Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_086510640.1 BZY95_RS14570 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_002151265.1:WP_086510640.1 Length = 416 Score = 435 bits (1119), Expect = e-126 Identities = 215/407 (52%), Positives = 287/407 (70%), Gaps = 1/407 (0%) Query: 225 KFSYPKSRINVLLLENVHPIGVEIMKQEGY-NVEVVSSAMSEEELCEKIKNVSIIGIRSK 283 K S KS+I +LLLE VH V+ GY N+E + +++ E L EK+++ +GIRS+ Sbjct: 3 KTSLDKSKIKILLLEGVHQSAVDNFLNAGYTNIEHLPTSLDEAALIEKVRDAHFLGIRSR 62 Query: 284 TQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIF 343 TQ+T++V A +L AVG FCIGTNQ+DL +GI VFNAP+SNTRSV EL ++E I Sbjct: 63 TQLTERVFAAAEKLNAVGCFCIGTNQVDLNAALIRGIPVFNAPYSNTRSVAELVLAEAIM 122 Query: 344 LMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDI 403 L+R + +K + HQG W KSA S E RGK LGI+GYGNIGAQLSVLAE++G NV +YD+ Sbjct: 123 LLRGIPEKNARAHQGGWLKSAKNSHEARGKTLGIVGYGNIGAQLSVLAESLGFNVIFYDV 182 Query: 404 VERLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGH 463 V +L +GNA ++ SL+ELL D++SLHV K ++ K+++ MK IL+N SRG Sbjct: 183 VTKLGMGNANQVASLEELLARADVVSLHVPELPSTKWMIGKDQLVLMKPSGILINASRGS 242 Query: 464 VVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQE 523 VV + L +AL++G L GAA+DVFP EPK NDE F S L G PN ILTPH+GGSTLEAQE Sbjct: 243 VVVIEDLAEALQAGRLYGAAIDVFPVEPKGNDEEFVSPLRGIPNVILTPHVGGSTLEAQE 302 Query: 524 NIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASY 583 NI V K+I Y ++G T SVNFP + LP D HR++HIH N PGVL++IN+VL+ Sbjct: 303 NIGIEVSEKLITYSDNGTTVTSVNFPEVALPAHPDKHRVLHIHDNVPGVLSEINRVLSES 362 Query: 584 KINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRILY 630 INI GQYL+TN+K+GYV+ D+DK Y ++AL+++ T+R R+LY Sbjct: 363 GINISGQYLQTNDKVGYVVIDVDKAYGEQALEALRKVNHTLRVRVLY 409 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: 26 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: 416 Length adjustment: 35 Effective length of query: 595 Effective length of database: 381 Effective search space: 226695 Effective search space used: 226695 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