Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_015820139.1 TERTU_RS01735 phosphoglycerate dehydrogenase
Query= BRENDA::Q9I6H5 (409 letters) >NCBI__GCF_000023025.1:WP_015820139.1 Length = 411 Score = 595 bits (1534), Expect = e-175 Identities = 292/408 (71%), Positives = 352/408 (86%) Query: 2 SKTSLDKSKIKFLLLEGVHQNAVDTLKAAGYTNIEYLKTALSGDELKERIADAHFIGIRS 61 ++TSLDK+KIKFLLLEGVHQ+AV++L AGYTN++Y+KTAL+ +EL ERI DAHF+G+RS Sbjct: 4 AQTSLDKAKIKFLLLEGVHQSAVESLNRAGYTNVDYVKTALAEEELIERIKDAHFVGLRS 63 Query: 62 RTQLTEEVFDCAKKLIAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEAI 121 RTQLT V + A KL+A GCFCIGTNQVDL+AA+E G+AVFNAP+SNTRSVAELV+AEAI Sbjct: 64 RTQLTRRVIEHAPKLVAAGCFCIGTNQVDLDAAQEHGVAVFNAPFSNTRSVAELVIAEAI 123 Query: 122 LLLRGIPEKNASCHRGGWIKSAANSFEIRGKKLGIVGYGSIGTQLSVLAEALGMQVFFYD 181 LLLRGIP KNA CHRG W KSA S+EIRGK +GIVGYGSIG+Q+SV+AEA+GMQV F+D Sbjct: 124 LLLRGIPAKNAGCHRGEWDKSAVGSYEIRGKTMGIVGYGSIGSQVSVMAEAMGMQVVFFD 183 Query: 182 TVTKLPLGNAVQIGSLHELLGMSDIVSLHVPELPSTQWMIGEKEIRAMKKGGILINAARG 241 VTKLPLGNAVQ SL ELL ++D+VSLHVPEL +T+ +IGE E+ AMK L+NA+RG Sbjct: 184 VVTKLPLGNAVQSKSLTELLQVADVVSLHVPELEATKNLIGENELAAMKPQSFLLNASRG 243 Query: 242 TVVELDHLAAAIKDEHLIGAAIDVFPVEPKSNDEEFASPLRGLDRVILTPHIGGSTAEAQ 301 TVV++D LAAA++ +HL GAAIDVFPVEPK N+EEF SPLR D VILTPHIGGST EAQ Sbjct: 244 TVVDIDALAAALESKHLAGAAIDVFPVEPKGNNEEFVSPLRRFDNVILTPHIGGSTMEAQ 303 Query: 302 ANIGLEVAEKLVKYSDNGTSVSSVNFPEVALPSHPGKHRLLHIHANIPGVMSEINKVFAD 361 NIG EVAEKL+KYSDNGT+ SSVNFPEVALP+H HRLLH+H N+PGVM+ IN++F++ Sbjct: 304 ENIGYEVAEKLIKYSDNGTTTSSVNFPEVALPAHREVHRLLHVHQNVPGVMTAINRIFSE 363 Query: 362 NGINVSGQYLQTNEKVGYVVIDVDAEYSDLALEKLQQVNGTIRSRVLF 409 N IN++GQYLQT E VGYVVIDVD+ YSDLAL++L++V GT+R RVLF Sbjct: 364 NNINIAGQYLQTKESVGYVVIDVDSAYSDLALKQLREVEGTVRCRVLF 411 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: 476 Number of extensions: 10 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: 409 Length of database: 411 Length adjustment: 31 Effective length of query: 378 Effective length of database: 380 Effective search space: 143640 Effective search space used: 143640 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