GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iolA in Pseudomonas fluorescens FW300-N2C3

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate AO356_25585 AO356_25585 2-hydroxymuconic semialdehyde dehydrogenase

Query= reanno::WCS417:GFF2142
         (499 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25585 AO356_25585
           2-hydroxymuconic semialdehyde dehydrogenase
          Length = 486

 Score =  246 bits (629), Expect = 1e-69
 Identities = 162/456 (35%), Positives = 246/456 (53%), Gaps = 8/456 (1%)

Query: 5   IEHYINDQRVSRDDRYQDVFNPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTPPIR 64
           I+H+I+ + V   D + + +NPATGE  G VA    + V++AVAAA+ AF  WA+TP   
Sbjct: 2   IKHWIDGREVESKDVFVN-YNPATGEAIGEVASGGAEEVAQAVAAAKEAFPKWANTPAKE 60

Query: 65  RARVLFEYLHLLRERKDDLARIIVAEHGKVFTDAQGE-VDRGIDILEFACGIPNLLKGEH 123
           RAR++ +   L+ +    LA +   + G      +   + R     +F   +   + G H
Sbjct: 61  RARLMRKLGELIEQNVPKLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDG-H 119

Query: 124 SDQVSRGMDNWTMRQPLGVVAGVTPFNFPVMVPMWMYPIAIAAGNTFILKPSPTDPSASL 183
           +  V   M N+T+ QP+GV A V+P+N P M   W     +A GNT +LK S   P  + 
Sbjct: 120 TYPVDDQMLNYTLYQPVGVCALVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTAN 179

Query: 184 FMAELLREAGLPKGVFNVVQGDKESV-DALIEHPDVKAVSFVGSTPIAQYIYETGARNGK 242
            +  L  EAG+P GV NV+QG   +  DAL+ HPDV+A+SF G T   + I +T     K
Sbjct: 180 ELGRLAVEAGIPNGVLNVIQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQTAGLK-K 238

Query: 243 RVQGLGGAKNHMVVMPDADIEKTVDALMGAAYGSAGERCMAISVAVLVGDVGDKVIAALT 302
               LGG K+ +++  DAD+E+ +DA +   +   GERC A S   +   V  + +A   
Sbjct: 239 YSMELGG-KSPVLIFEDADLERALDAALFTIFSLNGERCTAGSRIFIQESVYPQFVAEFA 297

Query: 303 ERAKHLRITDGRDLKAEMGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYVPTEPG-LE 361
            RAK L + D +D K ++G ++++A  ++++GYI+ G++ GA LL  G +     P  L 
Sbjct: 298 ARAKRLIVGDPQDPKTQVGSMITQAHYDKVTGYIKIGLEEGATLLAGGLERPANLPAHLS 357

Query: 362 NGFWLGATLFDHVTEEMSIYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSCFTRDG 421
           +G ++  T+F  V  +M I +EEIFGPV+  +   D AEA++L N  E+G     +T+D 
Sbjct: 358 HGQFIQPTVFADVNNKMRIAQEEIFGPVVCLIPFKDEAEALQLANDTEYGLASYIWTQDI 417

Query: 422 NIAREFARRIEVGMVGINVPISVPMAWHGFGGWKKS 457
             A   A  IE GMV IN   +V      FGG K S
Sbjct: 418 GKAHRLAHGIEAGMVFINSQ-NVRDLRQPFGGVKGS 452


Lambda     K      H
   0.320    0.136    0.407 

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: 551
Number of extensions: 22
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: 499
Length of database: 486
Length adjustment: 34
Effective length of query: 465
Effective length of database: 452
Effective search space:   210180
Effective search space used:   210180
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: 52 (24.6 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 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