Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_068175438.1 HTA01S_RS22370 phosphoglycerate dehydrogenase
Query= BRENDA::A4VGK3 (468 letters) >NCBI__GCF_001592305.1:WP_068175438.1 Length = 420 Score = 593 bits (1529), Expect = e-174 Identities = 296/407 (72%), Positives = 347/407 (85%) Query: 62 QTSLDKSKIKFLLLEGVHQNAVDTLKAAGYTNIEDLKTALSGDELKEKIADAHFIGIRSR 121 +TS+DK KI+FLLLEG+H +AV L+AAGY+ IE L AL D+L KIADAHF+GIRSR Sbjct: 14 KTSIDKHKIRFLLLEGIHPSAVSVLRAAGYSQIESLPGALPDDQLLAKIADAHFVGIRSR 73 Query: 122 TQLTEEVFDCAKKLIAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEAIL 181 TQLT +V A++L AVGCFCIGTNQVDL AARERGIAVFNAP+SNTRSVAELVLAEAIL Sbjct: 74 TQLTAKVLSHAQRLAAVGCFCIGTNQVDLAAARERGIAVFNAPFSNTRSVAELVLAEAIL 133 Query: 182 LLRGIPEKNASCHRGGWIKSAANSFEIRGKKLGIIGYGSIGTQLSVLAEALGMQVFFYDV 241 L+RGIPEKNA HRGGW+KSA+NSFEIRGK LGI+GYG+IGTQLSVLAEALGM V F+DV Sbjct: 134 LMRGIPEKNAVAHRGGWLKSASNSFEIRGKTLGIVGYGAIGTQLSVLAEALGMHVVFFDV 193 Query: 242 VTKLPLGNATQIGSLYELLGMCDIVSLHVPELPSTQWMIGEKEIRAMKKGAILINAARGT 301 TKLPLGNA + SL EL+ D+VSLHVPE P+TQWMIG ++ MK A+LINA+RGT Sbjct: 194 ATKLPLGNARPLTSLDELMATADVVSLHVPETPATQWMIGAAQLARMKPSAVLINASRGT 253 Query: 302 VVELDHLAAAIKDEHLIGAAIDVFPVEPKSNDEEFESPLRGLDRVILTPHIGGSTAEAQA 361 VV++D LA+A+ ++ L+GAAIDVFP EP SN + FESPLRGLD VILTPHIGGST EAQ Sbjct: 254 VVQVDALASALHNQALLGAAIDVFPEEPHSNKDVFESPLRGLDNVILTPHIGGSTLEAQE 313 Query: 362 NIGLEVAEKLVKYSDNGTSVSSVNFPEVALPSHPGKHRLLHIHQNIPGVMSEINKVFADN 421 NIG+EVAEKLVKYSDNGTS S+VNFPEVALP+HPGKHRLLHIH+N+PGV+S IN+VF+D+ Sbjct: 314 NIGIEVAEKLVKYSDNGTSTSAVNFPEVALPAHPGKHRLLHIHRNVPGVLSGINRVFSDH 373 Query: 422 GINICGQFLQTNEKVGYVVIDVDKEYSDLALEKLQHVNGTIRSRVLF 468 GINI Q+LQT E VGYVV+D+D +S+LAL +L V GT+RSRVLF Sbjct: 374 GINISAQYLQTREDVGYVVMDIDAAHSELALAELARVPGTLRSRVLF 420 Lambda K H 0.318 0.135 0.385 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: 566 Number of extensions: 14 Number of successful extensions: 1 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: 468 Length of database: 420 Length adjustment: 32 Effective length of query: 436 Effective length of database: 388 Effective search space: 169168 Effective search space used: 169168 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 (21.7 bits) S2: 51 (24.3 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