Align cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_013089932.1 BC1002_RS10060 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::A0A0M3VI47 (457 letters) >NCBI__GCF_000092885.1:WP_013089932.1 Length = 445 Score = 202 bits (513), Expect = 2e-56 Identities = 140/403 (34%), Positives = 203/403 (50%), Gaps = 45/403 (11%) Query: 96 AVSTPIYQTATFK-----QPSATVN---GPYDYTRSGNPTRDALERLLAKLDKADRAFCF 147 A +TPIYQT +F +A N + Y+R NPT E +A L+ A Sbjct: 23 ARATPIYQTTSFSFRDSDHAAALFNMERAGHVYSRISNPTVAVFEERVAALENGAGAIGT 82 Query: 148 GSGMAALS-AVSQLFENGDEIIAGDDIYGGSDRLLSSVIPRTGVVVKRVNTSDLEEVASA 206 SG AAL A++ L G I+A +YGGS LL + R G+ V DL+ +A Sbjct: 83 ASGQAALHLAIATLMGAGSHIVASSALYGGSHNLLHYTLRRFGIETTFVKPGDLDAWRAA 142 Query: 207 FGPATKLVWLESPTNPRLQISDIGKIAEMAHARGVLVLVDNSIMSPVLCQPLELGADIVM 266 P T+L++ E+ NP L++ DI +A++A A V +LVD++ +P L +P E GAD V Sbjct: 143 LRPNTRLLFGETLGNPGLEVLDIAALAQIARAHRVPLLVDSTFTTPYLLRPFEHGADFVY 202 Query: 267 HSATKFIGGHSYIMAGVIAVKGERLAKE-----------------MYFLQNAV------- 302 HSATKF+GGH + GV+ V G R E M F + + Sbjct: 203 HSATKFLGGHGTTIGGVL-VDGGRFDFEASGLFLEFTEPYDGFHGMVFAEESTVAPFLLR 261 Query: 303 ---------GSGLAPFDCWLCLQGIKTMELRVEKQQKSAQKIAEFLAFHPRVKKVNYAGL 353 G+ L P W LQGI+T+ LR+E+ + +++ +FLA H V+ V Y L Sbjct: 262 ARREGLRDFGACLHPQAAWQLLQGIETLPLRMERHVANTRRVVDFLAGHAAVESVAYPEL 321 Query: 354 PGHPGRDL-HYSQAKGAGSVLSF-LTGSLALSKHVVESTKYFSITVSFGSVKSLISMPCF 411 P HP L +GAG+V SF L G A + +E+ FS + G +SL+ P Sbjct: 322 PTHPDHALAKRLLPRGAGAVFSFNLRGDRAAGRAFIEALTLFSHLANVGDARSLVIHPAS 381 Query: 412 MSHASIPVAVREARGLTEDLVRISVGIENVDDLIADLDQALSS 454 +H + A A G+TE +R+S+G+E+ DDLI DL +AL + Sbjct: 382 TTHFRMDAAALAAAGITEGTIRLSIGLEDPDDLIDDLKRALKA 424 Lambda K H 0.318 0.134 0.386 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: 407 Number of extensions: 26 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: 457 Length of database: 445 Length adjustment: 33 Effective length of query: 424 Effective length of database: 412 Effective search space: 174688 Effective search space used: 174688 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 (21.7 bits) S2: 51 (24.3 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