GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artJ in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for L-Arginine, periplasmic substrate-binding component (characterized)
to candidate H281DRAFT_06484 H281DRAFT_06484 amino acid ABC transporter substrate-binding protein, PAAT family

Query= reanno::BFirm:BPHYT_RS07735
         (264 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_06484 H281DRAFT_06484 amino
           acid ABC transporter substrate-binding protein, PAAT
           family
          Length = 266

 Score =  503 bits (1294), Expect = e-147
 Identities = 255/266 (95%), Positives = 260/266 (97%), Gaps = 2/266 (0%)

Query: 1   MKMNWRNIAALALFAAASAT--AGTAAAADIKEVHFGVEASYAPFESKSPSGELQGFDID 58
           MKMNWRN AALALFA A+AT  AG+AAAADIKEV FGVEASYAPFESKSPSGELQGFDID
Sbjct: 1   MKMNWRNTAALALFATATATVTAGSAAAADIKEVRFGVEASYAPFESKSPSGELQGFDID 60

Query: 59  VGNAVCAKLKAKCVWVENSFDGLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPN 118
           VGNAVCAKLKAKCVWVENSFDGLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPN
Sbjct: 61  VGNAVCAKLKAKCVWVENSFDGLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPN 120

Query: 119 QMIAKKGSGLLPTPASLKGKHVGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLAS 178
           QMIAKKGSGLLPTPASLKGKHVGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLAS
Sbjct: 121 QMIAKKGSGLLPTPASLKGKHVGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLAS 180

Query: 179 GRLDAAFQDAEAASKGFLKKPQGAGFEFAGPAVTDEKLLGAGVGFGVRKGDKALKDALNQ 238
           GRLDA+FQDAEAASKGFLKKPQGAGFEFAGPAV+DEKLLGAGVGFG+RKGD ALKDALNQ
Sbjct: 181 GRLDASFQDAEAASKGFLKKPQGAGFEFAGPAVSDEKLLGAGVGFGIRKGDAALKDALNQ 240

Query: 239 ALKELKADGTIDRFAAKYFDVKVVLK 264
           ALKELKADGTIDRFAAKYFDVKVVLK
Sbjct: 241 ALKELKADGTIDRFAAKYFDVKVVLK 266


Lambda     K      H
   0.317    0.133    0.383 

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: 375
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: 264
Length of database: 266
Length adjustment: 25
Effective length of query: 239
Effective length of database: 241
Effective search space:    57599
Effective search space used:    57599
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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