Query 008004
Match_columns 581
No_of_seqs 259 out of 547
Neff 5.6
Searched_HMMs 46136
Date Thu Mar 28 18:12:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008004.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008004hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00482 membrane-attack compl 100.0 3.3E-28 7.2E-33 276.5 20.6 325 12-371 243-625 (844)
2 smart00457 MACPF membrane-atta 99.9 1.4E-25 2.9E-30 219.1 17.9 169 127-317 4-194 (194)
3 PF01823 MACPF: MAC/Perforin d 99.9 1.2E-25 2.7E-30 218.9 9.9 178 119-315 16-212 (212)
4 PTZ00481 Membrane attack compl 99.8 3.1E-19 6.8E-24 187.9 13.0 147 134-317 189-348 (524)
5 PRK00523 hypothetical protein; 18.6 70 0.0015 27.1 1.5 17 308-324 26-42 (72)
6 PRK01844 hypothetical protein; 17.8 76 0.0016 26.9 1.5 31 294-324 10-41 (72)
7 PF00908 dTDP_sugar_isom: dTDP 15.7 1.1E+02 0.0025 29.9 2.4 36 19-58 76-114 (176)
8 PF12651 RHH_3: Ribbon-helix-h 15.5 1.3E+02 0.0028 22.7 2.2 18 300-317 24-41 (44)
9 TIGR02834 spo_ytxC putative sp 14.9 1.2E+02 0.0026 32.0 2.5 44 287-335 146-192 (276)
10 PF07319 DnaI_N: Primosomal pr 14.7 2.1E+02 0.0045 25.0 3.6 12 364-375 81-92 (94)
No 1
>PTZ00482 membrane-attack complex/perforin (MACPF) Superfamily; Provisional
Probab=99.96 E-value=3.3e-28 Score=276.52 Aligned_cols=325 Identities=19% Similarity=0.219 Sum_probs=208.8
Q ss_pred HHHhhhcccceeecccccccccC--CCCCC--ceEEec-------CccceeeeecCCeeecCCCCcccccccccceeecc
Q 008004 12 ANSVQALGRGFDVNFDTRLLYCK--GVAGS--RVVEVD-------EEHKKDLFLYDEIVVPNVSRDIKNSQESIGRQSSG 80 (581)
Q Consensus 12 ~~ai~~lG~GyDlt~D~rl~~ck--~~~gs--rli~id-------~~~~r~l~~P~g~~v~~v~~~ikc~kger~r~~Sd 80 (581)
.+++++||.||||..---|..-- -.+|- .+|++. ..+.+.+.+|.|++|+ +.+.|.+++..+..++
T Consensus 243 ~~gleYLG~GYDIi~GNPlGd~~~~vDPGYR~pII~~~~~~n~~~~~nd~~~~~P~G~wIR---~e~sC~rSe~i~eI~s 319 (844)
T PTZ00482 243 FPGLYFLGIGYDSLFGNPLGEPDSLTDPGYRGQIILMNWAQSNDGVANDLATLQPLNGWIR---KENACSRSESIKECSS 319 (844)
T ss_pred cccceecccceeceecCCCCCccccCCCcccchhhcccccccccccCccccccCCCCceec---cccceeccccceeecc
Confidence 68999999999999421111000 00111 222221 0122445688898887 5668999999987666
Q ss_pred ccchhhHHHHhhcceeeecCcC-CceEEEEEeec-cchhhccccceeeEEeeeEEEEEEEEE--cCCCCCchhHHhh---
Q 008004 81 VCTYPQMVEYFNEKANLSGGFP-LGSFNAAFSFT-ASKHIDAAATKTLSMDGFYIPLAKVEL--KSPLVLQENVKRA--- 153 (581)
Q Consensus 81 v~sf~qmse~fn~~~slsg~ip-~g~fna~f~~s-~S~~~~~astKsl~~~~~~i~ly~f~L--~~~l~Ls~eF~ka--- 153 (581)
