GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artQ in Azospirillum brasilense Sp245

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 AZOBR_RS00680 AZOBR_RS00680 ABC transporter permease

Query= TCDB::Q9HU30
         (231 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS00680 AZOBR_RS00680 ABC
           transporter permease
          Length = 234

 Score =  196 bits (498), Expect = 3e-55
 Identities = 108/224 (48%), Positives = 149/224 (66%), Gaps = 1/224 (0%)

Query: 6   HGFGEQLLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPET 65
           +G+G QLL G  MT+ +S++A  +GL+ G LGA AK S+  AL  +   YTT+VRGVPE 
Sbjct: 10  NGWGGQLLGGAAMTVAVSVSAFVLGLVFGSLGASAKLSRNLALTGVAEVYTTVVRGVPEL 69

Query: 66  LWVLMIYFGTVSGLNALGDLFGKPD-LALSPFAAGTLALGLCFGAYATEVFRGALLSIPR 124
           L + +++FG    + A+G +FG    + L+ F+ G LA+GL  GAY+TEV RGA+ ++P 
Sbjct: 70  LVIYLLFFGGSGAVMAVGRVFGYEGYIELNAFSIGVLAVGLISGAYSTEVIRGAVQAVPH 129

Query: 125 GHREAGQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQ 184
           G  EA +A G+S   I  RI++PQ  R ALPGLGN++ + LKDTAL+S+  L EIMR + 
Sbjct: 130 GQIEAARACGMSRWLILRRILVPQTLRYALPGLGNVWQLTLKDTALISVTALAEIMRVSH 189

Query: 185 VASNATKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRGFVR 228
           VA+ +T++PF FY TAA +YL LT V  VA    ER A RG  R
Sbjct: 190 VAAGSTRQPFLFYTTAAVLYLLLTTVSTVAFERAERYANRGVRR 233


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: 171
Number of extensions: 9
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: 234
Length adjustment: 23
Effective length of query: 208
Effective length of database: 211
Effective search space:    43888
Effective search space used:    43888
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 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 (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 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