Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate Ga0059261_2264 Ga0059261_2264 D-3-phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >FitnessBrowser__Korea:Ga0059261_2264 Length = 525 Score = 204 bits (520), Expect = 6e-57 Identities = 129/369 (34%), Positives = 198/369 (53%), Gaps = 15/369 (4%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294 VL+ + + P +I ++ G V+ ++ + EEL I + IRS T++TK++L+ A Sbjct: 4 VLISDKMDPKAAQIFRERGVEVDEITGK-TPEELKAIIGQYDGLAIRSATKVTKEILDAA 62 Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLK 354 L VG IG + +D+ KG+ V N PF N+ + E AI+ + L R L + + Sbjct: 63 TNLKVVGRAGIGVDNVDIPNASAKGVVVMNTPFGNSITTAEHAIALMFALARQLPEANTQ 122 Query: 355 MHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD---IVERLALGN 411 G+W K+ EV GK LG+IG GNIG+ ++ A + M V YD ER Sbjct: 123 TQAGLWPKNGFMGVEVTGKTLGLIGAGNIGSIVADRAHGLRMKVVAYDPFLSPERAVEMG 182 Query: 412 ATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALR 471 K++ L++LL D I+LH + +NIL+ E + K KKG ++N +RG ++D AL+ Sbjct: 183 VEKVE-LEQLLARADFITLHTPLTEQTRNILSAENLAKTKKGVRIINCARGGLIDEAALK 241 Query: 472 DALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPG 531 D L+SGH+AGAA+DVF TEP E L PN + TPH+G ST EAQ N+A V Sbjct: 242 DLLDSGHVAGAALDVFVTEPAK-----EHALFNTPNFVATPHLGASTSEAQVNVAIQVAE 296 Query: 532 KIIEYINSGNTFNSVNFPNI---QLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKINIV 588 ++ +Y+ +G N++N P++ + P +K L + G LA N L I+ Sbjct: 297 QMADYLVNGGVTNALNMPSLTAEEAPRVKPYMELAEKLGSLVGQLAHGN--LDRVSIHAE 354 Query: 589 GQYLKTNEK 597 G + N+K Sbjct: 355 GAAAEVNQK 363 Score = 28.9 bits (63), Expect = 6e-04 Identities = 16/67 (23%), Positives = 33/67 (49%), Gaps = 2/67 (2%) Query: 558 DAHRLIHIHQNAPGVLAKINQVLASYKINIVGQYLKTNEKIG--YVITDIDKRYSNDVID 615 D H L ++++APG + +I L +NI +L E G ++ +D + ++I Sbjct: 450 DGHMLYVVNEDAPGFIGRIGTTLGDAGVNIGTFHLGRREAGGEAVLLLSVDDAVTPELIA 509 Query: 616 ALKEIEG 622 ++ + G Sbjct: 510 QVRALPG 516 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: 657 Number of extensions: 29 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: 525 Length adjustment: 36 Effective length of query: 594 Effective length of database: 489 Effective search space: 290466 Effective search space used: 290466 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 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