BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= psy8417
         (326 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

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



>pdb|2FV2|A Chain A, Crystal Structure Analysis Of Human Rcd-1 Conserved Region
 pdb|2FV2|B Chain B, Crystal Structure Analysis Of Human Rcd-1 Conserved Region
 pdb|2FV2|C Chain C, Crystal Structure Analysis Of Human Rcd-1 Conserved Region
 pdb|2FV2|D Chain D, Crystal Structure Analysis Of Human Rcd-1 Conserved Region
          Length = 268

 Score =  490 bits (1262), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 235/267 (88%), Positives = 250/267 (93%)

Query: 43  EREKIYQWILELSIPETRENALLELSKKREVVPDLAPMLWHSFGTIAALLQEIINIYPTI 102
           +REKIYQWI ELS PETRENALLELSKKRE VPDLAPMLWHSFGTIAALLQEI+NIYP+I
Sbjct: 1   DREKIYQWINELSSPETRENALLELSKKRESVPDLAPMLWHSFGTIAALLQEIVNIYPSI 60

Query: 103 NPATLTAHQSNRVCNALALLQCVASHQETRSLFLAAHIPLFLYPFLHTTSKTRPFEYLRL 162
           NP TLTAHQSNRVCNALALLQCVASH ETRS FLAAHIPLFLYPFLHT SKTRPFEYLRL
Sbjct: 61  NPPTLTAHQSNRVCNALALLQCVASHPETRSAFLAAHIPLFLYPFLHTVSKTRPFEYLRL 120

Query: 163 TSLGVIGALVKTDEQEVITFLLTTEIIPLCLRIMESGSELSKTVATFILQKILLDDSGLS 222
           TSLGVIGALVKTDEQEVI FLLTTEIIPLCLRIMESGSELSKTVATFILQKILLDD+GL+
Sbjct: 121 TSLGVIGALVKTDEQEVINFLLTTEIIPLCLRIMESGSELSKTVATFILQKILLDDTGLA 180

Query: 223 YICQTYDRFSHVAMILGKMVISLEKDQSSRLLKHVVRCYLRLSDNARAREALRQCLPDQL 282
           YICQTY+RFSHVAMILGKMV+ L K+ S+RLLKHVVRCYLRLSDN RAREALRQCLPDQL
Sbjct: 181 YICQTYERFSHVAMILGKMVLQLSKEPSARLLKHVVRCYLRLSDNPRAREALRQCLPDQL 240

Query: 283 RDSTFSVCLNDDKSTKNWLAQLIKNLE 309
           +D+TF+  L DD +TK WLAQL+KNL+
Sbjct: 241 KDTTFAQVLKDDTTTKRWLAQLVKNLQ 267


>pdb|1J8Y|F Chain F, Signal Recognition Particle Conserved Gtpase Domain From
           A. Ambivalens T112a Mutant
          Length = 297

 Score = 32.0 bits (71), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 3/43 (6%)

Query: 67  LSKKREVV-PDLAPMLWHSFGTIAALLQEIINIYPTINPATLT 108
           LS+K E++  D A    H +G  AALL+E+ NIY  I P  +T
Sbjct: 177 LSEKMEIIIVDTAGR--HGYGEEAALLEEMKNIYEAIKPDEVT 217


>pdb|1J8M|F Chain F, Signal Recognition Particle Conserved Gtpase Domain From
           A. Ambivalens
          Length = 297

 Score = 32.0 bits (71), Expect = 0.50,   Method: Compositional matrix adjust.
 Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 3/43 (6%)

Query: 67  LSKKREVV-PDLAPMLWHSFGTIAALLQEIINIYPTINPATLT 108
           LS+K E++  D A    H +G  AALL+E+ NIY  I P  +T
Sbjct: 177 LSEKMEIIIVDTAGR--HGYGEEAALLEEMKNIYEAIKPDEVT 217


>pdb|2V95|A Chain A, Struture Of Corticosteroid-Binding Globulin In Complex
           With Cortisol
          Length = 371

 Score = 29.6 bits (65), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 5/68 (7%)

Query: 162 LTSLGVIGALVKTDEQEVITFLLTTEIIPLCLRIMESGSELSKTVATFILQKILLDDSGL 221
           L SLG    L +T E E+     + + +   L+  ++G E++   A F+LQK+ L DS L
Sbjct: 57  LQSLGF--NLTETSEAEIHQ---SFQYLNYLLKQSDTGLEMNMGNAMFLLQKLKLKDSFL 111

Query: 222 SYICQTYD 229
           + + Q Y+
Sbjct: 112 ADVKQYYE 119


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.322    0.136    0.392 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,193,443
Number of Sequences: 62578
Number of extensions: 290050
Number of successful extensions: 640
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 635
Number of HSP's gapped (non-prelim): 8
length of query: 326
length of database: 14,973,337
effective HSP length: 99
effective length of query: 227
effective length of database: 8,778,115
effective search space: 1992632105
effective search space used: 1992632105
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)