GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Burkholderia phytofirmans PsJN

Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate BPHYT_RS32510 BPHYT_RS32510 ABC transporter permease

Query= TCDB::Q8YXD0
         (288 letters)



>FitnessBrowser__BFirm:BPHYT_RS32510
          Length = 286

 Score =  149 bits (375), Expect = 9e-41
 Identities = 95/289 (32%), Positives = 159/289 (55%), Gaps = 14/289 (4%)

Query: 1   MDIQTIQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTFGVN 60
           M++  +Q IVNGI VG +  L AVGL++ +G+LR  NFAHG F  LGAY  +    + ++
Sbjct: 1   MNVYLLQ-IVNGIGVGMLYFLLAVGLSIVFGLLRFVNFAHGAFYLLGAYFCYQAMQWSMS 59

Query: 61  IWLSMIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTL-IIISIGLALFLRNGIILIWGGR 119
            W +++V  V    +  + EKL+   +R + A      I++++GLAL ++   ILIWG  
Sbjct: 60  FWTALVVVPVVVGALAWVVEKLI---LRHVYAQQHEFHILVTVGLALVVQECAILIWGPL 116

Query: 120 NQNYNLP-ITPALDIFGVKV-PQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLD 177
             N  +P +   + I+G  V P+ +L V+    +    L ++L+ T++G A+RA ++  +
Sbjct: 117 GDNVAVPDVLNGVVIWGSFVYPKYRLFVIGFTAVLAALLWWVLEGTRLGSAVRAGSESTE 176

Query: 178 LAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGN 237
           +  + GI+V +V    + +     +L G +   I  V P MG   +   F  V++GG+GN
Sbjct: 177 MVSLLGINVLRVFSLVFALGAATAALAGVLAAPIRGVDPFMGIEALSVAFVVVVVGGMGN 236

Query: 238 PYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLI---MILVLLIRPKGL 283
             GA+    ++GIVQ V    + + + +G  L+I   M  VLL+RP GL
Sbjct: 237 FLGALVGGLLVGIVQSV----MSTLWPEGARLMIYVAMAAVLLLRPNGL 281


Lambda     K      H
   0.328    0.144    0.426 

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: 244
Number of extensions: 15
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: 288
Length of database: 286
Length adjustment: 26
Effective length of query: 262
Effective length of database: 260
Effective search space:    68120
Effective search space used:    68120
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: 47 (22.7 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