GapMind for Amino acid biosynthesis

 

Aligments for a candidate for serB in Dyella japonica UNC79MFTsu3.2

Align 2-oxoglutarate reductase; EC 1.1.1.399; EC 1.1.1.95; EC 3.1.3.3 (characterized, see rationale)
to candidate N515DRAFT_3581 N515DRAFT_3581 D-3-phosphoglycerate dehydrogenase

Query= uniprot:L0G228_ECHVK
         (630 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3581 N515DRAFT_3581
           D-3-phosphoglycerate dehydrogenase
          Length = 410

 Score =  423 bits (1088), Expect = e-123
 Identities = 212/409 (51%), Positives = 292/409 (71%), Gaps = 3/409 (0%)

Query: 225 KFSYPKSRINVLLLENVHPIGVEIMKQEGYN-VEVVSSAMSEEELCEKIKNVSIIGIRSK 283
           K SYPK+ I VLLLE V    VE+ ++ GY+ +E    ++ E EL  +I    I+GIRS+
Sbjct: 2   KTSYPKADIKVLLLEGVSQSAVEVFRRAGYSQIEFHEKSLPEAELKARIAEAHIVGIRSR 61

Query: 284 TQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIF 343
           + +T  VLE A RL+AVG FCIGTNQ+DLET +++G+ VFNAP+SNTRSV EL I+E I 
Sbjct: 62  SHLTADVLEQARRLIAVGCFCIGTNQVDLETARQQGVPVFNAPYSNTRSVAELVIAEAIM 121

Query: 344 LMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDI 403
           L+R +  K    H+G W KSA+GSFEVR K LGI+GYG+IG Q+ VLAE++GM V ++DI
Sbjct: 122 LLRGIPQKNALCHRGGWTKSAAGSFEVRDKVLGIVGYGHIGTQVGVLAESLGMRVIFHDI 181

Query: 404 VERLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGH 463
             +L+LGNA    SLD+LLE  D+++LHV      K ++   ++ KM+KGA L+N SRG 
Sbjct: 182 ETKLSLGNARAAGSLDDLLERADVVTLHVPETPATKLMIGATELAKMRKGAALINASRGT 241

Query: 464 VVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQE 523
           VVD+ AL  AL +GH+AGAAVDVFP EPK ND+PF S L+G  N ILTPHIGGSTLEAQ+
Sbjct: 242 VVDIDALAAALRTGHVAGAAVDVFPLEPKGNDDPFVSPLVGMDNVILTPHIGGSTLEAQD 301

Query: 524 NIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASY 583
           NI   V  K++ Y ++G+T ++VNFP + LP   ++ RL+HIH+N PGVL++IN++ ++ 
Sbjct: 302 NIGIEVASKLVRYSDNGSTLSAVNFPEVTLPEHPNSRRLLHIHRNVPGVLSRINELFSAG 361

Query: 584 KINIVGQYLKTNEKIGYVITDI--DKRYSNDVIDALKEIEGTIRFRILY 630
            INI  Q+L+T+ ++GYV+ D+  D+  +  + D L  I GT+R R+LY
Sbjct: 362 NINIDAQFLQTDSQVGYVVIDVSADEAQAGALKDRLAAIPGTLRSRVLY 410


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: 607
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: 630
Length of database: 410
Length adjustment: 34
Effective length of query: 596
Effective length of database: 376
Effective search space:   224096
Effective search space used:   224096
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 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