+ ++....+..+++++|+++ .+.|+|+.+|. ..........|.|..+. +|..|.+.| ..++.|+++|+++
T Consensus 320 i---sdy~ksLS~dasvsgs~~g~~sFSAS~gYk~f~~~lskk~~k~fi~ks-~C~~Y~~~L~~~~~~~Lt~~F~~aL~~ 395 (844)
T PTZ00482 320 L---SDYTKNLSAEASVSGSYMGINSFSASTGYKKFLQEVSKRTTKTYLLKS-NCVKYTAGLPPYFKWNQTTAFKNAVNG 395 (844)
T ss_pred H---HHhhhheeeeeecccccccceeeecccchHHHHHHHhhcceeEEEEee-eEEEEEEeccccCCCccCHHHHHHHHh
Confidence 4 445678888888888754 46788888774 33333345566687777 999999999 4478899999984
Q ss_pred CCCCCC------------------------hhHHHHHHhccccEEEEEEEEccEEEEEEEeeecCCCCHHHHHHHHhhcc
Q 008004 154 IPASWD------------------------PPSLASFIENFGTHVITSVTIGGKDVIYVKQHQSSPLSTMEIKTYVQDVG 209 (581)
Q Consensus 154 LP~~yd------------------------~~~Y~~FIe~YGTHyitsvtLGGkdvi~Vkq~~sS~lt~~evk~cLs~~a 209 (581)
||..|+ ...|++||++|||||+++++|||+-. ...+.+.+. .+...+.|+++.+
T Consensus 396 LP~~f~~~~~~~~Cs~~~Y~~n~~~e~C~~i~~W~~f~~~yGTH~~~~~~lGG~I~-~~~~le~s~-~e~lkk~~lsVkA 473 (844)
T PTZ00482 396 LPPVFDGLEAESECSSDVYEQDKTAEECENVPIWISFFEQYGTHIIMELQLGGKIT-KQVTVKNSS-VEQMKKDGVSVKA 473 (844)
T ss_pred cchhhhcccccccCCHHHhhhcccccccccHHHHHHHHHHcCceEEEEEEeccEEE-EEEEecchh-HHHHHhcCcceee
Confidence 699887 35699999999999999999999932 122222222 1334677777666
Q ss_pred ceeEe--cccccccccccccccCCCCCCcccCCccCCCCCCCCcccCCcCeEEEEEeecCCcc-----hhhHHHHHHhcc
Q 008004 210 NQRFS--DKDSLTSSGQLKLKDKGLDPGLFNSQGIYPQPTSAPYLTGKEDVTVIFRRRGGDDL-----EQNHRQWARTVR 282 (581)
Q Consensus 210 ~~~f~--~~~~~~s~~~~~~~ek~k~~~sf~~q~~~~r~~~~s~~s~~ed~~VI~~vrGG~~~-----~~~~~~Wl~SV~ 282 (581)
.+... .++...+.......+. ..++.+ ..+... ..++||.+. +..|.+|++||+
T Consensus 474 ~~k~~~g~~S~ggs~~~ss~~es---kss~~~------------~~~sk~----t~ViGG~~~~d~~d~~~~~~W~~SV~ 534 (844)
T PTZ00482 474 QVKAQFGFASAGGSTNVSSDNSS---ASNEYS------------YNMSEQ----LLVIGGNPIKDVTKEENLAEWSKTVS 534 (844)
T ss_pred eehhccccceecccccccchhhh---hhhhhh------------hccceE----EEEECCCCCCCCCChHHHHHHHHHhh
Confidence 54321 1111111100000000 000111 001112 224788763 578999999999
Q ss_pred cCCceeeeeeeehhhhcCCchhHHHHHHHHHHHHH-cCCCHHHH--------HHHhhhccccceeeccCCCCCCcccCCC
Q 008004 283 SSPDVIEMTFFPITALLDGITGKEHLTRAIGLYLE-CKPQIEEL--------RYFLEFQIPRVWAPVQTKIPGQQRKEPV 353 (581)
Q Consensus 283 ~~P~vI~~kL~PI~eLL~~~p~k~~Lk~AI~~YL~-yKP~ieeL--------~~flefq~p~~waPc~n~lpg~~r~~~~ 353 (581)
.+|+||+++|.||++||+..+++++|++||+.|++ +.-.+++. ...|+. ...+..+ |.......
