GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadB in Shewanella amazonensis SB2B

Align Enoyl-CoA hydratase (EC 4.2.1.17); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate 6935814 Sama_0032 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= reanno::SB2B:6935814
         (716 letters)



>lcl|FitnessBrowser__SB2B:6935814 Sama_0032 multifunctional fatty
           acid oxidation complex subunit alpha (RefSeq)
          Length = 716

 Score = 1400 bits (3623), Expect = 0.0
 Identities = 716/716 (100%), Positives = 716/716 (100%)

Query: 1   MIYQSPTIQVELTADKIARLCFNAPGSVNKFDRETLASLNAALDVLKDSDAKAAVLTSGK 60
           MIYQSPTIQVELTADKIARLCFNAPGSVNKFDRETLASLNAALDVLKDSDAKAAVLTSGK
Sbjct: 1   MIYQSPTIQVELTADKIARLCFNAPGSVNKFDRETLASLNAALDVLKDSDAKAAVLTSGK 60

Query: 61  DTFIVGADITEFLALFAEEDAKLMEWIAQANVVFNKLEDLPFPTVSAIKGFALGGGCEAI 120
           DTFIVGADITEFLALFAEEDAKLMEWIAQANVVFNKLEDLPFPTVSAIKGFALGGGCEAI
Sbjct: 61  DTFIVGADITEFLALFAEEDAKLMEWIAQANVVFNKLEDLPFPTVSAIKGFALGGGCEAI 120

Query: 121 LATDFRVADTSAKIGLPETKLGLIPGFGGTVRLPRLIGADNALEWITTGKDQRPEDALKV 180
           LATDFRVADTSAKIGLPETKLGLIPGFGGTVRLPRLIGADNALEWITTGKDQRPEDALKV
Sbjct: 121 LATDFRVADTSAKIGLPETKLGLIPGFGGTVRLPRLIGADNALEWITTGKDQRPEDALKV 180

Query: 181 GAIDAVVAPENLEAAAIQMLNDALAGKLDWQARRARKQAPLTLPKLEAMMSFTTAKGMVY 240
           GAIDAVVAPENLEAAAIQMLNDALAGKLDWQARRARKQAPLTLPKLEAMMSFTTAKGMVY
Sbjct: 181 GAIDAVVAPENLEAAAIQMLNDALAGKLDWQARRARKQAPLTLPKLEAMMSFTTAKGMVY 240

Query: 241 AVAGKHYPAPMAAVSVVEQAAGMSRAEALVVEHNAFIKLAKTDVATALIGIFLNDQLVKG 300
           AVAGKHYPAPMAAVSVVEQAAGMSRAEALVVEHNAFIKLAKTDVATALIGIFLNDQLVKG
Sbjct: 241 AVAGKHYPAPMAAVSVVEQAAGMSRAEALVVEHNAFIKLAKTDVATALIGIFLNDQLVKG 300

Query: 301 KAKKASKLAKDIKHAAVLGAGIMGGGIAYQSASKGTPIVMKDINQAALDLGVNEAAKLLS 360
           KAKKASKLAKDIKHAAVLGAGIMGGGIAYQSASKGTPIVMKDINQAALDLGVNEAAKLLS
Sbjct: 301 KAKKASKLAKDIKHAAVLGAGIMGGGIAYQSASKGTPIVMKDINQAALDLGVNEAAKLLS 360

Query: 361 AQVARGRSTPDKMAKVLNNITPALDYAPLKDVNVVVEAVVENPKVKAMVLADVENVVADD 420
           AQVARGRSTPDKMAKVLNNITPALDYAPLKDVNVVVEAVVENPKVKAMVLADVENVVADD
Sbjct: 361 AQVARGRSTPDKMAKVLNNITPALDYAPLKDVNVVVEAVVENPKVKAMVLADVENVVADD 420

Query: 421 AIIASNTSTISIDLLAKSLKNPARFCGMHFFNPVHKMPLVEVIRGKDTSEETVASVVAYA 480
           AIIASNTSTISIDLLAKSLKNPARFCGMHFFNPVHKMPLVEVIRGKDTSEETVASVVAYA
Sbjct: 421 AIIASNTSTISIDLLAKSLKNPARFCGMHFFNPVHKMPLVEVIRGKDTSEETVASVVAYA 480

Query: 481 SKMGKTPIVVNDCPGFFVNRVLFPYFAGFNGLLADGGDFAAIDKVMEKQFGWPMGPAYLL 540
           SKMGKTPIVVNDCPGFFVNRVLFPYFAGFNGLLADGGDFAAIDKVMEKQFGWPMGPAYLL
Sbjct: 481 SKMGKTPIVVNDCPGFFVNRVLFPYFAGFNGLLADGGDFAAIDKVMEKQFGWPMGPAYLL 540

Query: 541 DVVGLDTGHHAQAVMADGFPDRMGKSDKDAIDVMYEAGRLGQKNGKGFYQYSIDKRGKPK 600
           DVVGLDTGHHAQAVMADGFPDRMGKSDKDAIDVMYEAGRLGQKNGKGFYQYSIDKRGKPK
Sbjct: 541 DVVGLDTGHHAQAVMADGFPDRMGKSDKDAIDVMYEAGRLGQKNGKGFYQYSIDKRGKPK 600

Query: 601 KDVDPASYTMLAEAFGAQKAFEADEIIARTMIPMIIETVRCLEEGIVASPAEADMGLVYG 660
           KDVDPASYTMLAEAFGAQKAFEADEIIARTMIPMIIETVRCLEEGIVASPAEADMGLVYG
Sbjct: 601 KDVDPASYTMLAEAFGAQKAFEADEIIARTMIPMIIETVRCLEEGIVASPAEADMGLVYG 660

Query: 661 LGFPPFRGGVFRYLDTMGVANFVALADKYAHLGGLYQVTDAMRELASNNGSYYPKA 716
           LGFPPFRGGVFRYLDTMGVANFVALADKYAHLGGLYQVTDAMRELASNNGSYYPKA
Sbjct: 661 LGFPPFRGGVFRYLDTMGVANFVALADKYAHLGGLYQVTDAMRELASNNGSYYPKA 716


Lambda     K      H
   0.319    0.135    0.385 

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: 1748
Number of extensions: 67
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: 716
Length of database: 716
Length adjustment: 40
Effective length of query: 676
Effective length of database: 676
Effective search space:   456976
Effective search space used:   456976
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 (21.7 bits)
S2: 55 (25.8 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