Query 026468
Match_columns 238
No_of_seqs 58 out of 60
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 08:23:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026468.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026468hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08536 Whirly: Whirly transc 100.0 2.2E-62 4.7E-67 406.0 16.8 137 64-200 1-139 (139)
2 PF02035 Coagulin: Coagulin; 52.0 15 0.00032 31.8 3.0 51 60-117 76-126 (174)
3 PF07490 Tir_receptor_N: Trans 46.7 28 0.0006 32.1 4.0 61 133-198 84-145 (266)
4 KOG1335 Dihydrolipoamide dehyd 18.1 8.2E+02 0.018 25.0 8.9 98 56-177 189-295 (506)
5 KOG0288 WD40 repeat protein Ti 17.1 1.5E+02 0.0033 29.8 3.6 33 41-75 394-426 (459)
6 PRK00919 GMP synthase subunit 16.6 1.1E+02 0.0023 28.9 2.4 41 187-233 208-248 (307)
7 PRK04179 rpl37e 50S ribosomal 15.2 47 0.001 24.9 -0.3 16 101-116 40-55 (62)
8 PTZ00073 60S ribosomal protein 14.6 49 0.0011 26.6 -0.3 14 103-116 40-53 (91)
9 PF09341 Pcc1: Transcription f 14.2 3E+02 0.0066 20.0 3.8 48 153-206 18-67 (76)
10 PF11314 DUF3117: Protein of u 13.7 4.3E+02 0.0094 19.2 4.3 40 85-130 6-45 (51)
No 1
>PF08536 Whirly: Whirly transcription factor; InterPro: IPR013742 This is a family of plant transcription factors. ; PDB: 3R9Y_A 3N1I_A 3N1K_A 3RA0_A 3N1H_A 3N1J_A 3N1L_A 3R9Z_A 1L3A_D.
Probab=100.00 E-value=2.2e-62 Score=406.00 Aligned_cols=137 Identities=59% Similarity=1.011 Sum_probs=121.2
Q ss_pred eEeecceeEEEeecCCceeecCCCCeEEeeeceEEEEEeecccCcccccccceEEEeChhhhhhhhhcCCCCceeeeeCc
Q 026468 64 YVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDP 143 (238)
Q Consensus 64 sVYkgKAALsv~pi~P~F~~~~sG~~kv~R~G~IlLeFAPavG~rqYDW~kKq~FsLS~tEvG~LLsl~~~~s~effHDP 143 (238)
+||||||||+|+|++|+|++++||+++++|+|+||||||||+|+|||||+|||+|+|||+|||+||+++++++|||||||
T Consensus 1 sVYk~kaAl~v~p~~P~f~~~~sg~~kv~R~G~vlLefapa~g~r~YDW~kKq~FsLS~tEvG~ll~l~~~~s~effHdP 80 (139)
T PF08536_consen 1 SVYKGKAALSVRPIKPTFTSLDSGYFKVSREGSVLLEFAPAVGPRQYDWSKKQTFSLSPTEVGSLLSLGARESCEFFHDP 80 (139)
T ss_dssp EEEESSEEEEEEEE--EEEE-TTSCEEEEC--EEEEEEEEBCSTTEB-GGG-EEEEE-HHHHHHHHT--TT--EEEEE-T
T ss_pred CccccceeEEEEecCCccEECCCCcEEEeeccEEEEEEccccCCcccccccceEEEEcHHHhhhhhhhccCCceEEEecc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccCCCcccceeeEEEeeCCCC--ceEEEEEeecccCCCceEEEeecHHHHHHHHHHHH
Q 026468 144 AMLSSNAGQMRKSLSIKANADG--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACS 200 (238)
Q Consensus 144 ~~g~S~~g~v~K~Lkiep~pdG--~f~nLsV~n~~~~~~~~~~vpVT~gEf~v~rsl~~ 200 (238)
+|++|++|+++|+|+|||+||| |||||+|+|++.+++++|+||||+|||+|||++|+
T Consensus 81 ~~~~s~~G~v~K~Lkv~p~~dgsg~f~~Lsv~~~~~~~~~~~~ipVt~aEfavl~s~f~ 139 (139)
T PF08536_consen 81 NMGSSNEGKVRKSLKVEPLPDGSGYFFNLSVQNKLLNGDENFSIPVTKAEFAVLRSAFN 139 (139)
T ss_dssp TTTSTTTTSEEEEEEEEE-TTSSEEEEEEEEEECCCTEEEEEEEEEEHHHHHHHHHHHH
T ss_pred ccCCCCCCceEEEEEeEECCCCCceEEEEEEecccccccceEEEechHHHHHHHHHhhC
Confidence 9999999999999999999996 99999999999999999999999999999999986
No 2
