Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate 201343 SO2191 cystathionine beta-lyase (NCBI ptt file)
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__MR1:201343 Length = 399 Score = 169 bits (427), Expect = 2e-46 Identities = 125/393 (31%), Positives = 190/393 (48%), Gaps = 20/393 (5%) Query: 11 ITQNWKPATQAIRGGTARSEW--GETSEALFLTSGYAYDCAGDAAARFSGDQQG-MTYSR 67 +T + ATQ + G + +W G + +F S +D D G M Y R Sbjct: 1 MTDKHQLATQIVSVGRDK-KWTKGVINPPVFRASTIVFDTMEDMRHAAKNKTNGEMFYGR 59 Query: 68 LQNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLT 127 PT + ++ LEG SG AA++AALL L AGDHL+ + + R Sbjct: 60 RGTPTHFAFQAAVSELEGGAGTALYPSGAAAISAALLSFLQAGDHLLMVDSVYEPTRDFC 119 Query: 128 DTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGI 187 L F IETT D + IRPNTKV F E+P + TM+V D+ +C IA E G+ Sbjct: 120 SHILAGFNIETTYYDPLIGEGIRALIRPNTKVLFLESPGSITMEVQDVPTLCRIAHEHGL 179 Query: 188 VTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRN 247 VT++DN +A+P +P + G DV +ATK + G V+ G E++ L Sbjct: 180 VTILDNTWASPINSKPFEMGVDVSIQAATKYIVGHSDVMIGTATANEQYWPQ-LRERSYL 238 Query: 248 TGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNL 305 G T SP + ++ +GL TL +R+ + +NALKVA +L+ R V + P + P H Sbjct: 239 LGQTTSPDDVYLATRGLRTLGVRMAQHEKNALKVANWLQTRPEVDHLRHPAFETCPGHEF 298 Query: 306 AMSQMAAAGPIFSIELDGGRTQA-HGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAE 364 +A+ +FS L G +A L++ + + + G SL+ G+ Sbjct: 299 FKRDFSASNGLFSFVLKQGDQEAVTALVENMQHFKMGFSWGGYESLIL--------GIFG 350 Query: 365 DQRLLMG----VGEGMLRLNVGLEDPEDLIADL 393 +R+ + ++R+++GLEDPEDLIADL Sbjct: 351 IERIRSATKWDASKPLIRVHIGLEDPEDLIADL 383 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: 329 Number of extensions: 18 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: 399 Length adjustment: 31 Effective length of query: 371 Effective length of database: 368 Effective search space: 136528 Effective search space used: 136528 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