Align 2-oxoglutarate reductase; EC 1.1.1.399; EC 1.1.1.95; EC 3.1.3.3 (characterized, see rationale)
to candidate GFF3804 Psest_3873 Phosphoglycerate dehydrogenase and related dehydrogenases
Query= uniprot:L0G228_ECHVK (630 letters) >FitnessBrowser__psRCH2:GFF3804 Length = 411 Score = 447 bits (1151), Expect = e-130 Identities = 225/405 (55%), Positives = 298/405 (73%), Gaps = 1/405 (0%) Query: 227 SYPKSRINVLLLENVHPIGVEIMKQEGY-NVEVVSSAMSEEELCEKIKNVSIIGIRSKTQ 285 S KS+I LLLE VH V+ +K GY N+E + A+S EEL EKI +V IGIRS+TQ Sbjct: 7 SLDKSKIKFLLLEGVHQNAVDTLKAAGYTNIEYLKGALSTEELKEKIADVHFIGIRSRTQ 66 Query: 286 ITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLM 345 +T++V + A +L+AVG FCIGTNQ++L +E+GIAVFNAP+SNTRSV EL ++E I L+ Sbjct: 67 LTEEVFDAAKKLIAVGCFCIGTNQVNLNAARERGIAVFNAPYSNTRSVAELVLAEAILLL 126 Query: 346 RNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDIVE 405 R + +K H+G W KSA+ SFE+RGKKLGIIGYG+IG QLSVLAE +GM VF+YD+V Sbjct: 127 RGIPEKNASCHRGGWIKSAANSFEIRGKKLGIIGYGSIGTQLSVLAEALGMQVFFYDVVT 186 Query: 406 RLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVV 465 +L LGNAT+I SL ELL CDI+SLHV + ++ +++I MKKGAIL+N +RG VV Sbjct: 187 KLPLGNATQIGSLYELLGMCDIVSLHVPELPSTQWMIGEKEIRAMKKGAILINAARGTVV 246 Query: 466 DVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENI 525 ++ L A++ HL GAA+DVFP EPK+NDE FES L G ILTPHIGGST EAQ NI Sbjct: 247 ELDHLAAAIKDEHLIGAAIDVFPVEPKSNDEEFESPLRGLDRVILTPHIGGSTAEAQANI 306 Query: 526 AQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKI 585 V K+++Y ++G + +SVNFP + LP HRL+HIHQN PGV+++IN+V A I Sbjct: 307 GLEVAEKLVKYSDNGTSVSSVNFPEVALPSHPGKHRLLHIHQNIPGVMSEINKVFADNGI 366 Query: 586 NIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRILY 630 NI GQ+L+TNEK+GYV+ D+DK YS+ ++ L+ + GTIR R+L+ Sbjct: 367 NICGQFLQTNEKVGYVVIDVDKEYSDLALEKLQHVNGTIRSRVLF 411 Lambda K H 0.317 0.136 0.377 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: 642 Number of extensions: 28 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: 630 Length of database: 411 Length adjustment: 34 Effective length of query: 596 Effective length of database: 377 Effective search space: 224692 Effective search space used: 224692 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: 52 (24.6 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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