Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_041550394.1 SARO_RS13605 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000013325.1:WP_041550394.1 Length = 528 Score = 213 bits (542), Expect = 2e-59 Identities = 133/386 (34%), Positives = 208/386 (53%), Gaps = 15/386 (3%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294 VL+ + + P I + G +V+V++ + E+L +I + IRS T++TK +L+ A Sbjct: 6 VLISDKMDPNAARIFTEMGCDVDVITGE-TPEQLIARIGEYDGLAIRSSTKVTKAILDAA 64 Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLK 354 L +G IG + +D+ +G+ V N PF N+ + E AI+ + L R + + + Sbjct: 65 TNLKVIGRAGIGVDNVDIPAASAQGVVVMNTPFGNSITTAEHAIAMMFALARQIPEANAQ 124 Query: 355 MHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALGNA 412 G+W K+ EV GK LG+IG GNIG+ ++ A + M V +D + A+ Sbjct: 125 TQAGLWPKNGFMGVEVTGKTLGLIGAGNIGSIVASRALGLKMKVVAFDPFLTPERAVEMG 184 Query: 413 TKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALRD 472 + L+ LL D I+LH + +NIL++E I K KKG ++N +RG +VD AL+D Sbjct: 185 VEKADLETLLAKADFITLHTPLTDQTRNILSRENIAKCKKGVRIINCARGGLVDEAALKD 244 Query: 473 ALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPGK 532 AL+SGH+AGAA+DVF TEP ES L G PN I TPH+G ST EAQ N+A V + Sbjct: 245 ALDSGHVAGAALDVFETEPAK-----ESPLFGTPNFICTPHLGASTTEAQVNVALQVAEQ 299 Query: 533 IIEYINSGNTFNSVNFPNI---QLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKINIVG 589 + +++ +G N++N P++ + P L+ L + G LA N L I + G Sbjct: 300 MADFLVTGGVTNALNMPSLSAEEAPKLRPYMALAEKLGSLVGQLAHDN--LTKIAIEVEG 357 Query: 590 QYLKTNEK--IGYVITDIDKRYSNDV 613 + N+K V+ + K+YS V Sbjct: 358 AAAQLNQKPITAAVLAGLMKQYSQTV 383 Score = 33.1 bits (74), Expect = 3e-05 Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 2/67 (2%) Query: 558 DAHRLIHIHQNAPGVLAKINQVLASYKINIVGQYLKTNEKIG--YVITDIDKRYSNDVID 615 D L ++ +APG + +I +L INI +L E G ++ +D S DV+ Sbjct: 452 DGDMLYIVNSDAPGFIGRIGTLLGQNTINIGTFHLGRREAGGEAVLLLSLDNPVSEDVLK 511 Query: 616 ALKEIEG 622 +EI+G Sbjct: 512 EAREIQG 518 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: 635 Number of extensions: 31 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: 528 Length adjustment: 36 Effective length of query: 594 Effective length of database: 492 Effective search space: 292248 Effective search space used: 292248 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