T Consensus 535 ~nP~pI~~~l~PI~~Ll~~~~~ke~y~kAI~~Yi~l~G~~p~~~~~~~~~~I~~~l~~-----~t~i~~~--g~~~i~a~ 607 (844)
T PTZ00482 535 TLPMPINIELLPISTLFPSDDLKESYEKAVIYYSRLYGLSPHDTMQKDEKDIVKILTA-----ATTVTWS--GAPPISAE 607 (844)
T ss_pred cCCcceEEEeEEHHHhcCChhhHHHHHHHHHHHHHHhCCChhHhhccccccHHHHHhh-----CcEEeec--CCCceeEE
Confidence 99999999999999999998889999999999999 44444442 122221 1112211 33456678
Q ss_pred CCceeEEeeccEEEEeee
Q 008004 354 CPSLQFSMMGQKLYITQE 371 (581)
Q Consensus 354 ~pslqfs~mgpklyv~t~ 371 (581)
||.=+-.+||.-|-++..
T Consensus 608 CP~g~vIlfGFiL~~~~~ 625 (844)
T PTZ00482 608 CPHGQVVLFGFAMRQNFW 625 (844)
T ss_pred CCCCCEEEEEEEEEeecc
Confidence 999999999999988753
No 2
>smart00457 MACPF membrane-attack complex / perforin.
Probab=99.94 E-value=1.4e-25 Score=219.07 Aligned_cols=169 Identities=23% Similarity=0.366 Sum_probs=119.4
Q ss_pred EEeeeEEEEEEEEEcCCCCCchhHHh---hCCCCCChhHHHHHHhccccEEEEEEEEccE-EEEEEEe-e--ecCCCCHH
Q 008004 127 SMDGFYIPLAKVELKSPLVLQENVKR---AIPASWDPPSLASFIENFGTHVITSVTIGGK-DVIYVKQ-H--QSSPLSTM 199 (581)
Q Consensus 127 ~~~~~~i~ly~f~L~~~l~Ls~eF~k---aLP~~yd~~~Y~~FIe~YGTHyitsvtLGGk-dvi~Vkq-~--~sS~lt~~ 199 (581)
+.+.+.|.+|++++ .+++|+++|++ +||..|++++|++||++||||||++++|||+ ..+...+ + +..+++..
T Consensus 4 ~~~~v~~~~y~~~~-~~~~l~~~f~~~l~~Lp~~~~~~~~~~fi~~yGTH~i~s~~~Gg~~~~~~~~~~~~~~~~~~~~~ 82 (194)
T smart00457 4 ARWTVRNRLYSVKL-DDIPLALEFLKALRDLPDQYNRGAYARFIDKYGTHYITSATLGGEYSLLLVLDKKSLERKGLTSE 82 (194)
T ss_pred EEEEEEEEEEEecC-CCCCcCHHHHHHHHhCccccCHHHHHHHHHHhCCeEEEeeeeeeeEEEEEEEcHHHHHhcCCCHH
Confidence 44555555555554 47999999998 7899999999999999999999999999999 4443332 2 45579999
Q ss_pred HHHHHHhhccceeEecccccccccccccccCCCCCCcccCCccCCCCCCCCcccCCcCeEEEEEeecCCcc---------
Q 008004 200 EIKTYVQDVGNQRFSDKDSLTSSGQLKLKDKGLDPGLFNSQGIYPQPTSAPYLTGKEDVTVIFRRRGGDDL--------- 270 (581)
Q Consensus 200 evk~cLs~~a~~~f~~~~~~~s~~~~~~~ek~k~~~sf~~q~~~~r~~~~s~~s~~ed~~VI~~vrGG~~~--------- 270 (581)
++++|++. +...|.. +.+. ..|.... +... ... . ...++ .+..++||...
