Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate Dsui_1954 Dsui_1954 cysteine synthase B
Query= SwissProt::P9WP51 (464 letters) >FitnessBrowser__PS:Dsui_1954 Length = 299 Score = 204 bits (518), Expect = 4e-57 Identities = 121/302 (40%), Positives = 178/302 (58%), Gaps = 18/302 (5%) Query: 7 ISELIGGTPLVRLNSV----VPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLK 62 + + +G TPLV+L + + + AK+E NP GS KDR A+ MI AE G+++ Sbjct: 5 LEDFVGNTPLVQLKRLPGEAIAQRGNVILAKLEGNNPAGSVKDRPALSMISHAEQRGEIR 64 Query: 63 PGGTIVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPP 122 PG T++E TSGNTG+ LA+ A RGY+ + V P+ S ++R + AYGAE+++ P Sbjct: 65 PGDTLIEATSGNTGIALAMAAAMRGYRMILVMPENQSLERRQTMRAYGAELILTPR---D 121 Query: 123 HDPASYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGT 182 V++++ + G DQ+ANP+ P +H+ TGPEIW DT+G+VTHFV+ +GT Sbjct: 122 GGMELARDVAEKMCDEGKGIIL-DQFANPDNPLAHFEGTGPEIWRDTKGQVTHFVSSMGT 180 Query: 183 GGTITGAGRYLKEVSGGRVRIVGADP-EGSVYSGGAGRPYLVEGVGEDFWPAAYDPSVPD 241 GTI G ++LK+ R++IVG P EGS G P E + P Y+ S D Sbjct: 181 TGTIIGTSQFLKK-KNPRIQIVGCQPEEGSQIPGIRKWP-------EAYLPKIYERSRVD 232 Query: 242 EIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRGY 301 + VS +++ DMTRRLAREE + G S G A+ AL++A E +A IV ++ D G Y Sbjct: 233 RLEYVSQAEAEDMTRRLAREEGLFAGISSGGALAVALRLAREL-ENATIVTIVCDRGDRY 291 Query: 302 MS 303 +S Sbjct: 292 LS 293 Lambda K H 0.316 0.135 0.398 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: 368 Number of extensions: 22 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 464 Length of database: 299 Length adjustment: 30 Effective length of query: 434 Effective length of database: 269 Effective search space: 116746 Effective search space used: 116746 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: 49 (23.5 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