Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate H281DRAFT_06500 H281DRAFT_06500 Lactate dehydrogenase
Query= BRENDA::O58256 (333 letters) >FitnessBrowser__Burk376:H281DRAFT_06500 Length = 308 Score = 154 bits (390), Expect = 2e-42 Identities = 99/294 (33%), Positives = 157/294 (53%), Gaps = 17/294 (5%) Query: 18 ELKKYADVEIILYPSGEELKGVIGRFDGIIVSPTTKITREVLENAERLKVISCHSAGYDN 77 E+++YA ++ P+ E + I+ + ++ +L + LK+I+ G+D Sbjct: 23 EVRRYAQEDLQRDPAVSE------GIEAILTRSSYQVPASLLASLPNLKIIATSGVGFDG 76 Query: 78 IDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLMRKIHYADKFIRRGEWESHAKIWTG 137 I L+ A RG+ VT G+L AV E +GL+++L+R+I AD+F+R W Sbjct: 77 IPLDAARSRGVIVTNTPGVLDAAVCELAIGLLLSLLRRIPSADRFVRDEAWAHEL----- 131 Query: 138 FKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKLYYWSRHRKVNVEKELKARYMDIDEL 197 F SL GK++GI+G+G IG+ IARRL F V++ Y VE A D+ EL Sbjct: 132 FPLTSSLAGKRIGIVGLGRIGQGIARRLAGFDVEIAYCGS----KVEGLPYAMISDVREL 187 Query: 198 LEKSDIVILALPLTRDTYHIINEERVKKL-EGKYLVNIGRGALVDEKAVTEAIKQGKLKG 256 +DI+I+ P T H+I+ + L +LVN+ RG +VDE A+ +A+++G ++G Sbjct: 188 ASFADILIVCCPGGDRTRHLIDGAVLSALGSSGFLVNVSRGTVVDEAALIDALEKGLIRG 247 Query: 257 YATDVFEKEPVREHELFKYEWETVLTPHYAGLALEAQEDVGFRAVENLLKVLRG 310 A DVFEKEP+ L VLTPH E + + A++N+ +VL G Sbjct: 248 AALDVFEKEPLIGSRLATLS-NVVLTPHAGSATEETRHTMLRLALDNIHRVLDG 300 Score = 23.9 bits (50), Expect = 0.006 Identities = 11/34 (32%), Positives = 20/34 (58%), Gaps = 3/34 (8%) Query: 16 LEELKKYADVEIILYPSGEELKGVIGRFDGIIVS 49 + EL +AD+ I+ P G+ + +I DG ++S Sbjct: 184 VRELASFADILIVCCPGGDRTRHLI---DGAVLS 214 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: 252 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 333 Length of database: 308 Length adjustment: 28 Effective length of query: 305 Effective length of database: 280 Effective search space: 85400 Effective search space used: 85400 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