Query 042280
Match_columns 301
No_of_seqs 150 out of 908
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 04:42:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042280.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042280hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2335 Secreted and surface p 99.9 8.9E-22 1.9E-26 169.9 10.2 126 144-279 47-184 (187)
2 smart00554 FAS1 Four repeated 99.8 5E-20 1.1E-24 144.4 6.5 90 180-277 1-99 (99)
3 KOG1437 Fasciclin and related 99.8 1.7E-18 3.7E-23 174.9 13.9 219 21-282 407-647 (682)
4 PF02469 Fasciclin: Fasciclin 99.8 1E-18 2.2E-23 142.7 6.1 113 155-276 2-128 (128)
5 smart00554 FAS1 Four repeated 99.7 5.8E-18 1.3E-22 132.7 6.6 88 22-115 1-99 (99)
6 COG2335 Secreted and surface p 99.7 1.3E-16 2.8E-21 138.0 6.7 91 16-115 78-182 (187)
7 PF02469 Fasciclin: Fasciclin 99.6 9.2E-16 2E-20 125.1 3.4 94 17-114 22-128 (128)
8 KOG1437 Fasciclin and related 99.5 3.3E-14 7.3E-19 144.0 12.8 231 21-291 273-521 (682)
9 PF02680 DUF211: Uncharacteriz 14.3 90 0.0019 24.5 1.0 15 261-275 68-82 (95)
10 PF01479 S4: S4 domain; Inter 11.6 3.5E+02 0.0075 17.4 3.3 19 246-264 27-45 (48)
No 1
>COG2335 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]
Probab=99.86 E-value=8.9e-22 Score=169.95 Aligned_cols=126 Identities=21% Similarity=0.287 Sum_probs=101.4
Q ss_pred HHHHHHHHhhc-ChHHHHHHHH-HhhcccccCCCCCceEEEecCCHHHhhccC----------ChHHHhcccccccccCc
Q 042280 144 FEEASGVLRSK-GYSLMGSFLE-LQLLGFSDRSGIAELTVFAPFDGVMMDYVG----------NVSEYSSLLLRHTVPCK 211 (301)
Q Consensus 144 ~~~~~~~L~~~-gfs~f~~~L~-~~l~~l~~~~~~~~~TvFAPtD~Af~~l~~----------~~~~l~~iL~yHVvp~~ 211 (301)
-.++.+..... .|+++..++. +++-+. +...|+||||||||+||.+++. +...|..+|.||||+|+
T Consensus 47 ~~~iV~~a~~~~~f~tl~~a~~aa~Lv~~--L~~~gp~TVFaPtn~AFa~lp~~T~~~Ll~pen~~~L~~iLtYHVv~Gk 124 (187)
T COG2335 47 RADIVESAANNPSFTTLVAALKAAGLVDT--LNETGPFTVFAPTNEAFAKLPAGTLDALLKPENKPLLTKILTYHVVEGK 124 (187)
T ss_pred hhHHHHHHccCcchHHHHHHHHhhhhHHH--hcCCCCeEEecCCHHHHHhCChhHHHHHhCccchhhhheeeEEEEEcCc
Confidence 35677766444 4999998884 333222 2335689999999999999853 45678899999999999
Q ss_pred ccccccCCCCCCCceeeccCCcEEEEEEcCCCcccEEECcEEEeCCceeeeCCeEEEEEccccCCCCc
Q 042280 212 ISWSDLVGFDDGDALKTFLNGFKINVTRSDGDDDLLMLNGVVISSPNLYYSDWLVVHGIHEVLAVPAT 279 (301)
Q Consensus 212 l~~~dL~~~~~g~~l~Tll~g~~l~v~~~~~~~~~i~VNg~~I~~pDi~~~~~gVIHgId~VL~p~~~ 279 (301)
++.+++.. .....|+ +|..+.|...++ +++||++.|+.+|+.. +|||||+||+||+||..
T Consensus 125 ~~~~~l~~---~~~v~t~-~G~~~~i~~~~~---~~~Vn~a~v~~~di~a-~NgvIhvID~Vl~Pp~~ 184 (187)
T COG2335 125 ITAADLKS---SGSVKTV-QGADLKIKVTGG---GVYVNDATVTIADINA-SNGVIHVIDKVLIPPMD 184 (187)
T ss_pred ccHHHhhc---cccceee-cCceEEEEEcCC---cEEEeeeEEEeccEec-cCcEEEEEeeeccCCCc
Confidence 99999875 3347775 999999999988 8999999999999965 57999999999999864
No 2
>smart00554 FAS1 Four repeated domains in the Fasciclin I family of proteins, present in many other contexts.
