Aligments for a candidate for hom in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Aligments for a candidate for hom in Acidovorax sp. GW101-3H11

Align Homoserine dehydrogenase; EC 1.1.1.3 (characterized, see rationale)
to candidate Ac3H11_1507 Homoserine dehydrogenase (EC 1.1.1.3)

Query= uniprot:A0A1L6J6Q3
         (430 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1507
          Length = 444

 Score =  333 bits (854), Expect = 6e-96
 Identities = 192/431 (44%), Positives = 267/431 (61%), Gaps = 16/431 (3%)

Query: 3   EPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFDWV 62
           +P++V L G+GTVG+GV  ++  N + I+RRAGR IEI  V+  D  + + V       V
Sbjct: 2   KPIQVGLLGIGTVGSGVFNVLARNQDEISRRAGRGIEITMVADLDVERAKAVVGEGIQVV 61

Query: 63  DDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQVAE 122
           +D   +  +P  D+V+ELIGG  G A AL    +AAGK +VTANKA++A HG E+   A 
Sbjct: 62  NDARAIIANPDIDIVIELIGGY-GIARALVLEAIAAGKHVVTANKALLAVHGTEIFAAAS 120

Query: 123 KSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGEVL 182
                + FEAAVAGG+P+IK LREG  AN+I  + GI+NGT NFILS+M ++G DF  VL
Sbjct: 121 AKGVMVAFEAAVAGGIPIIKALREGLTANRIQWLAGIINGTTNFILSEMRSKGLDFDVVL 180

Query: 183 AEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAEAA 242
            EAQ  G+AEADP+FDI+GVDAAHK++++++IAFG    F    + GI  L AADI  A 
Sbjct: 181 KEAQRLGYAEADPTFDIEGVDAAHKVTLMSAIAFGIPVQFDKAYVEGITKLGAADIKYAE 240

Query: 243 ALGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQGAG 302
            LGYRI+LLGI   +  G+  RVHP LVP    +A+V G  NAVV +G+ VG  L+ G G
Sbjct: 241 QLGYRIKLLGITKRADKGIELRVHPSLVPSKRLIANVEGAMNAVVVQGDAVGTTLYYGKG 300

Query: 303 AGDGPTASAVVADLIDIARTEFG-PPYAMPATSLAAE---------PVAPTGERRGRAYL 352
           AG  PTASAV+ADL+DIAR     P + +P  +  +          PV P  E     YL
Sbjct: 301 AGSEPTASAVIADLVDIARLHTADPEHRVPHLAFQSNTLQGAMDQLPVLPMSEVVTSYYL 360

Query: 353 RFTVADKVGVLAEIAAAMRDAGVSIESLIQR-----GAMADGSVLVAIVTHEVPERSIAQ 407
           R  VAD+ GVLA++   + +AGVSI++++QR     G        + I+TH+  E ++  
Sbjct: 361 RLRVADQAGVLAKVTGLLAEAGVSIDAVLQREADEVGGEGSTQTDLIILTHDTREGTMDA 420

Query: 408 ALEKLRGSPSL 418
            + +++  P++
Sbjct: 421 VIAQMQALPTV 431


Lambda     K      H
   0.319    0.136    0.388 

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: 492
Number of extensions: 17
Number of successful extensions: 3
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: 430
Length of database: 444
Length adjustment: 32
Effective length of query: 398
Effective length of database: 412
Effective search space:   163976
Effective search space used:   163976
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: 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 (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 paper from 2022 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