Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate AZOBR_RS02140 AZOBR_RS02140 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__azobra:AZOBR_RS02140 Length = 402 Score = 365 bits (938), Expect = e-105 Identities = 189/388 (48%), Positives = 257/388 (66%), Gaps = 3/388 (0%) Query: 16 KPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEM 75 +P ++ + GG RS + ET EAL+ TSG+ Y A +A + F D YSR +NPT M Sbjct: 15 RPRSRLVHGGVRRSSFDETCEALYQTSGFVYGSAEEAESAFVNDGSRHVYSRFRNPTTAM 74 Query: 76 LEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFG 135 E R+ EGA AT SGMAA+ AL L GD ++ R+ F SC W+ +FG Sbjct: 75 FEDRLCEYEGAAWAYATTSGMAAVHGALWSNLRTGDRIVAPRSLFISCYWVIKELSARFG 134 Query: 136 IETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAF 195 +E VD D Q+ +A+ TKV F ETP+NP ++VVDL+AV A+A + G VVDNAF Sbjct: 135 VEAVFVDGTDLSQWEEALAKPTKVVFLETPSNPGLEVVDLRAVSALAHKAGAKVVVDNAF 194 Query: 196 ATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAV-CGTEEFINNTLLPFHRNTGPTLSP 254 ATP LQRP + GADVV YSATK +DGQGR L G + +++ ++ + P+ R+TGPT+SP Sbjct: 195 ATPVLQRPFEMGADVVIYSATKHIDGQGRCLGGIILTNDKQYGSDVIHPYLRHTGPTISP 254 Query: 255 FNAWVVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPGLPSHPQHNLAMSQMAA 312 FNAW++LKGLETL+LR+ QS AL VA FLEG +V RV +PGL SHPQH+L SQM Sbjct: 255 FNAWLLLKGLETLELRVSAQSAAALTVAEFLEGHAKVERVLYPGLASHPQHDLVRSQMTG 314 Query: 313 AGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGV 372 G + SI L GG+ +A L+ L ++ ISNN+GDS+SL+THP +TTHS + +++ + Sbjct: 315 GGTMLSIFLKGGKEEAFRALNDLRMVMISNNLGDSKSLITHPDTTTHSKLTVEEKAAANI 374 Query: 373 GEGMLRLNVGLEDPEDLIADLDQALGSV 400 +LRL+VGLED +D++ DLD+AL S+ Sbjct: 375 RPNLLRLSVGLEDAQDIVEDLDRALASL 402 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: 406 Number of extensions: 7 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 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