GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Pseudomonas fluorescens FW300-N2E3

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate AO353_25680 AO353_25680 acyl-CoA dehydrogenase

Query= reanno::Phaeo:GFF1011
         (386 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25680
          Length = 375

 Score =  281 bits (720), Expect = 2e-80
 Identities = 150/367 (40%), Positives = 226/367 (61%), Gaps = 2/367 (0%)

Query: 17  LRDMVHRWAQERVRPMAQEIDQKNEFPAELWQEMGELGLLGITVPEEFGGAGMSYLAHTV 76
           + D   ++AQER++P A E D+++ FP E   EM ELG  G+ VPE++GG    YLA+ +
Sbjct: 10  ISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAM 69

Query: 77  AVEEIARASASVSLSYGAHSNL-CVNQIKLNGNAEQKAKYLPRLVSGEHVGALAMSEAGA 135
           A+EEIA    + S     H+++ CV  +K  GN +QK ++L  L SG  +GA A++E  A
Sbjct: 70  ALEEIAAGDGACSTIMSVHNSVGCVPILKF-GNDDQKERFLKPLASGAMLGAFALTEPQA 128

Query: 136 GSDVVSMSLRAEKRNDHYRLNGNKYWITNGPDADTLVVYAKTDPDAGSKGMTAFLIEKEF 195
           GSD  S+  RA    DHY LNG K +IT+G +A  ++V+A TDP AG +G++AF++  + 
Sbjct: 129 GSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDS 188

Query: 196 KGFSTSQHFDKLGMRGSNTAELVFEDVEVPFENVLGEEGKGVRVLMSGLDYERVVLAGIG 255
            G+  ++  DKLG   S+T +++FEDV+VP  N LGEEG+G ++ ++ L+  RV +A   
Sbjct: 189 PGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQS 248

Query: 256 TGIMAACMDEMMPYMKERKQFGQPIGNFQLMQGKIADMYTAMNTARAYVYEVAKACDKGT 315
            G+  A  +    Y +ER+ FG+PI   Q +  ++ADM T +  AR  V+  A   D G 
Sbjct: 249 VGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGK 308

Query: 316 VTRQDAAACCLYASEVAMTQAHQAVQAFGGAGYLSDNPVGRIFRDAKLMEIGAGTSEIRR 375
               +A+   L+ASE+A      A+Q  GG GYLSD P+ RI+RD ++ +I  GTS+I+R
Sbjct: 309 PALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQR 368

Query: 376 MLIGREL 382
           M+I R L
Sbjct: 369 MVISRNL 375


Lambda     K      H
   0.318    0.132    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: 337
Number of extensions: 20
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: 386
Length of database: 375
Length adjustment: 30
Effective length of query: 356
Effective length of database: 345
Effective search space:   122820
Effective search space used:   122820
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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