Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate Dsui_2043 Dsui_2043 cysteine synthase
Query= SwissProt::P9WP51 (464 letters) >FitnessBrowser__PS:Dsui_2043 Length = 501 Score = 278 bits (712), Expect = 2e-79 Identities = 171/456 (37%), Positives = 247/456 (54%), Gaps = 20/456 (4%) Query: 9 ELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLKPGGTIV 68 +LIG TPLV + G + K+E NPGGS KDR+A MI+AAE G +KPG T+V Sbjct: 53 DLIGATPLVEVTHF-DTGPCRLFLKLESQNPGGSIKDRVARSMIDAAEKEGLIKPGSTLV 111 Query: 69 EPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPPHDPASY 128 E T+GNTG+ L LV +RGYK V V PDK+S++K L A GA VV+ + V P Y Sbjct: 112 EATAGNTGLALTLVGAQRGYKVVLVVPDKMSQEKIFALKALGARVVMTRSDVGVGHPEYY 171 Query: 129 YSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGTGGTITG 188 ++ RL +I GAW +Q+ NP P +H TGPE+W+ +G++ V G+G+GGT+TG Sbjct: 172 QDMAQRLASEIPGAWYVNQFGNPNNPKAHETGTGPELWSQLKGRIDAVVCGVGSGGTLTG 231 Query: 189 AGRYLKEVSGGRVRIVGADPEGSVYSGGAGRPY-------LVEGVGEDFWPAAYDPSVPD 241 R+ ++ S RV++V ADP GSV + Y LVEG+GEDF P D + Sbjct: 232 LTRFFRQKS-PRVKMVLADPAGSVLADYVAHGYIKEAGSWLVEGIGEDFIPPICDLTGVR 290 Query: 242 EIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRGY 301 E V D++SF R L R+E ++ G S G + AAL+ +V + D G Y Sbjct: 291 EAYTVPDAESFAAARELLRKEGIMGGSSTGTLLAAALRYCRTRTKPEHVVTFVCDHGNRY 350 Query: 302 MSKIFNDAWMSSYGFLRSRLDGSTEQSTVGDVLRRKSGALPALVHTHPSETVRDAIGILR 361 +SK++ND WM+ GFL + G + D++ R++ A+V P++TV A G + Sbjct: 351 LSKMYNDFWMADQGFLPKDVRGD-----LRDIIGRRADE-GAVVTVAPTDTVLTAYGRFK 404 Query: 362 EYGVSQMPVVGAEPPVMAGEVAGSVSERELLSAVFEGRAKLADAVSAHMSPPLRMIGAGE 421 Y VSQ+PV E G + G + E +LL A+ + A V M+ L + Sbjct: 405 LYDVSQLPVTNDE-----GRIVGLIDESDLLLAITKDEANFRQPVKKFMTSRLTTLPPTA 459 Query: 422 LVSAAGKALRDWDALMVVEEGKPVGVITRYDLLGFL 457 +S +VV+ + +G++TR DLL L Sbjct: 460 PISDLLPLFDQGLVPIVVDGDRFLGLVTRIDLLNHL 495 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: 629 Number of extensions: 32 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: 464 Length of database: 501 Length adjustment: 34 Effective length of query: 430 Effective length of database: 467 Effective search space: 200810 Effective search space used: 200810 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: 52 (24.6 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