Query 010545
Match_columns 507
No_of_seqs 159 out of 340
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 01:47:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010545.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010545hhsearch_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-103 1E-107 804.2 26.4 427 35-498 82-519 (519)
2 PF06087 Tyr-DNA_phospho: Tyro 100.0 6.1E-98 1E-102 796.7 9.4 404 32-473 1-443 (443)
3 PF13091 PLDc_2: PLD-like doma 95.1 0.017 3.7E-07 50.5 2.9 38 353-405 73-110 (126)
4 smart00155 PLDc Phospholipase 90.7 0.2 4.2E-06 32.8 2.1 25 353-381 3-27 (28)
5 PRK13912 nuclease NucT; Provis 89.7 0.38 8.3E-06 45.5 4.0 38 352-404 117-154 (177)
6 PF00614 PLDc: Phospholipase D 86.6 0.44 9.5E-06 31.5 1.5 25 123-150 2-26 (28)
7 smart00155 PLDc Phospholipase 86.0 0.93 2E-05 29.5 2.9 25 123-150 2-26 (28)
8 PF09565 RE_NgoFVII: NgoFVII r 84.2 1 2.3E-05 46.2 3.8 42 356-406 82-123 (296)
9 COG1502 Cls Phosphatidylserine 82.5 0.96 2.1E-05 48.3 2.9 40 353-407 353-392 (438)
10 cd00138 PLDc Phospholipase D. 81.9 1.4 3.1E-05 40.6 3.5 39 352-405 111-149 (176)
11 PRK01642 cls cardiolipin synth 79.0 1.8 3.8E-05 47.6 3.5 38 353-405 398-435 (483)
12 PRK11263 cardiolipin synthase 77.4 1.9 4.1E-05 46.4 3.1 39 353-406 286-324 (411)
13 PRK12452 cardiolipin synthetas 73.3 3 6.5E-05 46.1 3.4 38 353-405 424-461 (509)
14 cd00138 PLDc Phospholipase D. 71.5 4.8 0.0001 37.1 3.9 38 123-163 111-149 (176)
15 PF13091 PLDc_2: PLD-like doma 71.3 6.1 0.00013 34.1 4.3 30 124-156 73-102 (126)
16 PRK09428 pssA phosphatidylseri 66.6 6.3 0.00014 43.0 4.0 42 350-406 351-392 (451)
17 PRK13912 nuclease NucT; Provis 61.4 6.9 0.00015 36.9 2.8 31 122-155 116-146 (177)
18 PF09565 RE_NgoFVII: NgoFVII r 46.8 18 0.00038 37.4 3.1 27 125-151 80-107 (296)
19 COG3886 Predicted HKD family n 40.3 24 0.00052 34.0 2.7 32 352-384 117-148 (198)
20 PHA02820 phospholipase-D-like 38.5 26 0.00057 37.9 3.1 37 353-404 112-148 (424)
21 PLN03008 Phospholipase D delta 25.7 63 0.0014 37.9 3.5 39 353-404 715-753 (868)
22 PLN02352 phospholipase D epsil 22.4 55 0.0012 38.0 2.2 19 127-148 609-627 (758)
23 PF06087 Tyr-DNA_phospho: Tyro 21.4 89 0.0019 34.0 3.5 34 353-387 100-134 (443)
No 1
>KOG2031 consensus Tyrosyl-DNA phosphodiesterase [Replication, recombination and repair]
Probab=100.00 E-value=4.5e-103 Score=804.24 Aligned_cols=427 Identities=43% Similarity=0.726 Sum_probs=354.2
Q ss_pred eEEEEecCCCCCCCCCceeecccc---cccHHhhhhhhcccChhhhcccCCCCCCCCeEEEEeCCCCChhhhhhhcCCCc
