GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Marinicella litoralis KMM 3900

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_099020245.1 CCS90_RS14235 acyl-CoA dehydrogenase

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



>NCBI__GCF_002591915.1:WP_099020245.1
          Length = 386

 Score =  164 bits (415), Expect = 4e-45
 Identities = 114/372 (30%), Positives = 191/372 (51%), Gaps = 8/372 (2%)

Query: 19  LTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGL 78
           L E+++   D+A +FA  ++AP   +          + R  GE+G LG   PE+YGG GL
Sbjct: 5   LNEDQQAFVDAAKEFAISEMAPLAAKWDEESIFPVDVIRNTGELGFLGIYSPEKYGGLGL 64

Query: 79  NYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFG 138
           + +   LI  E+ +  +   + +++ +    + +  FG+E+  + +  +L SGE +  + 
Sbjct: 65  SRLDASLIFEEMSKHCTSTTAYLTIHNMCAWM-LTTFGSESLAETWGTQLTSGELLASYC 123

Query: 139 LTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAGDIRG---FV 195
           LTEP HGSD G++ T A K D  Y L GSK +I+ +   ++ +V A+      RG   F+
Sbjct: 124 LTEPGHGSDAGNLKTTAVKTDDTYVLNGSKTFISGAGSTEILIVMARTGEAGPRGVSCFM 183

Query: 196 LEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIF-PDVRGLKGPFTCLNSARYG 254
           +     G+S      K+G  +  T  I  ++V +P E +   +  G K     L+  R  
Sbjct: 184 VPADLAGISYGKKEDKMGWNSQPTRLITFEDVTIPAEYLIGQEGEGFKFAMKGLDGGRIN 243

Query: 255 ISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGRM 314
           I+  +LG A+A  + A+ Y L+R+QFG+ LA+ Q +Q KLADM TE+  A Q  +RL  +
Sbjct: 244 IASCSLGTAQAALNQAQSYMLERKQFGQSLASFQALQFKLADMLTELIAARQ-MVRLAAV 302

Query: 315 K--DEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYE 372
           K  ++   A    ++ KR +      I   A  + GG G   E+ + RH+ +  V    E
Sbjct: 303 KLDNKHPQASAYCAMAKRFATDVCFQICDEALQLHGGYGYIKEYPLERHVRDTRVHRILE 362

Query: 373 GTHDVHALILGR 384
           GT+++  LI+ R
Sbjct: 363 GTNEIMRLIISR 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: 334
Number of extensions: 20
Number of successful extensions: 5
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: 386
Length adjustment: 30
Effective length of query: 363
Effective length of database: 356
Effective search space:   129228
Effective search space used:   129228
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