Query 006900
Match_columns 626
No_of_seqs 195 out of 340
Neff 5.7
Searched_HMMs 46136
Date Thu Mar 28 16:06:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006900.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006900hhsearch_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 1E-101 3E-106 819.5 26.4 491 63-616 3-518 (519)
2 PF06087 Tyr-DNA_phospho: Tyro 100.0 8.5E-93 1.8E-97 778.1 10.6 394 161-592 1-443 (443)
3 cd00060 FHA Forkhead associate 97.6 0.00012 2.6E-09 63.4 6.2 94 7-108 2-101 (102)
4 TIGR01663 PNK-3'Pase polynucle 97.0 0.00095 2E-08 75.9 5.6 97 3-109 11-109 (526)
5 PF00498 FHA: FHA domain; Int 96.9 0.0014 3.1E-08 53.4 4.4 62 33-98 2-67 (68)
6 TIGR03354 VI_FHA type VI secre 91.2 0.37 8.1E-06 53.3 6.1 88 10-100 4-96 (396)
7 PLN02927 antheraxanthin epoxid 89.3 1.1 2.4E-05 52.9 8.2 102 8-112 535-649 (668)
8 smart00240 FHA Forkhead associ 88.4 0.62 1.4E-05 35.5 3.7 38 37-74 10-48 (52)
9 COG1716 FOG: FHA domain [Signa 82.9 1.7 3.6E-05 42.3 4.5 67 31-103 90-159 (191)
10 PF00614 PLDc: Phospholipase D 82.4 1 2.3E-05 31.3 2.0 25 252-279 2-26 (28)
11 smart00155 PLDc Phospholipase 79.1 2.2 4.8E-05 29.1 2.8 25 252-279 2-26 (28)
12 cd00138 PLDc Phospholipase D. 70.2 5.1 0.00011 38.1 3.8 38 252-292 111-149 (176)
13 PF13091 PLDc_2: PLD-like doma 66.7 7.8 0.00017 34.6 4.1 37 253-292 73-110 (126)
14 PF13091 PLDc_2: PLD-like doma 61.4 5.2 0.00011 35.7 1.9 32 482-524 73-110 (126)
15 PRK13912 nuclease NucT; Provis 54.2 10 0.00023 37.0 2.8 83 196-283 51-145 (177)
16 PF09565 RE_NgoFVII: NgoFVII r 37.6 30 0.00065 37.1 3.2 26 255-280 81-107 (296)
17 TIGR02500 type_III_yscD type I 29.3 70 0.0015 35.7 4.6 37 24-60 14-54 (410)
18 cd00138 PLDc Phospholipase D. 26.9 47 0.001 31.4 2.4 32 482-524 112-149 (176)
19 PRK13912 nuclease NucT; Provis 23.0 80 0.0017 30.8 3.2 33 481-524 117-155 (177)
20 COG4110 Uncharacterized protei 20.1 83 0.0018 30.9 2.5 37 55-93 128-166 (200)
No 1
>KOG2031 consensus Tyrosyl-DNA phosphodiesterase [Replication, recombination and repair]
Probab=100.00 E-value=1.5e-101 Score=819.50 Aligned_cols=491 Identities=37% Similarity=0.619 Sum_probs=388.8
Q ss_pred EEeecCCcEEEeeCC--cccccCcccccccccCCcccccCCCccceeeeeccccccccCCCCCccchhhhhhhhccccCC
Q 006900 63 LVVDGTNPVVVKSGD--QRKKLSSNEHVSIADGDIIELIPGHHFFKYVTLSRSQKRVSNDGATNGELSSKKMRQQDEQDN 140 (626)
Q Consensus 63 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~ 140 (626)
+++.+.++..++|++ ++.+.-...+.+..+++-++.+++++..+.+..... |- ....
