GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Lutibaculum baratangense AMV1

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_081718345.1 N177_RS02595 ABC transporter permease

Query= TCDB::Q9HU30
         (231 letters)



>NCBI__GCF_000496075.1:WP_081718345.1
          Length = 248

 Score =  102 bits (254), Expect = 7e-27
 Identities = 70/223 (31%), Positives = 111/223 (49%), Gaps = 2/223 (0%)

Query: 8   FGEQLLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETLW 67
           +G ++L+G W T++L   ++ +G  + L  A  + S    +  L   Y    RG P    
Sbjct: 27  YGFRMLSGFWTTIELVTLSLLIGAAISLPVAAGRLSPNPVIGALAYGYVYFFRGTPLLAQ 86

Query: 68  VLMIYFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIPRGHR 127
             ++Y+G  S   A  D  G        +        L   AY  E+  GA+ ++PR   
Sbjct: 87  TFLVYYGAGS-FRAELDAVGLWTFFRDAWFCAVFTFSLNTSAYQAEILAGAIRTVPRSQI 145

Query: 128 EAGQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQVAS 187
           EAGQALGLS   I  RIVLPQ   VAL   GN  ++++K +A+ S+IT+ ++M + + A 
Sbjct: 146 EAGQALGLSRYVIATRIVLPQALVVALRPYGNEVVLMIKGSAIASIITIYDLMGETRRAF 205

Query: 188 NATKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRGFVRNE 230
           + + + F  Y+ AA +YL L   +      +ERR  R  VR++
Sbjct: 206 SRSFD-FQTYIWAAILYLVLVETLRRLWDVMERRLTRHLVRDD 247


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: 145
Number of extensions: 9
Number of successful extensions: 3
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: 248
Length adjustment: 23
Effective length of query: 208
Effective length of database: 225
Effective search space:    46800
Effective search space used:    46800
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