GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00885 in Limnohabitans curvus MWH-C5

Align ABC transporter permease (characterized, see rationale)
to candidate WP_108401790.1 B9Z44_RS04225 branched-chain amino acid ABC transporter permease

Query= uniprot:A0A165KC95
         (309 letters)



>NCBI__GCF_003063475.1:WP_108401790.1
          Length = 309

 Score =  507 bits (1306), Expect = e-148
 Identities = 250/309 (80%), Positives = 283/309 (91%)

Query: 1   MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60
           MD+LLQQ+INGLVLGSMYAL+ALGYTMVYGII LINFAHGEVLMIGAL SWS IG++Q  
Sbjct: 1   MDVLLQQVINGLVLGSMYALVALGYTMVYGIINLINFAHGEVLMIGALCSWSVIGLLQPL 60

Query: 61  MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120
           MP  PGWV+LL++ ++A + AA LN+ IEK+AYRPLR++P+LAPLITAIGMSILLQTLAM
Sbjct: 61  MPDTPGWVLLLISMVLASIAAAALNYAIEKIAYRPLRNAPKLAPLITAIGMSILLQTLAM 120

Query: 121 IIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180
           I+WKPNYKP+PT+LP++PFEIG A ITPTQ++ILG+TAVALA L +LVN T LGRAMRAT
Sbjct: 121 IVWKPNYKPFPTLLPTTPFEIGEAVITPTQLMILGLTAVALAVLSWLVNRTKLGRAMRAT 180

Query: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAV 240
           AENPRVASLMGVKPD+VISATFIIGAVLA IAG+M+A NYGTA H MGFLPGLKAFTAAV
Sbjct: 181 AENPRVASLMGVKPDVVISATFIIGAVLATIAGVMWAMNYGTAHHAMGFLPGLKAFTAAV 240

Query: 241 FGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300
           FGGIGNL GAVVGG+LLGLIE+IGSGY+G LTGG+LGSHYTDI AF+VLII LTLRPSGL
Sbjct: 241 FGGIGNLGGAVVGGLLLGLIESIGSGYLGELTGGVLGSHYTDILAFVVLIITLTLRPSGL 300

Query: 301 LGERVADRA 309
           LGERVADRA
Sbjct: 301 LGERVADRA 309


Lambda     K      H
   0.327    0.142    0.419 

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: 371
Number of extensions: 7
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: 309
Length of database: 309
Length adjustment: 27
Effective length of query: 282
Effective length of database: 282
Effective search space:    79524
Effective search space used:    79524
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