GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acdH in Pseudomonas fluorescens FW300-N1B4

Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate Pf1N1B4_4789 Butyryl-CoA dehydrogenase (EC 1.3.99.2)

Query= metacyc::MONOMER-17424
         (375 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4789 Butyryl-CoA
           dehydrogenase (EC 1.3.99.2)
          Length = 383

 Score =  448 bits (1152), Expect = e-130
 Identities = 220/373 (58%), Positives = 283/373 (75%)

Query: 3   VNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62
           +++EQ  I D  R FA+  + P A+ W+K        + +M ELGL GM+VPE+WGG+  
Sbjct: 6   LSEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDGLVAKMGELGLLGMVVPEEWGGTYV 65

Query: 63  GYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFA 122
            YVAYA+A+EEI+AGDGA   +MS+HNSVGC P+L +G E+QK+Q+L  LA+G  +G F 
Sbjct: 66  DYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQQWLPDLASGQAIGCFC 125

Query: 123 LTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAF 182
           LTEPQAGS+A +L+TRA L    +V+NG+KQF+++G+ A + IVFAVTDPE GKRGISAF
Sbjct: 126 LTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGKRAKLAIVFAVTDPELGKRGISAF 185

Query: 183 IVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRI 242
           +VPT++ G+ V R E K+G  ASDTC +  +N  VP AN LG  G+G  IAL+NLEGGRI
Sbjct: 186 LVPTETAGFIVDRSEHKMGIRASDTCAVTLNNCTVPEANLLGERGKGLAIALSNLEGGRI 245

Query: 243 GIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAAA 302
           GIA+QA+G+ARAAFE A  YA +R  F KP+IEHQ++A  LADM T+++ AR ++LHAA 
Sbjct: 246 GIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSIANMLADMHTRLNAARLLILHAAR 305

Query: 303 LRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEG 362
           LR AG+P L EAS AKLFASEMAEKVCS A+Q  GGYGYL D+P+ER YRD R+ QIYEG
Sbjct: 306 LRSAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVERYYRDARITQIYEG 365

Query: 363 TSDIQRMVIARNL 375
           +S+IQRMVIAR L
Sbjct: 366 SSEIQRMVIAREL 378


Lambda     K      H
   0.319    0.134    0.382 

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: 432
Number of extensions: 12
Number of successful extensions: 1
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: 383
Length adjustment: 30
Effective length of query: 345
Effective length of database: 353
Effective search space:   121785
Effective search space used:   121785
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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