Query 007385
Match_columns 605
No_of_seqs 246 out of 414
Neff 4.9
Searched_HMMs 46136
Date Thu Mar 28 22:52:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007385.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007385hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00457 MACPF membrane-atta 100.0 4.4E-28 9.5E-33 236.3 15.2 168 127-318 3-193 (194)
2 PF01823 MACPF: MAC/Perforin d 99.9 7.9E-27 1.7E-31 226.0 6.6 177 122-317 18-212 (212)
3 PTZ00482 membrane-attack compl 99.9 2.7E-23 5.8E-28 237.6 15.3 283 12-326 243-577 (844)
4 PTZ00481 Membrane attack compl 99.8 3.2E-19 6.9E-24 189.5 11.1 157 136-329 190-366 (524)
5 PF12651 RHH_3: Ribbon-helix-h 46.9 16 0.00034 28.2 2.1 18 302-319 24-41 (44)
6 PF02095 Extensin_1: Extensin- 39.5 12 0.00026 20.9 0.3 6 320-325 4-9 (10)
7 PF00908 dTDP_sugar_isom: dTDP 17.5 1E+02 0.0022 30.6 2.6 36 19-59 76-114 (176)
8 cd03131 GATase1_HTS Type 1 glu 14.6 1E+02 0.0023 30.5 1.9 15 453-467 64-78 (175)
9 PF09305 TACI-CRD2: TACI, cyst 13.7 55 0.0012 25.3 -0.3 13 334-346 27-40 (41)
10 PF03983 SHD1: SLA1 homology d 13.5 2.5E+02 0.0054 24.2 3.5 28 562-589 17-48 (70)
No 1
>smart00457 MACPF membrane-attack complex / perforin.
Probab=99.95 E-value=4.4e-28 Score=236.35 Aligned_cols=168 Identities=24% Similarity=0.371 Sum_probs=125.5
Q ss_pred eeEeeEEEEEEEEEEcCCCCCCchhHh---ccCCCCCChHHHHHHHhccceEEEEceEecCE-EEE-EEe--ehhcCCCC
Q 007385 127 LAFDGMFISLYSVALEKSQMVLRDRVK---KAVPATWEPAALASFIETYGTHIIVGVRMGGK-DVI-YVK--QKHSSTLQ 199 (605)
Q Consensus 127 la~dg~~I~ly~frL~~~~L~LseeF~---k~LPs~Yd~~aYa~FIe~YGTHYItsgtLGGk-dvi-yVr--q~ksSglT 199 (605)
++.+.+.|.+|++++. +++|+++|+ ++||..|++++|++||++||||||++++|||+ ..+ .++ +++..+++
T Consensus 3 ~~~~~v~~~~y~~~~~--~~~l~~~f~~~l~~Lp~~~~~~~~~~fi~~yGTH~i~s~~~Gg~~~~~~~~~~~~~~~~~~~ 80 (194)
T smart00457 3 VARWTVRNRLYSVKLD--DIPLALEFLKALRDLPDQYNRGAYARFIDKYGTHYITSATLGGEYSLLLVLDKKSLERKGLT 80 (194)
T ss_pred EEEEEEEEEEEEecCC--CCCcCHHHHHHHHhCccccCHHHHHHHHHHhCCeEEEeeeeeeeEEEEEEEcHHHHHhcCCC
Confidence 4566666666666665 589999999 69999999999999999999999999999999 444 333 35566899
Q ss_pred HHHHHHHHHhhcCeeEe-cccCcccccchhhhcccchhhhhhhcccccCCCCcccccccCcEEEEEeecCC---------
Q 007385 200 PADVQKRLKEMADKRFL-DANGQYSLSSEQVYQNDKFDIREQRLRFADTSPSSSYSYKEDMVCICKRRGGS--------- 269 (605)
Q Consensus 200 ~~EVk~CL~~~a~~~F~-~~~~~sc~k~~~~~~~~k~~~~~~~~~f~~~~~~s~vs~~eDi~vI~~vRGG~--------- 269 (605)
.++++.|++. +...|. ..+...|.+.....+ ...+| ...+ .++.++||.
