Query psy6917
Match_columns 132
No_of_seqs 171 out of 255
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 21:44:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6917.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6917hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2435|consensus 100.0 3.1E-39 6.7E-44 266.3 9.3 125 1-126 93-320 (323)
2 PF08547 CIA30: Complex I inte 99.9 4.2E-23 9.1E-28 155.4 4.8 73 27-100 1-157 (157)
3 PF03425 CBM_11: Carbohydrate 95.7 0.027 5.9E-07 43.1 5.5 52 53-107 114-169 (178)
4 PF14330 DUF4387: Domain of un 37.7 24 0.00052 25.6 1.8 17 87-103 7-23 (99)
5 PF10974 DUF2804: Protein of u 29.0 1.1E+02 0.0023 25.8 4.6 58 23-84 252-326 (333)
6 KOG4276|consensus 27.0 57 0.0012 24.1 2.3 51 26-76 38-100 (113)
7 PF12340 DUF3638: Protein of u 24.4 22 0.00047 29.2 -0.4 35 18-54 24-59 (229)
8 PF04620 FlaA: Flagellar filam 23.6 3.1E+02 0.0068 22.2 6.2 59 55-113 151-214 (217)
9 PF08435 Calici_coat_C: Calici 21.4 1.2E+02 0.0027 24.9 3.5 32 1-32 144-186 (230)
10 PF13715 DUF4480: Domain of un 20.6 95 0.0021 20.1 2.2 36 64-99 1-40 (88)
No 1
>KOG2435|consensus
Probab=100.00 E-value=3.1e-39 Score=266.25 Aligned_cols=125 Identities=50% Similarity=0.813 Sum_probs=121.4
Q ss_pred Cchhhhhhhhc---cCceeeecCCCceEEEEEc-CCCCCCeEEeeccccCCccceEEE----------------------
Q psy6917 1 MWKDEVQDKLY---MDPVGDVYPNETKVIWKFN-ESTLDDWIVTTDSDHNEGLSKASL---------------------- 54 (132)
Q Consensus 1 ~~~~e~~~~~~---~~~~~~~~~~~~~vlf~F~-~~~l~~W~v~sD~v~GeG~S~a~l---------------------- 54 (132)
+++.|++.+|+ ++||+++++++.+|+|+|+ +++|+.|+++||+++| |+|+|+|
T Consensus 93 ~lkeeIkl~w~~eE~~pllevr~~eakvvf~F~~kEdLdkWtv~sDsd~g-G~StasLe~sd~G~~alf~G~~ss~~~kd 171 (323)
T KOG2435|consen 93 LLKEEIKLHWRGEEGHPLLEVRLEEAKVVFQFRGKEDLDKWTVTSDSDIG-GRSTASLEMSDNGQSALFYGTLSSEAPKD 171 (323)
T ss_pred HHHHHHHHHhccccCccceeecCCcceEEEEccChhhcceeEeecccccC-CeeeEEEEecCCCcceeeccccccccccC
Confidence 47899999997 8999999999999999999 9999999999999999 9999999
Q ss_pred -----------------------------------------------------------------------------EEe
Q psy6917 55 -----------------------------------------------------------------------------AIP 57 (132)
Q Consensus 55 -----------------------------------------------------------------------------~IP 57 (132)
+||
T Consensus 172 g~i~RsGyc~Mrs~~RkaF~rk~~~dw~qfn~L~LrvRGDGRsy~inihte~~~dq~wndsys~flft~gGp~wq~~KIP 251 (323)
T KOG2435|consen 172 GEITRSGYCAMRSRPRKAFERKMSYDWSQFNTLYLRVRGDGRSYMINIHTETDFDQRWNDSYSYFLFTRGGPYWQEVKIP 251 (323)
T ss_pred cceeeeeeeeeeccchhhhcceecccccccceEEEEEecCCceEEEEecCccchhhhcccceeeEEecCCCCceeEEecc
Confidence 799
Q ss_pred CCCceeccCCeecCCCCCCCccCccEEEEEEecCCCCceEEEEeEEEEEeCCCchhhhhhhcccccceE
Q psy6917 58 FSKFFLQSKGRIQDIQNPLDTDRISSIGLSLVDQNNGPFQLELDYIGIEYDPNHTEEFAYEMYLFENEV 126 (132)
Q Consensus 58 fs~F~~t~RGr~~d~q~~L~~~~I~~iGf~I~dkq~GpF~LeId~I~a~~d~~~~ee~aye~y~~~~~~ 126 (132)
||+|++|++||++|.|.+||+++|.+|||+++||.+|||.||||+|++.+|++|+|+||||+|..++|.
