GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hom in Desulfovibrio vulgaris Miyazaki F

Align Homoserine dehydrogenase; EC 1.1.1.3 (characterized, see rationale)
to candidate 8500664 DvMF_1412 homoserine dehydrogenase (RefSeq)

Query= uniprot:B8DRS3_DESVM
         (436 letters)



>lcl|FitnessBrowser__Miya:8500664 DvMF_1412 homoserine dehydrogenase
           (RefSeq)
          Length = 436

 Score =  853 bits (2205), Expect = 0.0
 Identities = 436/436 (100%), Positives = 436/436 (100%)

Query: 1   MGSDSDKPGGKRLVIGMAGFGTVGSGLARVLDENRQWITERTGREMVIKTILVRDLAKPR 60
           MGSDSDKPGGKRLVIGMAGFGTVGSGLARVLDENRQWITERTGREMVIKTILVRDLAKPR
Sbjct: 1   MGSDSDKPGGKRLVIGMAGFGTVGSGLARVLDENRQWITERTGREMVIKTILVRDLAKPR 60

Query: 61  AWPVPQGATLTADPAVLTDDPEIDVLVELMGGIAAPHAIIKRALEAGKHVVTANKALLAE 120
           AWPVPQGATLTADPAVLTDDPEIDVLVELMGGIAAPHAIIKRALEAGKHVVTANKALLAE
Sbjct: 61  AWPVPQGATLTADPAVLTDDPEIDVLVELMGGIAAPHAIIKRALEAGKHVVTANKALLAE 120

Query: 121 DGYDLYRLAEQKNVGLHHEASVAGGIPIVQTLKESLAGNRIGSLVGILNGTANYILSEMT 180
           DGYDLYRLAEQKNVGLHHEASVAGGIPIVQTLKESLAGNRIGSLVGILNGTANYILSEMT
Sbjct: 121 DGYDLYRLAEQKNVGLHHEASVAGGIPIVQTLKESLAGNRIGSLVGILNGTANYILSEMT 180

Query: 181 SNGLDFATALAQAQELGYAEADPTLDIEGHDTAHKLVLLIRLAYGMDYPYAELPVQGIAG 240
           SNGLDFATALAQAQELGYAEADPTLDIEGHDTAHKLVLLIRLAYGMDYPYAELPVQGIAG
Sbjct: 181 SNGLDFATALAQAQELGYAEADPTLDIEGHDTAHKLVLLIRLAYGMDYPYAELPVQGIAG 240

Query: 241 IDRMDIEFARELGFRIKLLAQVREVDGKLEAGVFPTLVKHTFLIARVGGAYNAIRLEGNA 300
           IDRMDIEFARELGFRIKLLAQVREVDGKLEAGVFPTLVKHTFLIARVGGAYNAIRLEGNA
Sbjct: 241 IDRMDIEFARELGFRIKLLAQVREVDGKLEAGVFPTLVKHTFLIARVGGAYNAIRLEGNA 300

Query: 301 VGPVFLHGLGAGSLPTASAVLADLMTVARGAAPHNTGFQRQVPPRADILPPADAESSYYV 360
           VGPVFLHGLGAGSLPTASAVLADLMTVARGAAPHNTGFQRQVPPRADILPPADAESSYYV
Sbjct: 301 VGPVFLHGLGAGSLPTASAVLADLMTVARGAAPHNTGFQRQVPPRADILPPADAESSYYV 360

Query: 361 RAMVPDNPGVLRDLAGAMADHSISIAQAIQKGQHPQGVPLVFMTHAAKASAIQGAIAQVQ 420
           RAMVPDNPGVLRDLAGAMADHSISIAQAIQKGQHPQGVPLVFMTHAAKASAIQGAIAQVQ
Sbjct: 361 RAMVPDNPGVLRDLAGAMADHSISIAQAIQKGQHPQGVPLVFMTHAAKASAIQGAIAQVQ 420

Query: 421 AAGLLLAPPVCYRVLQ 436
           AAGLLLAPPVCYRVLQ
Sbjct: 421 AAGLLLAPPVCYRVLQ 436


Lambda     K      H
   0.319    0.137    0.394 

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: 796
Number of extensions: 19
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: 436
Length of database: 436
Length adjustment: 32
Effective length of query: 404
Effective length of database: 404
Effective search space:   163216
Effective search space used:   163216
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 (21.7 bits)
S2: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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