Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate PP_1308 PP_1308 methionine gamma-lyase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Putida:PP_1308 Length = 398 Score = 277 bits (709), Expect = 3e-79 Identities = 159/384 (41%), Positives = 229/384 (59%), Gaps = 4/384 (1%) Query: 18 ATQAIRGG-TARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEML 76 +T+AI G S G ++ T+ YA+ AA F+G++ G YSR+ NPT+ +L Sbjct: 11 STRAIHHGYDPLSHGGALVPPVYQTATYAFPTVEYGAACFAGEEPGHFYSRISNPTLALL 70 Query: 77 EQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGI 136 EQR+A LEG EA A ASGM A+T+ L L GD LI GR +G + +FG+ Sbjct: 71 EQRMASLEGGEAGLALASGMGAITSTLWTLLRPGDELIVGRTLYGCTFAFLHHGIGEFGV 130 Query: 137 ETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFA 196 + VD D + AI T++ +FETPANP M +VD+ AV R + VVDN + Sbjct: 131 KVRHVDLNDAKALKAAISSKTRMIYFETPANPNMQLVDIAAVVEAVRGHDVHVVVDNTYC 190 Query: 197 TPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRN-TGPTLSPF 255 TP LQRP++ GAD+V +SATK + G G + AG V G + ++ L ++ TG LSP Sbjct: 191 TPYLQRPLELGADLVVHSATKYLSGHGDITAGLVVGRKVLVDRIRLEGLKDMTGAVLSPH 250 Query: 256 NAWVVLKGLETLDLRIQRQSENALKVARFL--EGRVPRVNFPGLPSHPQHNLAMSQMAAA 313 +A ++++G++TL LR+ R NA +VA FL + +V +++PGLPS Q+ LA QM Sbjct: 251 DAALLMRGIKTLALRMDRHCANAQQVAEFLVRQPQVELIHYPGLPSFAQYALAQRQMRLP 310 Query: 314 GPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVG 373 G + + EL GG ++AL L + ++GD+ SL HPAS THS +R G+ Sbjct: 311 GGMIAFELKGGIEAGRRFMNALQLFARAVSLGDAESLAQHPASMTHSSYTPQERAHHGIS 370 Query: 374 EGMLRLNVGLEDPEDLIADLDQAL 397 EG++RL+VGLED EDL+AD++QAL Sbjct: 371 EGLVRLSVGLEDVEDLLADVEQAL 394 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: 358 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: 398 Length adjustment: 31 Effective length of query: 371 Effective length of database: 367 Effective search space: 136157 Effective search space used: 136157 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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