GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Hyphomicrobium sulfonivorans WDL6

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_068463039.1 APY04_RS11295 NAD-dependent formate dehydrogenase

Query= BRENDA::O58256
         (333 letters)



>NCBI__GCF_001541235.1:WP_068463039.1
          Length = 401

 Score =  145 bits (365), Expect = 2e-39
 Identities = 88/243 (36%), Positives = 141/243 (58%), Gaps = 7/243 (2%)

Query: 54  ITREVLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLM 113
           +T E L+ A++LK+      G D++DL+ A K G+ V +V+   S +VAE  V +I++L+
Sbjct: 104 LTEERLKKAKKLKLAITAGIGSDHVDLDAAMKNGVTVAEVTYSNSISVAEHVVMMILSLV 163

Query: 114 RKIHYADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKLY 173
           R    + +++++G W     I    +R   L G  VG +G G IG A+ RRL PF VKL+
Sbjct: 164 RNYLPSYEWVKKGGWN----IADCVERSYDLEGMNVGTVGAGRIGLAVLRRLKPFDVKLH 219

Query: 174 YWSRHR-KVNVEKELKARY-MDIDELLEKSDIVILALPLTRDTYHIINEERVKKLE-GKY 230
           Y  RHR    VEKEL   Y  D++ L++  D+V +  PL  +T H+ + + + K++ G Y
Sbjct: 220 YTDRHRLPKEVEKELGLIYHKDVESLVKVCDVVTINAPLHSETEHLFDAKMISKMKHGAY 279

Query: 231 LVNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKEPVREHELFKYEWETVLTPHYAGLAL 290
           L+N  R  +VD  AV +A++ G+L GYA DV+  +P  +   ++      +TPH +G +L
Sbjct: 280 LINTARAKIVDRDAVVKALESGQLAGYAGDVWFPQPAPKDHPWRKMPHHGMTPHISGTSL 339

Query: 291 EAQ 293
            AQ
Sbjct: 340 SAQ 342


Lambda     K      H
   0.319    0.139    0.393 

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: 316
Number of extensions: 19
Number of successful extensions: 4
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: 333
Length of database: 401
Length adjustment: 30
Effective length of query: 303
Effective length of database: 371
Effective search space:   112413
Effective search space used:   112413
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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