Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate Dsui_3185 Dsui_3185 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__PS:Dsui_3185 Length = 395 Score = 371 bits (952), Expect = e-107 Identities = 186/389 (47%), Positives = 264/389 (67%), Gaps = 3/389 (0%) Query: 14 NWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTV 73 +W+ T A+R G RS++ E SEAL+LTS + ++ A AAARFSG+++G YSR NPT+ Sbjct: 8 DWQLETLAVRAGQERSQFNEHSEALYLTSSFVFENAAQAAARFSGEEEGNVYSRFSNPTL 67 Query: 74 EMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPK 133 + + R+A LEGAE+ TASGM+A+ + ++ L AGDH++ FG+ L + L + Sbjct: 68 SLFQDRLAALEGAESAICTASGMSAIMSLVMAHLKAGDHVVASAGLFGATIQLFNNILAR 127 Query: 134 FGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDN 193 FGI TT P+++ AIRP TK+FF ETP+NP +V D+ A+ IA +GI+ VDN Sbjct: 128 FGISTTYASQTRPEEWAAAIRPETKLFFLETPSNPLTEVADIAALAEIAHAKGILVAVDN 187 Query: 194 AFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLS 253 F TPALQRP++ GAD+V +SATK +DGQGRVL GAV G+++ + + F R GPTLS Sbjct: 188 CFCTPALQRPLELGADLVVHSATKYLDGQGRVLGGAVVGSKK-LTEEVFKFLRTAGPTLS 246 Query: 254 PFNAWVVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPGLPSHPQHNLAMSQMA 311 FNAWV+ KGLETL +R+ QS NAL++A +LE +V RV +PGL SHPQH LAM Q Sbjct: 247 AFNAWVLAKGLETLKIRMAAQSANALELATWLEAHPKVARVFYPGLASHPQHALAMRQQK 306 Query: 312 AAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMG 371 + G I S E+ GG+ +A ++D L+ I+ N+GD ++ +THPA+TTH ++ + R G Sbjct: 307 SGGAIVSFEVKGGKPEAWKVVDNCRLLSITANLGDVKTTITHPATTTHGRISAEARATAG 366 Query: 372 VGEGMLRLNVGLEDPEDLIADLDQALGSV 400 +G+G+LR+ VGLE DL ADL++ L + Sbjct: 367 IGDGLLRIAVGLEAVPDLQADLERGLAQL 395 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: 404 Number of extensions: 14 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: 395 Length adjustment: 31 Effective length of query: 371 Effective length of database: 364 Effective search space: 135044 Effective search space used: 135044 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