BLASTP 2.2.18 [Mar-02-2008]


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= 0001.0656.p
         (368 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310029|ref|YP_003774121.1| tRNA (5-methylaminomethyl-2-thi...   748   0.0  

>gi|300310029|ref|YP_003774121.1| tRNA
           (5-methylaminomethyl-2-thiouridylate)-methyltransferase
           [Herbaspirillum seropedicae SmR1]
          Length = 368

 Score =  748 bits (1930), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 357/368 (97%), Positives = 365/368 (99%)

Query: 1   MSKKRVVIGMSGGVDSSVSAWLLKQQGYEVIGLFMKNWEDDDDSEYCSTREDWIDAVSVA 60
           MSKKRVVIGMSGGVDSSVSAWLLK+QGYEVIGLFMKNWEDDDDSEYCSTREDWIDAVSVA
Sbjct: 1   MSKKRVVIGMSGGVDSSVSAWLLKEQGYEVIGLFMKNWEDDDDSEYCSTREDWIDAVSVA 60

Query: 61  DVVGVDIEAVNFASEYKDRVFAEFLREYQAGRTPNPDVLCNAEIKFKAFLDHAMKLGADL 120
           DVVGVDIEAVNFASEYKDRVFAEFLREYQAGRTPNPDVLCNAEIKFKAFLDHAMKLGADL
Sbjct: 61  DVVGVDIEAVNFASEYKDRVFAEFLREYQAGRTPNPDVLCNAEIKFKAFLDHAMKLGADL 120

Query: 121 IATGHYARVRQGPQGDFQLLKALDASKDQSYFLHRLNQEQLSRTIFPLGEIHKTEVRKIA 180
           IATGHYARVRQGPQGDFQLLKALDASKDQSYFLHRLNQEQLSRT+FPLGEIHKTEVR+IA
Sbjct: 121 IATGHYARVRQGPQGDFQLLKALDASKDQSYFLHRLNQEQLSRTVFPLGEIHKTEVRRIA 180

Query: 181 EQLQLPNAKKKDSTGICFIGERPFREFLNRYLSYKPGPIKTADGQTVGEHVGLSFYTLGQ 240
           EQLQLPNAKKKDSTGICFIGERPFREFLNRYLSYKPGPIKTADGQTVGEHVGLSFYTLGQ
Sbjct: 181 EQLQLPNAKKKDSTGICFIGERPFREFLNRYLSYKPGPIKTADGQTVGEHVGLSFYTLGQ 240

Query: 241 RKGIGIGGLKAHQNADGHGDAWYVARKDVDNNTLYIVQGHDHPWLLSPTLSAGQVSWVAG 300
           RKGIGIGGLKAHQNADGHGDAWYVARKDV+NNTLYIVQGHDHPWLLSPTLSAGQVSWVAG
Sbjct: 241 RKGIGIGGLKAHQNADGHGDAWYVARKDVENNTLYIVQGHDHPWLLSPTLSAGQVSWVAG 300

Query: 301 HAPQRPALSAKTRYRQADVPCGFADAGSTFSLAFDTPQWAVTPGQSAVLYDGEVCLGGGI 360
           HAPQ  ALSAKTRYRQADVPCGF+DAG++FSLAFDTPQWAVTPGQSAVLYDG+VCLGGGI
Sbjct: 301 HAPQMAALSAKTRYRQADVPCGFSDAGASFSLAFDTPQWAVTPGQSAVLYDGDVCLGGGI 360

Query: 361 IETGALPD 368
           IE GALPD
Sbjct: 361 IENGALPD 368


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.318    0.136    0.418 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 1,227,103
Number of extensions: 51917
Number of successful extensions: 127
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 127
Number of HSP's successfully gapped: 1
Length of query: 368
Length of database: 1,619,870
Length adjustment: 87
Effective length of query: 281
Effective length of database: 1,207,925
Effective search space: 339426925
Effective search space used: 339426925
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 (21.7 bits)
S2: 131 (55.1 bits)