RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2476
         (151 letters)



>gnl|CDD|218216 pfam04699, P16-Arc, ARP2/3 complex 16 kDa subunit (p16-Arc).  The
           Arp2/3 protein complex has been implicated in the
           control of actin polymerisation. The human complex
           consists of seven subunits which include the actin
           related proteins Arp2 and Arp3, and five others referred
           to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc.
           The precise function of p16-Arc is currently unknown.
           Its structure consists of a single domain containing a
           bundle of seven alpha helices.
          Length = 152

 Score =  182 bits (465), Expect = 2e-60
 Identities = 64/151 (42%), Positives = 91/151 (60%), Gaps = 7/151 (4%)

Query: 8   SAFRKIDVDQYNEDNYKEEE------QGEVPQLGAGVDESEILSLLNQGKHQDALKTVLK 61
           + FRKID+D  +E+++ + +        EV     G DE ++ SLL+ G  + AL+  L 
Sbjct: 1   TDFRKIDIDALDEESFVDLDKEDLPDTPEVSSADIGPDEQQVRSLLSSGDFEGALQLALS 60

Query: 62  NAPLGSKNQHVKDSALNLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKGFEIPSE- 120
           N P G+ +Q VKD AL   L+VL +IKS+ ++  V +LD +  D LMKY+YKG   PS  
Sbjct: 61  NPPYGTDDQAVKDQALQTVLEVLTSIKSADIENAVKSLDSEQQDVLMKYLYKGMATPSGQ 120

Query: 121 KSSSHLLTWHEKVFAIGGLGSIVRVLTDSKR 151
                LL+WHEK+  + GLGSIVRVLTD + 
Sbjct: 121 SQGGVLLSWHEKLVEVAGLGSIVRVLTDRRT 151


>gnl|CDD|237643 PRK14228, PRK14228, camphor resistance protein CrcB; Provisional.
          Length = 122

 Score = 27.8 bits (62), Expect = 1.4
 Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 1/22 (4%)

Query: 127 LTWHEKVFAIGGLGSIVRVLTD 148
           L W   V  IGG+GS++R L D
Sbjct: 5   LVW-IGVMLIGGIGSVLRFLVD 25


>gnl|CDD|131575 TIGR02523, type_IV_pilV, type IV pilus modification protein PilV.
           Pilus systems categorized as type IV pilins differ
           greatly from one another, with some showing greater
           similarty to type II or type III secretion systems than
           to each other. Members of this protein family represent
           the PilV protein of type IV pilus systems as found in
           Pseudomonas aeruginosa PAO1, Pseudomonas syringae
           DC3000, Neisseria meningitidis MC58, Xylella fastidiosa
           9a5c, etc [Cell envelope, Surface structures, Protein
           fate, Protein modification and repair].
          Length = 139

 Score = 27.0 bits (60), Expect = 2.6
 Identities = 9/31 (29%), Positives = 13/31 (41%)

Query: 75  SALNLTLKVLLAIKSSQMDETVSNLDQDLLD 105
               L LK +   +S+      S L  +LLD
Sbjct: 22  GMAALQLKAVRYTRSASTRTIASMLAYNLLD 52


>gnl|CDD|222983 PHA03098, PHA03098, kelch-like protein; Provisional.
          Length = 534

 Score = 27.8 bits (62), Expect = 2.8
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 9/71 (12%)

Query: 87  IKSSQMDETVS-NLDQDLLDTLMKYIYKG-FEIPSEKSSSHLLTWHEKVFAIGGL----- 139
            K++  +  ++ N+D D  + ++KYIY G   I S      L         I  L     
Sbjct: 41  FKNNFKENEINLNIDYDSFNEVIKYIYTGKINITSNNVKDIL--SIANYLIIDFLINLCI 98

Query: 140 GSIVRVLTDSK 150
             I++++ D+ 
Sbjct: 99  NYIIKIIDDNN 109


>gnl|CDD|217837 pfam04003, Utp12, Dip2/Utp12 Family.  This domain is found at the
           C-terminus of proteins containing WD40 repeats. These
           proteins are part of the U3 ribonucleoprotein the yeast
           protein is called Utp12 or DIP2.
          Length = 109

 Score = 26.4 bits (59), Expect = 3.9
 Identities = 12/49 (24%), Positives = 23/49 (46%)

Query: 81  LKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKGFEIPSEKSSSHLLTW 129
           LKVL  I  S ++ T+ +L    +  L++++ +  +         LL W
Sbjct: 7   LKVLEKIPPSDIELTLLSLPFSYVLRLLEFLAERLQAERSPHLEFLLRW 55


>gnl|CDD|215617 PLN03182, PLN03182, xyloglucan 6-xylosyltransferase; Provisional.
          Length = 429

 Score = 27.0 bits (60), Expect = 4.4
 Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 8/39 (20%)

Query: 99  LDQDLLDTLMKYIYKGFEIPSEKSSSHLLT---WHEKVF 134
           +D D L T M      FEIP EK   + L    W E V+
Sbjct: 204 MDSDALFTDM-----TFEIPLEKYEGYNLVIHGWDELVY 237