Probab=99.80 E-value=5e-20 Score=144.45 Aligned_cols=90 Identities=39% Similarity=0.547 Sum_probs=77.4
Q ss_pred EEEecCCHHHhhccCC-h-----H-HHhcccccccccCcccccccCCCCCCCceeeccCCcEEEEEEcC--CCcccEEEC
Q 042280 180 TVFAPFDGVMMDYVGN-V-----S-EYSSLLLRHTVPCKISWSDLVGFDDGDALKTFLNGFKINVTRSD--GDDDLLMLN 250 (301)
Q Consensus 180 TvFAPtD~Af~~l~~~-~-----~-~l~~iL~yHVvp~~l~~~dL~~~~~g~~l~Tll~g~~l~v~~~~--~~~~~i~VN 250 (301)
|+|||+|+||+++... . + .++++|+|||+|++++.++|.. +..++|+ .|..|.+++.+ + .+++|
T Consensus 1 TvfaP~d~Af~~~~~~~~~~l~~~~~l~~ll~~Hiv~~~~~~~~l~~---~~~~~Tl-~g~~l~v~~~~~~~---~i~in 73 (99)
T smart00554 1 TVFAPTDEAFQKLPPGTLNSLLADPKLKNLLLYHVVPGRLSSADLLN---GGTLPTL-AGSKLRVTRSGDSG---TVTVN 73 (99)
T ss_pred CEeCcCHHHHHhcCHHHHHHHhCCHHHHHHHHhcEeCceEcHHHhcc---CCccccC-CCCEEEEEEeCCCC---eEEEc
Confidence 8999999999987431 1 1 6789999999999999998864 6779997 68899999877 5 89999
Q ss_pred cEEEeCCceeeeCCeEEEEEccccCCC
Q 042280 251 GVVISSPNLYYSDWLVVHGIHEVLAVP 277 (301)
Q Consensus 251 g~~I~~pDi~~~~~gVIHgId~VL~p~ 277 (301)
+++|+.+|+.++ ||+||+||+||.||
T Consensus 74 ~~~v~~~di~~~-nGvih~Id~vL~P~ 99 (99)
T smart00554 74 GARIVEADIAAT-NGVVHVIDRVLLPP 99 (99)
T ss_pred ceEEEECCEecC-CeEEEEECceeCCC
Confidence 999999999765 79999999999875
No 3
>KOG1437 consensus Fasciclin and related adhesion glycoproteins [Cell wall/membrane/envelope biogenesis; Extracellular structures]
Probab=99.78 E-value=1.7e-18 Score=174.89 Aligned_cols=219 Identities=18% Similarity=0.125 Sum_probs=147.2
Q ss_pred eEEEecCChhhhcCCC-CC----HHHhhhcccCCccCccccCCCCCCCcccccCCCceEEEEEeCCC-----CeEEEee-
Q 042280 21 LTIFSPSDSAFVSSGQ-PS----LSLLEFHFSPLSLPLYSLKKLPCNSKIPTLSPSHSLVITSFPSD-----CNVSLKG- 89 (301)
Q Consensus 21 ~TiFAPtd~Af~~~~~-~~----~~lL~yHiv~g~~~~~~L~~~~~~~~l~Tll~g~~l~vt~~~~~-----~~v~in~- 89 (301)
+|+|+|.|+||.+... .. ..+|+|||++.++..+++.+. ++.++|+ .+..+..-+++.. ..+.++|
T Consensus 407 ~t~~lp~n~~fd~~~~~~~r~l~~qIL~~HII~~~~~~~~~y~~--~~~v~t~-g~~~l~~fv~r~~~s~~~t~i~~~~~ 483 (682)
