Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate PP_4594 PP_4594 putative Cystathionine gamma-synthase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Putida:PP_4594 Length = 393 Score = 238 bits (608), Expect = 2e-67 Identities = 140/390 (35%), Positives = 220/390 (56%), Gaps = 8/390 (2%) Query: 11 ITQNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQN 70 +T + KP A R A ++ A+F A A R D+ +YSR+ N Sbjct: 3 LTMSDKPRNFATRTIHAGEQFSVADNAIFP----AIVTASSFTKRSLDDKPEYSYSRVGN 58 Query: 71 PTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSC-RWLTDT 129 PT E +A LE A ASG+ A TA +L L H++ +G R + D Sbjct: 59 PTRHAYETCVAALEEGVGAVACASGVNA-TATVLELLPKDAHVVVMNGVYGGTFRIMEDY 117 Query: 130 QLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVT 189 + G+ TT VD D + AI+P T++ + E+P NP + +VD+KAVC +A+ +GI+T Sbjct: 118 RSRTSGLTTTYVDLNDIEAVAAAIKPETQLIWIESPTNPLLHLVDIKAVCDLAKAKGILT 177 Query: 190 VVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTG 249 +DN F +P QRP+ G D+V +SA+K + G + G V + + L G Sbjct: 178 CIDNTFCSPWNQRPITLGVDLVMHSASKYIGGHSDLTGGVVVAANDALLARLRRISMAIG 237 Query: 250 PTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPGLPSHPQHNLAM 307 PF+ ++ L+GL+TLD+R++RQ NAL+VARFLEG +V +V +PGL SHPQH L Sbjct: 238 AVQGPFDCYLALRGLKTLDVRMERQCANALQVARFLEGHAQVEQVYYPGLESHPQHELCK 297 Query: 308 SQMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQR 367 QM + G + ++++ G R + L++AL + +++++G S++ H S +H ++ +Q+ Sbjct: 298 RQMRSGGAVVAMKVKGDRAALNRLVEALQIFVLADSLGGVESMINHSWSMSHCSLSPEQK 357 Query: 368 LLMGVGEGMLRLNVGLEDPEDLIADLDQAL 397 +MG+ E +LRL+VG+ED DL+ DLD AL Sbjct: 358 GVMGISENLLRLSVGIEDYRDLVEDLDGAL 387 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: 345 Number of extensions: 12 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: 393 Length adjustment: 31 Effective length of query: 371 Effective length of database: 362 Effective search space: 134302 Effective search space used: 134302 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