RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

Searching..................................................done

Query= psy3950
         (338 letters)



>gnl|CDD|217504 pfam03345, DDOST_48kD, Oligosaccharyltransferase 48 kDa subunit
           beta.  Members of this family are involved in
           asparagine-linked protein glycosylation. In particular,
           dolichyl-diphosphooligosaccharide-protein
           glycosyltransferase (DDOST), also known as
           oligosaccharyltransferase EC:2.4.1.119, transfers the
           high-mannose sugar GlcNAc(2)-Man(9)-Glc(3) from a
           dolichol-linked donor to an asparagine acceptor in a
           consensus Asn-X-Ser/Thr motif. In most eukaryotes, the
           DDOST complex is composed of three subunits, which in
           humans are described as a 48kD subunit, ribophorin I,
           and ribophorin II. However, the yeast DDOST appears to
           consist of six subunits (alpha, beta, gamma, delta,
           epsilon, zeta). The yeast beta subunit is a 45kD
           polypeptide, previously discovered as the Wbp1 protein,
           with known sequence similarity to the human 48kD subunit
           and the other orthologues. This family includes the
           48kD-like subunits from several eukaryotes; it also
           includes the yeast DDOST beta subunit Wbp1.
          Length = 421

 Score =  430 bits (1108), Expect = e-151
 Identities = 167/343 (48%), Positives = 218/343 (63%), Gaps = 13/343 (3%)

Query: 4   GNLLIAGSS-SSSDLLRELASESGFEMDEEGAAVIDHLNYDV-KDAEKHTLIVADPSNLV 61
           GN+L+A SS +  D +REL SE G E+DE    V+DH NYDV   +  HT++V DP+NL+
Sbjct: 78  GNVLVALSSETIPDAIRELLSELGIELDERNTVVVDHFNYDVSSASGDHTVLVLDPNNLI 137

Query: 62  DSEVIVGKKPSSPLLYQGTGLIVDPANPLVLSVLSADSSAYSYNPDKPIKEYPHAVGKNT 121
            S+  VG     P+L++G G ++   NPLVL +L A S+AYSYNP +  +E P AVG   
Sbjct: 138 RSDTKVGFGGEKPILFRGVGALLGN-NPLVLPILRAPSTAYSYNPKEKEEEVPWAVGSQG 196

Query: 122 VLVAALQARNNARVVFSGSLYFFSNEAFNSPVQKAIGGKKFDKSSNEAVVAALSAWVFKE 181
            LV+ALQARNNARVVF GSL FFS+E F++ V+KA    K  K+ N      L+ WVFKE
Sbjct: 197 FLVSALQARNNARVVFVGSLEFFSDEWFSASVKKA---GKHVKTGNREFAKELTKWVFKE 253

Query: 182 NGVIRVKSVSHHKVGE-ENPPVAYTIMDNVVFRLELERKSGNTWVPHNANDVQMEFVRID 240
            GV++V  V+HHK GE    P  YTI D VV+ +E+   S   WVP  A+D+Q+EF  +D
Sbjct: 254 KGVLKVGKVTHHKAGEPSYNPEIYTIKDEVVYSIEISEYSNGKWVPFEADDIQLEFTMLD 313

Query: 241 PFVRTTLKSIAQ----GKYETVFKIPDVYGVYQFKVIYNRIGYTGISNATQVSVRPLEHT 296
           P+ R TLK   +    G Y T FK+PDV+GV+ FKV Y R G T I   TQV+VR L H 
Sbjct: 314 PYYRLTLKPSRRTSDSGVYSTSFKLPDVHGVFTFKVDYKRPGLTFIEEKTQVTVRHLAHD 373

Query: 297 QYER--FISSAYPYYASAFSMMFGVFVFSIVFLHYKDDEKSKS 337
           +Y R  FI++A+PYYAS FS++ G   F  VFL+ K   K  S
Sbjct: 374 EYPRSWFITNAWPYYASIFSVIIGFLAFVAVFLYSKPVGKVAS 416


