GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Flavobacterium sp. LM5

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_024981451.1 BXU11_RS04315 acyl-CoA dehydrogenase

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



>NCBI__GCF_002017945.1:WP_024981451.1
          Length = 379

 Score =  216 bits (551), Expect = 7e-61
 Identities = 133/378 (35%), Positives = 199/378 (52%), Gaps = 5/378 (1%)

Query: 15  LDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYG 74
           +D  LTEE  M++ +A  FAQ +L   V+E   H +      + MG +G LG  +  +YG
Sbjct: 1   MDFNLTEEHLMIQQAARDFAQTELQAGVIERDEHSKFPTEQVKMMGNLGFLGMMVDPKYG 60

Query: 75  GSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWI 134
           G+GL+ + Y L   E+ ++D+    +MSV +SLV   + ++ +E QK KYL  LA GE I
Sbjct: 61  GAGLDSISYVLAMTEIAKVDASAAVIMSVNNSLVCAGLEKYCSEEQKMKYLVPLAKGEVI 120

Query: 135 GCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDA----GD 190
           G F L+EP  GSD  S  T A  +   Y L G+K WITN   A  ++V A+ D       
Sbjct: 121 GAFCLSEPEAGSDATSQKTTAIDMGDHYLLNGTKNWITNGGTASTYLVIAQTDIEKGHKG 180

Query: 191 IRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEEN-IFPDVRGLKGPFTCLN 249
           I  F++EKGW G        K+G+R S T  ++  +V VP+EN I  D  G       LN
Sbjct: 181 INAFIVEKGWAGFEIGPKEKKMGIRGSDTHSLMFTDVKVPKENRIGADGFGFAFAMNVLN 240

Query: 250 SARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCL 309
             R GI+  ALG A   +  A +Y+ +R+ FG+ +  +Q I  KLADM  +IT A    +
Sbjct: 241 GGRIGIASQALGIATGAYELALKYSKERKAFGKEIFNHQAIAFKLADMYVKITAAKLLIM 300

Query: 310 RLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVN 369
           +    KD G       ++ K  +   AL++A  A  + GGNG   E+ V R + + ++  
Sbjct: 301 KAACEKDAGQDIAHSGAMAKLYASEIALEVANEAVQIHGGNGYVAEYHVERMMRDSKITQ 360

Query: 370 TYEGTHDVHALILGRAQT 387
            YEGT ++  +++ R  T
Sbjct: 361 IYEGTSEIQRIVISRGLT 378


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: 318
Number of extensions: 12
Number of successful extensions: 3
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: 379
Length adjustment: 30
Effective length of query: 363
Effective length of database: 349
Effective search space:   126687
Effective search space used:   126687
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