Query 014528
Match_columns 423
No_of_seqs 156 out of 335
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 06:01:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014528.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014528hhsearch_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 2E-96 4E-101 739.8 26.3 371 3-414 138-519 (519)
2 PF06087 Tyr-DNA_phospho: Tyro 100.0 4E-89 8.6E-94 710.3 12.4 349 3-389 61-443 (443)
3 PF13091 PLDc_2: PLD-like doma 95.6 0.0093 2E-07 50.7 2.8 38 269-321 73-110 (126)
4 smart00155 PLDc Phospholipase 91.0 0.19 4.1E-06 32.1 2.2 25 269-297 3-27 (28)
5 PRK13912 nuclease NucT; Provis 90.8 0.28 6.1E-06 45.2 4.0 37 269-320 118-154 (177)
6 PF00614 PLDc: Phospholipase D 89.8 0.23 4.9E-06 32.2 1.7 25 39-66 2-26 (28)
7 PF09565 RE_NgoFVII: NgoFVII r 87.4 0.59 1.3E-05 46.9 3.7 42 272-322 82-123 (296)
8 smart00155 PLDc Phospholipase 86.8 0.63 1.4E-05 29.7 2.4 25 39-66 2-26 (28)
9 cd00138 PLDc Phospholipase D. 85.3 0.91 2E-05 40.7 3.6 38 269-321 112-149 (176)
10 cd00138 PLDc Phospholipase D. 83.2 3.8 8.2E-05 36.7 6.7 38 39-79 111-149 (176)
11 COG1502 Cls Phosphatidylserine 80.2 1.3 2.8E-05 46.0 2.8 40 269-323 353-392 (438)
12 PRK11263 cardiolipin synthase 79.6 1.6 3.4E-05 45.8 3.2 39 269-322 286-324 (411)
13 PRK01642 cls cardiolipin synth 79.6 1.7 3.7E-05 46.4 3.5 38 269-321 398-435 (483)
14 PF13091 PLDc_2: PLD-like doma 77.5 2.8 6E-05 35.3 3.6 37 40-79 73-110 (126)
15 PRK12452 cardiolipin synthetas 74.1 2.7 5.8E-05 45.3 3.2 38 269-321 424-461 (509)
16 PRK09428 pssA phosphatidylseri 70.4 5.1 0.00011 42.6 4.2 41 267-322 352-392 (451)
17 PRK13912 nuclease NucT; Provis 66.9 6.2 0.00014 36.2 3.5 31 38-71 116-146 (177)
18 PF09565 RE_NgoFVII: NgoFVII r 54.8 10 0.00022 38.2 2.8 27 41-67 80-107 (296)
19 PHA02820 phospholipase-D-like 48.5 16 0.00034 38.6 3.2 37 270-322 323-359 (424)
20 COG3886 Predicted HKD family n 39.5 26 0.00056 33.1 2.7 32 268-300 117-148 (198)
21 KOG3603 Predicted phospholipas 29.9 51 0.0011 34.8 3.3 39 267-320 166-204 (456)
22 PLN02352 phospholipase D epsil 27.0 36 0.00077 38.6 1.8 26 42-70 608-633 (758)
23 TIGR03705 poly_P_kin polyphosp 26.9 81 0.0018 35.4 4.5 40 270-321 581-620 (672)
24 PF06087 Tyr-DNA_phospho: Tyro 22.8 84 0.0018 33.3 3.5 34 269-303 100-134 (443)
No 1
>KOG2031 consensus Tyrosyl-DNA phosphodiesterase [Replication, recombination and repair]
Probab=100.00 E-value=2e-96 Score=739.80 Aligned_cols=371 Identities=43% Similarity=0.713 Sum_probs=318.4
Q ss_pred ceEEEEEecCc-hhhhhhhhccCCCcEEEEcCCCCCCCCccccceeeeeeCCceEEEEeCCCCCccccccccceEEeecc
Q 014528 3 ILLLLFYQTTW-WTLIGCCQRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDF 81 (423)
Q Consensus 3 ~~~~~~~~~~~-~~~~~~~~~~~~~n~~~~~p~mp~~fG~hHSKmmll~y~d~lRVVI~SANL~~~DW~~~tQ~vW~qdf 81 (423)
+++++.||+.+ +++.+..+ .+.|+++|.+.||++|||||+|||+|+|++|+||||+||||++.||++++|++|++|+
T Consensus 138 ~~i~l~~G~~d~~~~~~~~K--~~~l~~~~~~~LpipF~thHtKm~~l~y~~G~rvvv~taNl~~~Dw~~ktQ~~w~sp~ 215 (519)
