Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate RR42_RS31610 RR42_RS31610 cystathionine beta-lyase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Cup4G11:RR42_RS31610 Length = 402 Score = 191 bits (485), Expect = 3e-53 Identities = 137/393 (34%), Positives = 204/393 (51%), Gaps = 19/393 (4%) Query: 20 DTLAVRAGQRRTPEGEHGEA---LFTTSSYVFRTAA---DAAARFAGEVPGNVYSRYTNP 73 DT + AG +G HG + TS+ F + D AR A + Y R+ Sbjct: 6 DTQLIHAGTPPFVQG-HGPVNVPVVRTSTVRFENSDAYDDIRARHARGERVSSYGRHGMD 64 Query: 74 TVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYF 133 T R E+ IA LEG +A SG++AI ++L S GDH LV SV+ L Sbjct: 65 THRALEDAIAGLEGGNRAFLAPSGLAAISLTFLALLSPGDHALVVDSVYAPVRRLEQTLL 124 Query: 134 KRFGIQVDY--PPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALL 191 +R GI+V Y P DL +A +PNT+L ++ESPS+ L E++D+ L +IAH G ++ Sbjct: 125 RRLGIEVSYFSPSQDDL---DALIRPNTRLLYLESPSSLLYEVLDLPRLVQIAHRHGVVV 181 Query: 192 AVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTA-G 250 A DN + + QPL LG D+ I ++TKYI G M G V + E + + G Sbjct: 182 ATDNTWASGHALQPLALGVDISILASTKYISGHSDLMQGAVVVKDEALARRIADAHDGFG 241 Query: 251 PTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELAR 310 +S +A+L L+G+ TL +R+ H +ALA+A++LE + RV+Y LPS P H L Sbjct: 242 LAISADDAYLALRGIRTLAVRLAQHQRNALAVAQFLEAHEAVGRVFYPALPSDPGHALWL 301 Query: 311 RQQSGFGAVVSFDVKGGRDAAWR-FIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPED 369 R SG +VSF + AA R +D+ + + + G ++ + A RL+ Sbjct: 302 RDFSGANGLVSFSLPTADVAAARKLVDSLSLFGLGASWGGYESLVQVAAPE---RLAEHS 358 Query: 370 RARAGIGDSLIRVAVGLEDLDDLKADMARGLAA 402 R + +IR+ +GLE +DL AD+A+GLAA Sbjct: 359 YWRG--AEPVIRLHIGLEAPEDLIADLAQGLAA 389 Lambda K H 0.319 0.133 0.392 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: 380 Number of extensions: 24 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: 403 Length of database: 402 Length adjustment: 31 Effective length of query: 372 Effective length of database: 371 Effective search space: 138012 Effective search space used: 138012 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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