Alignments for a candidate for gltX in Burkholderia phytofirmans PsJN

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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis