Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate HSERO_RS16440 HSERO_RS16440 hypothetical protein
Query= BRENDA::O05394 (379 letters) >FitnessBrowser__HerbieS:HSERO_RS16440 Length = 413 Score = 216 bits (551), Expect = 7e-61 Identities = 133/405 (32%), Positives = 212/405 (52%), Gaps = 35/405 (8%) Query: 5 TLMIHGGITGDEKTGAVSVPIYQVSTYKQPKA--------GQHTGYEYSRTANPTRTALE 56 T ++H + G++ PI+ T+ A G+ GY Y R NPT ALE Sbjct: 11 TTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALE 70 Query: 57 ALVTELESGEAGYAFSSGMAAITAVMM-LFNSGDHVVLTDDVYGGTYRVMTKVLNRLGIE 115 +T++E G++ F++GMAAI A++ L GDHVV + ++G T + V G + Sbjct: 71 DKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWMTV-GAQGAK 129 Query: 116 STFVDTSSREEVEKAIRPNTKAIYIETPTNPLLKITDLTLMADIAKKAGVLLIVDNTFNT 175 + VD + + VE AI NT+ +++ET NP ++ DL + ++ ++ G+L +VDNT + Sbjct: 130 VSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTS 189 Query: 176 PYFQQPLTLGADIVLHSATKYLGGHSDVVGG-LVVTASKELGEELHFVQN---------- 224 PY +P T+GA +V++S TK +GGH + +GG L T + H +N Sbjct: 190 PYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTRYPHIAENYKKNPAPQWG 249 Query: 225 ----------STGGVLGPQDSWLLMRGIKTLGLRMEAIDQNARKIASFLENHPAVQTLYY 274 GG LGP+ + + G +T+ LR E +NA +A L+ V +YY Sbjct: 250 MAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYY 309 Query: 275 PGSSNHPGHELAKTQGAGFGGMISFDIGSEERVDAF--LGNLKLFTIAESLGAVESLISV 332 PG +HP H L+K FG ++SF++ ++ +D F L L+L +LG +L+ Sbjct: 310 PGLESHPQHALSKALFRSFGSLMSFEL--KDGIDCFDYLNRLRLAIPTSNLGDTRTLVIP 367 Query: 333 PARMTHASIPRERRLELGITDGLIRISVGIEDAEDLLEDIGQALE 377 A + ERR +GI + LIR+SVG+ED +DL+ D QAL+ Sbjct: 368 VAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALD 412 Lambda K H 0.316 0.134 0.375 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: 393 Number of extensions: 16 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: 379 Length of database: 413 Length adjustment: 31 Effective length of query: 348 Effective length of database: 382 Effective search space: 132936 Effective search space used: 132936 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 (21.6 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