GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF3804
          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.

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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:

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