T KOG2031|consen 138 KPITLVHGEPDEARLLAQTK--APILVTVKLASLPIPFGTHHTKMIILFYEEGCRVVVHTANLIHDDWNNKTQGFWCSPL 215 (519)
T ss_pred CceEEEecCCchHHHHhhhh--ccceeeeecccccccccccccceEEEeccCccEEEEecCCcceecccccccceeecCC
Confidence 46888999988 45443333 3779999999999999999999999999999999999999999999999999999998
Q ss_pred CCCCCCCCCCCCCcHHHHHHHHHhCCCCccccCCCCCCCccccccccccccccccceeEEEccCCCCCCCccchhcHHHH
Q 014528 82 PLKDQNNLSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKL 161 (423)
Q Consensus 82 P~~~~~~~~~~~~F~~dL~~yL~ay~~~~~~~~~~~l~~~~i~~~~L~~yDFS~~~v~LV~SVPG~h~g~~~~~~G~~~L 161 (423)
+.+.+.....++.|++||++||++|+++... .++++|+++|||.++|+||+||||++.|.....|||.||
T Consensus 216 ~~~~~~~g~~~~~Fk~DLi~YL~~Y~~~~l~----------~~i~~lkk~DfS~i~v~fIgStPG~f~gs~~~~WGh~kL 285 (519)
T KOG2031|consen 216 LKIGDKKGVSPTGFKQDLIEYLNSYRLPQLK----------EWIASLKKVDFSAINVRFIGSTPGKFQGSGLLSWGHNKL 285 (519)
T ss_pred cccccCCCCCCCchHHHHHHHHHHhccchhH----------HHHHHHHhcchhhceEEEEeecCCcccCcccccccHHHH
Confidence 8877667788999999999999999987543 347899999999999999999999888877767999999
Q ss_pred HHHHhhcCccCCCcccCeEEEecCCCCCchHHHHHHHHhccCCCCCCCCCCCC--CCCeEEccChhhhhcCcccCcCCcc
Q 014528 162 RTVLQECTFEKGFKKSPLVYQFSSLGSLDEKWMAELSSSMSSGFSEDKTPLGI--GEPLIVWPTVEDVRCSLEGYAAGNA 239 (423)
Q Consensus 162 ~~~L~~~~~~~~~~~~~i~~Q~SSiGsl~~~wl~~~~~sl~~~~~~~~~~~~~--~~~~iifPT~~~V~~S~~G~~~gg~ 239 (423)
+++|+.+......++.+++||+||+|+++..|...|...+.....++.++.+. ++++|||||+||||+|.+||.+|||
T Consensus 286 ~kiL~~~~~~~~~~r~~~v~q~sS~gsl~~~~~~~~~~~f~~~l~kdt~~~gk~~~~~yiIfPTveeVrtS~~G~~~Ggs 365 (519)
T KOG2031|consen 286 KKILKEHAASPYLERTPVVGQSSSIGSLGSLWSAWFIGDFVESLAKDTTPPGKLRPPFYIIFPTVEEVRTSLLGYAGGGS 365 (519)
T ss_pred HHHHHhhccCcccccCceeeeeeccccccchhhhhhhhhhccchhhccCCCCCCCCCeeEEcccHHHhhccccccccCce
Confidence 99999987655567899999999999999888777766665555555554443 4589999999999999999999999
Q ss_pred ccCCCccch-hHHHHHHHhhhcCCCCCCCCCCCcceeeeeec--CCceeEEEEeccccchhhhhccccCCc---eeeeee
Q 014528 240 IPSPQKNVD-KDFLKKYWAKWKASHTGRSRAMPHIKTFARYN--GQKLAWFLLTSANLSKAAWGALQKNNS---QLMIRS 313 (423)
Q Consensus 240 i~~~~~~~~-~~~l~~~~~kw~~~~~~R~~~~PH~K~y~r~~--~~~~~W~lltSaNLS~aAWG~~~k~~~---ql~irn 313 (423)
|||..++.+ +.|+++|||||.+.+++|+|||||||||||++ ++.+.|||||||||||||||.++++++ ||+|||
T Consensus 366 ipy~~~~~~kq~~lk~y~~kW~A~~s~R~ramPHiKtYmr~~~d~q~l~W~LlTSANLSKaAWG~l~kn~sk~~~LmIRs 445 (519)
T KOG2031|consen 366 LPYGKNTNEKQPWLKKYLCKWKAMDSRRSRAMPHIKTYMRFNLDDQKLAWFLLTSANLSKAAWGTLSKNKSKQPQLMIRS 445 (519)
T ss_pred ecccchhhhhhHHHHHHHHhhhhhhhhccccCCcceeeeeecCCCCEEEEEEEeccccchhhhhhhccCCCCCchheeee
Confidence 999876665 58999999999999999999999999999998 689999999999999999999999876 999999
Q ss_pred eeeeeEEcCCcccCC--CccccccCCCCccccCCCccchhhhcceeeeeecCCCCCCCCCCcccccccccCCCCCCCCCC
Q 014528 314 YELGVLILPSAKRHG--CGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSE 391 (423)
Q Consensus 314 yElGVl~~P~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vPy~lP~~~Y~~~ 391 (423)
||+||||+|..+.+. .+..|.. +..+.. ....+.||||||||++||++.
