Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate GFF1863 HP15_1820 methionine gamma-lyase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Marino:GFF1863 Length = 413 Score = 316 bits (809), Expect = 9e-91 Identities = 176/388 (45%), Positives = 252/388 (64%), Gaps = 17/388 (4%) Query: 15 LSLATLAIHGGQSPDPSTGAV--MPPIYATSTYAQSSP--------GEHQGFEYSRTHNP 64 +S+ TLA+ GQ TG + I+ TS++ S GE G YSR NP Sbjct: 19 MSVDTLAVRAGQI---RTGQLEHSDAIFPTSSFVYGSAAQAAARFGGEEPGNIYSRFTNP 75 Query: 65 TRFAYERCVAALEGGTRAFAFASGMAAT-STVMELLDAGSHVVAMDDLYGGTFRLFERVR 123 T A+E +AA+EGG RA A ASGM+A ST M LL +G HV+ ++G T LF++ Sbjct: 76 TVQAFEGRIAAMEGGERAVATASGMSAILSTCMALLKSGDHVICSRGVFGTTNVLFQKYM 135 Query: 124 RRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTV 183 R G++ +FV LTD ++A+IR++T+M++IETP+NP+ ++ D+ + +AR + L V Sbjct: 136 ARF-GVETTFVSLTDMEEWQASIRSETRMLFIETPSNPLCEVADMEILGQLARDNDALFV 194 Query: 184 VDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIG 243 VDN F +P+LQRPL GAD+V+HSATKYL+G VGG+ VVG + E FL+ S G Sbjct: 195 VDNCFCTPVLQRPLEQGADIVIHSATKYLDGQGRCVGGV-VVGSEKMMEEVYGFLR-SAG 252 Query: 244 GVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAK 303 PF++++ +GL+TLP+RMRAHC+NAL LA WLE PA+E+V Y GL SHPQH LAK Sbjct: 253 PTMSPFNAWVFQKGLETLPIRMRAHCDNALELALWLEQQPAVERVFYAGLQSHPQHELAK 312 Query: 304 RQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARR 363 +Q +GFGG++S LKG + A RF + T + ++ +LG V++ + HPA TH + + Sbjct: 313 KQQTGFGGVLSFQLKGAREEAWRFIDGTRMISITANLGDVKTTITHPATTTHGRLSPEDK 372 Query: 364 EQLGISDALVRLSVGIEDLGDLRGDLER 391 + GI++ L+R+SVGIE + DL+ DLER Sbjct: 373 ARAGITENLIRISVGIEAVEDLKTDLER 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: 453 Number of extensions: 26 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: 413 Length adjustment: 31 Effective length of query: 366 Effective length of database: 382 Effective search space: 139812 Effective search space used: 139812 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