T Consensus 3 ~ss~~~~~~p~~s~~~~~~s~~~~~~~isa~~~~~~~~~~n~~~~~~~~l~g~--~~-------------------~~~t 61 (519)
T KOG2031|consen 3 LSSNFNGLKPERSDVAEEKSQRKKSSRISAENDNAAPVTENHHKDDCVILKGS--RD-------------------IKLT 61 (519)
T ss_pred cccCCCCcccccccccchhcccccCccccccCcccccccccccchhhhhcCCC--cc-------------------cccC
Confidence 556777788888844 455556677888899999999999999866655221 10 0011
Q ss_pred CCCCCCcccccccccCCCCCCCceEEEEecC--CCCCCCCCceeechhcc---ccHhhhhhhhcccCHhhhhccCCCCCC
Q 006900 141 ENGKNSEEALCNFHVSRDKLPSTFRLLRVQG--LPAWANTSCVSIRDVIQ---GDIIVAILSNYMVDIDWLLPACPVLAK 215 (626)
Q Consensus 141 ~~~~~~~~~~~~~~~~~~~~~s~FrL~rv~g--~~~~~n~~~Itl~Dll~---~~L~~avl~nF~~Dl~WLl~~~p~~~~ 215 (626)
...+...++....+ .|.-+.++.+.+ .+.......+++.+|+. |++..++|||||+|++||+.+||..-+
T Consensus 62 ~~e~~~~~~~~~~~-----~p~~~~ft~v~~~s~~~~~s~~s~sl~~il~~i~g~~v~silfsfmvdid~Lv~~y~~~~~ 136 (519)
T KOG2031|consen 62 NQEKDDSERILTND-----NPKGAVFTTVKGDSVPRYDSMGSVSLMEILADIFGTPVNSILFSFMVDIDWLVGQYPPSVR 136 (519)
T ss_pred ccccccHHHHhccC-----CcccccccccccccccccCcccchHHHHHHHHhhCCchhheEEEEEeEHHHHHhhCcchhc
Confidence 11112222333333 333445555554 23323336667666653 589999999999999999999985445
Q ss_pred CCeEEEEeCCCCchhhhhhhcCCCceEEecCCCCCCCCCccceeEEEEeCCceEEEEeCCCCCccccccccceEEeeccC
Q 006900 216 IPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFP 295 (626)
Q Consensus 216 ~~~i~Vv~ge~~~~~~~~~~~~~~n~~l~~p~mp~~fGthHSKmmLL~y~dglRVVI~TANLi~~DW~~~tQ~vW~qDfP 295 (626)
.+.|+++||+.++.........+.+++++.+.||++|||||+|||+|+|++|+|||||||||++.||+++||++|+++++
T Consensus 137 ~~~i~l~~G~~d~~~~~~~~K~~~l~~~~~~~LpipF~thHtKm~~l~y~~G~rvvv~taNl~~~Dw~~ktQ~~w~sp~~ 216 (519)
T KOG2031|consen 137 IKPITLVHGEPDEARLLAQTKAPILVTVKLASLPIPFGTHHTKMIILFYEEGCRVVVHTANLIHDDWNNKTQGFWCSPLL 216 (519)
T ss_pred cCceEEEecCCchHHHHhhhhccceeeeecccccccccccccceEEEeccCccEEEEecCCcceecccccccceeecCCc
Confidence 56688899988743322233356789999999999999999999999999999999999999999999999999999988
Q ss_pred CCCCCCCCCCCCcHHHHHHHHHhcCCCccccCCCCCCCccccccccccccccccceEEEEecCCCccCCCcccccHHHHH
Q 006900 296 LKDQNNLSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLR 375 (626)
Q Consensus 296 ~~~~~s~~~~t~Fk~dL~~YL~ay~~~~~~~~~p~~g~~~i~~~~L~~yDFS~a~v~LVaSVPG~H~g~~~~~~G~~rL~ 375 (626)
+........++.|+.||++||++|++|... +|++.|++||||.++|+||+||||++.|.....|||+||+
T Consensus 217 ~~~~~~g~~~~~Fk~DLi~YL~~Y~~~~l~----------~~i~~lkk~DfS~i~v~fIgStPG~f~gs~~~~WGh~kL~ 286 (519)
T KOG2031|consen 217 KIGDKKGVSPTGFKQDLIEYLNSYRLPQLK----------EWIASLKKVDFSAINVRFIGSTPGKFQGSGLLSWGHNKLK 286 (519)
T ss_pred ccccCCCCCCCchHHHHHHHHHHhccchhH----------HHHHHHHhcchhhceEEEEeecCCcccCcccccccHHHHH
Confidence 877666789999999999999999987433 3468999999999999999999999888766679999999
Q ss_pred HHHhhccccCCCccCCeEEEecCCCcCchHHHHHHHHhccCCCCCCCCCCCC--CCceEeccCchhhhcCccCCcCCccc
Q 006900 376 TVLQECTFEKGFKKSPLVYQFSSLGSLDEKWMAELSSSMSSGFSEDKTPLGI--GEPLIVWPTVEDVRCSLEGYAAGNAI 453 (626)
Q Consensus 376 ~vL~~~~~~~~~~~~~i~~Q~SSIGsl~~~wL~ef~~sl~~~~~~~~~p~~~--~~~~IIfPTveeVr~S~~G~~~Ggsi 453 (626)
++|+++......++.+++||+||+|+|+..|...|...+.....++..+.+. ++++|||||+||||+|++||++||||
T Consensus 287 kiL~~~~~~~~~~r~~~v~q~sS~gsl~~~~~~~~~~~f~~~l~kdt~~~gk~~~~~yiIfPTveeVrtS~~G~~~Ggsi 366 (519)
T KOG2031|consen 287 KILKEHAASPYLERTPVVGQSSSIGSLGSLWSAWFIGDFVESLAKDTTPPGKLRPPFYIIFPTVEEVRTSLLGYAGGGSL 366 (519)
T ss_pred HHHHhhccCcccccCceeeeeeccccccchhhhhhhhhhccchhhccCCCCCCCCCeeEEcccHHHhhccccccccCcee
Confidence 9999987655567899999999999999888776666665554455444433 45899999999999999999999999
Q ss_pred cCCCccchh-hHHHHHhhhhccCCCCCCCCCCceeEEEeeC------------cccchHHhhcccccCCc---eeEecee
Q 006900 454 PSPQKNVDK-DFLKKYWAKWKASHTGRSRAMPHIKTFARYN------------GQKLAKAAWGALQKNNS---QLMIRSY 517 (626)
Q Consensus 454 ~~~~~~~~k-~~l~~~~~kw~~~~~gR~~a~PHiKty~r~~------------s~NLSkaAWG~l~k~~s---ql~IrnY 517 (626)
||..+++.+ .||++|||||.+.+++|+|||||||||||++ ||||||||||++++|++ |||||||
T Consensus 367 py~~~~~~kq~~lk~y~~kW~A~~s~R~ramPHiKtYmr~~~d~q~l~W~LlTSANLSKaAWG~l~kn~sk~~~LmIRsY 446 (519)
T KOG2031|consen 367 PYGKNTNEKQPWLKKYLCKWKAMDSRRSRAMPHIKTYMRFNLDDQKLAWFLLTSANLSKAAWGTLSKNKSKQPQLMIRSY 446 (519)
T ss_pred cccchhhhhhHHHHHHHHhhhhhhhhccccCCcceeeeeecCCCCEEEEEEEeccccchhhhhhhccCCCCCchheeeec
Confidence 998777664 7999999999999999999999999999985 79999999999999886 8999999
Q ss_pred eeEEEEcCCcccCCCccccccCCCCCccccCCccchhcccceeeeeeccCCCCCCCCCccccccccCCCCCCCCCCCCCC
Q 006900 518 ELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVP 597 (626)
Q Consensus 518 ElGVL~~P~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pvPy~LP~~~Y~~~D~P 597 (626)
|+||||+|..+....+++ .+..+|.++.. ....+.|||||||||+||++.|+|
T Consensus 447 EaGVLf~p~~~~~~kt~k------------------------~~~~tf~~~~~---~~~v~~vpvpydlPp~pY~~~d~~ 499 (519)
T KOG2031|consen 447 EAGVLFLPRFFANLKTFK------------------------VVEDTFPRDNN---GDGVIAVPVPYDLPPVPYSPKDEP 499 (519)
T ss_pred ccceEecchhhhcccccc------------------------ccceecccccC---CCCcceeccccCCCCcCCCccCCc
Confidence 999999999765322221 11122333332 133488999999999999999999
Q ss_pred ceecCCCCCcccCCCCccc
Q 006900 598 WSWDKRYTKKDVYGQVWPR 616 (626)
Q Consensus 598 W~~d~~y~~pD~~G~~w~~ 616 (626)
|++++.+.++||+|.+|++
T Consensus 500 ~~~~~~~~~~d~lG~vW~p 518 (519)
T KOG2031|consen 500 FFTDIYRQGPDWLGCVWTP 518 (519)
T ss_pred eeecccccCCcceeeccCC
Confidence 9999777789999999986
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=8.5e-93 Score=778.13 Aligned_cols=394 Identities=41% Similarity=0.694 Sum_probs=279.9
Q ss_pred CCceEEEEecCCCCC--CCCCceeechhccc-cHhhhhhhhcccCHhhhhccCCCC-CCCCeEEEEeCCCCc-hhhhhhh
Q 006900 161 PSTFRLLRVQGLPAW--ANTSCVSIRDVIQG-DIIVAILSNYMVDIDWLLPACPVL-AKIPHVLVIHGESDG-TLEHMKR 235 (626)
Q Consensus 161 ~s~FrL~rv~g~~~~--~n~~~Itl~Dll~~-~L~~avl~nF~~Dl~WLl~~~p~~-~~~~~i~Vv~ge~~~-~~~~~~~ 235 (626)
|++|.++++.++++. .|.++|||+|||++ +|+.|++||||+|++|||++|+.. ++...|++++|+... ....+..