T Consensus 446 YEaGVLf~p~~~~~~kt~k~~~~t--------------------------f~~~~~---~~~v~~vpvpydlPp~pY~~~ 496 (519)
T KOG2031|consen 446 YEAGVLFLPRFFANLKTFKVVEDT--------------------------FPRDNN---GDGVIAVPVPYDLPPVPYSPK 496 (519)
T ss_pred cccceEecchhhhcccccccccee--------------------------cccccC---CCCcceeccccCCCCcCCCcc
Confidence 999999999976542 2222221 212211 123478999999999999999
Q ss_pred CCCceecCCCCCccCCCCCCccc
Q 014528 392 DVPWSWDKRYTKKDVYGQVWPRH 414 (423)
Q Consensus 392 D~Pw~~~~~y~~~D~~G~~w~~~ 414 (423)
|+||+++..+..+|++|.+|++.
T Consensus 497 d~~~~~~~~~~~~d~lG~vW~p~ 519 (519)
T KOG2031|consen 497 DEPFFTDIYRQGPDWLGCVWTPN 519 (519)
T ss_pred CCceeecccccCCcceeeccCCC
Confidence 99999997777999999999863
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=4e-89 Score=710.29 Aligned_cols=349 Identities=43% Similarity=0.681 Sum_probs=246.2
Q ss_pred ceEEEEEecCchhhhhhhhc--cCCCcEEEEcCCCCCCCCccccceeeeeeCCc-eEEEEeCCCCCccccccccceEEee
Q 014528 3 ILLLLFYQTTWWTLIGCCQR--NKPANWILHKPPLPISFGTHHSKAMLLIYPRG-VRIIVHTANLIHVDWNNKSQGLWMQ 79 (423)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~--~~~~n~~~~~p~mp~~fG~hHSKmmll~y~d~-lRVVI~SANL~~~DW~~~tQ~vW~q 79 (423)
+.+++++|+....-...++. ...+||++|.|+||.+|||||||||||+|+|| ||||||||||++.||+++||+||+|
T Consensus 61 ~~i~~v~g~~~~~~~~~~~~~~~~~~nv~~~~~~mp~~~g~hHsKm~ll~y~~~~lRVvI~TaNl~~~Dw~~~~q~vw~~ 140 (443)
T PF06087_consen 61 IPITIVHGTKDPPDKREIRQQAAIYPNVKLIFPPMPIPFGTHHSKMMLLFYEDGSLRVVIPTANLTPYDWNNKTQGVWIQ 140 (443)
T ss_dssp EEEEEECTSEEHHHHHHHHHHHCCHTTEEEEEE---STT--B--EEEEEEETTCEEEEEEESS-BSHHHHCSSB-EEEE-
T ss_pred ceEEEEeCCCcchhhhhhhhhcccCCCeEEEccCCCcccccccceeEEEEeCCccEEEEEECCCCCHHHHCCcceeEEEe
Confidence 47889999444333334443 36779999999999999999999999999999 9999999999999999999999999
Q ss_pred cc-CCCCC---CCCCCCCCcHHHHHHHHHhCCCCccccCCCCCCCccccccccccccccccceeEEEccCCCCCCCccch
Q 014528 80 DF-PLKDQ---NNLSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKK 155 (423)
Q Consensus 80 df-P~~~~---~~~~~~~~F~~dL~~yL~ay~~~~~~~~~~~l~~~~i~~~~L~~yDFS~~~v~LV~SVPG~h~g~~~~~ 155 (423)
|| |++.. .....+++|++||++||++|+.+.... +++.|++||||.++|+||+||||+|. .+..+
T Consensus 141 d~lP~~~~~~~~~~~~~~~F~~dL~~yL~~y~~~~~~~----------~~~~l~~yDFS~~~v~lV~SvPG~h~-~~~~~ 209 (443)
T PF06087_consen 141 DFLPRLPSSKSSSEESGSRFKKDLVAYLNSYGKSPLDK----------LIERLRKYDFSSARVHLVASVPGKHK-EDKDK 209 (443)
