Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate 6937071 Sama_1242 methionine gamma-lyase (RefSeq)
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__SB2B:6937071 Length = 392 Score = 336 bits (861), Expect = 8e-97 Identities = 174/387 (44%), Positives = 246/387 (63%), Gaps = 2/387 (0%) Query: 16 KPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEM 75 K AT + GG R G L+ ++ + +D A ARF+GD+ G Y+RL NPT Sbjct: 6 KLATLVVHGGHERDAMGALVSPLYQSATFVFDNARQGGARFAGDEAGYIYTRLGNPTTAE 65 Query: 76 LEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFG 135 LE+++A+LEGAE ATASGM A++AALL LS GDHL+ RA +G L + +FG Sbjct: 66 LERKLAILEGAEEAAATASGMGAVSAALLANLSQGDHLVASRAVYGCTFALMTDLMARFG 125 Query: 136 IETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAF 195 IE T+VD ++P AIR NT+ F ETP NP +DV DL A+ AI + G++T+VDN F Sbjct: 126 IEVTLVDFKEPAAIEAAIRDNTRAIFCETPVNPHLDVFDLDAIAAIGKRHGLLTIVDNTF 185 Query: 196 ATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPF 255 TP LQRP+D G D+V +SATK ++G G V+AG V G++E I+ ++ G +SP Sbjct: 186 MTPLLQRPLDHGIDMVIHSATKYLNGHGDVIAGMVAGSKEQIDKVKYQIIKDIGAVMSPH 245 Query: 256 NAWVVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPGLPSHPQHNLAMSQMAAA 313 +AW++L+G++TLD+R+QR +NA K+A FLE RV RV +P L SH H +QM A Sbjct: 246 DAWLILRGMKTLDVRVQRHCDNAEKIADFLEAHPRVGRVYYPALKSHQGHRFLGTQMRRA 305 Query: 314 GPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVG 373 G + + EL + +D+L + I+ ++GD+ SL+ HPAS THS + RL G+ Sbjct: 306 GGVIAFELKSDIEGSINFVDSLKVFTIAVSLGDAESLIQHPASMTHSPYTPEARLEAGIT 365 Query: 374 EGMLRLNVGLEDPEDLIADLDQALGSV 400 + +LR++VGLED +DLIADL QAL + Sbjct: 366 DTLLRISVGLEDVDDLIADLSQALAKI 392 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: 356 Number of extensions: 10 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: 392 Length adjustment: 31 Effective length of query: 371 Effective length of database: 361 Effective search space: 133931 Effective search space used: 133931 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