GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Thioalkalivibrio denitrificans ALJD

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_077277352.1 B1C78_RS01365 3-phosphoglycerate dehydrogenase

Query= BRENDA::O08651
         (533 letters)



>NCBI__GCF_002000365.1:WP_077277352.1
          Length = 319

 Score =  156 bits (394), Expect = 1e-42
 Identities = 100/285 (35%), Positives = 152/285 (53%), Gaps = 10/285 (3%)

Query: 8   KILISDSLDPCCRKI-----LQDGGLQVVEKQNLSKEELIAELQDCEGLI-VRSATKVTA 61
           KI+I D    C R +     L D  + V        E L    +D E L+ +R  T +T 
Sbjct: 2   KIVIPDDYQDCVRTLACFARLADHEVTVYNDTVRDVETLAERFRDAEALVLIRERTPITD 61

Query: 62  DVINAAEKLQVVGRAGTGVDNVDLEAATRKGVLVMNTPNGNSLSAAELTCGMLMCLARQI 121
           +++    +L+++ + G G+ +VDLEA TR+GV V     G   +AAELT G+++   R I
Sbjct: 62  ELLERLPRLRLISQTGKGIAHVDLEACTRRGVAVA-VGTGAPFAAAELTWGLIIAAMRHI 120

Query: 122 PQATASMKDGKWDRKKFMGTELNGKTLGILGLGRIGREVAARMQAFGMKTVGYDPIISPE 181
           P   A+MK GKW  +  +GT L G+TLGI G G+IG  VA   +AF M+ + +    S E
Sbjct: 121 PAEVAAMKAGKWQTR--LGTGLRGRTLGIFGYGKIGSLVAHYGRAFAMRVLVWGREGSLE 178

Query: 182 VAASFGVQQLPLEE-IWPLCDFITVHTPLLPSTTGLLNDSTFAQCKKGVRVVNCARGGIV 240
            AA  G      +E ++   D +++H  L   T G++     A  K    +VN +R  ++
Sbjct: 179 RAAMVGFDTAKSQEDLFARSDVLSLHLALNEGTRGIVTADHLAAMKPTALLVNTSRAELI 238

Query: 241 DEGALLRALQSGQCAGAALDVFTEEPPRDRALVDHENVISCPHLG 285
            EGAL+ AL++G+   AA+DV+  EP RD  L+  +N +  PHLG
Sbjct: 239 AEGALVDALKAGRPGMAAVDVYENEPVRDHPLLHLDNALCTPHLG 283


Lambda     K      H
   0.318    0.134    0.394 

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: 341
Number of extensions: 18
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: 533
Length of database: 319
Length adjustment: 31
Effective length of query: 502
Effective length of database: 288
Effective search space:   144576
Effective search space used:   144576
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 Apr 10 2024. The underlying query database was built on Apr 09 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