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 567888889998876 68999999999997 899999999999999999999753 333468888995432 2222322
Q ss_pred --cCCCceEEecCCCCCCCCCccceeEEEEeCCc-eEEEEeCCCCCccccccccceEEeecc-CCCCC---CCCCCCCCc
Q 006900 236 --NKPANWILHKPPLPISFGTHHSKAMLLIYPRG-VRIIVHTANLIHVDWNNKSQGLWMQDF-PLKDQ---NNLSEECGF 308 (626)
Q Consensus 236 --~~~~n~~l~~p~mp~~fGthHSKmmLL~y~dg-lRVVI~TANLi~~DW~~~tQ~vW~qDf-P~~~~---~s~~~~t~F 308 (626)
...+||++|.|+||.+|||||||||||+|+|| ||||||||||+++||+++||+||+||| |++.. ...+.+++|
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 HHHHHHHHHhcCCCccccCCCCCCCccccccccccccccccceEEEEecCCCccCCCcccccHHHHHHHHhhccccC---
Q 006900 309 ENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEK--- 385 (626)
Q Consensus 309 k~dL~~YL~ay~~~~~~~~~p~~g~~~i~~~~L~~yDFS~a~v~LVaSVPG~H~g~~~~~~G~~rL~~vL~~~~~~~--- 385 (626)
++||++||++|+.+.... +++.|++||||.++|+||+||||+|. .+..+|||++|+++|++++...
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 999999999998543111 14789999999999999999999999 4556899999999999988754
Q ss_pred CCccCCeEEEecCCCcCc---hHHHH-HHHHhccCCCC---CC--------CCCCCCCCceEeccCchhhhcCccCCcCC
Q 006900 386 GFKKSPLVYQFSSLGSLD---EKWMA-ELSSSMSSGFS---ED--------KTPLGIGEPLIVWPTVEDVRCSLEGYAAG 450 (626)
Q Consensus 386 ~~~~~~i~~Q~SSIGsl~---~~wL~-ef~~sl~~~~~---~~--------~~p~~~~~~~IIfPTveeVr~S~~G~~~G 450 (626)
.....+|+||+||||+++ ..||. +|+.+|..... .. ......++++|||||+||||+|.+||.+|
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 45984 78888765432 00 01112356899999999999999999999
Q ss_pred ccccCCCc----cchhhHHHHHhhhhccC--CCCCCCCCCceeEEEeeC-------------cccchHHhhcccccCCce
Q 006900 451 NAIPSPQK----NVDKDFLKKYWAKWKAS--HTGRSRAMPHIKTFARYN-------------GQKLAKAAWGALQKNNSQ 511 (626)
Q Consensus 451 gsi~~~~~----~~~k~~l~~~~~kw~~~--~~gR~~a~PHiKty~r~~-------------s~NLSkaAWG~l~k~~sq 511 (626)
||||++.+ +.++.||+++||+|.+. .++|++++||+|+|+|++ |||||+||||+.+++++|
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 45578999999999998 899999999999999873 799999999999999999
Q ss_pred eEeceeeeEEEEcCCcccCCCccccccCCCCCccccCCccchhcccceeeeeeccCCCCCCCCCccccccccCCCCCCCC
Q 006900 512 LMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRY 591 (626)
Q Consensus 512 l~IrnYElGVL~~P~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pvPy~LP~~~Y 591 (626)
++||||||||||+|...... ..|.... . ...........+.|||||+||++||
T Consensus 390 l~i~nyElGVl~~P~~~~~~--~~~~~~~-----~--------------------~~~~~~~~~~~~~v~vPf~lP~~~Y 442 (443)
T PF06087_consen 390 LSIRNYELGVLFLPSSFGVM--LPVFSLD-----D--------------------PVYRSISSTNTVPVPVPFDLPPTPY 442 (443)
T ss_dssp CEESSBEEEEEEEGGGCTSS--SSCEEEE-----C--------------------CG-------GGGCEEESS-SSEEE-
T ss_pred eeecceEEEEEEecCccccc--ccccccc-----c--------------------ccccccccCCCceEEecCCCCCcCc
Confidence 99999999999999865411 1111110 0 0000112345689999999999999
Q ss_pred C
Q 006900 592 S 592 (626)
Q Consensus 592 ~ 592 (626)
+
T Consensus 443 ~ 443 (443)
T PF06087_consen 443 G 443 (443)
T ss_dssp -
T ss_pred C
Confidence 5
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=97.62 E-value=0.00012 Score=63.43 Aligned_cols=94 Identities=29% Similarity=0.426 Sum_probs=76.6
Q ss_pred eeEeeCCCCccCCCCCCcccCCC-CCccccCC----CccccccccccceeEEEecC-CccEEEEeecCCcEEEeeCCccc
Q 006900 7 GYLVPLDNNLREDNSLPKLPLSQ-GPNVIGRT----NIPVSDKRLSRKHITLTASA-DGSASLVVDGTNPVVVKSGDQRK 80 (626)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~----~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 80 (626)
.+|.+++.+ .....++|.. +.-+|||+ ++.+.|+.+||+|.+|.... ++...+...+.|++.|.. +
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 888889999999999865 2
Q ss_pred ccCcccccccccCCcccccCCCccceee
Q 006900 81 KLSSNEHVSIADGDIIELIPGHHFFKYV 108 (626)
Q Consensus 81 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~ 108 (626)
++.......+.++|.+++-++.+.|+++
T Consensus 74 ~~~~~~~~~l~~gd~i~ig~~~~~~~~~ 101 (102)
T cd00060 74 RVSPGEPVRLRDGDVIRLGNTSISFRFE 101 (102)
T ss_pred ECCCCCcEECCCCCEEEECCeEEEEEEe
Confidence 3333556779999999999888887654
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=96.96 E-value=0.00095 Score=75.91 Aligned_cols=97 Identities=24% Similarity=0.382 Sum_probs=80.9
Q ss_pred ccceeeEeeCCCCccCCCCCCcccCCCCCccccCC-CccccccccccceeEEEecCC-ccEEEEeecCCcEEEeeCCccc
Q 006900 3 ATKIGYLVPLDNNLREDNSLPKLPLSQGPNVIGRT-NIPVSDKRLSRKHITLTASAD-GSASLVVDGTNPVVVKSGDQRK 80 (626)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 80 (626)
..+|.+|+|.. ++-|.|+|..|.++|||. .--|.|++-||+.+.|.|..+ |.+.+.+-|.||-.|.. .