T Consensus 81 ~~~i~~cl~~-~~~~~~~~~s~~~c~~~~~~~~--------~~~~~----------~~~~--~~~~v~GG~~~~~~~l~~ 139 (194)
T smart00457 81 SEDISTCLGG-SSNSFAGSVSAEHCLQFSSYSK--------YLSTS----------LRRL--SHTQVLGGHVTVLCDLLR 139 (194)
T ss_pred HHHHHhhhce-eeeEEEEeecCceecccccccc--------ccccc----------ccce--eeEEEeCCchHHHHHHhc
Confidence 9999999997 334443 223345655221110 01111 0123 345567773
Q ss_pred ---CCCcccHHHHHhhccCCCCeEEeeccccccccCCCc---hhhHHHHHHHHHH
Q 007385 270 ---DNRNLSHNEWLHTVQFEPDVTSMSFIPITSLLNGVP---GSGFLSHAINLYL 318 (605)
Q Consensus 270 ---~~~~l~yseWl~SVk~nPdVIs~kL~PI~eLL~~vp---kr~nLkrAIeeYL 318 (605)
.+.. .|++|++||+.+|++|++++.|||+||++.| ++++|++||++||
T Consensus 140 ~~~~~~~-~~~~W~~sv~~~p~~I~~~l~Pi~~lv~~~~~~~~~~~l~~Al~~Yl 193 (194)
T smart00457 140 GPSTNSL-DFSDWAESVPNEPVLIDVSLAPIYELLPPNPLSQKREALRQALRSYL 193 (194)
T ss_pred CCCCChH-HHHHHHHHhhhCCceeEEeeEEHHHHhcCcchHHHHHHHHHHHHHHh
Confidence 2345 7999999999999999999999999999986 9999999999998
No 2
>PF01823 MACPF: MAC/Perforin domain; InterPro: IPR020864 The membrane attack complex/perforin (MACPF) domain is conserved in bacteria, fungi, mammals and plants. It was originally identified and named as being common to five complement components (C6, C7, C8-alpha, C8-beta, and C9) and perforin. These molecules perform critical functions in innate and adaptive immunity. The MAC family proteins and perforin are known to participate in lytic pore formation. In response to pathogen infection, a sequential and highly specific interaction between the constituent elements occurs to form transmembrane channels which are known as the membrane-attack complex (MAC).Only a few other MACPF proteins have been characterised and several are thought to form pores for invasion or protection [, , ]. Examples are proteins from malarial parasites [], the cytolytic toxins from sea anemones [], and proteins that provide plant immunity [, ]. Functionally uncharacterised MACPF proteins are also evident in pathogenic bacteria such as Chlamydia spp [] and Photorhabdus luminescens (Xenorhabdus luminescens) []. The MACPF domain is commonly found to be associated with other N- and C-terminal domains, such as TSP1 (see PDOC50092 from PROSITEDOC), LDLRA (see PDOC00929 from PROSITEDOC), EGF-like (see PDOC00021 from PROSITEDOC),Sushi/CCP/SCR (see PDOC50923 from PROSITEDOC), FIMAC or C2 (see PDOC00380 from PROSITEDOC). They probably control or target MACPF function [, ]. The MACPF domain oligomerizes, undergoes conformational change, and is required for lytic activity. The MACPF domain consists of a central kinked four-stranded antiparallel beta sheet surrounded by alpha helices and beta strands, forming two structural segments. Overall, the MACPF domain has a thin L-shaped appearance. MACPF domains exhibit limited sequence similarity but contain a signature [YW]-G-[TS]-H-[FY]-x(6)-G-G motif [, , ]. Some proteins known to contain a MACPF domain are listed below: Vertebrate complement proteins C6 to C9. Complement factors C6 to C9 assemble to form a scaffold, the membrane attack complex (MAC), that permits C9 polymerisation into pores that lyse Gram-negative pathogens [, ]. Vertebrate perforin. It is delivered by natural killer cells and cytotoxic T lymphocytes and forms oligomeric pores (12 to 18 monomers) in the plasma membrane of either virus-infected or transformed cells. Arabidopsis thaliana (Mouse-ear cress) constitutively activated cell death 1 (CAD1) protein. It is likely to act as a mediator that recognises plant signals for pathogen infection []. Arabidopsis thaliana (Mouse-ear cress) necrotic spotted lesions 1 (NSL1) protein []. Venomous sea anemone Phyllodiscus semoni (Night anemone) toxins PsTX-60A and PsTX-60B []. Venomous sea anemone Actineria villosa (Okinawan sea anemone) toxin AvTX-60A []. Plasmodium sporozoite microneme protein essential for cell traversal 2 (SPECT2). It is essential for the membrane-wounding activity of the sporozoite and is involved in its traversal of the sinusoidal cell layer prior to hepatocyte-infection []. P. luminescens Plu-MACPF. Although nonlytic, it was shown to bind to cell membranes []. Chlamydial putative uncharacterised protein CT153 []. ; PDB: 2QP2_A 3OJY_B 3NSJ_A 4E0S_B 3T5O_A 4A5W_B 2QQH_A 2RD7_A.
