Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate SMc01666 SMc01666 methionine gamma-lyase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Smeli:SMc01666 Length = 427 Score = 192 bits (488), Expect = 2e-53 Identities = 124/394 (31%), Positives = 198/394 (50%), Gaps = 31/394 (7%) Query: 32 GETSEALFLTSGYAYDCAGDAAARF----------SGDQQGMTYSRLQNPTVEMLEQRIA 81 G +FLTS + + A + F +G G+ YSR +P E++E R+A Sbjct: 34 GAVKPPIFLTSTFVFHSAEEGRDFFDFVSGRREPPAGVGAGLVYSRFNHPNSEIVEDRLA 93 Query: 82 LLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIETTVV 141 + E AEA +SGM+A+ LL + GD ++ + +G L G+ Sbjct: 94 IFERAEAGALFSSGMSAIATTLLAFVRPGDSILHSQPLYGGTETLLAKTFLNLGVSAVGF 153 Query: 142 DARDPQQFIDAI------RPNTKVFFFETPANPTMDVVDLKAVCAIARERGI------VT 189 + ++A + V ETPANPT +VD+ V IA G + Sbjct: 154 ADGTDEAAVNAAAEEAMSKGRVSVILIETPANPTNSLVDVALVRRIAERIGERQAHRPIV 213 Query: 190 VVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTG 249 DN P Q P++ GAD+ YS TK + G ++AGAV G++ I + + G Sbjct: 214 ACDNTLLGPVFQHPIEHGADLSLYSLTKYVGGHSDLIAGAVLGSKALIRQ-VKALRGSIG 272 Query: 250 PTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPGLPSH----PQH 303 L P + W++ + LETL +R+++ ++NA VA FL +V R+++ LP H P Sbjct: 273 TQLDPHSCWMIGRSLETLSVRMEKANDNARIVAEFLRDHPKVERIHY--LPFHDADTPVG 330 Query: 304 NLAMSQMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVA 363 + +Q AG FS ++ GG+ A L+AL + ++ ++G + SL +HPA+ THSGV Sbjct: 331 RVFATQCTGAGSTFSFDIAGGQEAAFRFLNALQIFKLAVSLGGTESLASHPAAMTHSGVP 390 Query: 364 EDQRLLMGVGEGMLRLNVGLEDPEDLIADLDQAL 397 + R +GV E +RL++G+E P+DL+AD+ AL Sbjct: 391 IEVRARIGVLESTIRLSIGIEHPDDLVADVANAL 424 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: 394 Number of extensions: 16 Number of successful extensions: 5 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: 427 Length adjustment: 31 Effective length of query: 371 Effective length of database: 396 Effective search space: 146916 Effective search space used: 146916 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