GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Amycolatopsis halophila YIM 93223

Align Short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_034268902.1 AMYHA_RS06270 acyl-CoA dehydrogenase family protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2983
         (375 letters)



>NCBI__GCF_000504245.1:WP_034268902.1
          Length = 381

 Score =  307 bits (787), Expect = 3e-88
 Identities = 169/375 (45%), Positives = 232/375 (61%), Gaps = 2/375 (0%)

Query: 1   MIPNDDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGC 60
           ++P+ + + +  + R+ A++ L P A E+++  RFP+E    +   G  G+   E+WGG 
Sbjct: 6   LLPSTEAEDLLALTREIARDELAPRADEYEQAERFPREQFRLLGKSGLLGLPYAERWGGG 65

Query: 61  DTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGA 120
           D  Y  Y   LEEIA+   +    +SVH ++ C  +  YGTDEQ++R+L  L  G +LGA
Sbjct: 66  DVPYEVYLQVLEEIASAWMSVGVGLSVH-TMSCFALAFYGTDEQRDRWLPDLLGGDLLGA 124

Query: 121 FALTEPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGIS 180
           +AL+E  AGSDA+ L TRA  +GD YV+NG K +IT G  A        T P AG +GIS
Sbjct: 125 YALSETHAGSDAAALSTRAVRDGDEYVVNGTKAWITHGGKADFYTTMVRTSP-AGSKGIS 183

Query: 181 AFIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGG 240
             +V  D+PG   A  E K+G  AS T Q++F D +VP    LGEEG G RIAL +L  G
Sbjct: 184 CLLVAADTPGLSAATPERKMGMTASTTSQMIFSDARVPTDRLLGEEGAGLRIALDSLASG 243

Query: 241 RVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300
           R+GIA+ +VG+A+AA + A  YA ER  FGK II+ Q V F LADMA  +  +R     A
Sbjct: 244 RLGIAACAVGLAQAALDEAVRYATERTQFGKSIIDFQGVEFLLADMAAAVESSRATYLEA 303

Query: 301 AALRDSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIY 360
           A  +D G P   +AS+AKL A++ A KV + A+Q LGG GY  DFPVER  R+ +V QI+
Sbjct: 304 ARRKDRGLPFARQASIAKLVATDSAMKVTTDAVQVLGGAGYTKDFPVERYMREAKVPQIF 363

Query: 361 EGTSDIQRMVISRNL 375
           EGT+ IQRMVI++ L
Sbjct: 364 EGTNQIQRMVIAKEL 378


Lambda     K      H
   0.320    0.135    0.394 

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: 326
Number of extensions: 16
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: 375
Length of database: 381
Length adjustment: 30
Effective length of query: 345
Effective length of database: 351
Effective search space:   121095
Effective search space used:   121095
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