Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_038209742.1 Q392_RS15870 phosphoglycerate dehydrogenase
Query= BRENDA::Q9I6H5 (409 letters) >NCBI__GCF_000745855.1:WP_038209742.1 Length = 410 Score = 624 bits (1610), Expect = 0.0 Identities = 310/408 (75%), Positives = 355/408 (87%) Query: 2 SKTSLDKSKIKFLLLEGVHQNAVDTLKAAGYTNIEYLKTALSGDELKERIADAHFIGIRS 61 +KTSLDKSKIKFLLLEG+H + V+ ++AAGY+ +E L AL +ELK R+AD HF+GIRS Sbjct: 3 TKTSLDKSKIKFLLLEGIHPSGVELIRAAGYSQVEVLSGALDAEELKARVADVHFLGIRS 62 Query: 62 RTQLTEEVFDCAKKLIAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEAI 121 RTQLT E+F A++L+AVG FCIGTNQ+DL AA E G+AVFNAPYSNTRSVAELVLAEAI Sbjct: 63 RTQLTPEIFAAARRLVAVGAFCIGTNQIDLGAALEHGVAVFNAPYSNTRSVAELVLAEAI 122 Query: 122 LLLRGIPEKNASCHRGGWIKSAANSFEIRGKKLGIVGYGSIGTQLSVLAEALGMQVFFYD 181 LLLRG+PEKNA HRGGW+KSA N+FEIRGK LGIVGYGSIG QLSVLAEALGM V FYD Sbjct: 123 LLLRGVPEKNAVAHRGGWLKSAENAFEIRGKTLGIVGYGSIGAQLSVLAEALGMHVVFYD 182 Query: 182 TVTKLPLGNAVQIGSLHELLGMSDIVSLHVPELPSTQWMIGEKEIRAMKKGGILINAARG 241 VT+LPLGNA Q+ SL+ELLG +DIVSLHVP+LPSTQWMIGE +I AMK G ILINA+RG Sbjct: 183 VVTRLPLGNAQQVRSLNELLGTADIVSLHVPQLPSTQWMIGEAQIAAMKPGAILINASRG 242 Query: 242 TVVELDHLAAAIKDEHLIGAAIDVFPVEPKSNDEEFASPLRGLDRVILTPHIGGSTAEAQ 301 TVVE++ LAAAI+ + L+GAA+DVFPVEPKSN +EF SPLRGLD VILTPHIGGST EAQ Sbjct: 243 TVVEIEPLAAAIRAKKLLGAAVDVFPVEPKSNKDEFVSPLRGLDNVILTPHIGGSTMEAQ 302 Query: 302 ANIGLEVAEKLVKYSDNGTSVSSVNFPEVALPSHPGKHRLLHIHANIPGVMSEINKVFAD 361 ANIG+EVAEKLVKYSDNGT+ SSVNFPEVALP+HPGKHRLLH+H N+PGV+S +N VFA+ Sbjct: 303 ANIGVEVAEKLVKYSDNGTTTSSVNFPEVALPAHPGKHRLLHVHRNVPGVLSAVNGVFAE 362 Query: 362 NGINVSGQYLQTNEKVGYVVIDVDAEYSDLALEKLQQVNGTIRSRVLF 409 GIN+S QYLQTNEKVGYVV D+DA S+ ALEKL QV GTIRS VLF Sbjct: 363 TGINISAQYLQTNEKVGYVVTDIDAGSSEAALEKLTQVPGTIRSWVLF 410 Lambda K H 0.317 0.135 0.381 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: 534 Number of extensions: 15 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: 409 Length of database: 410 Length adjustment: 31 Effective length of query: 378 Effective length of database: 379 Effective search space: 143262 Effective search space used: 143262 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: 50 (23.9 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