Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate PP_1654 PP_1654 cysteine synthase B
Query= SwissProt::P9WP51 (464 letters) >FitnessBrowser__Putida:PP_1654 Length = 299 Score = 207 bits (527), Expect = 4e-58 Identities = 117/298 (39%), Positives = 177/298 (59%), Gaps = 14/298 (4%) Query: 7 ISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLKPGGT 66 I++ +G TPLVRL + + + T+ K+E NP GS KDR A+ MI AE GQ+KPG T Sbjct: 8 IADCVGNTPLVRLQRIAGETSNTLLLKLEGNNPAGSVKDRPALSMIARAELRGQIKPGDT 67 Query: 67 IVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPPHDPA 126 ++E TSGNTG+ LA+ A +GYK + + PD + +++ + AYGAE+++ Sbjct: 68 LIEATSGNTGIALAMAAAIKGYKMILIMPDNSTAERKAAMTAYGAELIL---VTKEEGME 124 Query: 127 SYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGTGGTI 186 ++++L + G DQ+AN + P +HY +TGPEIW T+G +THFV+ +GT GTI Sbjct: 125 GARDLAEKLQAEGRGL-VLDQFANGDNPIAHYNSTGPEIWQQTQGTITHFVSSMGTTGTI 183 Query: 187 TGAGRYLKEVSGGRVRIVGADP-EGSVYSGGAGRPYLVEGVGEDFWPAAYDPSVPDEIIA 245 G +YLKE V+I+G P EGS G P E++ P +D + D ++ Sbjct: 184 MGCSQYLKE-QNPAVQIIGLQPMEGSAIPGIRRWP-------EEYLPKIFDATRVDRVVD 235 Query: 246 VSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRGYMS 303 +S ++ D TRRLAREE + G S G AV A L+++ E +A++V ++ D G Y+S Sbjct: 236 MSQQEAEDTTRRLAREEGIFCGVSSGGAVAAMLRLSREV-ENAVMVAIICDRGDRYLS 292 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: 353 Number of extensions: 15 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