Align O-acetyl-L-homoserine sulfhydrylase 1; OAH-sulfhydrylase 1; EC 2.5.1.- (characterized)
to candidate WP_011444472.1 SARO_RS04055 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::Q5SK88 (421 letters) >NCBI__GCF_000013325.1:WP_011444472.1 Length = 427 Score = 443 bits (1140), Expect = e-129 Identities = 230/423 (54%), Positives = 284/423 (67%), Gaps = 6/423 (1%) Query: 2 RFETLQLHAGYEPEPTTLSRQVPIYPTTSYVFKSPEHAANLFALKEFGNIYSRIMNPTVD 61 + ETL +HAG EP+PTT +R PIY T SYVF S EHAANLFAL EFGNIYSRIMNPT Sbjct: 4 KLETLTVHAGCEPDPTTKARITPIYQTASYVFDSAEHAANLFALAEFGNIYSRIMNPTNA 63 Query: 62 VLEKRLAALEGGKAALATASGHAAQFLALTTLAQAGDNIVSTPNLYGGTFNQFKVTLKRL 121 LE ++AALEGG AAL ASGHAAQF+ TL + G IV+ LYGGT NQF + Sbjct: 64 ALEAKIAALEGGVAALGVASGHAAQFIVFHTLMEPGCEIVAAKKLYGGTLNQFAHGFAKF 123 Query: 122 GIEVRFTSREERPEEFLALTDEKTRAWWVESIGNPALNIPDLEALAQAAREKGVALIVDN 181 G + F ++ A+TD KTR ++ES+ NP + D+ A+A+ A GV LIVDN Sbjct: 124 GWKAVFVDADDPAAVAAAITD-KTRGVFIESLANPGGVVQDIAAIAEVAHAAGVPLIVDN 182 Query: 182 TFGMGGYLLRPLAWGAALVTHSLTKWVGGHGAVIAGAIVDGGNFPWEGG-RYPLLTEPQP 240 T L RP+ GA +V HS TK++ GHG I G IVD G F W ++P L++P P Sbjct: 183 TMASPA-LCRPIEHGADIVVHSCTKFLNGHGNSIGGLIVDAGRFDWAASDKFPSLSQPNP 241 Query: 241 GYHGLRLTEAF---GELAFIVKARVDGLRDQGQALGPFEAWVVLLGMETLSLRAERHVEN 297 YHG LTEA G +AFI+ RV GLRD G A+ P A++ L GMETL+LR ERH N Sbjct: 242 SYHGAVLTEALKPVGPIAFIIGCRVLGLRDLGPAMAPMNAFLTLTGMETLALRIERHCAN 301 Query: 298 TLHLAHWLLEQPQVAWVNYPGLPHHPHHDRAQKYFKGKPGAVLTFGLKGGYEAAKRFISR 357 LHLA WL P+VAWV+Y GLP P+H A++Y GK GAV TFG+KGGYEA + + Sbjct: 302 ALHLAQWLQNHPKVAWVSYAGLPEDPYHQLAKQYLGGKGGAVFTFGVKGGYEAGVKLVQS 361 Query: 358 LKLISHLANVGDTRTLAIHPASTTHSQLSPEEQAQAGVSPEMVRLSVGLEHVEDLKAELK 417 +KL SHLAN+GDTR+L IHPASTTHSQL EE AG P+ VR+SVG+EH++D+ A+L Sbjct: 362 VKLFSHLANIGDTRSLIIHPASTTHSQLGEEELVAAGAGPDTVRVSVGIEHIDDIVADLA 421 Query: 418 EAL 420 +AL Sbjct: 422 QAL 424 Lambda K H 0.318 0.135 0.407 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: 483 Number of extensions: 18 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: 421 Length of database: 427 Length adjustment: 32 Effective length of query: 389 Effective length of database: 395 Effective search space: 153655 Effective search space used: 153655 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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