Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Ac3H11_34 Methionine gamma-lyase (EC 4.4.1.11)
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_34 Length = 434 Score = 310 bits (795), Expect = 4e-89 Identities = 176/399 (44%), Positives = 242/399 (60%), Gaps = 13/399 (3%) Query: 6 THSHDGDRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYA--------QSSPGEHQGFE 57 T + D A +T AIH G +P GA++PPI+ ++TYA + G+ G+ Sbjct: 2 TRTTDRSPATGFSTRAIHHGYNPADHQGALVPPIHTSATYAFPDVAYGARCFAGQEPGYF 61 Query: 58 YSRTHNPTRFAYERCVAALEGGTRAFAFASGMAA-TSTVMELLDAGSHVVAMDDLYGGTF 116 Y+R NPT E +AALE G A F SGM A T+T+ +L+ G ++A LYG TF Sbjct: 62 YTRIANPTLALLEGRLAALEEGAGAVVFGSGMGAITATLWSMLEPGDEILADLTLYGCTF 121 Query: 117 RLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIAR 176 R G+ VD+TDPA A+ A T+++++ETP NP ++LVDIAA++ +A Sbjct: 122 SFLHHGLGRF-GVTVRHVDMTDPARVAEALTAKTRVLYLETPANPNMRLVDIAAVSALAH 180 Query: 177 KHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMA 236 G VVDNT+ +P LQ+PL LGAD+ VHS TKYL GH D+ G AV D AELA+++ Sbjct: 181 AQGAKVVVDNTYCTPYLQQPLLLGADVSVHSMTKYLGGHGDLTAGAAVFAD-AELAQRVR 239 Query: 237 F--LQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLA 294 L++ G V D+ L +RGLKTL LRM HC++A +A+++ HPA V YPGL Sbjct: 240 LYGLKDMTGAVMSAQDAHLVMRGLKTLALRMDRHCQSAQKVAEFIAAHPAAAAVHYPGLP 299 Query: 295 SHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMT 354 S QH LAK+QM GG+++ L+GG A RF + +L T A SLG E+L HPA MT Sbjct: 300 SFAQHALAKQQMRQMGGMIAFELRGGLQAGVRFMDALQLVTRAVSLGDAETLAQHPASMT 359 Query: 355 HASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 H++ +R GI++ LVRLSVG+EDL DL D+ +AL Sbjct: 360 HSTYTPEQRAAHGIAEGLVRLSVGLEDLDDLLADIGQAL 398 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: 497 Number of extensions: 24 Number of successful extensions: 5 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: 434 Length adjustment: 31 Effective length of query: 366 Effective length of database: 403 Effective search space: 147498 Effective search space used: 147498 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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