
No 22
>PF13091 PLDc_2: PLD-like domain; PDB: 2ZE4_A 2ZE9_A 1BYS_A 1BYR_A 1V0T_A 1V0U_A 1V0V_A 1V0S_A 1V0R_A 1V0W_A ....
Probab=66.01 E-value=8.9 Score=34.28 Aligned_cols=37 Identities=19% Similarity=0.313 Sum_probs=23.3
Q ss_pred CCccceeEEEEeCCccEEEEeCCCCCcccccccc-ceEEee
Q 006675 253 GTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKS-QGLWMQ 292 (636)
Q Consensus 253 GtHHSKmmLL~y~dglRVVI~TANLi~~DW~~~t-Q~vW~q 292 (636)
+.+|.|+++. |+=.++|.|+||+...|..-. .++.+.
T Consensus 73 ~~~H~K~~i~---d~~~~iiGS~N~t~~~~~~n~E~~~~~~ 110 (126)
T PF13091_consen 73 NRLHAKFYII---DDKVAIIGSANLTSSSFRRNYELGVIID 110 (126)
T ss_dssp S-B--EEEEE---TTTEEEEES--CSCCCSCTSEEEEEEEE
T ss_pred cCCCcceEEe---cCccEEEcCCCCCcchhcCCcceEEEEE
Confidence 7899999988 344999999999999986553 344333
No 23
>PRK12452 cardiolipin synthetase; Reviewed
Probab=64.44 E-value=5.9 Score=45.48 Aligned_cols=39 Identities=15% Similarity=0.214 Sum_probs=31.3
Q ss_pred CCCcceeEEeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEcC
Q 006675 482 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILP 535 (636)
Q Consensus 482 a~PHiKty~r~~~~~i~W~lltSaNLSkaAWG~l~k~~sql~IrNyElGVL~~P 535 (636)
.+.|.|+.+-.+ .|+++||+||..-++.. |||+++++.-
T Consensus 424 ~~lHaK~~ivD~----~~a~vGS~Nld~RS~~~-----------n~E~~~~i~~ 462 (509)
T PRK12452 424 GFMHAKIVLVDD----KIATIGTANMDVRSFEL-----------NYEIISVLYE 462 (509)
T ss_pred CCeeeeEEEECC----CEEEEeCcccCHhHhhh-----------hhhccEEEEC
Confidence 467999987644 39999999998877753 9999998843
No 24
>PRK13912 nuclease NucT; Provisional
Probab=55.00 E-value=10 Score=37.19 Aligned_cols=30 Identities=17% Similarity=0.361 Sum_probs=25.3
Q ss_pred CCCCccceeEEEEeCCccEEEEeCCCCCccccc
Q 006675 251 SFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWN 283 (636)
Q Consensus 251 ~fGtHHSKmmLL~y~dglRVVI~TANLi~~DW~ 283 (636)
.++.||.|+|++ |+-.+++.|+|++..-+.
T Consensus 116 ~~~~~H~K~~vi---D~~~~~iGS~N~t~~s~~ 145 (177)
T PRK13912 116 YYGIMHQKVAII---DDKIVVLGSANWSKNAFE 145 (177)
T ss_pred cccccceeEEEE---cCCEEEEeCCCCChhHhc
Confidence 568899999988 777799999999976554
No 25
>PF09565 RE_NgoFVII: NgoFVII restriction endonuclease; InterPro: IPR019065 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This domain is found in NgoFVII restriction endonuclease, which recognises GCSGC but cleavage site is unknown. It is also found as the C-terminal domain of the res subunit of some type III restriction endonucleases.
Probab=38.41 E-value=28 Score=37.44 Aligned_cols=27 Identities=19% Similarity=0.263 Sum_probs=23.0
Q ss_pred CccceeEEEEeCCc-cEEEEeCCCCCcc
Q 006675 254 THHSKAMLLIYPRG-VRIIVHTANLIHV 280 (636)
Q Consensus 254 tHHSKmmLL~y~dg-lRVVI~TANLi~~ 280 (636)
.-|+||.+....++ .+.+|-||||+..
