RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy15525
         (112 letters)



>gnl|CDD|190277 pfam02320, UCR_hinge, Ubiquinol-cytochrome C reductase hinge
           protein.  The ubiquinol-cytochrome C reductase complex
           (cytochrome bc1 complex) is a respiratory multienzyme
           complex. This Pfam family represents the 'hinge' protein
           of the complex which is thought to mediate formation of
           the cytochrome c1 and cytochrome c complex.
          Length = 65

 Score = 84.3 bits (209), Expect = 3e-23
 Identities = 33/65 (50%), Positives = 42/65 (64%), Gaps = 1/65 (1%)

Query: 49  VDPQVTLREKCSEA-HCTKYLDKLQQCNDRVNSKQNTTESCYEELIDYAHCVDHCVAHDI 107
           VDP+ TLRE+C     C K   + Q+C +RVNS+ +T E C EEL DY HC+DHCVA  +
Sbjct: 1   VDPKDTLREECKNKEKCVKAKHEYQECVERVNSRSSTKEDCTEELFDYLHCLDHCVAPKL 60

Query: 108 HKYLK 112
              LK
Sbjct: 61  FNKLK 65


>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 = 31.5 bits (72), Expect = 0.054
 Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 4/60 (6%)

Query: 39 PSIKAEEEELVD----PQVTLREKCSEAHCTKYLDKLQQCNDRVNSKQNTTESCYEELID 94
            +   E ++V     P VT+ E  ++   TKY++K     D V  +  T E  Y   + 
Sbjct: 15 KELSKGETDVVSCESNPTVTVHEPKTKVDLTKYIEKHTFRFDYVFDEAVTNEEVYRSTVK 74


>gnl|CDD|226220 COG3696, COG3696, Putative silver efflux pump [Inorganic ion
           transport and metabolism].
          Length = 1027

 Score = 27.6 bits (62), Expect = 1.3
 Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 4/34 (11%)

Query: 9   IFKFPSIKAEEEELNTAQMAQQFFKAIFKFPSIK 42
               P +  +E      +M Q   +AI KFP ++
Sbjct: 564 PLTIPGVSLDE----ALRMLQAIERAIKKFPEVE 593


>gnl|CDD|181070 PRK07658, PRK07658, enoyl-CoA hydratase; Provisional.
          Length = 257

 Score = 26.5 bits (59), Expect = 2.8
 Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 3/38 (7%)

Query: 5  FFKA---IFKFPSIKAEEEELNTAQMAQQFFKAIFKFP 39
          FF A   I +F S+   E+    AQ+ Q  F+ + KF 
Sbjct: 57 FFSAGADIKEFTSVTEAEQATELAQLGQVTFERVEKFS 94


>gnl|CDD|217829 pfam03985, Paf1, Paf1.  Members of this family are components of
           the RNA polymerase II associated Paf1 complex. The Paf1
           complex functions during the elongation phase of
           transcription in conjunction with Spt4-Spt5 and
           Spt16-Pob3i.
          Length = 431

 Score = 26.6 bits (59), Expect = 3.2
 Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 4/49 (8%)

Query: 1   MAHQFFKAIFKFPSIKAEEEELNTAQMAQQFFKAIFKFPSIKAEEEELV 49
           M  QFF+  F   +    +E+      A     AIF    ++ EEEE V
Sbjct: 197 MDQQFFQVRFDGDAAPDGKEKHAQLTQASST--AIFG--PVELEEEEFV 241


>gnl|CDD|219368 pfam07299, FBP, Fibronectin-binding protein (FBP).  This family
          consists of several bacterial fibronectin-binding
          proteins which are thought to be involved in virulence
          in Listeria species.
          Length = 208

 Score = 26.1 bits (58), Expect = 3.6
 Identities = 13/41 (31%), Positives = 25/41 (60%), Gaps = 3/41 (7%)

Query: 33 KAIFKFPSIKAEEEELVDPQVTLREKCSEAHCTKYLDKLQQ 73
          K +  FP +  E++EL+D  +T+R   + A   K+L++L+ 
Sbjct: 40 KILDLFPELSPEQKELLDKLLTVR---TRAEAEKFLEELKP 77


>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
          Length = 1470

 Score = 26.3 bits (58), Expect = 3.8
 Identities = 15/41 (36%), Positives = 19/41 (46%)

Query: 58  KCSEAHCTKYLDKLQQCNDRVNSKQNTTESCYEELIDYAHC 98
           K +E    K+L K +   DRV  K  T E  +E L   A C
Sbjct: 103 KVAEEDNEKFLKKFRNRIDRVGIKLPTVEVRFEHLTVEADC 143


>gnl|CDD|226571 COG4086, COG4086, Predicted secreted protein [Function unknown].
          Length = 299

 Score = 26.3 bits (58), Expect = 4.0
 Identities = 15/58 (25%), Positives = 24/58 (41%)

Query: 39 PSIKAEEEELVDPQVTLREKCSEAHCTKYLDKLQQCNDRVNSKQNTTESCYEELIDYA 96
          P +   +  +  P VTL E  SE    + L ++    D  ++K  T E   E L +  
Sbjct: 25 PEVSLADATVGRPIVTLGEDLSETQKQQLLKEMGVDPDSADTKIVTAEEENEYLGEVT 82


>gnl|CDD|182467 PRK10445, PRK10445, endonuclease VIII; Provisional.
          Length = 263

 Score = 25.4 bits (56), Expect = 7.9
 Identities = 12/42 (28%), Positives = 19/42 (45%)

Query: 13 PSIKAEEEELNTAQMAQQFFKAIFKFPSIKAEEEELVDPQVT 54
          P I+   + L  A   +      F FP +K  E +L+  +VT
Sbjct: 5  PEIRRAADNLEAAIKGKPLTDVWFAFPQLKPYESQLIGQRVT 46


>gnl|CDD|227462 COG5133, COG5133, Uncharacterized conserved protein [Function
          unknown].
          Length = 181

 Score = 25.0 bits (54), Expect = 10.0
 Identities = 9/42 (21%), Positives = 18/42 (42%)

Query: 11 KFPSIKAEEEELNTAQMAQQFFKAIFKFPSIKAEEEELVDPQ 52
          + P     EE+L      ++      +   ++ EE +L+D Q
Sbjct: 16 QLPFRAESEEDLLLGSSLEERHPIESENGVLQNEEPDLIDQQ 57


  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    0.131    0.394 

Gapped
Lambda     K      H
   0.267   0.0710    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,499,919
Number of extensions: 446692
Number of successful extensions: 379
Number of sequences better than 10.0: 1
Number of HSP's gapped: 378
Number of HSP's successfully gapped: 28
Length of query: 112
Length of database: 10,937,602
Length adjustment: 76
Effective length of query: 36
Effective length of database: 7,566,698
Effective search space: 272401128
Effective search space used: 272401128
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: 53 (24.2 bits)