Q 010545 35 FRLLRVQGLPAWANTSCVSIRDVI---QGDIIVAILSNYMVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPAN 111 (507)
Q Consensus 35 F~L~~~~~~~~~~n~~~itl~Dll---~~~l~~a~l~sF~~Dl~WLl~~~~~~~~~~~i~vv~g~~~~~~~~~~~~~~~n 111 (507)
|.+++.+..|+.+....+++.+|+ .|++..+++||||+|++||+.+||...+.+.|+++||+.++.........+.+
T Consensus 82 ft~v~~~s~~~~~s~~s~sl~~il~~i~g~~v~silfsfmvdid~Lv~~y~~~~~~~~i~l~~G~~d~~~~~~~~K~~~l 161 (519)
T KOG2031|consen 82 FTTVKGDSVPRYDSMGSVSLMEILADIFGTPVNSILFSFMVDIDWLVGQYPPSVRIKPITLVHGEPDEARLLAQTKAPIL 161 (519)
T ss_pred ccccccccccccCcccchHHHHHHHHhhCCchhheEEEEEeEHHHHHhhCcchhccCceEEEecCCchHHHHhhhhccce
Confidence 333333345554444666666664 56899999999999999999999865556668889998774333333345678
Q ss_pred eEEecCCCCCCCCCccceeeEeeeCCccEEEEeCCCCCccccccccceEEEeecCCCCCCCCCCCCCcHHHHHHHHHhcC
Q 010545 112 WILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTLK 191 (507)
Q Consensus 112 ~~~~~p~mp~~fGthHSKmmlL~y~d~lRVVI~TANL~~~DW~~~tQ~vW~qdfP~~~~~~~~~~t~F~~dL~~yL~ay~ 191 (507)
+.++.+.||++|||||+|||+|+|++|+||||+||||++.||++++|++|+++++++.......++.|+.||++||++|+
T Consensus 162 ~~~~~~~LpipF~thHtKm~~l~y~~G~rvvv~taNl~~~Dw~~ktQ~~w~sp~~~~~~~~g~~~~~Fk~DLi~YL~~Y~ 241 (519)
T KOG2031|consen 162 VTVKLASLPIPFGTHHTKMIILFYEEGCRVVVHTANLIHDDWNNKTQGFWCSPLLKIGDKKGVSPTGFKQDLIEYLNSYR 241 (519)
T ss_pred eeeecccccccccccccceEEEeccCccEEEEecCCcceecccccccceeecCCcccccCCCCCCCchHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999888776677899999999999999999
Q ss_pred CCccccCCCCCCCccccccccccccccccceEEEEccCCCCCCCccchhcHHHHHHHHhhccccCCCcccCeEEEecCCC
Q 010545 192 WPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLG 271 (507)
Q Consensus 192 ~~~~~~~~~~l~~~~i~~~~l~~~DFS~~~v~LV~SvPG~h~g~~~~~~G~~~L~~~L~~~~~~~~~~~~~i~~Q~SSiG 271 (507)
++.+. .|+++|+++|||.++|+||+||||++.|.....|||.||+++|+++......++++++||+||+|
T Consensus 242 ~~~l~----------~~i~~lkk~DfS~i~v~fIgStPG~f~gs~~~~WGh~kL~kiL~~~~~~~~~~r~~~v~q~sS~g 311 (519)
T KOG2031|consen 242 LPQLK----------EWIASLKKVDFSAINVRFIGSTPGKFQGSGLLSWGHNKLKKILKEHAASPYLERTPVVGQSSSIG 311 (519)
T ss_pred cchhH----------HHHHHHHhcchhhceEEEEeecCCcccCcccccccHHHHHHHHHhhccCcccccCceeeeeeccc
Confidence 87543 34689999999999999999999988887766799999999999987655567899999999999
Q ss_pred cCchHHHHHHHHhccCCCCCCCCCCCC--CCcEEEccCchhhhcCcccCCCCccccCCCccch-hHHHHHHHhhhcCCCC
Q 010545 272 SLDEKWMAELSSSMSSGFSEDKTPLGI--GEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVD-KDFLKKYWAKWKASHT 348 (507)
Q Consensus 272 sl~~~wl~~f~~sl~~~~~~~~~~~~~--~~~~IifPT~e~Vr~S~~G~~~gg~i~~~~~~~~-~~~l~~~~~kw~~~~~ 348 (507)
