RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12283
         (788 letters)



>gnl|CDD|217651 pfam03635, Vps35, Vacuolar protein sorting-associated protein 35.
           Vacuolar protein sorting-associated protein (Vps) 35 is
           one of around 50 proteins involved in protein
           trafficking. In particular, Vps35 assembles into a
           retromer complex with at least four other proteins Vps5,
           Vps17, Vps26 and Vps29. Vps35 contains a central region
           of weaker sequence similarity, thought to indicate the
           presence of at least three domains.
          Length = 741

 Score = 1023 bits (2648), Expect = 0.0
 Identities = 399/747 (53%), Positives = 524/747 (70%), Gaps = 19/747 (2%)

Query: 13  RLLEEASHIVKTQSLQMKRCLDSDKLMDALKHASTMLSELRTSLLSPKNYYELYMAVTDE 72
           +LLEEA  +VK QS  MKRCLD  KLMDALKHAS MLSELRTS LSPK YYELYM V DE
Sbjct: 1   KLLEEAIAVVKQQSFLMKRCLDQGKLMDALKHASNMLSELRTSSLSPKQYYELYMKVFDE 60

Query: 73  LRQLELYLVDEFQRGRKVPDLYELVQYAGNIVPRLYLLITVALVYIKTNSSLKRDLLKDL 132
           L+ L  YLVDE  +G  + DLYELVQYAGNIVPRLYLLITV  VYIK+  +  +++LKD+
Sbjct: 61  LQYLSTYLVDEHPKGHHLADLYELVQYAGNIVPRLYLLITVGSVYIKSKDAPAKEILKDM 120

Query: 133 VEMCRGVQHPLRGLFLRNYLLQCTRNVLPDTPEDEGDQAEGTVRDSVDFILMNFAEMNKL 192
           VEMCRGVQHP RGLFLR YL Q T++ LPDT   E +   GTV+DS++F+L NF EMNKL
Sbjct: 121 VEMCRGVQHPTRGLFLRYYLSQRTKDKLPDTGSYE-EGGGGTVQDSIEFLLTNFIEMNKL 179

Query: 193 WVRMQHQGHSRDKERREREREELRILVGTNLVRLSELDSITRDKYKKLVLPGILEQVVSC 252
           WVR+QHQG SR++E+RE+ER+ELRILVG+NLVRLS+L+ +  + YK+ +LP ILEQVV+C
Sbjct: 180 WVRLQHQGPSREREKREKERKELRILVGSNLVRLSQLEGVDLEMYKETILPRILEQVVNC 239

Query: 253 RDAIAQEYLMECIIQVFPDEFHLATLTAFLKSCAELQAGVNVKNILIALIDRLSLYAQKN 312
           RD +AQEYL+E IIQVFPDEFHLATL   L +C +L  GV+VK ILI L+DRL+ YA+++
Sbjct: 240 RDVLAQEYLLEVIIQVFPDEFHLATLDTLLSACLQLNPGVDVKKILITLMDRLAAYAERS 299

Query: 313 KEFNS------------LFETFSEQVASIVQSRIDMPAEDIVALQVSLINLALKCYPDKV 360
            E  +            LFE F  Q+  ++++R D+P +DI+AL VSL+NL LKCYPD++
Sbjct: 300 NEGVAEVESTKEEEDVDLFEVFWNQLVKLIKARPDLPLQDIIALLVSLLNLTLKCYPDRL 359

Query: 361 DYIDKILQTTVETFQKLNIERVEYNTPVSRELMRLLKIFIDQYNNILTVIQLTYFAPLME 420
           DY+D++L   VE            ++ + +E++RLL   I  Y NILT ++L  + PL+ 
Sbjct: 360 DYVDQVLGFAVEKVSNYL-GAKLNSSEIEQEIVRLLLAPISTYKNILTALELPNYQPLLS 418

Query: 421 LFDFYGRKSVSAYLITNALNNDTLVPTSESVDSILTIVSSLVQDQDDQPAEEEDPEDFAE 480
             D+  RKSV+  +I N L N+TL+ T + V+ +  ++S L++DQ DQP++E + E+FAE
Sbjct: 419 SLDYSTRKSVALAIIDNILKNNTLITTLDDVERLFELISPLIKDQPDQPSDELETEEFAE 478