T Consensus 83 ~i~~cl~~-~~~~~~~---~~s~--~~c~~~~----~~~~--~~~-----~--~~~~~--~~~~v~GG~~~~~~~l~~~~ 141 (194)
T smart00457 83 DISTCLGG-SSNSFAG---SVSA--EHCLQFS----SYSK--YLS-----T--SLRRL--SHTQVLGGHVTVLCDLLRGP 141 (194)
T ss_pred HHHhhhce-eeeEEEE---eecC--ceecccc----cccc--ccc-----c--cccce--eeEEEeCCchHHHHHHhcCC
Confidence 99999986 2333321 1211 1222210 0000 000 0 00112 33455788521
Q ss_pred ---hhhHHHHHHhcccCCceeeeeeeehhhhcCCch---hHHHHHHHHHHHHH
Q 008004 271 ---EQNHRQWARTVRSSPDVIEMTFFPITALLDGIT---GKEHLTRAIGLYLE 317 (581)
Q Consensus 271 ---~~~~~~Wl~SV~~~P~vI~~kL~PI~eLL~~~p---~k~~Lk~AI~~YL~ 317 (581)
...|++|++||+.+|++|++++.||++||++.| ++++|++||++||.
T Consensus 142 ~~~~~~~~~W~~sv~~~p~~I~~~l~Pi~~lv~~~~~~~~~~~l~~Al~~Yl~ 194 (194)
T smart00457 142 STNSLDFSDWAESVPNEPVLIDVSLAPIYELLPPNPLSQKREALRQALRSYLK 194 (194)
T ss_pred CCChHHHHHHHHHhhhCCceeEEeeEEHHHHhcCcchHHHHHHHHHHHHHHhC
Confidence 368999999999999999999999999999985 99999999999983
No 3
>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=99.92 E-value=1.2e-25 Score=218.92 Aligned_cols=178 Identities=26% Similarity=0.416 Sum_probs=126.7
Q ss_pred ccccceeeEEeeeEEEEEEEEE--cCCCCCchhHHh---hCCCCCChhH---HHHHHhccccEEEEEEEEccE-EEEEEE
Q 008004 119 DAAATKTLSMDGFYIPLAKVEL--KSPLVLQENVKR---AIPASWDPPS---LASFIENFGTHVITSVTIGGK-DVIYVK 189 (581)
Q Consensus 119 ~~astKsl~~~~~~i~ly~f~L--~~~l~Ls~eF~k---aLP~~yd~~~---Y~~FIe~YGTHyitsvtLGGk-dvi~Vk 189 (581)
....+..+.+....|.+|++.+ ...+.|+++|++ +||..|+++. |.+||++|||||+++++|||+ ..++..
