Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate Echvi_3411 Echvi_3411 OAH/OAS sulfhydrylase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__Cola:Echvi_3411 Length = 436 Score = 225 bits (574), Expect = 2e-63 Identities = 142/426 (33%), Positives = 228/426 (53%), Gaps = 22/426 (5%) Query: 7 YGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTV 66 + F T LH+ + S PI+ + ++ + A A +F K+ G Y R NPT Sbjct: 6 FKFETLQLHAGHEPDSNTNSRAVPIYQTSSYVFNSAEHGANLFGLKEFGNIYTRIMNPTN 65 Query: 67 AALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSLWMTVGA 125 E ++ +E G + + ++G AA + +L GD+ V+S FL+G T N ++ Sbjct: 66 DVFEKRMAALEGGVAALAVSSGQAAQFIALSNILENGDNFVTSPFLYGGTYNQFKVSFKR 125 Query: 126 QGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDN 185 G + +++E I T+ ++VETI NP V D + + L ++ I VVDN Sbjct: 126 LGISARFASSEKAEDMEKLIDDRTKALYVETIGNPGFNVPDFEALSALSKKHDIPLVVDN 185 Query: 186 TM-TSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT--RYPHIAE---- 238 T YLFRP GA +VV S TK IGGHG ++GG + D G ++W ++P +E Sbjct: 186 TFGAGGYLFRPLAHGAHIVVASATKWIGGHGTSIGGIIVDGGNYNWGNGKFPQFSEPSEG 245 Query: 239 ----NY-----KKNPAPQWGMA---QIRAKALRDFGGSLGPEAAHHIAVGAETIALRQER 286 N+ + NP +A + R + LRDFG ++ P + + G ET++LR ER Sbjct: 246 YHGLNFWEVFGEGNPLGLPNIAFSIRARVEGLRDFGPAISPFNSFLLLQGLETLSLRAER 305 Query: 287 ECKNALALAQMLQADERVAAVYYPGLESHPQHALSKA-LFRSFGSLMSFELKDGIDCFDY 345 +NAL LA+ L+ +VA V YPGLESH H L+K L + FG +++FE+K G + + Sbjct: 306 TVENALTLAKWLENHPQVATVSYPGLESHGHHTLAKKYLKKGFGGVLTFEVKGGKEAGEK 365 Query: 346 L-NRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLV 404 L + L+L +N+GD +TL+I + T ++ + +A+ G+ ++R+S+G+E DD+ Sbjct: 366 LVDSLQLISHLANVGDAKTLIIQPSATTHQQLSEKEQAAAGVTPGMLRISLGIEHIDDIC 425 Query: 405 ADFRQA 410 AD QA Sbjct: 426 ADLEQA 431 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: 462 Number of extensions: 21 Number of successful extensions: 6 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: 436 Length adjustment: 32 Effective length of query: 381 Effective length of database: 404 Effective search space: 153924 Effective search space used: 153924 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 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