Align cystathionine gamma-lyase (subunit 2/2) (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_013450565.1 CALNI_RS02185 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::B3TNN8 (394 letters) >NCBI__GCF_000183405.1:WP_013450565.1 Length = 426 Score = 210 bits (535), Expect = 5e-59 Identities = 140/421 (33%), Positives = 217/421 (51%), Gaps = 53/421 (12%) Query: 7 LIHGGISEDKATGAVSVPIYMAST--FHQQKIGENQYE-------YSRSGNPTREAVEKL 57 L+H G D TGA +VPIY ++ F N + Y+R NPT++ +EK Sbjct: 8 LLHYGYEPD-GTGARAVPIYQTTSYVFKSTDHAANLFALKEFGNIYTRLMNPTQDVLEKR 66 Query: 58 IAELEGGTAGFAFASGSAAID-TVFSMFSAGDHFVIGNDVYGGTFRLIDAVLKRFGMTFT 116 +A L GT+ A +SG AI ++ ++ S GD+ V + +YGGT+ L +K+ Sbjct: 67 LAALHKGTSAIAVSSGQTAITYSILNITSPGDNIVSTSFLYGGTYNLFKYTMKKLCREVR 126 Query: 117 VVDTRDLAAVEEAITPNTKAIYLETPTNPLLRVTDIAAVAKIAKSHQILSIIDNTFSSPY 176 VD+ AI NTKAIY+E+ NP V D A+A IA H I I+DNT SPY Sbjct: 127 FVDSSKPENFANAIDENTKAIYIESIGNPKNNVNDYKAIADIAHKHGIPLIVDNTV-SPY 185 Query: 177 VQRPLEQGVDIVLHSASKYLGGHSDVIAGLVVTKDD---------QLAE----------- 216 + P E G DIV++S +K+ G+ + G +V K D ++ E Sbjct: 186 ILNPFEYGADIVVYSLTKFATGNGTSLGGAIVEKGDFPWNNGKFNEMTEPDDSYHGLVYW 245 Query: 217 -KIGYLQNA------------------IGGILAPQESWLLQRGIKTLSLRMRAHLANAEA 257 G+ A +G ++P ++++ G++TL LRM+ H NA Sbjct: 246 DAFGWHDKAAARGCIFTQKIRLQLLRDMGACISPFNAFMIIEGLETLPLRMKKHCDNALK 305 Query: 258 VFNYLSNQPLVSKIYYPGDPNNPDYEVAKKQMHG-FGAMISFELQDGLDP-KQFVEQLHV 315 V +L P V + YPG P++PD+E AKK + G +GA+I F ++ G + K+F+ L + Sbjct: 306 VAEFLEKHPNVGWVNYPGLPSHPDHENAKKYLKGNYGAIIGFGVKGGYEAGKRFINSLKM 365 Query: 316 ITLAESLGALESLIEIPALMTHGSIPRDIRLKNGIKDELIRLSVGVEDQKDLLADLERGF 375 I+ ++G SL+ PA TH + + R+K+G+ D+ IRLSVG+E+ +D++ DL Sbjct: 366 ISHLANIGDARSLVIHPASTTHQQLSPEDRIKSGVTDDFIRLSVGIENVEDIIEDLNNAL 425 Query: 376 N 376 N Sbjct: 426 N 426 Lambda K H 0.317 0.134 0.376 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: 417 Number of extensions: 25 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: 394 Length of database: 426 Length adjustment: 31 Effective length of query: 363 Effective length of database: 395 Effective search space: 143385 Effective search space used: 143385 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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