GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Lacinutrix algicola AKS293

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_055434784.1 ASC41_RS01020 acyl-CoA dehydrogenase

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



>NCBI__GCF_001418085.1:WP_055434784.1
          Length = 392

 Score =  400 bits (1027), Expect = e-116
 Identities = 200/378 (52%), Positives = 265/378 (70%)

Query: 15  LDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYG 74
           LD+ LTEE ++VRD+A ++ +  ++P + EA +  +   +I   + E+G  G  IPE+YG
Sbjct: 14  LDELLTEEHKLVRDAAREWVKRDVSPIIEEAAQKAEFPKSIISGLAEIGAFGPYIPEEYG 73

Query: 75  GSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWI 134
           G+GL+ + YGLI +E+ER DSG RS  SVQSSLVM PI ++G E Q+ KYLPKLASGEWI
Sbjct: 74  GAGLDQISYGLIMQEIERGDSGVRSTASVQSSLVMYPIWKYGNEEQRNKYLPKLASGEWI 133

Query: 135 GCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAGDIRGF 194
           G FGLTEP+HGS+P  M+T  + +   Y L G+KMWI+NSP  +V VVWAK++ G I G 
Sbjct: 134 GSFGLTEPDHGSNPAGMVTNFKDMGDHYLLNGAKMWISNSPFCNVAVVWAKNEEGRIHGL 193

Query: 195 VLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGLKGPFTCLNSARYG 254
           ++E+G +G + P  H K  LRAS TGE++ DNV VP+EN+ P+  GL  P  CL+SAR+G
Sbjct: 194 IVERGMEGFTTPETHNKWSLRASATGELIFDNVKVPKENLLPNKSGLGAPLGCLDSARFG 253

Query: 255 ISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGRM 314
           I+WGA+GAA  C+ TA +Y+ +R QFG+P+   QL QKKLA+M TEIT A     RLG M
Sbjct: 254 IAWGAIGAAMDCYDTALRYSKERLQFGKPIGQFQLQQKKLAEMITEITKAQLLAWRLGVM 313

Query: 315 KDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEGT 374
           ++ GTA     S+ KRN+   AL IAR AR MLGG GIS E+ + RH++NLE V TYEGT
Sbjct: 314 RENGTATSAQISMAKRNNVDMALTIARDARQMLGGMGISGEYSIMRHMMNLESVVTYEGT 373

Query: 375 HDVHALILGRAQTGIQAF 392
           HD+H LI G   TG+ AF
Sbjct: 374 HDIHLLITGLDVTGLNAF 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: 438
Number of extensions: 9
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: 392
Length adjustment: 31
Effective length of query: 362
Effective length of database: 361
Effective search space:   130682
Effective search space used:   130682
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