Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_086510087.1 BZY95_RS11630 glyoxylate/hydroxypyruvate reductase A
Query= reanno::SB2B:6938941 (308 letters) >NCBI__GCF_002151265.1:WP_086510087.1 Length = 311 Score = 110 bits (274), Expect = 6e-29 Identities = 94/312 (30%), Positives = 148/312 (47%), Gaps = 9/312 (2%) Query: 4 KLLLLTRENERYRSLLASCHLPELELLD-DNPANIRLADIWLAEPGLAAPLVNHASGLRW 62 ++LL + E +R LA LP E++ D+PA+ R +LA L+ + R Sbjct: 2 RILLHIDDIEAWRDALAE-RLPGAEIVTADDPADKRRDADYLAVWKPPEALLAEQTRARG 60 Query: 63 MQSTFAGVD-LLVKPRQRRDYLLTNVRGI-FGPLMSEYLFGYLLARQREHDLYKSQQQQK 120 + + AGVD LL P + +R L+ +Y+ +L QR+ D Y+ QQ + Sbjct: 61 IVNLGAGVDALLSNPALPAGVPIVKLRDAGMAELIGDYVRYGVLHFQRDFDRYRRQQASR 120 Query: 121 LWLPGSYKTLQGSELLLLGTGSIAKHLAQTAKHFGMKVAGINRSAKATEGFDEVATLEAL 180 W + + + +LG G+I +A G V G +RS K+ EG E L Sbjct: 121 EWHEHNVTAKRDWPVGVLGLGAIGARVAAMIAADGFPVHGWSRSPKSLEGITCHHGDEGL 180 Query: 181 PTLMARADAIASILPSTEATRGILNENILARMKPDAVLFNLGRGDVLDLDALERQLRQHP 240 L+ + + +LP T +TR I+N LA + A L N GRG ++D AL L + Sbjct: 181 VELLGQVRTLVLLLPGTNSTRHIINAAALAALPEGASLINPGRGSLIDEAALLAALGEGE 240 Query: 241 QQQ----AVLDVFNQEPLPEDHPIWGLGNVIVTPHIAAPSFPEQVAEIFSSNYHKFLLGE 296 Q+ A+LD F +EPLPE P+W + VTPH+A P+ ++ + + F G+ Sbjct: 241 QEGRLRGAILDAFPEEPLPESSPLWRHPRIWVTPHMAGPTPLDEAVDQVAEAIRAFEAGD 300 Query: 297 TLSHRVNFERGY 308 + V+ E GY Sbjct: 301 EV-ESVDPEAGY 311 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: 280 Number of extensions: 22 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: 308 Length of database: 311 Length adjustment: 27 Effective length of query: 281 Effective length of database: 284 Effective search space: 79804 Effective search space used: 79804 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