Align homocysteine synthase Met17; 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= CharProtDB::CH_124469 (429 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_549 Length = 458 Score = 446 bits (1147), Expect = e-130 Identities = 226/423 (53%), Positives = 286/423 (67%), Gaps = 5/423 (1%) Query: 9 ETLQLHAGQEPDAATSSRAVPIYATTSYVFRDCDHGGRLFGLQEPGYIYSRMMNPTADVF 68 ETL +HAG PD T + AVPIY T +Y F HG LF L+ PG IY+R+MNPT DV Sbjct: 35 ETLAVHAGYSPDPTTKAVAVPIYQTVAYAFDSAQHGADLFDLKVPGNIYTRIMNPTTDVL 94 Query: 69 EKRIAALEHGAAAIATSSGTSALFMALTTLAKAGDNIVSTSYLYGGTYNLFKVTLPRLGI 128 EKR+AALE G AA+A +SG +A+ A+ T+A+AGDNIVS S LYGGTYNLF TLP+ GI Sbjct: 95 EKRVAALEGGIAALAVASGMAAITYAIQTIAEAGDNIVSASTLYGGTYNLFAHTLPQQGI 154 Query: 129 TTKFVNGDDPNDLAAQIDENTKAVYVESIGNPMYNVPDFERIAEVAHAAGVPLMVDNTFG 188 TT+F + DP A ID TKA+++ESIGNP+ NV D IA+VAH GVPL+VDNT Sbjct: 155 TTRFADPRDPASFAQHIDARTKAIFIESIGNPLGNVTDIAAIAKVAHDHGVPLIVDNTV- 213 Query: 189 GGGYLVRPIDHGADIVTHSATKWIGGHGTTIGGVIVDSGKFDWKKNSKRFPEFNEPHPGY 248 YL+RPI+HGADIV HS TK++GGHG ++GG IVDSGKF W ++ RFP NEP Y Sbjct: 214 PSPYLLRPIEHGADIVVHSLTKYLGGHGNSVGGAIVDSGKFPWAEHKARFPRLNEPDVSY 273 Query: 249 HGMVFTETFGNLAYAFACRTQTLRDVGGNANPFGVFLLLQGLETLSLRMERHVQNAFALA 308 HG+V+TE G A+ R LR+ G +P FL+LQG+ETL+LRM+R N ALA Sbjct: 274 HGVVYTEALGPAAFIGRARVVPLRNTGAALSPQSAFLILQGIETLALRMDRICDNTLALA 333 Query: 309 KYLEKHPKVNWVSYPGLESHVSHKLAKKYLKNGYGAVLSFGAKGGPDQSR----KVVNAL 364 KYL+ HPKV WV Y GL H H L ++ +LSFG K R + ++AL Sbjct: 334 KYLQSHPKVEWVRYAGLPDHPDHALVQRQSGGKASGILSFGLKSTDADPRAAGARFLDAL 393 Query: 365 KLASQLANVGDAKTLVIAPAYTTHLQLTDEEQISAGVTKDLIRVAVGIEHIDDIIADFAQ 424 +L ++L N+GDAK+L PA TTH QL EE AGV++ ++R++VGIEHIDD+ AD Q Sbjct: 394 QLFTRLVNIGDAKSLATHPASTTHRQLNPEELAKAGVSESMVRLSVGIEHIDDLRADLVQ 453 Query: 425 ALE 427 AL+ Sbjct: 454 ALD 456 Lambda K H 0.318 0.135 0.399 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: 596 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: 429 Length of database: 458 Length adjustment: 32 Effective length of query: 397 Effective length of database: 426 Effective search space: 169122 Effective search space used: 169122 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 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