Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_012536942.1 AFE_RS09520 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000021485.1:WP_012536942.1 Length = 404 Score = 365 bits (938), Expect = e-105 Identities = 190/387 (49%), Positives = 257/387 (66%), Gaps = 2/387 (0%) Query: 16 KPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEM 75 +P T AIR G R++ E SEA+F TS + +D A +AA RF+G G Y+R NPTV Sbjct: 15 RPETIAIRAGIHRTQEQEHSEAIFPTSSFVFDSAEEAADRFAGRVPGNIYARFTNPTVRT 74 Query: 76 LEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFG 135 E+R+A LEGAEAC ATASGMAA A + L AGDH++ R+ FG+ L L +FG Sbjct: 75 FEERLAALEGAEACVATASGMAACLTAFMGILKAGDHVVASRSIFGTTVQLLGNILSRFG 134 Query: 136 IETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAF 195 +ET+ V D + A+RPNT++ F ETP+NP ++ D++A+ +A VVDN F Sbjct: 135 VETSFVPLADVPAWRAALRPNTRMLFLETPSNPLTEIGDMQALADLAHVHDAWLVVDNCF 194 Query: 196 ATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPF 255 TPALQ+P+ FGAD+V +SATK +DGQGR L GAVCG+ E +N+ F R GP+LSPF Sbjct: 195 CTPALQQPLKFGADLVIHSATKYLDGQGRTLGGAVCGSTELLNSGPRNFVRTAGPSLSPF 254 Query: 256 NAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAAA 313 NAWV LKGLETL LR++R NA K+A +LE R V RV +PGL SHPQ LA Q Sbjct: 255 NAWVQLKGLETLGLRMERHCANAQKIAEWLEARPEVARVYYPGLDSHPQQALAARQQRLP 314 Query: 314 GPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVG 373 G I S +L GG+ A +DAL L+ ++ N+GD+++ +THPASTTHS V+ + R GVG Sbjct: 315 GAILSFDLHGGQKAAWAFVDALRLLSLTANLGDAKTTITHPASTTHSRVSPEARAAAGVG 374 Query: 374 EGMLRLNVGLEDPEDLIADLDQALGSV 400 +G+LR++VGLE +DL D+++ ++ Sbjct: 375 DGLLRISVGLEHADDLREDMERGFAAL 401 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: 441 Number of extensions: 14 Number of successful extensions: 2 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: 404 Length adjustment: 31 Effective length of query: 371 Effective length of database: 373 Effective search space: 138383 Effective search space used: 138383 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