Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate Dsui_2039 Dsui_2039 OAH/OAS sulfhydrylase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__PS:Dsui_2039 Length = 428 Score = 248 bits (632), Expect = 3e-70 Identities = 153/429 (35%), Positives = 232/429 (54%), Gaps = 35/429 (8%) Query: 7 YGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTV 66 +GF T LH+ + GS PI+ + + ++ A +F + G Y R NPTV Sbjct: 6 FGFDTLSLHAGQVPDAATGSRATPIYQTAAYVFDSPEHAASLFNLQTFGNVYSRLSNPTV 65 Query: 67 AALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNS-LWMTVGA 125 A LE++I +E GK+ + A+GMAA + L GD +V++ L+G T++ L + Sbjct: 66 AVLEERIAALEGGKAAVAVASGMAAQMVALLNLCEAGDEIVAARTLYGGTHTQLDVNFRK 125 Query: 126 QGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDN 185 G VD+ D +N AIT T++++ ET+ NP V D++ + + G+ VDN Sbjct: 126 LGINTIFVDSDDPENFAKAITPRTKVIYAETMGNPGLNVLDIEAVARIANAAGLPLFVDN 185 Query: 186 TMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT--RYPHIAENYKKN 243 T SPYL RP GA +VV+S TK IGGHG LGG + ++G+F W ++ + E Sbjct: 186 TFASPYLCRPFEWGAAIVVHSATKFIGGHGTTLGGIIVESGKFPWDNGKFATMTE----- 240 Query: 244 PAPQWG-------------MAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKN 290 P+P + A+ R + LR FG +L P A + G ET++LR +R C N Sbjct: 241 PSPGYHGVKFYETFGNFGFTAKCRMEGLRTFGPALSPFNAFLLLQGVETLSLRMDRHCSN 300 Query: 291 ALALAQMLQADERVAAVYYPGLESHPQHALS-KALFRSFGSLMSFELKDG-------IDC 342 ALA+A+ L+A +V V YPGL S H L+ K L + G++++F +K G ID Sbjct: 301 ALAIARHLEAHPQVEWVNYPGLPSSKYHDLAQKYLPKGAGAVLTFGIKGGAAAGQEFIDS 360 Query: 343 FDYLNRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDD 402 ++L+ L +N+GD +TLVI A T +M E++ + G+ LIR+SVGLE DD Sbjct: 361 VEFLSHL------ANIGDAKTLVIHPASTTHRQMTPEQQTAAGVPPDLIRLSVGLETLDD 414 Query: 403 LVADFRQAL 411 ++ D QAL Sbjct: 415 ILWDIDQAL 423 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: 425 Number of extensions: 29 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: 428 Length adjustment: 32 Effective length of query: 381 Effective length of database: 396 Effective search space: 150876 Effective search space used: 150876 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 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