Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate AZOBR_RS03790 AZOBR_RS03790 D-2-hydroxyacid dehydrogenase
Query= reanno::SB2B:6938941 (308 letters) >FitnessBrowser__azobra:AZOBR_RS03790 Length = 308 Score = 115 bits (289), Expect = 1e-30 Identities = 95/305 (31%), Positives = 141/305 (46%), Gaps = 10/305 (3%) Query: 9 TRENERYRSLLASCHLPELELLD----DNPANIRLADIWLAEPGLAAPLVNHASGLRWMQ 64 T ++R+ S L LP LE+ +PA+I +A +W GL A L N L+ + Sbjct: 9 TDRSDRWLSEL-DARLPGLEVRVWPEMGDPADIEMALVWKPPHGLLATLPN----LKLIV 63 Query: 65 STFAGVD-LLVKPRQRRDYLLTNVRGIFGPLMSEYLFGYLLARQREHDLYKSQQQQKLWL 123 S AGV+ LL+ P L+ V M+ Y+ +L R D YK+ QQ W Sbjct: 64 SLGAGVESLLLDPTLPEVPLVRMVSEGLTVDMAGYVALQVLRWHRLLDEYKALQQAGRWE 123 Query: 124 PGSYKTLQGSELLLLGTGSIAKHLAQTAKHFGMKVAGINRSAKATEGFDEVATLEALPTL 183 P ++ +LG G + A+T +V G +R+ K G + + + L + Sbjct: 124 PLDPCPASEVKVGILGMGELGMASAKTLLSMDYRVLGWSRTPKTLPGVESFSGPDGLAAM 183 Query: 184 MARADAIASILPSTEATRGILNENILARMKPDAVLFNLGRGDVLDLDALERQLRQHPQQQ 243 + + + + +LP T TRG+LN + A + AV+ N RG L D L L Sbjct: 184 LGQCNLLVCLLPLTAETRGLLNRKLFAALPKGAVVVNAARGGHLVEDDLLAALESGHIAG 243 Query: 244 AVLDVFNQEPLPEDHPIWGLGNVIVTPHIAAPSFPEQVAEIFSSNYHKFLLGETLSHRVN 303 A LDVF EPLP HP W V VTPH+AA + P + A + + F G L + V+ Sbjct: 244 ASLDVFADEPLPAGHPFWTHPKVHVTPHVAAVTHPSRSAAVVAEAIIAFREGRPLPNLVD 303 Query: 304 FERGY 308 +GY Sbjct: 304 RSQGY 308 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: 245 Number of extensions: 13 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: 308 Length adjustment: 27 Effective length of query: 281 Effective length of database: 281 Effective search space: 78961 Effective search space used: 78961 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 09 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