>gnl|CDD|233013 TIGR00540, TPR_hemY_coli, heme biosynthesis-associated TPR protein.
            Members of this protein family are uncharacterized
           tetratricopeptide repeat (TPR) proteins invariably found
           in heme biosynthesis gene clusters. The absence of any
           invariant residues other than Ala argues against this
           protein serving as an enzyme per se. The gene symbol
           hemY assigned in E. coli is unfortunate in that an
           unrelated protein, protoporphyrinogen oxidase (HemG in
           E. coli) is designated HemY in Bacillus subtilis
           [Unknown function, General].
          Length = 367

 Score = 26.9 bits (60), Expect = 4.8
 Identities = 17/97 (17%), Positives = 34/97 (35%), Gaps = 7/97 (7%)

Query: 6   SSSAFRKIDVDQYNEDNYKEEEQGEVPQLGAGVDESEILSLLNQGKHQDALKTVLKNAPL 65
           + +A +  D +    D Y  E     P     V  +    LL+Q  ++ AL  +      
Sbjct: 106 ARAAQQMGDEE--RRDRYLAEAAELAPNSELAVLLTRAELLLDQRDYEAALAALDSLQAQ 163

Query: 66  GSKNQHVKDSALNLTLKVLLAIKS-SQMDETVSNLDQ 101
             ++  V    L L L+      +   + + +  L +
Sbjct: 164 APRHTAV----LRLALRAYQRSGNWDALLKLLPALRK 196


>gnl|CDD|234015 TIGR02788, VirB11, P-type DNA transfer ATPase VirB11.  The VirB11
           protein is found in the vir locus of Agrobacterium Ti
           plasmids where it is involved in the type IV secretion
           system for DNA transfer. VirB11 is believed to be an
           ATPase. VirB11 is a homolog of the P-like conjugation
           system TrbB protein and the Flp pilus sytem protein
           TadA.
          Length = 308

 Score = 26.5 bits (59), Expect = 5.2
 Identities = 12/59 (20%), Positives = 28/59 (47%), Gaps = 3/59 (5%)

Query: 3   KNTSSSAFRKIDVDQYNEDNYKEE---EQGEVPQLGAGVDESEILSLLNQGKHQDALKT 58
            +T S   RK  +  ++ D+Y+E+   +           ++ ++L LL+ G  ++ L+ 
Sbjct: 81  NDTVSITIRKPSLVDFSLDDYEEKGFFDTVRAQSGTLSDNDEQLLELLDAGDIKEFLRL 139


>gnl|CDD|237098 PRK12421, PRK12421, ATP phosphoribosyltransferase regulatory
           subunit; Provisional.
          Length = 392

 Score = 26.5 bits (59), Expect = 5.9
 Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 1/29 (3%)

Query: 39  DESEILSLLNQGKHQDALKTVLKNAPLGS 67
           +E E+  LL Q K    L  V +N  +GS
Sbjct: 182 EEEELFDLL-QRKALPELAEVCQNLGVGS 209


>gnl|CDD|173711 cd05621, STKc_ROCK2, Catalytic domain of the Protein
           Serine/Threonine Kinase, Rho-associated coiled-coil
           containing protein kinase 2.  Serine/Threonine Kinases
           (STKs), ROCK subfamily, ROCK2 (or ROK-alpha) isoform,
           catalytic (c) domain. STKs catalyze the transfer of the
           gamma-phosphoryl group from ATP to serine/threonine
           residues on protein substrates. The ROCK subfamily is
           part of a larger superfamily that includes the catalytic
           domains of other protein STKs, protein tyrosine kinases,
           RIO kinases, aminoglycoside phosphotransferase, choline
           kinase, and phosphoinositide 3-kinase. ROCK contains an
           N-terminal extension, a catalytic kinase domain, and a
           C-terminal extension, which contains a coiled-coil
           region encompassing a Rho-binding domain (RBD) and a
           pleckstrin homology (PH) domain. ROCK is auto-inhibited
           by the RBD and PH domain interacting with the catalytic
           domain, and is activated via interaction with Rho
           GTPases. ROCK2 was the first identified target of
           activated RhoA, and was found to play a role in stress
           fiber and focal adhesion formation. It is prominently
           expressed in the brain, heart, and skeletal muscles. It
           is implicated in vascular and neurological disorders,
           such as hypertension and vasospasm of the coronary and
           cerebral arteries. ROCK2 is also activated by caspase-2
           cleavage, resulting in thrombin-induced microparticle
           generation in response to cell activation. Mice
           deficient in ROCK2 show intrauterine growth retardation
           and embryonic lethality because of placental
           dysfunction.
          Length = 370

 Score = 26.1 bits (57), Expect = 7.6
 Identities = 11/26 (42%), Positives = 16/26 (61%)

Query: 16  DQYNEDNYKEEEQGEVPQLGAGVDES 41
           DQ+N DN +E     VP+L + +D S
Sbjct: 310 DQWNWDNIRETAAPVVPELSSDIDSS 335


  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
   0.310    0.128    0.344 

Gapped
Lambda     K      H
   0.267   0.0796    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,152,806
Number of extensions: 616763
Number of successful extensions: 437
Number of sequences better than 10.0: 1
Number of HSP's gapped: 435
Number of HSP's successfully gapped: 20
Length of query: 151
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 63
Effective length of database: 7,034,450
Effective search space: 443170350
Effective search space used: 443170350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 54 (24.5 bits)