>PF02035 Coagulin: Coagulin; InterPro: IPR000275 Coagulogen is a gel-forming protein of hemolymph that hinders the spread of invaders by immobilising them [, ]. The protein contains a single 175- residue polypeptide chain; this is cleaved after Arg-18 and Arg-46 by a clotting enzyme contained in the hemocyte and activated by a bacterial endotoxin (lipopolysaccharide). Cleavage releases two chains of coagulin, A and B, linked by two disulphide bonds, together with the peptide C [, ]. Gel formation results from interlinking of coagulin molecules. Secondary structure prediction suggests the C peptide forms an alpha- helix, which is released during the proteolytic conversion of coagulogen to coagulin gel []. The beta-sheet structure and 16 half-cystines found in the molecule appear to yield a compact protein stable to acid and heat. Mammalian blood coagulation is based on the proteolytically induced polymerisation of fibrinogens. Initially, fibrin monomers noncovalently interact with each other. The resulting homopolymers are further stabilised when the plasma transglutaminase (TGase) intermolecularly cross-links epsilon-(gamma-glutamyl)lysine bonds. In crustaceans, hemolymph coagulation depends on the TGase-mediated cross-linking of specific plasma-clotting proteins, but without the proteolytic cascade. In horseshoe crabs, the proteolytic coagulation cascade triggered by lipopolysaccharides and beta-1,3-glucans leads to the conversion of coagulogen into coagulin, resulting in noncovalent coagulin homopolymers through head-to-tail interaction. Horseshoe crab TGase, however, does not cross-link coagulins intermolecularly. Recently, we found that coagulins are cross-linked on hemocyte cell surface proteins called proxins. This indicates that a cross-linking reaction at the final stage of hemolymph coagulation is an important innate immune system of horseshoe crabs [].; GO: 0042381 hemolymph coagulation, 0005576 extracellular region; PDB: 1AOC_A.
Probab=52.02 E-value=15 Score=31.76 Aligned_cols=51 Identities=25% Similarity=0.541 Sum_probs=26.9
Q ss_pred eeceeEeecceeEEEeecCCceeecCCCCeEEeeeceEEEEEeecccCcccccccceE
Q 026468 60 FAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQH 117 (238)
Q Consensus 60 f~~ysVYkgKAALsv~pi~P~F~~~~sG~~kv~R~G~IlLeFAPavG~rqYDW~kKq~ 117 (238)
|+||+-|+..+-.+.+..-|.|.---+|-|. |+.| ||.+|-||--|+.|-.
T Consensus 76 f~pf~hf~secpvstrdcepvfgyt~a~efr------vivq-apragfrqcvwqhkcr 126 (174)
T PF02035_consen 76 FPPFHHFKSECPVSTRDCEPVFGYTVAGEFR------VIVQ-APRAGFRQCVWQHKCR 126 (174)
T ss_dssp STT----SSB--EEEE----SEEE-TTS-EE------EE---BCCCTB-B---EEEET
T ss_pred CCCcccccccCCcccccccccccceecceEE------EEEe-CchhhHHHHHHHhhhc
Confidence 5999999999999999999999876666554 4554 7999999999998853
No 3
>PF07490 Tir_receptor_N: Translocated intimin receptor (Tir) N-terminus; InterPro: IPR022633 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens, such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia []. The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself [], type III subunits in the outer membrane translocate secreted proteins through a channel-like structure. Exotoxins secreted by the type III system do not possess a secretion signal, and are considered unique for this reason []. Enteropathogenic and entero- haemorrhagic Escherichia coli secrete the bacterial adhesion mediation molecule intimin [], which targets the translocated intimin receptor, Tir. Tir is secreted by the bacteria and is embedded in the target cell's plasma membrane []. This facilitates bacterial cell attachment to the host.