+++..|...|...+..+..++..+.+. ++++|||||+||||+|.+||.+||||||..++.+ +.|+++|||||.+.++
T Consensus 312 sl~~~~~~~~~~~f~~~l~kdt~~~gk~~~~~yiIfPTveeVrtS~~G~~~Ggsipy~~~~~~kq~~lk~y~~kW~A~~s 391 (519)
T KOG2031|consen 312 SLGSLWSAWFIGDFVESLAKDTTPPGKLRPPFYIIFPTVEEVRTSLLGYAGGGSLPYGKNTNEKQPWLKKYLCKWKAMDS 391 (519)
T ss_pred cccchhhhhhhhhhccchhhccCCCCCCCCCeeEEcccHHHhhccccccccCceecccchhhhhhHHHHHHHHhhhhhhh
Confidence 999887766666655554444444433 4689999999999999999999999999876665 5899999999999999
Q ss_pred CCCCCCCcceeeeeec--CCceeEEEEeccccchhhhhccccCCc---eeeeeeeeeeeEEcCCcccCCCccccccCCCC
Q 010545 349 GRSRAMPHIKTFARYN--GQKLAWFLLTSANLSKAAWGALQKNNS---QLMIRSYELGVLILPSAKRHGCGFSCTSNIVP 423 (507)
Q Consensus 349 ~R~~~~pH~K~y~r~~--~~~~~W~lltSaNLS~aAWG~~~k~~~---ql~i~nyElGVl~~P~~~~~~~~~~~~~~~~~ 423 (507)
+|+|||||||||||++ ++.+.|+|||||||||||||+++++++ ||+|||||+||||+|..+.+..+++
T Consensus 392 ~R~ramPHiKtYmr~~~d~q~l~W~LlTSANLSKaAWG~l~kn~sk~~~LmIRsYEaGVLf~p~~~~~~kt~k------- 464 (519)
T KOG2031|consen 392 RRSRAMPHIKTYMRFNLDDQKLAWFLLTSANLSKAAWGTLSKNKSKQPQLMIRSYEAGVLFLPRFFANLKTFK------- 464 (519)
T ss_pred hccccCCcceeeeeecCCCCEEEEEEEeccccchhhhhhhccCCCCCchheeeecccceEecchhhhcccccc-------
Confidence 9999999999999999 689999999999999999999998875 8999999999999999765321111
Q ss_pred ccccCCCccchhcccceeeeeecCCCCCCCCCCcccccccccCCCCCCCCCCCCCceecCCCCCccCCCCCCccc
Q 010545 424 SEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTKKDVYGQVWPRH 498 (507)
Q Consensus 424 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vPy~lP~~~Y~~~D~Pw~~~~~y~~~D~~G~~w~~~ 498 (507)
++.-++.++.. ......||||||+|++||++.|+||++++.+..+||+|++|.+.
T Consensus 465 -----------------~~~~tf~~~~~---~~~v~~vpvpydlPp~pY~~~d~~~~~~~~~~~~d~lG~vW~p~ 519 (519)
T KOG2031|consen 465 -----------------VVEDTFPRDNN---GDGVIAVPVPYDLPPVPYSPKDEPFFTDIYRQGPDWLGCVWTPN 519 (519)
T ss_pred -----------------ccceecccccC---CCCcceeccccCCCCcCCCccCCceeecccccCCcceeeccCCC
Confidence 11111222221 12247899999999999999999999997777899999999873
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=6.1e-98 Score=796.74 Aligned_cols=404 Identities=42% Similarity=0.703 Sum_probs=286.8
Q ss_pred CCceEEEEecCCCCC--CCCCceeecccccc-cHHhhhhhhcccChhhhcccCCCC-CCCCeEEEEeCCCCC-hhhhhhh
Q 010545 32 PSTFRLLRVQGLPAW--ANTSCVSIRDVIQG-DIIVAILSNYMVDIDWLLPACPVL-AKIPHVLVIHGESDG-TLEHMKR 106 (507)
Q Consensus 32 ~~~F~L~~~~~~~~~--~n~~~itl~Dll~~-~l~~a~l~sF~~Dl~WLl~~~~~~-~~~~~i~vv~g~~~~-~~~~~~~ 106 (507)
|++|.++++.+.+.. .|.++|||+|||++ +|++|++||||+|++|||++|+.. +....|++++|+.+. ....++.
