GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Paraburkholderia bryophila 376MFSha3.1

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate H281DRAFT_01978 H281DRAFT_01978 glutamine--fructose-6-phosphate transaminase

Query= reanno::BFirm:BPHYT_RS02735
         (335 letters)



>FitnessBrowser__Burk376:H281DRAFT_01978
          Length = 338

 Score =  595 bits (1533), Expect = e-175
 Identities = 313/335 (93%), Positives = 324/335 (96%)

Query: 1   MLKEALASAETVAAQLTDTSRVEALAAKLAQQPRHVALTVARGSSDHAASYFASLTMSRL 60
           MLKEALASAETVAAQLTDTSRVEALAA+LAQQPRHVALTVARGSSDHAASYFASLTMSRL
Sbjct: 4   MLKEALASAETVAAQLTDTSRVEALAARLAQQPRHVALTVARGSSDHAASYFASLTMSRL 63

Query: 61  GVPVASLPMSVATLQQAPLQVRDQLALAFSQSGKSPDLVGTMEALRKAGALTVAAVNVSG 120
           GVPVASLPMSVATLQQAPLQVRDQLALAFSQSGKSPDLVGTM+ALR+AGALTVAAVN   
Sbjct: 64  GVPVASLPMSVATLQQAPLQVRDQLALAFSQSGKSPDLVGTMQALREAGALTVAAVNAPA 123

Query: 121 SPLADACEFELPLVAGPELSVAATKSYIAMLSISAQLVAHWQKDAELLAALKTLPEALCT 180
           SPLADACE+ LPLVAGPELSVAATKSYIAMLSISAQLVAHWQ+D +LLAAL  LP+AL T
Sbjct: 124 SPLADACEWHLPLVAGPELSVAATKSYIAMLSISAQLVAHWQRDPDLLAALNALPDALQT 183

Query: 181 AGKLDWSVAVEELRGIERMIVIGRGLGLAIAQEAALKLKETSGIQAEAFSSAEVRHGPME 240
           AGKLDWS AV+ELRGIERMIVIGRGLGLA+AQEAALKLKETSGIQAEAFSSAEVRHGPME
Sbjct: 184 AGKLDWSKAVDELRGIERMIVIGRGLGLAVAQEAALKLKETSGIQAEAFSSAEVRHGPME 243

Query: 241 LIDRDYPLLVFAPRGPEQAGLLQLARDMKARGARVLLAASVDVPEATLPLATTAHAALDP 300
           LIDRDYPLLVFAPRGPEQAGLLQLARDM+ARGARVLLAA  DVPEATLPLATTAHAALDP
Sbjct: 244 LIDRDYPLLVFAPRGPEQAGLLQLARDMQARGARVLLAAPSDVPEATLPLATTAHAALDP 303

Query: 301 IAAILSFYVMAAGLAAARGRNPDAPRHLNKVTETH 335
           IAAILSFYVMAAGLAAARGRNPDAPRHLNK+TETH
Sbjct: 304 IAAILSFYVMAAGLAAARGRNPDAPRHLNKITETH 338


Lambda     K      H
   0.317    0.128    0.352 

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: 551
Number of extensions: 17
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: 335
Length of database: 338
Length adjustment: 28
Effective length of query: 307
Effective length of database: 310
Effective search space:    95170
Effective search space used:    95170
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: 49 (23.5 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