Query 018486
Match_columns 355
No_of_seqs 250 out of 544
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 09:25:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018486.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018486hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00457 MACPF membrane-atta 99.9 8.2E-27 1.8E-31 211.8 16.1 161 130-291 6-194 (194)
2 PTZ00482 membrane-attack compl 99.9 7.3E-26 1.6E-30 239.3 20.4 317 10-341 243-624 (844)
3 PF01823 MACPF: MAC/Perforin d 99.9 9.8E-27 2.1E-31 211.7 10.2 162 128-289 26-212 (212)
4 PTZ00481 Membrane attack compl 99.9 1.5E-23 3.3E-28 204.4 15.2 170 134-318 190-382 (524)
5 PF14116 YyzF: YyzF-like prote 52.1 15 0.00033 26.0 2.5 38 278-317 2-42 (48)
6 PHA03141 helicase-primase prim 38.5 15 0.00032 29.9 0.9 30 306-342 15-44 (101)
7 PRK00523 hypothetical protein; 33.1 31 0.00066 26.5 1.8 18 282-299 26-43 (72)
8 PRK01844 hypothetical protein; 32.1 33 0.00071 26.4 1.8 32 268-299 10-42 (72)
9 PF04564 U-box: U-box domain; 32.0 46 0.001 25.1 2.7 44 245-293 28-71 (73)
10 PF12651 RHH_3: Ribbon-helix-h 26.6 61 0.0013 22.2 2.3 17 275-291 25-41 (44)
11 PF03672 UPF0154: Uncharacteri 23.5 60 0.0013 24.4 1.9 18 281-298 17-34 (64)
12 PF11403 Yeast_MT: Yeast metal 23.4 57 0.0012 21.4 1.5 19 309-327 9-28 (40)
13 PF14259 RRM_6: RNA recognitio 20.4 78 0.0017 22.6 2.0 50 152-208 4-59 (70)
14 smart00362 RRM_2 RNA recogniti 20.0 64 0.0014 22.1 1.4 23 152-174 5-27 (72)
No 1
>smart00457 MACPF membrane-attack complex / perforin.
Probab=99.95 E-value=8.2e-27 Score=211.77 Aligned_cols=161 Identities=24% Similarity=0.370 Sum_probs=117.0
Q ss_pred EEEEEEEEEEecCCCCcchHHHh---hCCCCCChHHHHHHHhccccEEEEEEEEccE-EEEEEe-ec--ccCCCCHHHHH
Q 018486 130 NFISLYKVKLAKLNLVLREEIRR---AVPYSWDPPLLASFIENYGTHIVTSITIGGR-DVVYIR-QH--QSSPLSMMDIE 202 (355)
Q Consensus 130 ~~i~l~~~~l~~~~l~L~~~F~~---~LP~~yd~~~y~~fIe~YGTHyit~v~lGGk-~v~~v~-~~--~ss~ls~~evk 202 (355)
..+.+..|+|+..+++|+++|.+ +||..|++++|.+||++||||||+++++||+ ..+... ++ ...+++.++++
T Consensus 6 ~~v~~~~y~~~~~~~~l~~~f~~~l~~Lp~~~~~~~~~~fi~~yGTH~i~s~~~Gg~~~~~~~~~~~~~~~~~~~~~~i~ 85 (194)
T smart00457 6 WTVRNRLYSVKLDDIPLALEFLKALRDLPDQYNRGAYARFIDKYGTHYITSATLGGEYSLLLVLDKKSLERKGLTSEDIS 85 (194)
T ss_pred EEEEEEEEEecCCCCCcCHHHHHHHHhCccccCHHHHHHHHHHhCCeEEEeeeeeeeEEEEEEEcHHHHHhcCCCHHHHH
Confidence 34455555555556899999998 6999999999999999999999999999999 444333 33 34479999999
