Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_028586001.1 G494_RS0120435 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000429965.1:WP_028586001.1 Length = 427 Score = 228 bits (582), Expect = 2e-64 Identities = 141/423 (33%), Positives = 223/423 (52%), Gaps = 14/423 (3%) Query: 4 KKTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGN 63 ++ GF T LH+ + GS PI+ + ++ ++D++ A++F K+ G Y R N Sbjct: 5 QRQLGFNTRQLHAGQVADPATGSRAVPIYQTTSYAFKDSQHAADLFALKEAGNIYTRIMN 64 Query: 64 PTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSLWMT 122 PT LE ++ +E G + ++G A + +GDH+VSS L+G T L T Sbjct: 65 PTTDVLEQRLADLEGGVGALAASSGHGAQVMAFLTICGQGDHIVSSNSLYGGTYTQLQYT 124 Query: 123 VGAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYV 182 + G VS D D ++ AI NT+L++ ET+ NP V + + + I V Sbjct: 125 LPRLGITVSFADPRDPESFARAIQPNTKLIYGETLGNPALTVFPFEEVAAIAAAVQIPLV 184 Query: 183 VDNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT--RYPHIAEN- 239 +DNT+ +PYL RP GA +V +S TK + GHGN++GG L D G FDW + E Sbjct: 185 IDNTLATPYLCRPLEWGANIVSHSTTKFLNGHGNSIGGILVDGGNFDWQSGKISSFTEPD 244 Query: 240 -------YKKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNAL 292 Y + AP + + + R + LRD G S P + G ET++LR ER NAL Sbjct: 245 PSYHGLIYAELGAPAF-ILKARVQVLRDIGVSQAPFNSWLTVQGIETLSLRMERHVANAL 303 Query: 293 ALAQMLQADERVAAVYYPGLESHPQHALS-KALFRSFGSLMSFELKDGIDC-FDYLNRLR 350 A+ L+ RV+ V YPGL SHP H + + L + G++++F ++ G++ +++ L+ Sbjct: 304 ETARFLEGHARVSWVSYPGLSSHPDHGRACRYLPQGAGAVIAFGIQGGVEAGRRFIDHLQ 363 Query: 351 LAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQA 410 L +N+GD ++L I A T ++ G+ E +IR+S+GLED +D+ D QA Sbjct: 364 LFSHVANVGDAKSLAIHPASTTHSQLSPAELLEAGVQEEMIRLSIGLEDLEDIFWDLDQA 423 Query: 411 LDA 413 L A Sbjct: 424 LTA 426 Lambda K H 0.319 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: 438 Number of extensions: 16 Number of successful extensions: 4 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: 413 Length of database: 427 Length adjustment: 32 Effective length of query: 381 Effective length of database: 395 Effective search space: 150495 Effective search space used: 150495 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