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 78889999999988765 3
Q ss_pred ccCcccccccccCCcccccCCCccceeee
Q 006900 81 KLSSNEHVSIADGDIIELIPGHHFFKYVT 109 (626)
Q Consensus 81 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~ 109 (626)
.|..+...+..+||++||.+|.|.|..+-
T Consensus 81 ~~~~~~~~~l~~g~~l~~v~~~~~~~~~f 109 (526)
T TIGR01663 81 ELKPGGEGELGHGDLLEIVNGLHPLTLQF 109 (526)
T ss_pred EecCCCeeeecCCCEEEEeccccceeEEe
Confidence 45567788899999999999999884444
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=96.86 E-value=0.0014 Score=53.44 Aligned_cols=62 Identities=34% Similarity=0.574 Sum_probs=49.7
Q ss_pred cccCC---CccccccccccceeEEEecCCccEEEEe-ecCCcEEEeeCCcccccCcccccccccCCcccc
Q 006900 33 VIGRT---NIPVSDKRLSRKHITLTASADGSASLVV-DGTNPVVVKSGDQRKKLSSNEHVSIADGDIIEL 98 (626)
Q Consensus 33 ~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~ 98 (626)
+|||+ +|++.|+.+||.|..|....++.+.|.- .++|++.|+. +++.+.+...+.++|+|++
T Consensus 2 ~iGR~~~~di~l~~~~iSr~Ha~i~~~~~~~~~i~d~~s~ngt~vng----~~l~~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 2 TIGRSPDCDIVLPDPSISRRHARISFDDDGQFYIEDLGSTNGTFVNG----QRLGPGEPVPLKDGDIIRF 67 (68)
T ss_dssp EEESSTTSSEEETSTTSSTTSEEEEEETTEEEEEEESSSSS-EEETT----EEESSTSEEEE-TTEEEEE
T ss_pred EEcCCCCCCEEECCHheeeeeeEEEEeceeeEEEEeCCCCCcEEECC----EEcCCCCEEECCCCCEEEc
Confidence 47776 7999999999999999999997777777 4699998832 6777778888999998865
No 6
>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=91.19 E-value=0.37 Score=53.33 Aligned_cols=88 Identities=19% Similarity=0.245 Sum_probs=65.8
Q ss_pred eeCCCCccCCCCCCcccCCCCCccccC---CCccccccc--cccceeEEEecCCccEEEEeecCCcEEEeeCCcccccCc
Q 006900 10 VPLDNNLREDNSLPKLPLSQGPNVIGR---TNIPVSDKR--LSRKHITLTASADGSASLVVDGTNPVVVKSGDQRKKLSS 84 (626)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (626)
+=+|...-+.+....+++..+..+||| +++++.|.. +||.|.+|+... |...|.--.+|.+.|+..+.| +..
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 TVLNAHQLTPGIAAQKTFGTNGGTIGRSEDCDWVLPDPERHVSGRHARIRYRD-GAYLLTDLSTNGVFLNGSGSP--LGR 80 (396)
T ss_pred EEeccccCCCCcceEEEECCCCEEEecCCCCCEEeCCCCCCcchhhcEEEEEC-CEEEEEECCCCCeEECCCCCC--CCC
Confidence 334555557777889999999999999 578888887 999999999874 555555558899999754433 444
Q ss_pred ccccccccCCcccccC
Q 006900 85 NEHVSIADGDIIELIP 100 (626)
Q Consensus 85 ~~~~~i~~~~~~~~~~ 100 (626)
+..+.+.+||+|.+=+
T Consensus 81 ~~~~~L~~GD~I~iG~ 96 (396)
T TIGR03354 81 GNPVRLEQGDRLRLGD 96 (396)
T ss_pred CCceEcCCCCEEEECC
Confidence 4556799999888743
No 7
>PLN02927 antheraxanthin epoxidase/zeaxanthin epoxidase
Probab=89.34 E-value=1.1 Score=52.88 Aligned_cols=102 Identities=18% Similarity=0.287 Sum_probs=77.6
Q ss_pred eEeeCCCCccCCCCCCcccC---CCCCccccCCC--------ccccccccccceeEEEecCCccEEEEeecCCcEEEee-
Q 006900 8 YLVPLDNNLREDNSLPKLPL---SQGPNVIGRTN--------IPVSDKRLSRKHITLTASADGSASLVVDGTNPVVVKS- 75 (626)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 75 (626)
||+|..... .....|+| -..|=+|||+. |++.|..+|+.|.+++...+.-.--+..-+|=-.|+.
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 789975443 33567888 78888999973 3889999999999999986655555666778777776
Q ss_pred CCcccccCcccccccccCCcccccCCCcc-ceeeeecc
Q 006900 76 GDQRKKLSSNEHVSIADGDIIELIPGHHF-FKYVTLSR 112 (626)
Q Consensus 76 ~~~~~~~~~~~~~~i~~~~~~~~~~~~~~-~~~~~~~~ 112 (626)
.+.|=++.++..+.+..+|+|++=..++. |+--.+..
T Consensus 612 ~~~r~~~~p~~~~~l~~~d~I~~g~~~~~~fr~~~~~~ 649 (668)
T PLN02927 612 EGRRYRATPNFPARFRSSDIIEFGSDKKAAFRVKVIRK 649 (668)
T ss_pred CCceEecCCCCceEeCCCCEEEeCCCcceeEEEEeecC
Confidence 44556678899999999999999888766 76444433
No 8
>smart00240 FHA Forkhead associated domain. Found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain.
Probab=88.40 E-value=0.62 Score=35.49 Aligned_cols=38 Identities=26% Similarity=0.389 Sum_probs=30.2
Q ss_pred CCccccccccccceeEEEecCCccEEEEeec-CCcEEEe
Q 006900 37 TNIPVSDKRLSRKHITLTASADGSASLVVDG-TNPVVVK 74 (626)
Q Consensus 37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ 74 (626)
.++.+.|..+||+|..|..+.++.+.+.--+ +|.+.|+
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 4599999999999999999999855555444 7877664
No 9
>COG1716 FOG: FHA domain [Signal transduction mechanisms]
Probab=82.89 E-value=1.7 Score=42.26 Aligned_cols=67 Identities=28% Similarity=0.354 Sum_probs=53.7
Q ss_pred CccccC---CCccccccccccceeEEEecCCccEEEEeecCCcEEEeeCCcccccCcccccccccCCcccccCCCc
Q 006900 31 PNVIGR---TNIPVSDKRLSRKHITLTASADGSASLVVDGTNPVVVKSGDQRKKLSSNEHVSIADGDIIELIPGHH 103 (626)
Q Consensus 31 ~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~ 103 (626)
...||| +++.+.|+.+||+|..|+...+...-.++..+|=+.|....-+ + +..+.+||.+.+.....
T Consensus 90 ~~tigr~~~~~i~~~~~~vSR~Ha~l~~~~~~~~~~d~~S~nGt~vn~~~v~----~--~~~l~~gd~i~i~~~~~ 159 (191)
T COG1716 90 VTTIGRDPDNDIVLDDDVVSRRHAELRREGNEVFLEDLGSTNGTYVNGEKVR----Q--RVLLQDGDVIRLGGTLA 159 (191)
T ss_pred eEEeccCCCCCEEcCCCccccceEEEEEeCCceEEEECCCCcceEECCeEcc----C--cEEcCCCCEEEECccce
Confidence 778999 6889999999999999999998888888888887777653222 2 56688899988876655
No 10
>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=82.44 E-value=1 Score=31.27 Aligned_cols=25 Identities=32% Similarity=0.369 Sum_probs=14.9
Q ss_pred CCCccceeEEEEeCCceEEEEeCCCCCc
Q 006900 252 FGTHHSKAMLLIYPRGVRIIVHTANLIH 279 (626)
Q Consensus 252 fGthHSKmmLL~y~dglRVVI~TANLi~ 279 (626)
.|+||+|++++ |+-+..|.++||..
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 57899999998 45588999999863
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=79.12 E-value=2.2 Score=29.15 Aligned_cols=25 Identities=28% Similarity=0.279 Sum_probs=20.5
Q ss_pred CCCccceeEEEEeCCceEEEEeCCCCCc
Q 006900 252 FGTHHSKAMLLIYPRGVRIIVHTANLIH 279 (626)
Q Consensus 252 fGthHSKmmLL~y~dglRVVI~TANLi~ 279 (626)
.+.+|+|+|+. |+-.++|.|+||..
