Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_011446196.1 SARO_RS12875 cystathionine beta-lyase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000013325.1:WP_011446196.1 Length = 410 Score = 165 bits (417), Expect = 3e-45 Identities = 131/397 (32%), Positives = 192/397 (48%), Gaps = 17/397 (4%) Query: 17 PATQAIRGGTARSEWGETSE--------ALFLTSGYAYDCAGDAAARFSGDQQGMTYSRL 68 P T+ + G R EW T + A++ S + Y A + + Y R Sbjct: 12 PGTRGVLAGR-REEWTGTPDHPGAVVNPAVWRASTHLYPDMAALRAHPANEDGRFYYGRR 70 Query: 69 QNPTVEMLEQRIALLE-GAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLT 127 PT L + + +E GA SG+AA+ LL L GD L+ A+ R + Sbjct: 71 GAPTQWALAEALTQIEPGAAGTVLYPSGVAAIAGVLLTMLRPGDVLLMTDNAYEPSRVMA 130 Query: 128 DTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGI 187 L FG+ET D F A TK E+P + TM+V D+ A+ A A+ RGI Sbjct: 131 RGLLRDFGVETRWFDPTSIGAFEAACCDRTKAVLLESPGSLTMEVQDVPALAAAAKARGI 190 Query: 188 VTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRN 247 V+V+DN +A+P + G D+VA S TK + G + G+ ++ L + Sbjct: 191 VSVLDNTWASPLGFAGLSHGVDIVAMSLTKHVSGHSDCMMGSASAGPDWYRKLRLR-SQG 249 Query: 248 TGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNL 305 G +SP +A ++L+GL T+ +R++ ++ +AL +A +LEGR V RV P LP P H L Sbjct: 250 LGLVVSPDDASLMLRGLRTMKMRLEAETASALAIAGWLEGRPEVARVLCPMLPGSPGHEL 309 Query: 306 AMSQMAAAGPIFSIELDGGRTQAH-GLLDALGLIDISNNIGDSRSLMT--HPASTTHSGV 362 A +FS L GG + A L+DAL L I + G SL T PAS + Sbjct: 310 WARDFAGGCGLFSFVLKGGSSAARDALIDALALFGIGYSWGGFESLATPVDPASIRTASA 369 Query: 363 AEDQRLLMGVGEGMLRLNVGLEDPEDLIADLDQALGS 399 + M G +RL++GLED DLIAD++QALG+ Sbjct: 370 WPLAGMAMEDRFG-VRLSIGLEDTADLIADIEQALGA 405 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: 409 Number of extensions: 17 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: 410 Length adjustment: 31 Effective length of query: 371 Effective length of database: 379 Effective search space: 140609 Effective search space used: 140609 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