GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Phyllobacterium endophyticum PEPV15

Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_106717507.1 CU100_RS15545 tartrate dehydrogenase

Query= BRENDA::P76251
         (361 letters)



>NCBI__GCF_003010935.1:WP_106717507.1
          Length = 357

 Score =  489 bits (1258), Expect = e-143
 Identities = 237/354 (66%), Positives = 288/354 (81%), Gaps = 6/354 (1%)

Query: 7   IAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDDWHEQL 66
           IA I GDGIGKEV+PEGIRVL+AAA R GF L  +  ++A C+YY+ HG+MMP++W E++
Sbjct: 8   IAVIEGDGIGKEVIPEGIRVLEAAARRHGFTLRQKWHDFAHCDYYARHGRMMPENWKEEI 67

Query: 67  SRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAGKQPGD 126
            +  AI+FGAVGWPD VPDHISLWGSLL+FRRE+DQYVNLRPVRL  GVPCPL+G++PGD
Sbjct: 68  GKPAAIFFGAVGWPDIVPDHISLWGSLLQFRREYDQYVNLRPVRLMDGVPCPLSGRRPGD 127

Query: 127 IDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQSRPRKTL 186
           IDF+VVRENTEGEYS++GGR+ EGTE E+V+QE+V TR+GVDRIL++AF+LAQ+RPRK +
Sbjct: 128 IDFWVVRENTEGEYSAIGGRMFEGTEREMVMQETVMTRKGVDRILKFAFDLAQTRPRKLV 187

Query: 187 TSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVVVASNLF 246
           TSATKSNG+AI+MPYWDERVEAMA +YPE+ W+K HIDIL A FV++P+ FDVVV SNLF
Sbjct: 188 TSATKSNGIAITMPYWDERVEAMASSYPEVSWNKFHIDILTANFVLKPQIFDVVVGSNLF 247

Query: 247 GDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIATIWAGAM 306
           GDILSDLGPAC GTIGIAPS N+NPE   PSLFEPVHGSAPDI G+N+ANPI  IW+ AM
Sbjct: 248 GDILSDLGPACAGTIGIAPSGNINPEGEHPSLFEPVHGSAPDIAGRNLANPIGQIWSAAM 307

Query: 307 MLDFLGNGDERFQQAHNGILAAIEEVIAH-GPKTPDMKGNATTPQVADAICKII 359
           MLD LG      +QA   I+ AIE V+     +T D+ G A T     AI  ++
Sbjct: 308 MLDHLGE-----KQAAADIMGAIEMVLKQPSLRTRDLGGAADTQTCGKAIADLL 356


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: 455
Number of extensions: 12
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: 357
Length adjustment: 29
Effective length of query: 332
Effective length of database: 328
Effective search space:   108896
Effective search space used:   108896
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 Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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