GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Stenotrophomonas chelatiphaga DSM 21508

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_057507944.1 ABB28_RS06925 acyl-CoA dehydrogenase

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



>NCBI__GCF_001431535.1:WP_057507944.1
          Length = 382

 Score =  211 bits (538), Expect = 2e-59
 Identities = 132/382 (34%), Positives = 203/382 (53%), Gaps = 6/382 (1%)

Query: 15  LDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYG 74
           +D   TEE+ M++D A + AQ+K+AP      R  +   A  + +GE GL+G  +P +YG
Sbjct: 1   MDFSFTEEQLMLQDVARRIAQEKIAPSAEHHDRTGEFPLANIQLLGENGLMGIEVPAEYG 60

Query: 75  GSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWI 134
           G+G++ + Y L   EV   D+ + ++MSV +SL    I   G EAQKQKY+  +A G  I
Sbjct: 61  GAGMDPIAYVLAMVEVAAGDAAHSTIMSVNNSLFCNGILTHGNEAQKQKYVRAIAEGTAI 120

Query: 135 GCFGLTEPNHGSDPGSMITRA-RKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAG---- 189
           G F LTEP  GSD  +M  RA ++ DG Y + G K WIT+ P+A   V++A  DA     
Sbjct: 121 GAFALTEPQSGSDATAMRCRAVKQADGSYVINGKKSWITSGPVAKYIVLFAMTDADKGAR 180

Query: 190 DIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVM-DNVFVPEENIFPDVRGLKGPFTCL 248
            I  F+++    G        K+G+RAS T EI   D V   E+ +  +  G K     L
Sbjct: 181 GISAFLIDTDNAGFGRGKTEPKLGIRASATCEIEFNDYVAQAEDLLGQEGEGFKIAMGVL 240

Query: 249 NSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGC 308
           ++ R GI+  A+G A A +    +Y  +R+ FG  +   Q+ Q K+ADM+ ++  AL   
Sbjct: 241 DAGRIGIASQAIGIARAAYEATLEYVKERKAFGAAIGTFQMTQAKIADMKCKLDAALLLT 300

Query: 309 LRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVV 368
           LR   +K EG       +I K  +   A+ I   A  + GG G S E  + R+  + ++ 
Sbjct: 301 LRAAWVKGEGKRFSNEAAIAKLTASEAAMWITHQAVQIHGGMGYSKEMPLERYFRDAKIT 360

Query: 369 NTYEGTHDVHALILGRAQTGIQ 390
             YEGT ++  L++ R +TG++
Sbjct: 361 EIYEGTSEIQRLVIARNETGLR 382


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: 365
Number of extensions: 17
Number of successful extensions: 4
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: 382
Length adjustment: 30
Effective length of query: 363
Effective length of database: 352
Effective search space:   127776
Effective search space used:   127776
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.

Links

Downloads

Related tools

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