GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26145
          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.

Links

Downloads

Related tools

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