Alignments for a candidate for serB in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Shewanella oneidensis MR-1

Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate 200048 SO0862 D-3-phosphoglycerate dehydrogenase (NCBI ptt file)

Query= reanno::Cola:Echvi_2777
         (630 letters)



>FitnessBrowser__MR1:200048
          Length = 409

 Score =  421 bits (1081), Expect = e-122
 Identities = 205/407 (50%), Positives = 288/407 (70%), Gaps = 1/407 (0%)

Query: 225 KFSYPKSRINVLLLENVHPIGVEIMKQEGY-NVEVVSSAMSEEELCEKIKNVSIIGIRSK 283
           K S  K +I +LLLE VH   V++ ++ GY N+E   +++ +E L E IK+   IGIRS+
Sbjct: 3   KHSLDKDKIKILLLEGVHQSAVDVFERAGYTNIEYHKASLGDEALHESIKDAHFIGIRSR 62

Query: 284 TQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIF 343
           TQ++  VL+ A +L+A+G FCIGTNQ+DL T +  GI VFNAPFSNTRSV EL + EII 
Sbjct: 63  TQLSADVLKRAEKLIAIGCFCIGTNQVDLATAESLGIPVFNAPFSNTRSVAELVLGEIIM 122

Query: 344 LMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDI 403
           LMR + ++    H+G W K+A+GS+EVRGK LG+IGYG+IG QL +LAE +GM V ++DI
Sbjct: 123 LMRGIPERNAIAHRGGWMKTAAGSYEVRGKTLGVIGYGHIGTQLGILAETLGMRVVFFDI 182

Query: 404 VERLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGH 463
            ++L LGNA +I S+++LL   D++SLHV    + K++++  +   M+KG+I +N SRG 
Sbjct: 183 EDKLPLGNAQQIHSMEQLLAQADVVSLHVPETPQTKDMISTAEFAAMRKGSIFINASRGT 242

Query: 464 VVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQE 523
           VVD+ AL  AL+  HLAGAA+DVFP EP++ND+ F S L G  N +LTPH+GGST EAQE
Sbjct: 243 VVDIDALTVALKERHLAGAAIDVFPVEPQSNDDEFISPLRGLDNVLLTPHVGGSTAEAQE 302

Query: 524 NIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASY 583
           NI   V GK+ +Y ++G+T ++VNFP + LP  K   RL+HIHQN PGVL KIN+  +  
Sbjct: 303 NIGIEVAGKLAKYSDNGSTVSAVNFPEVSLPMHKGTSRLLHIHQNRPGVLIKINKAFSEK 362

Query: 584 KINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRILY 630
            INI  QYL+T  +IGYV+ ++D   + + +  LK I+GT+R R+L+
Sbjct: 363 GINIAAQYLQTTAEIGYVVMEVDTHQAEEALVELKAIDGTLRTRVLF 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: 612
Number of extensions: 11
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
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