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_028586001.1 G494_RS0120435 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::B3TNN8 (394 letters) >NCBI__GCF_000429965.1:WP_028586001.1 Length = 427 Score = 230 bits (587), Expect = 5e-65 Identities = 147/413 (35%), Positives = 222/413 (53%), Gaps = 42/413 (10%) Query: 3 FDTKLIHGGISEDKATGAVSVPIYMASTFHQQK---------IGENQYEYSRSGNPTREA 53 F+T+ +H G D ATG+ +VPIY +++ + + E Y+R NPT + Sbjct: 10 FNTRQLHAGQVADPATGSRAVPIYQTTSYAFKDSQHAADLFALKEAGNIYTRIMNPTTDV 69 Query: 54 VEKLIAELEGGTAGFAFASGSAAIDTVF-SMFSAGDHFVIGNDVYGGTFRLIDAVLKRFG 112 +E+ +A+LEGG A +SG A F ++ GDH V N +YGGT+ + L R G Sbjct: 70 LEQRLADLEGGVGALAASSGHGAQVMAFLTICGQGDHIVSSNSLYGGTYTQLQYTLPRLG 129 Query: 113 MTFTVVDTRDLAAVEEAITPNTKAIYLETPTNPLLRVTDIAAVAKIAKSHQILSIIDNTF 172 +T + D RD + AI PNTK IY ET NP L V VA IA + QI +IDNT Sbjct: 130 ITVSFADPRDPESFARAIQPNTKLIYGETLGNPALTVFPFEEVAAIAAAVQIPLVIDNTL 189 Query: 173 SSPYVQRPLEQGVDIVLHSASKYLGGHSDVIAGLVV---------------TKDDQLAEK 217 ++PY+ RPLE G +IV HS +K+L GH + I G++V T+ D Sbjct: 190 ATPYLCRPLEWGANIVSHSTTKFLNGHGNSIGGILVDGGNFDWQSGKISSFTEPDPSYHG 249 Query: 218 IGYLQ---------------NAIGGILAPQESWLLQRGIKTLSLRMRAHLANAEAVFNYL 262 + Y + IG AP SWL +GI+TLSLRM H+ANA +L Sbjct: 250 LIYAELGAPAFILKARVQVLRDIGVSQAPFNSWLTVQGIETLSLRMERHVANALETARFL 309 Query: 263 SNQPLVSKIYYPGDPNNPDYEVAKKQM-HGFGAMISFELQDGLDP-KQFVEQLHVITLAE 320 VS + YPG ++PD+ A + + G GA+I+F +Q G++ ++F++ L + + Sbjct: 310 EGHARVSWVSYPGLSSHPDHGRACRYLPQGAGAVIAFGIQGGVEAGRRFIDHLQLFSHVA 369 Query: 321 SLGALESLIEIPALMTHGSIPRDIRLKNGIKDELIRLSVGVEDQKDLLADLER 373 ++G +SL PA TH + L+ G+++E+IRLS+G+ED +D+ DL++ Sbjct: 370 NVGDAKSLAIHPASTTHSQLSPAELLEAGVQEEMIRLSIGLEDLEDIFWDLDQ 422 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: 412 Number of extensions: 21 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: 1 Length of query: 394 Length of database: 427 Length adjustment: 31 Effective length of query: 363 Effective length of database: 396 Effective search space: 143748 Effective search space used: 143748 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