GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcdH in Paraburkholderia bryophila 376MFSha3.1

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate H281DRAFT_04737 H281DRAFT_04737 glutaryl-CoA dehydrogenase

Query= BRENDA::Q3JP94
         (395 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_04737 H281DRAFT_04737
           glutaryl-CoA dehydrogenase
          Length = 396

 Score =  728 bits (1880), Expect = 0.0
 Identities = 360/393 (91%), Positives = 373/393 (94%)

Query: 3   AATFHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIG 62
           AA FHW+DPLLLDQQL +DERMVRDAA AYAQ KL PRV EAFRHE TD  IFREMGE+G
Sbjct: 4   AAQFHWEDPLLLDQQLTEDERMVRDAAAAYAQDKLQPRVLEAFRHEKTDIEIFREMGELG 63

Query: 63  LLGPTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEK 122
           LLGPTIPEQYGGPGL+YV+YGLIAREVERVDSGYRSMMSVQSSLVMVPI+EFGS+AQK+K
Sbjct: 64  LLGPTIPEQYGGPGLNYVAYGLIAREVERVDSGYRSMMSVQSSLVMVPIYEFGSEAQKQK 123

Query: 123 YLPKLATGEWIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVW 182
           YLPKLATGEWIGCFGLTEPNHGSDPGSMVTRA+KV GGYSLSGSKMWITNSPIADVFVVW
Sbjct: 124 YLPKLATGEWIGCFGLTEPNHGSDPGSMVTRAKKVDGGYSLSGSKMWITNSPIADVFVVW 183

Query: 183 AKLDEDGRDEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKG 242
           AKL+E+G+D IRGFILEKG KGLSAP IH KVGLRASITGEIVLDE FVPEEN  P V G
Sbjct: 184 AKLEENGKDAIRGFILEKGWKGLSAPTIHSKVGLRASITGEIVLDEVFVPEENRFPEVSG 243

Query: 243 LRGPFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTE 302
           LRGPFTCLNSARYGIAWGALGAAESCWH ARQYVLDRKQFGRPLAANQLIQKKLADMQTE
Sbjct: 244 LRGPFTCLNSARYGIAWGALGAAESCWHTARQYVLDRKQFGRPLAANQLIQKKLADMQTE 303

Query: 303 ITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVAR 362
           ITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFG+AR
Sbjct: 304 ITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGIAR 363

Query: 363 HLVNLEVVNTYEGTHDIHALILGRAQTGIQAFF 395
           HLVNLEVVNTYEGTHDIHALILGRAQTGIQAFF
Sbjct: 364 HLVNLEVVNTYEGTHDIHALILGRAQTGIQAFF 396


Lambda     K      H
   0.320    0.138    0.414 

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: 616
Number of extensions: 15
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: 395
Length of database: 396
Length adjustment: 31
Effective length of query: 364
Effective length of database: 365
Effective search space:   132860
Effective search space used:   132860
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 (21.8 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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