GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Pseudomonas fluorescens FW300-N1B4

Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate Pf1N1B4_1384 L-pipecolate dehydrogenase (EC 1.5.99.3)

Query= uniprot:Q88CC3
         (496 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1384
          Length = 496

 Score =  799 bits (2063), Expect = 0.0
 Identities = 397/496 (80%), Positives = 432/496 (87%)

Query: 1   MVAGLLERLGVAAEAYTQGDYPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSV 60
           MVA LL+RLGV    Y  G  PVH+PIDGS+IA+V   G AE    I +A  AFE WR V
Sbjct: 1   MVAALLDRLGVNPALYQNGKVPVHSPIDGSRIAAVNWEGAAEVEQHISRADHAFELWRKV 60

Query: 61  PAPRRGELVRLFGEVLREHKADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLY 120
           PAPRRGELVR  G++LRE+KADLGELVS EAGKITQEGLGEVQEMIDICDFAVGLSRQLY
Sbjct: 61  PAPRRGELVRQLGDILREYKADLGELVSWEAGKITQEGLGEVQEMIDICDFAVGLSRQLY 120

Query: 121 GLTIASERPGHHMRETWHPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPL 180
           GLTIASERPGHHMRETWHPLG+VGVISAFNFPVAVWAWN  LALV GN V+WKPSEKTPL
Sbjct: 121 GLTIASERPGHHMRETWHPLGIVGVISAFNFPVAVWAWNATLALVCGNPVIWKPSEKTPL 180

Query: 181 TALACQALFEKALKAFGDAPAGLAQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGP 240
           TALACQALF++ LK F DAP  L+Q++IGGR+AGEA+VDDPRV LVSATGSTRMGREV P
Sbjct: 181 TALACQALFDRVLKNFSDAPPHLSQVIIGGRDAGEALVDDPRVALVSATGSTRMGREVAP 240

Query: 241 RVAARFGRSILELGGNNAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKD 300
           ++AARF RSILELGGNNAMIL PSADLD+AVR ILFSAVGTAGQRCTTLRRLI H S+K+
Sbjct: 241 KIAARFARSILELGGNNAMILGPSADLDMAVRAILFSAVGTAGQRCTTLRRLIAHESVKE 300

Query: 301 EVVARVKAAYGKVRIGDPRKDNLVGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQ 360
           E+V R+KAAY KVRIG P + NLVGPLIDK SF+ MQ AL +A  EGG+VFGG+RQL D+
Sbjct: 301 EIVTRLKAAYSKVRIGHPLEGNLVGPLIDKHSFENMQDALEQALSEGGRVFGGKRQLEDK 360

Query: 361 YPNAYYVSPAIAEMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTD 420
           +PNAYYVSPAI EMP QSDVV  ETFAPILYV+ Y+DFEEALRLNN VPQGLSSCIFTTD
Sbjct: 361 FPNAYYVSPAIVEMPEQSDVVCSETFAPILYVIGYNDFEEALRLNNAVPQGLSSCIFTTD 420

Query: 421 IREAERFQSASGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYMRRQTNT 480
           +REAERF SA GSDCGIANVNIG SGAEIGGAFGGEKETGGGRESGSDAW+GYMRRQTNT
Sbjct: 421 VREAERFMSAVGSDCGIANVNIGPSGAEIGGAFGGEKETGGGRESGSDAWRGYMRRQTNT 480

Query: 481 VNYSRELPLAQGIVFD 496
           VNYS ELPLAQGI FD
Sbjct: 481 VNYSLELPLAQGITFD 496


Lambda     K      H
   0.318    0.135    0.396 

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: 848
Number of extensions: 23
Number of successful extensions: 1
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: 496
Length of database: 496
Length adjustment: 34
Effective length of query: 462
Effective length of database: 462
Effective search space:   213444
Effective search space used:   213444
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: 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