GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Burkholderia phytofirmans PsJN

Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate BPHYT_RS33975 BPHYT_RS33975 2-methylcitrate dehydratase

Query= BRENDA::P77243
         (483 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS33975 BPHYT_RS33975
           2-methylcitrate dehydratase
          Length = 483

 Score =  792 bits (2046), Expect = 0.0
 Identities = 378/483 (78%), Positives = 431/483 (89%)

Query: 1   MSAQINNIRPEFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKL 60
           MSA I+N+RP+ D  + DIVDYV +Y I S +A +TA +CL+DTLGCGLEAL YPAC KL
Sbjct: 1   MSAPISNVRPDPDSVLADIVDYVRDYRIDSALALETARHCLIDTLGCGLEALTYPACTKL 60

Query: 61  LGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120
           +GPIVPGT+VPNG +VPGT FQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI
Sbjct: 61  MGPIVPGTIVPNGAKVPGTSFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120

Query: 121 LATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVAST 180
           LATADWLSR+A+A+GKAPL MK VL AMIKAHEIQGCIALENSFN+VGLDHVLLVK+AST
Sbjct: 121 LATADWLSRSAIAAGKAPLAMKDVLIAMIKAHEIQGCIALENSFNKVGLDHVLLVKLAST 180

Query: 181 AVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAK 240
           AVV ++L LTR+E++NAVS A+VDG +LRTYRHAPNTG+RKSWAAGDATSRAVRLAL++K
Sbjct: 181 AVVGQLLDLTRDELINAVSQAFVDGHALRTYRHAPNTGSRKSWAAGDATSRAVRLALISK 240

Query: 241 TGEMGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAA 300
           TGEMGYPS LTA  WGFYDV FKG +F+FQRPYGSYVMENVLFKISFPAEFH+QTAVEA 
Sbjct: 241 TGEMGYPSVLTAKTWGFYDVLFKGNAFQFQRPYGSYVMENVLFKISFPAEFHAQTAVEAT 300

Query: 301 MTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYMVAIPLLFGR 360
           M L+ Q+ AAG++  DI K+TIRTHEA IRIIDKKGPLNNPADRDHCIQYMVA+PL+ GR
Sbjct: 301 MKLHAQLNAAGRSVDDISKITIRTHEAAIRIIDKKGPLNNPADRDHCIQYMVAVPLIHGR 360

Query: 361 LTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEV 420
           LTAADYED++AQD RID LR K+ C EDP FT DYHDPEKR+IANA+T+EF DG+ F+EV
Sbjct: 361 LTAADYEDSIAQDPRIDVLRAKMECVEDPQFTQDYHDPEKRSIANALTIEFNDGSSFDEV 420

Query: 421 VVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMPVNEYLDL 480
           +VEYPIGH RRR+DGIP LV+KFK NLAR+FP +QQ  IL+VSLD+ARLE MPVNEY+DL
Sbjct: 421 IVEYPIGHKRRREDGIPLLVEKFKTNLARRFPVKQQLAILDVSLDQARLEAMPVNEYVDL 480

Query: 481 YVI 483
           YVI
Sbjct: 481 YVI 483


Lambda     K      H
   0.321    0.136    0.406 

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: 787
Number of extensions: 12
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: 483
Length of database: 483
Length adjustment: 34
Effective length of query: 449
Effective length of database: 449
Effective search space:   201601
Effective search space used:   201601
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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 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