Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate WP_013089932.1 BC1002_RS10060 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::O05394 (379 letters) >NCBI__GCF_000092885.1:WP_013089932.1 Length = 445 Score = 248 bits (632), Expect = 3e-70 Identities = 150/416 (36%), Positives = 220/416 (52%), Gaps = 43/416 (10%) Query: 5 TLMIHGGITGDEKTGAVSVPIYQVSTYKQPKAG--------QHTGYEYSRTANPTRTALE 56 TL +H G D TGA + PIYQ +++ + + G+ YSR +NPT E Sbjct: 8 TLALHAGAAPDPATGARATPIYQTTSFSFRDSDHAAALFNMERAGHVYSRISNPTVAVFE 67 Query: 57 ALVTELESGEAGYAFSSGMAAI-TAVMMLFNSGDHVVLTDDVYGGTYRVMTKVLNRLGIE 115 V LE+G +SG AA+ A+ L +G H+V + +YGG++ ++ L R GIE Sbjct: 68 ERVAALENGAGAIGTASGQAALHLAIATLMGAGSHIVASSALYGGSHNLLHYTLRRFGIE 127 Query: 116 STFVDTSSREEVEKAIRPNTKAIYIETPTNPLLKITDLTLMADIAKKAGVLLIVDNTFNT 175 +TFV + A+RPNT+ ++ ET NP L++ D+ +A IA+ V L+VD+TF T Sbjct: 128 TTFVKPGDLDAWRAALRPNTRLLFGETLGNPGLEVLDIAALAQIARAHRVPLLVDSTFTT 187 Query: 176 PYFQQPLTLGADIVLHSATKYLGGHSDVVGGLVVTASK-------------ELGEELH-- 220 PY +P GAD V HSATK+LGGH +GG++V + E + H Sbjct: 188 PYLLRPFEHGADFVYHSATKFLGGHGTTIGGVLVDGGRFDFEASGLFLEFTEPYDGFHGM 247 Query: 221 -FVQNST----------------GGVLGPQDSWLLMRGIKTLGLRMEAIDQNARKIASFL 263 F + ST G L PQ +W L++GI+TL LRME N R++ FL Sbjct: 248 VFAEESTVAPFLLRARREGLRDFGACLHPQAAWQLLQGIETLPLRMERHVANTRRVVDFL 307 Query: 264 ENHPAVQTLYYPGSSNHPGHELAK-TQGAGFGGMISFDI-GSEERVDAFLGNLKLFTIAE 321 H AV+++ YP HP H LAK G G + SF++ G AF+ L LF+ Sbjct: 308 AGHAAVESVAYPELPTHPDHALAKRLLPRGAGAVFSFNLRGDRAAGRAFIEALTLFSHLA 367 Query: 322 SLGAVESLISVPARMTHASIPRERRLELGITDGLIRISVGIEDAEDLLEDIGQALE 377 ++G SL+ PA TH + GIT+G IR+S+G+ED +DL++D+ +AL+ Sbjct: 368 NVGDARSLVIHPASTTHFRMDAAALAAAGITEGTIRLSIGLEDPDDLIDDLKRALK 423 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: 433 Number of extensions: 18 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: 379 Length of database: 445 Length adjustment: 31 Effective length of query: 348 Effective length of database: 414 Effective search space: 144072 Effective search space used: 144072 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 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