T KOG1437|consen 407 ATLLLPTNNLFDDLTPLESRRLAEQILYNHIIPEYLTSSSMYNG--QTTVRTL-GKNKLLYFVYRHSVSANVTDILIGNE 483 (682)
T ss_pred eEEeeehhhhccCCChhhhHHHHHHHHHHhCcchhhhhhhhhcc--cceeecc-CCeEEEEEEecccccccceeeeccce
Confidence 7999999999998532 11 279999999999999998752 3367776 4556655555321 2344555
Q ss_pred EEEecCccc-cCCceEEEEeCCccCCCCCCCCCCCCCCCCCCCCCCccCCCchhhHHHHHHHHhhcC-hHHHHHHHHH-h
Q 042280 90 VNLTHKPIY-NDGLLVIYGINEFFNPGYGVSDSPFKTDQDAISPCGFSFNDSVNAFEEASGVLRSKG-YSLMGSFLEL-Q 166 (301)
Q Consensus 90 ~~I~~~di~-~ng~~vVH~Id~vL~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~g-fs~f~~~L~~-~ 166 (301)
++|...|+. .|| +||.||+|+.|. ++.+.|++.+ ++.+..+++. +
T Consensus 484 ~~Ii~aDi~~~nG--vvH~id~vl~p~------------------------------~l~~~l~~d~r~s~~~~~le~~~ 531 (682)
T KOG1437|consen 484 ACIIEADISVKNG--VVHIIDRVLDPV------------------------------SLMEDLKTDGRISGTVQGLEGVL 531 (682)
T ss_pred eeEEecccceecC--ceEEeeEEcCcc------------------------------cHHHHHhhccchhhhHHhhhhcC
Confidence 578899996 788 999999999992 2344555544 6666666643 3
Q ss_pred hcccccCCCCCceEEEecCCHHHhhccC------ChHHHhcccccccccCccc--ccccCCCCCCCceeeccCCcEEEEE
Q 042280 167 LLGFSDRSGIAELTVFAPFDGVMMDYVG------NVSEYSSLLLRHTVPCKIS--WSDLVGFDDGDALKTFLNGFKINVT 238 (301)
Q Consensus 167 l~~l~~~~~~~~~TvFAPtD~Af~~l~~------~~~~l~~iL~yHVvp~~l~--~~dL~~~~~g~~l~Tll~g~~l~v~ 238 (301)
+.+.. ...+.+|+|+|||+||.+... ....|.+++.||++++... ..+...-..+ .+-+. .|..+.+.
T Consensus 532 l~e~l--~~~~~~t~fvPt~ka~~~~~~~~~~~~~~~~l~~~l~yH~v~~~~~ls~~~~~~v~~~-~k~s~-~~~~~~~~ 607 (682)
T KOG1437|consen 532 LPEEL--TPEGNYTLFVPTNKAWQKSTKDEKSLFHKKALQDFLKYHLVPGQSRLSLGSSPYVMIQ-VKLSL-RGDHLFFS 607 (682)
T ss_pred Chhhh--ccCCceEEEeecccccccCCcchhhcchHHHHHHHHHhccccceeeeecccccceeee-eeEEE-ecccEEee
Confidence 32211 223459999999999997643 3356889999999998653 1211100000 11122 34444454
Q ss_pred EcCCCcccEEECcEEEeCCceeeeCCeEEEEEccccCCCCcchh
Q 042280 239 RSDGDDDLLMLNGVVISSPNLYYSDWLVVHGIHEVLAVPATTKE 282 (301)
Q Consensus 239 ~~~~~~~~i~VNg~~I~~pDi~~~~~gVIHgId~VL~p~~~~~~ 282 (301)
.... ...+|-.+++..|++.. ||++|.||.||.|+.....
