RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6972
         (133 letters)



>gnl|CDD|233155 TIGR00860, LIC, Cation transporter family protein.  The
           Ligand-gated Ion Channel (LIC) Family of
           Neurotransmitter Receptors TC 1.A.9)Members of the LIC
           family of ionotropic neurotransmitter receptors are
           found only in vertebrate and invertebrate animals. They
           exhibit receptor specificity for (1)acetylcholine, (2)
           serotonin, (3) glycine, (4) glutamate and (5)
           g-aminobutyric acid (GABA). All of these receptor
           channels are probably hetero- orhomopentameric. The best
           characterized are the nicotinic acetyl-choline receptors
           which are pentameric channels of a2bgd subunit
           composition. All subunits arehomologous. The three
           dimensional structures of the protein complex in both
           the open and closed configurations have been solved at
           0.9 nm resolution.The channel protein complexes of the
           LIC family preferentially transport cations or anions
           depending on the channel (e.g., the acetylcholine
           receptors are cationselective while glycine receptors
           are anion selective) [Transport and binding proteins,
           Cations and iron carrying compounds].
          Length = 459

 Score =  100 bits (250), Expect = 7e-26
 Identities = 44/107 (41%), Positives = 66/107 (61%)

Query: 2   YSCLKVDLIFTRDRAFYFTTVFIPGIILVTSSFITFWLEWNAVPARVMIGVTTMLNFFTT 61
           Y CL    +  R   +Y   ++IP I++V  S+++FWL  +A  ARV +G+TT+L   T 
Sbjct: 227 YPCLTFSFVLRRRPLYYLLQLYIPSILIVILSWVSFWLPADASGARVSLGITTLLTMTTF 286

Query: 62  SNGFRSTLPVVSNLTAMNVWDGVCMCFIYASLLEFVCVNYVGRKRPL 108
           S+G R +LP VS + A++V+  VCM F++ +LLE   VNYV  K P 
Sbjct: 287 SSGVRESLPAVSYVKAIDVYFAVCMAFVFLALLETAFVNYVHHKDPA 333


>gnl|CDD|202474 pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel
           transmembrane region.  This family includes the four
           transmembrane helices that form the ion channel.
          Length = 228

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 25/88 (28%), Positives = 43/88 (48%), Gaps = 2/88 (2%)

Query: 24  IPGIILVTSSFITFWLEWNAVPARVMIGVTTMLNFFTTSNGFRSTLPVVSNLTAMNVWDG 83
           IP +++   S++ FWL  +A P +V +G+TT+L         R +LP  S +  +     
Sbjct: 3   IPCVLISFLSWLVFWLPADAGPEKVTLGITTLLTMTVFLLLIRESLPKTSYVVPLIGKYL 62

Query: 84  VCMCFIYASLLEF-VCV-NYVGRKRPLH 109
           V   F++ + +E+ V V N   R    H
Sbjct: 63  VFTMFVFTASVEYAVVVLNVHHRSPSTH 90


>gnl|CDD|237101 PRK12430, PRK12430, putative bifunctional flagellar biosynthesis
           protein FliO/FliP; Provisional.
          Length = 379

 Score = 26.8 bits (59), Expect = 4.0
 Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 10/59 (16%)

Query: 17  FYFTTVFIPGIILVTSSF----ITFWLEWNAV------PARVMIGVTTMLNFFTTSNGF 65
           F  +  F+P  +L+ +SF    I F L  NA+      P ++++G+   L FF  S  F
Sbjct: 181 FLTSLTFLPAFLLMMTSFTRIVIVFGLLRNALGTPYAPPNQILLGLALFLTFFIMSPTF 239


>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG.  [DNA metabolism,
           DNA replication, recombination, and repair].
          Length = 630

 Score = 26.9 bits (60), Expect = 4.3
 Identities = 8/42 (19%), Positives = 12/42 (28%), Gaps = 2/42 (4%)

Query: 94  LEFVCVNYVGRKRP--LHNVVYRPGENPVTQTFQRNTYHKSM 133
            E +     G KR   L   +   G   +   F    + K  
Sbjct: 39  GEVLSHCIFGFKRRKVLKLRLKDGGYKKLELRFFNRAFLKKK 80


>gnl|CDD|223646 COG0573, PstC, ABC-type phosphate transport system, permease
          component [Inorganic ion transport and metabolism].
          Length = 310

