Aligments for a candidate for serB in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Aligments for a candidate for serB in Pseudomonas stutzeri RCH2

Align 2-oxoglutarate reductase; EC 1.1.1.399; EC 1.1.1.95; EC 3.1.3.3 (characterized, see rationale)
to candidate GFF3804 Psest_3873 Phosphoglycerate dehydrogenase and related dehydrogenases

Query= uniprot:L0G228_ECHVK
         (630 letters)



>lcl|FitnessBrowser__psRCH2:GFF3804 Psest_3873 Phosphoglycerate
           dehydrogenase and related dehydrogenases
          Length = 411

 Score =  447 bits (1151), Expect = e-130
 Identities = 225/405 (55%), Positives = 298/405 (73%), Gaps = 1/405 (0%)

Query: 227 SYPKSRINVLLLENVHPIGVEIMKQEGY-NVEVVSSAMSEEELCEKIKNVSIIGIRSKTQ 285
           S  KS+I  LLLE VH   V+ +K  GY N+E +  A+S EEL EKI +V  IGIRS+TQ
Sbjct: 7   SLDKSKIKFLLLEGVHQNAVDTLKAAGYTNIEYLKGALSTEELKEKIADVHFIGIRSRTQ 66

Query: 286 ITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLM 345
           +T++V + A +L+AVG FCIGTNQ++L   +E+GIAVFNAP+SNTRSV EL ++E I L+
Sbjct: 67  LTEEVFDAAKKLIAVGCFCIGTNQVNLNAARERGIAVFNAPYSNTRSVAELVLAEAILLL 126

Query: 346 RNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDIVE 405
           R + +K    H+G W KSA+ SFE+RGKKLGIIGYG+IG QLSVLAE +GM VF+YD+V 
Sbjct: 127 RGIPEKNASCHRGGWIKSAANSFEIRGKKLGIIGYGSIGTQLSVLAEALGMQVFFYDVVT 186

Query: 406 RLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVV 465
           +L LGNAT+I SL ELL  CDI+SLHV      + ++ +++I  MKKGAIL+N +RG VV
Sbjct: 187 KLPLGNATQIGSLYELLGMCDIVSLHVPELPSTQWMIGEKEIRAMKKGAILINAARGTVV 246

Query: 466 DVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENI 525
           ++  L  A++  HL GAA+DVFP EPK+NDE FES L G    ILTPHIGGST EAQ NI
Sbjct: 247 ELDHLAAAIKDEHLIGAAIDVFPVEPKSNDEEFESPLRGLDRVILTPHIGGSTAEAQANI 306

Query: 526 AQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKI 585
              V  K+++Y ++G + +SVNFP + LP     HRL+HIHQN PGV+++IN+V A   I
Sbjct: 307 GLEVAEKLVKYSDNGTSVSSVNFPEVALPSHPGKHRLLHIHQNIPGVMSEINKVFADNGI 366

Query: 586 NIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRILY 630
           NI GQ+L+TNEK+GYV+ D+DK YS+  ++ L+ + GTIR R+L+
Sbjct: 367 NICGQFLQTNEKVGYVVIDVDKEYSDLALEKLQHVNGTIRSRVLF 411


Lambda     K      H
   0.317    0.136    0.377 

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: 642
Number of extensions: 28
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: 630
Length of database: 411
Length adjustment: 34
Effective length of query: 596
Effective length of database: 377
Effective search space:   224692
Effective search space used:   224692
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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