Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_011306436.1 MBAR_RS07655 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000195895.1:WP_011306436.1 Length = 523 Score = 202 bits (514), Expect = 3e-56 Identities = 113/322 (35%), Positives = 192/322 (59%), Gaps = 9/322 (2%) Query: 233 INVLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLE 292 + VL+ +++ G+EI+K E + V+V S+ +SE+EL +KIK+ + IRS T +T+K++E Sbjct: 1 MKVLVSDSLSNEGLEILK-EHFKVDV-STGLSEDELVKKIKDYDALVIRSGTHVTQKIIE 58 Query: 293 NANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKT 352 A+ L +G +G + +D++ +KGI V N+P N S E I+ ++ + RN+ Sbjct: 59 AADNLKIIGRAGVGIDNVDVDAATKKGIIVANSPEGNMISAAEHTIAMMMAMSRNIPQAN 118 Query: 353 LKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALG 410 + W +S EV+GK LGIIG G IG++++ A + MN+ YD + E+ A+ Sbjct: 119 ASLKGKEWKRSKFTGVEVKGKTLGIIGLGRIGSEVAKRASGLEMNLMGYDPFVSEKRAIE 178 Query: 411 NATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPAL 470 K+ +++E+ + D I++H E +NIL++E+ MK ++N +RG +++ AL Sbjct: 179 LGVKLATVNEIAKEADYITVHTPLIKETRNILDEEQFALMKPTTRILNCARGGIINEEAL 238 Query: 471 RDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVP 530 ALESG +AGAA+DVF EP PF S L+ N ++TPH+G ST EAQ N+A + Sbjct: 239 AKALESGKIAGAAIDVFIEEP-----PFNSPLLSFDNVVVTPHLGASTKEAQVNVAVDIA 293 Query: 531 GKIIEYINSGNTFNSVNFPNIQ 552 ++ + G N++N P+++ Sbjct: 294 KEVASVLTGGPAKNAINIPSVK 315 Score = 31.6 bits (70), Expect = 9e-05 Identities = 15/66 (22%), Positives = 35/66 (53%), Gaps = 2/66 (3%) Query: 566 HQNAPGVLAKINQVLASYKINIVGQYLKTNE--KIGYVITDIDKRYSNDVIDALKEIEGT 623 H N P V+ VL INI G + +E + ++ +ID S+ +++ +++++G Sbjct: 456 HINRPNVIGPCCMVLGKNNINISGMQVGRSEIGGVTMMVLNIDSEVSDPILEEVRKVDGI 515 Query: 624 IRFRIL 629 + +++ Sbjct: 516 LDAKLV 521 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: 706 Number of extensions: 42 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: 523 Length adjustment: 36 Effective length of query: 594 Effective length of database: 487 Effective search space: 289278 Effective search space used: 289278 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