T ss_dssp --E-B-ECTS-S--SSTTHHHHHHHHHHHTT--HHHHH----------CHHHHHTEE-CCGTSEEEEE-SECCC-GGGGG
T ss_pred cccCcccccccccCCCCCchHHHHHHHHHHhCCcchhH----------HHHHHHhcCCccCceEEEeccCcccc-CCCcc
Confidence 98 98754 234678999999999999998544211 15889999999999999999999999 55668
Q ss_pred hcHHHHHHHHhhcCccC---CCcccCeEEEecCCCCCc---hHHH-HHHHHhccCCCC---CC--------CCCCCCCCC
Q 014528 156 WGHMKLRTVLQECTFEK---GFKKSPLVYQFSSLGSLD---EKWM-AELSSSMSSGFS---ED--------KTPLGIGEP 217 (423)
Q Consensus 156 ~G~~~L~~~L~~~~~~~---~~~~~~i~~Q~SSiGsl~---~~wl-~~~~~sl~~~~~---~~--------~~~~~~~~~ 217 (423)
|||++|+++|++++... .....+|+||+||||+++ ..|| .+|+.+|..... .. .......++
T Consensus 210 ~G~~~L~~~L~~~~~~~~~~~~~~~~~~~Q~SSIGs~~~~~~~Wl~~~f~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 (443)
T PF06087_consen 210 WGHMRLRKVLKRLGLPSNKDKDKESDIVCQFSSIGSLGSSPKDWLTSEFLTSLYPASFSSPSTPSSKSSSSQQENNRPPL 289 (443)
T ss_dssp SHHHHHHHHHHHCCTT---TTCCCCEEEEE-SBB---SSSTTTTTTTHHHHHCCHHCCT------HHHHHHHCCHHTEEE
T ss_pred hhHHHHHHHHHhccccccCCcCCCCeEEEEcccccccCcchhhhHHHHHHHHHhhccccccccccccccccccccCCCCc
Confidence 99999999999987654 346789999999999994 4587 468887764332 00 011123568
Q ss_pred eEEccChhhhhcCcccCcCCccccCCCc----cchhHHHHHHHhhhcCC--CCCCCCCCCcceeeeeec---CCceeEEE
Q 014528 218 LIVWPTVEDVRCSLEGYAAGNAIPSPQK----NVDKDFLKKYWAKWKAS--HTGRSRAMPHIKTFARYN---GQKLAWFL 288 (423)
Q Consensus 218 ~iifPT~~~V~~S~~G~~~gg~i~~~~~----~~~~~~l~~~~~kw~~~--~~~R~~~~PH~K~y~r~~---~~~~~W~l 288 (423)
+|||||+||||+|.+|+.+|||||++.+ +..+.+|+++||+|.+. .++|++++||+|+|+|++ .+.++|+|
T Consensus 290 ~IvfPT~e~Vr~S~~G~~~ggsi~~~~~~~~~~~~~~~l~~~~~~w~~~~~~~~R~~~~pH~K~y~~~~~~~~~~~~W~~ 369 (443)
T PF06087_consen 290 KIVFPTVEEVRNSPEGYNGGGSIPFKYKWWEPNFPQEWLRPYFHKWYASDDPSGRSRAPPHIKTYMRFSKNDFKSLGWFY 369 (443)
T ss_dssp EEE--BCHHHCTSTTGGGGGGGSB--HC--GHHCCHHHHHHCCE-EEEC-TGCTTTTS-B--EEEEEEE-TTTSEECEEE
T ss_pred eEECCCHHHHhhCccCCcCceeEEecchhccccchHHHHHHHHhhhccccccCCCCCcCcceEEEEEecCCCCCccceEE
Confidence 9999999999999999999999999865 33468999999999988 899999999999999997 57899999
Q ss_pred EeccccchhhhhccccCCceeeeeeeeeeeEEcCCcccCCCccccccCCCCccccCCCccchhhhcceeeeeecCCCCCC
Q 014528 289 LTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDA 368 (423)
Q Consensus 289 ltSaNLS~aAWG~~~k~~~ql~irnyElGVl~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 368 (423)
+||||||+||||+.+++++|++||||||||||+|..... ...|.+..+..+ ..
