Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate SMa1347 SMa1347 dehydrogenase
Query= BRENDA::P9WNX3 (528 letters) >FitnessBrowser__Smeli:SMa1347 Length = 324 Score = 178 bits (451), Expect = 3e-49 Identities = 110/300 (36%), Positives = 161/300 (53%), Gaps = 9/300 (3%) Query: 11 KLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVA 70 +L P A L ++R PD + LL A+ ++VR+ + P L+ V Sbjct: 9 RLHPDAEAMLKAASDLRVASAPDPETLLREGEGAEIVIVRAP--IPPAFFGNVPALRAVV 66 Query: 71 RAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTW- 129 R G GLD + DAATA GVL+ N P N + AEH + LA RQ D LR W Sbjct: 67 RHGAGLDMIPYDAATAAGVLIANVPAVNAPTVAEHVFMVTLALLRQFRPMDRDLRNMGWS 126 Query: 130 --KRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELL 187 + S ++ G+ +GV+G+G +G+ V RIA +G + SP G+ L Sbjct: 127 TGRAHSDRALDLAGRIMGVIGMGNVGKAVF-RIAKYGFQLEIVANSRSPESLPD-GVRFL 184 Query: 188 SLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITG 247 S+DDLL+ AD + + P TP+T GL+ +E +A+ KPG I+VN +RG +VD+AAL +A+ Sbjct: 185 SVDDLLSTADIVVLCCPLTPKTTGLLSRERIARMKPGAILVNVSRGPVVDDAALIEALER 244 Query: 248 GHVRAAGLDVFATEPC-TDSPLFELAQVVVTPHLGASTAEAQDRAGTD-VAESVRLALAG 305 G + A LDVF+T+P + P F V+VTPHL + E+ R G AE++R+ G Sbjct: 245 GRIGGAALDVFSTQPLPPEHPYFRQDNVIVTPHLAGISEESMMRMGKGAAAEAIRVMEGG 304 Lambda K H 0.317 0.133 0.370 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: 369 Number of extensions: 19 Number of successful extensions: 5 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: 528 Length of database: 324 Length adjustment: 31 Effective length of query: 497 Effective length of database: 293 Effective search space: 145621 Effective search space used: 145621 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: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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