Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_068175438.1 HTA01S_RS22370 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_001592305.1:WP_068175438.1 Length = 420 Score = 414 bits (1065), Expect = e-120 Identities = 209/407 (51%), Positives = 282/407 (69%), Gaps = 1/407 (0%) Query: 225 KFSYPKSRINVLLLENVHPIGVEIMKQEGYN-VEVVSSAMSEEELCEKIKNVSIIGIRSK 283 K S K +I LLLE +HP V +++ GY+ +E + A+ +++L KI + +GIRS+ Sbjct: 14 KTSIDKHKIRFLLLEGIHPSAVSVLRAAGYSQIESLPGALPDDQLLAKIADAHFVGIRSR 73 Query: 284 TQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIF 343 TQ+T KVL +A RL AVG FCIGTNQ+DL +E+GIAVFNAPFSNTRSV EL ++E I Sbjct: 74 TQLTAKVLSHAQRLAAVGCFCIGTNQVDLAAARERGIAVFNAPFSNTRSVAELVLAEAIL 133 Query: 344 LMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDI 403 LMR + +K H+G W KSAS SFE+RGK LGI+GYG IG QLSVLAE +GM+V ++D+ Sbjct: 134 LMRGIPEKNAVAHRGGWLKSASNSFEIRGKTLGIVGYGAIGTQLSVLAEALGMHVVFFDV 193 Query: 404 VERLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGH 463 +L LGNA + SLDEL+ T D++SLHV + ++ ++ +MK A+L+N SRG Sbjct: 194 ATKLPLGNARPLTSLDELMATADVVSLHVPETPATQWMIGAAQLARMKPSAVLINASRGT 253 Query: 464 VVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQE 523 VV V AL AL + L GAA+DVFP EP +N + FES L G N ILTPHIGGSTLEAQE Sbjct: 254 VVQVDALASALHNQALLGAAIDVFPEEPHSNKDVFESPLRGLDNVILTPHIGGSTLEAQE 313 Query: 524 NIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASY 583 NI V K+++Y ++G + ++VNFP + LP HRL+HIH+N PGVL+ IN+V + + Sbjct: 314 NIGIEVAEKLVKYSDNGTSTSAVNFPEVALPAHPGKHRLLHIHRNVPGVLSGINRVFSDH 373 Query: 584 KINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRILY 630 INI QYL+T E +GYV+ DID +S + L + GT+R R+L+ Sbjct: 374 GINISAQYLQTREDVGYVVMDIDAAHSELALAELARVPGTLRSRVLF 420 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: 582 Number of extensions: 16 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: 420 Length adjustment: 35 Effective length of query: 595 Effective length of database: 385 Effective search space: 229075 Effective search space used: 229075 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 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