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 Ac3H11_549 O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_549 Length = 458 Score = 411 bits (1056), Expect = e-119 Identities = 207/433 (47%), Positives = 291/433 (67%), Gaps = 9/433 (2%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +T+ +HAG D ++ AVPIY T +Y F++++HG+ LF L+VPG +Y+R NPT++ Sbjct: 35 ETLAVHAGYSP--DPTTKAVAVPIYQTVAYAFDSAQHGADLFDLKVPGNIYTRIMNPTTD 92 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 VLE+R+AALEGG AALAV+SG AA T AIQ +A GDNIVS S LYGGTYN F + + Sbjct: 93 VLEKRVAALEGGIAALAVASGMAAITYAIQTIAEAGDNIVSASTLYGGTYNLFAHTLPQQ 152 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 GI RF + +P F + D RTKA+++E+IGNP NV D I +AH HG+P++VDNT Sbjct: 153 GITTRFADPRDPASFAQHIDARTKAIFIESIGNPLGNVTDIAAIAKVAHDHGVPLIVDNT 212 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 Y +PI++GADIV HS TK++GGHG ++GG IVDSGKFPW ++ +FP+ ++P Sbjct: 213 V-PSPYLLRPIEHGADIVVHSLTKYLGGHGNSVGGAIVDSGKFPWAEHKARFPRLNEPDV 271 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 YHG +Y EA G A+I R LR+ G ++P ++FL+LQG+ETL+LR +R +N L Sbjct: 272 SYHGVVYTEALGPAAFIGRARVVPLRNTGAALSPQSAFLILQGIETLALRMDRICDNTLA 331 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 LAK+L+ P V WV Y GL H H ++ G+LSFG+K + DP + + Sbjct: 332 LAKYLQSHPKVEWVRYAGLPDHPDHALVQRQSGGKASGILSFGLK-----STDADP-RAA 385 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 GA+ +D L+L + L N+GDAK+L P TTH+QLN +E +GV++ ++R+SVGIE ID Sbjct: 386 GARFLDALQLFTRLVNIGDAKSLATHPASTTHRQLNPEELAKAGVSESMVRLSVGIEHID 445 Query: 426 DIIADFQQSFETV 438 D+ AD Q+ + V Sbjct: 446 DLRADLVQALDAV 458 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: 565 Number of extensions: 26 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: 444 Length of database: 458 Length adjustment: 33 Effective length of query: 411 Effective length of database: 425 Effective search space: 174675 Effective search space used: 174675 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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