Align 2-oxoglutarate reductase; EC 1.1.1.399; EC 1.1.1.95; EC 3.1.3.3 (characterized, see rationale)
to candidate 6938846 Sama_2949 D-3-phosphoglycerate dehydrogenase (RefSeq)
Query= uniprot:L0G228_ECHVK (630 letters) >FitnessBrowser__SB2B:6938846 Length = 409 Score = 420 bits (1079), Expect = e-122 Identities = 205/407 (50%), Positives = 286/407 (70%), Gaps = 1/407 (0%) Query: 225 KFSYPKSRINVLLLENVHPIGVEIMKQEGY-NVEVVSSAMSEEELCEKIKNVSIIGIRSK 283 K S K +I LLLE VH V+++++ GY N+E +++++E L IK+ +GIRS+ Sbjct: 3 KHSLDKDKIKFLLLEGVHQSAVDVLERAGYTNIEYHKASLADEALVASIKDAHFVGIRSR 62 Query: 284 TQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIF 343 TQ++ +VL A +L+ +G FCIGTNQ+DL++ + GI VFNAPFSNTRSV EL + EII Sbjct: 63 TQLSAEVLSKAEKLVGIGCFCIGTNQVDLKSAELAGIPVFNAPFSNTRSVAELVLGEIIM 122 Query: 344 LMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDI 403 LMR + + H+G W KSA+GS EVRGK LG+IGYG+IG QL +LAE +GM V ++DI Sbjct: 123 LMRGIPQRNALCHRGGWLKSANGSVEVRGKTLGVIGYGHIGTQLGILAETLGMRVKFFDI 182 Query: 404 VERLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGH 463 ++L LGNA ++ S +ELL D++SLHV + KN++ ++ MKKG+ L+N SRG Sbjct: 183 EDKLPLGNAQQVHSFEELLANADVVSLHVPETPQTKNMIGHTELATMKKGSFLINASRGT 242 Query: 464 VVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQE 523 VVD+ AL AL+ H+AGAA+DVFP EPK+ND+ F+S L G N ILTPH+GGST EAQE Sbjct: 243 VVDIDALSAALKEEHIAGAAIDVFPVEPKSNDDVFQSPLRGLDNVILTPHVGGSTEEAQE 302 Query: 524 NIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASY 583 NI V GK+ +Y ++G+T ++VNFP + LP K RL+HIH+N PG+L KINQ + Sbjct: 303 NIGIEVAGKLAKYSDNGSTVSAVNFPEVSLPMHKGTSRLLHIHKNRPGILIKINQAFSEK 362 Query: 584 KINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRILY 630 INI QYL+T IGYV+ ++D + + ++ L+ IEGTIR R+L+ Sbjct: 363 GINISAQYLQTTADIGYVVMEVDTHQAEEALEQLRGIEGTIRTRLLH 409 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: 648 Number of extensions: 20 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: 409 Length adjustment: 34 Effective length of query: 596 Effective length of database: 375 Effective search space: 223500 Effective search space used: 223500 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