Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_005455198.1 SACCYDRAFT_RS07930 bifunctional o-acetylhomoserine/o-acetylserine sulfhydrylase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000244975.1:WP_005455198.1 Length = 432 Score = 238 bits (606), Expect = 3e-67 Identities = 146/424 (34%), Positives = 227/424 (53%), Gaps = 18/424 (4%) Query: 7 YGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTV 66 + F T +H+ Q G+ PI+ + ++ + D + A++F +PG Y R NPT Sbjct: 5 WSFETKQIHAGAQPDPATGARATPIYQTTSYVFRDTQHGADLFSLAEPGNIYTRIMNPTQ 64 Query: 67 AALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGA 125 LE ++ +E G + + FA+G AA A V L GDHVV S L+G T +L+ T+ Sbjct: 65 DVLEQRVAALEGGVAALAFASGSAATTAAVLNLAGAGDHVVVSPALYGGTYNLFRHTLPK 124 Query: 126 QGAKVSMV-DATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVD 184 G +V+ + D D+ +A NT+L F ET+ANP + V D++ + ++ E G+ VVD Sbjct: 125 LGIEVTFLSDQDDLDEWRSAAKPNTKLFFAETLANPGSNVLDIRGVADVAHEIGVPLVVD 184 Query: 185 NTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTRYPHIAENYKKNP 244 NT+ +P+L RP GA +VV+S TK +GGHG + G L D G FD+ P + + P Sbjct: 185 NTIPTPFLLRPIEHGADVVVHSATKYLGGHGTTVAGVLVDGGTFDFGAQPERFPGFNE-P 243 Query: 245 APQWG-------------MAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNA 291 P + A+ R + LRD G ++ P A I G ET++LR ER NA Sbjct: 244 DPSYNGLKFWEALGPGAFAAKARVQLLRDTGAAIAPLNAFLILQGIETLSLRMERHVSNA 303 Query: 292 LALAQMLQADERVAAVYYPGLESHPQH-ALSKALFRSFGSLMSFELKDGIDC-FDYLNRL 349 ALA+ L+ + V VYY L S P H A K L + G+++SFEL+ G++ +++ Sbjct: 304 KALAEWLEQRDEVERVYYASLPSSPHHEAAQKYLPQGAGAVLSFELRGGVEAGRAFVDGT 363 Query: 350 RLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQ 409 L N+GD R+L++ A T ++ + + + G+ L+R++VGLE +DL AD Sbjct: 364 ELHSQLVNIGDVRSLIVHPASTTHSQLTPQEQLAGGVTPGLVRLAVGLEGLEDLQADLEA 423 Query: 410 ALDA 413 A Sbjct: 424 GFRA 427 Lambda K H 0.319 0.134 0.391 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: 451 Number of extensions: 22 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: 413 Length of database: 432 Length adjustment: 32 Effective length of query: 381 Effective length of database: 400 Effective search space: 152400 Effective search space used: 152400 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 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