GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livM in Synechococcus elongatus PCC 7942

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Synpcc7942_2494 Synpcc7942_2494 putative branched-chain amino acid ABC transporter, permease protein

Query= uniprot:A0A165KER0
         (358 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_2494 Synpcc7942_2494 putative
           branched-chain amino acid ABC transporter, permease
           protein
          Length = 307

 Score =  136 bits (343), Expect = 6e-37
 Identities = 100/309 (32%), Positives = 159/309 (51%), Gaps = 44/309 (14%)

Query: 44  LGLNIVVGY-AGLLDLGYVAFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVI 102
           LGL++ +   AG L L   AFYA+G YL A++++  L  +        P     +L + +
Sbjct: 21  LGLSVYLPLMAGQLSLASPAFYALGGYLAAILSTKGLTAS--------PEYSVGALLLEM 72

Query: 103 PVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQI 162
            +AA+ AA    ++G P L+LRG YLAI T+   EI+R+   NL    ++T G  G    
Sbjct: 73  GLAAIAAAVLAFLVGYPVLRLRGIYLAIATIALVEIVRVVALNL----SITGGAVG---- 124

Query: 163 DSVKVFGLDLGKRLEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIRED 222
               +FG+             +S   Y ++ L L++++V  C+RLQ  R G    AIRED
Sbjct: 125 ----IFGIPQ---------PFSSAVGYLWIALPLLLIAVAACWRLQQVRTGLVLAAIRED 171

Query: 223 EIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLG 282
           E+AA A+ +NT   K+LAF +GA    + GA+   F    +P   +   S+  +A V++G
Sbjct: 172 ELAASAIAVNTTRYKVLAFVLGAVLASLVGAVSAHFLNTWNPRQGTFDASITFLAFVLIG 231

Query: 283 GIGHIPGVILGAVLLSALPEVLRYVA-------GPLQAMTDGRLDSAILRQLLIALAMII 335
           G     G +LG ++L+ALPE+LR +        G  + + DGRL       L+  L +++
Sbjct: 232 GSRSAFGPVLGGMVLTALPELLRAIGSVPGLWPGLSRLLQDGRL-------LIFGLLLVL 284

Query: 336 IMLLRPRGL 344
             +  P+GL
Sbjct: 285 GSIYFPQGL 293


Lambda     K      H
   0.328    0.144    0.430 

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: 294
Number of extensions: 17
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: 358
Length of database: 307
Length adjustment: 28
Effective length of query: 330
Effective length of database: 279
Effective search space:    92070
Effective search space used:    92070
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: 49 (23.5 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