Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate 3609021 Dshi_2410 O-succinylhomoserine sulfhydrylase (RefSeq)
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Dino:3609021 Length = 392 Score = 382 bits (982), Expect = e-111 Identities = 190/385 (49%), Positives = 263/385 (68%), Gaps = 3/385 (0%) Query: 19 TQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARF-SGDQQGMTYSRLQNPTVEMLE 77 T+ + GT RS++GE +EA+FLT G+ YD A A ARF Y+R NPTV M E Sbjct: 8 TKLVHAGTRRSQYGEVAEAIFLTQGFVYDTAEAAEARFIEAGADEFIYARYGNPTVRMFE 67 Query: 78 QRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIE 137 RIA +EG E ATASGMAA+ AL L AGDH++ RA FGSC ++ + L ++G+E Sbjct: 68 DRIAAVEGTEDAFATASGMAAVNGALASMLRAGDHVVSARALFGSCLYILEEVLTRYGVE 127 Query: 138 TTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFAT 197 T VD D + AIRP+TK FFET +NPT++V+D++AV +A G + +VDN FAT Sbjct: 128 VTFVDGTDLAAWRAAIRPDTKAVFFETISNPTLEVIDIEAVAKLAHAVGALVIVDNVFAT 187 Query: 198 PALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNA 257 P R D GADV+ YSATK +DGQGR L G +CGT +F+ P+ ++TG +LSPFNA Sbjct: 188 PIFSRAKDQGADVIVYSATKHIDGQGRCLGGVICGTRDFVRKVAEPYLKHTGGSLSPFNA 247 Query: 258 WVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAAAGP 315 WV+LK +ETLDLR++ Q+E A +A LEG + +V FP LPSHPQ++LA +QMAA G Sbjct: 248 WVMLKSMETLDLRVRAQAETAQALAETLEGHAALEKVIFPHLPSHPQYDLARAQMAAGGT 307 Query: 316 IFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEG 375 + ++++ GG+ A L+AL ++ ISNN+GD++S+ THPA+TTH + +QR +G+ +G Sbjct: 308 VLALDIKGGKAGAFRFLNALEIVTISNNLGDAKSIATHPATTTHQRLTPEQRAGLGITDG 367 Query: 376 MLRLNVGLEDPEDLIADLDQALGSV 400 ++RL+VGLED DL+ DL AL +V Sbjct: 368 LIRLSVGLEDAGDLLRDLQTALAAV 392 Lambda K H 0.319 0.134 0.396 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: 385 Number of extensions: 14 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: 402 Length of database: 392 Length adjustment: 31 Effective length of query: 371 Effective length of database: 361 Effective search space: 133931 Effective search space used: 133931 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 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