Aligments for a candidate for amaB in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Aligments for a candidate for amaB in Caulobacter crescentus NA1000

Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate CCNA_01274 CCNA_01274 piperideine-6-carboxylate dehydrogenase

Query= uniprot:Q88CC3
         (496 letters)



>lcl|FitnessBrowser__Caulo:CCNA_01274 CCNA_01274
           piperideine-6-carboxylate dehydrogenase
          Length = 507

 Score =  646 bits (1666), Expect = 0.0
 Identities = 327/493 (66%), Positives = 386/493 (78%), Gaps = 2/493 (0%)

Query: 5   LLERLGVAAEAYTQGDYPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPR 64
           +L +LG        G+ PV  PIDG+ +  V      +  A++  A  AF  WR VPAPR
Sbjct: 15  ILAKLGAPPLPADAGE-PVRGPIDGAILGHVVYDDARQIEAKVAAACRAFADWRVVPAPR 73

Query: 65  RGELVRLFGEVLREHKADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTI 124
           RGELVRLFGE LR  KADL  LV++EAGKI  E  GEVQEMIDICDFAVGLSRQL+GLTI
Sbjct: 74  RGELVRLFGEELRAAKADLAALVTLEAGKIASEAAGEVQEMIDICDFAVGLSRQLHGLTI 133

Query: 125 ASERPGHHMRETWHPLGVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALA 184
           ASERPGH MRETWHPLG V VISAFNFPVAVWAWN  LALV G+ V+WKPSEKTPLTALA
Sbjct: 134 ASERPGHAMRETWHPLGPVAVISAFNFPVAVWAWNACLALVCGDPVIWKPSEKTPLTALA 193

Query: 185 CQALFEKALKAFGDAPAGLAQLVIGGREAGEAMVDDPRVPLVSATGSTRMGREVGPRVAA 244
            QA+ E+AL  F DAP GL+ +V+G R+AGE +  DPR+PLVSATGSTRMGR V P VA 
Sbjct: 194 TQAILERALARFRDAPQGLSSVVLGARDAGERLARDPRIPLVSATGSTRMGRAVAPMVAE 253

Query: 245 RFGRSILELGGNNAMILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVA 304
           RFGRSILELGGNNAMI+ PSADL LA+R I+FSA GTAGQRCT+LRRLIVH S+ D+V  
Sbjct: 254 RFGRSILELGGNNAMIVTPSADLSLALRAIVFSAAGTAGQRCTSLRRLIVHESLVDKVSD 313

Query: 305 RVKAAYGKVRIGDPR-KDNLVGPLIDKQSFDAMQGALAKARDEGGQVFGGERQLADQYPN 363
            V+AA+ ++ +GDPR    L+GPLIDK ++DA   A+ + R EGG V GGER L D++P+
Sbjct: 314 AVEAAFQRLSVGDPRDPKTLLGPLIDKAAYDAFIAAMNQVRAEGGSVAGGERVLIDEHPD 373

Query: 364 AYYVSPAIAEMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIRE 423
           AYYV PA+A +PA +  ++ ETFAP+L+V+ Y+ F+ A+ + N+VPQGLSSC+ T D+RE
Sbjct: 374 AYYVRPALARLPAPAPCMQRETFAPLLHVVPYNSFDMAIAIQNDVPQGLSSCVMTNDVRE 433

Query: 424 AERFQSASGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYMRRQTNTVNY 483
           AERF +A+GSDCGIANVNIG SGAEIGGAFGGEKETGGGRESGSD+WK YMRRQT TVNY
Sbjct: 434 AERFLAAAGSDCGIANVNIGPSGAEIGGAFGGEKETGGGRESGSDSWKQYMRRQTATVNY 493

Query: 484 SRELPLAQGIVFD 496
           S  LPLAQG+ FD
Sbjct: 494 SGALPLAQGVRFD 506


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: 780
Number of extensions: 28
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: 496
Length of database: 507
Length adjustment: 34
Effective length of query: 462
Effective length of database: 473
Effective search space:   218526
Effective search space used:   218526
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources