Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate 5209311 Shew_1789 cystathionine beta-lyase (RefSeq)
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__PV4:5209311 Length = 395 Score = 149 bits (375), Expect = 2e-40 Identities = 117/375 (31%), Positives = 171/375 (45%), Gaps = 25/375 (6%) Query: 32 GETSEALFLTSGYAYDCAGDAAARFSGDQQG-MTYSRLQNPTVEMLEQRIALLEGAEACR 90 G + +F S +D D G M Y R PT + IA LEG Sbjct: 19 GVINPPVFRASTVVFDTIEDMRHATKNRANGAMFYGRRGTPTHFAFQAAIAELEGGVGTA 78 Query: 91 ATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIETTVVDARDPQQFI 150 SG AA++ ALL L AGDHL+ A+ R L D L FGIETT D Sbjct: 79 LYPSGSAAISGALLSFLKAGDHLLMVDTAYEPTRDLCDKLLKGFGIETTYYDPLIGDGIE 138 Query: 151 DAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATPALQRPMDFGADV 210 IRPNTKV F E+P + T++V D+ + AIA +V ++DN +A+P RP + G D+ Sbjct: 139 ALIRPNTKVLFLESPGSITLEVQDVPTLSAIAHRHNLVVMLDNTWASPINCRPFELGVDI 198 Query: 211 VAYSATKMMDGQGRVLAGAVCGT----EEFINNTLLPFHRNTGPTLSPFNAWVVLKGLET 266 +ATK + G V+ G ++ N+ L G S + ++ +GL T Sbjct: 199 SIQAATKYIVGHSDVMLGTATANQAHWDQLRENSYL-----MGQCTSADDIYLASRGLRT 253 Query: 267 LDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAAAGPIFSIELDGG 324 L +R+ + +N L+VA L R V + P S P H +A+ +FS L G Sbjct: 254 LGVRMAQHEKNGLEVANLLATRPEVDHLRHPAFASCPGHEFFKRDFSASNGLFSFVLKRG 313 Query: 325 RTQA-HGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGV----GEGMLRL 379 +A ++ + + + G SL+ GV +L + ++RL Sbjct: 314 NIKAITAFVEGMDHFKMGFSWGGYESLIL--------GVFGIDKLRTATQWDSSKPLIRL 365 Query: 380 NVGLEDPEDLIADLD 394 +VGLE+PEDLI DL+ Sbjct: 366 HVGLENPEDLIKDLE 380 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: 335 Number of extensions: 19 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: 395 Length adjustment: 31 Effective length of query: 371 Effective length of database: 364 Effective search space: 135044 Effective search space used: 135044 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