Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate 7026177 Shewana3_3319 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (RefSeq)
Query= BRENDA::P9WNX3 (528 letters) >FitnessBrowser__ANA3:7026177 Length = 329 Score = 151 bits (382), Expect = 3e-41 Identities = 108/310 (34%), Positives = 154/310 (49%), Gaps = 25/310 (8%) Query: 16 TVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDA---EVLAAAPK--LKIVA 70 T AA G Q+E D + V A+ V A D+ EVL K KI+A Sbjct: 19 TNAAFGAQIEYF-----DYRLCMQTVKLAEGFEVVCAFVNDSLCEEVLVELAKGGTKIIA 73 Query: 71 RAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWK 130 G +NVD+ AA G+ VVN P + S AEH +AL+L +R+I A R+ + Sbjct: 74 MRCAGFNNVDLVAAKRLGMQVVNVPAYSPESVAEHTVALMLTLNRKIHKAYQRTRDANFS 133 Query: 131 RSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLD 190 G +FGKTVGV+G G+IG + + FG V+A+DPY +PA A L +E LD Sbjct: 134 LEGLVGFNMFGKTVGVIGTGKIGVATIKVLLGFGCKVIAFDPYPNPAVEA-LNVEYQDLD 192 Query: 191 DLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHV 250 + A +D IS+H P T + L++KE+ AK KPGV+++N +RGGL++ +A+ G + Sbjct: 193 TIYANSDIISLHCPLTADNHHLLNKESFAKMKPGVMVINTSRGGLLNAFDAMEALKLGQI 252 Query: 251 RAAGLDVFATEP-----------CTDSPLFELA---QVVVTPHLGASTAEAQDRAGTDVA 296 + GLDV+ E D L+ V+ T H T EA Sbjct: 253 GSLGLDVYENEKELFFEDKSNQIIQDDVFRRLSACHNVIFTGHQAFLTEEALGAIAHTTL 312 Query: 297 ESVRLALAGE 306 +V+ LAGE Sbjct: 313 SNVKALLAGE 322 Lambda K H 0.317 0.133 0.370 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: 325 Number of extensions: 14 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: 528 Length of database: 329 Length adjustment: 31 Effective length of query: 497 Effective length of database: 298 Effective search space: 148106 Effective search space used: 148106 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 (21.6 bits) S2: 50 (23.9 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