GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Acidovorax sp. GW101-3H11

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate Ac3H11_2322 2-methylcitrate synthase (EC 2.3.3.5)

Query= BRENDA::Q2Z1A8
         (398 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2322
          Length = 385

 Score =  662 bits (1709), Expect = 0.0
 Identities = 325/382 (85%), Positives = 348/382 (91%)

Query: 16  TASEPAAPRVKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHLLV 75
           T  E    + KKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAE CEFEEIAHLLV
Sbjct: 3   TTVETPGFKPKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAEVCEFEEIAHLLV 62

Query: 76  HGKLPTKSELAAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEKED 135
           HGKLPT++EL AYKAKLK+LRGLP +VK ALE +PA++HPMDVMRTGVS LG  LPEK+D
Sbjct: 63  HGKLPTRAELRAYKAKLKALRGLPLSVKQALEQLPAASHPMDVMRTGVSALGCALPEKDD 122

Query: 136 HNTPGARDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEKPSALW 195
           HN PGARDIADRLMASLGSMLLYWYH++ +GRRIEVETDDDSIG HFLHLLHG  PSA W
Sbjct: 123 HNLPGARDIADRLMASLGSMLLYWYHWASSGRRIEVETDDDSIGAHFLHLLHGTPPSAAW 182

Query: 196 ERAMHTSLNLYAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEVAFEIQ 255
           ERAMHTSLNLYAEHEFNASTFTARV+AGTGSDMYS+I+GAIGALRGPKHGGANEVAFEIQ
Sbjct: 183 ERAMHTSLNLYAEHEFNASTFTARVVAGTGSDMYSAITGAIGALRGPKHGGANEVAFEIQ 242

Query: 256 KRYDNPDEAQADITRRVGNKEVVIGFGHPVYTTGDPRNQVIKEVAKKLSKDAGSMKMFDI 315
           KRYD+PDEA+ADI RRV  KEVVIGFGHPVYT  DPRN VIK VA  LS++AGS KMFDI
Sbjct: 243 KRYDSPDEAEADIRRRVDAKEVVIGFGHPVYTVSDPRNVVIKGVAHNLSQEAGSTKMFDI 302

Query: 316 AERLETVMWDIKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNK 375
           AERLE+VMW++KKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNK
Sbjct: 303 AERLESVMWEVKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNK 362

Query: 376 IIRPSANYTGPENLKFVPIGKR 397
           IIRPSANYTGPE+L FVPI  R
Sbjct: 363 IIRPSANYTGPEDLVFVPIEHR 384


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: 595
Number of extensions: 15
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: 385
Length adjustment: 31
Effective length of query: 367
Effective length of database: 354
Effective search space:   129918
Effective search space used:   129918
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