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= 012390
         (464 letters)

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

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



>pdb|1VJ7|A Chain A, Crystal Structure Of The Bifunctional Catalytic Fragment
           Of Relseq, The RelaSPOT HOMOLOG FROM STREPTOCOCCUS
           EQUISIMILIS.
 pdb|1VJ7|B Chain B, Crystal Structure Of The Bifunctional Catalytic Fragment
           Of Relseq, The RelaSPOT HOMOLOG FROM STREPTOCOCCUS
           EQUISIMILIS
          Length = 393

 Score =  154 bits (389), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 91/233 (39%), Positives = 140/233 (60%), Gaps = 10/233 (4%)

Query: 232 FVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLS 291
           FV KA   A  AH  Q+R SG+PY++H ++ A +LA +  ++  VA G LHD ++D  ++
Sbjct: 27  FVKKALDYATAAHFYQVRKSGEPYIVHPIQVAGILADLHLDAVTVACGFLHDVVEDTDIT 86

Query: 292 YDYIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMA-DARAVLI 350
            D I   FG  V D+V+GV+KL ++   + E   A           M +AM+ D R +L+
Sbjct: 87  LDNIEFDFGKDVRDIVDGVTKLGKVEYKSHEEQLAENH------RKMLMAMSKDIRVILV 140

Query: 351 KLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQH 410
           KLADRLHNM TL  L   K++R ++ET+EI+ PLA+RLGIS  K +LE+L F++LN  + 
Sbjct: 141 KLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGISRIKWELEDLAFRYLNETEF 200

Query: 411 TELSSKLVECF--DEAMVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKM 461
            ++S  + E     EA+V   + K++    ++ + F  + GR K +YSI+ KM
Sbjct: 201 YKISHMMNEKRREREALVDDIVTKIKSYTTEQGL-FGDVYGRPKHIYSIYRKM 252


>pdb|3NR1|A Chain A, A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Plays A
           Role In Starvation Responses
 pdb|3NR1|B Chain B, A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Plays A
           Role In Starvation Responses
          Length = 178

 Score = 61.2 bits (147), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 55/173 (31%), Positives = 82/173 (47%), Gaps = 23/173 (13%)

Query: 240 AERAHRGQMR--ASGDPYLLHCVETAMLL---AAIGANSTVVAAGLLHDTLDDAFLSYDY 294
           A R HR Q R    G PY+ H +  A +L   A I  +  V+ A LLHDT++D   + D 
Sbjct: 14  AARKHRQQRRKDPEGTPYINHPIGVARILTHEAGI-TDIVVLQAALLHDTVEDTDTTLDE 72

Query: 295 IFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMADARAVLIKLAD 354
           +   FGA V  LVE V+    L KL R+           RL       +   A L+KLAD
Sbjct: 73  VELHFGAQVRRLVEEVTDDKTLPKLERK-----------RLQVEQAPHSSPGAKLVKLAD 121

Query: 355 RLHNMMTLDALPLCKRQRFAKETLEIFVPLANRL--GISTWKVQLENLCFKHL 405
           +L+N+  L+    C  + +++  ++ +   A ++  G+     QLE    KHL
Sbjct: 122 KLYNLRDLNR---CTPEGWSEHRVQEYFEWAAQVVKGLQGTNRQLEE-ALKHL 170


>pdb|3NQW|A Chain A, A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Plays A
           Role In Starvation Responses
 pdb|3NQW|B Chain B, A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Plays A
           Role In Starvation Responses
          Length = 179

 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 40/123 (32%), Positives = 58/123 (47%), Gaps = 15/123 (12%)

Query: 244 HRGQMRASGD--PYLLHCVETAMLLA--AIGANSTVVAAGLLHDTLDDAFLSYDYIFRTF 299
           HR Q R      PY+ H +  + +L+  A   +  V+ A LLHD ++D   S++ + + F
Sbjct: 20  HRQQRRKDPQETPYVNHVINVSTILSVEACITDEGVLMAALLHDVVEDTDASFEDVEKLF 79

Query: 300 GAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMADARAVLIKLADRLHNM 359
           G  V  LV  V+    L K  R+           RL     A +  RA LIKLAD+L N+
Sbjct: 80  GPDVCGLVREVTDDKSLEKQERK-----------RLQIENAAKSSCRAKLIKLADKLDNL 128

Query: 360 MTL 362
             L
Sbjct: 129 RDL 131


  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
   0.321    0.134    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,781,110
Number of Sequences: 62578
Number of extensions: 368585
Number of successful extensions: 714
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 707
Number of HSP's gapped (non-prelim): 3
length of query: 464
length of database: 14,973,337
effective HSP length: 102
effective length of query: 362
effective length of database: 8,590,381
effective search space: 3109717922
effective search space used: 3109717922
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: 53 (25.0 bits)