T Consensus 608 ~~~~---~~~vn~e~~~~~~i~~~-n~~~h~i~~vl~p~~l~~~ 647 (682)
T KOG1437|consen 608 LVNP---RGDVNKERLVGIDIMGT-NGVVHVIDLVLKPPDLPFL 647 (682)
T ss_pred eecc---ccceeeeeeeccceeee-cceeEEEEEEcccCcchhh
Confidence 4444 56778889999999754 7899999999999865443
No 4
>PF02469 Fasciclin: Fasciclin domain; InterPro: IPR000782 The FAS1 (fasciclin-like) domain is an extracellular module of about 140 amino acid residues. It has been suggested that the FAS1 domain represents an ancient cell adhesion domain common to plants and animals []; related FAS1 domains are also found in bacteria []. The crystal structure of FAS1 domains 3 and 4 of fasciclin I from Drosophila melanogaster (Fruit fly) has been determined, revealing a novel domain fold consisting of a seven-stranded beta wedge and at least five alpha helices; two well-ordered N-acetylglucosamine groups attached to a conserved asparagine are located in the interface region between the two FAS1 domains []. Fasciclin I is an insect neural cell adhesion molecule involved in axonal guidance that is attached to the membrane by a GPI-anchored protein. FAS1 domains are present in many secreted and membrane-anchored proteins. These proteins are usually GPI anchored and consist of: (i) a single FAS1 domain, (ii) a tandem array of FAS1 domains, or (iii) FAS1 domain(s) interspersed with other domains. Proteins known to contain a FAS1 domain include: Fasciclin I (4 FAS1 domains). Human TGF-beta induced Ig-H3 (BIgH3) protein (4 FAS1 domains), where the FAS1 domains mediate cell adhesion through an interaction with alpha3/beta1 integrin; mutation in the FAS1 domains result in corneal dystrophy []. Volvox major cell adhesion protein (2 FAS1 domains) []. Arabidopsis fasciclin-like arabinogalactan proteins (2 FAS1 domains) []. Mammalian stabilin protein, a family of fasciclin-like hyaluronan receptor homologues (7 FAS1 domains)[]. Human extracellular matrix protein periostin (4 FAS1 domains). Bacterial immunogenic protein MPT70 (1 FAS1 domain) []. The FAS1 domains of both human periostin (Q15063 from SWISSPROT) and BIgH3 (Q15582 from SWISSPROT) proteins were found to contain vitamin K-dependent gamma-carboxyglutamate residues []. Gamma-carboxyglutamate residues are more commonly associated with GLA domains (IPR000294 from INTERPRO), where they occur through post-translational modification catalysed by the vitamin K-dependent enzyme gamma-glutamylcarboxylase.; PDB: 1O70_A 1W7D_A 1W7E_A 1NYO_A 1X3B_A 2VXP_A.
Probab=99.75 E-value=1e-18 Score=142.68 Aligned_cols=113 Identities=34% Similarity=0.443 Sum_probs=84.4
Q ss_pred ChHHHHHHHH-Hhhcccc-cCCCCCceEEEecCCHHHhhcc--------CChHHHhcccccccccCcccccccCCCCCC-
Q 042280 155 GYSLMGSFLE-LQLLGFS-DRSGIAELTVFAPFDGVMMDYV--------GNVSEYSSLLLRHTVPCKISWSDLVGFDDG- 223 (301)
Q Consensus 155 gfs~f~~~L~-~~l~~l~-~~~~~~~~TvFAPtD~Af~~l~--------~~~~~l~~iL~yHVvp~~l~~~dL~~~~~g- 223 (301)
+|+.|..+++ ..+.... +. .+.+|||||+|+||+++. ...+.++++|+|||+++.++.++|.. +
T Consensus 2 ~~s~f~~~l~~~~l~~~l~~~--~~~~TvfaP~d~a~~~~~~~~~~~~~~~~~~l~~~l~~hiv~~~~~~~~l~~---~~ 76 (128)
T PF02469_consen 2 DLSTFSRLLEQAGLADLLNDS--DGNYTVFAPTDDAFQKLSQETNSSLADSKEQLKSLLKYHIVPGSITSSDLRN---GK 76 (128)
T ss_dssp TTHHHHHHHHHTTCHHHHGCS--SSSEEEEEE-HHHHHHSHHHHHHHHHTHHHHHHHHHHHTEEES---HCHHHC---HH
T ss_pred CHHHHHHHHHHcCCHHHHhcC--CCCEEEEEECHHHHHhccccccchhhhhhhhHhhhhhhEEEcCceehhhhcc---cc
Confidence 4778888884 4443222 22 235999999999998762 13466889999999999998888874 4
Q ss_pred CceeeccCCcEEEEEEc--CCCcccEEECc-EEEeCCceeeeCCeEEEEEccccCC
Q 042280 224 DALKTFLNGFKINVTRS--DGDDDLLMLNG-VVISSPNLYYSDWLVVHGIHEVLAV 276 (301)
Q Consensus 224 ~~l~Tll~g~~l~v~~~--~~~~~~i~VNg-~~I~~pDi~~~~~gVIHgId~VL~p 276 (301)
..++|++.|..+.|+.. ++ .++||+ ++|+.+|+.+ .||+||.||+||.|
T Consensus 77 ~~~~t~~~g~~~~v~~~~~~~---~~~v~~~a~i~~~~~~~-~nG~ih~id~vL~P 128 (128)
T PF02469_consen 77 QTLETLLNGQPLRVSSSPSNG---TIYVNGKARIVKSDIEA-SNGVIHIIDDVLIP 128 (128)
T ss_dssp EEEEBSSTTCEEEEEEEGGTT---EEEECCEEEESEEEEEE-SSEEEEEESS-TSS
T ss_pred ccceeccCCCEEEEEEEecCC---ceEecCceEEEeCCEEe-CCEEEEEECceECc
Confidence 57888568999999887 44 899999 9999999965 57999999999976
No 5
>smart00554 FAS1 Four repeated domains in the Fasciclin I family of proteins, present in many other contexts.