Probab=46.73 E-value=28 Score=32.09 Aligned_cols=61 Identities=20% Similarity=0.287 Sum_probs=41.4
Q ss_pred CCCceeeeeCcCccC-CCcccceeeEEEeeCCCCceEEEEEeecccCCCceEEEeecHHHHHHHHHH
Q 026468 133 PRDSSEFFHDPAMLS-SNAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTA 198 (238)
Q Consensus 133 ~~~s~effHDP~~g~-S~~g~v~K~Lkiep~pdG~f~nLsV~n~~~~~~~~~~vpVT~gEf~v~rsl 198 (238)
-...+|..||-.-.- =|..--..+|+||-++||.++-+-.+|+. -.+|.++..||+-++.+
T Consensus 84 L~ggfEVLHD~G~LDtLN~~IGss~FrvE~q~dG~h~AiGqk~gv-----EtsV~Ls~qE~~sLQai 145 (266)
T PF07490_consen 84 LHGGFEVLHDKGPLDTLNKQIGSSVFRVETQEDGSHVAIGQKNGV-----ETSVTLSEQELASLQAI 145 (266)
T ss_pred eccceEEeeccCchhhHHhhhCccceEEEeccCCceEeeeccCCe-----EEEEEeCHHHhhhhhcc
Confidence 345789999833210 01111136899999999988777766643 34899999999988765
No 4
>KOG1335 consensus Dihydrolipoamide dehydrogenase [Energy production and conversion]
Probab=18.07 E-value=8.2e+02 Score=25.03 Aligned_cols=98 Identities=20% Similarity=0.270 Sum_probs=55.3
Q ss_pred CCeeeeceeEeecceeEEEeecCCceeecCCCCeEE------eeece--EEEEEeecccCcccccccceEEEeChhhhhh
Q 026468 56 GGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKV------KRKGV--ILLTFAPAIGERKYDWAKKQHFALSPTEVGS 127 (238)
Q Consensus 56 ~~rvf~~ysVYkgKAALsv~pi~P~F~~~~sG~~kv------~R~G~--IlLeFAPavG~rqYDW~kKq~FsLS~tEvG~ 127 (238)
|......=.|..+..||++.-+|-.++..+.|++=+ .|-|. -.+||.+.+|+. .| -|+-.
T Consensus 189 PGI~IDekkIVSStgALsL~~vPk~~~viG~G~IGLE~gsV~~rLGseVT~VEf~~~i~~~-mD-----------~Eisk 256 (506)
T KOG1335|consen 189 PGITIDEKKIVSSTGALSLKEVPKKLTVIGAGYIGLEMGSVWSRLGSEVTVVEFLDQIGGV-MD-----------GEISK 256 (506)
T ss_pred CCeEecCceEEecCCccchhhCcceEEEEcCceeeeehhhHHHhcCCeEEEEEehhhhccc-cC-----------HHHHH
Confidence 344445567788889999999998888887766433 22221 234555555443 33 11111
Q ss_pred hh-hcCCCCceeeeeCcCccCCCcccceeeEEEeeCCCCceEEEEEeeccc
Q 026468 128 LL-TMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNIL 177 (238)
Q Consensus 128 LL-sl~~~~s~effHDP~~g~S~~g~v~K~Lkiep~pdG~f~nLsV~n~~~ 177 (238)
.. .+..+..+.|-- ..|+.++++..|| -+++++.|...
T Consensus 257 ~~qr~L~kQgikF~l-----------~tkv~~a~~~~dg-~v~i~ve~ak~ 295 (506)
T KOG1335|consen 257 AFQRVLQKQGIKFKL-----------GTKVTSATRNGDG-PVEIEVENAKT 295 (506)
T ss_pred HHHHHHHhcCceeEe-----------ccEEEEeeccCCC-ceEEEEEecCC
Confidence 11 112223444442 3577888888887 56666666543
No 5
>KOG0288 consensus WD40 repeat protein TipD [General function prediction only]
Probab=17.11 E-value=1.5e+02 Score=29.85 Aligned_cols=33 Identities=24% Similarity=0.391 Sum_probs=26.2
Q ss_pred cccccccccccCCCCCCeeeeceeEeecceeEEEe
Q 026468 41 GMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVD 75 (238)
Q Consensus 41 ~~st~~~~~~~~~~~~~rvf~~ysVYkgKAALsv~ 75 (238)
-|| ....|.++|+...+||. ++|++||....++
T Consensus 394 vfS-pd~~YvaAGS~dgsv~i-W~v~tgKlE~~l~ 426 (459)
T KOG0288|consen 394 VFS-PDGSYVAAGSADGSVYI-WSVFTGKLEKVLS 426 (459)
T ss_pred EEC-CCCceeeeccCCCcEEE-EEccCceEEEEec
Confidence 355 45558899999999997 8899999876654
No 6
>PRK00919 GMP synthase subunit B; Validated
Probab=16.61 E-value=1.1e+02 Score=28.90 Aligned_cols=41 Identities=20% Similarity=0.171 Sum_probs=30.1
Q ss_pred ecHHHHHHHHHHHHhhhhhhccccccCCCcccccceeeeeecCCccc
