Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_038211315.1 Q392_RS19580 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000745855.1:WP_038211315.1 Length = 429 Score = 272 bits (696), Expect = 1e-77 Identities = 166/418 (39%), Positives = 224/418 (53%), Gaps = 45/418 (10%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEH---------QGFEYSRTHNPTRFAY 69 T ++H G SP+P+T AV+PPIY T YA S +H G Y+R NPT+ Sbjct: 9 TRSVHAGYSPEPTTKAVVPPIYQTVAYAFDS-AQHGADLFDLKVPGNIYTRIMNPTQDVL 67 Query: 70 ERCVAALEGGTRAFAFASG-MAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAG 128 E+ VAALEGG A A ASG MA T + + +AG ++V+ LYGGT+ LF + G Sbjct: 68 EQRVAALEGGIAALALASGQMAITYAIQTITEAGDNIVSSTALYGGTYNLFAHTLPQF-G 126 Query: 129 LDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTF 188 + F D DPA+F I TK V++E+ NP + DIAAIA IA +HG+ +VDNT Sbjct: 127 IHVRFADHRDPASFGKLIDERTKAVFVESLGNPAGNITDIAAIAAIAHQHGVPLIVDNTV 186 Query: 189 ASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAV------------------------ 224 SP L RP+ GAD+VVHS TKYL GH VGG V Sbjct: 187 PSPYLLRPIEHGADIVVHSLTKYLGGHGTSVGGAIVDSGKFPWAQHKERFRRLNEPDVSY 246 Query: 225 --------VGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALA 276 +G A + + GG PF++FL L+G++TL LRM C+N L +A Sbjct: 247 HGVVYTEALGPAAYIGRARVVPLRNTGGAISPFNAFLILQGIETLALRMDRICDNTLRVA 306 Query: 277 QWLETHPAIEKVIYPGLASHPQHVLAKRQMSG-FGGIVSIVLKGGFDAAKRFCEKTELFT 335 + L+ HPA+ V Y GL HP H LAK+ M G G+++ + GG +F + +LFT Sbjct: 307 RHLKAHPAVRWVNYAGLEDHPDHALAKKYMGGRASGLLTFGIGGGRAEGAKFLDALQLFT 366 Query: 336 LAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 ++G V SL HPA TH + + G+S+ VRL VGIE + DL DL++AL Sbjct: 367 RLVNIGDVRSLATHPASTTHRQLSPEELAKAGVSEETVRLCVGIEHIDDLLADLDQAL 424 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: 526 Number of extensions: 27 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: 429 Length adjustment: 31 Effective length of query: 366 Effective length of database: 398 Effective search space: 145668 Effective search space used: 145668 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 Jul 25 2024. The underlying query database was built on Jul 25 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