GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Herbaspirillum aquaticum IEH 4430

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_088756986.1 CEJ45_RS20840 2-methylcitrate synthase

Query= BRENDA::Q2Z1A8
         (398 letters)



>NCBI__GCF_002213425.1:WP_088756986.1
          Length = 384

 Score =  701 bits (1808), Expect = 0.0
 Identities = 339/373 (90%), Positives = 357/373 (95%)

Query: 26  KKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHLLVHGKLPTKSEL 85
           KKSVALSGVTAGNTALCTVG+TGNDLHYRGYDILD+A++CEFEEIAHLLVHGKLPT +EL
Sbjct: 12  KKSVALSGVTAGNTALCTVGKTGNDLHYRGYDILDVADSCEFEEIAHLLVHGKLPTAAEL 71

Query: 86  AAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEKEDHNTPGARDIA 145
            AYKAKLK+LRGLPANVKAALEW+PA++HPMDVMRTGVS LG VLPEK+DHNTPGARDIA
Sbjct: 72  RAYKAKLKALRGLPANVKAALEWLPAASHPMDVMRTGVSALGCVLPEKDDHNTPGARDIA 131

Query: 146 DRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEKPSALWERAMHTSLNL 205
           DRLMASLGSMLLYWYHYSHNG RIEVETDDDSIG HFLHLLHGEKPS  WE+AMHTSL L
Sbjct: 132 DRLMASLGSMLLYWYHYSHNGNRIEVETDDDSIGAHFLHLLHGEKPSEAWEKAMHTSLIL 191

Query: 206 YAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEVAFEIQKRYDNPDEAQ 265
           YAEHEFNASTFT RVIAGTGSDMYS+I+GAIGALRGPKHGGANEVAFEIQKRYDNPDEA+
Sbjct: 192 YAEHEFNASTFTGRVIAGTGSDMYSAITGAIGALRGPKHGGANEVAFEIQKRYDNPDEAE 251

Query: 266 ADITRRVGNKEVVIGFGHPVYTTGDPRNQVIKEVAKKLSKDAGSMKMFDIAERLETVMWD 325
           ADI RRV NKEVVIGFGHPVYT  DPRN+VIKEVA+KLSK+AGS KMFDIAERLETVMWD
Sbjct: 252 ADIRRRVENKEVVIGFGHPVYTISDPRNKVIKEVARKLSKEAGSTKMFDIAERLETVMWD 311

Query: 326 IKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKIIRPSANYTG 385
           IKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKIIRPSANY G
Sbjct: 312 IKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKIIRPSANYVG 371

Query: 386 PENLKFVPIGKRK 398
           PE+LKFVPIGKRK
Sbjct: 372 PEDLKFVPIGKRK 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: 635
Number of extensions: 13
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: 384
Length adjustment: 31
Effective length of query: 367
Effective length of database: 353
Effective search space:   129551
Effective search space used:   129551
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 24 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