GapMind for catabolism of small carbon sources

 

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

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate AO356_26145 AO356_26145 aldehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26145 AO356_26145 aldehyde
           dehydrogenase
          Length = 477

 Score =  570 bits (1470), Expect = e-167
 Identities = 294/479 (61%), Positives = 356/479 (74%), Gaps = 5/479 (1%)

Query: 2   SVPVQHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWE 61
           SVPV    +I+GQF     +A +DV NPAT A++SR+P   A D  +A+  A  AQ +W 
Sbjct: 3   SVPV-FQNFINGQFT--HSEAHLDVFNPATGALLSRVPASNAADVDQALATARAAQKDWS 59

Query: 62  ALPAIERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARR 121
           A PAIERA +LR+I+A +RE  + ++  I  E GKI  LAEVEV FTADY+DYMAEWARR
Sbjct: 60  AKPAIERAGYLRRIAAKLRENVAHLAHTITLEQGKISALAEVEVHFTADYLDYMAEWARR 119

Query: 122 YEGEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFT 181
            EGEII SDRPGENI LF++ LGV  GILPWNFPFFLIARKMAPALLTGNTIVIKPSE T
Sbjct: 120 IEGEIITSDRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVIKPSEET 179

Query: 182 PNNAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATA 241
           PNN   FA++V    LP GVFN+V G G+ VG  L+G+  V M+S TGSV+ G +IM  A
Sbjct: 180 PNNCFEFARLVAATDLPPGVFNVVCGDGQ-VGAALSGHKGVDMISFTGSVATGSRIMTAA 238

Query: 242 AKNITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQF 301
           A NITK+ LELGGKAPAIV+ DADL LAVKAI DSR+IN+GQVCNCAERVYV++ + DQF
Sbjct: 239 APNITKLNLELGGKAPAIVLADADLALAVKAIRDSRIINTGQVCNCAERVYVERKVADQF 298

Query: 302 VNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVE-G 360
           + R+  AM A ++G+P    D+ MGPLIN   L+ VE KV  A+ +GA +  GG   +  
Sbjct: 299 IERISAAMSATRYGDPIAEADVEMGPLINRQGLDSVEHKVRTALSQGASLVSGGSVADRS 358

Query: 361 KGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNL 420
            G+++ PT+L      M IM EE FGPVLP+   D L++AI++AND DYGLTSSIYT++L
Sbjct: 359 SGFHFQPTVLAGCNASMDIMREEIFGPVLPIQIIDDLDEAIALANDCDYGLTSSIYTRDL 418

Query: 421 NVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYLQS 479
           + AM AI+GL FGETY+NRENFEAMQGFHAG RKSGIGGADGKHGL+EY  T  VYLQS
Sbjct: 419 SRAMHAIRGLDFGETYVNRENFEAMQGFHAGVRKSGIGGADGKHGLYEYTHTHAVYLQS 477


Lambda     K      H
   0.318    0.135    0.392 

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: 616
Number of extensions: 17
Number of successful extensions: 3
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: 479
Length of database: 477
Length adjustment: 34
Effective length of query: 445
Effective length of database: 443
Effective search space:   197135
Effective search space used:   197135
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: 51 (24.3 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