T Consensus 2 ~~~~H~K~~v~---D~~~~~iGs~N~~~ 26 (28)
T smart00155 2 DGVLHTKLMIV---DDEIAYIGSANLDG 26 (28)
T ss_pred CCcEEeEEEEE---cCCEEEEeCccCCC
Confidence 46799999987 45589999999875
No 12
>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=70.23 E-value=5.1 Score=38.08 Aligned_cols=38 Identities=21% Similarity=0.239 Sum_probs=29.7
Q ss_pred CCCccceeEEEEeCCceEEEEeCCCCCccccc-cccceEEee
Q 006900 252 FGTHHSKAMLLIYPRGVRIIVHTANLIHVDWN-NKSQGLWMQ 292 (626)
Q Consensus 252 fGthHSKmmLL~y~dglRVVI~TANLi~~DW~-~~tQ~vW~q 292 (626)
.+++|+|+||. |+=.++|.|+|+....|. +.+.++.+.
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 58999999999 556899999999998884 334455444
No 13
>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=66.69 E-value=7.8 Score=34.59 Aligned_cols=37 Identities=19% Similarity=0.301 Sum_probs=23.7
Q ss_pred CCccceeEEEEeCCceEEEEeCCCCCccccccc-cceEEee
Q 006900 253 GTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNK-SQGLWMQ 292 (626)
Q Consensus 253 GthHSKmmLL~y~dglRVVI~TANLi~~DW~~~-tQ~vW~q 292 (626)
+.+|.|+++.- +=.++|.|+|++...|..- +.++.+.
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 78999999993 3399999999999998655 3344443
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=61.43 E-value=5.2 Score=35.72 Aligned_cols=32 Identities=31% Similarity=0.499 Sum_probs=21.7
Q ss_pred CCCceeEEEe------eCcccchHHhhcccccCCceeEeceeeeEEEEc
Q 006900 482 AMPHIKTFAR------YNGQKLAKAAWGALQKNNSQLMIRSYELGVLIL 524 (626)
Q Consensus 482 a~PHiKty~r------~~s~NLSkaAWG~l~k~~sql~IrnYElGVL~~ 524 (626)
...|.|+|+- ++|+||+..+|. +|+|+||++.
T Consensus 73 ~~~H~K~~i~d~~~~iiGS~N~t~~~~~-----------~n~E~~~~~~ 110 (126)
T PF13091_consen 73 NRLHAKFYIIDDKVAIIGSANLTSSSFR-----------RNYELGVIID 110 (126)
T ss_dssp S-B--EEEEETTTEEEEES--CSCCCSC-----------TSEEEEEEEE
T ss_pred cCCCcceEEecCccEEEcCCCCCcchhc-----------CCcceEEEEE
Confidence 3669999875 468999999992 5889999994
No 15
>PRK13912 nuclease NucT; Provisional
Probab=54.23 E-value=10 Score=37.01 Aligned_cols=83 Identities=12% Similarity=0.113 Sum_probs=47.3
Q ss_pred hhhcccCHhhhhccCCC-CCCCCeEEEEeCC-CCc---h--hhhhhhcCCCceEEec--C---CCCCCCCCccceeEEEE
Q 006900 196 LSNYMVDIDWLLPACPV-LAKIPHVLVIHGE-SDG---T--LEHMKRNKPANWILHK--P---PLPISFGTHHSKAMLLI 263 (626)
Q Consensus 196 l~nF~~Dl~WLl~~~p~-~~~~~~i~Vv~ge-~~~---~--~~~~~~~~~~n~~l~~--p---~mp~~fGthHSKmmLL~ 263 (626)
+..|.+.-+.+.+.+-. .++-..|-|+..+ ... . ...+.+ ..|+.++. + .....++.||.|+|++
T Consensus 51 i~~Y~~~~~~i~~aL~~Aa~RGV~VrIlld~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~~~~~~~~~H~K~~vi- 127 (177)
T PRK13912 51 IAIYSFTHKDIAKALKSAAKRGVKISIIYDYESNHNNDQSTIGYLDK--YPNIKVCLLKGLKAKNGKYYGIMHQKVAII- 127 (177)
T ss_pred EEEEEEchHHHHHHHHHHHHCCCEEEEEEeCccccCcchhHHHHHHh--CCCceEEEecCccccCcccccccceeEEEE-
Confidence 45688888888887732 2233445555332 111 0 111111 22333221 1 1122568899999998
Q ss_pred eCCceEEEEeCCCCCccccc
Q 006900 264 YPRGVRIIVHTANLIHVDWN 283 (626)
Q Consensus 264 y~dglRVVI~TANLi~~DW~ 283 (626)
|+-.+++.|+|++..-+.
