Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_015945316.1 DHAF_RS22855 3-phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000021925.1:WP_015945316.1 Length = 387 Score = 182 bits (462), Expect = 2e-50 Identities = 121/379 (31%), Positives = 192/379 (50%), Gaps = 37/379 (9%) Query: 270 EKIKNVSIIGIRSKTQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSN 329 ++ ++ + + +RS + ++ N + GA G N I L+ C EKGI VFN P +N Sbjct: 26 DRYEDANGVLVRSTSMHDLELPPNIEAIARAGA---GVNNIPLDKCAEKGIVVFNTPGAN 82 Query: 330 TRSVVELAISEIIFLMRNL------------HDKTLKMHQGIWNKSASGSFEVRGKKLGI 377 V E+ I+ +I RNL + K+ + NK+ E++GKKLG+ Sbjct: 83 ANGVKEMVIATMIMAARNLVGGVNWVNSCQTDPEVAKLVEK--NKAKFAGTEIKGKKLGV 140 Query: 378 IGYGNIGAQLSVLAENMGMNVFYYDIVERLALGNATK-------IDSLDELLETCDIISL 430 IG G IG ++ A + M+V YD +++ +A K I + +E+ CD I++ Sbjct: 141 IGLGAIGILVANAANKLEMDVCGYD--PYISVEHAWKLSKYIKPIKNTEEIYRECDFITI 198 Query: 431 HVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALRDALESGHLAGAAVDVFPTE 490 HV N+ +LNK+ +MK G I++N SR +VD AL +AL++G +A D FP Sbjct: 199 HVPLTDSNRGMLNKQAFEQMKDGVIILNFSRDTLVDEEALIEALKTGKVAKYVTD-FPN- 256 Query: 491 PKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPGKIIEYINSGNTFNSVNFPN 550 PK + G I PH+G ST E++EN A +I+ Y+ GN NSVNFPN Sbjct: 257 PK---------VCGVEGVIAIPHLGASTAESEENCAVMAVEQIMNYLEHGNIKNSVNFPN 307 Query: 551 IQLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKINIVGQYLKTNEKIGYVITDIDKRYS 610 + A R+ H+N P +L + LA +NI K+ Y + DI+ + Sbjct: 308 CDMGVCNQAGRIAINHKNIPNMLGQFTSTLAKENVNISDLMNKSKGSYAYTLIDIETPAA 367 Query: 611 NDVIDALKEIEGTIRFRIL 629 ++I LKEI+G ++ R++ Sbjct: 368 PEMITKLKEIDGVLKVRVI 386 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: 543 Number of extensions: 36 Number of successful extensions: 4 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: 387 Length adjustment: 34 Effective length of query: 596 Effective length of database: 353 Effective search space: 210388 Effective search space used: 210388 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