Probab=99.93 E-value=7.9e-27 Score=225.97 Aligned_cols=177 Identities=22% Similarity=0.322 Sum_probs=131.7
Q ss_pred ccceeeeEeeEEEEEEEEEEc-CCCCCCchhHh---ccCCCCCChHH---HHHHHhccceEEEEceEecCE-EEEEE-e-
Q 007385 122 ANTKTLAFDGMFISLYSVALE-KSQMVLRDRVK---KAVPATWEPAA---LASFIETYGTHIIVGVRMGGK-DVIYV-K- 191 (605)
Q Consensus 122 a~tKsla~dg~~I~ly~frL~-~~~L~LseeF~---k~LPs~Yd~~a---Ya~FIe~YGTHYItsgtLGGk-dviyV-r- 191 (605)
..++.+......|.+|++.|. ..++.|+++|+ ++||..|++.. |.+||++|||||++++.|||+ .+++. +
T Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~F~~~l~~L~~~~~~~~~~~y~~f~~~yGTH~v~~~~lGG~~~~~~~~~~ 97 (212)
T PF01823_consen 18 SSSNKFIISKSNCSRYQFSLNDSDDLPLTPEFLSDLNALPAEYNSDNTDEYYRFFDKYGTHYVTSVTLGGKLIYIYSVSK 97 (212)
T ss_dssp STTEEEEEEEEEEEEEEEEE-HSSSBHBGHHHHHHHHTSHSS--HHHHHHHHHHHHHH-SEEEEEEEEEEEEEEEEEEEH
T ss_pred cccEEEEEEEEEEEEEEEEEecCCCCCcCHHHHHHHHhhCcccCccchHHHHHHHHHhCcEEEEEEEEcceeEEEEEeee
Confidence 344457888889999999994 56889999997 78999999988 999999999999999999999 66654 3
Q ss_pred -ehhcCCCCHHHHHHHHHhhcCeeEecccCcccccchhhhcccchhhhhhhcccccCCCCcccccccCcEEEEEeecCCC
Q 007385 192 -QKHSSTLQPADVQKRLKEMADKRFLDANGQYSLSSEQVYQNDKFDIREQRLRFADTSPSSSYSYKEDMVCICKRRGGSD 270 (605)
Q Consensus 192 -q~ksSglT~~EVk~CL~~~a~~~F~~~~~~sc~k~~~~~~~~k~~~~~~~~~f~~~~~~s~vs~~eDi~vI~~vRGG~~ 270 (605)
+.........+++.|++..+...|.......|.......+. .. .......+ ....++||++
T Consensus 98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~--------~~~~~~~~--~~~~~~GG~~ 159 (212)
T PF01823_consen 98 SSLESSKESSIEMKICVSASASASFAGVSVSGSASNSSSQSQ--------SS--------SFSQSNSS--SSIIVIGGDP 159 (212)
T ss_dssp HHHHHTTSSHHHHHHHHHHHHHHHTHCHCCCHHTCTTTHHHH--------CC--------HHHCHEEE--EEEEEESS-C
T ss_pred hhhccccccchhhhheeeeeeeeeecccccccccccCccccc--------cc--------ccccccee--EEEEEECCcc
Confidence 34566788899999999988766633333333331111100 00 00111123 5677889986
Q ss_pred ------CCcccHHHHHhhccCCCCeEEeeccccccccCCCc-hhhHHHHHHHHH
Q 007385 271 ------NRNLSHNEWLHTVQFEPDVTSMSFIPITSLLNGVP-GSGFLSHAINLY 317 (605)
Q Consensus 271 ------~~~l~yseWl~SVk~nPdVIs~kL~PI~eLL~~vp-kr~nLkrAIeeY 317 (605)
+.. .+.+|++||+++|.+|+++|.||++|++..+ ++.+|++||++|
T Consensus 160 ~~~~~~~~~-~~~~W~~sv~~~p~~i~~~l~PI~~li~~~~~k~~~l~~ai~~Y 212 (212)
T PF01823_consen 160 SSAAASDND-NFSEWASSVKDNPVPIDFELQPIYDLIPDNPFKKENLKKAIEEY 212 (212)
T ss_dssp TTHHCCCHH-HHHHHHHHHCTS-EEEEEEEEEGGGGGCTTTTHHHHHHHHHHHH
T ss_pred ccccccCcc-cHHHHHHHHhCCCeeEEEEeEEHHHHcCCcHHHHHHHHHHHHhC
Confidence 355 8999999999999999999999999999998 999999999998
No 3
>PTZ00482 membrane-attack complex/perforin (MACPF) Superfamily; Provisional
Probab=99.90 E-value=2.7e-23 Score=237.61 Aligned_cols=283 Identities=19% Similarity=0.234 Sum_probs=179.7
Q ss_pred HHHHhhccceeecccchhh----hcccCCCCCcceEEecC-------CCceeEEcCCCeeecCCCCCccccccceeEEee
Q 007385 12 EVAIGSIGRGYDIAIDLRL----KYCKGDLKDSRLIEIDK-------DGGREIVLPGGISIPNVSKSIKCDKGERTRFRS 80 (605)
Q Consensus 12 ~~ai~~lG~G~Dlt~D~rl----~~cK~~~~~srli~id~-------~~~r~l~~Pgg~~v~~v~~~ikCdk~~s~~~~S 80 (605)
..+++.||.|||+..==.| .--+.|= ..++|++.= ...+....|-|+-|. +.+.|.+.+....-+
T Consensus 243 ~~gleYLG~GYDIi~GNPlGd~~~~vDPGY-R~pII~~~~~~n~~~~~nd~~~~~P~G~wIR---~e~sC~rSe~i~eI~ 318 (844)
T PTZ00482 243 FPGLYFLGIGYDSLFGNPLGEPDSLTDPGY-RGQIILMNWAQSNDGVANDLATLQPLNGWIR---KENACSRSESIKECS 318 (844)
T ss_pred cccceecccceeceecCCCCCccccCCCcc-cchhhcccccccccccCccccccCCCCceec---cccceeccccceeec
Confidence 5789999999999761111 0111100 023444421 122455677776555 456799998877777
Q ss_pred cHhhHHHHHHhcccceecccccC-CcceeEEEEEcceeehhh--ccceeeeEeeEEEEEEEEEEcC-CCCCCchhHh---
Q 007385 81 DVLSFQQMSEQFNQELSLTGKIP-SGLFNAMFEFSGYWQKDA--ANTKTLAFDGMFISLYSVALEK-SQMVLRDRVK--- 153 (605)
Q Consensus 81 dv~~f~qmse~fn~~~sl~gkIp-sg~fna~f~~sGs~skdA--a~tKsla~dg~~I~ly~frL~~-~~L~LseeF~--- 153 (605)
+..+++ ..++.+.++++..+ .+.|+++.++.-- .++. ...|.|..+. +|..|.+.|.. .+..|+++|+
T Consensus 319 sisdy~---ksLS~dasvsgs~~g~~sFSAS~gYk~f-~~~lskk~~k~fi~ks-~C~~Y~~~L~~~~~~~Lt~~F~~aL 393 (844)
T PTZ00482 319 SLSDYT---KNLSAEASVSGSYMGINSFSASTGYKKF-LQEVSKRTTKTYLLKS-NCVKYTAGLPPYFKWNQTTAFKNAV 393 (844)
T ss_pred cHHHhh---hheeeeeecccccccceeeecccchHHH-HHHHhhcceeEEEEee-eEEEEEEeccccCCCccCHHHHHHH
Confidence 666665 47888888888765 2445555554311 1222 2444576666 89999999996 3458999999
Q ss_pred ccCCCCCC------------------------hHHHHHHHhccceEEEEceEecCE-EEEEEeehhcCCCCHH-HHHHHH
Q 007385 154 KAVPATWE------------------------PAALASFIETYGTHIIVGVRMGGK-DVIYVKQKHSSTLQPA-DVQKRL 207 (605)
Q Consensus 154 k~LPs~Yd------------------------~~aYa~FIe~YGTHYItsgtLGGk-dviyVrq~ksSglT~~-EVk~CL 207 (605)
..||..|+ ...|.+||++|||||+++++|||+ ..++ + ..+.+.+ ..+.|+
T Consensus 394 ~~LP~~f~~~~~~~~Cs~~~Y~~n~~~e~C~~i~~W~~f~~~yGTH~~~~~~lGG~I~~~~--~--le~s~~e~lkk~~l 469 (844)
T PTZ00482 394 NGLPPVFDGLEAESECSSDVYEQDKTAEECENVPIWISFFEQYGTHIIMELQLGGKITKQV--T--VKNSSVEQMKKDGV 469 (844)
T ss_pred HhcchhhhcccccccCCHHHhhhcccccccccHHHHHHHHHHcCceEEEEEEeccEEEEEE--E--ecchhHHHHHhcCc
Confidence 57899887 457999999999999999999999 3221 1 1233333 367787
Q ss_pred HhhcCeeE--ecccCcccccchhhhcccchhhhhhhcccccCCCCcccccccCcEEEEEeecCCC-----CCcccHHHHH
Q 007385 208 KEMADKRF--LDANGQYSLSSEQVYQNDKFDIREQRLRFADTSPSSSYSYKEDMVCICKRRGGSD-----NRNLSHNEWL 280 (605)
Q Consensus 208 ~~~a~~~F--~~~~~~sc~k~~~~~~~~k~~~~~~~~~f~~~~~~s~vs~~eDi~vI~~vRGG~~-----~~~l~yseWl 280 (605)
++++.+.. ...+...+..... +.+....|. ....+ --..++||.. ++. .|.+|+
T Consensus 470 sVkA~~k~~~g~~S~ggs~~~ss--------~~eskss~~--------~~~~s--k~t~ViGG~~~~d~~d~~-~~~~W~ 530 (844)
T PTZ00482 470 SVKAQVKAQFGFASAGGSTNVSS--------DNSSASNEY--------SYNMS--EQLLVIGGNPIKDVTKEE-NLAEWS 530 (844)
T ss_pred ceeeeehhccccceecccccccc--------hhhhhhhhh--------hhccc--eEEEEECCCCCCCCCChH-HHHHHH
Confidence 77665432 1111111111000 000011111 00011 1133678853 445 799999
Q ss_pred hhccCCCCeEEeeccccccccCCCchhhHHHHHHHHHHh-cCCChhh
Q 007385 281 HTVQFEPDVTSMSFIPITSLLNGVPGSGFLSHAINLYLR-YKPPIEE 326 (605)
Q Consensus 281 ~SVk~nPdVIs~kL~PI~eLL~~vpkr~nLkrAIeeYL~-ykp~ie~ 326 (605)
+||+++|++|+++|.|||+||+..+++++|++||+.|++ |.=.+++
T Consensus 531 ~SV~~nP~pI~~~l~PI~~Ll~~~~~ke~y~kAI~~Yi~l~G~~p~~ 577 (844)
T PTZ00482 531 KTVSTLPMPINIELLPISTLFPSDDLKESYEKAVIYYSRLYGLSPHD 577 (844)
T ss_pred HHhhcCCcceEEEeEEHHHhcCChhhHHHHHHHHHHHHHHhCCChhH
