GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gltX in Burkholderia phytofirmans PsJN

Align glutamine-tRNA ligase (EC 6.1.1.18); glutamate-tRNAGln ligase (EC 6.1.1.24) (characterized)
to candidate BPHYT_RS14000 BPHYT_RS14000 glutaminyl-tRNA synthetase

Query= BRENDA::P00962
         (554 letters)



>FitnessBrowser__BFirm:BPHYT_RS14000
          Length = 569

 Score =  626 bits (1614), Expect = 0.0
 Identities = 314/557 (56%), Positives = 399/557 (71%), Gaps = 15/557 (2%)

Query: 9   TNFIRQIIDEDLASGKH-TTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQCNLRFD 67
           +NFIR IID+D  +GK    V TRFPPEPNGYLHIGHAKSICLNFG+A+ Y G C+LRFD
Sbjct: 12  SNFIRNIIDDDNRTGKWGQRVETRFPPEPNGYLHIGHAKSICLNFGVARSYGGVCHLRFD 71

Query: 68  DTNPVKEDIEYVESIKNDVEWLGFHWS----GNVRYSSDYFDQLHAYAIELINKGLAYVD 123
           DTNP KE +EYV+SI + V WLGF W       + Y+SDY+D+L+ +A  LI +G AYVD
Sbjct: 72  DTNPEKESVEYVDSIIDAVRWLGFEWEKDGKAELYYASDYYDKLYEFAELLIERGKAYVD 131

Query: 124 ELTPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASPF 183
             + E++R  RG+ T+ G  S +R+RSV+ENL LF +M+AG F+EG+  LRAKIDM+SP 
Sbjct: 132 SQSAEEMRANRGSATEVGTPSRFRERSVQENLDLFRRMKAGEFQEGEHVLRAKIDMSSPN 191

Query: 184 IVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYDW 243
             MRDPV+YRI+FA H++TG+KWCIYPMYD+THCISDALE ITHSLCTLEF+D+R LYDW
Sbjct: 192 FNMRDPVIYRIRFAHHYRTGDKWCIYPMYDYTHCISDALENITHSLCTLEFEDHRPLYDW 251

Query: 244 VLDNI------TIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGL 297
           +L+ +      T P+ P+Q EFSRLNL Y + SKRKL  LVT+ HV+GWDDPRMPTI G+
Sbjct: 252 ILNELAEAGVFTRPL-PQQIEFSRLNLTYAITSKRKLLQLVTEGHVDGWDDPRMPTIVGV 310

Query: 298 RRRGYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENY 357
           RRRG+T  SI+ FC+RIGVTK D+ I+M+  E  +R+DL+E APR  AV+DPVKL+I+N+
Sbjct: 311 RRRGFTPESIQLFCERIGVTKVDSWIDMSVFEGALRDDLDEKAPRTAAVLDPVKLIIDNF 370

Query: 358 -QGEGEMVTMPNHPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAY 416
            +G  E    P HP+ PEMG R+ P S E+WI+R D+ E   K Y RL  G +VRLR  Y
Sbjct: 371 PEGVTEPCNAPVHPHHPEMGVREFPISRELWIERDDYNETPPKGYFRLFPGNKVRLRYGY 430

Query: 417 VIKAERVEKDAEGNITTIFCTYDADTLS-KDPADGRKVKGVIHWVSAAHALPVEIRLYDR 475
           VI+    +KD +GNI  + C Y  D+ S  + A+  KVKG IHWVSAA A P E+R+YDR
Sbjct: 431 VIECIGADKDEKGNIVAVHCNYFPDSKSGTEGANNYKVKGNIHWVSAAAACPAEVRIYDR 490

Query: 476 LFSVPNPGAAD-DFLSVINPESLVIKQGFAEPSLKDAVAGKAFQFEREGYFCLDSRHSTA 534
           LF  P P A   DFL  +NP+S  +   + EP  ++A+  + +QFER GYF  D   S  
Sbjct: 491 LFKEPQPDAGGRDFLEALNPDSKRVVNAYLEPGAREALPEQRYQFERHGYFVADRVDSKP 550

Query: 535 EKPVFNRTVGLRDTWAK 551
            KPVFNR V LRD+W K
Sbjct: 551 GKPVFNRIVSLRDSWGK 567


Lambda     K      H
   0.319    0.137    0.416 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1032
Number of extensions: 46
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 554
Length of database: 569
Length adjustment: 36
Effective length of query: 518
Effective length of database: 533
Effective search space:   276094
Effective search space used:   276094
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 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory