GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Pseudomonas fluorescens FW300-N2E2

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate Pf6N2E2_1751 Aldehyde dehydrogenase A (EC 1.2.1.22) / Glycolaldehyde dehydrogenase (EC 1.2.1.21)

Query= SwissProt::Q9I6M5
         (483 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1751 Aldehyde
           dehydrogenase A (EC 1.2.1.22) / Glycolaldehyde
           dehydrogenase (EC 1.2.1.21)
          Length = 477

 Score =  320 bits (820), Expect = 7e-92
 Identities = 176/463 (38%), Positives = 269/463 (58%), Gaps = 4/463 (0%)

Query: 12  QAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKE 71
           Q Y+  A+V +D  + ++V+NPA G+++G VP+   AE  +AI AA +A  AW A  A E
Sbjct: 7   QNYIANAFVASD--EHLEVHNPANGQLLGRVPQGSTAEVEQAIAAARQAQRAWAARPAIE 64

Query: 72  RANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRIYGDTI 131
           RA  LR+    + E+ + LAR +T EQGK L  A+ E+ + A +L++  E A+R+ G+ +
Sbjct: 65  RAGYLRKIASKVREHGERLARTITAEQGKVLELARVEVNFTADYLDYMAEWARRLEGEVL 124

Query: 132 PGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALA 191
              +  + I ++++P+GV A I PWNFP  +I RK  PAL  G T+V+KP+ +TP +   
Sbjct: 125 SSDRAGESIFLLRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVIKPSEETPINCFE 184

Query: 192 LAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKK 251
            A L     +P GVF+VV G+   VG  L+ +P +  ++FTGS   G ++MA  A +I K
Sbjct: 185 FARLVAETDLPAGVFNVVCGTGATVGHALSGHPGIDLISFTGSVGTGSRIMAAAAPNITK 244

Query: 252 VSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLKA 311
           ++LELGG AP IV  DADLD A+     S+  N GQ C CA R+YV+  V DAF+D + A
Sbjct: 245 LNLELGGKAPAIVLADADLDLAIRAITASRVINTGQVCNCAERVYVERKVADAFIDGIAA 304

Query: 312 AVAKLNIGNGL-EAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALG-GTFFE 369
           ++A    G+ L E G+  GPLI+  A+ KV + +  A  +GA++++GG    LG G  ++
Sbjct: 305 SMAATRYGDPLAEHGLDMGPLINRAALDKVAQMVRTASGQGAQIITGGAVADLGQGFHYQ 364

Query: 370 PTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARVFRV 429
           PT+L        + + E FGP+ P+    D  E IA++ND+E+GL S  Y   L+   + 
Sbjct: 365 PTVLAGCSAKMEIMRKEIFGPVLPIQIVDDLDEAIALANDSEYGLTSSIYTASLSAAMQA 424

Query: 430 AEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDY 472
              L++G   IN            G + SG+G    K+G+ +Y
Sbjct: 425 TRLLDFGETYINRENFEAMQGFHAGTRKSGIGGADGKHGLYEY 467


Lambda     K      H
   0.317    0.135    0.391 

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: 521
Number of extensions: 17
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: 483
Length of database: 477
Length adjustment: 34
Effective length of query: 449
Effective length of database: 443
Effective search space:   198907
Effective search space used:   198907
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 paper from 2022 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