Aligments for a candidate for prpC in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for prpC in Burkholderia phytofirmans PsJN

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate BPHYT_RS33965 BPHYT_RS33965 methylcitrate synthase

Query= BRENDA::Q2Z1A8
         (398 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS33965 BPHYT_RS33965 methylcitrate
           synthase
          Length = 395

 Score =  670 bits (1729), Expect = 0.0
 Identities = 321/373 (86%), Positives = 350/373 (93%)

Query: 26  KKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHLLVHGKLPTKSEL 85
           KKSVALSGVTAGNTALCTVG+TGNDLHYRGYDILDIA  CEFEEIA+LLVH KLPT++EL
Sbjct: 23  KKSVALSGVTAGNTALCTVGKTGNDLHYRGYDILDIASACEFEEIAYLLVHEKLPTQAEL 82

Query: 86  AAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEKEDHNTPGARDIA 145
            AYK KLK+LRGLPANVKAALEW+PA+AHPMDVMRTGVSVLGTVLPEK+DHN PGARDIA
Sbjct: 83  TAYKIKLKALRGLPANVKAALEWIPAAAHPMDVMRTGVSVLGTVLPEKDDHNLPGARDIA 142

Query: 146 DRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEKPSALWERAMHTSLNL 205
           D+LMASLGSMLLYWYHYSHNG+RIEVETDDDSIGGHFLHLLHG +PS  W  AMH SLNL
Sbjct: 143 DKLMASLGSMLLYWYHYSHNGKRIEVETDDDSIGGHFLHLLHGVEPSKEWVDAMHVSLNL 202

Query: 206 YAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEVAFEIQKRYDNPDEAQ 265
           YAEHEFNASTFT RVIAGTGSD+YS+I+GAIGALRGPKHGGANEVAFEIQ RY  PDEA+
Sbjct: 203 YAEHEFNASTFTGRVIAGTGSDIYSAITGAIGALRGPKHGGANEVAFEIQSRYQTPDEAE 262

Query: 266 ADITRRVGNKEVVIGFGHPVYTTGDPRNQVIKEVAKKLSKDAGSMKMFDIAERLETVMWD 325
           ADI +RV NKEVVIGFGHPVYT  DPRN+VIKE+AKKLSK+AG+ K+F+IAERLE+VMWD
Sbjct: 263 ADIRKRVENKEVVIGFGHPVYTISDPRNKVIKEIAKKLSKEAGNSKLFNIAERLESVMWD 322

Query: 326 IKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKIIRPSANYTG 385
            KKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIART+GW+AHIIEQRIDNKIIRPSANYTG
Sbjct: 323 AKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTAGWSAHIIEQRIDNKIIRPSANYTG 382

Query: 386 PENLKFVPIGKRK 398
           PENLK++P+ +RK
Sbjct: 383 PENLKYLPLNRRK 395


Lambda     K      H
   0.317    0.133    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: 625
Number of extensions: 11
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: 398
Length of database: 395
Length adjustment: 31
Effective length of query: 367
Effective length of database: 364
Effective search space:   133588
Effective search space used:   133588
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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