T Consensus 370 lgShNLS~aAWG~~~~~~~~l~i~nyElGVl~~P~~~~~--~~~~~~~~~~~~-------------------------~~ 422 (443)
T PF06087_consen 370 LGSHNLSKAAWGKRSKNGSQLSIRNYELGVLFLPSSFGV--MLPVFSLDDPVY-------------------------RS 422 (443)
T ss_dssp EES--BSHHHH-EEETTTTCCEESSBEEEEEEEGGGCTS--SSSCEEEECCG----------------------------
T ss_pred eCcccCCHHHhcccccCCceeeecceEEEEEEecCcccc--cccccccccccc-------------------------cc
Confidence 999999999999999999999999999999998886441 122222111100 01
Q ss_pred CCCCcccccccccCCCCCCCC
Q 014528 369 GASSEVVYLPVPYELPPQRYS 389 (423)
Q Consensus 369 ~~~~~~~~~~vPy~lP~~~Y~ 389 (423)
......+.|||||+||++||+
T Consensus 423 ~~~~~~~~v~vPf~lP~~~Y~ 443 (443)
T PF06087_consen 423 ISSTNTVPVPVPFDLPPTPYG 443 (443)
T ss_dssp ----GGGCEEESS-SSEEE--
T ss_pred cccCCCceEEecCCCCCcCcC
Confidence 123446889999999999996
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=95.58 E-value=0.0093 Score=50.68 Aligned_cols=38 Identities=34% Similarity=0.488 Sum_probs=26.7
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEc
Q 014528 269 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLIL 321 (423)
Q Consensus 269 ~~PH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~irnyElGVl~~ 321 (423)
-..|.|+|+-.+ + .+++||+|||..|| -+|+|+||++.
T Consensus 73 ~~~H~K~~i~d~-~---~~iiGS~N~t~~~~-----------~~n~E~~~~~~ 110 (126)
T PF13091_consen 73 NRLHAKFYIIDD-K---VAIIGSANLTSSSF-----------RRNYELGVIID 110 (126)
T ss_dssp S-B--EEEEETT-T---EEEEES--CSCCCS-----------CTSEEEEEEEE
T ss_pred cCCCcceEEecC-c---cEEEcCCCCCcchh-----------cCCcceEEEEE
Confidence 366999998732 2 79999999999999 27899999983
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=91.01 E-value=0.19 Score=32.10 Aligned_cols=25 Identities=24% Similarity=0.190 Sum_probs=19.4
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchh
Q 014528 269 AMPHIKTFARYNGQKLAWFLLTSANLSKA 297 (423)
Q Consensus 269 ~~PH~K~y~r~~~~~~~W~lltSaNLS~a 297 (423)
...|.|+++-.+ .|+++||+||+..
T Consensus 3 ~~~H~K~~v~D~----~~~~iGs~N~~~~ 27 (28)
T smart00155 3 GVLHTKLMIVDD----EIAYIGSANLDGR 27 (28)
T ss_pred CcEEeEEEEEcC----CEEEEeCccCCCC
Confidence 457999987533 3899999999864
No 5
>PRK13912 nuclease NucT; Provisional
Probab=90.78 E-value=0.28 Score=45.15 Aligned_cols=37 Identities=30% Similarity=0.329 Sum_probs=29.9
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEE
Q 014528 269 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLI 320 (423)
Q Consensus 269 ~~PH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~irnyElGVl~ 320 (423)
..+|.|+++-.. .|+++||+|++..++. .|+|+||++
T Consensus 118 ~~~H~K~~viD~----~~~~iGS~N~t~~s~~-----------~N~E~~lii 154 (177)
T PRK13912 118 GIMHQKVAIIDD----KIVVLGSANWSKNAFE-----------NNYEVLLIT 154 (177)
T ss_pred cccceeEEEEcC----CEEEEeCCCCChhHhc-----------cCCceEEEE
Confidence 468999987532 4899999999987764 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=89.75 E-value=0.23 Score=32.15 Aligned_cols=25 Identities=32% Similarity=0.323 Sum_probs=15.0
Q ss_pred CCccccceeeeeeCCceEEEEeCCCCCc
Q 014528 39 FGTHHSKAMLLIYPRGVRIIVHTANLIH 66 (423)
Q Consensus 39 fG~hHSKmmll~y~d~lRVVI~SANL~~ 66 (423)
.++||+|++++- +-+.+|.++||..
