Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate YP_004145039.1 Mesci_5982 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000185905.1:YP_004145039.1 Length = 395 Score = 415 bits (1066), Expect = e-120 Identities = 197/387 (50%), Positives = 275/387 (71%), Gaps = 2/387 (0%) Query: 13 QNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPT 72 +NWKP T + GT RS +GETSEA++LT GY Y+ A A ARF G++ G YSR NPT Sbjct: 6 RNWKPQTALVHSGTLRSGFGETSEAIYLTQGYVYETAQAAEARFKGEEPGFIYSRYANPT 65 Query: 73 VEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLP 132 V+M E+R+ LEGAE RATASGMA +TAALLC AGDH++ RA FGSCRW+ +T P Sbjct: 66 VDMFEKRMCALEGAEDARATASGMAGVTAALLCSAKAGDHIVAARALFGSCRWVVETLAP 125 Query: 133 KFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVD 192 ++GIE T+VD D + A++PNTK+FF E+P NPT++VVD+ AV ++A G +VD Sbjct: 126 RYGIEATLVDGTDIANWEKAVKPNTKLFFLESPTNPTLEVVDIAAVASLANSIGARLIVD 185 Query: 193 NAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTL 252 N FATP Q+P+ GA +V YSATK +DGQGR L G + +++I+ L + R+TGP+L Sbjct: 186 NVFATPLQQKPLQLGAHIVVYSATKHIDGQGRCLGGVILSDKKWIDENLHDYFRHTGPSL 245 Query: 253 SPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQM 310 SPFNAW +LKGLETL LR+++Q+E+A ++A FL R + RV +PG HPQ ++ QM Sbjct: 246 SPFNAWTLLKGLETLPLRVRQQTESAGRIADFLAERPEIARVIYPGRADHPQADIVKKQM 305 Query: 311 AAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLM 370 + + +++ GG+ A L +AL ++ ISNN+GD++SL+THPA+TTH ++++ R + Sbjct: 306 SGGSTLICLDVKGGKQAAFALQNALDIVLISNNLGDAKSLITHPATTTHKNLSDEARAEL 365 Query: 371 GVGEGMLRLNVGLEDPEDLIADLDQAL 397 G+G G LRL+VGLED +DL+ D+ QAL Sbjct: 366 GIGPGTLRLSVGLEDTDDLLEDIAQAL 392 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: 421 Number of extensions: 11 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 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