>gnl|CDD|225819 COG3280, TreY, Maltooligosyl trehalose synthase [Carbohydrate
           transport and metabolism].
          Length = 889

 Score = 33.6 bits (77), Expect = 0.15
 Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 71  PSSPLLYQGTGLI----VDPAN--PLVLSVLSADSSAYSYNPDKPIKEYPHAVGKNTVLV 124
           P  P +YQGT L     VDP N  P+  +  +    A      + ++ +   + K  V  
Sbjct: 719 PGVPDIYQGTELWDFSLVDPDNRRPVDFATRAQALKALQEGDFELLEHWLDGI-KQAVTA 777

Query: 125 AALQARNNARVVFSGSLY 142
           AAL+ R     +F+G  Y
Sbjct: 778 AALRLRREHPELFAGGDY 795


>gnl|CDD|133433 cd05297, GH4_alpha_glucosidase_galactosidase, Glycoside Hydrolases
           Family 4; Alpha-glucosidases and alpha-galactosidases.
           Glucosidases cleave glycosidic bonds to release glucose
           from oligosaccharides. Alpha-glucosidases and
           alpha-galactosidases release alpha-D-glucose and
           alpha-D-galactose, respectively, via the hydrolysis of
           alpha-glycopyranoside bonds. Some bacteria
           simultaneously translocate and phosphorylate
           disaccharides via the phosphoenolpyruvate-dependent
           phosphotransferase system (PEP-PTS). After
           translocation, these phospho-disaccharides may be
           hydrolyzed by the GH4 glycoside hydrolases such as the
           alpha-glucosidases. Other organsisms (such as archaea
           and Thermotoga maritima) lack the PEP-PTS system, but
           have several enzymes normally associated with the
           PEP-PTS operon. Alpha-glucosidases and
           alpha-galactosidases are part of the NAD(P)-binding
           Rossmann fold superfamily, which includes a wide variety
           of protein families including the NAD(P)-binding domains
           of alcohol dehydrogenases, tyrosine-dependent
           oxidoreductases, glyceraldehyde-3-phosphate
           dehydrogenases, formate/glycerate dehydrogenases,
           siroheme synthases, 6-phosphogluconate dehydrogenases,
           aminoacid dehydrogenases, repressor rex, and NAD-binding
           potassium channel domains, among others.
          Length = 423

 Score = 31.4 bits (72), Expect = 0.76
 Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 4/32 (12%)

Query: 255 YETVFKIPDVYGVYQFKVIYNR-IGYTGISNA 285
            ET F+IP+ YG YQ         G  GI  A
Sbjct: 90  TETDFEIPEKYGYYQT---VGDTSGPGGIFRA 118


>gnl|CDD|180745 PRK06915, PRK06915, acetylornithine deacetylase; Validated.
          Length = 422

 Score = 30.4 bits (69), Expect = 1.4
 Identities = 35/153 (22%), Positives = 58/153 (37%), Gaps = 34/153 (22%)

Query: 17  LLRELASESGFEMDEEGA--AVID-----HLNYDV-----KDAEKHTLIVADPSNLVDSE 64
           LL+ L  E     DE GA   VI+      L+ D+     K  + H   V+  ++  DS 
Sbjct: 22  LLKRLIQEKSVSGDESGAQAIVIEKLRELGLDLDIWEPSFKKLKDHPYFVSPRTSFSDSP 81

Query: 65  VIVGKKPSSPLLYQGTG----LIVDPANPLVLSVLSADSSAYSYNPDKPIKE----YPHA 116
            IV          +G+G    +I+   N  +  V   D + + ++P          Y   
Sbjct: 82  NIVATL-------KGSGGGKSMIL---NGHIDVVPEGDVNQWDHHPYSGEVIGGRIYGRG 131

