GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 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)



>FitnessBrowser__SynE:Synpcc7942_2494
          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:

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