Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate 206086 DVU0663 cysteine synthase A
Query= SwissProt::P9WP51 (464 letters) >MicrobesOnline__882:206086 Length = 308 Score = 249 bits (636), Expect = 9e-71 Identities = 143/310 (46%), Positives = 191/310 (61%), Gaps = 16/310 (5%) Query: 1 MRIAQHISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQ 60 M IA +++L+G TP+VRLN V V AK+E NP S KDRIA+ M+EAA A G+ Sbjct: 1 MDIASSMTDLVGKTPMVRLNKVTLGCVAEVVAKLENFNPCSSVKDRIALNMVEAAIARGE 60 Query: 61 LKPGGTIVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAV 120 + PG +VEPTSGNTGVGLA V RG K V P+ +S ++R +L A+G +V+ P A Sbjct: 61 IAPGAVLVEPTSGNTGVGLAFVCAVRGLKLVLTMPESMSAERRALLKAFGTTLVLTPAA- 119 Query: 121 PPHDPASYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGI 180 ++R+V D GA Q+ANP+ PA+H TTGPEIWADT+G + FVAG+ Sbjct: 120 --KGMRGAVEEAERIVADTPGAVMLQQFANPDNPAAHEATTGPEIWADTDGMIDCFVAGV 177 Query: 181 GTGGTITGAGRYLKEVSGGR---VRIVGADP-EGSVYSGGAGRPYLVEGVGEDFWPAAYD 236 GTGGTITG GRYLK GR +R++ +P E +V SGGA P+ ++G+G F P D Sbjct: 178 GTGGTITGTGRYLK----GRNPDIRVIAVEPAESAVLSGGAPGPHAIQGIGAGFVPPVLD 233 Query: 237 PSVPDEIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVA---EEAGPDALIVVL 293 SV DE++ V +D+ M RRL +EE +L G S G V AA+ A E AG +V + Sbjct: 234 TSVYDEVMPVPGADALTMARRLLQEEGILCGISSGANVHAAIAYARRPENAG--KRVVCI 291 Query: 294 LPDGGRGYMS 303 + D G Y+S Sbjct: 292 ICDTGERYLS 301 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: 426 Number of extensions: 19 Number of successful extensions: 3 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: 308 Length adjustment: 30 Effective length of query: 434 Effective length of database: 278 Effective search space: 120652 Effective search space used: 120652 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 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