Aligments for a candidate for serB in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Aligments for a candidate for serB in Pseudomonas fluorescens FW300-N1B4

Align 2-oxoglutarate reductase; EC 1.1.1.399; EC 1.1.1.95; EC 3.1.3.3 (characterized, see rationale)
to candidate Pf1N1B4_2272 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

Query= uniprot:L0G228_ECHVK
         (630 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2272
          Length = 409

 Score =  435 bits (1118), Expect = e-126
 Identities = 213/407 (52%), Positives = 297/407 (72%), Gaps = 1/407 (0%)

Query: 225 KFSYPKSRINVLLLENVHPIGVEIMKQEGY-NVEVVSSAMSEEELCEKIKNVSIIGIRSK 283
           K S  KS+I  LLLE VH   V+++K  GY ++E ++ ++ E +L EKI +   IGIRS+
Sbjct: 3   KTSLDKSKIKFLLLEGVHQSAVDVLKAAGYTSIEYLTGSLPEAQLKEKIADAHFIGIRSR 62

Query: 284 TQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIF 343
           TQ+T+++ ++A +L+AVG FCIGTNQ+DL   +E+GIAVFNAP+SNTRSV EL ++E I 
Sbjct: 63  TQLTEEIFDHAKKLVAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEAIL 122

Query: 344 LMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDI 403
           L+R + +K    H+G W KSA+ SFE+RGKKLGI+GYG+IG QLSVLAE +GM V++YD 
Sbjct: 123 LLRGIPEKNASCHRGGWIKSAANSFEIRGKKLGIVGYGSIGTQLSVLAEGLGMQVYFYDT 182

Query: 404 VERLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGH 463
           V +L LGNAT++ +L ELL   DI++LHV      + ++ +++I  +KKG IL+N +RG 
Sbjct: 183 VTKLPLGNATQVGNLHELLGMSDIVTLHVPETAATQWMIGEKEIRAIKKGGILINAARGT 242

Query: 464 VVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQE 523
           VV++ AL DA++  HL GAA+DVFP EP++N+E FES L G  N ILTPHIGGST EAQ 
Sbjct: 243 VVELDALADAIKDKHLIGAAIDVFPVEPRSNEEEFESPLRGLDNVILTPHIGGSTAEAQA 302

Query: 524 NIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASY 583
           NI   V  K+++Y ++G + +SVNFP + LP     HRL+HIH+N PGV+++IN+V A  
Sbjct: 303 NIGLEVAEKLVKYSDNGTSVSSVNFPEVALPAHPGKHRLLHIHENIPGVMSEINKVFAEN 362

Query: 584 KINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRILY 630
            INI GQ+L+TNEK+GYV+ D+D  YS    + L+ I GTIR R+L+
Sbjct: 363 GINISGQFLQTNEKVGYVVIDVDAEYSEMAQEKLQHINGTIRCRVLF 409


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: 641
Number of extensions: 23
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: 409
Length adjustment: 34
Effective length of query: 596
Effective length of database: 375
Effective search space:   223500
Effective search space used:   223500
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.

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Protein sequences (fasta format)
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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