Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_011372397.1 SUDEN_RS04000 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000012965.1:WP_011372397.1 Length = 421 Score = 192 bits (487), Expect = 2e-53 Identities = 124/418 (29%), Positives = 210/418 (50%), Gaps = 16/418 (3%) Query: 11 TTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALE 70 T LH K + G++ PI+ + + + A++F KQ G Y R NPT E Sbjct: 5 TRALHEGYTKDSQ-GTMAVPIYQTTAYEFNSVEHAADLFSLKQLGNIYTRLNNPTTDVFE 63 Query: 71 DKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSL-WMTVGAQGAK 129 + +E G++ + ++GM+A + G+++V + L+G + +L T+ G + Sbjct: 64 KRFASLEGGEAALATSSGMSATFFAIVNATAAGENIVCAKQLYGGSLTLNTHTLKRFGIE 123 Query: 130 VSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTS 189 D D+ ++E+ I TR++F E++ NP VAD++ I ++ + GIL VVDNT+ + Sbjct: 124 ARYFDVHDMSSLESLIDDKTRVIFFESLTNPSIDVADIEAITKIADKYGILSVVDNTVAT 183 Query: 190 PYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTRYPHIAENYKKNPAPQW- 248 P L RP GA +VV+S +K G G A+GG L + + + NP P + Sbjct: 184 PVLCRPFEFGADIVVHSASKYTTGQGLAIGGILVERKNLVEKLRSNPRYEHFNNPDPSYH 243 Query: 249 GMAQI-----------RAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQM 297 G+ + R RD G L P + G ET++LR + KNALALA+ Sbjct: 244 GLIYVNIGLPPFTLRARLSLSRDLGAVLSPFNSWLFIQGIETLSLRMKEHSKNALALAEF 303 Query: 298 LQADERVAAVYYPGLESHPQHALSKALF--RSFGSLMSFELKDGIDCFDYLNRLRLAIPT 355 L++ +V V YPGL+S+ + ++ F L+SFE+ + ++ +L Sbjct: 304 LESHPKVKKVNYPGLKSNANYKNAQKYFDGGECSGLLSFEVASLQEATKIVDATKLYSLV 363 Query: 356 SNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 N+GD+++++ A T ++ + + G+ LIR+S GLE DL+ D +QAL+A Sbjct: 364 VNIGDSKSIITHPASTTHQQLNEQELIACGVPSGLIRISCGLESIKDLIDDMKQALEA 421 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: 415 Number of extensions: 18 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: 421 Length adjustment: 31 Effective length of query: 382 Effective length of database: 390 Effective search space: 148980 Effective search space used: 148980 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