Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_012041083.1 BBTA_RS03595 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000015165.1:WP_012041083.1 Length = 402 Score = 397 bits (1019), Expect = e-115 Identities = 195/387 (50%), Positives = 264/387 (68%), Gaps = 2/387 (0%) Query: 15 WKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVE 74 ++P T+ + G+ RSE+GET+EAL+LT G+ Y A + ARF G+ G YSR NPT Sbjct: 15 YRPETRLVHSGSLRSEFGETAEALYLTQGFVYATAEECEARFKGEDPGFIYSRFSNPTTA 74 Query: 75 MLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKF 134 M E+R+ LEGAEACR+ A+GMAA+T A+L L AGDH++ +A FGSCR++ + LP++ Sbjct: 75 MFERRMIELEGAEACRSAATGMAAVTTAILAPLRAGDHVVAAKALFGSCRYVVEDLLPRY 134 Query: 135 GIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNA 194 GIE+T+VD D Q+ A+RPNTK FF E+P NPT+DV+D+ A+ IA G +VDN Sbjct: 135 GIESTLVDGLDLDQWQKAVRPNTKSFFLESPTNPTLDVMDIPAIAEIAHAHGARLIVDNV 194 Query: 195 FATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSP 254 FATP Q P+ GADVV YSATK +DGQGR L G + +E FI + F R TGP++SP Sbjct: 195 FATPIWQSPLALGADVVVYSATKHIDGQGRCLGGVILSSEAFIAEHIHNFMRQTGPSISP 254 Query: 255 FNAWVVLKGLETLDLRIQRQSENALKVARFL--EGRVPRVNFPGLPSHPQHNLAMSQMAA 312 FNAWV+LKGLETL +R++ Q+ENA KVA FL ++ R+ +PG HPQ QM A Sbjct: 255 FNAWVLLKGLETLAVRVRAQTENAAKVADFLATHPKISRLIYPGREDHPQAATVRKQMRA 314 Query: 313 AGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGV 372 + E+ GG+ A L+ L L ISNN+GDS++L+THPA+TTH ++ + R +G+ Sbjct: 315 GSTLVGFEVKGGKAGAFRTLNGLKLARISNNLGDSKTLVTHPATTTHQRLSPEARAELGI 374 Query: 373 GEGMLRLNVGLEDPEDLIADLDQALGS 399 EG +R + GLE +DLIADLD ALG+ Sbjct: 375 SEGFIRFSAGLEHADDLIADLDAALGA 401 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: 425 Number of extensions: 16 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: 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