Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_012116516.1 XAUT_RS23015 cystathionine beta-lyase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000017645.1:WP_012116516.1 Length = 398 Score = 166 bits (420), Expect = 1e-45 Identities = 113/337 (33%), Positives = 169/337 (50%), Gaps = 11/337 (3%) Query: 64 TYSRLQNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSC 123 +Y R NPT E E + LEG + T SG++A + +LL L AGDHL+ A+ Sbjct: 61 SYGRRGNPTTEGFETALRALEGGDGIALTPSGLSACSISLLSVLDAGDHLLMVDTAYRPT 120 Query: 124 RWLTDTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIAR 183 R D L + G+ETT D + IR NT+ F E+P + + ++ D+ A+ A+AR Sbjct: 121 RTFCDQVLKRLGVETTYYDPLVGSGIAELIRDNTRAIFLESPGSQSFEMQDVPAITAVAR 180 Query: 184 ERGIVTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLP 243 RGI T++DN +ATP +P FG D+ + TK + G + G + ++ Sbjct: 181 ARGITTLIDNTWATPLFFKPHAFGVDISIQAGTKYIGGHADLNLGTISAVGPAWKK-VIA 239 Query: 244 FHRNTGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHP 301 H G T+SP +A + +GL TL +R+ + L+VA++L+ R V RV P LP+ P Sbjct: 240 THGTLGITISPDDAALGARGLRTLAVRLAHHQRSGLEVAQWLQDRPEVSRVLHPALPTDP 299 Query: 302 QHNLAMSQMAAAGPIFSIELDGGRTQA-HGLLDALGLIDISNNIGDSRSL-MTHPASTTH 359 H + A +FS+ L +A DAL L + + G SL + Sbjct: 300 GHAIWKRDFTGATGLFSLILKEVPERAVAAFFDALALFGMGYSWGGYESLAIPFDCRDYR 359 Query: 360 SGVAEDQRLLMGVGEGMLRLNVGLEDPEDLIADLDQA 396 + D + G G +RL++GLED DL ADLDQA Sbjct: 360 TATVWD---VEGPG---VRLHIGLEDVADLKADLDQA 390 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: 405 Number of extensions: 19 Number of successful extensions: 4 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: 398 Length adjustment: 31 Effective length of query: 371 Effective length of database: 367 Effective search space: 136157 Effective search space used: 136157 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