Query 030060
Match_columns 183
No_of_seqs 51 out of 53
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 07:53:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030060.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030060hhsearch_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 7.8E-60 1.7E-64 378.0 14.5 116 64-179 1-118 (139)
2 PF02035 Coagulin: Coagulin; 89.5 0.35 7.6E-06 40.4 3.1 50 60-116 76-125 (174)
3 PF10657 RC-P840_PscD: Photosy 37.8 32 0.00069 28.6 2.7 40 90-141 40-79 (144)
4 KOG0288 WD40 repeat protein Ti 37.1 38 0.00082 32.8 3.4 56 41-98 394-456 (459)
5 PF13437 HlyD_3: HlyD family s 23.3 2.1E+02 0.0046 20.2 4.7 78 93-180 22-103 (105)
6 COG3737 Uncharacterized conser 22.0 1.6E+02 0.0034 24.3 4.1 55 81-140 18-75 (127)
7 PRK04179 rpl37e 50S ribosomal 21.8 27 0.00059 25.4 -0.2 16 101-116 40-55 (62)
8 PTZ00073 60S ribosomal protein 21.3 28 0.00061 27.0 -0.3 14 103-116 40-53 (91)
9 PF08624 CRC_subunit: Chromati 20.7 58 0.0013 26.8 1.4 49 84-142 14-69 (139)
10 PF06788 UPF0257: Uncharacteri 19.2 1.7E+02 0.0037 26.0 4.1 45 135-179 33-86 (236)
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=7.8e-60 Score=377.96 Aligned_cols=116 Identities=59% Similarity=0.956 Sum_probs=100.1
Q ss_pred eeeecceeEEeeccCCceeecCCCCeEEeeeeeEEEEeecccCCcccccccceEEEeChhhHhhhhhccCCCceeeeeCC
Q 030060 64 YVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDP 143 (183)
Q Consensus 64 sIYKgKAAlsv~p~~P~F~~l~SG~~kv~R~G~vlLeFAPa~G~RqYDW~kKq~FaLS~tEvG~Llsl~~~~s~effHDP 143 (183)
+||||||||+|+|++|+|+.++||+++++|+|+||||||||+|+|||||+|||+|+|||+|+|+||+|+++++|||||||
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 CCCCCCCCceeeeEEeEeCCCC--ceEEEEEeeccccc
Q 030060 144 AMLSSNAGQMRKSLSIKANADG--FFISLICIASSHGL 179 (183)
Q Consensus 144 ~~g~S~~G~vrK~LkveP~~dG--~f~~LsV~n~~~~~ 179 (183)
+|++|++|+|||+|||||+||| |||||+|+|+++|.
T Consensus 81 ~~~~s~~G~v~K~Lkv~p~~dgsg~f~~Lsv~~~~~~~ 118 (139)
T PF08536_consen 81 NMGSSNEGKVRKSLKVEPLPDGSGYFFNLSVQNKLLNG 118 (139)
T ss_dssp TTTSTTTTSEEEEEEEEE-TTSSEEEEEEEEEECCCTE
T ss_pred ccCCCCCCceEEEEEeEECCCCCceEEEEEEecccccc
Confidence 9999999999999999999996 99999999999884
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=89.49 E-value=0.35 Score=40.42 Aligned_cols=50 Identities=26% Similarity=0.548 Sum_probs=28.3
Q ss_pred eeceeeeecceeEEeeccCCceeecCCCCeEEeeeeeEEEEeecccCCcccccccce
Q 030060 60 FAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQ 116 (183)
Q Consensus 60 y~~ysIYKgKAAlsv~p~~P~F~~l~SG~~kv~R~G~vlLeFAPa~G~RqYDW~kKq 116 (183)
|+||.-|+..+-.+.+..-|.|.-.-+|.+. |++| ||.+|-||--|+.|-
T Consensus 76 f~pf~hf~secpvstrdcepvfgyt~a~efr------vivq-apragfrqcvwqhkc 125 (174)
T PF02035_consen 76 FPPFHHFKSECPVSTRDCEPVFGYTVAGEFR------VIVQ-APRAGFRQCVWQHKC 125 (174)
T ss_dssp STT----SSB--EEEE----SEEE-TTS-EE------EE---BCCCTB-B---EEEE
T ss_pred CCCcccccccCCcccccccccccceecceEE------EEEe-CchhhHHHHHHHhhh
Confidence 5999999999999999999999988888765 5677 999999999999885
No 3
>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=37.81 E-value=32 Score=28.55 Aligned_cols=40 Identities=40% Similarity=0.536 Sum_probs=29.9