 Score = 26.4 bits (59), Expect = 4.9
 Identities = 10/50 (20%), Positives = 19/50 (38%), Gaps = 3/50 (6%)

Query: 14 DRAFYFTTVFIPGIILVTSSFITFWLEWNAVPARVMIGVTTMLNFFTTSN 63
          ++ F         I+++    I  +L   A+PA    G++    FF    
Sbjct: 18 EKLFKALLFAAAVIVVLALLLILVFLLIEAIPAFQKFGLS---LFFLFGT 64


>gnl|CDD|184658 PRK14401, PRK14401, membrane protein; Provisional.
          Length = 187

 Score = 25.9 bits (57), Expect = 7.2
 Identities = 16/66 (24%), Positives = 21/66 (31%), Gaps = 13/66 (19%)

Query: 19  FTTVFIPGIILVTSSF---------ITFW----LEWNAVPARVMIGVTTMLNFFTTSNGF 65
           F  V  PG  L T +F            W         +P   ++G    L   T S GF
Sbjct: 106 FFLVLAPGTTLGTVAFGLAVAGLYRALLWRQRRKGLYPIPFGAVVGYPVGLLVATRSGGF 165

Query: 66  RSTLPV 71
            + L  
Sbjct: 166 LALLAG 171


>gnl|CDD|129395 TIGR00294, TIGR00294, GTP cyclohydrolase, MptA/FolE2 family.  This
           family includes type I GTP cyclohydrolases involved in
           methanopterin in archaea (MptA) and de novo
           tetrahydrofolate biosynthesis in bacteria (FolE2)
           [Biosynthesis of cofactors, prosthetic groups, and
           carriers, Other].
          Length = 308

 Score = 26.0 bits (57), Expect = 7.3
 Identities = 8/22 (36%), Positives = 11/22 (50%)

Query: 107 PLHNVVYRPGENPVTQTFQRNT 128
            LH ++ RP E  V +T   N 
Sbjct: 226 ELHEILKRPDEKAVVETAHENP 247


>gnl|CDD|238663 cd01367, KISc_KIF2_like, Kinesin motor domain, KIF2-like group.
           KIF2 is a protein expressed in neurons, which has been
           associated with axonal transport and neuron development;
           alternative splice forms have been implicated in
           lysosomal translocation. This catalytic (head) domain
           has ATPase activity and belongs to the larger group of
           P-loop NTPases. Kinesins are microtubule-dependent
           molecular motors that play important roles in
           intracellular transport and in cell division. In this
           subgroup the motor domain is found in the middle
           (M-type) of the protein chain. M-type kinesins are (+)
           end-directed motors, i.e. they transport cargo towards
           the (+) end of the microtubule. Kinesin motor domains
           hydrolyze ATP at a rate of about 80 per second, and move
           along the microtubule at a speed of about 6400 Angstroms
           per second (KIF2 may be slower). To achieve that,
           kinesin head groups work in pairs. Upon replacing ADP
           with ATP, a kinesin motor domain increases its affinity
           for microtubule binding and locks in place. Also, the
           neck linker binds to the motor domain, which repositions
           the other head domain through the coiled-coil domain
           close to a second tubulin dimer, about 80 Angstroms
           along the microtubule. Meanwhile, ATP hydrolysis takes
           place, and when the second head domain binds to the
           microtubule, the first domain again replaces ADP with
           ATP, triggering a conformational change that pulls the
           first domain forward.
          Length = 322

 Score = 25.7 bits (57), Expect = 7.9
 Identities = 11/32 (34%), Positives = 13/32 (40%), Gaps = 4/32 (12%)

Query: 97  VCVNYVGRKRPLHNVVYRPGENPVTQTFQRNT 128
           V V    RKRPL++     GE  V       T
Sbjct: 5   VAV----RKRPLNDKELSKGETDVVSCESNPT 32


  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
   0.330    0.140    0.455 

Gapped
Lambda     K      H
   0.267   0.0824    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,647,553
Number of extensions: 559418
Number of successful extensions: 724
Number of sequences better than 10.0: 1
Number of HSP's gapped: 721
Number of HSP's successfully gapped: 34
Length of query: 133
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 47
Effective length of database: 7,123,158
Effective search space: 334788426
Effective search space used: 334788426
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 53 (24.0 bits)