Align Cystathionine beta-synthase; Beta-thionase; Hemoprotein H-450; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate PfGW456L13_4472 Cysteine synthase (EC 2.5.1.47)
Query= SwissProt::P32232 (561 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4472 Length = 324 Score = 221 bits (562), Expect = 4e-62 Identities = 139/321 (43%), Positives = 191/321 (59%), Gaps = 20/321 (6%) Query: 72 KILPDILRKIGNTPMVRINRISKNAGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERAG 131 +I D IGNTP+V+INRI+ +L K E N G SVK RI MI DAE +G Sbjct: 3 RIFADNAHSIGNTPLVQINRIAPRG---VTILVKIEGRNPGYSVKCRIGANMIWDAEGSG 59 Query: 132 TLKPGDTIIEPTSGNTGIGLALAAAVKGYRCIIVMPEKMSMEKVDVLRALGAEIVRTPTN 191 LKPG TI+EPTSGNTGIGLA AA +GY+ ++ MP MS+E+ VL+ALGAE+V T Sbjct: 60 KLKPGMTIVEPTSGNTGIGLAFVAAARGYKLMLTMPASMSIERRKVLKALGAELVLT--- 116 Query: 192 ARFDSPESHVGVAWRLKNEI----PNSHILD-QYRNASNPLAHYDDTAEEILQQCDGKVD 246 P + A EI P+ + + Q+ N +NP H T EI DG VD Sbjct: 117 ----EPAKGMKGAIEKAGEIVAGDPSKYFMPAQFDNPANPAIHEKTTGPEIWNDTDGAVD 172 Query: 247 MLVASAGTGGTITGIARKLKEKCPGCKIIGVDPE---GSILAEPEELNQTEQTAYEVEGI 303 +LVA GTGGTITG++R +K G I+ V E ++ + + + + ++++GI Sbjct: 173 VLVAGVGTGGTITGVSRYIK-NTQGKPILSVAVEPVVSPVITQALAGEEIKPSPHKIQGI 231 Query: 304 GYDFIPTVLDRAVVDRWFKSNDDDSFAFARMLISQEGLLCGGSSGSAMAVAVKAAQELK- 362 G F+P LD ++VDR +D++S A A L+ +EG+LCG SSG+AMAVAV+ A+ + Sbjct: 232 GAGFVPKNLDLSIVDRVELVSDEESKAMALRLMQEEGILCGISSGAAMAVAVRLAETPEM 291 Query: 363 EGQRCVVILPDSVRNYMSKFL 383 +G+ VVILPDS Y+S L Sbjct: 292 QGKTFVVILPDSGERYLSSML 312 Lambda K H 0.317 0.134 0.401 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: 430 Number of extensions: 26 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: 561 Length of database: 324 Length adjustment: 32 Effective length of query: 529 Effective length of database: 292 Effective search space: 154468 Effective search space used: 154468 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 09 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