Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate PP_1707 PP_1707 D-isomer specific 2-hydroxyacid dehydrogenase family protein
Query= BRENDA::O58256 (333 letters) >FitnessBrowser__Putida:PP_1707 Length = 316 Score = 152 bits (384), Expect = 1e-41 Identities = 108/326 (33%), Positives = 169/326 (51%), Gaps = 20/326 (6%) Query: 1 MRPKV----GVLLKMKREALEEL----KKYADVEIILYPSGEELKGVIGRFDGIIVSPTT 52 M+P+V +L+ RE LE+L + Y + Y S G G+I T Sbjct: 1 MKPEVLQLSPILIPQIRERLEQLFTVHRYYEQADKEAYVSQHA-----GNIRGVITGGHT 55 Query: 53 KITREVLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINL 112 I++ ++ L+VI+ + G D +DL A RGI VT G L+E VA+ +GL+I L Sbjct: 56 GISQALMARLPNLEVIAVNGVGTDAVDLAYARDRGIQVTATIGALTEDVADLAIGLLIGL 115 Query: 113 MRKIHYADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKL 172 R I D+F+R G W + + G +VGI+GMG +G+A+A+R FG + Sbjct: 116 CRGICTGDRFVRAGRWATSTTPLAPLPLARQVSGMRVGIVGMGRVGRAVAQRAAAFGCPI 175 Query: 173 YYWSRHRKVNVEKELKARYMDIDELLEKSDIVILALPLTRDTYHIINEERVKKLEGK-YL 231 Y + + ++V +A D+ +L + SD +ILA + +IN + ++ L + YL Sbjct: 176 RY-TDLQALDVPYGFEA---DLLQLAKDSDALILAAAADKGE-ALINRDVLQALGSEGYL 230 Query: 232 VNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKEPVREHELFKYEWETVLTPHYAGLALE 291 +NI RG LVDE A+ A++ G++ G A DVF EP LF+ E + VL PH A ++ Sbjct: 231 INIARGKLVDEPALIAALQAGEIGGAALDVFADEPRAPEALFERE-DVVLQPHRASATVQ 289 Query: 292 AQEDVGFRAVENLLKVLRGEVPEDLV 317 + +G V +L+ V G P+ LV Sbjct: 290 TRTRMGEMVVASLVDVFAGRTPQGLV 315 Lambda K H 0.319 0.139 0.393 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: 242 Number of extensions: 11 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: 333 Length of database: 316 Length adjustment: 28 Effective length of query: 305 Effective length of database: 288 Effective search space: 87840 Effective search space used: 87840 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 (21.7 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