GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Burkholderia phytofirmans PsJN

Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.- (characterized)
to candidate BPHYT_RS25670 BPHYT_RS25670 carboxyvinyl-carboxyphosphonate phosphorylmutase

Query= SwissProt::P54528
         (301 letters)



>FitnessBrowser__BFirm:BPHYT_RS25670
          Length = 292

 Score =  196 bits (499), Expect = 4e-55
 Identities = 106/293 (36%), Positives = 162/293 (55%), Gaps = 7/293 (2%)

Query: 5   VNKQSSQEELAGRFRKLMSAPDILQIPGAHDGMAALLAKEAGFSAIYLSGAAYTASR-GL 63
           V +QS ++ L  RF +     +I+  PG  D ++A +A   GF  +Y++G    AS  GL
Sbjct: 3   VTQQSKRQALKARFAR----NEIVTAPGIFDMISAKIADSMGFECLYMTGFGTVASYLGL 58

Query: 64  PDLGIITSAEIAERAKDLVRAADLPLLVDIDTGFGGVLNAARTAREMLEARVAAVQMEDQ 123
           PD G+ T  ++  R        + P++ D DTG+GG+LN A T R   +A  A +Q+EDQ
Sbjct: 59  PDAGLATYTDMVNRVAAFCGGTNTPMICDADTGYGGLLNVAHTVRGYEQAGAAGIQLEDQ 118

Query: 124 QLPKKCGHLNGKQLVPIKEMAQKIKAIKQAAPS--LIVVARTDARAQEGLDAAIKRSEAY 181
           + PKKCGH  G++++P+ +M +KIK   ++       +VARTDAR   GLD A++R EAY
Sbjct: 119 EFPKKCGHTPGRRVIPVDDMVRKIKVAAESRSDRDFQIVARTDARTSLGLDEALRRGEAY 178

Query: 182 IEAGADAIFPEALQAENEFRQFAERIPVPLLANMTEFGKTPYYRADEFEDMGFHMVIYPV 241
            +AGAD +F E+ ++  E         VPLL N+ E G+TP     E E +GF + IYP 
Sbjct: 179 AKAGADVLFIESPESIEELETIGRTFNVPLLVNIVEGGRTPQLAPRELEKLGFSLAIYPA 238

Query: 242 TSLRAAAKACERMFGLMKEHGSQKEGLHDMQTRKELYDTISYYDYEALDKTIA 294
           +   A AKA + M+G +  H S    +  M    E+ + + + +  A D+  A
Sbjct: 239 SGFLAVAKALKEMYGQILAHRSTVAAVDAMYPFSEMCELMGFPEVWAFDRAHA 291


Lambda     K      H
   0.318    0.133    0.370 

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: 230
Number of extensions: 13
Number of successful extensions: 3
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: 301
Length of database: 292
Length adjustment: 26
Effective length of query: 275
Effective length of database: 266
Effective search space:    73150
Effective search space used:    73150
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: 48 (23.1 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