GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artQ in Cupriavidus basilensis 4G11

Align ABC transporter for L-Arginine, permease component 2 (characterized)
to candidate RR42_RS29650 RR42_RS29650 histidine ABC transporter permease

Query= reanno::BFirm:BPHYT_RS07675
         (229 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS29650 RR42_RS29650 histidine ABC
           transporter permease
          Length = 229

 Score =  384 bits (986), Expect = e-112
 Identities = 195/229 (85%), Positives = 208/229 (90%)

Query: 1   MFLYGFGPVLLAGTIQTIELSVLSLAAAVLLGLAGAAAKLSFNRPLRAIATGYTTLIRSV 60
           MFLYGFGP+LLAGTI+TIELS+LSLA A++LGL GA AKLSFNRPLR +   YTTLIRSV
Sbjct: 1   MFLYGFGPLLLAGTIRTIELSLLSLATAIVLGLLGATAKLSFNRPLRELGRCYTTLIRSV 60

Query: 61  PDLVLMLLLFYSIQIAVNNLTDALNLPQFDIDPFVAGVLTLGFIYGAYFTETFRGAFLAV 120
           PDLVLMLLLFYSIQI +NNLTDA+ LPQFDIDPFVAGVLTLGFIYGAYFTETFRGAFL+V
Sbjct: 61  PDLVLMLLLFYSIQIGINNLTDAVGLPQFDIDPFVAGVLTLGFIYGAYFTETFRGAFLSV 120

Query: 121 PRGQLEAGSAYGMSGARVFTRILFPQMMRFALPGIGNNWQVLVKATALVSIIGLADVVKA 180
           PRGQLEAG+AYGM+G  VF RILFPQMMRFA+PGIGNNWQVLVKATALVSIIGLAD+VKA
Sbjct: 121 PRGQLEAGAAYGMNGTLVFRRILFPQMMRFAIPGIGNNWQVLVKATALVSIIGLADIVKA 180

Query: 181 AQDAGKSTFNMFFFILVAALIYLAITTASNLVLIWLEKRYSIGVRHAEL 229
           AQDAGKSTF MFFFIL AA IYL ITT SNLVL WL K YS GVRHAEL
Sbjct: 181 AQDAGKSTFKMFFFILCAAFIYLVITTFSNLVLAWLAKHYSSGVRHAEL 229


Lambda     K      H
   0.329    0.142    0.411 

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: 266
Number of extensions: 9
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: 229
Length of database: 229
Length adjustment: 23
Effective length of query: 206
Effective length of database: 206
Effective search space:    42436
Effective search space used:    42436
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, 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