Query: 117 V----GKNTVLVAALQARNNARVVFSGSLYFFS 145
                G N  L+ A++A   + +   G + F S
Sbjct: 132 TTDMKGGNVALLLAMEALIESGIELKGDVIFQS 164


>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
           family.  Included in this family of heterogeneous
           ribonucleoproteins are PTB (polypyrimidine tract binding
           protein ) and hnRNP-L. These proteins contain four RNA
           recognition motifs (rrm: pfam00067).
          Length = 481

 Score = 29.4 bits (66), Expect = 2.7
 Identities = 15/60 (25%), Positives = 24/60 (40%)

Query: 147 EAFNSPVQKAIGGKKFDKSSNEAVVAALSAWVFKENGVIRVKSVSHHKVGEENPPVAYTI 206
           E F       +   KF    NE     L  W   E+ V  + +++HH++ E N    Y +
Sbjct: 413 ELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHL 472


>gnl|CDD|233849 TIGR02401, trehalose_TreY, malto-oligosyltrehalose synthase.  This
           enzyme, formally named (1->4)-alpha-D-glucan
           1-alpha-D-glucosylmutase, is the TreY enzyme of the
           TreYZ pathway of trehalose biosynthesis, an alternative
           to the OtsAB pathway. Trehalose may be incorporated into
           more complex compounds but is best known as compatible
           solute. It is one of the most effective osmoprotectants,
           and unlike the various betaines does not require
           nitrogen for its synthesis [Energy metabolism,
           Biosynthesis and degradation of polysaccharides].
          Length = 825

 Score = 29.3 bits (66), Expect = 3.2
 Identities = 21/85 (24%), Positives = 29/85 (34%), Gaps = 19/85 (22%)

Query: 71  PSSPLLYQGTGL----IVDPAN---------PLVLSVLSADSSAYSYNPDKPIKEYPHAV 117
           P  P +YQGT      +VDP N            L  L+  + +      +        +
Sbjct: 658 PGVPDIYQGTEFWDLSLVDPDNRRPVDYAARRAALLQLTTPNWS------ELELWLLDGL 711

Query: 118 GKNTVLVAALQARNNARVVFSGSLY 142
            K  V  AALQ R     +F    Y
Sbjct: 712 VKLAVTAAALQLRREHPELFGQGDY 736


>gnl|CDD|241356 cd13202, FERM_C_MyoX, Myosin X (MyoX, Myo10) FERM domain C-lobe.
           MyoX, a MyTH-FERM myosin, is a molecular motor that has
           crucial functions in the transport and/or tethering of
           integrins in the actin-based extensions known as
           filopodia, microtubule binding, and in netrin-mediated
           axon guidance. It functions as a dimer. MyoX walks on
           bundles of actin, rather than single filaments, unlike
           the other unconventional myosins. MyoX is present in
           organisms ranging from humans to choanoflagellates, but
           not in Drosophila and Caenorhabditis elegans.MyoX
           consists of a N-terminal motor/head region, a neck made
           of 3 IQ motifs, and a tail consisting of a coiled-coil
           domain, a PEST region, 3 PH domains, a myosin tail
           homology 4 (MyTH4), and a FERM domain at its very
           C-terminus. The MyoX FERM domain binds to the NPXY motif
           of several beta-integrins, a key family of cell surface
           receptors that are involved in cell adhesion and
           migration. In addition the FERM domain binds to the
           cytoplasmic domains of the netrin receptors DCC (deleted
           in colorectal cancer) and neogenin. The FERM domain also
           forms a supramodule with its MyTH4 domain which binds to
           the negatively charged E-hook region in the tails of
           alpha- and beta-tubulin forming a proposed motorized
           link between actin filaments and microtubules. The FERM
           domain has a cloverleaf tripart structure (FERM_N,
           FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe,
           C-lobe/F1, F2, F3). The C-lobe/F3 within the FERM domain
           is part of the PH domain family. The FERM domain is
           found in the cytoskeletal-associated proteins such as
           ezrin, moesin, radixin, 4.1R, and merlin. These proteins
           provide a link between the membrane and cytoskeleton and
           are involved in signal transduction pathways. The FERM
           domain is also found in protein tyrosine phosphatases
           (PTPs) , the tyrosine kinases FAK and JAK, in addition
           to other proteins involved in signaling. This domain is
           structurally similar to the PH and PTB domains and
           consequently is capable of binding to both peptides and
           phospholipids at different sites.
          Length = 111

