Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_050461123.1 AKL27_RS02665 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_001189915.1:WP_050461123.1 Length = 423 Score = 259 bits (662), Expect = 1e-73 Identities = 158/422 (37%), Positives = 222/422 (52%), Gaps = 45/422 (10%) Query: 15 LSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEH---------QGFEYSRTHNPT 65 + L T+A+HGG SPDP+T A PIY T +YA +H G Y+R NPT Sbjct: 1 MRLETIAVHGGYSPDPTTKAAAVPIYQTVSYAFDDT-QHGADLFDLKVAGNIYTRIMNPT 59 Query: 66 RFAYERCVAALEGGTRAFAFASGMAA-TSTVMELLDAGSHVVAMDDLYGGTFRLFERVRR 124 + E+ VA LEGG A A ASG AA T + + +AG ++V+ LYGGT+ LF Sbjct: 60 QDVLEKRVAELEGGIAALALASGQAAITYAIQTIAEAGDNIVSASTLYGGTYNLFAHTLP 119 Query: 125 RTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVV 184 + G++ F D DP +F I TK V++E+ NP+ + DI IA IA +HG+ +V Sbjct: 120 QF-GIETRFADYRDPESFGKLIDDKTKAVFVESIGNPLGNITDIEKIAEIAHRHGVPLIV 178 Query: 185 DNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAV-------------------- 224 DNT SP L RP+ GAD+VVHS TKYL GH + +GG V Sbjct: 179 DNTVPSPYLLRPIDFGADIVVHSLTKYLGGHGNSLGGAIVDSGKFPWAEHKQKFKRLNEP 238 Query: 225 ------------VGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENA 272 +G A + + G PF++FL L+G++TL LRM N Sbjct: 239 DVSYHGVVYTEALGAAAYIGRARVVPLRNTGAAISPFNAFLILQGIETLALRMERITSNT 298 Query: 273 LALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGF-GGIVSIVLKGGFDAAKRFCEKT 331 +AQ+L+ H ++ V Y GL HP H LA++ + G GI++ +KGG RF + Sbjct: 299 AHIAQFLQQHAKVQWVNYAGLPDHPDHALAQKYLGGRPSGILTFGVKGGLAGGTRFQDAL 358 Query: 332 ELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLER 391 +LFT ++G +SL HPA TH + + G+++ VRLS+GIE + DL DLE+ Sbjct: 359 KLFTRLVNIGDAKSLACHPASTTHRQLNPEELVKAGVTEDTVRLSIGIEHIDDLLADLEQ 418 Query: 392 AL 393 AL Sbjct: 419 AL 420 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: 509 Number of extensions: 23 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 397 Length of database: 423 Length adjustment: 31 Effective length of query: 366 Effective length of database: 392 Effective search space: 143472 Effective search space used: 143472 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 10 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