Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate GFF3511 HP15_3453 cysteine synthase A
Query= SwissProt::P9WP51 (464 letters) >FitnessBrowser__Marino:GFF3511 Length = 323 Score = 218 bits (556), Expect = 2e-61 Identities = 133/310 (42%), Positives = 179/310 (57%), Gaps = 12/310 (3%) Query: 2 RIAQHISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQL 61 RI + S IG TPLVRLN V DGA T+ AK+E NP S K RI MI AE G L Sbjct: 3 RIYEDNSLSIGNTPLVRLNRV-NDGA-TIWAKIEGRNPAYSVKCRIGSAMIWDAEKRGTL 60 Query: 62 KPGGTIVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVP 121 K G TIVEPTSGNTG+ LA VA RGYK + P +S ++R VL A GAE+V+ T Sbjct: 61 KAGMTIVEPTSGNTGIALAYVAAARGYKLILTMPASMSLERRKVLKALGAELVL--TEPA 118 Query: 122 PHDPASYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIG 181 P + + D D + P Q+ NP P H TTGPEIW DT+G++ FVAG+G Sbjct: 119 KGMPGAIAKAEEIFSSDPDNYFLPQQFQNPANPRIHEDTTGPEIWEDTDGEIDIFVAGVG 178 Query: 182 TGGTITGAGRYLKEVSGGRVRIVGADPEGS-----VYSGG--AGRPYLVEGVGEDFWPAA 234 TGGT+TG RY+K G ++ + +P S + +G P+ ++G+G F P Sbjct: 179 TGGTLTGVSRYIKGTKGKQIATIAVEPTDSPVITQMMNGEDIKPAPHKIQGIGAGFVPKN 238 Query: 235 YDPSVPDEIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDAL-IVVL 293 D + D++ VS+ ++ DM RL +EE +L G SCG AV AA++++++ IVV+ Sbjct: 239 LDLEMVDQVETVSNEEAMDMAHRLMQEEGILCGISCGAAVAAAVRISKQPEYQGKNIVVV 298 Query: 294 LPDGGRGYMS 303 LPD Y+S Sbjct: 299 LPDTAERYLS 308 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: 397 Number of extensions: 23 Number of successful extensions: 4 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: 323 Length adjustment: 30 Effective length of query: 434 Effective length of database: 293 Effective search space: 127162 Effective search space used: 127162 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