GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Klebsiella michiganensis M5al

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate BWI76_RS23920 BWI76_RS23920 D-3-phosphoglycerate dehydrogenase

Query= BRENDA::P0A9T0
         (410 letters)



>FitnessBrowser__Koxy:BWI76_RS23920
          Length = 410

 Score =  749 bits (1935), Expect = 0.0
 Identities = 375/410 (91%), Positives = 398/410 (97%)

Query: 1   MAKVSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLR 60
           MAKVSLEKDKIKFLLVEGVHQKA++SLRAAGYTNIEFHKGALD E+LK SIRDAHFIGLR
Sbjct: 1   MAKVSLEKDKIKFLLVEGVHQKAVDSLRAAGYTNIEFHKGALDSEELKASIRDAHFIGLR 60

Query: 61  SRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEL 120
           SRTHLTE++  AAEKLVA+GCFCIGTNQVDL+AAAKRGIPVFNAPFSNTRSVAELVIGEL
Sbjct: 61  SRTHLTEEIFAAAEKLVAVGCFCIGTNQVDLNAAAKRGIPVFNAPFSNTRSVAELVIGEL 120

Query: 121 LLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFY 180
           LL+LRGVP ANAKAHRGVWNKLA GSFEARGKKLGIIGYGHIGTQLGILAESLGM+VYFY
Sbjct: 121 LLMLRGVPAANAKAHRGVWNKLAVGSFEARGKKLGIIGYGHIGTQLGILAESLGMHVYFY 180

Query: 181 DIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASR 240
           DIE+KLPLGNATQVQHLSDLLNMSDVVSLHVPEN STKNM+GA+E++LMKPG+LLINASR
Sbjct: 181 DIESKLPLGNATQVQHLSDLLNMSDVVSLHVPENASTKNMIGAEELALMKPGALLINASR 240

Query: 241 GTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEA 300
           GTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPF SPLCEFDNV+LTPHIGGSTQEA
Sbjct: 241 GTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFNSPLCEFDNVILTPHIGGSTQEA 300

Query: 301 QENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGRRLMHIHENRPGVLTALNKIFAE 360
           QENIGLEVAGKL KYSDNGSTLSAVNFPEVSLPLHGGRRL+HIHENRPGVLTALN+IFA 
Sbjct: 301 QENIGLEVAGKLAKYSDNGSTLSAVNFPEVSLPLHGGRRLLHIHENRPGVLTALNQIFAA 360

Query: 361 QGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410
           QG+NIAAQYLQT+ QMGYVVIDIEA+EDVA+ ALQAMKAIPGTIRARLL+
Sbjct: 361 QGINIAAQYLQTTPQMGYVVIDIEAEEDVAQAALQAMKAIPGTIRARLLF 410


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: 647
Number of extensions: 10
Number of successful extensions: 1
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: 410
Length adjustment: 31
Effective length of query: 379
Effective length of database: 379
Effective search space:   143641
Effective search space used:   143641
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