GapMind for catabolism of small carbon sources

 

Aligments for a candidate for actP in Azospirillum brasilense Sp245

Align Acetate transporter (characterized, see rationale)
to candidate AZOBR_RS02940 AZOBR_RS02940 actetate permease

Query= uniprot:G8AHY6
         (572 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS02940 AZOBR_RS02940 actetate
           permease
          Length = 572

 Score = 1107 bits (2862), Expect = 0.0
 Identities = 572/572 (100%), Positives = 572/572 (100%)

Query: 1   MRSLVNRVGVAAVAAGALIPASVHAAAVEGAVQKQATNFSAIVMFLVFVLATLGITYWAA 60
           MRSLVNRVGVAAVAAGALIPASVHAAAVEGAVQKQATNFSAIVMFLVFVLATLGITYWAA
Sbjct: 1   MRSLVNRVGVAAVAAGALIPASVHAAAVEGAVQKQATNFSAIVMFLVFVLATLGITYWAA 60

Query: 61  RRTKSAKDFYAAGGGITGFQNGLAIAGDYMSAASFLGIAGLVYTSGFDGLIFSVGWLVGW 120
           RRTKSAKDFYAAGGGITGFQNGLAIAGDYMSAASFLGIAGLVYTSGFDGLIFSVGWLVGW
Sbjct: 61  RRTKSAKDFYAAGGGITGFQNGLAIAGDYMSAASFLGIAGLVYTSGFDGLIFSVGWLVGW 120

Query: 121 PIILFLVAERLRNLGKYTFADVASYRFQQTPMRTMAACGSLATVTFYLIAQMVGAGKLIQ 180
           PIILFLVAERLRNLGKYTFADVASYRFQQTPMRTMAACGSLATVTFYLIAQMVGAGKLIQ
Sbjct: 121 PIILFLVAERLRNLGKYTFADVASYRFQQTPMRTMAACGSLATVTFYLIAQMVGAGKLIQ 180

Query: 181 LLFGMDYLWAVVIVGVLMIAYVTFGGMLATTWVQIIKAVLLLSGASFMAFAVLAKFGFSP 240
           LLFGMDYLWAVVIVGVLMIAYVTFGGMLATTWVQIIKAVLLLSGASFMAFAVLAKFGFSP
Sbjct: 181 LLFGMDYLWAVVIVGVLMIAYVTFGGMLATTWVQIIKAVLLLSGASFMAFAVLAKFGFSP 240

Query: 241 EAMFSTAVQVHPKATGIMAPGALITDPVSAISLGMALMFGTAGLPHILMRFFTVSDAKEA 300
           EAMFSTAVQVHPKATGIMAPGALITDPVSAISLGMALMFGTAGLPHILMRFFTVSDAKEA
Sbjct: 241 EAMFSTAVQVHPKATGIMAPGALITDPVSAISLGMALMFGTAGLPHILMRFFTVSDAKEA 300

Query: 301 RKSVFYATGFIGYFYILTFIIGFGAIVLLLAPDATGAYPFLDAAKLAAAGGKPNPSMIIG 360
           RKSVFYATGFIGYFYILTFIIGFGAIVLLLAPDATGAYPFLDAAKLAAAGGKPNPSMIIG
Sbjct: 301 RKSVFYATGFIGYFYILTFIIGFGAIVLLLAPDATGAYPFLDAAKLAAAGGKPNPSMIIG 360

Query: 361 GSNMAAIHTAHAVGGDLFFGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRAS 420
           GSNMAAIHTAHAVGGDLFFGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRAS
Sbjct: 361 GSNMAAIHTAHAVGGDLFFGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRAS 420

Query: 421 EHDEIRVSKITTVIIGIVSIFLGIAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMT 480
           EHDEIRVSKITTVIIGIVSIFLGIAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMT
Sbjct: 421 EHDEIRVSKITTVIIGIVSIFLGIAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMT 480

Query: 481 TRGAVLGGWIGLVSSVSLLIMGPTVWKSVLGNPAALFPYDNPGVFTIPLSFLAIWFFSIT 540
           TRGAVLGGWIGLVSSVSLLIMGPTVWKSVLGNPAALFPYDNPGVFTIPLSFLAIWFFSIT
Sbjct: 481 TRGAVLGGWIGLVSSVSLLIMGPTVWKSVLGNPAALFPYDNPGVFTIPLSFLAIWFFSIT 540

Query: 541 DNSKAAQDEREAYKAQYIRSQTGLGAEGASAH 572
           DNSKAAQDEREAYKAQYIRSQTGLGAEGASAH
Sbjct: 541 DNSKAAQDEREAYKAQYIRSQTGLGAEGASAH 572


Lambda     K      H
   0.327    0.138    0.410 

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: 1344
Number of extensions: 52
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: 572
Length of database: 572
Length adjustment: 36
Effective length of query: 536
Effective length of database: 536
Effective search space:   287296
Effective search space used:   287296
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 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