T Consensus 2 ~~~~H~K~~vvD---~~~a~vGg~nl~~ 26 (28)
T PF00614_consen 2 GGSHHQKFVVVD---DRVAFVGGANLCD 26 (28)
T ss_dssp TBEE---EEEET---TTEEEEE---SSH
T ss_pred CcceeeEEEEEc---CCEEEECceecCC
Confidence 589999999984 4489999999864
No 7
>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=87.39 E-value=0.59 Score=46.87 Aligned_cols=42 Identities=31% Similarity=0.237 Sum_probs=30.5
Q ss_pred cceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEcC
Q 014528 272 HIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILP 322 (423)
Q Consensus 272 H~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~irnyElGVl~~P 322 (423)
|.|+|+-..+...-=+|+||||||.- ||..+ +.||..|+.-+
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 99999976554444599999999985 55432 67887776644
No 8
>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=86.79 E-value=0.63 Score=29.67 Aligned_cols=25 Identities=28% Similarity=0.279 Sum_probs=20.6
Q ss_pred CCccccceeeeeeCCceEEEEeCCCCCc
Q 014528 39 FGTHHSKAMLLIYPRGVRIIVHTANLIH 66 (423)
Q Consensus 39 fG~hHSKmmll~y~d~lRVVI~SANL~~ 66 (423)
.+.+|+|+++. |+-.++|.|+||..
T Consensus 2 ~~~~H~K~~v~---D~~~~~iGs~N~~~ 26 (28)
T smart00155 2 DGVLHTKLMIV---DDEIAYIGSANLDG 26 (28)
T ss_pred CCcEEeEEEEE---cCCEEEEeCccCCC
Confidence 37899999987 45589999999975
No 9
>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=85.26 E-value=0.91 Score=40.73 Aligned_cols=38 Identities=26% Similarity=0.260 Sum_probs=31.0
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEc
Q 014528 269 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLIL 321 (423)
Q Consensus 269 ~~PH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~irnyElGVl~~ 321 (423)
...|.|+++-.+ + -+++||+|++..+|. .|.|+||++.
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 577999988542 2 599999999999988 5789999873
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=83.22 E-value=3.8 Score=36.67 Aligned_cols=38 Identities=21% Similarity=0.239 Sum_probs=29.4
Q ss_pred CCccccceeeeeeCCceEEEEeCCCCCccccc-cccceEEee
Q 014528 39 FGTHHSKAMLLIYPRGVRIIVHTANLIHVDWN-NKSQGLWMQ 79 (423)
Q Consensus 39 fG~hHSKmmll~y~d~lRVVI~SANL~~~DW~-~~tQ~vW~q 79 (423)
.+.+|+|+||. |+=.++|.|+|+....+. +.+.++.+.
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 455899999999998885 334455444
No 11
>COG1502 Cls Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthases and related enzymes [Lipid metabolism]
Probab=80.20 E-value=1.3 Score=45.97 Aligned_cols=40 Identities=28% Similarity=0.326 Sum_probs=32.3
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEcCC
Q 014528 269 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPS 323 (423)
Q Consensus 269 ~~PH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~irnyElGVl~~P~ 323 (423)
+..|.|+++-.+ .|+++||+||+..|+. .|+|++|++...
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 578999988533 3799999999999875 479999999543
No 12
>PRK11263 cardiolipin synthase 2; Provisional
Probab=79.64 E-value=1.6 Score=45.80 Aligned_cols=39 Identities=21% Similarity=0.189 Sum_probs=30.8
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEcC
Q 014528 269 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILP 322 (423)
Q Consensus 269 ~~PH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~irnyElGVl~~P 322 (423)
-+.|.|+++-.+ .|+++||+||...++. .|+|++|++.-
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 467999988533 4999999999886652 69999999853
No 13
>PRK01642 cls cardiolipin synthetase; Reviewed
Probab=79.59 E-value=1.7 Score=46.44 Aligned_cols=38 Identities=18% Similarity=0.268 Sum_probs=30.5
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEc
Q 014528 269 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLIL 321 (423)
Q Consensus 269 ~~PH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~irnyElGVl~~ 321 (423)
-+.|.|+++-.+ .|+++||+|++..++. .|+|+||++.
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 467999987532 4899999999877762 6999999984
No 14
>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=77.50 E-value=2.8 Score=35.26 Aligned_cols=37 Identities=19% Similarity=0.301 Sum_probs=23.6
Q ss_pred CccccceeeeeeCCceEEEEeCCCCCccccccc-cceEEee
Q 014528 40 GTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNK-SQGLWMQ 79 (423)
Q Consensus 40 G~hHSKmmll~y~d~lRVVI~SANL~~~DW~~~-tQ~vW~q 79 (423)
+.+|+|+++.- +=.++|.|+|++...|..- +.++.+.
T Consensus 73 ~~~H~K~~i~d---~~~~iiGS~N~t~~~~~~n~E~~~~~~ 110 (126)
T PF13091_consen 73 NRLHAKFYIID---DKVAIIGSANLTSSSFRRNYELGVIID 110 (126)
T ss_dssp S-B--EEEEET---TTEEEEES--CSCCCSCTSEEEEEEEE
T ss_pred cCCCcceEEec---CccEEEcCCCCCcchhcCCcceEEEEE
Confidence 68999999983 3399999999999998665 3344443
No 15
>PRK12452 cardiolipin synthetase; Reviewed
Probab=74.07 E-value=2.7 Score=45.33 Aligned_cols=38 Identities=16% Similarity=0.215 Sum_probs=30.2
Q ss_pred CCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEc
Q 014528 269 AMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLIL 321 (423)
Q Consensus 269 ~~PH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~irnyElGVl~~ 321 (423)
...|.|+.+-.+ .|+++||+||..-++. .|||+++++.
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 467999988533 3999999999887764 3999999884
No 16
>PRK09428 pssA phosphatidylserine synthase; Provisional
Probab=70.36 E-value=5.1 Score=42.58 Aligned_cols=41 Identities=32% Similarity=0.460 Sum_probs=33.1
Q ss_pred CCCCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEcC
Q 014528 267 SRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILP 322 (423)
Q Consensus 267 ~~~~PH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~irnyElGVl~~P 322 (423)
...+-|.|+.+-.+ .|+++||+||-.-+|. .|+|+||++.-
T Consensus 352 ~~~~~HaK~i~vD~----~~~~iGS~Nld~RS~~-----------ln~E~~l~i~d 392 (451)
T PRK09428 352 GDNSYHLKGIWVDD----RWMLLTGNNLNPRAWR-----------LDLENALLIHD 392 (451)
T ss_pred CCCcceEEEEEEeC----CEEEEcCCCCChhHhh-----------hcccceEEEEC
Confidence 45677999987532 4999999999998886 58999999843
No 17
>PRK13912 nuclease NucT; Provisional
Probab=66.87 E-value=6.2 Score=36.22 Aligned_cols=31 Identities=19% Similarity=0.390 Sum_probs=25.6
Q ss_pred CCCccccceeeeeeCCceEEEEeCCCCCcccccc
Q 014528 38 SFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNN 71 (423)
Q Consensus 38 ~fG~hHSKmmll~y~d~lRVVI~SANL~~~DW~~ 71 (423)
.++.+|+|+|++ |+-.++|.|+|++...+..
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 467899999998 6777999999999765553
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=54.77 E-value=10 Score=38.19 Aligned_cols=27 Identities=19% Similarity=0.263 Sum_probs=23.1
Q ss_pred ccccceeeeeeCCc-eEEEEeCCCCCcc
Q 014528 41 THHSKAMLLIYPRG-VRIIVHTANLIHV 67 (423)
Q Consensus 41 ~hHSKmmll~y~d~-lRVVI~SANL~~~ 67 (423)
.-|+||.+..-.++ .+..|.||||+..
T Consensus 80 ~~HgKlY~f~k~g~~~~a~IGSANfS~~ 107 (296)
T PF09565_consen 80 PYHGKLYIFSKNGKPFRAYIGSANFSQI 107 (296)
T ss_pred CcccEEEEEecCCCceEEEEeecccccc
Confidence 35999998766666 9999999999995
No 19
>PHA02820 phospholipase-D-like protein; Provisional
Probab=48.46 E-value=16 Score=38.56 Aligned_cols=37 Identities=14% Similarity=0.169 Sum_probs=28.4
Q ss_pred CCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEcC
Q 014528 270 MPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILP 322 (423)
Q Consensus 270 ~PH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~irnyElGVl~~P 322 (423)
+-|.|+.+-. +|+++||+|++.-. .-.|+|+++++..