Confidence 999999999999999999999988899999999999998 4433333
No 4
>PTZ00481 Membrane attack complex/ Perforin (MACPF) Superfamily; Provisional
Probab=99.79 E-value=3.2e-19 Score=189.48 Aligned_cols=157 Identities=18% Similarity=0.330 Sum_probs=121.5
Q ss_pred EEEEEEcCCCCCCchhHh---ccCCCCCChHHHHHHHhccceEEEEceEecCE--EEEEEeehhc------CCCCHHHHH
Q 007385 136 LYSVALEKSQMVLRDRVK---KAVPATWEPAALASFIETYGTHIIVGVRMGGK--DVIYVKQKHS------STLQPADVQ 204 (605)
Q Consensus 136 ly~frL~~~~L~LseeF~---k~LPs~Yd~~aYa~FIe~YGTHYItsgtLGGk--dviyVrq~ks------SglT~~EVk 204 (605)
+.+.+|++++|+|+++|+ ++||.+||+++|++||++||||||++++|||. .++.+|+|.. .|++.++|+
T Consensus 190 v~r~~mRsdnLmLh~eFqraL~~LP~eYd~g~Y~~FIe~YGTHYITsv~LGG~VE~vTs~RtC~~slps~~~GlS~~qVk 269 (524)
T PTZ00481 190 VIRMTFKTDNLKLNRFAQRAIDALPEDYQPDVYNEFLNAWGTHISVDTFIGGMIEKQTVFKDCVFFTPQFNGGLSPEQVE 269 (524)
T ss_pred eEEEEEecCCceeCHHHHHHHHhcchhcCHHHHHHHHHhcCceEEEEeeEcCEEEEEeehhhhhhhchhhhcCCCHHHHH
Confidence 456778899999999999 78999999999999999999999999999999 6789999973 489999999
Q ss_pred HHHHhhcCeeEecccCcccccchhhhcccchhhhhhhcccccCCCCcccccccCcEEEEEeecCCCCCcccHHHHHhhcc
Q 007385 205 KRLKEMADKRFLDANGQYSLSSEQVYQNDKFDIREQRLRFADTSPSSSYSYKEDMVCICKRRGGSDNRNLSHNEWLHTVQ 284 (605)
Q Consensus 205 ~CL~~~a~~~F~~~~~~sc~k~~~~~~~~k~~~~~~~~~f~~~~~~s~vs~~eDi~vI~~vRGG~~~~~l~yseWl~SVk 284 (605)
+||..|+.-.. ++.+ |+......-++ +-||+ ++ .-++|.+|+.
T Consensus 270 ~cLn~ELqgn~-----------~~Gy-----------------~~~rrkvslD~------i~GGN--PE-~i~nr~~Tfs 312 (524)
T PTZ00481 270 QALRNELNGNP-----------AEGF-----------------FTARRQVTLDH------KFGGN--PE-DVANWEQTIS 312 (524)
T ss_pred HHHHHHhcCCC-----------Cccc-----------------eeeeeeeehhh------hcCCC--hh-Hhhhhhhhhc
Confidence 99999875110 0000 01111111122 23664 55 5789999999
Q ss_pred CCCCeEEeeccccccccCCCch-hhHHHHHHHH--------HHhcCCChhhhhh
Q 007385 285 FEPDVTSMSFIPITSLLNGVPG-SGFLSHAINL--------YLRYKPPIEELHQ 329 (605)
Q Consensus 285 ~nPdVIs~kL~PI~eLL~~vpk-r~nLkrAIee--------YL~ykp~ie~l~~ 329 (605)
.||+.|+|.-.||.+-++..|. |+||++||.- |..|--.+.|=+.
