GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__PV4:5210768
          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:

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