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~F~~~l~~L~~~~~~~~~~~y~~f~~~yGTH~v~~~~lGG~~~~~~~~ 95 (212)
T PF01823_consen 16 SSSSSNKFIISKSNCSRYQFSLNDSDDLPLTPEFLSDLNALPAEYNSDNTDEYYRFFDKYGTHYVTSVTLGGKLIYIYSV 95 (212)
T ss_dssp CCSTTEEEEEEEEEEEEEEEEE-HSSSBHBGHHHHHHHHTSHSS--HHHHHHHHHHHHHH-SEEEEEEEEEEEEEEEEEE
T ss_pred hhcccEEEEEEEEEEEEEEEEEecCCCCCcCHHHHHHHHhhCcccCccchHHHHHHHHHhCcEEEEEEEEcceeEEEEEe
Confidence 3444555888888999999999 458999999975 7899999988 999999999999999999999 544443
Q ss_pred e-e--ecCCCCHHHHHHHHhhccceeEecccccccccccccccCCCCCCcccCCccCCCCCCCCcccCCcCeEEEEEeec
Q 008004 190 Q-H--QSSPLSTMEIKTYVQDVGNQRFSDKDSLTSSGQLKLKDKGLDPGLFNSQGIYPQPTSAPYLTGKEDVTVIFRRRG 266 (581)
Q Consensus 190 q-~--~sS~lt~~evk~cLs~~a~~~f~~~~~~~s~~~~~~~ek~k~~~sf~~q~~~~r~~~~s~~s~~ed~~VI~~vrG 266 (581)
+ + ........+++.|++..+...|.......+......... ...+. .....+...++|
T Consensus 96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~----------------~~~~~~~~~~~G 156 (212)
T PF01823_consen 96 SKSSLESSKESSIEMKICVSASASASFAGVSVSGSASNSSSQSQ---SSSFS----------------QSNSSSSIIVIG 156 (212)
T ss_dssp EHHHHHHTTSSHHHHHHHHHHHHHHHTHCHCCCHHTCTTTHHHH---CCHHH----------------CHEEEEEEEEES
T ss_pred eehhhccccccchhhhheeeeeeeeeecccccccccccCccccc---ccccc----------------ccceeEEEEEEC
Confidence 3 2 344666788889998877654422111111110000000 00000 012335566799
Q ss_pred CCcc------hhhHHHHHHhcccCCceeeeeeeehhhhcCCch-hHHHHHHHHHHH
Q 008004 267 GDDL------EQNHRQWARTVRSSPDVIEMTFFPITALLDGIT-GKEHLTRAIGLY 315 (581)
Q Consensus 267 G~~~------~~~~~~Wl~SV~~~P~vI~~kL~PI~eLL~~~p-~k~~Lk~AI~~Y 315 (581)
|++. ...+.+|++||.++|+||+++|.||++||+..+ ++.+|++||++|
T Consensus 157 G~~~~~~~~~~~~~~~W~~sv~~~p~~i~~~l~PI~~li~~~~~k~~~l~~ai~~Y 212 (212)
T PF01823_consen 157 GDPSSAAASDNDNFSEWASSVKDNPVPIDFELQPIYDLIPDNPFKKENLKKAIEEY 212 (212)
T ss_dssp S-CTTHHCCCHHHHHHHHHHHCTS-EEEEEEEEEGGGGGCTTTTHHHHHHHHHHHH
T ss_pred CccccccccCcccHHHHHHHHhCCCeeEEEEeEEHHHHcCCcHHHHHHHHHHHHhC
Confidence 9973 679999999999999999999999999999988 999999999998
No 4
>PTZ00481 Membrane attack complex/ Perforin (MACPF) Superfamily; Provisional
Probab=99.80 E-value=3.1e-19 Score=187.92 Aligned_cols=147 Identities=22% Similarity=0.367 Sum_probs=117.2
Q ss_pred EEEEEEE-cCCCCCchhHHh---hCCCCCChhHHHHHHhccccEEEEEEEEccE-E-EEEEEeee------cCCCCHHHH
Q 008004 134 PLAKVEL-KSPLVLQENVKR---AIPASWDPPSLASFIENFGTHVITSVTIGGK-D-VIYVKQHQ------SSPLSTMEI 201 (581)
Q Consensus 134 ~ly~f~L-~~~l~Ls~eF~k---aLP~~yd~~~Y~~FIe~YGTHyitsvtLGGk-d-vi~Vkq~~------sS~lt~~ev 201 (581)
.+.+.+| +++++|+++|++ +||.+||+++|++||++|||||+++++|||. + ++.+|+|. ..|++..+|
