Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate WP_057508382.1 ABB28_RS09420 cystathionine beta-synthase
Query= SwissProt::P9WP51 (464 letters) >NCBI__GCF_001431535.1:WP_057508382.1 Length = 456 Score = 260 bits (664), Expect = 8e-74 Identities = 170/465 (36%), Positives = 246/465 (52%), Gaps = 22/465 (4%) Query: 1 MRIAQHISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQ 60 M I + +LIG TP+V+ + G + K+E NPGGS KDRI + MIEAAE G Sbjct: 1 MPIHASVLDLIGQTPIVKAQRL-DTGVCELFLKLESANPGGSIKDRIGLSMIEAAEKRGD 59 Query: 61 LKPGGTIVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAV 120 LKPG T+VE T+GNTG+GLALVAQ++GYK V V PDK+S +K L A GAEV + + V Sbjct: 60 LKPGATLVEGTAGNTGLGLALVAQQKGYKLVLVVPDKMSREKIFNLKAMGAEVRLTRSDV 119 Query: 121 PPHDPASYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGI 180 P Y ++ + I GA+ +Q+ NP+ PA+H TGPEI G + V G Sbjct: 120 AKGHPEYYQDLAKTIADQIPGAYFINQFGNPDNPAAHEFGTGPEILEQMGGDLDAIVFGC 179 Query: 181 GTGGTITGAGRYLKEVSGGRVRIVGADPEGSVYS--------GGAGRPYLVEGVGEDFWP 232 G+ GT+TG R +S + +V ADP GS+ + +LVEG+GEDF P Sbjct: 180 GSSGTMTGLSRAFSTLS-PKTELVLADPVGSILAEYINDGVLNDKSGSWLVEGIGEDFLP 238 Query: 233 AAYDPSVPDEIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVV 292 + D S + A++D++SF R L +E +L G S G + AALK +E ++V Sbjct: 239 SISDFSRVKKAYAITDAESFHTARELLGKEGILGGSSTGTLLAAALKYCKEQTTPKKVLV 298 Query: 293 LLPDGGRGYMSKIFNDAWMSSYGFLRSRLDGSTEQSTVGDVLRRKSGALPALVHTHPSET 352 L+ D G Y+SK++ND WM GFL G + D++ R G +V P++ Sbjct: 299 LVCDTGNKYLSKMYNDYWMLDNGFLERPQHGD-----LRDLILRPYGQRDTVV-IGPNDL 352 Query: 353 VRDAIGILREYGVSQMPVVGAEPPVMAGEVAGSVSERELLSAVFEGRAKLADAVSAHMSP 412 + A ++ Y VSQ+PVV + + G V E ++L V+ A+ D VS M Sbjct: 353 LTTAYQRMKLYDVSQLPVVDGD------TLVGIVDESDVLLHVYGDEARFRDTVSTAMVS 406 Query: 413 PLRMIGAGELVSAAGKALRDWDALMVVEEGKPVGVITRYDLLGFL 457 L + + A ++++ +G+ITR DLL +L Sbjct: 407 KLDRLDVKSPIEALLPVFDRGQVAIIMDGDTFLGLITRIDLLNYL 451 Lambda K H 0.316 0.135 0.398 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: 569 Number of extensions: 37 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: 464 Length of database: 456 Length adjustment: 33 Effective length of query: 431 Effective length of database: 423 Effective search space: 182313 Effective search space used: 182313 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: 51 (24.3 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