Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_012674243.1 SULAZ_RS08320 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000021545.1:WP_012674243.1 Length = 529 Score = 179 bits (454), Expect = 3e-49 Identities = 119/358 (33%), Positives = 192/358 (53%), Gaps = 22/358 (6%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294 VL+ +++ P G+EI+ + + EL E +K+ I RS+T +TK++LE A Sbjct: 4 VLVTDDISPKGLEILNNDEMIDLDYQPEIKFNELLEIVKDYDAIITRSRTPVTKELLERA 63 Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLK 354 +L VG +G + +DLE +GI V N P +NT E+ ++ + ++R LH Sbjct: 64 EKLKVVGRAGVGVDNVDLEEASRRGILVINTPGANTIGAAEITMAHLYAVLRKLHLAHKS 123 Query: 355 MHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDIV------ERLA 408 M +G W++ E+ GK +GIIG GN+G+Q+++ + G V YD ERL Sbjct: 124 MLEGQWDRKRFMGEELDGKVVGIIGLGNVGSQVAIRCKAAGAKVIAYDPYIPREKGERLG 183 Query: 409 LGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVP 468 + ID+L +L++ DII+LH E +N++ K++ MKKG +N +RG +VD Sbjct: 184 V---ELIDNLHDLIKMSDIITLHCPLTEETRNMIGKKEFDLMKKGVYFINCARGGIVDED 240 Query: 469 ALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQEN---- 524 AL +A++ G +AG +DVF EP ++ L PN L+PHIG +T E+Q+N Sbjct: 241 ALYEAVKEGKIAGLGLDVFSKEPPDDR---IRRLFEFPNISLSPHIGANTYESQDNVAIK 297 Query: 525 IAQFV----PGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRL-IHIHQNAPGVLAKIN 577 IAQ+V G+ +E + + F NI+ +L+ A +L + Q A G +IN Sbjct: 298 IAQYVIAALKGQFVEVAVNAPFTITEGFENIK-AYLELAEKLGSFLTQYAGGHFTEIN 354 Score = 33.1 bits (74), Expect = 3e-05 Identities = 47/195 (24%), Positives = 78/195 (40%), Gaps = 28/195 (14%) Query: 451 KKGAILVNLSRGHVVDVP-----ALRDALE---SGHLAGAAVDVFPTEPKNNDEPFESEL 502 K G+ L + GH ++ +RD +E + L G V T + PF ++ Sbjct: 337 KLGSFLTQYAGGHFTEINIEVRGTIRDHIEPIVAFFLKGYLSPVLDTPVNIINAPFIAKE 396 Query: 503 IGCPNTILTPHIGGSTLEAQENIAQFVP----GKIIEYINSGNTFNSVNFPNIQL----- 553 G +I ST EA N +F+ + E + G F P I L Sbjct: 397 RGI-------NIIKSTREAGLNFKEFIKITAKAQDKEVVVGGTAFYD-KLPRIMLVDNYW 448 Query: 554 -PFLKDAHRLIHIHQNAPGVLAKINQVLASYKINIVGQYLKTNE--KIGYVITDIDKRYS 610 L+ +++ PGV+ K+ +LA + INI G L E KI +D + + Sbjct: 449 IDIEPSGVILMFENKDVPGVIGKLGTILARHNINIAGFRLGRLEKGKIALGALQLDDKLN 508 Query: 611 NDVIDALKEIEGTIR 625 V++ + +I I+ Sbjct: 509 EAVLEEIHQIPEIIK 523 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: 818 Number of extensions: 46 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: 529 Length adjustment: 36 Effective length of query: 594 Effective length of database: 493 Effective search space: 292842 Effective search space used: 292842 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 Apr 10 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