Query 026312
Match_columns 240
No_of_seqs 58 out of 60
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 06:24:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026312.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026312hhsearch_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 9.3E-62 2E-66 402.6 16.3 137 64-200 1-139 (139)
2 PF02035 Coagulin: Coagulin; 79.4 0.97 2.1E-05 38.9 1.3 51 60-117 76-126 (174)
3 PF07490 Tir_receptor_N: Trans 44.2 40 0.00086 31.1 4.6 62 132-198 83-145 (266)
4 PF10657 RC-P840_PscD: Photosy 32.5 40 0.00086 28.8 2.5 40 90-141 40-79 (144)
5 TIGR02588 conserved hypothetic 30.0 1.4E+02 0.0031 25.0 5.4 49 55-108 47-97 (122)
6 KOG1335 Dihydrolipoamide dehyd 25.2 4.3E+02 0.0094 26.9 8.6 128 56-207 189-348 (506)
7 KOG0288 WD40 repeat protein Ti 15.9 1.7E+02 0.0037 29.5 3.6 33 41-75 394-426 (459)
8 PRK04179 rpl37e 50S ribosomal 14.1 53 0.0011 24.7 -0.3 16 101-116 40-55 (62)
9 PTZ00073 60S ribosomal protein 13.8 55 0.0012 26.3 -0.3 14 103-116 40-53 (91)
10 TIGR02636 galM_Leloir galactos 13.5 2.1E+02 0.0046 26.7 3.5 112 94-216 57-170 (335)
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=9.3e-62 Score=402.57 Aligned_cols=137 Identities=59% Similarity=1.011 Sum_probs=121.2
Q ss_pred eEeecceeEEeeecCCceeeccCCCeEEeeeceEEEEEeecccccccccccceEEEeCchhhhhhhhcCCCCceeeeeCc
Q 026312 64 YVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDP 143 (240)
Q Consensus 64 sVYkgKAAlsv~p~~P~F~~~~sg~~~v~R~G~IlLeFAPavG~rqYDW~kKq~FsLS~tEvG~LLsl~~~~s~effHdP 143 (240)
+||||||||+|+|++|+|++++||+++++|+|+||||||||+|+|||||+|||+|+|||+|||+||+|+++++|||||||
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 cccCCCcCccceeEEEeeCCCC--ceEEEEEeecccCCCceEEEeecHHHHHHHHHHHH
Q 026312 144 AMLSSNAGQMRKSLSIKANADG--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACS 200 (240)
Q Consensus 144 ~~g~S~~g~v~K~Lkiep~pdG--~f~nLsV~n~~~~~~~~~~vpVt~gEf~virsl~~ 200 (240)
+|++|++|+|+|+|+|||+||| |||||+|+|++++++++|+||||+|||+|||++|+
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=79.44 E-value=0.97 Score=38.87 Aligned_cols=51 Identities=25% Similarity=0.436 Sum_probs=26.8
Q ss_pred eeceeEeecceeEEeeecCCceeeccCCCeEEeeeceEEEEEeecccccccccccceE
Q 026312 60 FAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQH 117 (240)
Q Consensus 60 f~~ysVYkgKAAlsv~p~~P~F~~~~sg~~~v~R~G~IlLeFAPavG~rqYDW~kKq~ 117 (240)
|+||+-|+..+-.+.+..-|.|.-- ++.+=.|+.| ||.+|-||--|+.|-.
