Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate AO353_23290 AO353_23290 cystathionine beta-synthase
Query= SwissProt::P9WP51 (464 letters) >FitnessBrowser__pseudo3_N2E3:AO353_23290 Length = 458 Score = 261 bits (667), Expect = 3e-74 Identities = 170/455 (37%), Positives = 247/455 (54%), Gaps = 20/455 (4%) Query: 10 LIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLKPGGTIVE 69 LIG TPLVR+ S G T+ K+E NPGGS KDRI + MI+AAE G+L+PGGTIVE Sbjct: 12 LIGNTPLVRV-SRFDTGPCTLFLKLESQNPGGSIKDRIGLAMIDAAERDGRLQPGGTIVE 70 Query: 70 PTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPPHDPASYY 129 T+GNTG+GLALV + +GY+ V V PDK+S +K L A GAEV + + V P Y Sbjct: 71 ATAGNTGLGLALVGRAKGYRVVLVVPDKMSTEKVLHLKAMGAEVHITRSDVGKGHPEYYQ 130 Query: 130 SVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGTGGTITGA 189 V+ RL ++I A+ DQ+ NP P +H +T PEIWA E + V G+G+ GT+TG Sbjct: 131 DVAARLAQEIPDAFFADQFNNPANPLAHECSTAPEIWAQAEHDLDAIVVGVGSAGTLTGL 190 Query: 190 GRYLKEVSGGRVRIVGADPEGSVY-----SGGAGRP--YLVEGVGEDFWPAAYDPSVPDE 242 R+ + V + +V ADP GSV SG G P + VEG+GEDF P+ D S + Sbjct: 191 TRFFRRVQPD-LEMVLADPVGSVMAEYSRSGTLGTPGSWAVEGIGEDFIPSIADLSSVRQ 249 Query: 243 IIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRGYM 302 ++SD +SFD R+L R E +L G S G + AAL+ E +V + D G Y+ Sbjct: 250 AYSISDEESFDHARQLLRAEGILGGSSTGTLLAAALRYCREQTEPKRVVSFVCDTGTRYL 309 Query: 303 SKIFNDAWMSSYGFLRSRLDGSTEQSTVGDVLRRKSGALPALVHTHPSETVRDAIGILRE 362 SKI+ND WM+ G L + G + D++ R+ ++ P +T+ A +R Sbjct: 310 SKIYNDQWMTDQGLLARKRYGD-----LRDLIARRFED-GRVISVGPDDTLLTAFQRMRL 363 Query: 363 YGVSQMPVVGAEPPVMAGEVAGSVSERELLSAVFEGRAKLADAVSAHMSPPLRMIGAGEL 422 VSQ+PV+ V + G + E ++L V + + V++ M+ + + G Sbjct: 364 ADVSQLPVL-----VGGKRLVGVIDESDILLGVHKDASHFRMTVASAMTDKVETLPPGAS 418 Query: 423 VSAAGKALRDWDALMVVEEGKPVGVITRYDLLGFL 457 ++ L ++ + G+ITR D+L L Sbjct: 419 LAELQAELDRGLVAVIADASGFHGLITRVDMLNHL 453 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: 607 Number of extensions: 37 Number of successful extensions: 3 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: 458 Length adjustment: 33 Effective length of query: 431 Effective length of database: 425 Effective search space: 183175 Effective search space used: 183175 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 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