GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Pseudomonas fluorescens GW456-L13

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate PfGW456L13_943 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

Query= BRENDA::P0A9T0
         (410 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_943
          Length = 409

 Score =  540 bits (1391), Expect = e-158
 Identities = 272/412 (66%), Positives = 336/412 (81%), Gaps = 5/412 (1%)

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+GCFCIGTNQVDLDAA +RGI VFNAP+SNTRSVAELV+ E 
Sbjct: 61  SRTQLTEEIFDHAKKLVAVGCFCIGTNQVDLDAARERGIAVFNAPYSNTRSVAELVLAEA 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+VSLHVPE  +T+ MMG KEI  +K G +LINA+R
Sbjct: 181 DTITKLPLGNATQVGNLHELLAMSDIVSLHVPETAATQWMMGEKEIRAIKKGGILINAAR 240

Query: 241 GTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEA 300
           GTVV++  L  A+  KHL GAAIDVFP EP +N + F SPL   DNV+LTPHIGGST EA
Sbjct: 241 GTVVELDHLAAAIKDKHLIGAAIDVFPVEPRSNDEEFESPLRGLDNVILTPHIGGSTAEA 300

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

Query: 360 EQGVNIAAQYLQTSAQMGYVVIDIEAD-EDVAEKALQAMKAIPGTIRARLLY 410
           E G+NI+ Q+LQT+ ++GYVVID++A+  D+A++ LQ +K   GTIR+R+L+
Sbjct: 361 ENGINISGQFLQTNEKVGYVVIDVDAEYSDLAQEKLQHVK---GTIRSRVLF 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: 518
Number of extensions: 21
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: 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.

Links

Downloads

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:

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