GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proW in Burkholderia phytofirmans PsJN

Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate BPHYT_RS14815 BPHYT_RS14815 methionine ABC transporter permease

Query= SwissProt::P14176
         (354 letters)



>FitnessBrowser__BFirm:BPHYT_RS14815
          Length = 217

 Score = 75.9 bits (185), Expect = 9e-19
 Identities = 61/197 (30%), Positives = 104/197 (52%), Gaps = 21/197 (10%)

Query: 148 TLALVLTALLFCIVIGLPLGIWLARSPRAA--------KIIRPLLDAMQTTPAFVYLVPI 199
           TL +V  + L   ++GLPLG+ L  + R          + +  +++A+++TP  + LV +
Sbjct: 16  TLVMVGISGLVGALVGLPLGVVLYLTDRQGVLQNIAVNRAMGVIVNAVRSTPFIILLVAV 75

Query: 200 V----MLFG--IGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEASRSFGASPRQMLF 253
           +    ++ G  IG    VV   I A P I RL    + +V   LIEA+++ GA+  Q++F
Sbjct: 76  IPFTRLVVGSSIGTAAAVVPLTIAAAPFIARLVETALREVDRGLIEAAQAMGATTSQIVF 135

Query: 254 KVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLR-GIGR-LDMGLATVGGV 311
           KV LP ++P ++AG+  T +  +    +A  I  GGLG + +R G  R L   + TV   
Sbjct: 136 KVLLPESLPGVVAGLTITFVSLVGYSAMAGAIGGGGLGDLGIRYGYQRFLPEVMLTV--- 192

Query: 312 GIVILAIILDRLTQAVG 328
             V++ I+  +L Q+ G
Sbjct: 193 --VVILIVFVQLVQSFG 207


Lambda     K      H
   0.326    0.141    0.435 

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: 188
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: 354
Length of database: 217
Length adjustment: 25
Effective length of query: 329
Effective length of database: 192
Effective search space:    63168
Effective search space used:    63168
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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