GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24010 in Synechococcus elongatus PCC 7942

Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine

Query= uniprot:B2TBJ8
         (250 letters)



>FitnessBrowser__SynE:Synpcc7942_0247
          Length = 377

 Score = 79.3 bits (194), Expect = 1e-19
 Identities = 46/129 (35%), Positives = 73/129 (56%)

Query: 97  YMCAVLSLALCTAGYTAEIIRGGLMAVPVGQIEAGYSIGLSGFALLRRVIGPIALRQCLP 156
           +   +L L   T  +  EIIRGG+++VP GQ EA  ++GL+    L +++ P ALR  +P
Sbjct: 245 FTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIVP 304

Query: 157 AYSTEAVLLVKSTALASLVTVWEVTGVAQQIIQQTYRTTEVFICAALIYLFLNFVIVRLL 216
           + +++ V   K+++LA  V   ++   AQ  + QT R  EVF+   L YL +N VI   +
Sbjct: 305 SLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISAGM 364

Query: 217 GMLETRLSR 225
             L+ RL R
Sbjct: 365 NGLQQRLQR 373



 Score = 36.6 bits (83), Expect = 8e-07
 Identities = 17/64 (26%), Positives = 34/64 (53%)

Query: 13  KQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPLLIQMF 72
           + L+  +  +L +    LIL  ++  +      S +WL  + +R Y+ V R +PLL+Q+ 
Sbjct: 80  RALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLI 139

Query: 73  LVYY 76
           + Y+
Sbjct: 140 VWYF 143


Lambda     K      H
   0.331    0.143    0.431 

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: 226
Number of extensions: 13
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 250
Length of database: 377
Length adjustment: 27
Effective length of query: 223
Effective length of database: 350
Effective search space:    78050
Effective search space used:    78050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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:

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