GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaB in Burkholderia phytofirmans PsJN

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2; 3-carboxymuconate lactonizing enzyme; CMLE (uncharacterized)
to candidate BPHYT_RS14615 BPHYT_RS14615 fumarate hydratase

Query= curated2:Q9I6Q8
         (459 letters)



>FitnessBrowser__BFirm:BPHYT_RS14615
          Length = 466

 Score = 69.3 bits (168), Expect = 3e-16
 Identities = 75/235 (31%), Positives = 103/235 (43%), Gaps = 17/235 (7%)

Query: 71  LAEAVATAGNSAIPLVKALGRQVAAGDAEAERYVHLGATSQDAMDSGLVLQLRRALAL-L 129
           L E +A   +  +  V+   R+V   D      V+ G +S D   + + +    A+   L
Sbjct: 107 LNEVIANRASELLGGVRGEERKVHPNDD-----VNRGQSSNDVFPTAMHVAAAYAIVKHL 161

Query: 130 EQDLQRLAEVLADQAERHADTPLAGRTWLQHATPVTLGMKLAGLLGALTRHRQRLRELRP 189
           +  L+ L + L  +A+  AD    GRT LQ ATP+TLG + +G +  L    + +    P
Sbjct: 162 QPALKTLRDTLDGKAKAFADIVKIGRTHLQDATPLTLGQEFSGYVAQLDHGIRHVETALP 221

Query: 190 RLLVLQFGG-ASGT-LAALGEQALPVAAALAEELGLALPEQPWHTQ----RDRLVEFASV 243
            L  L  GG A GT L A  + A  VAAA+ +  GL     P   +     D LV     
Sbjct: 222 HLYELAQGGTAVGTGLNAHPQFADKVAAAIGKLTGLPFVSAPNKFEVMAAADALVFAHGA 281

Query: 244 LGLVAGSLGKFGRDVSLLM---QTEAGEVFEPAGAGRGGSSTMPHKRNPVSSAVL 295
           L  VA SL K   DV  L    +   GE+  P      GSS MP K NP  S  L
Sbjct: 282 LKTVAASLNKIANDVRWLASGPRCGLGELSIP--ENEPGSSIMPGKVNPTQSEAL 334


Lambda     K      H
   0.320    0.133    0.386 

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: 348
Number of extensions: 14
Number of successful extensions: 2
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: 459
Length of database: 466
Length adjustment: 33
Effective length of query: 426
Effective length of database: 433
Effective search space:   184458
Effective search space used:   184458
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 (21.8 bits)
S2: 51 (24.3 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