T Consensus 128 --D~~~~~iGS~N~t~~s~~ 145 (177)
T PRK13912 128 --DDKIVVLGSANWSKNAFE 145 (177)
T ss_pred --cCCEEEEeCCCCChhHhc
Confidence 777799999999976554
No 16
>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=37.56 E-value=30 Score=37.12 Aligned_cols=26 Identities=19% Similarity=0.272 Sum_probs=23.0
Q ss_pred ccceeEEEEeCCc-eEEEEeCCCCCcc
Q 006900 255 HHSKAMLLIYPRG-VRIIVHTANLIHV 280 (626)
Q Consensus 255 hHSKmmLL~y~dg-lRVVI~TANLi~~ 280 (626)
-|+||.+....++ .+.+|-||||+..
T Consensus 81 ~HgKlY~f~k~g~~~~a~IGSANfS~~ 107 (296)
T PF09565_consen 81 YHGKLYIFSKNGKPFRAYIGSANFSQI 107 (296)
T ss_pred cccEEEEEecCCCceEEEEeecccccc
Confidence 5999998877766 9999999999995
No 17
>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=29.31 E-value=70 Score=35.65 Aligned_cols=37 Identities=32% Similarity=0.618 Sum_probs=32.5
Q ss_pred cccCCCCCcccc-CC---CccccccccccceeEEEecCCcc
Q 006900 24 KLPLSQGPNVIG-RT---NIPVSDKRLSRKHITLTASADGS 60 (626)
Q Consensus 24 ~~~~~~~~~~~~-~~---~~~~~~~~~~~~~~~~~~~~~~~ 60 (626)
.++|..|.-+|| ++ +|+..|..++|.|++|+...+|.
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 79999999999999999998774
No 18
>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=26.93 E-value=47 Score=31.41 Aligned_cols=32 Identities=22% Similarity=0.258 Sum_probs=26.3
Q ss_pred CCCceeEEE------eeCcccchHHhhcccccCCceeEeceeeeEEEEc
Q 006900 482 AMPHIKTFA------RYNGQKLAKAAWGALQKNNSQLMIRSYELGVLIL 524 (626)
Q Consensus 482 a~PHiKty~------r~~s~NLSkaAWG~l~k~~sql~IrnYElGVL~~ 524 (626)
...|.|+++ .++|+|++..+|. .|.|+||++.
T Consensus 112 ~~~H~K~~iiD~~~~~vGS~N~~~~~~~-----------~~~e~~~~~~ 149 (176)
T cd00138 112 GVLHTKLVIVDDETAYIGSANLDGRSLT-----------LNSEVGVVIY 149 (176)
T ss_pred cceeeeEEEEcCCEEEEECCcCChhhhh-----------hhcceEEEEe
Confidence 567999866 4579999999988 4789999884
No 19
>PRK13912 nuclease NucT; Provisional
Probab=22.98 E-value=80 Score=30.81 Aligned_cols=33 Identities=18% Similarity=0.213 Sum_probs=25.3
Q ss_pred CCCCceeEEE------eeCcccchHHhhcccccCCceeEeceeeeEEEEc
Q 006900 481 RAMPHIKTFA------RYNGQKLAKAAWGALQKNNSQLMIRSYELGVLIL 524 (626)
Q Consensus 481 ~a~PHiKty~------r~~s~NLSkaAWG~l~k~~sql~IrnYElGVL~~ 524 (626)
...+|.|+++ ..+|+|++..++. .|+|+||++.
T Consensus 117 ~~~~H~K~~viD~~~~~iGS~N~t~~s~~-----------~N~E~~lii~ 155 (177)
T PRK13912 117 YGIMHQKVAIIDDKIVVLGSANWSKNAFE-----------NNYEVLLITD 155 (177)
T ss_pred ccccceeEEEEcCCEEEEeCCCCChhHhc-----------cCCceEEEEC
Confidence 3467999876 3578999987765 4899999883
No 20
>COG4110 Uncharacterized protein involved in stress response [General function prediction only]
Probab=20.08 E-value=83 Score=30.95 Aligned_cols=37 Identities=16% Similarity=0.425 Sum_probs=31.8
Q ss_pred ecCCccEEEEeecCCcEEEee--CCcccccCcccccccccC
Q 006900 55 ASADGSASLVVDGTNPVVVKS--GDQRKKLSSNEHVSIADG 93 (626)
Q Consensus 55 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~i~~~ 93 (626)
.++||.+.+-+-+++||++.- ++.|+..|+..+ |.+-
T Consensus 128 ~~~dGvvTik~P~~~~I~~qm~e~~~r~~mCAiA~--i~N~ 166 (200)
T COG4110 128 DKTDGVVTIKVPDQPPIETQLTEGENRRTMCAIAR--LVNE 166 (200)
T ss_pred cccCCEEEEecCCCCceEEEccCCcccceeEEEEE--Eecc
Confidence 578999999999999999986 788999999888 5443
Done!