Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_020176501.1 A3OQ_RS0116385 cystathionine beta-lyase
Query= BRENDA::L7N4M1 (449 letters) >NCBI__GCF_000385335.1:WP_020176501.1 Length = 395 Score = 155 bits (392), Expect = 2e-42 Identities = 130/429 (30%), Positives = 192/429 (44%), Gaps = 51/429 (11%) Query: 10 ADPTAHWSFETKQIHAGQHPDPTTNARALPIYATTSYTF---DDTAHAAALFGLEIPGNI 66 AD + TK +HAG+ P + PIY ++ F DD + F Sbjct: 6 ADSRKNLKNRTKLVHAGRKPSEQSGFVNTPIYRGSTVLFPTLDDLLNRRMPF-------T 58 Query: 67 YTRIGNPTTDVVEQRIAALEGGVAALFLSSGQAAETFAILNLAGAGDHIVSSPRLYGGTY 126 Y G+PTT+ ++ L G + + +G AA A+L + AGDHI+ S +Y Sbjct: 59 YGTQGSPTTEALQTAWTELSGAKGTVIVPTGLAAIAIALLAVVKAGDHILVSDSVYRPNR 118 Query: 127 NLFHYSLAKLGIEVSFVDDPDDLDTWQAAVRPNTKAFFAETISNPQIDLLDTPAVSEVAH 186 N L ++G+E ++ + +A +RPNT F ET + ++ D PA+ VA Sbjct: 119 NFCDTILKRMGVETTYYEPLIGAGI-EALIRPNTSVIFLETPGSQTFEVQDIPAIVAVAR 177 Query: 187 RNGVPLIVDNTIATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDWTQGRF 246 G+ I+DNT ATP Q A G DI + + TKYL GH + G++ N W Sbjct: 178 AKGICTILDNTWATPLFFQAHAHGVDISLEAGTKYLSGHSDLLLGLVT--ANEVWY---- 231 Query: 247 PGFTTPDPSYHGVVFAELGPPAFALKARVQLLRDYGSAASPFNAFLVAQGLETLSLRIER 306 P+ H AFA+ P + FL +G+ TL LR+ Sbjct: 232 -------PALHATY------DAFAM------------CPGPEDVFLALRGMRTLELRLNE 266 Query: 307 HVANAQRVAEFLAARDDVLSVNYAGLPSSPWHERAKRLAPKGTGAVLSFELAG-GIEAGK 365 +A++L R +VL V + LPS P HE KR G+ + S LA +A Sbjct: 267 AQRQGLAMAQWLGGRKEVLKVLHPALPSCPGHEIWKR-DFLGSSGLFSILLAPCSQQALA 325 Query: 366 AFVNALKLHSHVANIGDVRSLVIHPASTTHAQLSP-AEQLATGVSPGLVRLAVGIEGIDD 424 AF++ L+L + G SLVI T+ +P A Q P L R ++G+E I+D Sbjct: 326 AFLDGLELFGMGFSWGGFESLVIPFDCKTYRTATPWAPQ-----GPAL-RFSIGLEDIED 379 Query: 425 ILADLELGF 433 + ADL GF Sbjct: 380 LKADLAAGF 388 Lambda K H 0.318 0.134 0.394 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: 436 Number of extensions: 24 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: 449 Length of database: 395 Length adjustment: 32 Effective length of query: 417 Effective length of database: 363 Effective search space: 151371 Effective search space used: 151371 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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