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 456777788888775 57899999999998 799999999999999999999853 322367888884322 2222222
Q ss_pred --cCCCceEEecCCCCCCCCCccceeeEeeeCCc-cEEEEeCCCCCccccccccceEEEeec-CCCCC---CCCCCCCCc
Q 010545 107 --NKPANWILHKPPLPISFGTHHSKAMLLIYPRG-VRIIVHTANLIHVDWNNKSQGLWMQDF-PLKDQ---NNLSEECGF 179 (507)
Q Consensus 107 --~~~~n~~~~~p~mp~~fGthHSKmmlL~y~d~-lRVVI~TANL~~~DW~~~tQ~vW~qdf-P~~~~---~~~~~~t~F 179 (507)
....|+++|.|+||.+|||||||||||+|+|| ||||||||||+++||+++||+||+||| |++.. ...+.+++|
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 24579999999999999999999999999999 999999999999999999999999998 98754 234678999
Q ss_pred HHHHHHHHHhcCCCccccCCCCCCCccccccccccccccccceEEEEccCCCCCCCccchhcHHHHHHHHhhccccC---
Q 010545 180 ENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEK--- 256 (507)
Q Consensus 180 ~~dL~~yL~ay~~~~~~~~~~~l~~~~i~~~~l~~~DFS~~~v~LV~SvPG~h~g~~~~~~G~~~L~~~L~~~~~~~--- 256 (507)
++||++||++|+.+.... +++.|++||||.++|+||+||||+|. .+..+|||++|+++|+++....
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 4556899999999999987654
Q ss_pred CCcccCeEEEecCCCcCc---hHHH-HHHHHhccCCCCC-CC----------CCCCCCCcEEEccCchhhhcCcccCCCC
Q 010545 257 GFKKSPLVYQFSSLGSLD---EKWM-AELSSSMSSGFSE-DK----------TPLGIGEPLIVWPTVEDVRCSLEGYAAG 321 (507)
Q Consensus 257 ~~~~~~i~~Q~SSiGsl~---~~wl-~~f~~sl~~~~~~-~~----------~~~~~~~~~IifPT~e~Vr~S~~G~~~g 321 (507)
...+.+++||+||||+++ ..|| .+|+.+|...... .. .....++++|||||+||||+|..|+.+|
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 4788887654320 00 1112356899999999999999999999
Q ss_pred ccccCCCc----cchhHHHHHHHhhhcCC--CCCCCCCCCcceeeeeec---CCceeEEEEeccccchhhhhccccCCce
Q 010545 322 NAIPSPQK----NVDKDFLKKYWAKWKAS--HTGRSRAMPHIKTFARYN---GQKLAWFLLTSANLSKAAWGALQKNNSQ 392 (507)
Q Consensus 322 g~i~~~~~----~~~~~~l~~~~~kw~~~--~~~R~~~~pH~K~y~r~~---~~~~~W~lltSaNLS~aAWG~~~k~~~q 392 (507)
||||++.+ +..+.+|+++||+|.+. .++|++++||+|+|+|++ .+.++|+|+||||||+||||+.+++++|
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 34468999999999988 899999999999999997 5789999999999999999999999999
Q ss_pred eeeeeeeeeeEEcCCcccCCCccccccCCCCccccCCCccchhcccceeeeeecCCCCCCCCCCcccccccccCCCCCCC
Q 010545 393 LMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRY 472 (507)
Q Consensus 393 l~i~nyElGVl~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vPy~lP~~~Y 472 (507)
++||||||||||+|..... ...|.+.....+ .....+..+.|||||+||++||
T Consensus 390 l~i~nyElGVl~~P~~~~~--~~~~~~~~~~~~-------------------------~~~~~~~~~~v~vPf~lP~~~Y 442 (443)
T PF06087_consen 390 LSIRNYELGVLFLPSSFGV--MLPVFSLDDPVY-------------------------RSISSTNTVPVPVPFDLPPTPY 442 (443)
T ss_dssp CEESSBEEEEEEEGGGCTS--SSSCEEEECCG--------------------------------GGGCEEESS-SSEEE-
T ss_pred eeecceEEEEEEecCcccc--cccccccccccc-------------------------cccccCCCceEEecCCCCCcCc
Confidence 9999999999999986541 122222111100 0112344678999999999999
Q ss_pred C
Q 010545 473 S 473 (507)
Q Consensus 473 ~ 473 (507)
+
T Consensus 443 ~ 443 (443)
T PF06087_consen 443 G 443 (443)
T ss_dssp -
T ss_pred C
Confidence 6
No 3
>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=95.08 E-value=0.017 Score=50.46 Aligned_cols=38 Identities=34% Similarity=0.465 Sum_probs=26.9
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEc
Q 010545 353 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLIL 405 (507)
Q Consensus 353 ~~pH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~i~nyElGVl~~ 405 (507)
...|.|+|+-.+. .+++||+|||..|| -+|+|+||++.