Q ss_pred HHHHhhcccccc-ccccccccC---cccccCC--ceEEEEEeecCCcc------------hhhHHHHHHhhccCCceeee
Q 018486 203 NYVKDIGDERFM-DSKSQSSAA---PLKYKDK--DVTVIFRRRGGDDL------------EQSHAKWAETVQLAPDVINM 264 (355)
Q Consensus 203 ~cl~~~~~~~f~-~~~~~s~~~---~~~~~~~--~~~vi~~~~GG~~l------------~~~~~~W~~SV~~~P~vI~~ 264 (355)
+|++. +...|. +.+...... ....... ..+.+..++||... ...|.+|++||+.+|++|++
T Consensus 86 ~cl~~-~~~~~~~~~s~~~c~~~~~~~~~~~~~~~~~~~~~v~GG~~~~~~~l~~~~~~~~~~~~~W~~sv~~~p~~I~~ 164 (194)
T smart00457 86 TCLGG-SSNSFAGSVSAEHCLQFSSYSKYLSTSLRRLSHTQVLGGHVTVLCDLLRGPSTNSLDFSDWAESVPNEPVLIDV 164 (194)
T ss_pred hhhce-eeeEEEEeecCceecccccccccccccccceeeEEEeCCchHHHHHHhcCCCCChHHHHHHHHHhhhCCceeEE
Confidence 99986 233332 111110000 0011110 12334456788521 25799999999999999999
Q ss_pred eeeehhhhccCch---hHHHHHHHHHHHHH
Q 018486 265 TFTPIVSLLEGVP---GIKHLARAIELYLE 291 (355)
Q Consensus 265 ~l~PI~eLl~~~p---~k~~Lk~AI~~Yl~ 291 (355)
++.||++||++.| ++++|++||++||.
T Consensus 165 ~l~Pi~~lv~~~~~~~~~~~l~~Al~~Yl~ 194 (194)
T smart00457 165 SLAPIYELLPPNPLSQKREALRQALRSYLK 194 (194)
T ss_pred eeEEHHHHhcCcchHHHHHHHHHHHHHHhC
Confidence 9999999999985 99999999999984
No 2
>PTZ00482 membrane-attack complex/perforin (MACPF) Superfamily; Provisional
Probab=99.94 E-value=7.3e-26 Score=239.33 Aligned_cols=317 Identities=18% Similarity=0.210 Sum_probs=189.2
Q ss_pred HHhhccccceeeecCchhhcc--CCCCCC--CceEEecCCC------CccceeecCCeeeCCCCcceeecCcceeEEeec
Q 018486 10 RYSIQALGRGFDVTSDIRLLY--CKGAPG--SRLVHIDEDH------HAGDLVVSDGVLVPNVSVDIECSKGNRSIERIP 79 (355)
Q Consensus 10 ~~~~~~lG~GyD~t~d~r~~~--~k~~~~--srli~~~~~~------~~~~l~~p~g~~v~~v~~~i~~~k~~~~~~~sd 79 (355)
.+++++||.||||..---+.. -.-.|| .++|.+.=.. +.+....|.|+-| .+.+.|.+++..+..++
T Consensus 243 ~~gleYLG~GYDIi~GNPlGd~~~~vDPGYR~pII~~~~~~n~~~~~nd~~~~~P~G~wI---R~e~sC~rSe~i~eI~s 319 (844)
T PTZ00482 243 FPGLYFLGIGYDSLFGNPLGEPDSLTDPGYRGQIILMNWAQSNDGVANDLATLQPLNGWI---RKENACSRSESIKECSS 319 (844)
T ss_pred cccceecccceeceecCCCCCccccCCCcccchhhcccccccccccCccccccCCCCcee---ccccceeccccceeecc
Confidence 689999999999985322211 001122 2344432100 1122345666433 34578999998888777
Q ss_pred cccHHHhhhhccceeeeeeccC-CceEEEEEeecchhhHhHHHHhhcceec-----EEEEEEEEEEecC-CCCcchHHHh
Q 018486 80 VCSFHEMAGYFNEKSGISGNIP-LGSFNAMFNFTGCWQADAAATKSLAMVG-----NFISLYKVKLAKL-NLVLREEIRR 152 (355)
Q Consensus 80 v~~f~~ms~~fn~~~~L~~~ip-~g~f~~~f~~s~s~~~~~a~~ks~~~d~-----~~i~l~~~~l~~~-~l~L~~~F~~ 152 (355)