T Consensus 313 ~NPvplK~n~ipiW~afpagpqvk~NlqqaI~nriesM~qr~~~~q~qv~eqRr 366 (524)
T PTZ00481 313 QNPALLKINRFLSWDNLTANPQVKANLQQAIMNRIESMKQRQISYQQQVREQRR 366 (524)
T ss_pred cCceeeeeeeeeehhhcccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999998775 9999999976 4444444555444
No 5
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=46.86 E-value=16 Score=28.18 Aligned_cols=18 Identities=39% Similarity=0.709 Sum_probs=16.1
Q ss_pred CCCchhhHHHHHHHHHHh
Q 007385 302 NGVPGSGFLSHAINLYLR 319 (605)
Q Consensus 302 ~~vpkr~nLkrAIeeYL~ 319 (605)
+++|+..-++.||++||+
T Consensus 24 t~i~~S~Ll~eAle~~l~ 41 (44)
T PF12651_consen 24 TGIPKSKLLREALEDYLE 41 (44)
T ss_pred HCCCHHHHHHHHHHHHHH
Confidence 458899999999999997
No 6
>PF02095 Extensin_1: Extensin-like protein repeat; InterPro: IPR003883 Extensins are plant cell-wall proteins; they can account for up to 20% of the dry weight of the cell wall. They are highly-glycosylated, possibly reflecting their interactions with cell-wall carbohydrates. Amongst their functions is cell wall strengthening in response to mechanical stress (e.g., during attack by pests, plant-bending in the wind, etc.). This repeat occurs within extensin-like proteins.; GO: 0005199 structural constituent of cell wall
Probab=39.47 E-value=12 Score=20.86 Aligned_cols=6 Identities=83% Similarity=1.824 Sum_probs=5.2
Q ss_pred cCCChh
Q 007385 320 YKPPIE 325 (605)
Q Consensus 320 ykp~ie 325 (605)
||||+|
T Consensus 4 ykPpve 9 (10)
T PF02095_consen 4 YKPPVE 9 (10)
T ss_pred cCCCcc
Confidence 899987
No 7
>PF00908 dTDP_sugar_isom: dTDP-4-dehydrorhamnose 3,5-epimerase; InterPro: IPR000888 Deoxythymidine diphosphate (dTDP)-4-keto-6-deoxy-d-hexulose 3, 5-epimerase (RmlC, 5.1.3.13 from EC) is involved in the biosynthesis of dTDP-l-rhamnose, which is an essential component of the bacterial cell wall, converting dTDP-4-keto-6-deoxy-D-glucose to dTDP-4-keto-L-rhamnose. The crystal structure of RmlC from Methanobacterium thermoautotrophicum was determined in the presence and absence of a substrate analogue. RmlC is a homodimer comprising a central jelly roll motif, which extends in two directions into longer beta-sheets. Binding of dTDP is stabilised by ionic interactions to the phosphate group and by a combination of ionic and hydrophobic interactions with the base. The active site, which is located in the centre of the jelly roll, is formed by residues that are conserved in all known RmlC sequence homologues. The active site is lined with a number of charged residues and a number of residues with hydrogen-bonding potentials, which together comprise a potential network for substrate binding and catalysis. The active site is also lined with aromatic residues which provide favorable environments for the base moiety of dTDP and potentially for the sugar moiety of the substrate [].; GO: 0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity, 0009103 lipopolysaccharide biosynthetic process; PDB: 1EPZ_A 1EP0_A 1NXM_A 1NZC_D 2IXL_C 1NYW_B 2IXC_D 1PM7_B 1UPI_A 3RYK_B ....
Probab=17.51 E-value=1e+02 Score=30.57 Aligned_cols=36 Identities=31% Similarity=0.638 Sum_probs=24.9
Q ss_pred cceeecccchhh---hcccCCCCCcceEEecCCCceeEEcCCCe
Q 007385 19 GRGYDIAIDLRL---KYCKGDLKDSRLIEIDKDGGREIVLPGGI 59 (605)
Q Consensus 19 G~G~Dlt~D~rl---~~cK~~~~~srli~id~~~~r~l~~Pgg~ 59 (605)
|+=||+.-|+|- .|-| --.+.+++++.+-|+||.|+
T Consensus 76 G~i~dV~vDlR~~SpTfg~-----~~~~~Ls~~n~~~l~IP~G~ 114 (176)
T PF00908_consen 76 GEIFDVAVDLRKGSPTFGK-----WVSVELSAENPRQLYIPPGV 114 (176)
T ss_dssp SEEEEEEEE-BTTSTTTT------EEEEEEETTT--EEEE-TTE
T ss_pred CeEEEEEEECCCCCCCCCE-----EEEEEeCccccCEEEeCCcc
Confidence 788999999987 3555 25678899999999999984
No 8
