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_012171767.1 AZC_RS16705 hypothetical protein
Query= BRENDA::B3TNN8 (394 letters) >NCBI__GCF_000010525.1:WP_012171767.1 Length = 389 Score = 240 bits (612), Expect = 6e-68 Identities = 147/386 (38%), Positives = 221/386 (57%), Gaps = 25/386 (6%) Query: 10 GGISEDKATGAVSVP-IYMASTFHQQKIGE---------NQYEYSRSGNPTREAVEKLIA 59 GG S + A +VP I+ S F + +Q YSR NPT A E+ +A Sbjct: 14 GGWSREVNLLAAAVPPIFQTSLFTFDTYADMAAVYAGRSHQLIYSRGDNPTVMAFERAVA 73 Query: 60 ELEGGTAGFAFASGSAAID-TVFSMFSAGDHFVIGNDVYGGTFRLIDAVLKRFGMTFTVV 118 ELEG AG AF+SG AI TV ++ SAGD V +VY +RL + +L RFG+ V Sbjct: 74 ELEGAEAGRAFSSGMGAISATVLALVSAGDRIVTVRNVYSDAYRLFELMLSRFGVVVDYV 133 Query: 119 DTRDLAAVEEAITPNTKAIYLETPTNPLLRVTDIAAVAKIAKSHQILSIIDNTFSSPYVQ 178 D D AVE A+ P K +YLE+PT+ + DIA +A+ A++H ++S+IDN++++P Q Sbjct: 134 DGTDAEAVE-AVLPGAKLLYLESPTSLAFELQDIARLARAARTHGVVSVIDNSWATPLFQ 192 Query: 179 RPLEQGVDIVLHSASKYLGGHSDVIAGLVVTKDDQLAEKIGYLQNA----IGGILAPQES 234 RP+ GVD+V+H+ASKYLGGHSD +AG+VV AE +G + + +G L+P E+ Sbjct: 193 RPIAHGVDLVVHAASKYLGGHSDTVAGVVVGS----AELVGRINASSYAYLGAKLSPFEA 248 Query: 235 WLLQRGIKTLSLRMRAHLANAEAVFNYLSNQPLVSKIYYPGDPNNPDYEVAKKQMHGFGA 294 WLL RG+ TL +RM H+++ A+ L P V + +P ++P + + GF Sbjct: 249 WLLLRGLHTLPMRMARHMSSGLALAERLRAHPDVELVRHPAFSDHP----GRASLSGFAG 304 Query: 295 MISFELQDGLDPKQFVEQLHVITLAESLGALESLIEIPALMTHGSIPRDIRLKNGIKDEL 354 + SFE+ + +D FV+ L ++ + S G ESL+ +PAL + + GI L Sbjct: 305 VFSFEVGEAIDVPTFVDALRLVRIGVSWGGPESLV-VPALAPLQLAKANCFARFGISPRL 363 Query: 355 IRLSVGVEDQKDLLADLERGFNELKR 380 IRLS G+ED+ + AD+E+ + +R Sbjct: 364 IRLSAGMEDETLIWADIEQALHGARR 389 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: 357 Number of extensions: 21 Number of successful extensions: 7 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: 394 Length of database: 389 Length adjustment: 31 Effective length of query: 363 Effective length of database: 358 Effective search space: 129954 Effective search space used: 129954 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