GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Mesorhizobium ciceri WSM1271

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate YP_004140220.1 Mesci_1006 polar amino acid ABC transporter inner membrane subunit

Query= reanno::Smeli:SMc02119
         (397 letters)



>NCBI__GCF_000185905.1:YP_004140220.1
          Length = 269

 Score = 90.5 bits (223), Expect = 5e-23
 Identities = 73/223 (32%), Positives = 113/223 (50%), Gaps = 32/223 (14%)

Query: 190 TLLAFVIAVAASVFFARYARK-----RQLATGERLPVLWTVLGLIIGLPLVTFLV----T 240
           T++AFV+A A  +  A          RQ+A           + +I G+P++  L      
Sbjct: 53  TVVAFVLASAIGLGIALMGMSGSRWLRQIAR--------FYVEIIRGVPILVLLFWIAFA 104

Query: 241 GAP--------ITFDIPVAGKFNLTGGSVVGPEFMSLF---LALSFYTAAFIAEIVRAGI 289
           GAP        +T  +  AG F    G ++  +   L+   +AL+   +AFI+E+ RAGI
Sbjct: 105 GAPAFVAAWNALTAPLQSAGLF----GELLVRDVSLLWRAIMALTIGYSAFISEVFRAGI 160

Query: 290 RGVSKGQTEAAHALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADL 349
           + V KGQ EAA ALG+  A   RL+V PQA+R I+PPL + ++ L K+SSL   +G AD+
Sbjct: 161 QAVEKGQIEAAKALGLTRAQRFRLIVFPQAIRTILPPLGNDFVALVKDSSLVSVLGVADI 220

Query: 350 VAVGGTILNQTGQSIEIVSIWLIVYLSLSLATSLFMNWYNARM 392
             +G      + +  E  SI   +YL L++  SL +     R+
Sbjct: 221 TQMGKVYAAGSFRFFETYSITAYIYLILTVGLSLALRALERRL 263


Lambda     K      H
   0.327    0.141    0.412 

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: 243
Number of extensions: 9
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: 397
Length of database: 269
Length adjustment: 28
Effective length of query: 369
Effective length of database: 241
Effective search space:    88929
Effective search space used:    88929
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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