T Consensus 189 nv~r~~mRsdnLmLh~eFqraL~~LP~eYd~g~Y~~FIe~YGTHYITsv~LGG~VE~vTs~RtC~~slps~~~GlS~~qV 268 (524)
T PTZ00481 189 NVIRMTFKTDNLKLNRFAQRAIDALPEDYQPDVYNEFLNAWGTHISVDTFIGGMIEKQTVFKDCVFFTPQFNGGLSPEQV 268 (524)
T ss_pred eeEEEEEecCCceeCHHHHHHHHhcchhcCHHHHHHHHHhcCceEEEEeeEcCEEEEEeehhhhhhhchhhhcCCCHHHH
Confidence 3456667 889999999998 6899999999999999999999999999999 4 99999986 248999999
Q ss_pred HHHHhhccceeEecccccccccccccccCCCCCCcccCCccCCCCCCCCcccCCcCeEEEEEeecCCcchhhHHHHHHhc
Q 008004 202 KTYVQDVGNQRFSDKDSLTSSGQLKLKDKGLDPGLFNSQGIYPQPTSAPYLTGKEDVTVIFRRRGGDDLEQNHRQWARTV 281 (581)
Q Consensus 202 k~cLs~~a~~~f~~~~~~~s~~~~~~~ek~k~~~sf~~q~~~~r~~~~s~~s~~ed~~VI~~vrGG~~~~~~~~~Wl~SV 281 (581)
+.||..++.... . +-+ |. -| + .+.+ -.+.||++. ...+|.+|+
T Consensus 269 k~cLn~ELqgn~------~----~Gy---------~~-----~r-----r-----kvsl-D~i~GGNPE--~i~nr~~Tf 311 (524)
T PTZ00481 269 EQALRNELNGNP------A----EGF---------FT-----AR-----R-----QVTL-DHKFGGNPE--DVANWEQTI 311 (524)
T ss_pred HHHHHHHhcCCC------C----ccc---------ee-----ee-----e-----eeeh-hhhcCCChh--Hhhhhhhhh
Confidence 999999875211 0 000 00 00 0 0001 123699764 589999999
Q ss_pred ccCCceeeeeeeehhhhcCCchh-HHHHHHHHHHHHH
Q 008004 282 RSSPDVIEMTFFPITALLDGITG-KEHLTRAIGLYLE 317 (581)
Q Consensus 282 ~~~P~vI~~kL~PI~eLL~~~p~-k~~Lk~AI~~YL~ 317 (581)
..||++|++.-.|||+-++..|. |+||++||..-++
T Consensus 312 s~NPvplK~n~ipiW~afpagpqvk~NlqqaI~nrie 348 (524)
T PTZ00481 312 SQNPALLKINRFLSWDNLTANPQVKANLQQAIMNRIE 348 (524)
T ss_pred ccCceeeeeeeeeehhhcccCcHHHHHHHHHHHHHHH
Confidence 99999999999999999999777 9999999987664
No 5
>PRK00523 hypothetical protein; Provisional
Probab=18.57 E-value=70 Score=27.12 Aligned_cols=17 Identities=18% Similarity=0.237 Sum_probs=14.2
Q ss_pred HHHHHHHHHHcCCCHHH
Q 008004 308 LTRAIGLYLECKPQIEE 324 (581)
Q Consensus 308 Lk~AI~~YL~yKP~iee 324 (581)
-++-++.||+++|||.|
T Consensus 26 ark~~~k~l~~NPpine 42 (72)
T PRK00523 26 SKKMFKKQIRENPPITE 42 (72)
T ss_pred HHHHHHHHHHHCcCCCH
Confidence 45667889999999988
No 6
>PRK01844 hypothetical protein; Provisional
Probab=17.80 E-value=76 Score=26.93 Aligned_cols=31 Identities=26% Similarity=0.307 Sum_probs=19.7
Q ss_pred ehhhhcCCchh-HHHHHHHHHHHHHcCCCHHH
Q 008004 294 PITALLDGITG-KEHLTRAIGLYLECKPQIEE 324 (581)
Q Consensus 294 PI~eLL~~~p~-k~~Lk~AI~~YL~yKP~iee 324 (581)
+|-.|+-+.-. --.-++.++.||+++|||.|
T Consensus 10 ~I~~li~G~~~Gff~ark~~~k~lk~NPpine 41 (72)
T PRK01844 10 GVVALVAGVALGFFIARKYMMNYLQKNPPINE 41 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCH
Confidence 34444444322 23345667889999999988
