Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate GFF2323 PGA1_c23540 O-succinylhomoserine sulfhydrylase MetZ
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Phaeo:GFF2323 Length = 396 Score = 367 bits (941), Expect = e-106 Identities = 187/392 (47%), Positives = 263/392 (67%), Gaps = 6/392 (1%) Query: 11 ITQNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARF--SGDQQGMTYSRL 68 +++ W T+ + GGT RS++ E SEA++LT G+ YD A A ARF +G + Y+R Sbjct: 1 MSETWNKRTKLVHGGTRRSQYNEVSEAIYLTQGFVYDTAEQAEARFIETGPDE-FIYARY 59 Query: 69 QNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTD 128 NPTV M E+RIA LEGAE ATASGMAA+ AL L AGDH++ +A FGSC ++ + Sbjct: 60 GNPTVAMFEERIAALEGAEDAFATASGMAAVNGALTSILKAGDHVVSAKALFGSCLYILE 119 Query: 129 TQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIV 188 L ++G+E T VD D + A+RP+TK FFE+ +NPT++V+D+ AV +A G Sbjct: 120 NILTRYGVEVTFVDGTDLDAWRAALRPDTKAVFFESMSNPTLEVIDIAAVAELAHAVGAT 179 Query: 189 TVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNT 248 VVDN F+TP ++ GADVV YSATK +DGQGRVL G + GT +FI T+ P+ ++T Sbjct: 180 VVVDNVFSTPVFSNAIEQGADVVIYSATKHIDGQGRVLGGVILGTRDFIRGTVEPYMKHT 239 Query: 249 GPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLA 306 G +LSPFNAW +LKGLET+ LR+ Q+E AL++A+ L G + R+ +PGL H QH L Sbjct: 240 GGSLSPFNAWTLLKGLETISLRVNAQAETALELAQALSGHPALSRLMYPGLEDHAQHALV 299 Query: 307 MSQMAA-AGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAED 365 Q+ G + S++L GG+ A L+AL + ISNN+GD++S+ THPA+TTH ++E+ Sbjct: 300 QRQLGGKGGTVLSLDLKGGKDAAFRFLNALTIPVISNNLGDAKSIATHPATTTHQRLSEE 359 Query: 366 QRLLMGVGEGMLRLNVGLEDPEDLIADLDQAL 397 + +G+ G++R +VGLED DLIADL QAL Sbjct: 360 LKSELGITPGLVRFSVGLEDAGDLIADLTQAL 391 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: 412 Number of extensions: 18 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: 402 Length of database: 396 Length adjustment: 31 Effective length of query: 371 Effective length of database: 365 Effective search space: 135415 Effective search space used: 135415 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