GapMind for Amino acid biosynthesis

 

Aligments for a candidate for serA in Shewanella loihica PV-4

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate 5210768 Shew_3196 D-3-phosphoglycerate dehydrogenase (RefSeq)

Query= BRENDA::P0A9T0
         (410 letters)



>lcl|FitnessBrowser__PV4:5210768 Shew_3196 D-3-phosphoglycerate
           dehydrogenase (RefSeq)
          Length = 409

 Score =  572 bits (1473), Expect = e-168
 Identities = 283/411 (68%), Positives = 345/411 (83%), Gaps = 3/411 (0%)

Query: 1   MAKVSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLR 60
           MAK SL+KDKIK LL+EGVHQ A++  + AGY NIE+HK +L +E+L  SI+DAHF+G+R
Sbjct: 1   MAKHSLDKDKIKILLLEGVHQSAVDVFKRAGYNNIEYHKASLGEEELLASIKDAHFVGIR 60

Query: 61  SRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEL 120
           SRT LT+ V++ AEKLV+IGCFCIGTNQVDL AA K GIPVFNAPFSNTRSVAELV+GE+
Sbjct: 61  SRTQLTKAVLDKAEKLVSIGCFCIGTNQVDLAAAEKLGIPVFNAPFSNTRSVAELVLGEI 120

Query: 121 LLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFY 180
           ++LLRG+P+ NA AHRG W K A GSFEARGK LG+IGYGHIGTQLGILAE+LGM V F+
Sbjct: 121 IMLLRGIPQRNALAHRGGWLKSANGSFEARGKTLGVIGYGHIGTQLGILAETLGMRVIFF 180

Query: 181 DIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASR 240
           DIE+KLPLGNA Q+  L  LL+++DVVSLHVPE P TKNM+G+KE++ M+ GS+LINASR
Sbjct: 181 DIEDKLPLGNAQQIHSLEQLLSLADVVSLHVPETPQTKNMIGSKELAAMRQGSILINASR 240

Query: 241 GTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEA 300
           GTVVDI AL +A+   H+ GAAIDVFP EP +N D F SPL   DNVLLTPH+GGSTQEA
Sbjct: 241 GTVVDIDALAEAIRGDHIVGAAIDVFPVEPKSNDDEFVSPLRGLDNVLLTPHVGGSTQEA 300

Query: 301 QENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLH-GGRRLMHIHENRPGVLTALNKIFA 359
           QENIG+EVAGKL KYSDNGST++AVNFPEVSL  H    RL+HIH NRPG+L  +N+ FA
Sbjct: 301 QENIGIEVAGKLAKYSDNGSTMTAVNFPEVSLAQHKDTSRLLHIHHNRPGILIKINQAFA 360

Query: 360 EQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410
           E+G+NIAAQYLQT+A++GYVV+++ +D+  A++AL+ MKAI GTIR RLL+
Sbjct: 361 EKGINIAAQYLQTTAEIGYVVMEVNSDQ--ADEALEEMKAIDGTIRTRLLH 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: 495
Number of extensions: 15
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.

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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 paper from 2022 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