Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_012170707.1 AZC_RS11290 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000010525.1:WP_012170707.1 Length = 427 Score = 253 bits (645), Expect = 1e-71 Identities = 158/423 (37%), Positives = 221/423 (52%), Gaps = 42/423 (9%) Query: 12 DRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQ--------GFEYSRTHN 63 +R +TLAIH G PDP+TGA PIY T+++ G Y+R N Sbjct: 3 ERTPGFSTLAIHAGAQPDPTTGARATPIYQTTSFVFDDVDHAAALFGLQTFGNIYTRIGN 62 Query: 64 PTRFAYERCVAALEGGTRAFAFASGMAATSTVME-LLDAGSHVVAMDDLYGGTFRLFERV 122 PT E VAALEGGT A A ASG AA V LL +G VA LYGG+ F Sbjct: 63 PTVAVLEERVAALEGGTAALAVASGHAAQHLVFHTLLTSGDEFVASRKLYGGSINQFNHA 122 Query: 123 RRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLT 182 + + G + ++ D + ++F+ AI TK ++IE+ NP + DI AI+ +A+K G+ Sbjct: 123 FK-SYGWNVAWADPDNVSSFERAITPKTKAIFIESLANPGGIVTDIKAISAVAKKAGIPL 181 Query: 183 VVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAV------------------ 224 +VDNT A+P L RP+ GAD+V+HSATK+L GH + +GG+ V Sbjct: 182 IVDNTLATPYLWRPIEHGADIVIHSATKFLGGHGNSIGGVIVDAGTFDWTASGRYPFLTQ 241 Query: 225 -------------VGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCEN 271 G+ A +G PF++FL L G++TL LR++ H +N Sbjct: 242 PRPEYQGIVLHETFGNFAFAIAARVLGLRDLGPALSPFNAFLILTGIETLGLRVQRHSDN 301 Query: 272 ALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQM-SGFGGIVSIVLKGGFDAAKRFCEK 330 ALA+A +L THPA+E V Y GL H LAK + G G + + LKGG+ A Sbjct: 302 ALAVANFLSTHPAVEGVSYAGLPGDRYHDLAKAYLPKGAGAVFTFRLKGGYQAGVNLVSN 361 Query: 331 TELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLE 390 ELF+ ++G SL+ HPA TH + ++ G +VRLSVGIED+ D+ DL+ Sbjct: 362 VELFSHLANIGDTRSLIIHPASTTHRQLSDEQKTLAGAGPEVVRLSVGIEDVADIIADLD 421 Query: 391 RAL 393 +AL Sbjct: 422 QAL 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: 511 Number of extensions: 27 Number of successful extensions: 5 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: 427 Length adjustment: 31 Effective length of query: 366 Effective length of database: 396 Effective search space: 144936 Effective search space used: 144936 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