T Consensus 323 f~HaK~~vvD-----~~a~IGTsN~D~rs-----------f~~n~ev~~~i~~ 359 (424)
T PHA02820 323 VNHAKYMVTD-----KTAYIGTSNWTGNY-----------FTDTCGVSINITP 359 (424)
T ss_pred eeeeeEEEEc-----ccEEEECCcCCHHH-----------HhccCcEEEEEec
Confidence 6699987632 48999999997543 3469999999954
No 20
>COG3886 Predicted HKD family nuclease [DNA replication, recombination, and repair]
Probab=39.53 E-value=26 Score=33.06 Aligned_cols=32 Identities=22% Similarity=0.241 Sum_probs=24.0
Q ss_pred CCCCcceeeeeecCCceeEEEEeccccchhhhh
Q 014528 268 RAMPHIKTFARYNGQKLAWFLLTSANLSKAAWG 300 (423)
Q Consensus 268 ~~~PH~K~y~r~~~~~~~W~lltSaNLS~aAWG 300 (423)
.+-.|.|-|++--...+. +.+||.|||++|--
T Consensus 117 ~~~fH~KgYiFe~~~~~t-aiiGSsNlt~sALt 148 (198)
T COG3886 117 SANFHTKGYIFEHNTGIT-AIIGSSNLTDSALT 148 (198)
T ss_pred ccccccceeEEEecceEE-EEEccchhhhhhcc
Confidence 366799999954433333 89999999999853
No 21
>KOG3603 consensus Predicted phospholipase D [General function prediction only]
Probab=29.89 E-value=51 Score=34.85 Aligned_cols=39 Identities=31% Similarity=0.434 Sum_probs=0.0
Q ss_pred CCCCCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEE
Q 014528 267 SRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLI 320 (423)
Q Consensus 267 ~~~~PH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~irnyElGVl~ 320 (423)
++-+.|+|+.+- ..+=+|+||||+ -.+..+|++ |+||++
T Consensus 166 g~GvlHtKf~vv----D~khfylGSaNf-------DWrSlTqvk----ElGv~v 204 (456)
T KOG3603|consen 166 GGGVLHTKFWVV----DIKHFYLGSANF-------DWRSLTQVK----ELGVVV 204 (456)
T ss_pred cCceEEEEEEEE----ecceEEEecccc-------chhhcccee----EeeeEE
No 22
>PLN02352 phospholipase D epsilon
Probab=26.97 E-value=36 Score=38.56 Aligned_cols=26 Identities=27% Similarity=0.401 Sum_probs=20.6
Q ss_pred cccceeeeeeCCceEEEEeCCCCCccccc
Q 014528 42 HHSKAMLLIYPRGVRIIVHTANLIHVDWN 70 (423)
Q Consensus 42 hHSKmmll~y~d~lRVVI~SANL~~~DW~ 70 (423)
-||||||. |.--|+|.|||+...-..
T Consensus 608 VHSKlMIV---DD~~viIGSANIN~RSM~ 633 (758)
T PLN02352 608 VHSKLMIV---DDTYILIGSANVNQRSMD 633 (758)
T ss_pred EeeeEEEE---cCcEEEEccccccccccc
Confidence 39999987 556789999999876544
No 23
>TIGR03705 poly_P_kin polyphosphate kinase 1. Members of this protein family are the enzyme polyphosphate kinase 1 (PPK1). This family is found in many prokaryotes and also in Dictyostelium. Sequences in the seed alignment were taken from prokaryotic consecutive two-gene pairs in which the other gene encodes an exopolyphosphatase. It synthesizes polyphosphate from the terminal phosphate of ATP but not GTP, in contrast to PPK2.
Probab=26.94 E-value=81 Score=35.40 Aligned_cols=40 Identities=23% Similarity=0.214 Sum_probs=27.1
Q ss_pred CCcceeeeeecCCceeEEEEeccccchhhhhccccCCceeeeeeeeeeeEEc
Q 014528 270 MPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLIL 321 (423)
Q Consensus 270 ~PH~K~y~r~~~~~~~W~lltSaNLS~aAWG~~~k~~~ql~irnyElGVl~~ 321 (423)
+=|+|+|.-.+++ -.|+|+||||+-. .+ .=+|+|+.+.+.
T Consensus 581 Leh~rIy~f~~~~-d~~~~igSAn~m~-------Rn----l~~r~E~~~~i~ 620 (672)
T TIGR03705 581 LEHSRIYYFGNGG-EEKVYISSADWMT-------RN----LDRRVEVLFPIE 620 (672)
T ss_pred hCcCEEEEEeCCC-CcEEEEECCCCCC-------Cc----ccceEEEEEEEc
Confidence 3388887654443 3499999999832 21 348899999764
No 24
>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=22.76 E-value=84 Score=33.26 Aligned_cols=34 Identities=21% Similarity=0.354 Sum_probs=22.8
Q ss_pred CCCcceeeeeecCCc-eeEEEEeccccchhhhhccc
Q 014528 269 AMPHIKTFARYNGQK-LAWFLLTSANLSKAAWGALQ 303 (423)
Q Consensus 269 ~~PH~K~y~r~~~~~-~~W~lltSaNLS~aAWG~~~ 303 (423)
...|+|+++-+-.+. + -+.+.||||...-|+..+
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 567999977654444 5 499999999999999854
Done!