GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lat in Escherichia coli BW25113

Align lysine ε-aminotransferase (EC 2.6.1.36) (characterized)
to candidate 15866 b1748 succinylornithine transaminase, PLP-dependent (NCBI)

Query= metacyc::MONOMER-12388
         (457 letters)



>lcl|FitnessBrowser__Keio:15866 b1748 succinylornithine
           transaminase, PLP-dependent (NCBI)
          Length = 406

 Score =  115 bits (289), Expect = 2e-30
 Identities = 95/327 (29%), Positives = 146/327 (44%), Gaps = 29/327 (8%)

Query: 124 RLFFVDGGALAVENALKAALDWKAQKLGLAEPDTDRLQVLHLERSFHGRSGYTMSLTNTE 183
           R+FF + GA A E ALK A  +   + G     + +  ++  + +FHGR+ +T+S     
Sbjct: 98  RVFFCNSGAEANEAALKLARKFAHDRYG-----SHKSGIVAFKNAFHGRTLFTVSAG--- 149

Query: 184 PSKTARFPKFGWPRISSPALQHPPAEHTGANQEAERRALEAAREAFAAADGMIACFIAEP 243
                     G P  S      P         +    A      A A  D      I EP
Sbjct: 150 ----------GQPAYSQDFAPLPA--------DIRHAAYNDINSASALIDDSTCAVIVEP 191

Query: 244 IQGEGGDNHLSAEFLQAMQRLCHENDALFVLDEVQSGCGITGTAWAYQQLGLQPDLVAFG 303
           IQGEGG    S  FLQ ++ LC+ ++AL + DEVQ+G G TG  +AY   G+ PDL+   
Sbjct: 192 IQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTTA 251

Query: 304 KKTQVCGVMGGGRIDEVPENVFAVSSRISSTWGGNLADMVRATRLLETIERTQVFDTVVQ 363
           K       +G     E    V  V +   +T+GGN      A ++LE I   ++ + V Q
Sbjct: 252 KALGGGFPVGALLATEECARVMTVGTH-GTTYGGNPLASAVAGKVLELINTPEMLNGVKQ 310

Query: 364 RGKYFRDGLEDLAARHPSVVTNARGRGLMCAVDL-PDTRTRNEVLRLMYTEHQVIALPCG 422
           R  +F + L  +  R+  + +  RG GL+    L  D   + + +     +  V+ L  G
Sbjct: 311 RHDWFVERLNTINHRY-GLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVMVLIAG 369

Query: 423 GRSLRFRPALTIAEHEIDQALQALASS 449
           G  +RF PAL ++E E+   L   A++
Sbjct: 370 GNVVRFAPALNVSEEEVTTGLDRFAAA 396


Lambda     K      H
   0.320    0.135    0.403 

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: 360
Number of extensions: 22
Number of successful extensions: 3
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: 457
Length of database: 406
Length adjustment: 32
Effective length of query: 425
Effective length of database: 374
Effective search space:   158950
Effective search space used:   158950
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: 51 (24.3 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 preprint 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