Probab=99.73 E-value=5.8e-18 Score=132.69 Aligned_cols=88 Identities=28% Similarity=0.452 Sum_probs=74.7
Q ss_pred EEEecCChhhhcCCCC---------CH-HHhhhcccCCccCccccCCCCCCCcccccCCCceEEEEEeCCCCeEEEeeEE
Q 042280 22 TIFSPSDSAFVSSGQP---------SL-SLLEFHFSPLSLPLYSLKKLPCNSKIPTLSPSHSLVITSFPSDCNVSLKGVN 91 (301)
Q Consensus 22 TiFAPtd~Af~~~~~~---------~~-~lL~yHiv~g~~~~~~L~~~~~~~~l~Tll~g~~l~vt~~~~~~~v~in~~~ 91 (301)
|+|||+|+||+++... .+ ++|+||+++++++.++|.+ +..++|+. |..|+++..++.+.+++|+++
T Consensus 1 TvfaP~d~Af~~~~~~~~~~l~~~~~l~~ll~~Hiv~~~~~~~~l~~---~~~~~Tl~-g~~l~v~~~~~~~~i~in~~~ 76 (99)
T smart00554 1 TVFAPTDEAFQKLPPGTLNSLLADPKLKNLLLYHVVPGRLSSADLLN---GGTLPTLA-GSKLRVTRSGDSGTVTVNGAR 76 (99)
T ss_pred CEeCcCHHHHHhcCHHHHHHHhCCHHHHHHHHhcEeCceEcHHHhcc---CCccccCC-CCEEEEEEeCCCCeEEEcceE
Confidence 8999999999987531 22 8999999999999999975 56788885 889999987433789999999
Q ss_pred EecCccc-cCCceEEEEeCCccCCC
Q 042280 92 LTHKPIY-NDGLLVIYGINEFFNPG 115 (301)
Q Consensus 92 I~~~di~-~ng~~vVH~Id~vL~P~ 115 (301)
|+.+|+. .|| +||+||+||.|+
T Consensus 77 v~~~di~~~nG--vih~Id~vL~P~ 99 (99)
T smart00554 77 IVEADIAATNG--VVHVIDRVLLPP 99 (99)
T ss_pred EEECCEecCCe--EEEEECceeCCC
Confidence 9999996 666 999999999985
No 6
>COG2335 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]
Probab=99.66 E-value=1.3e-16 Score=137.99 Aligned_cols=91 Identities=25% Similarity=0.411 Sum_probs=75.6
Q ss_pred CCCCceEEEecCChhhhcCCC--------CC----H-HHhhhcccCCccCccccCCCCCCCcccccCCCceEEEEEeCCC
Q 042280 16 HHSPFLTIFSPSDSAFVSSGQ--------PS----L-SLLEFHFSPLSLPLYSLKKLPCNSKIPTLSPSHSLVITSFPSD 82 (301)
Q Consensus 16 ~~~~~~TiFAPtd~Af~~~~~--------~~----~-~lL~yHiv~g~~~~~~L~~~~~~~~l~Tll~g~~l~vt~~~~~ 82 (301)
+.++ ||||||+|+||.+++. |. + .+|.|||++|+++.+++.+. ..+.|+ .|..++|... +
T Consensus 78 ~~gp-~TVFaPtn~AFa~lp~~T~~~Ll~pen~~~L~~iLtYHVv~Gk~~~~~l~~~---~~v~t~-~G~~~~i~~~--~ 150 (187)
T COG2335 78 ETGP-FTVFAPTNEAFAKLPAGTLDALLKPENKPLLTKILTYHVVEGKITAADLKSS---GSVKTV-QGADLKIKVT--G 150 (187)
T ss_pred CCCC-eEEecCCHHHHHhCChhHHHHHhCccchhhhheeeEEEEEcCcccHHHhhcc---ccceee-cCceEEEEEc--C
Confidence 3555 5999999999999752 22 2 79999999999999999863 346665 7999999886 3
Q ss_pred CeEEEeeEEEecCccc-cCCceEEEEeCCccCCC
Q 042280 83 CNVSLKGVNLTHKPIY-NDGLLVIYGINEFFNPG 115 (301)
Q Consensus 83 ~~v~in~~~I~~~di~-~ng~~vVH~Id~vL~P~ 115 (301)
++++||+++|+..|+. +|| +||+||+||.|+
T Consensus 151 ~~~~Vn~a~v~~~di~a~Ng--vIhvID~Vl~Pp 182 (187)
