Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate PP_2001 PP_2001 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Putida:PP_2001 Length = 403 Score = 308 bits (788), Expect = 2e-88 Identities = 167/384 (43%), Positives = 245/384 (63%), Gaps = 13/384 (3%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTY--------AQSSPGEHQGFEYSRTHNPTRFAYE 70 TLA+ GQ+ P G ++ TS+Y A GE G YSR NP+ A+E Sbjct: 21 TLAVRAGQNRTPE-GEHSEALFLTSSYVFRTAADAAARFAGETPGNVYSRYTNPSVRAFE 79 Query: 71 RCVAALEGGTRAFAFASGMAAT-STVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGL 129 +AA+EG +A ++GMAA + VM L AG HV+ ++G T LFE+ +R G+ Sbjct: 80 ERLAAMEGAEQAVGTSTGMAAILAVVMSLCSAGDHVLVSQSVFGSTISLFEKYFKRF-GV 138 Query: 130 DFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFA 189 + +V L D ++ AI+A+TK++ +E+P+NP+ +LVDI A++ IA G + VVDN F+ Sbjct: 139 EVDYVPLVDLTGWEKAIKANTKLLIVESPSNPLAELVDITALSEIAHAQGAMLVVDNCFS 198 Query: 190 SPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPF 249 +P LQ+PL LGAD+V HSATK+++G +GG+ V G ++ E + FL+ + G PF Sbjct: 199 TPALQQPLKLGADIVFHSATKFIDGQGRCMGGV-VAGRTEQMKEVVGFLRTA-GPTLSPF 256 Query: 250 DSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGF 309 ++++ +GL+TL LRMRAHCE+A ALA+WLE +EKV Y GL SHPQH LAKRQMSGF Sbjct: 257 NAWIFTKGLETLRLRMRAHCESAQALAEWLEQQDGVEKVHYAGLPSHPQHELAKRQMSGF 316 Query: 310 GGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGIS 369 G +VS +KGG + A RF + T + ++ +LG ++ + HPA +H + RE GI Sbjct: 317 GAVVSFEVKGGKEGAWRFIDATRVISITTNLGDSKTTIAHPATTSHGRLSPQEREAAGIR 376 Query: 370 DALVRLSVGIEDLGDLRGDLERAL 393 D+L+R++VG+ED+ DL+ DL R L Sbjct: 377 DSLIRVAVGLEDVADLQADLARGL 400 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: 413 Number of extensions: 18 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: 397 Length of database: 403 Length adjustment: 31 Effective length of query: 366 Effective length of database: 372 Effective search space: 136152 Effective search space used: 136152 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