GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_25585
          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:

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