T Consensus 73 ~~~H~K~~i~d~~----~~iiGS~N~t~~~~-----------~~n~E~~~~~~ 110 (126)
T PF13091_consen 73 NRLHAKFYIIDDK----VAIIGSANLTSSSF-----------RRNYELGVIID 110 (126)
T ss_dssp S-B--EEEEETTT----EEEEES--CSCCCS-----------CTSEEEEEEEE
T ss_pred cCCCcceEEecCc----cEEEcCCCCCcchh-----------cCCcceEEEEE
Confidence 4679999987432 89999999999999 27899999984
No 4
>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=90.71 E-value=0.2 Score=32.78 Aligned_cols=25 Identities=24% Similarity=0.190 Sum_probs=20.0
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchh
Q 010545 353 AMPHIKTFARYNGQKLAWFLLTSANLSKA 381 (507)
Q Consensus 353 ~~pH~K~y~r~~~~~~~W~lltSaNLS~a 381 (507)
...|.|+++-.+ .|+++||+||+..
T Consensus 3 ~~~H~K~~v~D~----~~~~iGs~N~~~~ 27 (28)
T smart00155 3 GVLHTKLMIVDD----EIAYIGSANLDGR 27 (28)
T ss_pred CcEEeEEEEEcC----CEEEEeCccCCCC
Confidence 467999988654 4899999999864
No 5
>PRK13912 nuclease NucT; Provisional
Probab=89.74 E-value=0.38 Score=45.49 Aligned_cols=38 Identities=29% Similarity=0.305 Sum_probs=30.6
Q ss_pred CCCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEE
Q 010545 352 RAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLI 404 (507)
Q Consensus 352 ~~~pH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~i~nyElGVl~ 404 (507)
...+|.|+++-.. .|+++||+|++..++. .|+|+||++
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 3468999987633 5899999999987764 489999987
No 6
>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=86.58 E-value=0.44 Score=31.49 Aligned_cols=25 Identities=32% Similarity=0.369 Sum_probs=14.9
Q ss_pred CCCccceeeEeeeCCccEEEEeCCCCCc
Q 010545 123 FGTHHSKAMLLIYPRGVRIIVHTANLIH 150 (507)
Q Consensus 123 fGthHSKmmlL~y~d~lRVVI~TANL~~ 150 (507)
.++||+|++++ |+-+.+|.++||..
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 7
>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=85.98 E-value=0.93 Score=29.53 Aligned_cols=25 Identities=28% Similarity=0.279 Sum_probs=20.6
Q ss_pred CCCccceeeEeeeCCccEEEEeCCCCCc
Q 010545 123 FGTHHSKAMLLIYPRGVRIIVHTANLIH 150 (507)
Q Consensus 123 fGthHSKmmlL~y~d~lRVVI~TANL~~ 150 (507)
.+.+|+|+++. |+-.++|.|+||..