T Consensus 76 f~pf~hf~secpvstrdcepvfgyt------~a~efrvivq-apragfrqcvwqhkcr 126 (174)
T PF02035_consen 76 FPPFHHFKSECPVSTRDCEPVFGYT------VAGEFRVIVQ-APRAGFRQCVWQHKCR 126 (174)
T ss_dssp STT----SSB--EEEE----SEEE-------TTS-EEEE---BCCCTB-B---EEEET
T ss_pred CCCcccccccCCcccccccccccce------ecceEEEEEe-CchhhHHHHHHHhhhc
Confidence 5999999999999999999999654 4445557777 9999999999998853
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=44.15 E-value=40 Score=31.10 Aligned_cols=62 Identities=19% Similarity=0.296 Sum_probs=42.4
Q ss_pred CCCCceeeeeCccccCC-CcCccceeEEEeeCCCCceEEEEEeecccCCCceEEEeecHHHHHHHHHH
Q 026312 132 GPRDSSEFFHDPAMLSS-NAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTA 198 (240)
Q Consensus 132 ~~~~s~effHdP~~g~S-~~g~v~K~Lkiep~pdG~f~nLsV~n~~~~~~~~~~vpVt~gEf~virsl 198 (240)
.-.+.+|..||-.-.-. +..--..+|+||-++||.++-|-.+|+. -.+|.++..||+-++++
T Consensus 83 ~L~ggfEVLHD~G~LDtLN~~IGss~FrvE~q~dG~h~AiGqk~gv-----EtsV~Ls~qE~~sLQai 145 (266)
T PF07490_consen 83 TLHGGFEVLHDKGPLDTLNKQIGSSVFRVETQEDGSHVAIGQKNGV-----ETSVTLSEQELASLQAI 145 (266)
T ss_pred eeccceEEeeccCchhhHHhhhCccceEEEeccCCceEeeeccCCe-----EEEEEeCHHHhhhhhcc
Confidence 34467899999652211 1112235899999999988777666633 34788999999988764
No 4
>PF10657 RC-P840_PscD: Photosystem P840 reaction centre protein PscD; InterPro: IPR019608 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. The photosynthetic reaction centres (RCs) of aerotolerant organisms contain a heterodimeric core, built up of two strongly homologous polypeptides each of which contributes five transmembrane peptide helices to hold a pseudo-symmetric double set of redox components. Two molecules of PscD are housed within a subunit. PscD may be involved in stabilising the PscB component since it is found to co-precipitate with FMO (Fenna-Mathews-Olson BChl a-protein) and PscB. It may also be involved in the interaction with ferredoxin [].
Probab=32.52 E-value=40 Score=28.80 Aligned_cols=40 Identities=40% Similarity=0.536 Sum_probs=29.6
Q ss_pred EEeeeceEEEEEeecccccccccccceEEEeCchhhhhhhhcCCCCceeeee
Q 026312 90 KVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFH 141 (240)
Q Consensus 90 ~v~R~G~IlLeFAPavG~rqYDW~kKq~FsLS~tEvG~LLsl~~~~s~effH 141 (240)
+.+|.|.+=||++|+.|-|+ |||++ +++...-...+|+|-
T Consensus 40 kRD~~g~Lql~i~pasGrrk----------Lspt~--emi~~l~~geIel~V 79 (144)
T PF10657_consen 40 KRDRYGKLQLTISPASGRRK----------LSPTP--EMIDKLISGEIELFV 79 (144)
T ss_pred ecccCCceEEEEecCCCccc----------cCCcH--HHHHHHhcCceEEEE
Confidence 68999999999999999888 66653 445444445666663
No 5
>TIGR02588 conserved hypothetical protein TIGR02588. The function of this protein is unknown. It is always found as part of a two-gene operon with TIGR02587, a protein that appears to span the membrane seven times. It is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Sinorhizobium meliloti, and Gloeobacter violaceus, so far, all of which are bacterial.
