Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate SMc02217 SMc02217 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Smeli:SMc02217 Length = 394 Score = 423 bits (1088), Expect = e-123 Identities = 200/392 (51%), Positives = 282/392 (71%), Gaps = 2/392 (0%) Query: 11 ITQNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQN 70 +++NW+PATQ + GGT RS++GETSEA+FLT G+ YD + A ARF G+ G Y+R + Sbjct: 1 MSKNWRPATQLVHGGTLRSQYGETSEAIFLTQGFVYDSSEAAEARFKGETDGFIYARYGS 60 Query: 71 PTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQ 130 PT +M E+R+ +LEGAE RATASGMAA++AA+LCQ+ AGDH++ RA FGSCRW+ +T Sbjct: 61 PTNDMFEKRMCMLEGAEDARATASGMAAVSAAILCQVKAGDHIVAARALFGSCRWVVETL 120 Query: 131 LPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTV 190 PK+G+E T+VD RD + + DA+RPNTKVFF E+P NPT++V+D+ V +A + G V Sbjct: 121 APKYGVECTLVDGRDLKNWEDAVRPNTKVFFLESPTNPTLEVIDIAGVARLADQIGAKVV 180 Query: 191 VDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGP 250 VDN FATP Q+P++ GA VV YSATK +DGQGR L G V +++++ L + R+TGP Sbjct: 181 VDNVFATPLFQKPLELGAHVVVYSATKHIDGQGRCLGGVVLSDKQWVDENLHDYFRHTGP 240 Query: 251 TLSPFNAWVVLKGLETLDLRIQRQSENALKVARFL--EGRVPRVNFPGLPSHPQHNLAMS 308 +SPFNAW +LKG+ETL LR+++Q+E+A +VA FL + +V RV +PG HPQ ++ Sbjct: 241 AMSPFNAWTLLKGIETLPLRVKQQTESARRVADFLAEQPQVARVIYPGRKDHPQADVIAK 300 Query: 309 QMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRL 368 QM+ + + EL GG+ A L +AL +I ISNN+GDS+SL+THPA+TTH + ++ R Sbjct: 301 QMSGGSTLVAFELKGGKEAAFALQNALEIIRISNNLGDSKSLITHPATTTHKNLTDEARA 360 Query: 369 LMGVGEGMLRLNVGLEDPEDLIADLDQALGSV 400 +G+ G +R + G+ED EDLI D +AL V Sbjct: 361 ELGISAGTVRFSAGIEDSEDLIEDFARALKGV 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: 411 Number of extensions: 10 Number of successful extensions: 2 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: 394 Length adjustment: 31 Effective length of query: 371 Effective length of database: 363 Effective search space: 134673 Effective search space used: 134673 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 03 2021. The underlying query database was built on Aug 03 2021.
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