Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate 5209311 Shew_1789 cystathionine beta-lyase (RefSeq)
Query= BRENDA::L7N4M1 (449 letters) >FitnessBrowser__PV4:5209311 Length = 395 Score = 155 bits (391), Expect = 3e-42 Identities = 127/420 (30%), Positives = 187/420 (44%), Gaps = 43/420 (10%) Query: 19 ETKQIHAGQHPDPTTNARALPIYATTSYTFD---DTAHAAALFGLEIPGNIYTRIGNPTT 75 ETK + G+ + P++ ++ FD D HA Y R G PT Sbjct: 4 ETKIVSVGRDKKWSKGVINPPVFRASTVVFDTIEDMRHATK--NRANGAMFYGRRGTPTH 61 Query: 76 DVVEQRIAALEGGVAALFLSSGQAAETFAILNLAGAGDHIVSSPRLYGGTYNLFHYSLAK 135 + IA LEGGV SG AA + A+L+ AGDH++ Y T +L L Sbjct: 62 FAFQAAIAELEGGVGTALYPSGSAAISGALLSFLKAGDHLLMVDTAYEPTRDLCDKLLKG 121 Query: 136 LGIEVSFVDDPDDLDTWQAAVRPNTKAFFAETISNPQIDLLDTPAVSEVAHRNGVPLIVD 195 GIE ++ D P D +A +RPNTK F E+ + +++ D P +S +AHR+ + +++D Sbjct: 122 FGIETTYYD-PLIGDGIEALIRPNTKVLFLESPGSITLEVQDVPTLSAIAHRHNLVVMLD 180 Query: 196 NTIATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDWTQGRFPGFTTPDPS 255 NT A+P +P G DI + +ATKY+ GH + G W Q R + Sbjct: 181 NTWASPINCRPFELGVDISIQAATKYIVGHSDVMLGT-ATANQAHWDQLRENSYL----- 234 Query: 256 YHGVVFAELGPPAFALKARVQLLRDYGSAASPFNAFLVAQGLETLSLRIERHVANAQRVA 315 G S + +L ++GL TL +R+ +H N VA Sbjct: 235 -------------------------MGQCTSADDIYLASRGLRTLGVRMAQHEKNGLEVA 269 Query: 316 EFLAARDDVLSVNYAGLPSSPWHERAKRLAPKGTGAVLSFEL-AGGIEAGKAFVNALKLH 374 LA R +V + + S P HE KR G + SF L G I+A AFV + Sbjct: 270 NLLATRPEVDHLRHPAFASCPGHEFFKRDFSASNG-LFSFVLKRGNIKAITAFVEGMDHF 328 Query: 375 SHVANIGDVRSLVIHPASTTHAQLSPAEQLATGVSPGLVRLAVGIEGIDDILADLELGFA 434 + G SL++ +L A Q + S L+RL VG+E +D++ DLE GFA Sbjct: 329 KMGFSWGGYESLILGVFGID--KLRTATQWDS--SKPLIRLHVGLENPEDLIKDLEAGFA 384 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: 441 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 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