Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_011840397.1 RSPH17029_RS02535 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000015985.1:WP_011840397.1 Length = 393 Score = 379 bits (972), Expect = e-109 Identities = 192/394 (48%), Positives = 267/394 (67%), Gaps = 5/394 (1%) Query: 11 ITQNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARF--SGDQQGMTYSRL 68 +T++WK TQ + GG+ RS++GE +EA+FLT G+ YD A A ARF +G + Y+R Sbjct: 1 MTKDWKTRTQLVHGGSRRSQYGEMAEAIFLTQGFVYDSAEQAEARFIETGADE-FIYARY 59 Query: 69 QNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTD 128 NPT M E+RIA +EG E ATASGMAA+ L + AGDHL+ RA FGSC ++ + Sbjct: 60 GNPTTRMFEERIAAVEGTEDAFATASGMAAIHGVLTSIVRAGDHLVAARALFGSCIYILE 119 Query: 129 TQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIV 188 L +FG+E T VD D Q+ A+RP TK FFE+ +NPT++V D+ A+ IA G + Sbjct: 120 EVLGRFGVEVTFVDGTDLDQWRAAVRPGTKAVFFESVSNPTLEVADIGAIAEIAHAVGAL 179 Query: 189 TVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNT 248 +VDN FATP + GADVV YSATK +DGQGR L G VC ++ FI L PF ++T Sbjct: 180 VIVDNVFATPVFSTAVRQGADVVIYSATKHIDGQGRALGGVVCASQAFIRKVLEPFMKHT 239 Query: 249 GPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPGLPSHPQHNLA 306 G ++SPFNAW++L G+ TLDLR + ++ A K+AR LEG ++ RV P L SHPQH++A Sbjct: 240 GGSMSPFNAWLMLNGMATLDLRCRAMADTAEKIARALEGHPQLGRVIHPALESHPQHDMA 299 Query: 307 MSQMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQ 366 +QM G + +++L GG+ A LDAL ++ ISNN+GD+RS+ THPA+TTH +++ Q Sbjct: 300 KAQMERPGTMIALDLAGGKEAAFRFLDALKIVKISNNLGDARSIATHPATTTHQRLSDAQ 359 Query: 367 RLLMGVGEGMLRLNVGLEDPEDLIADLDQALGSV 400 + +G+ G++RL+VGLED +DLIADL QAL + Sbjct: 360 KAHLGITPGLVRLSVGLEDADDLIADLKQALAVI 393 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: 424 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: 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 Aug 31 2024. The underlying query database was built on Jul 25 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