GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Sphingomonas koreensis DSMZ 15582

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate Ga0059261_3793 Ga0059261_3793 Acyl-CoA dehydrogenases

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



>FitnessBrowser__Korea:Ga0059261_3793
          Length = 381

 Score =  168 bits (425), Expect = 3e-46
 Identities = 115/362 (31%), Positives = 180/362 (49%), Gaps = 5/362 (1%)

Query: 28  DSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGLNYVCYGLIA 87
           D+  +F   +L P   E    +     I  EM  +GL G +I E++GG GL  +    +A
Sbjct: 13  DTVRRFVAQRLRPLESEVEAADAIPDTIVEEMKALGLFGLSIAEEFGGLGLTMLEECRVA 72

Query: 88  REVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFGLTEPNHGSD 147
            E+ R    +RS       +    +   GT  QK  +LP++ASGE I  F LTEP+ GSD
Sbjct: 73  IEMGRTTPAFRSTFGTNVGIGSQGLVMAGTSEQKAAWLPRIASGEIITSFALTEPDVGSD 132

Query: 148 PGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAK--DDAG--DIRGFVLEKGWQGL 203
            G++  RA +    YRL+G+K +ITN+  A +F V A+  D+ G   +  F++ +   G+
Sbjct: 133 SGAVKARAVRDGDVYRLSGTKRFITNADKASLFTVMARTGDEPGARGVSAFLVPRDLPGI 192

Query: 204 SAPAIHGKVGLRASITGEIVMDNVFVPEEN-IFPDVRGLKGPFTCLNSARYGISWGALGA 262
           S      K+G + +   +++ D+V VP  N +  +  G K     L+  R  IS  ++G 
Sbjct: 193 SIGEPEKKMGQKGAKVADVIFDDVPVPAANRLGEEGEGFKIAMRVLDRGRLHISAVSVGV 252

Query: 263 AEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGRMKDEGTAAV 322
           AE        Y  +R+QFG+P+A +QLIQ  LAD +TE   A    L     KD G   V
Sbjct: 253 AERLIADCVAYASERKQFGKPIAEHQLIQAMLADSKTECLAARALVLETAAAKDAGKDVV 312

Query: 323 EITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEGTHDVHALIL 382
             ++  K  +      +A  A  +LGG G  +++G+ R   ++ +   YEGT  +  LI+
Sbjct: 313 MESAAAKLFATEMVGRVADRAVQILGGAGYIEDYGIERLYRDVRLFRIYEGTSQIQQLII 372

Query: 383 GR 384
            R
Sbjct: 373 AR 374


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: 343
Number of extensions: 18
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: 381
Length adjustment: 30
Effective length of query: 363
Effective length of database: 351
Effective search space:   127413
Effective search space used:   127413
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