GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Klebsiella michiganensis M5al

Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate BWI76_RS10680 BWI76_RS10680 tartrate dehydrogenase

Query= BRENDA::P76251
         (361 letters)



>FitnessBrowser__Koxy:BWI76_RS10680
          Length = 372

 Score =  662 bits (1709), Expect = 0.0
 Identities = 315/359 (87%), Positives = 335/359 (93%)

Query: 1   MMKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPD 60
           M KT+RIAAIPGDGIGKEVLPEG+RVLQAAAERWG ALSFE  EWASC+YY+ HG MMPD
Sbjct: 1   MNKTLRIAAIPGDGIGKEVLPEGVRVLQAAAERWGLALSFEHFEWASCDYYAQHGAMMPD 60

Query: 61  DWHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLA 120
           DW  QL  FDAIYFGAVGWPD VPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLA
Sbjct: 61  DWRAQLQTFDAIYFGAVGWPDIVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLA 120

Query: 121 GKQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQS 180
           GKQPGDIDFYVVRENTEGEYS+LGG VN GTEHEVVIQESVFTRRGVDRILRYAFELAQS
Sbjct: 121 GKQPGDIDFYVVRENTEGEYSALGGHVNPGTEHEVVIQESVFTRRGVDRILRYAFELAQS 180

Query: 181 RPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVV 240
           RPR+TLTSATKSNGLAISMP+WD+RVEAMA+ YPE++WDKQHIDILCARFV+QPERFDVV
Sbjct: 181 RPRRTLTSATKSNGLAISMPFWDQRVEAMAQEYPEVKWDKQHIDILCARFVLQPERFDVV 240

Query: 241 VASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIAT 300
           V SNLFGDILSDLGPACTGTIGIAPSANLNP+RTFPSLFE VHGSAPDIYGKNIANPIAT
Sbjct: 241 VGSNLFGDILSDLGPACTGTIGIAPSANLNPDRTFPSLFEAVHGSAPDIYGKNIANPIAT 300

Query: 301 IWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHGPKTPDMKGNATTPQVADAICKII 359
           IWAGAMMLDFLGNGD R+Q AH+GILAAIE+ IA GPKTPDM+G A+T QV +AIC+ I
Sbjct: 301 IWAGAMMLDFLGNGDARYQAAHDGILAAIEQTIASGPKTPDMQGTASTQQVGEAICQAI 359


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: 605
Number of extensions: 19
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: 361
Length of database: 372
Length adjustment: 30
Effective length of query: 331
Effective length of database: 342
Effective search space:   113202
Effective search space used:   113202
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