Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate GFF5281 PS417_27040 3-phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >FitnessBrowser__WCS417:GFF5281 Length = 409 Score = 443 bits (1139), Expect = e-129 Identities = 218/407 (53%), Positives = 300/407 (73%), Gaps = 1/407 (0%) Query: 225 KFSYPKSRINVLLLENVHPIGVEIMKQEGY-NVEVVSSAMSEEELCEKIKNVSIIGIRSK 283 K S KS+I LLLE VHP V+++K GY ++E ++S++ E +L EKI + IGIRS+ Sbjct: 3 KTSLDKSKIKFLLLEGVHPSAVDVLKAAGYTSIEYITSSLPEAQLKEKIADAHFIGIRSR 62 Query: 284 TQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIF 343 TQ+T+++ ++A +L+AVG FCIGTNQ+DL +E+GIAVFNAP+SNTRSV EL ++E I Sbjct: 63 TQLTEEIFDHAKKLVAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEAIL 122 Query: 344 LMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDI 403 L+R + +K H+G W KSA+ SFE+RGKKLGI+GYG+IG QLSVLAE +GM VF+YD Sbjct: 123 LLRGIPEKNASCHRGGWIKSAANSFEIRGKKLGIVGYGSIGTQLSVLAEGLGMQVFFYDT 182 Query: 404 VERLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGH 463 + +L LGNAT++ SL ELL DI++LHV E + ++ +++I +KKG IL+N +RG Sbjct: 183 LTKLPLGNATQVASLTELLGMSDIVTLHVPETAETQWMIGEKEIRAIKKGGILINAARGT 242 Query: 464 VVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQE 523 VV++ AL DA++ HL GAA+DVFP EP++ND+ FES L G N ILTPHIGGST EAQ Sbjct: 243 VVELDALADAIKDKHLIGAAIDVFPEEPRSNDDIFESPLRGLDNVILTPHIGGSTAEAQA 302 Query: 524 NIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASY 583 NI V K+++Y ++G + +SVNFP + LP HRL+HIHQN PGV+ +IN+V A Sbjct: 303 NIGLEVSEKLVKYSDNGTSVSSVNFPEVALPAHPGKHRLLHIHQNIPGVMMEINKVFAEN 362 Query: 584 KINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRILY 630 INI GQ+L+TNEK+GYV+ D+D YS+ + L+ I GTIR R+L+ Sbjct: 363 GINISGQFLQTNEKVGYVVIDVDAEYSDLAQEKLQHINGTIRSRVLF 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: 632 Number of extensions: 27 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 Apr 09 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