GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Cupriavidus basilensis 4G11

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate RR42_RS14475 RR42_RS14475 methylcitrate synthase

Query= BRENDA::Q2Z1A8
         (398 letters)



>FitnessBrowser__Cup4G11:RR42_RS14475
          Length = 387

 Score =  728 bits (1880), Expect = 0.0
 Identities = 355/377 (94%), Positives = 366/377 (97%)

Query: 22  APRVKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHLLVHGKLPT 81
           AP+ KKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHLLVHGKLPT
Sbjct: 11  APKPKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHLLVHGKLPT 70

Query: 82  KSELAAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEKEDHNTPGA 141
           ++ELAAYKAKLK+LRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEK+DHNTPGA
Sbjct: 71  RAELAAYKAKLKALRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEKDDHNTPGA 130

Query: 142 RDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEKPSALWERAMHT 201
           RDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDD+IG HFLHLLHG+KPSALWERAM T
Sbjct: 131 RDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDDTIGAHFLHLLHGQKPSALWERAMQT 190

Query: 202 SLNLYAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEVAFEIQKRYDNP 261
           SLNLYAEHEFNASTF  RVIAGTGSDMYSSI GAIGALRGPKHGGANEVAFEIQKRYD+P
Sbjct: 191 SLNLYAEHEFNASTFAGRVIAGTGSDMYSSICGAIGALRGPKHGGANEVAFEIQKRYDSP 250

Query: 262 DEAQADITRRVGNKEVVIGFGHPVYTTGDPRNQVIKEVAKKLSKDAGSMKMFDIAERLET 321
           DEA  DI+RRV NKEVVIGFGHPVYTTGDPRNQVIKEVA++LSKDAGSMKMFDIAERLET
Sbjct: 251 DEAHIDISRRVENKEVVIGFGHPVYTTGDPRNQVIKEVARRLSKDAGSMKMFDIAERLET 310

Query: 322 VMWDIKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKIIRPSA 381
            MWD KKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKIIRPSA
Sbjct: 311 TMWDAKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKIIRPSA 370

Query: 382 NYTGPENLKFVPIGKRK 398
           NYTGPENLKFVPIGKRK
Sbjct: 371 NYTGPENLKFVPIGKRK 387


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: 649
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: 387
Length adjustment: 31
Effective length of query: 367
Effective length of database: 356
Effective search space:   130652
Effective search space used:   130652
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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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