RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13552
         (173 letters)



>gnl|CDD|220394 pfam09773, Meckelin, Meckelin (Transmembrane protein 67).  Members
           of this family are thought to be related to the ciliary
           basal body. Defects result in Meckel syndrome type 3, an
           autosomal recessive disorder characterized by a
           combination of renal cysts and variably associated
           features including developmental anomalies of the
           central nervous system (typically encephalocele),
           hepatic ductal dysplasia and cysts, and polydactyly.
           Joubert syndrome type 6 is also a manifestation of
           certain mutations; it is an autosomal recessive
           congenital malformation of the cerebellar vermis and
           brainstem with abnormalities of axonal decussation
           (crossing in the brain) affecting the corticospinal
           tract and superior cerebellar peduncles. Individuals
           with Joubert syndrome have motor and behavioral
           abnormalities, including an inability to walk due to
           severe clumsiness and 'mirror' movements, and cognitive
           and behavioural disturbances.
          Length = 847

 Score =  142 bits (360), Expect = 7e-40
 Identities = 51/120 (42%), Positives = 72/120 (60%)

Query: 8   PLLKLGVAICTYLVVYLTQWLLLIGVYENFIKNGIHQFVDLCSVANVSVFILTTENYGYY 67
           P L+  +    +L + L Q +L    Y  F+ + + QFVDLCSV+N+S+FIL+   +GYY
Sbjct: 560 PTLRYALVTFVWLAIGLVQVILEFQFYYRFVCHPLQQFVDLCSVSNISIFILSEPQFGYY 619

Query: 68  IHGRSAHGFADTDMESMATQMLREEEDLVGHRGLLPGTEQQTFEMTVPRQLRTYYKRVMA 127
           IHG S HG ADT ME M + + RE + +   RGL   ++ QTFE+ V   LR Y +R  A
Sbjct: 620 IHGESIHGHADTSMEEMQSNLRREAQGMCPVRGLGGQSDCQTFEVFVGPHLRQYLERCYA 679


>gnl|CDD|224347 COG1430, COG1430, Uncharacterized conserved protein [Function
           unknown].
          Length = 126

 Score = 26.5 bits (59), Expect = 4.4
 Identities = 18/67 (26%), Positives = 25/67 (37%), Gaps = 9/67 (13%)

Query: 76  FADTDMESMATQMLREEEDLVGHRGLLPGTEQQTFEMTVPRQLRTYYKRVMAPLSMALKD 135
            ADT  +     M R    L    G+L       F     R++  + K  M PL +   D
Sbjct: 20  VADTFAKRARGLMFRT--SLPDDHGML-------FVFPETRRVAFWMKNTMLPLDIIFID 70

Query: 136 LDYQVKD 142
            D +V D
Sbjct: 71  SDGRVVD 77


>gnl|CDD|238671 cd01375, KISc_KIF9_like, Kinesin motor domain, KIF9-like subgroup;
           might play a role in cell shape remodeling. 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 most kinesins, the motor domain is found at
           the N-terminus (N-type). N-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. 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 = 334

 Score = 27.1 bits (60), Expect = 5.1
 Identities = 9/24 (37%), Positives = 12/24 (50%)

Query: 98  HRGLLPGTEQQTFEMTVPRQLRTY 121
            RGL+P   +Q F     R  +TY
Sbjct: 107 DRGLIPRALEQVFREVAMRATKTY 130


>gnl|CDD|215457 PLN02852, PLN02852, ferredoxin-NADP+ reductase.
          Length = 491

 Score = 27.0 bits (60), Expect = 7.0
 Identities = 12/34 (35%), Positives = 14/34 (41%), Gaps = 4/34 (11%)

Query: 71  RSAHGFADTDMESMATQMLREEE----DLVGHRG 100
           R     A TD+   A + LR        LVG RG
Sbjct: 187 RPTDELASTDIAEHALEALRGSSVRKVYLVGRRG 220


>gnl|CDD|180963 PRK07405, PRK07405, RNA polymerase sigma factor SigD; Validated.
          Length = 317

 Score = 26.6 bits (59), Expect = 8.1
 Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 1/32 (3%)

Query: 108 QTFEMTVPRQLRTYYKRVMAPLSMALKDLDYQ 139
           +  E+T P+Q+R Y +R   PLS+ L+  D Q
Sbjct: 192 EELELT-PKQVREYLERARQPLSLDLRVGDNQ 222


  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
   0.324    0.140    0.411 

Gapped
Lambda     K      H
   0.267   0.0658    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,048,524
Number of extensions: 830364
Number of successful extensions: 834
Number of sequences better than 10.0: 1
Number of HSP's gapped: 834
Number of HSP's successfully gapped: 12
Length of query: 173
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 83
Effective length of database: 6,945,742
Effective search space: 576496586
Effective search space used: 576496586
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 55 (25.1 bits)