 Score = 27.3 bits (61), Expect = 5.2
 Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 13/65 (20%)

Query: 251 AQGKYETVFKIPDVYGVYQFKVIYNRIG------YTGISNATQVSV------RPLEHTQY 298
           A  KY  + +    YG   F+V  N+ G      + G+S A  VS+       PLE   Y
Sbjct: 6   AMAKYMAIIREWPGYGSTLFEVECNKEGGFPQELWLGVS-AKGVSLYKRGEPEPLESFPY 64

Query: 299 ERFIS 303
           E+ +S
Sbjct: 65  EKILS 69


>gnl|CDD|183376 PRK11909, PRK11909, cobalt transport protein CbiM; Provisional.
          Length = 230

 Score = 27.8 bits (62), Expect = 7.1
 Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 16/83 (19%)

Query: 259 FKIPDV-YGVYQF-------KVIYNRIG-YTGISNAT-----QVSVRP-LEHTQYERFIS 303
           F +P V Y VY+        +VI + IG Y GI+ A      +  ++P L HT     + 
Sbjct: 115 FVLPFVGYYVYKLLSILKVRRVIASAIGGYVGINAAALATGIEFGLQPFLFHTANGTPLY 174

Query: 304 SAYPYYASAFSMMFG-VFVFSIV 325
             Y    S  +M+F  + V  IV
Sbjct: 175 CPYGLNVSIPAMLFAHLTVAGIV 197


>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
           envelope biogenesis, outer membrane / Carbohydrate
           transport and metabolism].
          Length = 314

 Score = 28.0 bits (62), Expect = 8.4
 Identities = 14/46 (30%), Positives = 19/46 (41%)

Query: 95  LSADSSAYSYNPDKPIKEYPHAVGKNTVLVAALQARNNARVVFSGS 140
           L+A SS    N   P +     V     L+ A +A    R VF+ S
Sbjct: 71  LAAQSSVPDSNASDPAEFLDVNVDGTLNLLEAARAAGVKRFVFASS 116


>gnl|CDD|215746 pfam00144, Beta-lactamase, Beta-lactamase.  This family appears to
           be distantly related to pfam00905 and PF00768
           D-alanyl-D-alanine carboxypeptidase.
          Length = 326

 Score = 27.9 bits (62), Expect = 8.8
 Identities = 21/97 (21%), Positives = 32/97 (32%), Gaps = 19/97 (19%)

Query: 10  GSSSSSDLLRELASESGFEMDEEGAAVIDHLNYDVKDAEKHTLIVADPSNLVDSE----- 64
             S++ DL R       F +   G  ++                       + +      
Sbjct: 218 LKSTARDLAR-------FLLLLLGGLLLSAATLAQLTDWLRG--GTTGVGGIRAGLGLGW 268

Query: 65  VIVGKKPSSPLLYQGTG-----LIVDPANPLVLSVLS 96
           V+  K  + P L+  TG     L VDP   LV+ VLS
Sbjct: 269 VLADKTGAGPGLFGHTGGYGTYLAVDPDIGLVVVVLS 305


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.316    0.133    0.376 

Gapped
Lambda     K      H
   0.267   0.0761    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,216,777
Number of extensions: 1661498
Number of successful extensions: 1642
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1634
Number of HSP's successfully gapped: 19
Length of query: 338
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 240
Effective length of database: 6,590,910
Effective search space: 1581818400
Effective search space used: 1581818400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.4 bits)