Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_058930869.1 AU252_RS11760 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_001484605.1:WP_058930869.1 Length = 402 Score = 370 bits (949), Expect = e-107 Identities = 192/390 (49%), Positives = 263/390 (67%), Gaps = 7/390 (1%) Query: 15 WKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVE 74 W TQA+RGG R+ + ET+E +FL SG+ Y+ A A F+G+ + YSR NP+V Sbjct: 10 WSAETQAVRGGLDRTNFQETTEPVFLNSGFVYESAAAAERAFTGEDERFVYSRYGNPSVA 69 Query: 75 MLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKF 134 ++R+ LLEG EAC ATASGM+A+ AL L+AGD ++ R+ FGSC + + LP++ Sbjct: 70 TFQERLRLLEGTEACFATASGMSAVFTALGALLAAGDRVVAARSLFGSCFVILNEILPRW 129 Query: 135 GIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNA 194 G+ET VD D +Q+ A+ T FFE+P+NP ++VD+ AV +A G VVDN Sbjct: 130 GVETVFVDGPDLEQWAAALSEPTTAVFFESPSNPMQEIVDIAAVSELAHAAGATVVVDNV 189 Query: 195 FATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSP 254 FATP LQR GADV+ YS TK +DGQGRVL GA+ GT+EFI+ + R+TGP LS Sbjct: 190 FATPLLQRCGQLGADVIVYSGTKHIDGQGRVLGGAILGTKEFIDGPVKQLMRHTGPALSA 249 Query: 255 FNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAA 312 FNAWV+ KGLET+ LR+ S +AL++A +LE + V V +P L SHPQ+ LA QM A Sbjct: 250 FNAWVLTKGLETMALRVNHSSASALRLAEWLEQQPAVSWVRYPLLKSHPQYELAAKQMKA 309 Query: 313 AGPIFSIEL--DGGRT---QAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQR 367 G + ++EL GGR+ A LLDAL +IDISNN+GD++SL+THPA+TTH + + R Sbjct: 310 GGTVLTLELATTGGRSGKEAAFALLDALRIIDISNNLGDAKSLITHPATTTHRAMGPEGR 369 Query: 368 LLMGVGEGMLRLNVGLEDPEDLIADLDQAL 397 +G+ +G++RL+VGLED +DLI DL+QAL Sbjct: 370 AAIGLSDGVVRLSVGLEDVDDLIGDLEQAL 399 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: 449 Number of extensions: 17 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: 402 Length adjustment: 31 Effective length of query: 371 Effective length of database: 371 Effective search space: 137641 Effective search space used: 137641 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 10 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