T Consensus 252 fSKff~t~kGriqDrq~e~nl~~vssig~sl~dk~dGpF~LEIDfIGv~~d~~H~EdFayE~y~~p~~r 320 (323)
T KOG2435|consen 252 FSKFFFTNKGRIQDRQHELNLDKVSSIGFSLADKVDGPFFLEIDFIGVFTDPAHTEDFAYENYPEPNPR 320 (323)
T ss_pred hhhheeccccceeecccccCccceeeEeEEEeeccCCcceeeEEEEEEecCCCcccceeeecccccccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999765
No 2
>PF08547 CIA30: Complex I intermediate-associated protein 30 (CIA30); InterPro: IPR013857 Mitochondrial complex I intermediate-associated protein 30 (CIA30) is present in human and mouse, and also in Schizosaccharomyces pombe (Fission yeast) which does not contain the NADH dehydrogenase component of complex I, or many of the other essential subunits. This means it is possible that it is not directly involved in oxidative phosphorylation [, ].
Probab=99.87 E-value=4.2e-23 Score=155.44 Aligned_cols=73 Identities=45% Similarity=0.803 Sum_probs=71.4
Q ss_pred EEEc-CCCCCCeEEeeccccCCccceEEE---------------------------------------------------
Q psy6917 27 WKFN-ESTLDDWIVTTDSDHNEGLSKASL--------------------------------------------------- 54 (132)
Q Consensus 27 f~F~-~~~l~~W~v~sD~v~GeG~S~a~l--------------------------------------------------- 54 (132)
|+|+ |+++++|++++|+||| |.|+|.+
T Consensus 1 f~F~~~~~~~~W~~~~D~vmG-G~S~~~~~~~~~~~~~~F~G~ls~~~~~GFa~~r~~~~~~~~dls~y~~l~l~vrgdG 79 (157)
T PF08547_consen 1 FDFNSPQDLENWRVVSDTVMG-GVSTASLEFSPEDGSAVFSGNLSTENNGGFASVRTPSFPSPLDLSGYDGLELRVRGDG 79 (157)
T ss_pred CcCCCChhhCCeEEEcceEeC-CeEEEEEEEECCCCEEEEEEEEecCCCCceEEEEEccCCCcCCCCCCcEEEEEEEcCC
Confidence 6899 9999999999999999 9999999
Q ss_pred --------------------------------EEeCCCceeccCCeecCCCCCCCccCccEEEEEEecCCCCceEEEE
Q psy6917 55 --------------------------------AIPFSKFFLQSKGRIQDIQNPLDTDRISSIGLSLVDQNNGPFQLEL 100 (132)
Q Consensus 55 --------------------------------~IPfs~F~~t~RGr~~d~q~~L~~~~I~~iGf~I~dkq~GpF~LeI 100 (132)
+|||++|+|++||++++++++||+++|++|||+++|+|+|||+|||
T Consensus 80 r~Y~~~l~~~~~~~~~~y~~~f~t~~~~w~~v~iPFs~F~~~~rG~~v~~~~~l~~~~I~~ig~~~~~~~~G~F~L~I 157 (157)
T PF08547_consen 80 RTYKVNLRTDNDEPSDSYQARFQTPPGEWQTVRIPFSDFVPTFRGRPVDDAPPLDPSRIRSIGFMISDKQEGPFELEI 157 (157)
T ss_pred ceEEEEEEeCCCCCCceEEEEEeccCCccEEEEEEHHHCceeeCCcccCCCCCcChHHceEEEEEEecCCCCCEEEeC
Confidence 8999999999999999999999999999999999999999999997
No 3
>PF03425 CBM_11: Carbohydrate binding domain (family 11); InterPro: IPR005087 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This entry represents CBM11 from CAZY which binds both beta-1,4-glucan and beta-1,3-1,4-mixed linked glucans.; GO: 0008810 cellulase activity, 0030245 cellulose catabolic process; PDB: 1V0A_A.
Probab=95.70 E-value=0.027 Score=43.14 Aligned_cols=52 Identities=23% Similarity=0.288 Sum_probs=32.9
Q ss_pred EEEEeCCCcee----ccCCeecCCCCCCCccCccEEEEEEecCCCCceEEEEeEEEEEe
Q psy6917 53 SLAIPFSKFFL----QSKGRIQDIQNPLDTDRISSIGLSLVDQNNGPFQLELDYIGIEY 107 (132)
Q Consensus 53 ~l~IPfs~F~~----t~RGr~~d~q~~L~~~~I~~iGf~I~dkq~GpF~LeId~I~a~~ 107 (132)
.++|||++|.. +--|.-. ..+||+.+|.+|.|.+... .|++.|.||.|+++.
T Consensus 114 ~V~IPF~~f~~~~~~~p~g~~~--~~~ldl~~v~~~~~~~~~~-~~~~~~~iDdI~l~~ 169 (178)
T PF03425_consen 114 TVEIPFSDFTQRPDYQPGGWGA--DGTLDLTNVWEFAFYVNGG-GGAGTFYIDDIRLYG 169 (178)
T ss_dssp EEEEEGGG-EE--S---TT------SS--TTSEEEEEEEESSS----EEEEEEEEEEE-
T ss_pred EEEEEHHHcccccccCCCCCCc--ccccChHHcEEEEEEEcCC-CceeEEEEEeEEEEe
Confidence 44999999987 1122111 2457999999999998744 445999999999993
No 4
>PF14330 DUF4387: Domain of unknown function (DUF4387)
Probab=37.70 E-value=24 Score=25.62 Aligned_cols=17 Identities=41% Similarity=0.825 Sum_probs=14.6
Q ss_pred EEecCCCCceEEEEeEE
Q psy6917 87 SLVDQNNGPFQLELDYI 103 (132)
Q Consensus 87 ~I~dkq~GpF~LeId~I 103 (132)
.|..|.+|||.|.+|=|
T Consensus 7 vIRSKNAGPf~lT~DI~ 23 (99)
T PF14330_consen 7 VIRSKNAGPFELTFDII 23 (99)
T ss_pred HHhccCCCCcEEEEEEE
Confidence 46779999999999965
No 5
>PF10974 DUF2804: Protein of unknown function (DUF2804); InterPro: IPR021243 This is a family of proteins with unknown function.
Probab=29.04 E-value=1.1e+02 Score=25.78 Aligned_cols=58 Identities=19% Similarity=0.432 Sum_probs=40.8
Q ss_pred ceEEEEEc-CCCCCCeEEeeccccCCccceEEE---------------EEeCCCceeccCCeecC-CCCCCCccCccEE
Q psy6917 23 TKVIWKFN-ESTLDDWIVTTDSDHNEGLSKASL---------------AIPFSKFFLQSKGRIQD-IQNPLDTDRISSI 84 (132)
Q Consensus 23 ~~vlf~F~-~~~l~~W~v~sD~v~GeG~S~a~l---------------~IPfs~F~~t~RGr~~d-~q~~L~~~~I~~i 84 (132)
+.|.|+|+ ..-.+.|++.|+. |+-.-+| .--++.++=+|.|+++. +...+.++++..+
T Consensus 252 ~~V~f~~~~~~~~~pW~i~s~d----g~vdL~FtP~~~r~~~~nl~~i~s~~~Q~fG~f~G~~~~~dG~~i~l~~~~G~ 326 (333)
T PF10974_consen 252 PPVRFEYDREDPMKPWRITSDD----GRVDLTFTPIFDRKEKTNLGVIASNFHQVFGRFSGTLRLDDGEKIELDDVPGF 326 (333)
T ss_pred CcEEEEecCcCCCCCeEEEcCC----CeEEEEEEEeeeeecccceEEEEeeeEEEEEEEEEEEEcCCCCEEEECCeEEe
Confidence 67889999 5667999999973 4444444 55677788899998876 4456666665443
No 6
>KOG4276|consensus
Probab=27.04 E-value=57 Score=24.14 Aligned_cols=51 Identities=25% Similarity=0.376 Sum_probs=42.2
Q ss_pred EEEEc-CCCCCCeEE----eeccccCCccceEEE-------EEeCCCceeccCCeecCCCCCC
Q psy6917 26 IWKFN-ESTLDDWIV----TTDSDHNEGLSKASL-------AIPFSKFFLQSKGRIQDIQNPL 76 (132)
Q Consensus 26 lf~F~-~~~l~~W~v----~sD~v~GeG~S~a~l-------~IPfs~F~~t~RGr~~d~q~~L 76 (132)
-|.|. ..|-+.|+- ++|..|+|-.|.|+. .+||.-|...-.|+-.+.|.+.
