Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate Ac3H11_34 Methionine gamma-lyase (EC 4.4.1.11)
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_34 Length = 434 Score = 248 bits (633), Expect = 2e-70 Identities = 146/385 (37%), Positives = 211/385 (54%), Gaps = 5/385 (1%) Query: 18 ATQAIRGG-TARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEML 76 +T+AI G G + ++ YA+ A F+G + G Y+R+ NPT+ +L Sbjct: 14 STRAIHHGYNPADHQGALVPPIHTSATYAFPDVAYGARCFAGQEPGYFYTRIANPTLALL 73 Query: 77 EQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGI 136 E R+A LE SGM A+TA L L GD ++ +G L +FG+ Sbjct: 74 EGRLAALEEGAGAVVFGSGMGAITATLWSMLEPGDEILADLTLYGCTFSFLHHGLGRFGV 133 Query: 137 ETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFA 196 VD DP + +A+ T+V + ETPANP M +VD+ AV A+A +G VVDN + Sbjct: 134 TVRHVDMTDPARVAEALTAKTRVLYLETPANPNMRLVDIAAVSALAHAQGAKVVVDNTYC 193 Query: 197 TPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINN--TLLPFHRNTGPTLSP 254 TP LQ+P+ GADV +S TK + G G + AGA + + L TG +S Sbjct: 194 TPYLQQPLLLGADVSVHSMTKYLGGHGDLTAGAAVFADAELAQRVRLYGLKDMTGAVMSA 253 Query: 255 FNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAA 312 +A +V++GL+TL LR+ R ++A KVA F+ V++PGLPS QH LA QM Sbjct: 254 QDAHLVMRGLKTLALRMDRHCQSAQKVAEFIAAHPAAAAVHYPGLPSFAQHALAKQQMRQ 313 Query: 313 AGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGV 372 G + + EL GG +DAL L+ + ++GD+ +L HPAS THS +QR G+ Sbjct: 314 MGGMIAFELRGGLQAGVRFMDALQLVTRAVSLGDAETLAQHPASMTHSTYTPEQRAAHGI 373 Query: 373 GEGMLRLNVGLEDPEDLIADLDQAL 397 EG++RL+VGLED +DL+AD+ QAL Sbjct: 374 AEGLVRLSVGLEDLDDLLADIGQAL 398 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: 398 Number of extensions: 11 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: 434 Length adjustment: 32 Effective length of query: 370 Effective length of database: 402 Effective search space: 148740 Effective search space used: 148740 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