Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_038209742.1 Q392_RS15870 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000745855.1:WP_038209742.1 Length = 410 Score = 427 bits (1098), Expect = e-124 Identities = 219/410 (53%), Positives = 290/410 (70%), Gaps = 1/410 (0%) Query: 222 MNKKFSYPKSRINVLLLENVHPIGVEIMKQEGYN-VEVVSSAMSEEELCEKIKNVSIIGI 280 M K S KS+I LLLE +HP GVE+++ GY+ VEV+S A+ EEL ++ +V +GI Sbjct: 1 MTTKTSLDKSKIKFLLLEGIHPSGVELIRAAGYSQVEVLSGALDAEELKARVADVHFLGI 60 Query: 281 RSKTQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISE 340 RS+TQ+T ++ A RL+AVGAFCIGTNQIDL E G+AVFNAP+SNTRSV EL ++E Sbjct: 61 RSRTQLTPEIFAAARRLVAVGAFCIGTNQIDLGAALEHGVAVFNAPYSNTRSVAELVLAE 120 Query: 341 IIFLMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFY 400 I L+R + +K H+G W KSA +FE+RGK LGI+GYG+IGAQLSVLAE +GM+V + Sbjct: 121 AILLLRGVPEKNAVAHRGGWLKSAENAFEIRGKTLGIVGYGSIGAQLSVLAEALGMHVVF 180 Query: 401 YDIVERLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLS 460 YD+V RL LGNA ++ SL+ELL T DI+SLHV + ++ + +I MK GAIL+N S Sbjct: 181 YDVVTRLPLGNAQQVRSLNELLGTADIVSLHVPQLPSTQWMIGEAQIAAMKPGAILINAS 240 Query: 461 RGHVVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLE 520 RG VV++ L A+ + L GAAVDVFP EPK+N + F S L G N ILTPHIGGST+E Sbjct: 241 RGTVVEIEPLAAAIRAKKLLGAAVDVFPVEPKSNKDEFVSPLRGLDNVILTPHIGGSTME 300 Query: 521 AQENIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVL 580 AQ NI V K+++Y ++G T +SVNFP + LP HRL+H+H+N PGVL+ +N V Sbjct: 301 AQANIGVEVAEKLVKYSDNGTTTSSVNFPEVALPAHPGKHRLLHVHRNVPGVLSAVNGVF 360 Query: 581 ASYKINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRILY 630 A INI QYL+TNEK+GYV+TDID S ++ L ++ GTIR +L+ Sbjct: 361 AETGINISAQYLQTNEKVGYVVTDIDAGSSEAALEKLTQVPGTIRSWVLF 410 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: 23 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: 410 Length adjustment: 34 Effective length of query: 596 Effective length of database: 376 Effective search space: 224096 Effective search space used: 224096 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