GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Pseudomonas fluorescens FW300-N2C3

Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate AO356_26735 AO356_26735 tartrate dehydrogenase

Query= BRENDA::P76251
         (361 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26735
          Length = 359

 Score =  585 bits (1508), Expect = e-172
 Identities = 273/355 (76%), Positives = 312/355 (87%)

Query: 1   MMKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPD 60
           M K  RIAAI GDGIGKEVLPEG+RVL+ AA++W   LS E ++WA C+YY  HG+MMP 
Sbjct: 1   MSKPFRIAAIAGDGIGKEVLPEGLRVLEQAAKKWQLDLSIEVLDWAHCDYYLEHGQMMPA 60

Query: 61  DWHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLA 120
           DW  QL  FDAIYFGAVGWPD VPDHISLWGSLLKFRR+FDQYVN+RPVRLFPGVPCPLA
Sbjct: 61  DWFAQLKDFDAIYFGAVGWPDKVPDHISLWGSLLKFRRDFDQYVNIRPVRLFPGVPCPLA 120

Query: 121 GKQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQS 180
           G++ GDIDF V+RENTEGEYSS+GG++ EGTEHE V+QESVFTRRGVDRIL++AF+LAQ+
Sbjct: 121 GREAGDIDFVVIRENTEGEYSSIGGKMFEGTEHEFVLQESVFTRRGVDRILKFAFDLAQT 180

Query: 181 RPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVV 240
           RPRK LT+ATKSNG++ISMPYWDER   MA+ YP++ WDKQHIDILCARFV+QP+RFDVV
Sbjct: 181 RPRKRLTAATKSNGISISMPYWDERTALMAQQYPDVTWDKQHIDILCARFVLQPDRFDVV 240

Query: 241 VASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIAT 300
           VASNLFGDILSDLGPAC GTIGIAPSANL+PER FPSLFEPVHGSAPDIYG+NIANPIA 
Sbjct: 241 VASNLFGDILSDLGPACAGTIGIAPSANLDPERRFPSLFEPVHGSAPDIYGRNIANPIAM 300

Query: 301 IWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHGPKTPDMKGNATTPQVADAI 355
           IW+GA+MLDFLGNGDER++ AH+GIL AIE+VIA GP TPD+ G  +T  V  AI
Sbjct: 301 IWSGALMLDFLGNGDERYRAAHDGILRAIEQVIAEGPITPDLGGQGSTQDVGQAI 355


Lambda     K      H
   0.321    0.138    0.432 

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: 533
Number of extensions: 10
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: 361
Length of database: 359
Length adjustment: 29
Effective length of query: 332
Effective length of database: 330
Effective search space:   109560
Effective search space used:   109560
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: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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