Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_059149611.1 V474_RS00340 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_001046635.1:WP_059149611.1 Length = 527 Score = 203 bits (517), Expect = 1e-56 Identities = 123/368 (33%), Positives = 199/368 (54%), Gaps = 13/368 (3%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294 VL+ + + P I + G +V+V++ +E+++ +I + IRS T++TK++L A Sbjct: 6 VLISDKMDPNAARIFTEMGCDVDVITGENAEQQIA-RIGEYDGLAIRSSTRVTKEMLAAA 64 Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLK 354 L +G IG + +D+ +G+ V N PF N+ + E AI+ I L R L + + Sbjct: 65 KNLKVIGRAGIGVDNVDIPAASSQGVVVMNTPFGNSITTAEHAIALIFALARQLPEANAQ 124 Query: 355 MHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALGNA 412 G+W K+ EV GK LG+IG GNIG+ ++ A + M V +D + A+ Sbjct: 125 TQAGLWPKNGFMGVEVTGKTLGLIGAGNIGSIVASRALGLRMKVVAFDPFLTPERAVEMG 184 Query: 413 TKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALRD 472 + L+ LL D I+LH + +NIL+ E + K KKG +VN +RG ++D AL+ Sbjct: 185 VEKADLETLLARADFITLHTPLTDQTRNILSAENLAKTKKGVRIVNCARGGLIDEAALKA 244 Query: 473 ALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPGK 532 L+SGH+AGAA+DVF TEP +S L G PN I TPH+G ST EAQ N+A V + Sbjct: 245 GLDSGHIAGAALDVFQTEPAK-----DSPLFGTPNFICTPHLGASTTEAQVNVALQVAEQ 299 Query: 533 IIEYINSGNTFNSVNFPNI---QLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKINIVG 589 + +++ +G N++N P++ + P LK +L + + G L + I++ G Sbjct: 300 MADFLVNGGVTNALNMPSLSAEEAPKLKPYMKLAEVLGSMVGQLTV--DSVPRISIHVEG 357 Query: 590 QYLKTNEK 597 + N+K Sbjct: 358 AAAELNQK 365 Score = 27.7 bits (60), Expect = 0.001 Identities = 20/93 (21%), Positives = 45/93 (48%), Gaps = 11/93 (11%) Query: 539 SGNTFNSVNFPNIQLPFLK-----DAHRLIHIHQNAPGVLAKINQVLASYKINI----VG 589 +G FN+V +++ +K D L ++++APG + +I ++ INI +G Sbjct: 428 AGTLFNNVEPRLVEMFGIKVEAELDGSMLYIVNEDAPGFIGRIGTLMGEQGINIGTFNLG 487 Query: 590 QYLKTNEKIGYVITDIDKRYSNDVIDALKEIEG 622 + E + ++ +D + DV++ + + G Sbjct: 488 RRTTGGEAV--LLLSVDTPVAADVLEQARALPG 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: 617 Number of extensions: 28 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: 527 Length adjustment: 36 Effective length of query: 594 Effective length of database: 491 Effective search space: 291654 Effective search space used: 291654 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 Jul 26 2024. The underlying query database was built on Jul 25 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