GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artM in Burkholderia phytofirmans PsJN

Align ABC transporter for L-Arginine, permease component 1 (characterized)
to candidate BPHYT_RS05500 BPHYT_RS05500 histidine/lysine/arginine/ornithine ABC transporter permease HisM

Query= reanno::BFirm:BPHYT_RS07680
         (237 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS05500 BPHYT_RS05500
           histidine/lysine/arginine/ornithine ABC transporter
           permease HisM
          Length = 237

 Score =  370 bits (949), Expect = e-107
 Identities = 174/232 (75%), Positives = 206/232 (88%)

Query: 1   MIDILNQFWRAFLYWDGQRMSGLAVTLWLLVASVGIGFCAAIPLAVARVSKKRWLSTPVR 60
           MI+I+ ++WR +LY DG R++G+ +TLWLLV S+G+GFC +IPLAVARVSKK+WLS  V 
Sbjct: 1   MIEIIQEYWRNYLYTDGYRLTGVVITLWLLVVSIGLGFCLSIPLAVARVSKKKWLSRLVW 60

Query: 61  LYTYVFRGTPLYVQLLLIYTGMYSLEFVRSHQLLDAFFRSGFHCAILAFALNTCAYTTEI 120
           LYTYVFRGTPLYVQLLL YTG+YSLE +R+H+L +AFFR G HC +LAF LNTCAYTTEI
Sbjct: 61  LYTYVFRGTPLYVQLLLCYTGLYSLEIIRNHELTNAFFRDGMHCTLLAFTLNTCAYTTEI 120

Query: 121 FAGAIRSTSHGEVEAARAYGMSWFTMYRRIVIPSALRRALPLYSNEVILMLHATTVAFTA 180
           FAGAI++T +GE+EAARAYGMS FT+YRR+++PSALRRALP YSNEVILMLHATTVAFTA
Sbjct: 121 FAGAIKATPYGEIEAARAYGMSSFTLYRRVILPSALRRALPYYSNEVILMLHATTVAFTA 180

Query: 181 TVPDILKVARDANSATYQSFDAFGLAALIYLVVSFVLVALFRRAERHWLGYL 232
           TVPDILK+ARD NSATYQSF+AFG+AAL+YL +SF LV LFRRAER WL YL
Sbjct: 181 TVPDILKIARDVNSATYQSFNAFGIAALLYLCISFALVWLFRRAERRWLAYL 232


Lambda     K      H
   0.331    0.139    0.437 

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: 307
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: 237
Length of database: 237
Length adjustment: 23
Effective length of query: 214
Effective length of database: 214
Effective search space:    45796
Effective search space used:    45796
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 46 (22.3 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 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