GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_01274
          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:

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