+.+++ ..+..++++++..+ .+.|+++.+|. .++...+..-.+ ..-..|.+.|... +..|+++|++
T Consensus 320 isdy~---ksLS~dasvsgs~~g~~sFSAS~gYk-----~f~~~lskk~~k~fi~ks~C~~Y~~~L~~~~~~~Lt~~F~~ 391 (844)
T PTZ00482 320 LSDYT---KNLSAEASVSGSYMGINSFSASTGYK-----KFLQEVSKRTTKTYLLKSNCVKYTAGLPPYFKWNQTTAFKN 391 (844)
T ss_pred HHHhh---hheeeeeecccccccceeeecccchH-----HHHHHHhhcceeEEEEeeeEEEEEEeccccCCCccCHHHHH
Confidence 66655 34666777777533 23444444432 233332221122 2223566777662 3479999999
Q ss_pred h---CCCCCC------------------------hHHHHHHHhccccEEEEEEEEccEEEEEEeecccCCCCH-HHHHHH
Q 018486 153 A---VPYSWD------------------------PPLLASFIENYGTHIVTSITIGGRDVVYIRQHQSSPLSM-MDIENY 204 (355)
Q Consensus 153 ~---LP~~yd------------------------~~~y~~fIe~YGTHyit~v~lGGk~v~~v~~~~ss~ls~-~evk~c 204 (355)
+ ||..|+ ...|++||++|||||+++++|||+-...+ . .++.+. +..+.|
T Consensus 392 aL~~LP~~f~~~~~~~~Cs~~~Y~~n~~~e~C~~i~~W~~f~~~yGTH~~~~~~lGG~I~~~~-~--le~s~~e~lkk~~ 468 (844)
T PTZ00482 392 AVNGLPPVFDGLEAESECSSDVYEQDKTAEECENVPIWISFFEQYGTHIIMELQLGGKITKQV-T--VKNSSVEQMKKDG 468 (844)
T ss_pred HHHhcchhhhcccccccCCHHHhhhcccccccccHHHHHHHHHHcCceEEEEEEeccEEEEEE-E--ecchhHHHHHhcC
Confidence 5 899887 34699999999999999999999933211 1 122222 335666
Q ss_pred HHhhccccc--ccc--cccc--ccC---cccccCCceEEEEEeecCCcc-----hhhHHHHHHhhccCCceeeeeeeehh
Q 018486 205 VKDIGDERF--MDS--KSQS--SAA---PLKYKDKDVTVIFRRRGGDDL-----EQSHAKWAETVQLAPDVINMTFTPIV 270 (355)
Q Consensus 205 l~~~~~~~f--~~~--~~~s--~~~---~~~~~~~~~~vi~~~~GG~~l-----~~~~~~W~~SV~~~P~vI~~~l~PI~ 270 (355)
+++.+.+.. .++ .++. .+. ...++....+--..++||.++ ...|.+|++||+.+|+||+++|.|||
T Consensus 469 lsVkA~~k~~~g~~S~ggs~~~ss~~eskss~~~~~~sk~t~ViGG~~~~d~~d~~~~~~W~~SV~~nP~pI~~~l~PI~ 548 (844)
T PTZ00482 469 VSVKAQVKAQFGFASAGGSTNVSSDNSSASNEYSYNMSEQLLVIGGNPIKDVTKEENLAEWSKTVSTLPMPINIELLPIS 548 (844)
T ss_pred cceeeeehhccccceecccccccchhhhhhhhhhhccceEEEEECCCCCCCCCChHHHHHHHHHhhcCCcceEEEeEEHH
Confidence 666554332 111 1111 111 011111111111234799764 46799999999999999999999999
Q ss_pred hhccCchhHHHHHHHHHHHHH-hCCChhHHhh----hhcccCCcccccCCCCC-ccCCCCCCceeEEeecceeEecC
Q 018486 271 SLLEGVPGIKHLARAIELYLE-YKPPIEDLQY----FLDYQIPRVWAPQHSNI-QRKEPVCSSLQFSLMGPKLYISP 341 (355)
Q Consensus 271 eLl~~~p~k~~Lk~AI~~Yl~-~kp~ieel~~----fle~~~p~~wap~~n~~-~~~~~~~~~l~f~~~g~~l~~~~ 341 (355)
+||++.++|++|++||+.|++ +.-.+++..+ -+...+ .....+.+++ ..-...||.=+--+||.-|-++.
T Consensus 549 ~Ll~~~~~ke~y~kAI~~Yi~l~G~~p~~~~~~~~~~I~~~l-~~~t~i~~~g~~~i~a~CP~g~vIlfGFiL~~~~ 624 (844)
T PTZ00482 549 TLFPSDDLKESYEKAVIYYSRLYGLSPHDTMQKDEKDIVKIL-TAATTVTWSGAPPISAECPHGQVVLFGFAMRQNF 624 (844)
T ss_pred HhcCChhhHHHHHHHHHHHHHHhCCChhHhhccccccHHHHH-hhCcEEeecCCCceeEECCCCCEEEEEEEEEeec
Confidence 999997789999999999999 4444444221 111122 1122233333 34456799999999999886653
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=99.94 E-value=9.8e-27 Score=211.70 Aligned_cols=162 Identities=27% Similarity=0.428 Sum_probs=119.5
Q ss_pred ecEEEEEEEEEEec-CCCCcchHHHh---hCCCCCChHH---HHHHHhccccEEEEEEEEccE-EEEEEe-ec--ccCCC
Q 018486 128 VGNFISLYKVKLAK-LNLVLREEIRR---AVPYSWDPPL---LASFIENYGTHIVTSITIGGR-DVVYIR-QH--QSSPL 196 (355)
Q Consensus 128 d~~~i~l~~~~l~~-~~l~L~~~F~~---~LP~~yd~~~---y~~fIe~YGTHyit~v~lGGk-~v~~v~-~~--~ss~l 196 (355)
....+.+|++.|.. .++.|+++|++ +||..|++.. |.+||++|||||+++++|||+ ..++.. ++ .....
T Consensus 26 ~~~~~~~~~~~~~~~~~~~L~~~F~~~l~~L~~~~~~~~~~~y~~f~~~yGTH~v~~~~lGG~~~~~~~~~~~~~~~~~~ 105 (212)
T PF01823_consen 26 SKSNCSRYQFSLNDSDDLPLTPEFLSDLNALPAEYNSDNTDEYYRFFDKYGTHYVTSVTLGGKLIYIYSVSKSSLESSKE 105 (212)
T ss_dssp EEEEEEEEEEEE-HSSSBHBGHHHHHHHHTSHSS--HHHHHHHHHHHHHH-SEEEEEEEEEEEEEEEEEEEHHHHHHTTS
T ss_pred EEEEEEEEEEEEecCCCCCcCHHHHHHHHhhCcccCccchHHHHHHHHHhCcEEEEEEEEcceeEEEEEeeehhhccccc
Confidence 55667799999954 57889999976 6999999988 999999999999999999999 554433 33 33455
Q ss_pred CHHHHHHHHHhhcccccccccc----cccc---CcccccCCceEEEEEeecCCcc------hhhHHHHHHhhccCCceee
Q 018486 197 SMMDIENYVKDIGDERFMDSKS----QSSA---APLKYKDKDVTVIFRRRGGDDL------EQSHAKWAETVQLAPDVIN 263 (355)
Q Consensus 197 s~~evk~cl~~~~~~~f~~~~~----~s~~---~~~~~~~~~~~vi~~~~GG~~l------~~~~~~W~~SV~~~P~vI~ 263 (355)
...+++.|++..+.+.+.+... +... ....+......+...++||++. ...+.+|++||.++|.||+
T Consensus 106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GG~~~~~~~~~~~~~~~W~~sv~~~p~~i~ 185 (212)
T PF01823_consen 106 SSIEMKICVSASASASFAGVSVSGSASNSSSQSQSSSFSQSNSSSSIIVIGGDPSSAAASDNDNFSEWASSVKDNPVPID 185 (212)
T ss_dssp SHHHHHHHHHHHHHHHTHCHCCCHHTCTTTHHHHCCHHHCHEEEEEEEEESS-CTTHHCCCHHHHHHHHHHHCTS-EEEE
T ss_pred cchhhhheeeeeeeeeecccccccccccCccccccccccccceeEEEEEECCccccccccCcccHHHHHHHHhCCCeeEE
Confidence 6778789999888766622211 1110 1112222334555667899863 6689999999999999999