T Consensus 2 ~~~~H~K~~v~---D~~~~~iGs~N~~~ 26 (28)
T smart00155 2 DGVLHTKLMIV---DDEIAYIGSANLDG 26 (28)
T ss_pred CCcEEeEEEEE---cCCEEEEeCccCCC
Confidence 46799999886 45589999999975
No 8
>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=84.18 E-value=1 Score=46.23 Aligned_cols=42 Identities=31% Similarity=0.237 Sum_probs=30.5
Q ss_pred cceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEcC
Q 010545 356 HIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILP 406 (507)
Q Consensus 356 H~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~i~nyElGVl~~P 406 (507)
|.|+|.=..+...-=+|+||||||.- ||..+ +.||..|+.-+
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 99999876554444699999999985 55432 67887776643
No 9
>COG1502 Cls Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthases and related enzymes [Lipid metabolism]
Probab=82.52 E-value=0.96 Score=48.32 Aligned_cols=40 Identities=28% Similarity=0.326 Sum_probs=33.5
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEcCC
Q 010545 353 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPS 407 (507)
Q Consensus 353 ~~pH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~i~nyElGVl~~P~ 407 (507)
+..|.|+++-.+ .|+++||+||+..++. .|+|++|++...
T Consensus 353 ~~lH~K~~iiD~----~~~~vGS~N~~~rS~~-----------lN~E~~~~i~d~ 392 (438)
T COG1502 353 AFLHSKVMIIDD----RTVLVGSANLDPRSLR-----------LNFEVGLVIEDP 392 (438)
T ss_pred CcceeeEEEEcC----CEEEEeCCcCCHhHHH-----------HhhhheeEEeCH
Confidence 578999988765 5799999999999875 479999999543
No 10
>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=81.89 E-value=1.4 Score=40.62 Aligned_cols=39 Identities=26% Similarity=0.234 Sum_probs=31.7
Q ss_pred CCCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEc
Q 010545 352 RAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLIL 405 (507)
Q Consensus 352 ~~~pH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~i~nyElGVl~~ 405 (507)
....|.|+++-.+ .-+++||+|++..+|. .|.|+||++.
T Consensus 111 ~~~~H~K~~iiD~----~~~~vGS~N~~~~~~~-----------~~~e~~~~~~ 149 (176)
T cd00138 111 GGVLHTKLVIVDD----ETAYIGSANLDGRSLT-----------LNSEVGVVIY 149 (176)
T ss_pred ccceeeeEEEEcC----CEEEEECCcCChhhhh-----------hhcceEEEEe
Confidence 3678999987643 2699999999999988 5789999873
No 11
>PRK01642 cls cardiolipin synthetase; Reviewed
Probab=79.03 E-value=1.8 Score=47.59 Aligned_cols=38 Identities=18% Similarity=0.268 Sum_probs=31.3
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEc
Q 010545 353 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLIL 405 (507)
Q Consensus 353 ~~pH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~i~nyElGVl~~ 405 (507)
...|.|+.+-.+ .|+++||+|++..++. .|+|+||++.
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 467999987654 5899999999877762 6999999984
No 12
>PRK11263 cardiolipin synthase 2; Provisional
Probab=77.44 E-value=1.9 Score=46.43 Aligned_cols=39 Identities=21% Similarity=0.189 Sum_probs=31.5
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEcC
Q 010545 353 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILP 406 (507)
Q Consensus 353 ~~pH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~i~nyElGVl~~P 406 (507)
-+.|.|+.+-.. .|+++||+||...++. .|+|++|++.-
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 467999988654 5999999999886652 69999999853
No 13
>PRK12452 cardiolipin synthetase; Reviewed
Probab=73.27 E-value=3 Score=46.15 Aligned_cols=38 Identities=16% Similarity=0.215 Sum_probs=31.0
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEc
Q 010545 353 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLIL 405 (507)
Q Consensus 353 ~~pH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~i~nyElGVl~~ 405 (507)
...|.|+.+-.+ .|+++||+||..-++. .|||+++++.
T Consensus 424 ~~lHaK~~ivD~----~~a~vGS~Nld~RS~~-----------~n~E~~~~i~ 461 (509)
T PRK12452 424 GFMHAKIVLVDD----KIATIGTANMDVRSFE-----------LNYEIISVLY 461 (509)
T ss_pred CCeeeeEEEECC----CEEEEeCcccCHhHhh-----------hhhhccEEEE
Confidence 467999988655 4999999999887764 3999999884
No 14
>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=71.47 E-value=4.8 Score=37.05 Aligned_cols=38 Identities=21% Similarity=0.239 Sum_probs=29.1
Q ss_pred CCCccceeeEeeeCCccEEEEeCCCCCccccc-cccceEEEe
Q 010545 123 FGTHHSKAMLLIYPRGVRIIVHTANLIHVDWN-NKSQGLWMQ 163 (507)
Q Consensus 123 fGthHSKmmlL~y~d~lRVVI~TANL~~~DW~-~~tQ~vW~q 163 (507)
.+.+|+|+||. |+=.++|.|+|+....+. +...++.+.
