GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aglG' in Synechococcus elongatus PCC 7942

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate Synpcc7942_0471 Synpcc7942_0471 ABC-type sugar transport system permease component-like

Query= uniprot:A8LLL4
         (385 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0471 Synpcc7942_0471 ABC-type
           sugar transport system permease component-like
          Length = 276

 Score =  113 bits (283), Expect = 6e-30
 Identities = 72/238 (30%), Positives = 119/238 (50%), Gaps = 13/238 (5%)

Query: 153 PPEF-----TFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWME 207
           PP+F     T  N+  +  +      + + F N+  V +    + +L  + AAY LA +E
Sbjct: 46  PPQFLPTQPTLDNFRRVWTE----NPLGQYFLNSTWVALLTVGLNLLFCSLAAYPLARLE 101

Query: 208 FPGRALLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRN 267
           F GR  L  LIV  +++P Q+ +IPL  L   +G+   YLG  L          I+LLR 
Sbjct: 102 FKGRQTLFLLIVATILIPFQVVMIPLYVLIINLGLRNTYLG--LVFPYLASAFGIFLLRQ 159

Query: 268 YMVGLPRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLID 327
              G+P+D+ E A++DG  D  ++  +++P + PAL + AIF F+ +W+D L   + L +
Sbjct: 160 AFQGIPKDLEEAARIDGCNDLGVWWNVMIPSARPALITLAIFVFIGSWSDFLWPLIILDE 219

Query: 328 ATGQTTVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385
               T  +   I  L      +W ++A  + +SI     VF ++QR++V    A  VK
Sbjct: 220 PDRYTLPL--GIATLASGFSLDWRLVAAGSVLSILPVFGVFLALQRYIVPSAAASGVK 275


Lambda     K      H
   0.323    0.138    0.419 

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: 286
Number of extensions: 20
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: 385
Length of database: 276
Length adjustment: 28
Effective length of query: 357
Effective length of database: 248
Effective search space:    88536
Effective search space used:    88536
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 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