Aligments for a candidate for gltX in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Aligments for a candidate for gltX in Pseudomonas fluorescens FW300-N2C3

Align glutamine-tRNA ligase (EC 6.1.1.18); glutamate-tRNAGln ligase (EC 6.1.1.24) (characterized)
to candidate AO356_01010 AO356_01010 glutamine--tRNA ligase

Query= BRENDA::P00962
         (554 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01010 AO356_01010
           glutamine--tRNA ligase
          Length = 566

 Score =  704 bits (1816), Expect = 0.0
 Identities = 343/551 (62%), Positives = 421/551 (76%), Gaps = 6/551 (1%)

Query: 6   ARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQCNLR 65
           A P NF+R II  DL SGKHT + TRFPPEPNGYLHIGHAKSIC+NFG+AQ++ G  +LR
Sbjct: 17  AVPVNFLRPIIQADLDSGKHTQIVTRFPPEPNGYLHIGHAKSICVNFGLAQEFGGVTHLR 76

Query: 66  FDDTNPVKEDIEYVESIKNDVEWLGFHWSGNVRYSSDYFDQLHAYAIELINKGLAYVDEL 125
           FDDTNP KED EY+++I++DV+WLGF WSG VRY+S YFDQLH +A+ELI  G AYV +L
Sbjct: 77  FDDTNPAKEDQEYIDAIESDVKWLGFEWSGEVRYASQYFDQLHDWAVELIKSGNAYVCDL 136

Query: 126 TPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASPFIV 185
           TPEQ +EYRG+L +PGKNSP+R+RSVEENL LF +MRAG F +G   LRAKIDMASP + 
Sbjct: 137 TPEQAKEYRGSLIEPGKNSPFRERSVEENLDLFARMRAGEFPDGARVLRAKIDMASPNMN 196

Query: 186 MRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYDWVL 245
           +RDP++YRI+ A HHQTG+KWCIYP YDFTH  SDA+EGITHS+CTLEF+ +R LY+W L
Sbjct: 197 LRDPIMYRIRHAHHHQTGDKWCIYPNYDFTHGQSDAIEGITHSICTLEFESHRPLYEWFL 256

Query: 246 DNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRRGYTAA 305
           +++ +P  PRQYEFSRLNL YT+ SKRKL  LV +KHV GWDDPRM T+SG RRRGYT A
Sbjct: 257 EHLPVPATPRQYEFSRLNLNYTITSKRKLKQLVDEKHVNGWDDPRMSTLSGFRRRGYTPA 316

Query: 306 SIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENY-QGEGEMV 364
           SIR FC+ IG  + D  ++   LE  IR+DL+ NAPRAM V+ P+K+VI NY Q + E +
Sbjct: 317 SIRNFCEMIGTNRSDGVVDFGMLEFSIRQDLDANAPRAMCVLRPLKVVITNYPQDQVENL 376

Query: 365 TMPNHPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAYVIKAERVE 424
            +P HP K E+G R++PF+ EI+IDR DF EE  K YKRL    EVRLR +YVI+A+   
Sbjct: 377 ELPRHPQKEELGVRKLPFAREIYIDRDDFMEEPPKGYKRLEPNGEVRLRGSYVIRADEAI 436

Query: 425 KDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPVEIRLYDRLFSVPNPGA 484
           KDA+GNI  + C+YD DTL K+P +GRKVKGVIHWV AA ++  E+RLYDRLF  PNP  
Sbjct: 437 KDADGNIVELRCSYDPDTLGKNP-EGRKVKGVIHWVPAAASVECEVRLYDRLFRSPNPEK 495

Query: 485 ADD---FLSVINPESLVIKQGF-AEPSLKDAVAGKAFQFEREGYFCLDSRHSTAEKPVFN 540
           A+D   FL  INP+SL +  G  AEPSL +A     FQFEREGYF  D + S   +PVFN
Sbjct: 496 AEDSASFLDNINPDSLQVLTGCRAEPSLGNAQPEDRFQFEREGYFVADIKDSKPGQPVFN 555

Query: 541 RTVGLRDTWAK 551
           RTV LRD+W +
Sbjct: 556 RTVTLRDSWGQ 566


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: 1038
Number of extensions: 37
Number of successful extensions: 4
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: 566
Length adjustment: 36
Effective length of query: 518
Effective length of database: 530
Effective search space:   274540
Effective search space used:   274540
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)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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