Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_012282233.1 HM1_RS05105 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000019165.1:WP_012282233.1 Length = 526 Score = 179 bits (453), Expect = 4e-49 Identities = 103/323 (31%), Positives = 173/323 (53%), Gaps = 9/323 (2%) Query: 233 INVLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLE 292 + VL+ + + G++++ G V ++E+++ E I + +RS+T+ITK+++E Sbjct: 1 MRVLVCDPISQKGIDVLTSAGDVAVDVKLKLTEDQIVEIIAEYDAVVVRSETKITKRIIE 60 Query: 293 NANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKT 352 A+RL A+G +G + ID+E KGI V NAP NT + EL ++ I+ + RN+ Sbjct: 61 AADRLKAIGRAGVGVDNIDVEAATRKGIVVVNAPEGNTIAAAELTVAHILAIARNVGSAN 120 Query: 353 LKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD---IVERLAL 409 L + G W++S E++GK LGI+G G IG++++ A M V YD VE+ A Sbjct: 121 LSLKGGKWDRSKYTGIELKGKTLGILGLGKIGSEVAKRARAFDMTVIAYDPYASVEK-AK 179 Query: 410 GNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPA 469 + L+ + D I++H+ + +++ + MK+G +VN +RG ++D A Sbjct: 180 SLGVTVTDLETVFRQSDFITVHMPKTKDTYRMISAAQFAIMKEGVRIVNCARGGIIDEQA 239 Query: 470 LRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFV 529 L DA++SG +A A +DVF EP +S L TPH+G ST EAQ N+A V Sbjct: 240 LYDAIQSGKVAAAGLDVFEKEPCT-----DSPLFALDQVTATPHLGASTKEAQVNVAIDV 294 Query: 530 PGKIIEYINSGNTFNSVNFPNIQ 552 I+ + +VN P ++ Sbjct: 295 AYDILRVLRGEAVSAAVNIPAVK 317 Score = 30.8 bits (68), Expect = 2e-04 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 2/79 (2%) Query: 546 VNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKINIVGQYLKTNEKIG--YVIT 603 V+ + + H L+ H + P ++ ++ ++ + +NI G +L + G I Sbjct: 438 VSIDGYDMDMAPEGHMLVVPHTDKPRIIGQLGTIIGEHNVNIAGMHLGRKDFGGNAVAIL 497 Query: 604 DIDKRYSNDVIDALKEIEG 622 ID V+ L +I+G Sbjct: 498 TIDGPVPAAVLTDLAKIDG 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: 670 Number of extensions: 36 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 630 Length of database: 526 Length adjustment: 36 Effective length of query: 594 Effective length of database: 490 Effective search space: 291060 Effective search space used: 291060 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 25 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