GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AO353_03045 in Burkholderia phytofirmans PsJN

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

Query= reanno::pseudo3_N2E3:AO353_03045
         (232 letters)



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

 Score =  210 bits (534), Expect = 2e-59
 Identities = 110/214 (51%), Positives = 142/214 (66%), Gaps = 1/214 (0%)

Query: 18  GLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRGTPMLVQLFLIYYG 77
           G+V TL LL +S+  G   ++PL + RVSK+  ++   WLYTYV RGTP+ VQL L Y G
Sbjct: 22  GVVITLWLLVVSIGLGFCLSIPLAVARVSKKKWLSRLVWLYTYVFRGTPLYVQLLLCYTG 81

Query: 78  LAQFEAVRESFLW-PWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEAAKAMGM 136
           L   E +R   L   +      C  LAF +NT AYT EI AG+++ATP GEIEAA+A GM
Sbjct: 82  LYSLEIIRNHELTNAFFRDGMHCTLLAFTLNTCAYTTEIFAGAIKATPYGEIEAARAYGM 141

Query: 137 SRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQYYLPFE 196
           S F +Y+R++LPSALRRALP YSNEVI+ML  T++A   T+ DI   AR VN+  Y  F 
Sbjct: 142 SSFTLYRRVILPSALRRALPYYSNEVILMLHATTVAFTATVPDILKIARDVNSATYQSFN 201

Query: 197 AYITAGVFYLCMTFILVRLFKMAEHRWLGYLAPR 230
           A+  A + YLC++F LV LF+ AE RWL YL P+
Sbjct: 202 AFGIAALLYLCISFALVWLFRRAERRWLAYLRPQ 235


Lambda     K      H
   0.329    0.139    0.427 

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: 176
Number of extensions: 7
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: 232
Length of database: 237
Length adjustment: 23
Effective length of query: 209
Effective length of database: 214
Effective search space:    44726
Effective search space used:    44726
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 (21.8 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, the preprint on GapMind for carbon sources, 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