GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Brevibacterium jeotgali SJ5-8

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_101589126.1 BJEO58_RS08890 acyl-CoA dehydrogenase

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



>NCBI__GCF_900169175.1:WP_101589126.1
          Length = 388

 Score =  169 bits (428), Expect = 1e-46
 Identities = 119/376 (31%), Positives = 190/376 (50%), Gaps = 6/376 (1%)

Query: 19  LTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGL 78
           LTEE++ +      FA ++LAP  LE            R   E+G+ G  I E+YGG+GL
Sbjct: 13  LTEEQQELFAMCRTFADEELAPHALEWDAEGHFPVDSIRRTAELGMGGIYIDEEYGGAGL 72

Query: 79  NYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFG 138
             +   L+   +        S +S+ + +V   +  F TE QKQ++L  L S E +  + 
Sbjct: 73  GRMDAVLVFEALSTGCPAVASYISIHN-MVAKCLELFATEEQKQRWLLPLTSFEALSSYC 131

Query: 139 LTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAK---DDAGDIRGFV 195
           LTEPN GSD  ++ T AR+    Y L G K +I+ +  +D+++V A+   D A  I  F+
Sbjct: 132 LTEPNAGSDAAALKTSARRDGDSYILNGVKQFISGAGSSDLYLVMARTGQDGARGISAFI 191

Query: 196 LEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEEN-IFPDVRGLKGPFTCLNSARYG 254
           +E G +GLS      K+G +A  T ++ M+NV VP EN I  +  G +   + L+  R  
Sbjct: 192 VEDGTEGLSFGPNEKKMGWKAQPTRQVFMENVRVPVENRIGDEGTGFRIAMSGLDGGRLN 251

Query: 255 ISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGRM 314
           I   +LG A++    A  Y  +RQ FG+ L   Q ++ ++AD+QT++  A     R    
Sbjct: 252 IGASSLGGAQSALEKAITYMGERQAFGQDLTGFQALRFEVADLQTKLEAARSLLWRAASA 311

Query: 315 KDEGTAAVEITSIM-KRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEG 373
            D    +  + S M K  +     D+A  A  + GG G   E+GV + + +L V    EG
Sbjct: 312 YDAEDPSTTLLSAMGKLTATDTGFDVANRALQLFGGYGYLAEYGVEKLVRDLRVHQILEG 371

Query: 374 THDVHALILGRAQTGI 389
           T+++  +I+ R  TG+
Sbjct: 372 TNEIMRVIISRRSTGV 387


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: 322
Number of extensions: 16
Number of successful extensions: 6
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: 388
Length adjustment: 31
Effective length of query: 362
Effective length of database: 357
Effective search space:   129234
Effective search space used:   129234
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