T COG2335 151 GGVYVNDATVTIADINASNG--VIHVIDKVLIPP 182 (187)
T ss_pred CcEEEeeeEEEeccEeccCc--EEEEEeeeccCC
Confidence 4499999999999995 888 999999999998
No 7
>PF02469 Fasciclin: Fasciclin domain; InterPro: IPR000782 The FAS1 (fasciclin-like) domain is an extracellular module of about 140 amino acid residues. It has been suggested that the FAS1 domain represents an ancient cell adhesion domain common to plants and animals []; related FAS1 domains are also found in bacteria []. The crystal structure of FAS1 domains 3 and 4 of fasciclin I from Drosophila melanogaster (Fruit fly) has been determined, revealing a novel domain fold consisting of a seven-stranded beta wedge and at least five alpha helices; two well-ordered N-acetylglucosamine groups attached to a conserved asparagine are located in the interface region between the two FAS1 domains []. Fasciclin I is an insect neural cell adhesion molecule involved in axonal guidance that is attached to the membrane by a GPI-anchored protein. FAS1 domains are present in many secreted and membrane-anchored proteins. These proteins are usually GPI anchored and consist of: (i) a single FAS1 domain, (ii) a tandem array of FAS1 domains, or (iii) FAS1 domain(s) interspersed with other domains. Proteins known to contain a FAS1 domain include: Fasciclin I (4 FAS1 domains). Human TGF-beta induced Ig-H3 (BIgH3) protein (4 FAS1 domains), where the FAS1 domains mediate cell adhesion through an interaction with alpha3/beta1 integrin; mutation in the FAS1 domains result in corneal dystrophy []. Volvox major cell adhesion protein (2 FAS1 domains) []. Arabidopsis fasciclin-like arabinogalactan proteins (2 FAS1 domains) []. Mammalian stabilin protein, a family of fasciclin-like hyaluronan receptor homologues (7 FAS1 domains)[]. Human extracellular matrix protein periostin (4 FAS1 domains). Bacterial immunogenic protein MPT70 (1 FAS1 domain) []. The FAS1 domains of both human periostin (Q15063 from SWISSPROT) and BIgH3 (Q15582 from SWISSPROT) proteins were found to contain vitamin K-dependent gamma-carboxyglutamate residues []. Gamma-carboxyglutamate residues are more commonly associated with GLA domains (IPR000294 from INTERPRO), where they occur through post-translational modification catalysed by the vitamin K-dependent enzyme gamma-glutamylcarboxylase.; PDB: 1O70_A 1W7D_A 1W7E_A 1NYO_A 1X3B_A 2VXP_A.
