GapMind for catabolism of small carbon sources

 

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

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate AO356_26715 AO356_26715 4-aminobutyrate aminotransferase

Query= reanno::Putida:PP_4108
         (416 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 AO356_26715
           4-aminobutyrate aminotransferase
          Length = 430

 Score =  348 bits (894), Expect = e-100
 Identities = 187/413 (45%), Positives = 255/413 (61%), Gaps = 12/413 (2%)

Query: 6   ISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLT 65
           + + +   HP+ +   + AEVWD DG RY+DFVGGIGVLN+GH +P VV A+QAQ  +++
Sbjct: 19  VPRGLVTAHPLVIDRAQGAEVWDVDGARYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKVS 78

Query: 66  HYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAF 125
           H  F    + PYL L+++L + V         L  SGAEA ENA+K+AR  T + A+I+F
Sbjct: 79  HACFQVVAYKPYLDLVKRLCELVGGQQAYKAALFTSGAEAVENAVKIARAHTNRPAVISF 138

Query: 126 DGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVE 185
            GGFHGRTL    L G   PYKQ  G     V+H PYP+A  G + E AL+A++ L + +
Sbjct: 139 RGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGFSSEMALQALNELLATQ 198

Query: 186 LAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAF 245
           +A + VAA I EPVQG+GGFL+  P F QALR   ++ GI++I+DEIQ+GFGRTG+ F F
Sbjct: 199 VAPDRVAAIIIEPVQGDGGFLSAPPEFLQALRTLTEQHGIVLILDEIQTGFGRTGKWFGF 258

Query: 246 PRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQ 305
              GI+PDL+ +AKS+AGG+P+  VVGR  +M A   GGLGGTY GN +SCAAALA +  
Sbjct: 259 QHAGIQPDLVTVAKSLAGGLPISGVVGRAHIMDAPLPGGLGGTYGGNALSCAAALAVIDA 318

Query: 306 MTDENL----ATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAP 361
              E L       GER  Q ++    R       P IG + G G M  IE    D + +P
Sbjct: 319 YEQEQLLERGQVLGERLRQGLLRLQAR------HPRIGDVRGTGFMLAIELIKDDEARSP 372

Query: 362 -AQLA-KVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412
            A+L  ++++ AR   LL++  G  R+++R LAPL  E   ++E L ILE  L
Sbjct: 373 DAELTQQLIDQARVGRLLVIKCGVHRNVLRFLAPLVTEESQIDEALTILEAAL 425


Lambda     K      H
   0.320    0.137    0.402 

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: 514
Number of extensions: 12
Number of successful extensions: 2
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: 416
Length of database: 430
Length adjustment: 32
Effective length of query: 384
Effective length of database: 398
Effective search space:   152832
Effective search space used:   152832
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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