Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate PP_0659 PP_0659 Cystathionine gamma-synthase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Putida:PP_0659 Length = 423 Score = 243 bits (619), Expect = 1e-68 Identities = 134/379 (35%), Positives = 212/379 (55%), Gaps = 3/379 (0%) Query: 24 GGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEMLEQRIALL 83 G + + T + +++ Y Y+ G Q G YSR+ NPTV LE ++A L Sbjct: 23 GEQVQHPYNATQTPIVVSAAYGYNDIDAWYDVAQGKQPGFIYSRMSNPTVATLEAKLAEL 82 Query: 84 EGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIETTVVDA 143 E AE+ A +SGMAA++A L LS G ++ R ++G + + LP+ G++ + D Sbjct: 83 EQAESAVAFSSGMAAISAVLHTFLSNGKRVVSTRDSYGGTNKIFEEFLPRMGVQVCLCDT 142 Query: 144 RDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATPALQRP 203 D + I + + ETP NPT+ V+D++ + A A + G + V DN FATP Q P Sbjct: 143 LDTEALEREIAAGCDLLYLETPTNPTLKVLDIRRLSAAAHKVGALVVADNTFATPLNQNP 202 Query: 204 MDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNAWVVLKG 263 + G DVV +SATK + G G VL G VCG E + + + G L PF+A+++++G Sbjct: 203 LALGVDVVVHSATKFLSGHGDVLGGVVCGAEALMAQ-VRHYREINGAALDPFSAYLIIRG 261 Query: 264 LETLDLRIQRQSENALKVARFL--EGRVPRVNFPGLPSHPQHNLAMSQMAAAGPIFSIEL 321 ++TL +R+++Q +A+ +A +L E V VN+PGLP+H H +A +QM G I S L Sbjct: 262 IKTLAVRLRQQQASAMALAHYLSTEPLVEAVNYPGLPAHAGHAIAKAQMRGFGAIVSFVL 321 Query: 322 DGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEGMLRLNV 381 GG LL L + N+G ++ +T+H ++RL +G+ EG++R++V Sbjct: 322 KGGMPTVARLLPRLKYAHRAGNLGAVETIYGPARTTSHVENTLEERLALGISEGLVRISV 381 Query: 382 GLEDPEDLIADLDQALGSV 400 G+E+ +DL+ADL QA SV Sbjct: 382 GIEETDDLLADLAQACASV 400 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: 359 Number of extensions: 15 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: 423 Length adjustment: 31 Effective length of query: 371 Effective length of database: 392 Effective search space: 145432 Effective search space used: 145432 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