T Consensus 38 nW~fQgS~DgktWt~l~vH~DD~sl~epGstAtWpi~~a~~~~~fRffRi~q~G~nasgqThy 100 (113)
T KOG4276|consen 38 NWKFQGSKDGKTWTDLRVHVDDKSLCEPGSTATWPITAANDLLPFRFFRIVQNGKNASGQTHY 100 (113)
T ss_pred heeeeccccCCcceeEEEEeccccccCCCccccccccCcccccceEEEEEEecCCCCCCccce
Confidence 58888 889999975 689999999999998 5599888888888877766654
No 7
>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length. There are two conserved sequence motifs: LLE and NMG.
Probab=24.43 E-value=22 Score=29.23 Aligned_cols=35 Identities=9% Similarity=0.129 Sum_probs=19.0
Q ss_pred ecCCCceEEEEEc-CCCCCCeEEeeccccCCccceEEE
Q psy6917 18 VYPNETKVIWKFN-ESTLDDWIVTTDSDHNEGLSKASL 54 (132)
Q Consensus 18 ~~~~~~~vlf~F~-~~~l~~W~v~sD~v~GeG~S~a~l 54 (132)
.|+.|..+.-++- |++-. ..+-==-||+|+|+.-+
T Consensus 24 iR~~Q~~ia~~mi~~~~~~--n~v~QlnMGeGKTsVI~ 59 (229)
T PF12340_consen 24 IRPVQVEIAREMISPPSGK--NSVMQLNMGEGKTSVIV 59 (229)
T ss_pred eeHHHHHHHHHHhCCCCCC--CeEeeecccCCccchHH
Confidence 4555555555555 42211 12333459999998766
No 8
>PF04620 FlaA: Flagellar filament outer layer protein Flaa; InterPro: IPR006714 Periplasmic flagella are the organelles of spirochete mobility, and are structurally different from the flagella of other motile bacteria. They reside inside the cell within the periplasmic space, and confer mobility in viscous gel-like media such as connective tissue []. The flagella are composed of an outer sheath of FlaA proteins and a core filament of FlaB proteins. Each species usually has several FlaA protein species [].; GO: 0001539 ciliary or flagellar motility, 0030288 outer membrane-bounded periplasmic space
Probab=23.62 E-value=3.1e+02 Score=22.22 Aligned_cols=59 Identities=15% Similarity=0.282 Sum_probs=42.0
Q ss_pred EEeCCCceeccCCeecCCCC--CCCccCccEEEEEEec---CCCCceEEEEeEEEEEeCCCchh
Q psy6917 55 AIPFSKFFLQSKGRIQDIQN--PLDTDRISSIGLSLVD---QNNGPFQLELDYIGIEYDPNHTE 113 (132)
Q Consensus 55 ~IPfs~F~~t~RGr~~d~q~--~L~~~~I~~iGf~I~d---kq~GpF~LeId~I~a~~d~~~~e 113 (132)
+.+.-...|--|-|.+...+ |.....++=.||.|.. ...|+|.+-+|.+++..|..+.|
T Consensus 151 ~~~iP~~ip~~r~r~~q~~~~yp~~~~~l~f~gfrI~~dp~~~~g~f~iYfDdlkv~tD~~~v~ 214 (217)
T PF04620_consen 151 TVNIPPYIPDVRNRILQQYPRYPRSDPGLKFVGFRIDRDPDERGGDFYIYFDDLKVLTDKFVVE 214 (217)
T ss_pred EEECCCCCCccceeeeeecccCCCCCCceEEEEEEEECChhhcCCCEEEEEeeeEEEEEEEEEE
Confidence 45555666655555544223 3344558889999985 58999999999999999987664
No 9