Query: 481 EQGLLGRLVHQFKSDVPDQQYLILSTARKHFQAGGKKRIKHTLPPLVFQAYQLATQFSAL 540
           EQ  + RL+H  +SD  ++Q+ IL+T RKH   GG +RI++TLP LVF A +LA +  + 
Sbjct: 479 EQEKVARLIHLIRSDDVEKQFKILNTVRKHLGKGGPERIRYTLPTLVFAALRLARRLKSQ 538

Query: 541 REEDEMWSKKCSKIFRFCHQIILSLIK-AELAELPLRLFLQGAMTIGSIDFENHETISYE 599
            ++D+ W  K  KIF+F H  I  L   A  AEL L+L+LQ A+       E    I+YE
Sbjct: 539 EKKDDKWDAKIKKIFKFIHSTISILYNVAPAAELALKLYLQCAIVADQCGLEE---IAYE 595

Query: 600 FISQALSLYEEEISESKCQLAAITLLVGTFEKMSCFGEENAEPIRTQSALAASKLFKKPD 659
           F +QA ++YEE IS+SK Q  AI L++ T ++     EEN E + T+ AL ASKL KKPD
Sbjct: 596 FFTQAFTIYEESISDSKAQFQAIVLIISTLQRTRSLPEENYETLATKLALYASKLLKKPD 655

Query: 660 QCSGVCTCSHLFWSGKNSQGEEIRDGKRVLECLKKGVRIASQCMDMSVQVQLFIELLNHY 719
           QC  V  CSHLFW+ + S GE  RDGKRVLECL+K +RIA  CMD S  VQLF+E+LN Y
Sbjct: 656 QCRAVYLCSHLFWATELS-GEFYRDGKRVLECLQKALRIADSCMDNSQSVQLFVEILNRY 714

Query: 720 IYYFEKKNEHITVAMLNQLIGKIRDEL 746
           +YYFEK N H+TV  +N LI  I++ L
Sbjct: 715 LYYFEKGNTHVTVKYINGLIELIQENL 741


>gnl|CDD|218871 pfam06046, Sec6, Exocyst complex component Sec6.  Sec6 is a
           component of the multiprotein exocyst complex. Sec6
           interacts with Sec8, Sec10 and Exo70.These exocyst
           proteins localise to regions of active exocytosis-at the
           growing ends of interphase cells and in the medial
           region of cells undergoing cytokinesis-in an
           F-actin-dependent and exocytosis- independent manner.
          Length = 557

 Score = 32.3 bits (74), Expect = 1.1
 Identities = 22/121 (18%), Positives = 48/121 (39%), Gaps = 17/121 (14%)

Query: 258 QEYLMECIIQVFPDEFHLATLTAFLKSCAELQAGVNVKNILIALIDRLSLYAQKNKEFNS 317
           QEYL   + Q   +E     +  +L++    +             +++       ++   
Sbjct: 406 QEYLHPPLFQELLEELLDELVVEYLRALRNKRLVFKGAEERKQFAEKMK------RDAEQ 459

Query: 318 LFETFSE-QVASIVQSRID--------MPAEDIVALQVSLINLALKCYPD-KVDYIDKIL 367
           L++ F +   A+ + S+          +  ED  AL + +  L L  YPD   D+++ +L
Sbjct: 460 LYDFFQKLGDAAYLLSKFRVLEKLLDLLKLEDPDALILEVETL-LSSYPDISEDHVEAVL 518

Query: 368 Q 368
           +
Sbjct: 519 K 519


>gnl|CDD|215568 PLN03088, PLN03088, SGT1,  suppressor of G2 allele of SKP1;
           Provisional.
          Length = 356

 Score = 31.3 bits (71), Expect = 2.2
 Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 8/51 (15%)

Query: 322 FSEQVASIVQSRIDMPAEDIVALQVSLINLALKCYPDKVDYIDKILQTTVE 372
           F EQ+ S+V   I++P ED   LQ  L     K  PDK  Y  ++L T +E
Sbjct: 186 FGEQILSVV---IEVPGEDAYHLQPRLFG---KIIPDKCKY--EVLSTKIE 228


>gnl|CDD|233471 TIGR01569, A_tha_TIGR01569, plant integral membrane protein
           TIGR01569.  This model describes a region of ~160
           residues found exclusively in plant proteins, generally
           as the near complete length of the protein. At least 24
           different members are found in Arabidopsis thaliana.
           Members have four predicted transmembrane regions, the
           last of which is preceded by an invariant CXXXXX[FY]C
           motif. The family is not functionally characterized.
          Length = 154

