Align 2-oxoglutarate reductase; EC 1.1.1.399; EC 1.1.1.95; EC 3.1.3.3 (characterized, see rationale)
to candidate 3609936 Dshi_3318 D-3-phosphoglycerate dehydrogenase (RefSeq)
Query= uniprot:L0G228_ECHVK (630 letters) >FitnessBrowser__Dino:3609936 Length = 531 Score = 204 bits (518), Expect = 1e-56 Identities = 122/321 (38%), Positives = 177/321 (55%), Gaps = 10/321 (3%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSS-AMSEEELCEKIKNVSIIGIRSKTQITKKVLEN 293 VL+ + + V+I + G V+ S +++L E I + IRS T++T+K+L + Sbjct: 5 VLVSDKLSETAVQIFRDRGIEVDFEPSLGKDKDKLAEVIGKYDGLAIRSATKVTEKLLAH 64 Query: 294 ANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTL 353 A+ L VG IGT+ +D +KG+ V N PF N + E AI+ + + R + + + Sbjct: 65 ADNLKVVGRAGIGTDNVDKVAASKKGVIVMNTPFGNMITTAEHAIAMMFAVARQIPEASA 124 Query: 354 KMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD---IVERLALG 410 H G W KS E+ K LG+IG GNIG + A + M V YD ER Sbjct: 125 STHAGKWEKSKFMGVELTAKTLGVIGAGNIGGIVCERALGLKMKVIAYDPFLSEERADKL 184 Query: 411 NATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPAL 470 K+D LD LL D I+LHV + +NIL++E + K KKG ++N +RG +VD AL Sbjct: 185 GVEKVD-LDTLLARADFITLHVPLTDQTRNILSREALEKTKKGVRIINCARGGLVDEQAL 243 Query: 471 RDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVP 530 D L+SGH+AGAA DVF EP E+ L G PN + TPH+G ST EAQEN+A V Sbjct: 244 ADLLKSGHVAGAAFDVFAEEPAT-----ENPLFGLPNVVCTPHLGASTTEAQENVALQVA 298 Query: 531 GKIIEYINSGNTFNSVNFPNI 551 ++ Y+ SG N++N P++ Sbjct: 299 EQMSNYLLSGAVENALNMPSV 319 Score = 26.6 bits (57), Expect = 0.003 Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 2/60 (3%) Query: 560 HRLIHIHQNAPGVLAKINQVLASYKINIVGQYLKTNEKIGYVIT--DIDKRYSNDVIDAL 617 H L +++ PG++ + +L ++NI L NE G I +D DV D L Sbjct: 455 HMLYTTNKDTPGMIGTLGGILGENQVNIANFTLGRNETNGDAIAMLYLDAPLPRDVQDKL 514 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: 691 Number of extensions: 33 Number of successful extensions: 4 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: 630 Length of database: 531 Length adjustment: 36 Effective length of query: 594 Effective length of database: 495 Effective search space: 294030 Effective search space used: 294030 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: 53 (25.0 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