Q ss_pred eeeeehhhhccCch-hHHHHHHHHHHH
Q 018486 264 MTFTPIVSLLEGVP-GIKHLARAIELY 289 (355)
Q Consensus 264 ~~l~PI~eLl~~~p-~k~~Lk~AI~~Y 289 (355)
++|.||++||++.+ +|++|++||++|
T Consensus 186 ~~l~PI~~li~~~~~k~~~l~~ai~~Y 212 (212)
T PF01823_consen 186 FELQPIYDLIPDNPFKKENLKKAIEEY 212 (212)
T ss_dssp EEEEEGGGGGCTTTTHHHHHHHHHHHH
T ss_pred EEeEEHHHHcCCcHHHHHHHHHHHHhC
Confidence 99999999999988 999999999998
No 4
>PTZ00481 Membrane attack complex/ Perforin (MACPF) Superfamily; Provisional
Probab=99.91 E-value=1.5e-23 Score=204.41 Aligned_cols=170 Identities=22% Similarity=0.366 Sum_probs=137.6
Q ss_pred EEEEEEecCCCCcchHHHh---hCCCCCChHHHHHHHhccccEEEEEEEEccE--EEEEEeecc------cCCCCHHHHH
Q 018486 134 LYKVKLAKLNLVLREEIRR---AVPYSWDPPLLASFIENYGTHIVTSITIGGR--DVVYIRQHQ------SSPLSMMDIE 202 (355)
Q Consensus 134 l~~~~l~~~~l~L~~~F~~---~LP~~yd~~~y~~fIe~YGTHyit~v~lGGk--~v~~v~~~~------ss~ls~~evk 202 (355)
+.+.+|+.+.|+|+++|++ +||.+|+++.|.+||++|||||+++++|||. .++.+|+|. ..|++.++|+
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 5788899999999999998 5999999999999999999999999999999 779999995 2489999999
Q ss_pred HHHHhhccccccccccccccCccccc-C-CceEEEEEeecCCcchhhHHHHHHhhccCCceeeeeeeehhhhccCchh-H
Q 018486 203 NYVKDIGDERFMDSKSQSSAAPLKYK-D-KDVTVIFRRRGGDDLEQSHAKWAETVQLAPDVINMTFTPIVSLLEGVPG-I 279 (355)
Q Consensus 203 ~cl~~~~~~~f~~~~~~s~~~~~~~~-~-~~~~vi~~~~GG~~l~~~~~~W~~SV~~~P~vI~~~l~PI~eLl~~~p~-k 279 (355)
.||..++.-.. +..|- - +.+.+- .+-||++. ...+|.+|+..||++|++.-.|||+-++..|. |
T Consensus 270 ~cLn~ELqgn~----------~~Gy~~~rrkvslD-~i~GGNPE--~i~nr~~Tfs~NPvplK~n~ipiW~afpagpqvk 336 (524)
T PTZ00481 270 QALRNELNGNP----------AEGFFTARRQVTLD-HKFGGNPE--DVANWEQTISQNPALLKINRFLSWDNLTANPQVK 336 (524)
T ss_pred HHHHHHhcCCC----------Cccceeeeeeeehh-hhcCCChh--HhhhhhhhhccCceeeeeeeeeehhhcccCcHHH
Confidence 99999876221 22331 1 122111 23599873 58999999999999999999999999999776 9
Q ss_pred HHHHHHHHH--------HHHhCCChhHHhhhhcccCCc-ccccCCCCC
Q 018486 280 KHLARAIEL--------YLEYKPPIEDLQYFLDYQIPR-VWAPQHSNI 318 (355)
Q Consensus 280 ~~Lk~AI~~--------Yl~~kp~ieel~~fle~~~p~-~wap~~n~~ 318 (355)
+||++||.. |..|...+.|-++ +|..-|+ .|| .++||
T Consensus 337 ~NlqqaI~nriesM~qr~~~~q~qv~eqRr-ie~~~P~ta~A-iqgng 382 (524)