Q 026468 187 VSTAEFAVMKTACSVCTNEIASRSQLGSPAVICCSQVTSVLGDSRSK 233 (238)
Q Consensus 187 VT~gEf~v~rsl~~y~lP~LLGW~a~~np~~~~~~~~~~~~~~~~~~ 233 (238)
|-.||..++.++-..-+=+ |++|+ ++-+.|.+.|.||.|+-
T Consensus 208 v~~ae~~~~~~~~~~~~~~---~q~~~---~~~~~~~~g~~g~~r~~ 248 (307)
T PRK00919 208 VREANAIVEEEVEKYGPDK---WQYFA---ALLGVKATGVKGDNRVY 248 (307)
T ss_pred HHHHHHHHHHHHHhcCCcc---cceEE---EEcCceeeeecCCcccc
Confidence 6677777777777754433 89875 44557889999999974
No 7
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=15.24 E-value=47 Score=24.95 Aligned_cols=16 Identities=31% Similarity=0.773 Sum_probs=12.1
Q ss_pred EeecccCcccccccce
Q 026468 101 FAPAIGERKYDWAKKQ 116 (238)
Q Consensus 101 FAPavG~rqYDW~kKq 116 (238)
|-|+.--|+|+|++|-
T Consensus 40 ygps~k~R~YnWs~Ka 55 (62)
T PRK04179 40 FGRSKRIRRYSWQNKK 55 (62)
T ss_pred CCcccccccccHHHHh
Confidence 4466667999999874
No 8
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=14.64 E-value=49 Score=26.56 Aligned_cols=14 Identities=36% Similarity=0.923 Sum_probs=12.0
Q ss_pred ecccCcccccccce
Q 026468 103 PAIGERKYDWAKKQ 116 (238)
Q Consensus 103 PavG~rqYDW~kKq 116 (238)
|+.--|+|+|+.|-
T Consensus 40 psak~R~YnWs~Ka 53 (91)
T PTZ00073 40 PSAKMRRYNWSVKA 53 (91)
T ss_pred chhhccccchhhhh
Confidence 77778999999885
No 9
>PF09341 Pcc1: Transcription factor Pcc1; InterPro: IPR015419 Pcc1 is a proposed transcription factor involved in the expression of genes regulated by alpha-factor and galactose; component of the EKC/KEOPS protein complex with Kae1, Gon7, Bud32, and Cgi121; related to human cancer-testis antigens [].; PDB: 2BNR_C 2P5W_C 3KLA_C 2F54_C 2P5E_C 2F53_C 3ENO_E 3ENC_B.
Probab=14.23 E-value=3e+02 Score=19.95 Aligned_cols=48 Identities=10% Similarity=0.250 Sum_probs=33.7
Q ss_pred ceeeEEEeeCC--CCceEEEEEeecccCCCceEEEeecHHHHHHHHHHHHhhhhhh
Q 026468 153 MRKSLSIKANA--DGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACSVCTNEI 206 (238)
Q Consensus 153 v~K~Lkiep~p--dG~f~nLsV~n~~~~~~~~~~vpVT~gEf~v~rsl~~y~lP~L 206 (238)
+..+|+.++-+ ++...++++.+ +.+.|.+..-+...||...+-.+..|
T Consensus 18 i~~sL~~d~e~~~~~~~~~~~~~~------~~L~i~~~A~d~~~LRasvns~l~~l 67 (76)
T PF09341_consen 18 IYRSLKPDKELKPSRVKRELSVDG------NKLVITIEAEDLRSLRASVNSFLDLL 67 (76)
T ss_dssp HHHHHHHHHH-SS-SSEEEEEEES------SEEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred HHHHhCCCCCCCCCcEEEEEEEeC------CEEEEEEEECCHHHHHHHHHHHHHHH
Confidence 34555555433 34666676654 57899999999999999998877654
No 10
>PF11314 DUF3117: Protein of unknown function (DUF3117); InterPro: IPR021465 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=13.66 E-value=4.3e+02 Score=19.17 Aligned_cols=40 Identities=25% Similarity=0.356 Sum_probs=33.1
Q ss_pred CCCCeEEeeeceEEEEEeecccCcccccccceEEEeChhhhhhhhh
Q 026468 85 DSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLT 130 (238)
Q Consensus 85 ~sG~~kv~R~G~IlLeFAPavG~rqYDW~kKq~FsLS~tEvG~LLs 130 (238)
+||-+.+.|+|.=++==.|.-|.. +...-|++.|...|-+
T Consensus 6 GdGPlEv~kEgR~ivmRvPleGGG------RLVvEl~~~Ea~~L~~ 45 (51)
T PF11314_consen 6 GDGPLEVTKEGRGIVMRVPLEGGG------RLVVELNPDEAKELGE 45 (51)
T ss_pred CCCCcEEeecCceEEEEEecCCCc------EEEEEeCHHHHHHHHH
Confidence 688999999998777778977654 5789999999888764
Done!