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=15.66 E-value=1.1e+02 Score=29.87 Aligned_cols=36 Identities=31% Similarity=0.460 Sum_probs=24.6
Q ss_pred ccceeecccccc---cccCCCCCCceEEecCccceeeeecCCe
Q 008004 19 GRGFDVNFDTRL---LYCKGVAGSRVVEVDEEHKKDLFLYDEI 58 (581)
Q Consensus 19 G~GyDlt~D~rl---~~ck~~~gsrli~id~~~~r~l~~P~g~ 58 (581)
|+=+|+.=|+|- .|.+ -..+.+++++.+.|.||.|+
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 777999999996 3555 25677888899999999984
No 8
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=15.54 E-value=1.3e+02 Score=22.71 Aligned_cols=18 Identities=39% Similarity=0.538 Sum_probs=15.3
Q ss_pred CCchhHHHHHHHHHHHHH
Q 008004 300 DGITGKEHLTRAIGLYLE 317 (581)
Q Consensus 300 ~~~p~k~~Lk~AI~~YL~ 317 (581)
+++|...-++.||++||+
T Consensus 24 t~i~~S~Ll~eAle~~l~ 41 (44)
T PF12651_consen 24 TGIPKSKLLREALEDYLE 41 (44)
T ss_pred HCCCHHHHHHHHHHHHHH
Confidence 346778999999999997
No 9
>TIGR02834 spo_ytxC putative sporulation protein YtxC. This uncharacterized protein is part of a panel of proteins conserved in all known endospore-forming Firmicutes (low-GC Gram-positive bacteria), including Carboxydothermus hydrogenoformans, and nowhere else.
Probab=14.92 E-value=1.2e+02 Score=32.02 Aligned_cols=44 Identities=34% Similarity=0.499 Sum_probs=32.9
Q ss_pred eeeeeeeehhhhcCCchhHHHHHHHHHHHHHcC---CCHHHHHHHhhhcccc
Q 008004 287 VIEMTFFPITALLDGITGKEHLTRAIGLYLECK---PQIEELRYFLEFQIPR 335 (581)
Q Consensus 287 vI~~kL~PI~eLL~~~p~k~~Lk~AI~~YL~yK---P~ieeL~~flefq~p~ 335 (581)
-|.|.|.+..+-| +.....||++|+-+| -=|.-|+||++-|.|+
T Consensus 146 FitFRLk~y~~~L-----~~~Ve~aidEy~~EkEYqeFI~lLryFV~~Qe~k 192 (276)
T TIGR02834 146 FVTFRLKPYVEEL-----RDIVEKAIDEYLMEKEYQEFIKLLRYFVEIQDSR 192 (276)
T ss_pred ceeeehHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcC
Confidence 4556666665544 467888999999865 4478899999999886
No 10
>PF07319 DnaI_N: Primosomal protein DnaI N-terminus; InterPro: IPR009928 This entry represents the N terminus (approximately 120 residues) of bacterial primosomal DnaI proteins, although one family member appears to be of viral origin. DnaI is one of the components of the Bacillus subtilis replication restart primosome, and is required for the DnaB75-dependent loading of the DnaC helicase [].; PDB: 2K7R_A.
Probab=14.68 E-value=2.1e+02 Score=25.01 Aligned_cols=12 Identities=33% Similarity=0.434 Sum_probs=10.5
Q ss_pred cEEEEeeeeEee
Q 008004 364 QKLYITQEQISV 375 (581)
Q Consensus 364 pklyv~t~~v~~ 375 (581)
|+|.|+...|+|
T Consensus 81 P~L~~~~~~Idv 92 (94)
T PF07319_consen 81 PKLVVNNGYIDV 92 (94)
T ss_dssp EEEEEETTEEEE
T ss_pred CeEEeeCCEeee
Confidence 999999888876
Done!