T PTZ00481 337 ANLQQAIMNRIESMKQRQISYQQQVREQRR-IERNGPRTAWA-IQGNG 382 (524)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHhcCCcceEE-EccCc
Confidence 999999986 4445556666655 6777787 788 77777
No 5
>PF14116 YyzF: YyzF-like protein
Probab=52.08 E-value=15 Score=25.99 Aligned_cols=38 Identities=21% Similarity=0.294 Sum_probs=27.8
Q ss_pred hHHHHHHHHHHHHHhC---CChhHHhhhhcccCCcccccCCCC
Q 018486 278 GIKHLARAIELYLEYK---PPIEDLQYFLDYQIPRVWAPQHSN 317 (355)
Q Consensus 278 ~k~~Lk~AI~~Yl~~k---p~ieel~~fle~~~p~~wap~~n~ 317 (355)
|++++..||+.|+.+. |.+++|..- +..|.+|.=|.+.
T Consensus 2 C~EHie~AiD~~Vde~e~aP~i~~l~~~--~~~~~~C~~C~~~ 42 (48)
T PF14116_consen 2 CEEHIELAIDDFVDEYEQAPDIEKLEEV--EKLPTTCEYCDQP 42 (48)
T ss_pred cHHHHHHHHHHHHHhhccCCCeEecccc--CCCCCcchhhCCC
Confidence 6789999999999964 666666432 3678888777554
No 6
>PHA03141 helicase-primase primase subunit; Provisional
Probab=38.50 E-value=15 Score=29.92 Aligned_cols=30 Identities=17% Similarity=0.473 Sum_probs=24.4
Q ss_pred cCCcccccCCCCCccCCCCCCceeEEeecceeEecCC
Q 018486 306 QIPRVWAPQHSNIQRKEPVCSSLQFSLMGPKLYISPD 342 (355)
Q Consensus 306 ~~p~~wap~~n~~~~~~~~~~~l~f~~~g~~l~~~~~ 342 (355)
-+|+.|+ ..++.||-|.+-.+|||+||-|+
T Consensus 15 LlP~sf~-------t~~p~~PplP~DCL~P~~fi~T~ 44 (101)
T PHA03141 15 LVPRAFV-------TSKPQKPPIPSDCLAPTLFLLTT 44 (101)
T ss_pred EecHHHc-------cCCCCCCCCCccccCCceEEEeC
Confidence 4556565 56778999999999999999875
No 7
>PRK00523 hypothetical protein; Provisional
Probab=33.12 E-value=31 Score=26.55 Aligned_cols=18 Identities=17% Similarity=0.335 Sum_probs=14.8
Q ss_pred HHHHHHHHHHhCCChhHH
Q 018486 282 LARAIELYLEYKPPIEDL 299 (355)
Q Consensus 282 Lk~AI~~Yl~~kp~ieel 299 (355)
-++-++.||+++|||.|=
T Consensus 26 ark~~~k~l~~NPpine~ 43 (72)
T PRK00523 26 SKKMFKKQIRENPPITEN 43 (72)
T ss_pred HHHHHHHHHHHCcCCCHH
Confidence 367789999999998773
No 8
>PRK01844 hypothetical protein; Provisional
Probab=32.13 E-value=33 Score=26.38 Aligned_cols=32 Identities=28% Similarity=0.447 Sum_probs=20.3
Q ss_pred ehhhhccCchh-HHHHHHHHHHHHHhCCChhHH
Q 018486 268 PIVSLLEGVPG-IKHLARAIELYLEYKPPIEDL 299 (355)
Q Consensus 268 PI~eLl~~~p~-k~~Lk~AI~~Yl~~kp~ieel 299 (355)
+|--|+-+.-. ==--++-.+.||+++|||.|=
T Consensus 10 ~I~~li~G~~~Gff~ark~~~k~lk~NPpine~ 42 (72)
T PRK01844 10 GVVALVAGVALGFFIARKYMMNYLQKNPPINEQ 42 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH
Confidence 44445544222 223377789999999998773
No 9
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=32.02 E-value=46 Score=25.07 Aligned_cols=44 Identities=18% Similarity=0.232 Sum_probs=27.2
Q ss_pred hhhHHHHHHhhccCCceeeeeeeehhhhccCchhHHHHHHHHHHHHHhC
Q 018486 245 EQSHAKWAETVQLAPDVINMTFTPIVSLLEGVPGIKHLARAIELYLEYK 293 (355)
Q Consensus 245 ~~~~~~W~~SV~~~P~vI~~~l~PI~eLl~~~p~k~~Lk~AI~~Yl~~k 293 (355)
.....+|++. ...-+++.-.-+...+|+++ ..|+++|++|++.+
T Consensus 28 r~~I~~~l~~-~~~~~P~t~~~l~~~~l~pn----~~Lk~~I~~~~~~~ 71 (73)
T PF04564_consen 28 RSAIERWLEQ-NGGTDPFTRQPLSESDLIPN----RALKSAIEEWCAEN 71 (73)
T ss_dssp HHHHHHHHCT-TSSB-TTT-SB-SGGGSEE-----HHHHHHHHHHHHHC
T ss_pred HHHHHHHHHc-CCCCCCCCCCcCCcccceEC----HHHHHHHHHHHHHc
Confidence 4578899988 33334444443444456554 48999999999854
No 10
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=26.65 E-value=61 Score=22.18 Aligned_cols=17 Identities=53% Similarity=0.778 Sum_probs=14.9
Q ss_pred CchhHHHHHHHHHHHHH
Q 018486 275 GVPGIKHLARAIELYLE 291 (355)
Q Consensus 275 ~~p~k~~Lk~AI~~Yl~ 291 (355)
++|...-++.||++||+
T Consensus 25 ~i~~S~Ll~eAle~~l~ 41 (44)
T PF12651_consen 25 GIPKSKLLREALEDYLE 41 (44)
T ss_pred CCCHHHHHHHHHHHHHH
Confidence 46778999999999998
No 11
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=23.50 E-value=60 Score=24.41 Aligned_cols=18 Identities=28% Similarity=0.462 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHhCCChhH
Q 018486 281 HLARAIELYLEYKPPIED 298 (355)
Q Consensus 281 ~Lk~AI~~Yl~~kp~iee 298 (355)
.-++-.+.|++++|||.|
T Consensus 17 ~ar~~~~k~l~~NPpine 34 (64)
T PF03672_consen 17 IARKYMEKQLKENPPINE 34 (64)
T ss_pred HHHHHHHHHHHHCCCCCH
Confidence 347778899999999866
No 12
>PF11403 Yeast_MT: Yeast metallothionein; InterPro: IPR022710 Metallothioneins are characterised by an abundance of cysteine residues and a lack of generic secondary structure motifs. This protein functions in primary metal storage, transport and detoxification []. For the first 40 residues in the protein the polypeptide wraps around the metal by forming two large parallel loops separated by a deep cleft containing the metal cluster []. ; PDB: 1AQS_A 1AQR_A 1RJU_V 1FMY_A 1AOO_A 1AQQ_A.
Probab=23.37 E-value=57 Score=21.35 Aligned_cols=19 Identities=16% Similarity=0.146 Sum_probs=10.4
Q ss_pred cccccCCCCC-ccCCCCCCc
Q 018486 309 RVWAPQHSNI-QRKEPVCSS 327 (355)
Q Consensus 309 ~~wap~~n~~-~~~~~~~~~ 327 (355)
|+|..|.||- -.|.++||.
T Consensus 9 cqcgscknneqcqkscscpt 28 (40)
T PF11403_consen 9 CQCGSCKNNEQCQKSCSCPT 28 (40)
T ss_dssp -SSSTTTT-TTSTTS-SS-T
T ss_pred eecCCccChHHHhhcCCCCC
Confidence 5677888888 345667764
No 13
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=20.39 E-value=78 Score=22.64 Aligned_cols=50 Identities=16% Similarity=0.237 Sum_probs=30.8
Q ss_pred hhCCCCCChHHHHHHHhccccEEEEEEEEccE------EEEEEeecccCCCCHHHHHHHHHhh
Q 018486 152 RAVPYSWDPPLLASFIENYGTHIVTSITIGGR------DVVYIRQHQSSPLSMMDIENYVKDI 208 (355)
Q Consensus 152 ~~LP~~yd~~~y~~fIe~YGTHyit~v~lGGk------~v~~v~~~~ss~ls~~evk~cl~~~ 208 (355)
..||...+..+...|++.||. +..+.+-.. ...+|.- -+.++.+.++...
T Consensus 4 ~nlp~~~~~~~l~~~f~~~g~--v~~v~~~~~~~~~~~~~a~v~f-----~~~~~a~~al~~~ 59 (70)
T PF14259_consen 4 SNLPPSTTEEDLRNFFSRFGP--VEKVRLIKNKDGQSRGFAFVEF-----SSEEDAKRALELL 59 (70)
T ss_dssp ESSTTT--HHHHHHHCTTSSB--EEEEEEEESTTSSEEEEEEEEE-----SSHHHHHHHHHHH
T ss_pred eCCCCCCCHHHHHHHHHhcCC--cceEEEEeeeccccCCEEEEEe-----CCHHHHHHHHHHC
Confidence 468998999999999999996 555555432 1111111 2567777777654
No 14
>smart00362 RRM_2 RNA recognition motif.
Probab=20.04 E-value=64 Score=22.09 Aligned_cols=23 Identities=13% Similarity=0.184 Sum_probs=19.5
Q ss_pred hhCCCCCChHHHHHHHhccccEE
Q 018486 152 RAVPYSWDPPLLASFIENYGTHI 174 (355)
Q Consensus 152 ~~LP~~yd~~~y~~fIe~YGTHy 174 (355)
..||..++..+..++++.||+-.
T Consensus 5 ~~l~~~~~~~~l~~~~~~~g~v~ 27 (72)
T smart00362 5 GNLPPDVTEEDLKELFSKFGPIE 27 (72)
T ss_pred cCCCCcCCHHHHHHHHHhcCCEE
Confidence 46888899999999999999743
Done!