GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Pseudomonas simiae WCS417

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF4238 PS417_21710 acetylornithine aminotransferase

Query= BRENDA::O30508
         (406 letters)



>FitnessBrowser__WCS417:GFF4238
          Length = 406

 Score =  653 bits (1685), Expect = 0.0
 Identities = 323/405 (79%), Positives = 358/405 (88%)

Query: 1   MSAPHAQVERADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAH 60
           MS   A V+RADFD+ MVPNYAPAAFIPVRGEGSRVWDQ+GRELIDFAGGIAV  LGHAH
Sbjct: 1   MSVEQAPVQRADFDQVMVPNYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAH 60

Query: 61  PALVKALTEQAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLAR 120
           PALV ALTEQA ++WHVSNVFTNEPALRLA KL+DATFAERVF  NSGAEANEAAFKLAR
Sbjct: 61  PALVGALTEQAHKLWHVSNVFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLAR 120

Query: 121 RYANDVYGPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALK 180
           R A D +G +KYEIIAA NSFHGRTLFTVNVGGQ KYSDGFGPK  GITHVPYNDL+ALK
Sbjct: 121 RVAFDRFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALK 180

Query: 181 AAISDKTCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFA 240
           AA+SDKTCAVVLEPIQGEGGVLPA+ AYL+GAR LCD +NALLVFDEVQ+GMGR G LFA
Sbjct: 181 AAVSDKTCAVVLEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFA 240

Query: 241 YMHYGVVPDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALD 300
           Y HYGV PDIL+SAKSLGGGFPI AMLTT  +AKHL VGTHGTTYGGNPLA AVAEA +D
Sbjct: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVID 300

Query: 301 VINTPEVLDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNA 360
           VINTPEVL GV AKH+ FK+RL++IG++YGIF E+RGMGLL+G  L+D +KGKA+DV NA
Sbjct: 301 VINTPEVLAGVNAKHDLFKARLEQIGKQYGIFTEVRGMGLLLGCVLSDAFKGKAKDVFNA 360

Query: 361 AEKEAVMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAKLVR 405
           AEKE +M+LQA PDVVRFAPSLV++DA+I EGL+RFERAV  L +
Sbjct: 361 AEKENLMILQAGPDVVRFAPSLVVEDADIKEGLDRFERAVKALTQ 405


Lambda     K      H
   0.318    0.135    0.394 

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: 593
Number of extensions: 17
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: 406
Length of database: 406
Length adjustment: 31
Effective length of query: 375
Effective length of database: 375
Effective search space:   140625
Effective search space used:   140625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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