RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17977
         (362 letters)



>gnl|CDD|217325 pfam03028, Dynein_heavy, Dynein heavy chain and region D6 of dynein
           motor.  This family represents the C-terminal region of
           dynein heavy chain. The chain also contains ATPase
           activity and microtubule binding ability and acts as a
           motor for the movement of organelles and vesicles along
           microtubules. Dynein is also involved in cilia and
           flagella movement. The dynein subunit consists of at
           least two heavy chains and a number of intermediate and
           light chains. The 380 kDa motor unit of dynein belongs
           to the AAA class of chaperone-like ATPases. The core of
           the 380 kDa motor unit contains a concatenated chain of
           six AAA modules, of which four correspond to the ATP
           binding sites with P-loop signatures described
           previously, and two are modules in which the P loop has
           been lost in evolution. This C-terminal domain carries
           the D6 region of the dynein motor where the P-loop has
           been lost in evolution but the general structure of a
           potential ATP binding site appears to be retained.
          Length = 706

 Score =  318 bits (818), Expect = e-103
 Identities = 135/386 (34%), Positives = 198/386 (51%), Gaps = 57/386 (14%)

Query: 17  PGIRSNLKRSLATIDEQVFNTHSLEGAWRKMVFGVCFFHAVIQERKKFGPLGWNILYEFN 76
            G+++NL R+L++  ++          +++++F +CFFHAV+QER+KFGPLGWN  YEFN
Sbjct: 233 TGLKANLLRALSSFTQETLEMCKKPAEFKRILFLLCFFHAVVQERRKFGPLGWNKSYEFN 292

Query: 77  DSDLECALGTLKMYC---AQDTIPWEALTYTFGEVNYGGRVTDYWDQRTLKTILLTYFGF 133
           + DL  +L  L  Y    A D +PWE L Y FGE+ YGGR+TD WD+R L+T L  +F  
Sbjct: 293 EGDLRISLDVLDNYLDANAPDKVPWEDLRYLFGEIMYGGRITDDWDRRLLRTYLEEFFTP 352

Query: 134 HTLAPDYVYSASGTYY-CPETEECNTLEMYREFVEELPIIEEPEIFGMHDNANIAFQMKE 192
               P+   +     +  P        E Y +++EELP    PE +G+H NA I F  ++
Sbjct: 353 RLFDPELELAPGDLGFAVPPG---TDYEGYLQYIEELPPESSPEWYGLHPNAEIGFLTQQ 409

Query: 193 TKNVIQTIMEVQPREGGSSEG--KSPDELVLEQCDSVIER---------IKTKIDKDNAH 241
           T+ +I+T++E+QPRE G S G   S +E+V +    ++E+         IK K  ++   
Sbjct: 410 TEKLIRTLLELQPREAGGSGGSGVSREEVVKQVLRDILEKLPKLFPIEEIKLKRTEEIKD 469

Query: 242 P---------------------SLLE-----KGNRTCQVYL----------IVPKLWSAK 265
           P                     SL E     KG  T    L           VP  W+  
Sbjct: 470 PLFRVLFQEIERMNKLLKEIRRSLKELDLGLKGELTMTNDLEDLAKALFKGRVPASWAKL 529

Query: 266 CYPSLKSLGSWIKDLALRIDFIAVWLNH-GPPVSFWISGFFFPQGFMTGCLQTHARRHDI 324
            YPSLK LGSW+ DL  RI  +  W    G P + W+SGFF PQ F+T  +Q+ AR++  
Sbjct: 530 AYPSLKPLGSWVTDLLRRIRQLQDWTEDFGKPKTVWLSGFFNPQSFLTAIMQSVARKNKW 589

Query: 325 AIDTLKIDFQMTNVVLSQEEIELAHR 350
            +D L +   +T     +EE + A R
Sbjct: 590 PLDKLCLQTDVTKK--EKEEFDSAPR 613



 Score = 31.1 bits (71), Expect = 1.1
 Identities = 8/16 (50%), Positives = 14/16 (87%)

Query: 3   KDTSNTTPLVFVLSPG 18
           +++S +TP+ F+LSPG
Sbjct: 112 EESSPSTPIFFILSPG 127


>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
          Length = 3164

 Score = 40.4 bits (94), Expect = 0.002
 Identities = 19/125 (15%), Positives = 30/125 (24%), Gaps = 8/125 (6%)

Query: 11   LVFVLSPGIRSNLKRSLATIDEQVFNTHSLEGAWR-KMVFGVCFFHAVIQERKKFGPLGW 69
             V    P         +       +              F + + HA +      GP   
Sbjct: 2976 FVSSTYPETGCGYADLVEI---DRYPFDYT-LVIACDDAFYLSWEHAAVASVISAGPKEN 3031

Query: 70   NILYEFNDSDLECALGTLKMYCAQ---DTIPWEALTYTFGEVNYGGRVTDYWDQRTLKTI 126
            N    F D D E     LK        +   W         + YG + +   D + +   
Sbjct: 3032 NEEIYFGDKDFEFKTHLLKNILFLNHLNARKWGNNRDLIFTIVYGKKHSLMEDSKVVDKY 3091

Query: 127  LLTYF 131
               Y 
Sbjct: 3092 CRGYG 3096


>gnl|CDD|217845 pfam04016, DUF364, Domain of unknown function (DUF364).  This
           domain of unknown function has a PLP-dependent
           transferase-like fold. Its genomic context suggests that
           it may have a role in anaerobic vitamin B12
           biosynthesis. This domain is often found at the
           C-terminus of proteins containing DUF4213, pfam13938.
          Length = 147

 Score = 28.7 bits (65), Expect = 2.6
 Identities = 13/42 (30%), Positives = 17/42 (40%), Gaps = 5/42 (11%)

Query: 190 MKETKNVIQTIMEVQPREGGSSEGKSPDEL---VLEQCDSVI 228
            K    V   ++E  P      EG  PDE    +L + D VI
Sbjct: 28  RKRGAEVY--VLERNPNLLDGEEGDLPDEAAEELLPEADVVI 67


>gnl|CDD|222680 pfam14323, GxGYxYP, GxGYxY sequence motif in domain of unknown
           function.  This family carries a characteristic sequence
           motif, GxGYxYP, but is of unknown function. Associated
           families are sugar-processing domains.
          Length = 463

 Score = 29.2 bits (66), Expect = 3.3
 Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 3/34 (8%)

Query: 90  YCAQDTIPWEALTYT-FGEVNYGGRVTDYWDQRT 122
           Y  Q  I  + L Y  +G  N  GR+T Y + + 
Sbjct: 352 YLKQPNI--DGLFYLNYGAQNDYGRITWYRNSKP 383


>gnl|CDD|200324 TIGR03781, Bac_Flav_CT_K, Bacteroides conjugative transposon TraK
           protein.  Members of this protein family are designated
           TraK and are found in a proposed transfer region of a
           class of conjugative transposon found in the Bacteroides
           lineage. PSI-BLAST reveals a distant relationship to
           proteins TrbF and VirB8 in Proteobacterial conjugal
           transfer systems [Cellular processes, DNA
           transformation].
          Length = 202

 Score = 28.6 bits (64), Expect = 4.8
 Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 3/29 (10%)

Query: 11  LVFVLSP---GIRSNLKRSLATIDEQVFN 36
           L F LSP    I  N++R+L   D+  FN
Sbjct: 79  LFFTLSPDKKAIEYNIERALYLADKSAFN 107


>gnl|CDD|129888 TIGR00806, rfc, RFC reduced folate carrier.  The Reduced Folate
          Carrier (RFC) Family (TC 2.A.48) Members of the RFC
          family mediate the uptake of folate, reduce folate,
          derivatives of reduced folate and the drug,
          methotrexate. Proteins of the RFC family are so-far
          restricted to animals. RFC proteins possess 12 putative
          transmembrane a-helical spanners (TMSs) and evidence
          for a 12 TMS topology has been published for the human
          RFC. The RFC transporters appear to transport reduced
          folate by an energy-dependent, pH-dependent,
          Na+-independent mechanism. Folate:H+ symport,
          folate:OH- antiport and folate:anion antiport
          mechanisms have been proposed, but the energetic
          mechanism is not well defined [Transport and binding
          proteins, Carbohydrates, organic alcohols, and acids].
          Length = 511

 Score = 28.7 bits (64), Expect = 5.2
 Identities = 7/20 (35%), Positives = 12/20 (60%)

Query: 42 GAWRKMVFGVCFFHAVIQER 61
           +WR +V  +CF+  + Q R
Sbjct: 23 KSWRVLVLYLCFYGFMAQFR 42


>gnl|CDD|217835 pfam03999, MAP65_ASE1, Microtubule associated protein (MAP65/ASE1
           family). 
          Length = 619

 Score = 28.7 bits (64), Expect = 5.6
 Identities = 9/33 (27%), Positives = 20/33 (60%), Gaps = 3/33 (9%)

Query: 218 ELVLEQCDSVIERIKTKIDKDNAHPSLLEKGNR 250
           E +LEQ ++ I+R+K +    +++  +LE   +
Sbjct: 322 EQLLEQHENEIKRLKEEY---SSNKEILELIEK 351


>gnl|CDD|234377 TIGR03866, PQQ_ABC_repeats, PQQ-dependent catabolism-associated
           beta-propeller protein.  Members of this protein family
           consist of seven repeats each of the YVTN family
           beta-propeller repeat (see TIGR02276). Members occur
           invariably as part of a transport operon that is
           associated with PQQ-dependent catabolism of alcohols
           such as phenylethanol.
          Length = 300

 Score = 28.5 bits (64), Expect = 6.0
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 10/64 (15%)

Query: 163 REFVEELPIIEEPEIFGMHDNANIAFQMKETKNVIQTIMEVQPRE-------GGSSEGK- 214
            E +  LP   +PE+F +H N  I +   E   ++ T+++++ R+       G   EG  
Sbjct: 63  GEVLHTLPSGPDPELFALHPNGKILYIANEDDALV-TVIDIETRKVLAEIPVGVEPEGMA 121

Query: 215 -SPD 217
            SPD
Sbjct: 122 VSPD 125


>gnl|CDD|182805 PRK10880, PRK10880, adenine DNA glycosylase; Provisional.
          Length = 350

 Score = 28.1 bits (63), Expect = 8.1
 Identities = 10/20 (50%), Positives = 10/20 (50%)

Query: 289 VWLNHGPPVSFWISGFFFPQ 308
           VWL   PP   W   F FPQ
Sbjct: 244 VWLEQRPPSGLWGGLFCFPQ 263


  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
   0.321    0.137    0.430 

Gapped
Lambda     K      H
   0.267   0.0721    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,729,839
Number of extensions: 1808743
Number of successful extensions: 1384
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1380
Number of HSP's successfully gapped: 18
Length of query: 362
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 264
Effective length of database: 6,590,910
Effective search space: 1740000240
Effective search space used: 1740000240
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 (21.9 bits)
S2: 60 (26.9 bits)