GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpE in Burkholderia phytofirmans PsJN

Align 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase; 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; HHED aldolase; 4-hydroxy-2-ketoheptane-1,7-dioate aldolase; HKHD aldolase; EC 4.1.2.52 (characterized)
to candidate BPHYT_RS28905 BPHYT_RS28905 alpha-dehydro-beta-deoxy-D-glucarate aldolase

Query= SwissProt::Q47098
         (262 letters)



>FitnessBrowser__BFirm:BPHYT_RS28905
          Length = 267

 Score =  299 bits (766), Expect = 4e-86
 Identities = 152/253 (60%), Positives = 183/253 (72%)

Query: 3   NSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAP 62
           N+FK AL  G+PQ GLW  L+ +Y  ELLA AGFDWLLID EHAPN+V++ L QLQA+A 
Sbjct: 6   NNFKRALAEGKPQFGLWAALADAYVTELLATAGFDWLLIDNEHAPNDVRSTLAQLQAVAA 65

Query: 63  YPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSAL 122
           Y S PVVRP  +D   IKQLLD+G QTLL+PM+  A++A +AV ATRYPP GIRGVGSAL
Sbjct: 66  YASHPVVRPVRSDSALIKQLLDIGAQTLLLPMIDTAEQAADAVAATRYPPQGIRGVGSAL 125

Query: 123 ARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGY 182
           ARASRWNRIPDYL  A D++CVLVQ+E+ + M+NL  I  V+GVDGVF GP+DLSA MG 
Sbjct: 126 ARASRWNRIPDYLNTAADELCVLVQVESVQGMENLSAIAAVDGVDGVFFGPSDLSASMGL 185

Query: 183 AGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARA 242
            G P    V+ AI   I  +  +GKA G+L  +  +A  YLE GA FVAVG DT LL+RA
Sbjct: 186 LGKPGDASVREAIRNGIQTVLRAGKAAGVLAPDPAIAADYLEAGATFVAVGTDTGLLSRA 245

Query: 243 AEALAARFGAQAT 255
           A  LAA +   AT
Sbjct: 246 AADLAASYKKTAT 258


Lambda     K      H
   0.317    0.133    0.387 

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: 248
Number of extensions: 3
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: 262
Length of database: 267
Length adjustment: 25
Effective length of query: 237
Effective length of database: 242
Effective search space:    57354
Effective search space used:    57354
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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.

Links

Downloads

Related tools

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