Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_003550455.1 RL_RS34795 cystathionine gamma-synthase family protein
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000009265.1:WP_003550455.1 Length = 427 Score = 192 bits (488), Expect = 2e-53 Identities = 136/414 (32%), Positives = 206/414 (49%), Gaps = 40/414 (9%) Query: 17 PATQAIRGG-TARSEWGETSEALFLTSGYAYDCAGDAAARFS----------GDQQGMTY 65 P TQ + G G +FLTS + + A D F G G+ Y Sbjct: 18 PETQMLNYGYDPELSEGAVKPPVFLTSTFVFKTAEDGRDFFDYVSGRREPPEGKGAGLVY 77 Query: 66 SRLQNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRW 125 SR +P E++E R+A+ E E+ +SGMAA+ LL + GD ++ + +G Sbjct: 78 SRFNHPNSEIVEDRLAVYERTESGVLFSSGMAAIATTLLAFVRPGDAILHSQPLYGG--- 134 Query: 126 LTDTQLPK---------FGIETTVVDARDPQQFIDAI-RPNTKVFFFETPANPTMDVVDL 175 T+T L K G V + + +A+ + V ETPANPT +VD+ Sbjct: 135 -TETLLAKTFLNLGAAAVGFADGVSEGSVQKAAEEAMAKGRVSVILIETPANPTNSLVDV 193 Query: 176 KAVCAIARERGI------VTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGA 229 + +A G + V DN P QRP++ GAD+ YS TK + G ++AGA Sbjct: 194 AMIRRVADAIGARQGHMPIIVCDNTLLGPVFQRPIEHGADISLYSLTKYVGGHSDLIAGA 253 Query: 230 VCGTEEFINNTLLPFHRNTGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEG-- 287 V G + I + G L P + W++ + LETL LR++R + NA VA FL Sbjct: 254 VLGRKAVIKQ-IKALRGAIGTQLDPHSCWMLGRSLETLQLRMERANSNARAVADFLRDHP 312 Query: 288 RVPRVNFPGLPSH----PQHNLAMSQMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNN 343 +V +V++ LP H P ++Q AG FS ++ GG+ + L+AL + ++ + Sbjct: 313 KVEKVHY--LPYHDPESPAGRTFIAQCTGAGSTFSFDIRGGQPASFKFLNALQIFKLAVS 370 Query: 344 IGDSRSLMTHPASTTHSGVAEDQRLLMGVGEGMLRLNVGLEDPEDLIADLDQAL 397 +G + SL +HPA+ THSGV D R +GV E +RL++G+E P+DLIADL+ AL Sbjct: 371 LGGTESLASHPAAMTHSGVPADVRQRIGVLESTIRLSIGIEHPDDLIADLEIAL 424 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: 418 Number of extensions: 14 Number of successful extensions: 5 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: 427 Length adjustment: 31 Effective length of query: 371 Effective length of database: 396 Effective search space: 146916 Effective search space used: 146916 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