GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artQ in Lactobacillus oryzae SG293

Align Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate WP_034528785.1 LOSG293_RS07410 amino acid ABC transporter permease

Query= TCDB::Q9HU30
         (231 letters)



>NCBI__GCF_000740055.1:WP_034528785.1
          Length = 221

 Score =  106 bits (265), Expect = 3e-28
 Identities = 62/194 (31%), Positives = 111/194 (57%), Gaps = 16/194 (8%)

Query: 11  QLLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETLWVLM 70
           ++LAG  ++  L++ +  + L+LGLL  +A+ S++  L +    + + +RGVP  + + +
Sbjct: 24  KILAGFPISALLTVVSFGLALVLGLLLTLAQLSRFRVLHWPARAFISFMRGVPMLVVLFI 83

Query: 71  IYFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIPRGHREAG 130
           IYFG    +NAL               A  +A  +   A+ +EVFR + ++I +G  EA 
Sbjct: 84  IYFGFE--INAL--------------PAAIVAFTINCSAFVSEVFRSSFIAIDKGQWEAA 127

Query: 131 QALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQVASNAT 190
            +LGL   R+  +++LPQ +R+A+P LGN+ L L K T+L ++IT+ ++   A++ + A 
Sbjct: 128 YSLGLPYRRVVLKVILPQAFRIAIPALGNILLDLFKGTSLAAMITVTDMFMDAKIIAGAN 187

Query: 191 KEPFTFYMTAAAIY 204
            +  T Y+T A IY
Sbjct: 188 LDYMTIYITIAIIY 201


Lambda     K      H
   0.327    0.143    0.431 

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: 117
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: 231
Length of database: 221
Length adjustment: 22
Effective length of query: 209
Effective length of database: 199
Effective search space:    41591
Effective search space used:    41591
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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