>cd03131 GATase1_HTS Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS). Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS). HTS, the first enzyme in methionine biosynthesis in Escherichia coli, transfers a succinyl group from succinyl-CoA to homoserine forming succinyl homoserine. It has been suggested that the succinyl group of succinyl-CoA is initially transferred to an enzyme nucleophile before subsequent transfer to homoserine. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with GATase1 domains a reactive cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. It has been proposed that this cys is in the active site of the molecule. However, as succinyl has been found bound to a conserved lysine residue, this conserved cys may play a role in dimer formation. HTS acti
Probab=14.63 E-value=1e+02 Score=30.50 Aligned_cols=15 Identities=40% Similarity=0.297 Sum_probs=12.3
Q ss_pred ceEEEecceEEEeec
Q 007385 453 DLSIVTGAQLHVENH 467 (605)
Q Consensus 453 ~~~ivtgaql~v~~~ 467 (605)
+..|||||.++.-++
T Consensus 64 DGlIITGApve~~~f 78 (175)
T cd03131 64 DGLIVTGAPVEHLPF 78 (175)
T ss_pred CEEEEeCCCcccCCc
Confidence 589999999976554
No 9
>PF09305 TACI-CRD2: TACI, cysteine-rich domain; InterPro: IPR015384 Cytokines can be grouped into a family on the basis of sequence, functional and structural similarities [, , ]. Tumor necrosis factor (TNF) (also known as TNF-alpha or cachectin) is a monocyte-derived cytotoxin that has been implicated in tumour regression, septic shock and cachexia [, ]. The protein is synthesised as a prohormone with an unusually long and atypical signal sequence, which is absent from the mature secreted cytokine []. A short hydrophobic stretch of amino acids serves to anchor the prohormone in lipid bilayers []. Both the mature protein and a partially-processed form of the hormone are secreted after cleavage of the propeptide []. There are a number of different families of TNF, but all these cytokines seem to form homotrimeric (or heterotrimeric in the case of LT-alpha/beta) complexes that are recognised by their specific receptors. This entry represents a cysteine-rich domain found in the TACI family of proteins. Members of this family are predominantly found in tumour necrosis factor receptor superfamily, member 13b (TACI), and are required for binding to the ligands APRIL and BAFF []. ; PDB: 1XU1_T 1XUT_A.
Probab=13.66 E-value=55 Score=25.30 Aligned_cols=13 Identities=31% Similarity=0.294 Sum_probs=7.8
Q ss_pred cCccceec-cccCC
Q 007385 334 QLPRQWAP-VFSEL 346 (605)
Q Consensus 334 q~pc~caP-c~n~l 346 (605)
|+|.+||+ |.|.+
T Consensus 27 qhpk~Ca~fC~~~~ 40 (41)
T PF09305_consen 27 QHPKQCAAFCENKP 40 (41)
T ss_dssp S--GGGHHHHHCTT
T ss_pred cCcHHHHHHHhcCC
Confidence 67888887 76654
No 10
>PF03983 SHD1: SLA1 homology domain 1, SHD1 ; InterPro: IPR007131 The SLA1 homology domain is found in the cytoskeleton assembly control protein SLA1, which is responsible for the correct formation of the actin cytoskeleton.; GO: 0008092 cytoskeletal protein binding, 0030674 protein binding, bridging, 0042802 identical protein binding, 0043130 ubiquitin binding; PDB: 2HBP_A.
Probab=13.47 E-value=2.5e+02 Score=24.17 Aligned_cols=28 Identities=29% Similarity=0.487 Sum_probs=21.4
Q ss_pred CCCcceEEeeeeeeeeCceEEEE----EEeec
Q 007385 562 DSPGYWVVSGARLVVEKGRISLR----VKYSL 589 (605)
Q Consensus 562 d~pg~w~vtgakl~~~~gki~l~----vk~sl 589 (605)
|.-|.+-|-+.-|.+.+|||.|| ||.++
T Consensus 17 D~tG~f~VeA~fv~~~dgkV~L~k~nG~~i~V 48 (70)
T PF03983_consen 17 DRTGKFKVEAEFVGVNDGKVHLHKTNGVKIAV 48 (70)
T ss_dssp BSSS--EEEEEEEEEETTEEEEE-TTS-EEEE
T ss_pred eCCCCEEEEEEEEEeeCCEEEEEecCCeEEEe
Confidence 45689999999999999999998 56655
Done!