GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Cupriavidus basilensis 4G11

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate RR42_RS15400 RR42_RS15400 acyl-CoA dehydrogenase

Query= BRENDA::Q3JP94
         (395 letters)



>FitnessBrowser__Cup4G11:RR42_RS15400
          Length = 397

 Score =  694 bits (1791), Expect = 0.0
 Identities = 341/395 (86%), Positives = 366/395 (92%), Gaps = 1/395 (0%)

Query: 2   AAATFHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEI 61
           A A FHW DPLLLD QL+ DERMVRDAA AY Q KLAPRV ++FR+E TD  IFREMGE+
Sbjct: 3   ANAEFHWADPLLLDDQLSADERMVRDAALAYCQDKLAPRVLQSFRNEKTDIEIFREMGEL 62

Query: 62  GLLGPTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKE 121
           GLLGPTIPE+YGGPGL+YV+YGLIAREVERVDSGYRSMMSVQSSLVMVPI EFGS+AQK+
Sbjct: 63  GLLGPTIPEEYGGPGLNYVAYGLIAREVERVDSGYRSMMSVQSSLVMVPIHEFGSEAQKQ 122

Query: 122 KYLPKLATGEWIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVV 181
           KYLPKLATGEWIGCFGLTEPNHGSDPGSM+TRA+KV GGY LSG+KMWITNSPIADVFVV
Sbjct: 123 KYLPKLATGEWIGCFGLTEPNHGSDPGSMITRAKKVAGGYELSGAKMWITNSPIADVFVV 182

Query: 182 WAKL-DEDGRDEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHV 240
           W KL  +DG++ IRGFILEKG KGLSAPAIHGKVGLR SITGEIV+D+ FVPEEN++P V
Sbjct: 183 WGKLVGDDGKEAIRGFILEKGWKGLSAPAIHGKVGLRTSITGEIVMDQVFVPEENLMPGV 242

Query: 241 KGLRGPFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQ 300
            GL+GPFTCLNSARYGIAWGALGAAE CWH ARQY LDRKQFGRPLAANQL+QKKLADMQ
Sbjct: 243 SGLKGPFTCLNSARYGIAWGALGAAEFCWHTARQYTLDRKQFGRPLAANQLVQKKLADMQ 302

Query: 301 TEITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGV 360
           TEITLGLQG LRLGRMKDEGTAAVEITSIMKRNSCGK+LDIAR+ARDMLGGNGISDEFGV
Sbjct: 303 TEITLGLQGCLRLGRMKDEGTAAVEITSIMKRNSCGKSLDIARVARDMLGGNGISDEFGV 362

Query: 361 ARHLVNLEVVNTYEGTHDIHALILGRAQTGIQAFF 395
            RH+VNLEVVNTYEGTHDIHALILGRAQTGIQAFF
Sbjct: 363 IRHVVNLEVVNTYEGTHDIHALILGRAQTGIQAFF 397


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: 595
Number of extensions: 14
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: 395
Length of database: 397
Length adjustment: 31
Effective length of query: 364
Effective length of database: 366
Effective search space:   133224
Effective search space used:   133224
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:

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