Probab=99.57 E-value=9.2e-16 Score=125.13 Aligned_cols=94 Identities=30% Similarity=0.476 Sum_probs=72.3
Q ss_pred CCCceEEEecCChhhhcCCC--------C--CH-HHhhhcccCCccCccccCCCCCCCcccccCCCceEEEEEeCCCCeE
Q 042280 17 HSPFLTIFSPSDSAFVSSGQ--------P--SL-SLLEFHFSPLSLPLYSLKKLPCNSKIPTLSPSHSLVITSFPSDCNV 85 (301)
Q Consensus 17 ~~~~~TiFAPtd~Af~~~~~--------~--~~-~lL~yHiv~g~~~~~~L~~~~~~~~l~Tll~g~~l~vt~~~~~~~v 85 (301)
....+|||||+|+||.+++. + .+ .+|+||++++.++.++|... ...+.|.+.|..++|+.+.+++.+
T Consensus 22 ~~~~~TvfaP~d~a~~~~~~~~~~~~~~~~~~l~~~l~~hiv~~~~~~~~l~~~--~~~~~t~~~g~~~~v~~~~~~~~~ 99 (128)
T PF02469_consen 22 SDGNYTVFAPTDDAFQKLSQETNSSLADSKEQLKSLLKYHIVPGSITSSDLRNG--KQTLETLLNGQPLRVSSSPSNGTI 99 (128)
T ss_dssp SSSSEEEEEE-HHHHHHSHHHHHHHHHTHHHHHHHHHHHTEEES---HCHHHCH--HEEEEBSSTTCEEEEEEEGGTTEE
T ss_pred CCCCEEEEEECHHHHHhccccccchhhhhhhhHhhhhhhEEEcCceehhhhccc--cccceeccCCCEEEEEEEecCCce
Confidence 44578999999999987631 1 12 89999999999999998852 156888668999999988446789
Q ss_pred EEee-EEEecCccc-cCCceEEEEeCCccCC
Q 042280 86 SLKG-VNLTHKPIY-NDGLLVIYGINEFFNP 114 (301)
Q Consensus 86 ~in~-~~I~~~di~-~ng~~vVH~Id~vL~P 114 (301)
++|+ ++|+..|+. .|| +||+||+||.|
T Consensus 100 ~v~~~a~i~~~~~~~~nG--~ih~id~vL~P 128 (128)
T PF02469_consen 100 YVNGKARIVKSDIEASNG--VIHIIDDVLIP 128 (128)
T ss_dssp EECCEEEESEEEEEESSE--EEEEESS-TSS
T ss_pred EecCceEEEeCCEEeCCE--EEEEECceECc
Confidence 9999 999999995 677 99999999988
No 8
>KOG1437 consensus Fasciclin and related adhesion glycoproteins [Cell wall/membrane/envelope biogenesis; Extracellular structures]
Probab=99.55 E-value=3.3e-14 Score=144.03 Aligned_cols=231 Identities=16% Similarity=0.191 Sum_probs=141.8
Q ss_pred eEEEecCChhhhcCCCCCH-HHhhhcccCCccCccccCCCCCCCcccccCC-------CceEEEEEeCCCCeEEEeeEEE
Q 042280 21 LTIFSPSDSAFVSSGQPSL-SLLEFHFSPLSLPLYSLKKLPCNSKIPTLSP-------SHSLVITSFPSDCNVSLKGVNL 92 (301)
Q Consensus 21 ~TiFAPtd~Af~~~~~~~~-~lL~yHiv~g~~~~~~L~~~~~~~~l~Tll~-------g~~l~vt~~~~~~~v~in~~~I 92 (301)
.|++||+|+||.+.+.... .++.||.+.|.+......+ .....+.+. ++...+....++....+||..+
T Consensus 273 rt~~a~tn~a~~~ip~~~~~~~~~~~~v~~~~~~~~i~~---~~~~~~s~~~~~~r~~~~~~~~a~g~~g~~~~~ng~~~ 349 (682)
T KOG1437|consen 273 RTHLAPTNEAFFTIPRGYPPRILGYHLVLGNLKYNHILD---NMKLGPSLAPGTVRLTGEGVAIAPGSSGERYHINGRAI 349 (682)
T ss_pred ccccccCcchhhcccccCCCcccccccchhhhhhhhhcc---cccccccccccceeeccccccccccCCCceEEeeccee
Confidence 5899999999977643332 5677888877765554442 111111111 1222222222345678898776
Q ss_pred ecCcccc-CCceEEEEeCCccCCCCCCCCCCCCCCCCCCCCCCccCCCchhhHHHHHHHHhhcChHHHHHHHHH-hh-cc
Q 042280 93 THKPIYN-DGLLVIYGINEFFNPGYGVSDSPFKTDQDAISPCGFSFNDSVNAFEEASGVLRSKGYSLMGSFLEL-QL-LG 169 (301)
Q Consensus 93 ~~~di~~-ng~~vVH~Id~vL~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~gfs~f~~~L~~-~l-~~ 169 (301)
