GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natG in Burkholderia phytofirmans PsJN

Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate BPHYT_RS34465 BPHYT_RS34465 glutamate/aspartate ABC transporter permease GltJ

Query= TCDB::Q8YPM8
         (308 letters)



>FitnessBrowser__BFirm:BPHYT_RS34465
          Length = 245

 Score =  108 bits (271), Expect = 1e-28
 Identities = 74/236 (31%), Positives = 116/236 (49%), Gaps = 21/236 (8%)

Query: 74  TYSLALWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLL 133
           TY   L+ GL+N++ +      L  +VG   GI R   +     +   YV +FR  PL++
Sbjct: 21  TYLGWLFSGLLNTVLLTVSAYALALVVGTGFGILRTLPSRPASMLGTAYVSVFRGVPLIV 80

Query: 134 QLLFWYFAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIF----YTG 189
           Q   W+F V   +P       LG             WF   P ++  L   IF    YTG
Sbjct: 81  QFFIWFFVVPELVPT-----ELGD------------WFKNLPPYTQFLSVSIFSLGIYTG 123

Query: 190 AFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNS 249
           + I E VR GIQ++ +GQ++AG +LGL  +   R V+ P   R I+ PLTS++L ++KNS
Sbjct: 124 SRICEQVRAGIQALPRGQFDAGFALGLTRAQTYRYVLLPVTFRTILGPLTSEFLIISKNS 183

Query: 250 SLAIAIGYPDIYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIMNAFNRTVQI 305
           ++A  IG  ++   A    + T +  E  + + L Y++L+  I   MN   R  ++
Sbjct: 184 AVASTIGLLELSGQARQLVDYTAQPYESFICVTLAYMALNFAILHGMNWIRRQTRL 239


Lambda     K      H
   0.328    0.143    0.430 

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: 186
Number of extensions: 11
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: 308
Length of database: 245
Length adjustment: 25
Effective length of query: 283
Effective length of database: 220
Effective search space:    62260
Effective search space used:    62260
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: 47 (22.7 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