Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_048061266.1 MTH_RS04590 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000008645.1:WP_048061266.1 Length = 522 Score = 186 bits (473), Expect = 2e-51 Identities = 111/345 (32%), Positives = 189/345 (54%), Gaps = 9/345 (2%) Query: 233 INVLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLE 292 + VL+ ++++ G+ +++ VV++ ++ EEL + IK+ I +RS+T++T++V+E Sbjct: 1 MKVLIADSINEKGISELEEVAE--VVVNTTITPEELLDAIKDFDAIVVRSRTKVTREVIE 58 Query: 293 NANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKT 352 A RL + +G + +D++ ++GI V NAP S + +V E +I ++ L R + Sbjct: 59 AAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIAD 118 Query: 353 LKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALG 410 + +G W K+ E+ GK LGIIG G IG+Q+ V + GM++ YD I + A Sbjct: 119 RSVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEE 178 Query: 411 NATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPAL 470 + L+ LL DI+++HV E ++++++++ MK A +VN +RG ++D AL Sbjct: 179 MGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDAL 238 Query: 471 RDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVP 530 AL+ G +AGAA+DVF EP P S L+ N +LTPHIG ST EAQ + A V Sbjct: 239 YRALKDGEIAGAALDVFEEEP-----PEGSPLLELENVVLTPHIGASTSEAQRDAAIIVA 293 Query: 531 GKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAK 575 +I G N +N P + K I + + ++A+ Sbjct: 294 NEIKTVFQGGAPRNVLNMPVMDSETYKSLKPYIELAEKMGAIIAQ 338 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: 642 Number of extensions: 28 Number of successful extensions: 3 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: 522 Length adjustment: 36 Effective length of query: 594 Effective length of database: 486 Effective search space: 288684 Effective search space used: 288684 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