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 456899999999998874 333444443
No 15
>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=71.33 E-value=6.1 Score=34.12 Aligned_cols=30 Identities=20% Similarity=0.275 Sum_probs=20.7
Q ss_pred CCccceeeEeeeCCccEEEEeCCCCCccccccc
Q 010545 124 GTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNK 156 (507)
Q Consensus 124 GthHSKmmlL~y~d~lRVVI~TANL~~~DW~~~ 156 (507)
+.+|.|+++.- +=.++|.|+|++...|..-
T Consensus 73 ~~~H~K~~i~d---~~~~iiGS~N~t~~~~~~n 102 (126)
T PF13091_consen 73 NRLHAKFYIID---DKVAIIGSANLTSSSFRRN 102 (126)
T ss_dssp S-B--EEEEET---TTEEEEES--CSCCCSCTS
T ss_pred cCCCcceEEec---CccEEEcCCCCCcchhcCC
Confidence 78999999983 4499999999999998655
No 16
>PRK09428 pssA phosphatidylserine synthase; Provisional
Probab=66.61 E-value=6.3 Score=43.00 Aligned_cols=42 Identities=31% Similarity=0.447 Sum_probs=33.9
Q ss_pred CCCCCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEcC
Q 010545 350 RSRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILP 406 (507)
Q Consensus 350 R~~~~pH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~i~nyElGVl~~P 406 (507)
+...+-|.|+.+-.+ .|+++||+||-.-+|. .|+|+||++.-
T Consensus 351 ~~~~~~HaK~i~vD~----~~~~iGS~Nld~RS~~-----------ln~E~~l~i~d 392 (451)
T PRK09428 351 DGDNSYHLKGIWVDD----RWMLLTGNNLNPRAWR-----------LDLENALLIHD 392 (451)
T ss_pred cCCCcceEEEEEEeC----CEEEEcCCCCChhHhh-----------hcccceEEEEC
Confidence 345678999977533 4999999999999886 58999999853
No 17
>PRK13912 nuclease NucT; Provisional
Probab=61.39 E-value=6.9 Score=36.92 Aligned_cols=31 Identities=19% Similarity=0.390 Sum_probs=25.6
Q ss_pred CCCCccceeeEeeeCCccEEEEeCCCCCcccccc
Q 010545 122 SFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNN 155 (507)
Q Consensus 122 ~fGthHSKmmlL~y~d~lRVVI~TANL~~~DW~~ 155 (507)
.++.+|+|+||+ |+-.++|.|+|++...+..
T Consensus 116 ~~~~~H~K~~vi---D~~~~~iGS~N~t~~s~~~ 146 (177)
T PRK13912 116 YYGIMHQKVAII---DDKIVVLGSANWSKNAFEN 146 (177)
T ss_pred cccccceeEEEE---cCCEEEEeCCCCChhHhcc
Confidence 568899999988 7777999999999765543
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=46.82 E-value=18 Score=37.39 Aligned_cols=27 Identities=19% Similarity=0.263 Sum_probs=23.2
Q ss_pred CccceeeEeeeCCc-cEEEEeCCCCCcc
Q 010545 125 THHSKAMLLIYPRG-VRIIVHTANLIHV 151 (507)
Q Consensus 125 thHSKmmlL~y~d~-lRVVI~TANL~~~ 151 (507)
.-|+||.+....++ .+.+|-||||+..