>PF08435 Calici_coat_C: Calicivirus coat protein C-terminal; InterPro: IPR013643 Bovine calicivirus is a positive-stranded ssRNA viruses that cause gastroenteritis []. The calicivirus genome contains two open reading frames, ORF1 and ORF2 [, ]. ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity. The regions of the poly-protein in which these activities lie are similar to proteins produced by the picornaviruses [, ]. ORF2 encodes a structural protein []. This signature finds ORF2, the structural coat protein. Two different families of caliciviruses can be distinguished on the basis of sequence similarity, namely those classified as small round structured viruses (SRSVs) and those classed as non-SRSVs. Rabbit hemorrhagic disease virus (RHDV) which causes a highly contagious disease of wild and domestic rabbits belongs to the family Caliciviridae []. The capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry. It is about 38nm in diameter and consists of 180 capsid proteins. The capsid encapsulates the genomic RNA and VP2 proteins and attaches the virion to target cells by binding histo-blood group antigens present on gastroduodenal epithelial cells. The Shell domain (S domain) contains elements essential for the formation of the icosahedron. The Protruding domain (P domain) is divided into sub-domains P1 and P2. An hypervariable region in P2 is thought to play an important role in receptor binding and immune reactivity. This is the calicivirus coat protein (IPR004005 from INTERPRO) C-terminal region. ; PDB: 3D26_B 2ZL6_B 1IHM_B 3BY2_A 3BY1_A 2ZL7_A 2ZL5_A 3LQ6_B 3LQE_A 3SEJ_A ....
Probab=21.45 E-value=1.2e+02 Score=24.94 Aligned_cols=32 Identities=16% Similarity=0.237 Sum_probs=23.6
Q ss_pred Cchhhhhhhhc-------cCceee-ec-CCCceEEEEEc--CC
Q psy6917 1 MWKDEVQDKLY-------MDPVGD-VY-PNETKVIWKFN--ES 32 (132)
Q Consensus 1 ~~~~e~~~~~~-------~~~~~~-~~-~~~~~vlf~F~--~~ 32 (132)
||.||+..|+. +|-.++ |. |..-|+||+|+ ++
T Consensus 144 llPqE~v~hF~~e~ap~q~~~ALl~YvnpdTgr~LfE~KLy~~ 186 (230)
T PF08435_consen 144 LLPQEWVQHFYQEQAPSQGDVALLRYVNPDTGRVLFEAKLYPE 186 (230)
T ss_dssp SS-HHHHHHHHHH--S-SSSEEEEEEEETTTTEEEEEEEEETT
T ss_pred cCCHHHHHHHHhccCccccceeEEEEecCCCCCEEEEEEecCC
Confidence 68899999985 554443 33 68899999999 65
No 10
>PF13715 DUF4480: Domain of unknown function (DUF4480)
Probab=20.55 E-value=95 Score=20.14 Aligned_cols=36 Identities=19% Similarity=0.339 Sum_probs=19.5
Q ss_pred ccCCeecCCC--CCCCccCccEEEEEEe--cCCCCceEEE
Q psy6917 64 QSKGRIQDIQ--NPLDTDRISSIGLSLV--DQNNGPFQLE 99 (132)
Q Consensus 64 t~RGr~~d~q--~~L~~~~I~~iGf~I~--dkq~GpF~Le 99 (132)
|.+|++.|.. .|+.-..|.-.+-..+ -..+|.|+|.
T Consensus 1 ti~G~V~d~~t~~pl~~a~V~~~~~~~~~~Td~~G~F~i~ 40 (88)
T PF13715_consen 1 TISGKVVDSDTGEPLPGATVYLKNTKKGTVTDENGRFSIK 40 (88)
T ss_pred CEEEEEEECCCCCCccCeEEEEeCCcceEEECCCeEEEEE
Confidence 4578888754 5665555544433111 1346666665
Done!