 Score = 29.7 bits (67), Expect = 3.0
 Identities = 24/92 (26%), Positives = 35/92 (38%), Gaps = 15/92 (16%)

Query: 501 YLILSTARKHFQAGGKKRIKHTLPPLVF----QAYQLATQFSA---------LREEDEMW 547
           Y +LS     F    K+R+   L  L F        L++  SA         L  ++  W
Sbjct: 57  YSLLSLVVSIF-GLLKRRVFFKLIALFFLDLVMLALLSSGTSAAAAVAYVGKLGNKEAGW 115

Query: 548 SKKCSKIFRFCHQIILSLIKAELAELPLRLFL 579
            K C    +FC +I  SL    L  + L + L
Sbjct: 116 LKICGVFGKFCDRIAGSLA-LSLFAVILLVLL 146


>gnl|CDD|241262 cd01228, PH_BCR-related, Breakpoint Cluster Region-related
           pleckstrin homology (PH) domain.  The BCR gene is one of
           the two genes in the BCR-ABL complex, which is
           associated with the Philadelphia chromosome, a product
           of a reciprocal translocation between chromosomes 22 and
           9. BCR is a GTPase-activating protein (GAP) for RAC1
           (primarily) and CDC42. The Dbl region of BCR has the
           most RhoGEF activity for Cdc42, and less activity
           towards Rac and Rho. Since BCR possesses both GAP and
           GEF activities, it may function to temporally regulate
           the activity of these GTPases. It also displays
           serine/threonine kinase activity. The BCR protein
           contains multiple domains including an N-terminal kinase
           domain, a RhoGEF domain, a PH domain, a C1 domain, a C2
           domain, and a C-terminal RhoGAP domain. ABR, a related
           smaller protein, is structurally similar to BCR, but
           lacks the N-terminal kinase domain and has GAP activity
           for both Rac and Cdc42. PH domains have diverse
           functions, but in general are involved in targeting
           proteins to the appropriate cellular location or in the
           interaction with a binding partner. They share little
           sequence conservation, but all have a common fold, which
           is electrostatically polarized. Less than 10% of PH
           domains bind phosphoinositide phosphates (PIPs) with
           high affinity and specificity. PH domains are
           distinguished from other PIP-binding domains by their
           specific high-affinity binding to PIPs with two vicinal
           phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
           PtdIns(3,4,5)P3 which results in targeting some PH
           domain proteins to the plasma membrane. A few display
           strong specificity in lipid binding. Any specificity is
           usually determined by loop regions or insertions in the
           N-terminus of the domain, which are not conserved across
           all PH domains. PH domains are found in cellular
           signaling proteins such as serine/threonine kinase,
           tyrosine kinases, regulators of G-proteins, endocytotic
           GTPases, adaptors, as well as cytoskeletal associated
           molecules and in lipid associated enzymes.
          Length = 179

 Score = 30.0 bits (68), Expect = 3.1
 Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 3/35 (8%)

Query: 125 KRDLLKD--LVEMCRGVQHPLRGLFLRNYLLQCTR 157
           +R L+KD  LVE+  G    LR LFL   +L C +
Sbjct: 13  RRQLVKDGFLVELSEGS-RKLRHLFLFTDVLLCAK 46


>gnl|CDD|205044 pfam12725, DUF3810, Protein of unknown function (DUF3810).  This
           family of proteins is functionally uncharacterized. This
           family of proteins is found in bacteria. Proteins in
           this family are typically between 333 and 377 amino
           acids in length. There is a conserved HEXXH sequence
           motif that is characteristic of metallopeptidases. This
           family may therefore belong to an as yet uncharacterized
           family of peptidase enzymes.
          Length = 317

 Score = 29.8 bits (68), Expect = 5.2
 Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 3/35 (8%)

Query: 374 FQKLNIERVEYNTPVSRELMRLLKIFIDQYNNILT 408
            ++L IE  EY+T    EL+ L +  I++ N +  
Sbjct: 84  SERLGIEVEEYST---EELLELTEYLIERLNELRL 115


