Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_011886200.1 glyoxylate/hydroxypyruvate reductase A
Query= reanno::SB2B:6938941 (308 letters) >NCBI__GCF_000016205.1:WP_011886200.1 Length = 313 Score = 111 bits (278), Expect = 2e-29 Identities = 98/318 (30%), Positives = 138/318 (43%), Gaps = 19/318 (5%) Query: 4 KLLLLTRENER--YRSLLASCHLPELELLDDNPANIRLAD---IWLAEPGLAAPLVNHAS 58 KLL T E +R LA LP+ EL + P + AD +W A L AP Sbjct: 2 KLLFYTPHQEAGAWRDALAHA-LPDAELREWQPGDTAAADYALVWRAPRALFAP----RE 56 Query: 59 GLRWMQSTFAGVD-LLVKPRQRRDYLLTNVRGI------FGPLMSEYLFGYLLARQREHD 111 LR + + AGVD LL R L +V + M EY+ +L R D Sbjct: 57 RLRAIFNLGAGVDALLALERAHPGTLPPDVPLVRLEDSGMAQQMIEYVTYAVLRYLRRFD 116 Query: 112 LYKSQQQQKLWLPGSYKTLQGSELLLLGTGSIAKHLAQTAKHFGMKVAGINRSAKATEGF 171 Y + Q ++ W + +LG G + +AQ G+ V G +RS K +G Sbjct: 117 EYDALQHERRWEVLEPHPRARFTVAVLGLGVLGAQVAQALAALGLPVRGYSRSPKQLDGI 176 Query: 172 DEVATLEALPTLMARADAIASILPSTEATRGILNENILARMKPDAVLFNLGRG-DVLDLD 230 A A + A + ++LPST T IL+ AR+ P A L N+ RG +++ D Sbjct: 177 ATFAGEHAFDACIDGAKVLVNLLPSTPDTDAILSARTFARLAPGAYLVNVARGAHLVEAD 236 Query: 231 ALERQLRQHPQQQAVLDVFNQEPLPEDHPIWGLGNVIVTPHIAAPSFPEQVAEIFSSNYH 290 L+ L A LDVF EPLP DHP W + +TPH AA + ++ E + Sbjct: 237 LLDA-LASGRIAAATLDVFEHEPLPADHPFWQAPRITITPHSAALTLRDEAVEQIAGKIR 295 Query: 291 KFLLGETLSHRVNFERGY 308 GE + V+ RGY Sbjct: 296 ALERGEPIGGIVDRARGY 313 Lambda K H 0.320 0.137 0.404 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: 263 Number of extensions: 19 Number of successful extensions: 2 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: 308 Length of database: 313 Length adjustment: 27 Effective length of query: 281 Effective length of database: 286 Effective search space: 80366 Effective search space used: 80366 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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:
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