GapMind for Amino acid biosynthesis

 

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

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Pf1N1B4_2272 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

Query= BRENDA::P0A9T0
         (410 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2272 D-3-phosphoglycerate
           dehydrogenase (EC 1.1.1.95)
          Length = 409

 Score =  540 bits (1390), Expect = e-158
 Identities = 268/411 (65%), Positives = 335/411 (81%), Gaps = 3/411 (0%)

Query: 1   MAKVSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLR 60
           M+K SL+K KIKFLL+EGVHQ A++ L+AAGYT+IE+  G+L + QLKE I DAHFIG+R
Sbjct: 1   MSKTSLDKSKIKFLLLEGVHQSAVDVLKAAGYTSIEYLTGSLPEAQLKEKIADAHFIGIR 60

Query: 61  SRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEL 120
           SRT LTE++ + A+KLVA+GCFCIGTNQVDL+AA +RGI VFNAP+SNTRSVAELV+ E 
Sbjct: 61  SRTQLTEEIFDHAKKLVAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEA 120

Query: 121 LLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFY 180
           +LLLRG+PE NA  HRG W K AA SFE RGKKLGI+GYG IGTQL +LAE LGM VYFY
Sbjct: 121 ILLLRGIPEKNASCHRGGWIKSAANSFEIRGKKLGIVGYGSIGTQLSVLAEGLGMQVYFY 180

Query: 181 DIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASR 240
           D   KLPLGNATQV +L +LL MSD+V+LHVPE  +T+ M+G KEI  +K G +LINA+R
Sbjct: 181 DTVTKLPLGNATQVGNLHELLGMSDIVTLHVPETAATQWMIGEKEIRAIKKGGILINAAR 240

Query: 241 GTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEA 300
           GTVV++ AL DA+  KHL GAAIDVFP EP +N + F SPL   DNV+LTPHIGGST EA
Sbjct: 241 GTVVELDALADAIKDKHLIGAAIDVFPVEPRSNEEEFESPLRGLDNVILTPHIGGSTAEA 300

Query: 301 QENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGR-RLMHIHENRPGVLTALNKIFA 359
           Q NIGLEVA KL+KYSDNG+++S+VNFPEV+LP H G+ RL+HIHEN PGV++ +NK+FA
Sbjct: 301 QANIGLEVAEKLVKYSDNGTSVSSVNFPEVALPAHPGKHRLLHIHENIPGVMSEINKVFA 360

Query: 360 EQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410
           E G+NI+ Q+LQT+ ++GYVVID++A  + +E A + ++ I GTIR R+L+
Sbjct: 361 ENGINISGQFLQTNEKVGYVVIDVDA--EYSEMAQEKLQHINGTIRCRVLF 409


Lambda     K      H
   0.318    0.135    0.383 

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: 511
Number of extensions: 21
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: 410
Length of database: 409
Length adjustment: 31
Effective length of query: 379
Effective length of database: 378
Effective search space:   143262
Effective search space used:   143262
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 (21.7 bits)
S2: 50 (23.9 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