+..|... +| +||.||.++.|+.. +.+++..+.+.-+++..++.. .+ .-
T Consensus 350 I~kd~i~~~~--~lh~id~~l~p~~~---------------------------~~l~~La~e~~~st~~rlv~elgll~~ 400 (682)
T KOG1437|consen 350 IQKDFIHTNG--LLHYIDYVLEPDSL---------------------------KNLMSLAREDEISTSMRLVAELGLLTA 400 (682)
T ss_pred EEEeeeccce--EEEEcccccCCchH---------------------------HHHHHHHhcccccHHHHHHHhccceEE
Confidence 6677764 45 99999999998622 245565555444555444422 12 21
Q ss_pred cccCCCCCceEEEecCCHHHhhccCCh--HHHhcccccccccCcccccccCCCCCCCceeeccCCcEEEEEE--cCCCc-
Q 042280 170 FSDRSGIAELTVFAPFDGVMMDYVGNV--SEYSSLLLRHTVPCKISWSDLVGFDDGDALKTFLNGFKINVTR--SDGDD- 244 (301)
Q Consensus 170 l~~~~~~~~~TvFAPtD~Af~~l~~~~--~~l~~iL~yHVvp~~l~~~dL~~~~~g~~l~Tll~g~~l~v~~--~~~~~- 244 (301)
+.. +. .+|+|+|+|+||+.+.... ..++.+|+|||+|.++..+++.. .++.++|+ ++..+..-. ..+.+
T Consensus 401 L~~--n~-e~t~~lp~n~~fd~~~~~~~r~l~~qIL~~HII~~~~~~~~~y~--~~~~v~t~-g~~~l~~fv~r~~~s~~ 474 (682)
T KOG1437|consen 401 LAP--ND-EATLLLPTNNLFDDLTPLESRRLAEQILYNHIIPEYLTSSSMYN--GQTTVRTL-GKNKLLYFVYRHSVSAN 474 (682)
T ss_pred EcC--CC-ceEEeeehhhhccCCChhhhHHHHHHHHHHhCcchhhhhhhhhc--ccceeecc-CCeEEEEEEeccccccc
Confidence 222 22 3999999999999864321 22579999999999999888763 23377786 665543332 22211
Q ss_pred -ccEEECc-EEEeCCceeeeCCeEEEEEccccCCCCcchhhhhccCCCC
Q 042280 245 -DLLMLNG-VVISSPNLYYSDWLVVHGIHEVLAVPATTKEATESSSQMG 291 (301)
Q Consensus 245 -~~i~VNg-~~I~~pDi~~~~~gVIHgId~VL~p~~~~~~~~~~~~~~~ 291 (301)
..+.+++ +.|...|+.. .+|++|.||+||.| ...-+..+.++.++
T Consensus 475 ~t~i~~~~~~~Ii~aDi~~-~nGvvH~id~vl~p-~~l~~~l~~d~r~s 521 (682)
T KOG1437|consen 475 VTDILIGNEACIIEADISV-KNGVVHIIDRVLDP-VSLMEDLKTDGRIS 521 (682)
T ss_pred ceeeeccceeeEEecccce-ecCceEEeeEEcCc-ccHHHHHhhccchh
Confidence 2466666 5688999975 57899999999976 33333444444333
No 9
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=14.26 E-value=90 Score=24.54 Aligned_cols=15 Identities=40% Similarity=0.304 Sum_probs=11.4
Q ss_pred eeCCeEEEEEccccC
Q 042280 261 YSDWLVVHGIHEVLA 275 (301)
Q Consensus 261 ~~~~gVIHgId~VL~ 275 (301)
...+|+||.||+|-.
T Consensus 68 e~~Gg~IHSIDeVva 82 (95)
T PF02680_consen 68 EELGGVIHSIDEVVA 82 (95)
T ss_dssp HHTT-EEEEEEEEEE
T ss_pred HHcCCeEEeeeeeee
Confidence 456899999999864
No 10
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=11.61 E-value=3.5e+02 Score=17.40 Aligned_cols=19 Identities=21% Similarity=0.315 Sum_probs=14.9
Q ss_pred cEEECcEEEeCCceeeeCC
Q 042280 246 LLMLNGVVISSPNLYYSDW 264 (301)
Q Consensus 246 ~i~VNg~~I~~pDi~~~~~ 264 (301)
.++|||..+..|+.....+
T Consensus 27 ~V~VNg~~v~~~~~~v~~~ 45 (48)
T PF01479_consen 27 RVKVNGKVVKDPSYIVKPG 45 (48)
T ss_dssp TEEETTEEESSTTSBESTT
T ss_pred EEEECCEEEcCCCCCCCCc
Confidence 7999999998887765543
Done!