Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate Echvi_3411 Echvi_3411 OAH/OAS sulfhydrylase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__Cola:Echvi_3411 Length = 436 Score = 515 bits (1326), Expect = e-150 Identities = 261/442 (59%), Positives = 332/442 (75%), Gaps = 22/442 (4%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 F+T+QLHAG E P N + SRAVPIY T+SYVF +++HG+ LFGL+ G +Y+R NPT+ Sbjct: 8 FETLQLHAGHE-PDSNTN-SRAVPIYQTSSYVFNSAEHGANLFGLKEFGNIYTRIMNPTN 65 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 +V E+R+AALEGG AALAVSSGQAAQ +A+ + GDN V++ +LYGGTYNQFK+SFKR Sbjct: 66 DVFEKRMAALEGGVAALAVSSGQAAQFIALSNILENGDNFVTSPFLYGGTYNQFKVSFKR 125 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 GI ARF + E+ EK+ D+RTKA+Y+ETIGNP +NVPDFE + A++ KH IP+VVDN Sbjct: 126 LGISARFASSEKAEDMEKLIDDRTKALYVETIGNPGFNVPDFEALSALSKKHDIPLVVDN 185 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 TFGAGGY +P+ +GA IV SATKWIGGHGT+IGGIIVD G + W + KFPQFS+P+ Sbjct: 186 TFGAGGYLFRPLAHGAHIVVASATKWIGGHGTSIGGIIVDGGNYNWGN--GKFPQFSEPS 243 Query: 245 EGYHGTIYNEAYG--------NLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRA 296 EGYHG + E +G N+A+ + R E LRD GP ++PF SFLLLQG+ETLSLRA Sbjct: 244 EGYHGLNFWEVFGEGNPLGLPNIAFSIRARVEGLRDFGPAISPFNSFLLLQGLETLSLRA 303 Query: 297 ERHGENALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNAD 356 ER ENAL LAKWLE P V+ VSYPGL SH HH AKKYL GFGGVL+F VK Sbjct: 304 ERTVENALTLAKWLENHPQVATVSYPGLESHGHHTLAKKYLKKGFGGVLTFEVKG----- 358 Query: 357 KETDPFKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIR 416 K +G ++VD+L+L S+LANVGDAKTL+I P TTH+QL++KE+ A+GVT ++R Sbjct: 359 -----GKEAGEKLVDSLQLISHLANVGDAKTLIIQPSATTHQQLSEKEQAAAGVTPGMLR 413 Query: 417 VSVGIEFIDDIIADFQQSFETV 438 +S+GIE IDDI AD +Q+F+ + Sbjct: 414 ISLGIEHIDDICADLEQAFQKI 435 Lambda K H 0.317 0.136 0.402 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: 664 Number of extensions: 23 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: 444 Length of database: 436 Length adjustment: 32 Effective length of query: 412 Effective length of database: 404 Effective search space: 166448 Effective search space used: 166448 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: 51 (24.3 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