GapMind for Amino acid biosynthesis

 

Aligments for a candidate for serB in Pseudomonas fluorescens GW456-L13

Align 2-oxoglutarate reductase; EC 1.1.1.399; EC 1.1.1.95; EC 3.1.3.3 (characterized, see rationale)
to candidate PfGW456L13_943 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

Query= uniprot:L0G228_ECHVK
         (630 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_943
           D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
          Length = 409

 Score =  434 bits (1115), Expect = e-126
 Identities = 212/407 (52%), Positives = 298/407 (73%), 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  TQLTEEIFDHAKKLVAVGCFCIGTNQVDLDAARERGIAVFNAPYSNTRSVAELVLAEAIL 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
           + +L LGNAT++ +L ELL   DI+SLHV      + ++ +++I  +KKG IL+N +RG 
Sbjct: 183 ITKLPLGNATQVGNLHELLAMSDIVSLHVPETAATQWMMGEKEIRAIKKGGILINAARGT 242

Query: 464 VVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQE 523
           VV++  L  A++  HL GAA+DVFP EP++NDE FES L G  N ILTPHIGGST EAQ 
Sbjct: 243 VVELDHLAAAIKDKHLIGAAIDVFPVEPRSNDEEFESPLRGLDNVILTPHIGGSTAEAQA 302

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

Query: 584 KINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRILY 630
            INI GQ+L+TNEK+GYV+ D+D  YS+   + L+ ++GTIR R+L+
Sbjct: 363 GINISGQFLQTNEKVGYVVIDVDAEYSDLAQEKLQHVKGTIRSRVLF 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: 634
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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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 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