Probab=30.03 E-value=1.4e+02 Score=25.01 Aligned_cols=49 Identities=14% Similarity=0.270 Sum_probs=36.0
Q ss_pred CCCeeeeceeEe--ecceeEEeeecCCceeeccCCCeEEeeeceEEEEEeeccccc
Q 026312 55 LGGRIFAPYYVY--KGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGER 108 (240)
Q Consensus 55 ~~~rvf~~ysVY--kgKAAlsv~p~~P~F~~~~sg~~~v~R~G~IlLeFAPavG~r 108 (240)
...+.|++|+|- +|++|-+|+.+- ++..|. .+..+|-.-++|.|.-..+
T Consensus 47 ~~gqyyVpF~V~N~gg~TAasV~V~g----eL~~~~-~v~E~~e~tiDfl~g~e~~ 97 (122)
T TIGR02588 47 QTGQYYVPFAIHNLGGTTAAAVNIRG----ELRQAG-AVVENAEVTIDYLASGSKE 97 (122)
T ss_pred eCCEEEEEEEEEeCCCcEEEEEEEEE----EEccCC-ceeEEeeEEEEEcCCCCeE
Confidence 345689999997 688999998875 444433 4778899999999844333
No 6
>KOG1335 consensus Dihydrolipoamide dehydrogenase [Energy production and conversion]
Probab=25.21 E-value=4.3e+02 Score=26.94 Aligned_cols=128 Identities=19% Similarity=0.277 Sum_probs=69.9
Q ss_pred CCeeeeceeEeecceeEEeeecCCceeeccCCCeEE------eeece--EEEEEeecccccccccccceEEEeCchhhhh
Q 026312 56 GGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKV------KRKGV--ILLTFAPAIGERKYDWAKKQHFALSPTEVGS 127 (240)
Q Consensus 56 ~~rvf~~ysVYkgKAAlsv~p~~P~F~~~~sg~~~v------~R~G~--IlLeFAPavG~rqYDW~kKq~FsLS~tEvG~ 127 (240)
|......=.|..+..||++.-+|-.++..+.|++=+ .|-|. -.+||.+.+|+. .| -|+-.
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 344445567788889999999998888877776433 23232 245555555543 33 11111
Q ss_pred hh-hcCCCCceeeeeCccccCCCcCccceeEEEeeCCCCceEEEEEeecccCCC-----------------------ceE
Q 026312 128 LL-TMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKTN-----------------------ERF 183 (240)
Q Consensus 128 LL-sl~~~~s~effHdP~~g~S~~g~v~K~Lkiep~pdG~f~nLsV~n~~~~~~-----------------------~~~ 183 (240)
.. .+..++.+.|. -..|+.++++..|| -++++|.|...+-+ +++
T Consensus 257 ~~qr~L~kQgikF~-----------l~tkv~~a~~~~dg-~v~i~ve~ak~~k~~tle~DvlLVsiGRrP~t~GLgle~i 324 (506)
T KOG1335|consen 257 AFQRVLQKQGIKFK-----------LGTKVTSATRNGDG-PVEIEVENAKTGKKETLECDVLLVSIGRRPFTEGLGLEKI 324 (506)
T ss_pred HHHHHHHhcCceeE-----------eccEEEEeeccCCC-ceEEEEEecCCCceeEEEeeEEEEEccCcccccCCChhhc
Confidence 11 12233444443 23466666666666 45555555432222 333
Q ss_pred EEeecHHHHHHHHHHHHhhhhhhc
Q 026312 184 VVPVSTAEFAVMKTACSFALPHLM 207 (240)
Q Consensus 184 ~vpVt~gEf~virsl~~y~lP~LL 207 (240)
.+...+.+-..+.+-|..-+|+|.
