Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_011777963.1 MVAN_RS03475 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000015305.1:WP_011777963.1 Length = 411 Score = 370 bits (950), Expect = e-107 Identities = 190/391 (48%), Positives = 260/391 (66%), Gaps = 11/391 (2%) Query: 19 TQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEMLEQ 78 T +RGG RS + ET+EAL+LTSGY Y+ A A F+G+ YSR NPTV M E+ Sbjct: 21 TIGVRGGLLRSGFEETAEALYLTSGYVYESAAAAEKAFTGEIDRYVYSRYGNPTVSMFEE 80 Query: 79 RIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIET 138 R+ L+EGA AC AT+SGM+A+ AL L AGD L+ R+ FGSC + + LP++G+ET Sbjct: 81 RLRLIEGAPACFATSSGMSAVFTALGALLGAGDRLVAARSLFGSCFVVCNEILPRWGVET 140 Query: 139 TVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATP 198 VD D Q+ A+ T+ FFETP+NP +VD+ AVC +A G V+DN FATP Sbjct: 141 VFVDGDDLSQWEQALSVPTQAVFFETPSNPMQSLVDIAAVCELAHAAGAKVVLDNVFATP 200 Query: 199 ALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNAW 258 LQ+ G DVV YS TK +DGQGRVL GA+ G++E+I+ + R+TGP LSPFNAW Sbjct: 201 ILQQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGSKEYIDEPVQKLMRHTGPALSPFNAW 260 Query: 259 VVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAAAGPI 316 +LKGLETL LR+Q Q+ +A ++A FLE V V +P L SHPQ++LA QM G + Sbjct: 261 TLLKGLETLSLRVQHQNSSAHRIAEFLEQHPSVSWVKYPFLESHPQYDLAKRQMTGGGTV 320 Query: 317 FSIEL---------DGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQR 367 + EL D + +A +LD L ++DISNN+GD++SL+THPA+TTH + + R Sbjct: 321 VTFELAGAGGAGNPDAAKERAFEVLDKLQIVDISNNLGDAKSLITHPATTTHRAMGPEGR 380 Query: 368 LLMGVGEGMLRLNVGLEDPEDLIADLDQALG 398 +G+G+G++R+++GLE EDL+ADLD+ALG Sbjct: 381 AAIGLGDGVVRISIGLEGTEDLLADLDRALG 411 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: 471 Number of extensions: 16 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: 411 Length adjustment: 31 Effective length of query: 371 Effective length of database: 380 Effective search space: 140980 Effective search space used: 140980 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