T Consensus 80 ~~HgKlY~f~k~g~~~~a~IGSANfS~~ 107 (296)
T PF09565_consen 80 PYHGKLYIFSKNGKPFRAYIGSANFSQI 107 (296)
T ss_pred CcccEEEEEecCCCceEEEEeecccccc
Confidence 35999988766666 9999999999995
No 26
>PHA02820 phospholipase-D-like protein; Provisional
Probab=37.68 E-value=29 Score=39.02 Aligned_cols=29 Identities=28% Similarity=0.512 Sum_probs=23.6
Q ss_pred CCCccceeEEEEeCCccEEEEeCCCCCcccccccc
Q 006675 252 FGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKS 286 (636)
Q Consensus 252 fGtHHSKmmLL~y~dglRVVI~TANLi~~DW~~~t 286 (636)
-|..|+|+|+ -||-.+.|.|+|+ ||...+
T Consensus 111 ~~~~HrK~~V---IDg~~~~iGS~Ni---d~rsl~ 139 (424)
T PHA02820 111 GGVLHTKFWI---SDNTHIYLGSANM---DWRSLT 139 (424)
T ss_pred cccceeeEEE---ECCCEEEEeCCcC---Chhhhh
Confidence 3789999998 4788999999999 665543
No 27
>PHA02820 phospholipase-D-like protein; Provisional
Probab=31.86 E-value=39 Score=38.00 Aligned_cols=37 Identities=35% Similarity=0.559 Sum_probs=26.2
Q ss_pred CCCcceeEEeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEE
Q 006675 482 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLI 533 (636)
Q Consensus 482 a~PHiKty~r~~~~~i~W~lltSaNLSkaAWG~l~k~~sql~IrNyElGVL~ 533 (636)
...|.|+.+-.. .|+|+||+|+. |..+. .|.|+||.+
T Consensus 112 ~~~HrK~~VIDg----~~~~iGS~Nid---~rsl~--------~n~E~gv~i 148 (424)
T PHA02820 112 GVLHTKFWISDN----THIYLGSANMD---WRSLT--------QVKELGIAI 148 (424)
T ss_pred ccceeeEEEECC----CEEEEeCCcCC---hhhhh--------hCCceEEEE
Confidence 458999887432 37999999994 44443 256888876
No 28
>TIGR02500 type_III_yscD type III secretion apparatus protein, YscD/HrpQ family. This family represents a conserved protein of bacterial type III secretion systems. Gene symbols are variable from species to species. Members are designated YscD in Yersinia, HrpQ in Pseudomonas syringae, and EscD in enteropathogenic Escherichia coli. In the Chlamydiae, this model describes the C-terminal 400 residues of a longer protein.
Probab=31.32 E-value=62 Score=36.15 Aligned_cols=37 Identities=32% Similarity=0.618 Sum_probs=32.4
Q ss_pred cccCCCCCcccc-CC---CccccccccccceeEEEecCCcc
Q 006675 24 KLPLSQGPNVIG-RT---NIPVSDKRLSRKHITLTASADGS 60 (636)
Q Consensus 24 ~~~~~~~~~~~~-~~---~~~~~~~~~~~~~~~~~~~~~~~ 60 (636)
.++|..|.-+|| ++ +|+..|..++|.|++|+...+|.
T Consensus 14 ~~~L~~g~~~iG~~~~~~di~L~d~~~~~~h~~l~v~~~~~ 54 (410)
T TIGR02500 14 ELPLPEGNLVLGTDAADCDIVLSDGGIAAVHVSLHVRLEGV 54 (410)
T ss_pred EEECCCCceEeccCCCCcEEEeCCCCccchheEEEEcCceE
Confidence 467889999999 65 78999999999999999998774
No 29
>COG3886 Predicted HKD family nuclease [DNA replication, recombination, and repair]
Probab=24.91 E-value=61 Score=32.81 Aligned_cols=32 Identities=22% Similarity=0.241 Sum_probs=24.0
Q ss_pred CCCCcceeEEeecCCceeEEEEeccccchhhhh
Q 006675 481 RAMPHIKTFARYNGQKLAWFLLTSANLSKAAWG 513 (636)
Q Consensus 481 ~a~PHiKty~r~~~~~i~W~lltSaNLSkaAWG 513 (636)
.+-.|.|-|++--...+. +.+||.|||+.|--
T Consensus 117 ~~~fH~KgYiFe~~~~~t-aiiGSsNlt~sALt 148 (198)
T COG3886 117 SANFHTKGYIFEHNTGIT-AIIGSSNLTDSALT 148 (198)
T ss_pred ccccccceeEEEecceEE-EEEccchhhhhhcc
Confidence 466799999954433333 88999999999853
No 30
>PF10382 DUF2439: Protein of unknown function (DUF2439); InterPro: IPR018838 This domain is found at the N-terminal of proteins implicated in telomere maintenance in Saccharomyces cerevisiae (Baker's yeast) [] and in meiotic chromosome segregation in Schizosaccharomyces pombe (Fission yeast) [].
Probab=20.22 E-value=2e+02 Score=24.99 Aligned_cols=61 Identities=16% Similarity=0.209 Sum_probs=42.3
Q ss_pred cccccceeEEEecCCcceEEEeecCCcEEEeeCCcccccccc-ccc--ccccCCccccCCCCccceeee
Q 006675 44 KRLSRKHITLTASADGSASLVVDGTNPVVVKSGDQRKKLSSN-EHV--SIADGDIIELIPGHHFFKYVT 109 (636)
Q Consensus 44 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~--~i~~~~~~~~~~~~~~~~~~~ 109 (636)
+++.+||++-+ ||.+.+. ++.|-|++-.+ +..++... .+. .+..|+.++++-|.++.-..+
T Consensus 10 ~q~~kK~K~W~---DG~l~~~-~~~~kv~Lyde-~~~~i~~~~~~~~~~~~~g~e~~l~~~~~LV~i~e 73 (83)
T PF10382_consen 10 HQKTKKRKKWH---DGFLKYH-SFNKKVMLYDE-DGNLIGSDFLKNSEELEEGDELELPKGGYLVQIEE 73 (83)
T ss_pred ccccccceeeE---CCEEEEE-eCCCEEEEEcC-CCCEEeEEEEecCCCCCCCCEEEEcCCCEEEEEec
Confidence 56788998885 9999888 77777777665 33344322 222 377899999998888875333
Done!