GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpC in Pseudomonas fluorescens FW300-N2E3

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate AO353_00895 AO353_00895 2-methylcitrate synthase

Query= reanno::pseudo6_N2E2:Pf6N2E2_6062
         (375 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_00895 AO353_00895
           2-methylcitrate synthase
          Length = 375

 Score =  713 bits (1841), Expect = 0.0
 Identities = 350/375 (93%), Positives = 360/375 (96%)

Query: 1   MAEAKVLSGAGLRGQVAGQTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGEL 60
           MAEAKVLSGAGLRGQVAGQTALSTVGQ GAGLTYRGYDVR+LAA A FEEVAY+LLYGEL
Sbjct: 1   MAEAKVLSGAGLRGQVAGQTALSTVGQEGAGLTYRGYDVRELAAQAHFEEVAYMLLYGEL 60

Query: 61  PTQAQLDAYTGKLRQLRDLPQALKEVLERIPADAHPMDVMRTGCSFLGNLEPEQDFSQQH 120
           P +AQL AY  KL +LRDLPQALKEVLERIPADAHPMDVMRTGCSFLGNLEPE DFS+QH
Sbjct: 61  PNKAQLAAYINKLSKLRDLPQALKEVLERIPADAHPMDVMRTGCSFLGNLEPEHDFSEQH 120

Query: 121 DKTDRLLAAFPAIMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHGKKPSELHVKVMNVS 180
           DKTDRLLAAFPAIMCYWYRFSH G+RI CVTDE SIGGHFLHLLH KKPSELHVKVMNVS
Sbjct: 121 DKTDRLLAAFPAIMCYWYRFSHDGKRINCVTDEESIGGHFLHLLHDKKPSELHVKVMNVS 180

Query: 181 LILYAEHEFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQ 240
           LILYAEHEFNASTFTARVCASTLSDLFSC+TAAIGSLRGPLHGGANEAAMEMIERF+SPQ
Sbjct: 181 LILYAEHEFNASTFTARVCASTLSDLFSCVTAAIGSLRGPLHGGANEAAMEMIERFASPQ 240

Query: 241 EAIEGTLGMLARKDKIMGFGHAIYKDNDPRNEVIKGWSKKLADEVGDTVLFPVSEAIDKT 300
           EAI+GTL MLARKDKIMGFGHAIYKDNDPRNEVIKGWSKKL+DEVGDTVLFPVSEAIDKT
Sbjct: 241 EAIKGTLDMLARKDKIMGFGHAIYKDNDPRNEVIKGWSKKLSDEVGDTVLFPVSEAIDKT 300

Query: 301 MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQRANNRIIRPSAE 360
           MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQRANNRIIRPSAE
Sbjct: 301 MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQRANNRIIRPSAE 360

Query: 361 YTGVEQRKFVPIEQR 375
           Y GVEQRKFVPIEQR
Sbjct: 361 YVGVEQRKFVPIEQR 375


Lambda     K      H
   0.321    0.135    0.406 

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: 597
Number of extensions: 7
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: 375
Length of database: 375
Length adjustment: 30
Effective length of query: 345
Effective length of database: 345
Effective search space:   119025
Effective search space used:   119025
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 (21.9 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