GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuA in Phaeobacter inhibens BS107

Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate GFF1551 PGA1_c15710 acyl-CoA dehydrogenase

Query= BRENDA::Q75N94
         (430 letters)



>lcl|FitnessBrowser__Phaeo:GFF1551 PGA1_c15710 acyl-CoA
           dehydrogenase
          Length = 406

 Score =  191 bits (486), Expect = 3e-53
 Identities = 122/348 (35%), Positives = 184/348 (52%), Gaps = 11/348 (3%)

Query: 78  EFPAEMWKKLGDAGFLGITANEDYGGLGMGYQAHCIVMEELSRASGSIALSYAAHSQLCV 137
           E   E+++++G+ G LG T  E YGGLG GY ++ +V  E+ R         +  S L +
Sbjct: 61  ETDPEIFREMGEMGLLGTTIPEQYGGLGAGYVSYGLVAREVERVDSGYRSMMSVQSSLVM 120

Query: 138 NQLSLNGSPEQKERFLPGLLSGDKIGALAMSEHSAGSDVVSMKTTAKEVDGGYVLNGTKM 197
             +   GS EQ++++LP L SG+ IG   ++E  AGSD   MKT A++ DGGY L G+KM
Sbjct: 121 YPIYAYGSEEQRQKYLPKLSSGEWIGCFGLTEPDAGSDPAGMKTRAEKTDGGYRLTGSKM 180

Query: 198 WITNGPDADFIVVYAKTEPQKGSKGITAFVVEKTFDGFSCARKLDKLGMRGSNTGELIFE 257
           WI+N P AD  VV+AK+E   G   I  FV+EK   G S  +  +K  +R S TGE++ +
Sbjct: 181 WISNAPIADVFVVWAKSEAHGGK--IRGFVLEKGMKGLSAPKIANKASLRASITGEIVMD 238

Query: 258 DVFVPKENVLGEVNRGVKVLMEGLDLERLVLSAGPLGIMQAALDLVLPYTHVRKQFGTPI 317
            V V  + +L  V  G+K     L+  R  +S G +G  +A       Y   RKQFG P+
Sbjct: 239 GVEVGDDALLPHV-EGLKGPFGCLNRARYGISWGAMGAAEACWHAARQYGLDRKQFGRPL 297

Query: 318 AHNQLIQGKLADMYTKLQASRAYTYSTARHIDNSASLSE-VSIRTQDCAGAILYAAERAT 376
           A+ QL Q KLA+M T++      +    R +D + +  E +SI  ++  G       +A 
Sbjct: 298 ANTQLFQLKLANMQTEITLGLQASLRVGRLMDEANAAPEMISIVKRNNCG-------KAL 350

Query: 377 ECALDAIQLMGGNGYINELPAGRLLRDAKLYEIGAGTSEIRRMVIGRA 424
           E A  A  + GGNG   E    R + + +      GT ++  +++GRA
Sbjct: 351 EIARHARDMHGGNGISLEFGVIRHMVNLETVNTYEGTHDVHALILGRA 398


Lambda     K      H
   0.317    0.134    0.380 

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: 389
Number of extensions: 24
Number of successful extensions: 4
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: 430
Length of database: 406
Length adjustment: 32
Effective length of query: 398
Effective length of database: 374
Effective search space:   148852
Effective search space used:   148852
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 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, the preprint on GapMind for carbon sources, 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