T Consensus 325 Gi~~D~r~rv~v~~~f~t~vP~i~ 348 (506)
T KOG1335|consen 325 GIELDKRGRVIVNTRFQTKVPHIY 348 (506)
T ss_pred ccccccccceeccccccccCCceE
Confidence 444444555556666677777765
No 7
>KOG0288 consensus WD40 repeat protein TipD [General function prediction only]
Probab=15.88 E-value=1.7e+02 Score=29.53 Aligned_cols=33 Identities=24% Similarity=0.391 Sum_probs=26.2
Q ss_pred cccccccccccCCCCCCeeeeceeEeecceeEEee
Q 026312 41 GMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVD 75 (240)
Q Consensus 41 ~~st~~~~~~~~~~~~~rvf~~ysVYkgKAAlsv~ 75 (240)
-|| ....|.++|+...+||. ++|++||....++
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 8
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=14.06 E-value=53 Score=24.67 Aligned_cols=16 Identities=31% Similarity=0.773 Sum_probs=12.3
Q ss_pred Eeecccccccccccce
Q 026312 101 FAPAIGERKYDWAKKQ 116 (240)
Q Consensus 101 FAPavG~rqYDW~kKq 116 (240)
|-|+.--|+|+|++|-
T Consensus 40 ygps~k~R~YnWs~Ka 55 (62)
T PRK04179 40 FGRSKRIRRYSWQNKK 55 (62)
T ss_pred CCcccccccccHHHHh
Confidence 4466677999999874
No 9
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=13.79 E-value=55 Score=26.30 Aligned_cols=14 Identities=36% Similarity=0.923 Sum_probs=11.9
Q ss_pred ecccccccccccce
Q 026312 103 PAIGERKYDWAKKQ 116 (240)
Q Consensus 103 PavG~rqYDW~kKq 116 (240)
|+.--|+|+|+.|-
T Consensus 40 psak~R~YnWs~Ka 53 (91)
T PTZ00073 40 PSAKMRRYNWSVKA 53 (91)
T ss_pred chhhccccchhhhh
Confidence 77778999999885
No 10
>TIGR02636 galM_Leloir galactose mutarotase. Members of this protein family act as galactose mutarotase (D-galactose 1-epimerase) and participate in the Leloir pathway for galactose/glucose interconversion. All members of the seed alignment for this model are found in gene clusters with other enzymes of the Leloir pathway. This enzyme family belongs to the aldose 1-epimerase family, described by pfam model pfam01263. However, the enzyme described as aldose 1-epimerase itself (EC 5.1.3.3) is called broadly specific for D-glucose, L-arabinose, D-xylose, D-galactose, maltose and lactose. The restricted genome context for genes in this family suggests members should act primarily on D-galactose.
Probab=13.52 E-value=2.1e+02 Score=26.66 Aligned_cols=112 Identities=18% Similarity=0.220 Sum_probs=61.9
Q ss_pred eceEEEEEeecccccccccccceEEEeCchhhhhhhhcCCCC-ceeeeeCccccCCCcCccceeEEEeeCCCCceEEEEE
Q 026312 94 KGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRD-SSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNV 172 (240)
Q Consensus 94 ~G~IlLeFAPavG~rqYDW~kKq~FsLS~tEvG~LLsl~~~~-s~effHdP~~g~S~~g~v~K~Lkiep~pdG~f~nLsV 172 (240)
-|.++.=||-.+.+.+|.|+- +.+.|..-|-+.-|==+... .--.|+-... .++..++=.+......+||-.++.+
T Consensus 57 ~Ga~igp~anRI~~g~f~~~G-~~y~L~~N~~~n~lHGg~~G~~~~~W~v~~~--~~~~~v~l~~~~~~~~~gyPg~l~~ 133 (335)
T TIGR02636 57 LGATVGRYANRIANGSFEIDG-ETYQLSINQGGNCLHGGPEGFDKRRWNIEEL--QEEVQVKFSLESPDGDQGFPGNLTV 133 (335)
T ss_pred cCCCcCCCCceecCCEEEECC-EEEEeccCCCCcccCCCCccccccEEeEeee--cCCCEEEEEEECCCcCCCCCeEEEE
Confidence 577888899999999999874 67799888765433111110 0011210000 1122343334434455677666654
Q ss_pred eecc-cCCCceEEEeecHHHHHHHHHHHHhhhhhhccchhhccCC
Q 026312 173 ANNI-LKTNERFVVPVSTAEFAVMKTACSFALPHLMGWDRLTNQL 216 (240)
Q Consensus 173 ~n~~-~~~~~~~~vpVt~gEf~virsl~~y~lP~LLGW~~~~n~~ 216 (240)
.-.- +...+.+.|.++.- ..=.+|.-||||.+.|-.
T Consensus 134 ~vtY~L~~~~~L~i~~~a~--------~d~~tp~nlt~H~YFnL~ 170 (335)
T TIGR02636 134 SVTYTLTDDNELTIEYEAT--------TDKATPFNLTNHVYFNLD 170 (335)
T ss_pred EEEEEECCCCEEEEEEEEE--------ECCceEEeccccceEEcC
Confidence 3322 22234455554432 234789999999987664
Done!