>gnl|CDD|221232 pfam11802, CENP-K, Centromere-associated protein K.  CENP-K is one
           of seven new CENP-A-nucleosome distal (CAD) centromere
           components (the others being CENP-L, CENP-O, CENP-P,
           CENP-Q, CENP-R and CENP-S) that are identified as
           assembling on the CENP-A nucleosome associated complex,
           NAC. The CENP-A NAC is essential, as disruption of the
           complex causes errors of chromosome alignment and
           segregation that preclude cell survival despite
           continued centromere-derived mitotic checkpoint
           signalling. CENP-K is centromere-associated through its
           interaction with one or more components of the CENP-A
           NAC.
          Length = 273

 Score = 29.1 bits (65), Expect = 7.8
 Identities = 19/52 (36%), Positives = 25/52 (48%)

Query: 522 TLPPLVFQAYQLATQFSALREEDEMWSKKCSKIFRFCHQIILSLIKAELAEL 573
           TLP    Q   L  Q  AL  E E W K+  +I      ++L+L K EL +L
Sbjct: 51  TLPESDAQLSLLIMQMKALTAEYEQWQKRTPEIISLNEDVLLTLGKEELQKL 102


>gnl|CDD|218134 pfam04535, DUF588, Domain of unknown function (DUF588).  This
           family of plant proteins contains a domain that may have
           a catalytic activity. It has a conserved arginine and
           aspartate that could form an active site. These proteins
           are predicted to contain 3 or 4 transmembrane helices.
          Length = 150

 Score = 28.4 bits (64), Expect = 8.7
 Identities = 9/25 (36%), Positives = 15/25 (60%)

Query: 547 WSKKCSKIFRFCHQIILSLIKAELA 571
           W K C++  RFC++   S+  + LA
Sbjct: 123 WMKICNQFGRFCNRAAASVALSFLA 147


>gnl|CDD|232935 TIGR00354, polC, DNA polymerase, archaeal type II, large subunit.
           This model represents the large subunit, DP2, of a two
           subunit novel Archaeal replicative DNA polymerase first
           characterized for Pyrococcus furiosus. Structure of DP2
           appears to be organized as a ~950 residue component
           separated from a ~300 residue component by a ~150
           residue intein. The other subunit, DP1, has sequence
           similarity to the eukaryotic DNA polymerase delta small
           subunit [DNA metabolism, DNA replication, recombination,
           and repair].
          Length = 1095

 Score = 29.5 bits (66), Expect = 8.8
 Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 17/83 (20%)

Query: 675 KNSQGEEIRDGKRVLECLKKGVRIASQCMDMSVQVQLFIELLNHYIYYFE-----KKNE- 728
           ++  G E++D  +++E   + V I   C +  V+V  FI+ L    Y  E     K  E 
Sbjct: 744 RDYYGAELKDENQIVELKPQDVIIPESCAEYLVRVANFIDDLLEKFYKMERFYNVKSVED 803

Query: 729 -----------HITVAMLNQLIG 740
                      H +  +L ++IG
Sbjct: 804 LIGHLVIGLAPHTSAGVLGRIIG 826


>gnl|CDD|110632 pfam01645, Glu_synthase, Conserved region in glutamate synthase.
           This family represents a region of the glutamate
           synthase protein. This region is expressed as a separate
           subunit in the glutamate synthase alpha subunit from
           archaebacteria, or part of a large multidomain enzyme in
           other organisms. The aligned region of these proteins
           contains a putative FMN binding site and Fe-S cluster.
          Length = 367

 Score = 29.2 bits (66), Expect = 9.5
 Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 11/87 (12%)

Query: 521 HTLPPLVFQAYQLATQFSALREEDEMWSKKCSKIFRFCHQIIL-------SLIKAELAEL 573
           H   P V +  Q A Q  +    D+ + +  ++         L         I  E  E 
Sbjct: 1   HRNEPEVIKTLQKAVQVESYPSYDK-YREPLNERVPIGALRDLLEFDYAEDPIPIEEVEP 59

Query: 574 PLRL---FLQGAMTIGSIDFENHETIS 597
            L +   F  GAM+ G++  E HE ++
Sbjct: 60  ALEIKTRFCTGAMSYGALSEEAHEALA 86


  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
   0.320    0.135    0.383 

Gapped
Lambda     K      H
   0.267   0.0801    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 40,006,840
Number of extensions: 4003020
Number of successful extensions: 3950
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3942
Number of HSP's successfully gapped: 31
Length of query: 788
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 683
Effective length of database: 6,280,432
Effective search space: 4289535056
Effective search space used: 4289535056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 63 (27.9 bits)