Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate AZOBR_RS02140 AZOBR_RS02140 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__azobra:AZOBR_RS02140 Length = 402 Score = 249 bits (637), Expect = 8e-71 Identities = 148/401 (36%), Positives = 225/401 (56%), Gaps = 11/401 (2%) Query: 4 RTTHSHDGDRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQG-------- 55 RT H + L + +HGG S +Y TS + S E + Sbjct: 3 RTDHRNPNVAGLRPRSRLVHGGVRRS-SFDETCEALYQTSGFVYGSAEEAESAFVNDGSR 61 Query: 56 FEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAAT-STVMELLDAGSHVVAMDDLYGG 114 YSR NPT +E + EG A+A SGMAA + L G +VA L+ Sbjct: 62 HVYSRFRNPTTAMFEDRLCEYEGAAWAYATTSGMAAVHGALWSNLRTGDRIVAPRSLFIS 121 Query: 115 TFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVI 174 + + + + R G++ FVD TD + ++ A+ TK+V++ETP+NP L++VD+ A++ + Sbjct: 122 CYWVIKELSARF-GVEAVFVDGTDLSQWEEALAKPTKVVFLETPSNPGLEVVDLRAVSAL 180 Query: 175 ARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQ 234 A K G VVDN FA+P+LQRP +GAD+V++SATK+++G +GGI + D ++ Sbjct: 181 AHKAGAKVVVDNAFATPVLQRPFEMGADVVIYSATKHIDGQGRCLGGIILTNDKQYGSDV 240 Query: 235 MAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLA 294 + G PF+++L L+GL+TL LR+ A AL +A++LE H +E+V+YPGLA Sbjct: 241 IHPYLRHTGPTISPFNAWLLLKGLETLELRVSAQSAAALTVAEFLEGHAKVERVLYPGLA 300 Query: 295 SHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMT 354 SHPQH L + QM+G G ++SI LKGG + A R + ++ +LG +SL+ HP T Sbjct: 301 SHPQHDLVRSQMTGGGTMLSIFLKGGKEEAFRALNDLRMVMISNNLGDSKSLITHPDTTT 360 Query: 355 HASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERALVN 395 H+ + V + I L+RLSVG+ED D+ DL+RAL + Sbjct: 361 HSKLTVEEKAAANIRPNLLRLSVGLEDAQDIVEDLDRALAS 401 Lambda K H 0.320 0.134 0.391 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: 450 Number of extensions: 19 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: 397 Length of database: 402 Length adjustment: 31 Effective length of query: 366 Effective length of database: 371 Effective search space: 135786 Effective search space used: 135786 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 (21.8 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