GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Limnohabitans curvus MWH-C5

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_108402939.1 B9Z44_RS14300 acyl-CoA dehydrogenase

Query= metacyc::G1G01-166-MONOMER
         (393 letters)



>NCBI__GCF_003063475.1:WP_108402939.1
          Length = 404

 Score =  661 bits (1705), Expect = 0.0
 Identities = 318/387 (82%), Positives = 355/387 (91%)

Query: 6   SFNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLL 65
           +F+W DP LLDQQL+E+ERMVRD+A+ + QDKLAPRVL +FRHEQTD  IFREMGE+GLL
Sbjct: 5   TFHWNDPFLLDQQLSEDERMVRDAAFAYCQDKLAPRVLNSFRHEQTDVEIFREMGELGLL 64

Query: 66  GATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYL 125
           G TIP +YGG GLNYV YGLIAREVER+DSGYRSMMSVQSSLVMVPI+EFGTE Q+QKYL
Sbjct: 65  GPTIPTEYGGPGLNYVAYGLIAREVERVDSGYRSMMSVQSSLVMVPIHEFGTETQRQKYL 124

Query: 126 PKLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAK 185
           P+LA GEWIGCFGLTEP+HGSDP SM +RA+KVDGGY L G+KMWITNSPIADVFVVWAK
Sbjct: 125 PRLAKGEWIGCFGLTEPDHGSDPSSMASRAKKVDGGYMLKGNKMWITNSPIADVFVVWAK 184

Query: 186 DDAGDIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGLKGPF 245
            D G IRGF+LEKGW+GLSAPAIHGKVGLR SITGEIVM++VFVPEEN+FP+VRGLKGPF
Sbjct: 185 TDDGAIRGFILEKGWEGLSAPAIHGKVGLRTSITGEIVMNDVFVPEENMFPEVRGLKGPF 244

Query: 246 TCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLAL 305
           TCLNSARYGI+WGALGAAE C++ +RQY LDR+QFGRPLAANQLIQKKLADM TEI+L +
Sbjct: 245 TCLNSARYGIAWGALGAAEDCFNRSRQYVLDRKQFGRPLAANQLIQKKLADMLTEISLGI 304

Query: 306 QGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNL 365
           Q CLRLGRMKD+G AA  ITSI+KRNSCGK+LDIARMARDM+GGNGISDEFGVARHLVNL
Sbjct: 305 QACLRLGRMKDDGLAATGITSILKRNSCGKSLDIARMARDMMGGNGISDEFGVARHLVNL 364

Query: 366 EVVNTYEGTHDVHALILGRAQTGIQAF 392
           EVVNTYEGTHD+HALILGRA TGI +F
Sbjct: 365 EVVNTYEGTHDIHALILGRAITGIASF 391


Lambda     K      H
   0.320    0.137    0.413 

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: 622
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: 393
Length of database: 404
Length adjustment: 31
Effective length of query: 362
Effective length of database: 373
Effective search space:   135026
Effective search space used:   135026
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 24 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