GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gtsD in Pseudomonas putida KT2440

Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate PP_1018 PP_1018 mannose/glucose ABC transporter - ATP binding subunit

Query= TCDB::Q88P35
         (384 letters)



>lcl|FitnessBrowser__Putida:PP_1018 PP_1018 mannose/glucose ABC
           transporter - ATP binding subunit
          Length = 384

 Score =  753 bits (1943), Expect = 0.0
 Identities = 384/384 (100%), Positives = 384/384 (100%)

Query: 1   MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60
           MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG
Sbjct: 1   MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60

Query: 61  AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA 120
           AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA
Sbjct: 61  AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA 120

Query: 121 KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL
Sbjct: 121 KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPP 240
           MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPP
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPP 240

Query: 241 MNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALEGREIILGIRPEQIALGAADGNG 300
           MNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALEGREIILGIRPEQIALGAADGNG
Sbjct: 241 MNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALEGREIILGIRPEQIALGAADGNG 300

Query: 301 LPAIRAEVQVTEPTGPDLLVFVTLNQTKVCCRLAPDVACRVGDTLNLQFDPARVLLFDAA 360
           LPAIRAEVQVTEPTGPDLLVFVTLNQTKVCCRLAPDVACRVGDTLNLQFDPARVLLFDAA
Sbjct: 301 LPAIRAEVQVTEPTGPDLLVFVTLNQTKVCCRLAPDVACRVGDTLNLQFDPARVLLFDAA 360

Query: 361 NGERLHLASTGATAKDNVAHFKGR 384
           NGERLHLASTGATAKDNVAHFKGR
Sbjct: 361 NGERLHLASTGATAKDNVAHFKGR 384


Lambda     K      H
   0.320    0.137    0.391 

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: 656
Number of extensions: 11
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: 384
Length of database: 384
Length adjustment: 30
Effective length of query: 354
Effective length of database: 354
Effective search space:   125316
Effective search space used:   125316
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 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