Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate Ga0059261_1458 Ga0059261_1458 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Korea:Ga0059261_1458 Length = 440 Score = 199 bits (506), Expect = 1e-55 Identities = 130/393 (33%), Positives = 203/393 (51%), Gaps = 28/393 (7%) Query: 32 GETSEALFLTSGYAYDCAGDAAARFSG-------DQQGMTYSRLQNPTVEMLEQRIALLE 84 G +F TS + + A F G +G+ YSR P E+LE R+ + E Sbjct: 52 GSLKPPIFATSTFVFPNAAAGKRHFEGVTGKRPGGAEGLVYSRFNGPNQEILEDRLGIWE 111 Query: 85 GAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIETTVVDAR 144 AE A +SGM+A+ L + GD ++ + + L L KFG+ A Sbjct: 112 EAEDALAFSSGMSAIATLFLAMVKPGDTIVHSGPLYAATETLIARILGKFGVHWLDFPAG 171 Query: 145 DPQQFIDAIRP-----NTKVFFFETPANPTMDVVDLKAVCAIARERGIVT-------VVD 192 ++ IDA+ N + + E+PANPT +VD++AV A I T +D Sbjct: 172 ATREEIDAVLSKAASGNVALIYLESPANPTNALVDVEAVAA--SRDAIFTGASKPPIAID 229 Query: 193 NAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNT-GPT 251 N F P +P+ GAD+V YS TK G ++AG V G++E IN L RNT G Sbjct: 230 NTFLGPLWAKPLQQGADLVVYSLTKYAGGHSDLVAGGVLGSKELINTIRLM--RNTIGTI 287 Query: 252 LSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPG-LPSHP-QHNLAM 307 P AW++L+ LETL+LR+ R ENA+KV +L +V V + G LP Q ++ Sbjct: 288 CDPNTAWMLLRSLETLELRMSRAGENAIKVCEYLRTHPKVESVGYLGFLPEGSRQRDIYD 347 Query: 308 SQMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQR 367 AG FS+ L GG +A LD+L + ++ ++G + +L + PA+ TH V + ++ Sbjct: 348 RHCTGAGSTFSLYLKGGEKEAFAFLDSLKIAKLAVSLGGTETLASAPAAMTHLSVPDARK 407 Query: 368 LLMGVGEGMLRLNVGLEDPEDLIADLDQALGSV 400 +G+ + ++R+++G+ED +DLIAD ++AL +V Sbjct: 408 KALGITDNLVRISIGVEDADDLIADFEEALKAV 440 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: 411 Number of extensions: 25 Number of successful extensions: 5 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: 440 Length adjustment: 32 Effective length of query: 370 Effective length of database: 408 Effective search space: 150960 Effective search space used: 150960 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