T Consensus 80 ~~HgKlY~f~k~g~~~~a~IGSANfS~~ 107 (296)
T PF09565_consen 80 PYHGKLYIFSKNGKPFRAYIGSANFSQI 107 (296)
T ss_pred CcccEEEEEecCCCceEEEEeecccccc
Confidence 36999998766666 9999999999995
No 19
>COG3886 Predicted HKD family nuclease [DNA replication, recombination, and repair]
Probab=40.28 E-value=24 Score=34.02 Aligned_cols=32 Identities=22% Similarity=0.241 Sum_probs=24.3
Q ss_pred CCCCcceeeeeecCCceeEEEEeccccchhhhh
Q 010545 352 RAMPHIKTFARYNGQKLAWFLLTSANLSKAAWG 384 (507)
Q Consensus 352 ~~~pH~K~y~r~~~~~~~W~lltSaNLS~aAWG 384 (507)
.+-.|.|-|++--...+. +.+||.|||++|--
T Consensus 117 ~~~fH~KgYiFe~~~~~t-aiiGSsNlt~sALt 148 (198)
T COG3886 117 SANFHTKGYIFEHNTGIT-AIIGSSNLTDSALT 148 (198)
T ss_pred ccccccceeEEEecceEE-EEEccchhhhhhcc
Confidence 467799999854444443 89999999999853
No 20
>PHA02820 phospholipase-D-like protein; Provisional
Probab=38.45 E-value=26 Score=37.88 Aligned_cols=37 Identities=35% Similarity=0.559 Sum_probs=26.3
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEE
Q 010545 353 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLI 404 (507)
Q Consensus 353 ~~pH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~i~nyElGVl~ 404 (507)
...|.|+.+-.. .++|+||+|+. |..+. .|.|+||.+
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 458999987543 58999999994 44432 346888876
No 21
>PLN03008 Phospholipase D delta
Probab=25.73 E-value=63 Score=37.95 Aligned_cols=39 Identities=18% Similarity=0.264 Sum_probs=28.1
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEE
Q 010545 353 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLI 404 (507)
Q Consensus 353 ~~pH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~i~nyElGVl~ 404 (507)
+--|+|+++-.+ .|+.+|||||..-..+- -|++|+++.+
T Consensus 715 IYvHsK~~ivDd----~~~~iGSaN~n~RS~~~---------~Rd~E~~~~~ 753 (868)
T PLN03008 715 IYVHAKGMIVDD----EYVLMGSANINQRSMAG---------TKDTEIAMGA 753 (868)
T ss_pred EEEeeeEEEECC----CEEEEeccccCHhhccC---------CCCceEeEEe
Confidence 344888877644 68999999996544332 3789999876
No 22
>PLN02352 phospholipase D epsilon
Probab=22.37 E-value=55 Score=38.03 Aligned_cols=19 Identities=37% Similarity=0.616 Sum_probs=0.0
Q ss_pred cceeeEeeeCCccEEEEeCCCC
Q 010545 127 HSKAMLLIYPRGVRIIVHTANL 148 (507)
Q Consensus 127 HSKmmlL~y~d~lRVVI~TANL 148 (507)
||||||. |.--|+|-|||+
T Consensus 609 HSKlMIV---DD~~viIGSANI 627 (758)
T PLN02352 609 HSKLMIV---DDTYILIGSANV 627 (758)
T ss_pred eeeEEEE---cCcEEEEccccc
No 23
>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=21.40 E-value=89 Score=33.96 Aligned_cols=34 Identities=21% Similarity=0.354 Sum_probs=22.8
Q ss_pred CCCcceeeeeecCCc-eeEEEEeccccchhhhhccc
Q 010545 353 AMPHIKTFARYNGQK-LAWFLLTSANLSKAAWGALQ 387 (507)
Q Consensus 353 ~~pH~K~y~r~~~~~-~~W~lltSaNLS~aAWG~~~ 387 (507)
..+|+|+++-+-.+. + -+.+.||||...-|+..+
T Consensus 100 g~hHsKm~ll~y~~~~l-RVvI~TaNl~~~Dw~~~~ 134 (443)
T PF06087_consen 100 GTHHSKMMLLFYEDGSL-RVVIPTANLTPYDWNNKT 134 (443)
T ss_dssp --B--EEEEEEETTCEE-EEEEESS-BSHHHHCSSB
T ss_pred ccccceeEEEEeCCccE-EEEEECCCCCHHHHCCcc
Confidence 677999976554444 5 499999999999999964
Done!