Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate AZOBR_RS02140 AZOBR_RS02140 O-succinylhomoserine sulfhydrylase
Query= metacyc::HP_RS00540-MONOMER (380 letters) >FitnessBrowser__azobra:AZOBR_RS02140 Length = 402 Score = 249 bits (635), Expect = 1e-70 Identities = 140/393 (35%), Positives = 228/393 (58%), Gaps = 18/393 (4%) Query: 1 MRMQTKLIHGGI---SEDATTGAVSVPIYQTSTYRQDA--------IGRHKGYEYSRSGN 49 +R +++L+HGG+ S D T A +YQTS + + + + YSR N Sbjct: 14 LRPRSRLVHGGVRRSSFDETCEA----LYQTSGFVYGSAEEAESAFVNDGSRHVYSRFRN 69 Query: 50 PTRFALEELIADLEGGVKGFAFASGLAGIH-AVFSLLQSGDHVLLGDDVYGGTFRLFNQV 108 PT E+ + + EG +A SG+A +H A++S L++GD ++ ++ + + ++ Sbjct: 70 PTTAMFEDRLCEYEGAAWAYATTSGMAAVHGALWSNLRTGDRIVAPRSLFISCYWVIKEL 129 Query: 109 LVKNGLSCTIIDTSDISQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTI 168 + G+ +D +D+SQ ++A+ TK ++LETPSNP L++ DL +++A G + Sbjct: 130 SARFGVEAVFVDGTDLSQWEEALAKPTKVVFLETPSNPGLEVVDLRAVSALAHKAGAKVV 189 Query: 169 VDNTFATPYYQNPLLLGADIVAHSGTKYLGGHSDVVAGLVTTNNEALAQEIAF-FQNAIG 227 VDN FATP Q P +GAD+V +S TK++ G + G++ TN++ ++ + G Sbjct: 190 VDNAFATPVLQRPFEMGADVVIYSATKHIDGQGRCLGGIILTNDKQYGSDVIHPYLRHTG 249 Query: 228 GVLGPQDSWLLQRGIKTLGLRMEAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAK 287 + P ++WLL +G++TL LR+ A AL VAEFLE H KVERV YPGL +HP ++L + Sbjct: 250 PTISPFNAWLLLKGLETLELRVSAQSAAALTVAEFLEGHAKVERVLYPGLASHPQHDLVR 309 Query: 288 KQMRGFSGMLSFTLK-NDSEAVAFVESLKLFILGESLGGVESLVGIPAFMTHACIPKTQR 346 QM G MLS LK EA + L++ ++ +LG +SL+ P TH+ + ++ Sbjct: 310 SQMTGGGTMLSIFLKGGKEEAFRALNDLRMVMISNNLGDSKSLITHPDTTTHSKLTVEEK 369 Query: 347 EAAGIRDGLVRLSVGIEHEQDLLEDLEQAFAKI 379 AA IR L+RLSVG+E QD++EDL++A A + Sbjct: 370 AAANIRPNLLRLSVGLEDAQDIVEDLDRALASL 402 Lambda K H 0.319 0.137 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: 390 Number of extensions: 17 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: 380 Length of database: 402 Length adjustment: 31 Effective length of query: 349 Effective length of database: 371 Effective search space: 129479 Effective search space used: 129479 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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