Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_019555914.1 F612_RS0101190 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000381085.1:WP_019555914.1 Length = 392 Score = 347 bits (891), Expect = e-100 Identities = 171/381 (44%), Positives = 252/381 (66%), Gaps = 2/381 (0%) Query: 19 TQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEMLEQ 78 T A+R G +++ E SEA+F TS + Y A AAARFSG+++G YSR NPTV E Sbjct: 8 TLAVRAGYDQTQEQENSEAIFPTSSFRYTSAAQAAARFSGEEKGNVYSRFTNPTVRAFEN 67 Query: 79 RIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIET 138 R+AL+EG EAC T+SGMAA+ + + +GDH+I ++ FG+ + L + L KFG+E Sbjct: 68 RLALMEGGEACVGTSSGMAAILSTFMALYESGDHVICSQSVFGTTKVLFNKYLVKFGLEV 127 Query: 139 TVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATP 198 T V D ++ AI+PNTK FF ETP+NP ++ DL + A+A+ G + +VDN F TP Sbjct: 128 TFVSQTDTSEWKKAIQPNTKAFFLETPSNPLTEIADLSTISALAKANGCLLIVDNCFCTP 187 Query: 199 ALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNAW 258 LQRP++ GAD++ +SATK +DGQGR + GAV G+ E ++ + F R GP++SPFNAW Sbjct: 188 ILQRPLEQGADIIIHSATKFLDGQGRGIGGAVVGSNELVDEHVRGFMRTAGPSMSPFNAW 247 Query: 259 VVLKGLETLDLRIQRQSENALKVARF--LEGRVPRVNFPGLPSHPQHNLAMSQMAAAGPI 316 + LKGLETL +R+ ++AL++A + L V +V +PGL SHPQ+ LA Q +A G + Sbjct: 248 IFLKGLETLPIRMAAHCQSALQLAEWLSLHPAVEQVFYPGLKSHPQYELACKQQSAGGGL 307 Query: 317 FSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEGM 376 S ++ G + +A ++D ++ I+ N+GD ++ +THPA+TTH V D RL G+ + + Sbjct: 308 VSFKVKGNQAEAWSVIDHTQMVSITANLGDVKTSITHPATTTHVRVEPDARLRAGITDNL 367 Query: 377 LRLNVGLEDPEDLIADLDQAL 397 +RL+VGLE ED+ ADL + L Sbjct: 368 IRLSVGLESIEDIKADLARGL 388 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: 377 Number of extensions: 9 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: 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 Jul 25 2024. The underlying query database was built on Jul 25 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