GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF in Burkholderia phytofirmans PsJN

Align 2-hydroxymuconate semialdehyde hydrolase; HMSH; EC 3.7.1.9; 2-hydroxymuconic semialdehyde hydrolase (uncharacterized)
to candidate BPHYT_RS23610 BPHYT_RS23610 alpha/beta hydrolase

Query= curated2:P19076
         (283 letters)



>FitnessBrowser__BFirm:BPHYT_RS23610
          Length = 331

 Score = 89.0 bits (219), Expect = 1e-22
 Identities = 91/288 (31%), Positives = 133/288 (46%), Gaps = 29/288 (10%)

Query: 4   PQNSPEIGREIIAAGIRTNL--HDSGAGFPLMMIHGSGPGVTAWANWRLVMPELAKSRRV 61
           P + P I RE IA  +  ++     G G P+++  G    +  W      + +LAK   V
Sbjct: 48  PDHKPWI-REQIAHTVNGDIAYFRFGHGTPIVLQTGFRATLAEWD--AAFLTDLAKRHEV 104

Query: 62  IAPDMLGFGYSERPADAQYNRDVWVDHAVGVLDALEIEQADLVGNSFGGGIALALAIRHP 121
           I  D  G G SE  A +   RD+ +D A  ++D L +     VG S GG IA  LA+  P
Sbjct: 105 IVFDNRGIGRSEPAASSFTARDMTLD-AAALIDTLRLSDVTFVGWSMGGAIAQQLALDAP 163

Query: 122 ERVRRLVLM-----GSAGVSFPITEGLDAVWGYNP--SFAEMRRLLDIFAFDRNLVNDEL 174
             VRR+VLM     GS GV  P+T  ++A    N   +F ++ R+L    F  N V+   
Sbjct: 164 LAVRRIVLMSAPAPGSLGV--PVTPDVEATLSGNAGTTFMDVMRVL----FPPNAVDAAQ 217

Query: 175 AELRYQ----ASIRPGFHESFAAMFPAPRQRWVDGLASAEAAIRALPH---ETLVIHGRE 227
              R      AS RP    + +A     +   +   +S EAA  AL +    TL++ G +
Sbjct: 218 RCFRQNMFQPASYRP---PAISATVTEGQSVLLHDWSSDEAAAAALKNVRLATLILTGAD 274

Query: 228 DQIIPLQTSLTLADWIARAQLHVFGQCGHWTQIEHAARFASLVGDFLA 275
           DQ++P Q S  LA  I  AQL V    GH    ++    A+ +  F+A
Sbjct: 275 DQVLPKQNSEALAGQIPHAQLLVVRSAGHAMMYQYPHALAAAINTFIA 322


Lambda     K      H
   0.323    0.137    0.424 

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: 224
Number of extensions: 13
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: 283
Length of database: 331
Length adjustment: 27
Effective length of query: 256
Effective length of database: 304
Effective search space:    77824
Effective search space used:    77824
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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