GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__WCS417:GFF4163 PS417_21325 arabinose ABC
           transporter permease
          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 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, 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