Aligments for a candidate for leuB in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS10680 BWI76_RS10680 tartrate
           dehydrogenase
          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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis