GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Collimonas arenae Ter10

Align Glutamate/aspartate import permease protein GltK (characterized)
to candidate WP_061533332.1 CAter10_RS10280 amino acid ABC transporter permease

Query= SwissProt::P0AER5
         (224 letters)



>NCBI__GCF_001584165.1:WP_061533332.1
          Length = 250

 Score =  131 bits (330), Expect = 1e-35
 Identities = 84/239 (35%), Positives = 126/239 (52%), Gaps = 20/239 (8%)

Query: 4   FDWSSIVPSLPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFA----------PVA 53
           F W  I   LP  ++G ++TLK+ V  VV G   G +L V R++              V 
Sbjct: 5   FQWQIIGEYLPLFIEGTLMTLKVAVICVVTGTFLGLLLGVGRVAEARHGAMKYFLRYAVQ 64

Query: 54  WFAKAYVNVFRSIPL-VMVLLWFYLIVPGFLQNVLGLSPKNDIR---------LISAMVA 103
           W  + YV+ FR  PL V +LL  + ++P  +    GL    DI           +SA++A
Sbjct: 65  WPVRFYVSFFRGTPLFVQILLIHFALMPLLINPNGGLLLSGDIAREVRSQYGAFLSAVLA 124

Query: 104 FSMFEAAYYSEIIRAGIQSISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGI 163
            ++   AY SEI RAGIQSI RGQS A+ +LGMT+ Q+++ ++LPQAFR M+P L    I
Sbjct: 125 ITLNSGAYVSEIFRAGIQSIDRGQSEASRSLGMTYLQTLRKVVLPQAFRRMLPPLGNNAI 184

Query: 164 VLFQDTSLVYVLSLADFFRTASTIGERDGTQVEMILFAGFVYFVISLSASLLVSYLKRR 222
            + +D+SL   + LA+    A T+        E  L    +Y+ I+L  S+ V +L++R
Sbjct: 185 AIVKDSSLASAIGLAELAYAARTVSGAYARYWEPYLTISLIYWGITLLLSVFVQHLEKR 243


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: 144
Number of extensions: 10
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: 224
Length of database: 250
Length adjustment: 23
Effective length of query: 201
Effective length of database: 227
Effective search space:    45627
Effective search space used:    45627
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: 46 (22.3 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