GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16925 in Pseudomonas simiae WCS417

Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate GFF4163 PS417_21325 arabinose ABC transporter permease

Query= uniprot:A0A161GM94
         (322 letters)



>FitnessBrowser__WCS417:GFF4163
          Length = 321

 Score =  542 bits (1397), Expect = e-159
 Identities = 274/305 (89%), Positives = 292/305 (95%)

Query: 18  RRFLDDWVMLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFD 77
           R+FLDDWVMLLAA+ IFVL  L IDNFLSPLNMRGLGLAIST GIAACTML+CLASGHFD
Sbjct: 17  RKFLDDWVMLLAALSIFVLSALFIDNFLSPLNMRGLGLAISTVGIAACTMLFCLASGHFD 76

Query: 78  LSVGSVIACAGVVAAVVMRDTNSVFLGISAALVMGLIVGLINGIVIAKLRVNALITTLAT 137
           LSVGSVIACAGVVA +V+RDT+SV LG+SAAL MGL+VGLINGIVIAKLR+NALI TLAT
Sbjct: 77  LSVGSVIACAGVVAGIVIRDTDSVVLGVSAALAMGLVVGLINGIVIAKLRINALIATLAT 136

Query: 138 MQIVRGLAYIFANGKAVGVSQESFFVFGNGQMFGVPVPILITIVCFLFFGWLLNYTTYGR 197
           MQIVRGLAYIF+NGKAVGV  E FFVFGNGQ+ GVPVPI+IT++CF+FFGWLLNYTTYGR
Sbjct: 137 MQIVRGLAYIFSNGKAVGVMDEGFFVFGNGQLLGVPVPIIITVLCFVFFGWLLNYTTYGR 196

Query: 198 NTMAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTV 257
           NTMAIGGNQEAALLAGVNVDRTKIIIFAVHG+IGALAGVILASRMTSGQPMIGQGFELTV
Sbjct: 197 NTMAIGGNQEAALLAGVNVDRTKIIIFAVHGLIGALAGVILASRMTSGQPMIGQGFELTV 256

Query: 258 ISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVID 317
           ISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAV+ID
Sbjct: 257 ISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVIID 316

Query: 318 RLKQR 322
           R+KQR
Sbjct: 317 RMKQR 321


Lambda     K      H
   0.330    0.144    0.420 

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: 455
Number of extensions: 12
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: 322
Length of database: 321
Length adjustment: 28
Effective length of query: 294
Effective length of database: 293
Effective search space:    86142
Effective search space used:    86142
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: 48 (23.1 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:

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