GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Skermanella stibiiresistens SB22

Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate WP_037452835.1 N825_RS14310 amino acid ABC transporter permease

Query= SwissProt::P0AER5
         (224 letters)



>NCBI__GCF_000576635.1:WP_037452835.1
          Length = 303

 Score =  132 bits (332), Expect = 7e-36
 Identities = 80/223 (35%), Positives = 131/223 (58%), Gaps = 6/223 (2%)

Query: 6   WSSIVPSL--PYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVF 63
           WS+I   L  P +++G+ +TL  TV A+VI I+ G ++A+MRLSS   ++ FA  Y+  F
Sbjct: 55  WSAIGEYLFDPTIIEGIKLTLLFTVLAMVISIVAGVVIAMMRLSSNPVLSGFASVYIWFF 114

Query: 64  RSIPL-VMVLLWF--YLIVPGFLQNVLGLSPKNDIRLISA-MVAFSMFEAAYYSEIIRAG 119
           R  PL V ++ WF   L +P      + L     I   +A ++A S+ E AY +EI+R G
Sbjct: 115 RGTPLLVQIIFWFNIQLFIPSIDIGPIHLETNTLISAFTAALLALSLNETAYMAEIVRGG 174

Query: 120 IQSISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLAD 179
           + ++ +GQS AA ALG T +Q++  ++LPQA R ++P +  Q I + + TSLV V++  D
Sbjct: 175 LLAVDKGQSEAATALGYTPFQTLTRVVLPQALRVIIPPVGNQTISMLKTTSLVSVVAAQD 234

Query: 180 FFRTASTIGERDGTQVEMILFAGFVYFVISLSASLLVSYLKRR 222
                  I  ++   +E++L A   Y V++  ASL+  +++RR
Sbjct: 235 LLTRVQNIYAKNFLIIELLLVASIWYLVMTTVASLVQGWIERR 277


Lambda     K      H
   0.330    0.140    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: 180
Number of extensions: 7
Number of successful extensions: 2
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: 224
Length of database: 303
Length adjustment: 24
Effective length of query: 200
Effective length of database: 279
Effective search space:    55800
Effective search space used:    55800
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 (21.9 bits)
S2: 47 (22.7 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