Alignments for a candidate for aspS2 in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Pseudomonas stutzeri RCH2

Align Aspartate--tRNA(Asp/Asn) ligase; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS; EC 6.1.1.23 (characterized)
to candidate GFF1456 Psest_1493 aspartyl-tRNA synthetase, bacterial type

Query= SwissProt::Q51422
         (591 letters)



>FitnessBrowser__psRCH2:GFF1456
          Length = 591

 Score = 1099 bits (2842), Expect = 0.0
 Identities = 544/591 (92%), Positives = 569/591 (96%)

Query: 1   MMRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAK 60
           MMRSHYCGQLNESLDGQE+TLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFA 
Sbjct: 1   MMRSHYCGQLNESLDGQEITLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAT 60

Query: 61  ADRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVG 120
           AD+VRSE+VVKITGKVRLRP GA NPN+ASG+IEVLGYEL+VLN AETPPFPL+EYSDVG
Sbjct: 61  ADKVRSEYVVKITGKVRLRPAGAVNPNIASGAIEVLGYELDVLNDAETPPFPLNEYSDVG 120

Query: 121 EETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYL 180
           EETRLRYRFIDLRRPEMA KLKLR+RIT+SIRRYLD+NGFLDVETPILGRPTPEGARDYL
Sbjct: 121 EETRLRYRFIDLRRPEMAEKLKLRSRITASIRRYLDENGFLDVETPILGRPTPEGARDYL 180

Query: 181 VPSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETS 240
           VPSRT+ G+FFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETS
Sbjct: 181 VPSRTHAGNFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETS 240

Query: 241 FLDESDIIGITEKMVRQLFKEVLDVEFDEFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300
           FLDE+DII ITE M+R+LFKEVLD+EF EFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD
Sbjct: 241 FLDEADIIDITEGMIRKLFKEVLDLEFGEFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300

Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360
           QL  VEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER
Sbjct: 301 QLNAVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360

Query: 361 AKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDL 420
           AKGVEGLQSPIVKFIPE NLNVILDRVGAVDGDIVFFGADKAKIV +ALGALRIK+GHDL
Sbjct: 361 AKGVEGLQSPIVKFIPEDNLNVILDRVGAVDGDIVFFGADKAKIVSEALGALRIKIGHDL 420

Query: 421 KLLTREWAPMWVVDFPMFEENDDGSLSALHHPFTSPKCTPAELEANPGAALSRAYDMVLN 480
           KLLT +WAP+WVVDFPMFEENDDGSLSALHHPFT+PKCTP ELEANP AALSRAYDMVLN
Sbjct: 421 KLLTCDWAPLWVVDFPMFEENDDGSLSALHHPFTAPKCTPQELEANPAAALSRAYDMVLN 480

Query: 481 GTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDRLV 540
           GTELGGGSIRIH K MQQ VFR+LGIDEAEQEEKFGFLLDALK+GAPPHGGLAFGLDRLV
Sbjct: 481 GTELGGGSIRIHRKEMQQTVFRILGIDEAEQEEKFGFLLDALKFGAPPHGGLAFGLDRLV 540

Query: 541 MLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQPKAE 591
           MLMTGA SIREVIAFPKTQSA DVMTQAPG+VD KALR+LHIRLREQPKAE
Sbjct: 541 MLMTGAQSIREVIAFPKTQSAADVMTQAPGAVDNKALRDLHIRLREQPKAE 591


Lambda     K      H
   0.321    0.140    0.411 

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: 1366
Number of extensions: 36
Number of successful extensions: 1
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: 591
Length of database: 591
Length adjustment: 37
Effective length of query: 554
Effective length of database: 554
Effective search space:   306916
Effective search space used:   306916
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
the source code
instructions for running GapMind on your computer
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