Q ss_pred EEeeeeeEEEEeecccCCcccccccceEEEeChhhHhhhhhccCCCceeeee
Q 030060 90 KVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFH 141 (183)
Q Consensus 90 kv~R~G~vlLeFAPa~G~RqYDW~kKq~FaLS~tEvG~Llsl~~~~s~effH 141 (183)
|-+|.|.+=||++||.|-|+ |||++ ++|...-+..+|+|-
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 45788999999999999887 67764 445555566777664
No 4
>KOG0288 consensus WD40 repeat protein TipD [General function prediction only]
Probab=37.13 E-value=38 Score=32.81 Aligned_cols=56 Identities=20% Similarity=0.287 Sum_probs=38.5
Q ss_pred ccccccccccCCCCCCCeeeeceeeeecceeEEeeccC-C------ceeecCCCCeEEeeeeeEE
Q 030060 41 GMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVL-P------TFMKLDSGDLKVKRKGVIL 98 (183)
Q Consensus 41 ~~st~~~~~s~~~~~~~Rvy~~ysIYKgKAAlsv~p~~-P------~F~~l~SG~~kv~R~G~vl 98 (183)
-|| .+..|.++|++..+||+ +.|++||....++-.- | .|.+.++|-+..+|++.+-
T Consensus 394 vfS-pd~~YvaAGS~dgsv~i-W~v~tgKlE~~l~~s~s~~aI~s~~W~~sG~~Llsadk~~~v~ 456 (459)
T KOG0288|consen 394 VFS-PDGSYVAAGSADGSVYI-WSVFTGKLEKVLSLSTSNAAITSLSWNPSGSGLLSADKQKAVT 456 (459)
T ss_pred EEC-CCCceeeeccCCCcEEE-EEccCceEEEEeccCCCCcceEEEEEcCCCchhhcccCCcceE
Confidence 355 45568999999999998 8999999887665322 1 3555566655556555543
No 5
>PF13437 HlyD_3: HlyD family secretion protein
Probab=23.26 E-value=2.1e+02 Score=20.19 Aligned_cols=78 Identities=10% Similarity=0.132 Sum_probs=49.8
Q ss_pred eeeeEEEEeecccCCcccccccceEEEeChhhHhhhhhccCCCceeeeeCCCCCCCCCCceeeeEEeEeCCCC--ceEEE
Q 030060 93 RKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADG--FFISL 170 (183)
Q Consensus 93 R~G~vlLeFAPa~G~RqYDW~kKq~FaLS~tEvG~Llsl~~~~s~effHDP~~g~S~~G~vrK~LkveP~~dG--~f~~L 170 (183)
..|..+++.++. . +-+..+.++..+++.|- ...+...+..++.....-.|+|...-. .+.+++ +.+.+
T Consensus 22 ~~g~~l~~i~~~-~------~~~v~~~v~~~~~~~i~--~~g~~v~v~~~~~~~~~~~g~V~~I~~-~~~~~~~~~~v~~ 91 (105)
T PF13437_consen 22 SAGQPLAEIVDT-D------DLWVEAYVPEKDIARIK--DPGQKVTVRLDPGPEKTIEGKVSSISP-SPDPQGGTYRVEI 91 (105)
T ss_pred CCCCEEEEEEcc-c------eEEEEEEEChHhhcceE--eCCCEEEEEECCCCCcEEEEEEEEEeC-cccCCCcEEEEEE
Confidence 456678887763 1 12467889998888765 567788999886544455565554333 223333 88888
Q ss_pred EEeec--ccccC
Q 030060 171 ICIAS--SHGLG 180 (183)
Q Consensus 171 sV~n~--~~~~~ 180 (183)
++.|. ..+|-
T Consensus 92 ~i~~~~~~~~lr 103 (105)
T PF13437_consen 92 SIDNPKDDSPLR 103 (105)
T ss_pred EECCCCCCCccC
Confidence 88887 44443
No 6
>COG3737 Uncharacterized conserved protein [Function unknown]
Probab=21.98 E-value=1.6e+02 Score=24.27 Aligned_cols=55 Identities=18% Similarity=0.397 Sum_probs=43.9
Q ss_pred eeecCCCCeEE---eeeeeEEEEeecccCCcccccccceEEEeChhhHhhhhhccCCCceeee
Q 030060 81 FMKLDSGDLKV---KRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFF 140 (183)
Q Consensus 81 F~~l~SG~~kv---~R~G~vlLeFAPa~G~RqYDW~kKq~FaLS~tEvG~Llsl~~~~s~eff 140 (183)
+..-++|++.+ +.+|++|+ .|. .-|||+-+..=.|+|+.+..+++.++.-++-++
T Consensus 18 ~~ayG~Gg~R~a~~sh~~SlL~--lpd---gv~~W~v~~~~~Lt~e~f~~vl~~a~~~Eilli 75 (127)
T COG3737 18 IDAYGAGGFRFADMSHRGSLLV--LPD---GVCDWEVATLSDLTPEDFERVLAEAPDVEILLI 75 (127)
T ss_pred hhhhcCCceEeccccccccEEE--ecC---ccccccccChhhCCHHHHHHHHhcCCCceEEEE
Confidence 55668899887 78899887 453 379999999999999999999988775554444
No 7
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=21.75 E-value=27 Score=25.41 Aligned_cols=16 Identities=31% Similarity=0.773 Sum_probs=12.4
Q ss_pred eecccCCcccccccce
Q 030060 101 FAPAIGERKYDWAKKQ 116 (183)
Q Consensus 101 FAPa~G~RqYDW~kKq 116 (183)
|-|+.--|.|+|++|-
T Consensus 40 ygps~k~R~YnWs~Ka 55 (62)
T PRK04179 40 FGRSKRIRRYSWQNKK 55 (62)
T ss_pred CCcccccccccHHHHh
Confidence 3477778999999874
No 8
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=21.34 E-value=28 Score=27.04 Aligned_cols=14 Identities=36% Similarity=0.923 Sum_probs=12.1
Q ss_pred cccCCcccccccce
Q 030060 103 PAIGERKYDWAKKQ 116 (183)
Q Consensus 103 Pa~G~RqYDW~kKq 116 (183)
|+.--|.|+|+.|-
T Consensus 40 psak~R~YnWs~Ka 53 (91)
T PTZ00073 40 PSAKMRRYNWSVKA 53 (91)
T ss_pred chhhccccchhhhh
Confidence 77778999999885
No 9
>PF08624 CRC_subunit: Chromatin remodelling complex Rsc7/Swp82 subunit; InterPro: IPR013933 This entry contains subunits of the chromatin remodelling complexes. Saccharomyces cerevisiae (Baker's yeast) P32832 from SWISSPROT and its paralogue P43554 from SWISSPROT have been identified as subunits of the RSC chromatin remodelling complex, and SWI/SNF chromatin remodelling complex respectively [].
Probab=20.70 E-value=58 Score=26.84 Aligned_cols=49 Identities=33% Similarity=0.579 Sum_probs=35.4
Q ss_pred cCCCCeEEeeeeeEEEEeecccCCcccccc-------cceEEEeChhhHhhhhhccCCCceeeeeC
Q 030060 84 LDSGDLKVKRKGVILLTFAPAIGERKYDWA-------KKQHFALSPTEVGSLLTMGPRDSSEFFHD 142 (183)
Q Consensus 84 l~SG~~kv~R~G~vlLeFAPa~G~RqYDW~-------kKq~FaLS~tEvG~Llsl~~~~s~effHD 142 (183)
.+.|--||++.|-++ |.|+|-.. ....|+||. |+.-++ |-+||.+|||.
T Consensus 14 Dp~GE~KId~~G~Ll-------gGR~y~~~TFtl~~rg~~lymL~t-d~ar~l--g~rDs~~ff~~ 69 (139)
T PF08624_consen 14 DPKGEKKIDKNGRLL-------GGREYRFRTFTLPGRGNRLYMLST-DPARCL--GFRDSYLFFRK 69 (139)
T ss_pred CCCcCeEeCCCCccc-------CCCEEEEEEEEeCCCCCeEEEEeH-HHHHHh--ccccHHHHHHh
Confidence 456778999999874 66666321 256889975 555444 99999999987
No 10
>PF06788 UPF0257: Uncharacterised protein family (UPF0257); InterPro: IPR010646 This is a group of proteins of unknown function.; GO: 0005886 plasma membrane
Probab=19.20 E-value=1.7e+02 Score=25.97 Aligned_cols=45 Identities=24% Similarity=0.315 Sum_probs=37.0
Q ss_pred CceeeeeCCCCCC---------CCCCceeeeEEeEeCCCCceEEEEEeeccccc
Q 030060 135 DSSEFFHDPAMLS---------SNAGQMRKSLSIKANADGFFISLICIASSHGL 179 (183)
Q Consensus 135 ~s~effHDP~~g~---------S~~G~vrK~LkveP~~dG~f~~LsV~n~~~~~ 179 (183)
=|.+|=|||-.|. .+.|+|.|.-.++=.++|-|=.|.-.+.-.|.
T Consensus 33 fSn~FdFDPlrGpVK~~tQt~~de~g~v~~~v~~~l~~eGCfd~l~~~~~~~n~ 86 (236)
T PF06788_consen 33 FSNEFDFDPLRGPVKEFTQTLYDEDGEVTKRVSLTLSREGCFDTLELYDKENNT 86 (236)
T ss_pred hhhhccCCcccCCceeeeEEEEcCCCcEEEEEEEEECCccceeeeeeccccccc
Confidence 3789999999885 69999999999999999977777766665544
Done!