Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate YP_002825570.1 NGR_c10280 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000018545.1:YP_002825570.1 Length = 427 Score = 258 bits (659), Expect = 2e-73 Identities = 152/423 (35%), Positives = 234/423 (55%), Gaps = 24/423 (5%) Query: 8 GFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVA 67 GF+T +H+ Q G+ PI+ + +F + DA A +F +Q G Y R NPT A Sbjct: 7 GFSTLAVHAGAQPDPTTGARATPIYQTTSFVFNDADHAAALFGLQQFGNIYSRIMNPTQA 66 Query: 68 ALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSLWMTVGAQ 126 LE++I +E G + + A+G AA + ++ GD+ V++ L+G + N + Sbjct: 67 VLEERIAALEGGTAALATASGHAAQLLVFHTIMGPGDNFVAARQLYGGSVNQFGQAFKSF 126 Query: 127 GAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNT 186 +V D D ++ E I A T+ +FVE++ANP D+ I E+ R G+ +VDNT Sbjct: 127 DWQVRWADCADPESFETQIDARTKAIFVESLANPGGIFVDIAAIAEVARRHGLPLIVDNT 186 Query: 187 MTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT---RYPHIAENYKKN 243 M +PYL RP GA +VV+SLTK IGGHGN++GG + D G FDW+ +YP ++E Sbjct: 187 MATPYLVRPLEHGADIVVHSLTKFIGGHGNSMGGIIVDGGTFDWSKSGKYPLLSE----- 241 Query: 244 PAPQWGMAQI-------------RAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKN 290 P P++G + R LRDFG ++ P A I G ET+ LR +R C N Sbjct: 242 PRPEYGGVVLHQAFGNFAFAIAARVLGLRDFGPAISPFNAFLIQTGVETLPLRMQRHCDN 301 Query: 291 ALALAQMLQADERVAAVYYPGLESHPQHALSKALF-RSFGSLMSFELKDGIDCFD-YLNR 348 ALA+A+ L+ + V+ + Y GLE P HAL K + G++ +F L G + ++ Sbjct: 302 ALAVARWLKGRDEVSWIRYAGLEDDPNHALQKRYSPKGAGAVFTFGLSGGYEAGKRFVEG 361 Query: 349 LRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFR 408 L + +N+GDTR+LVI A T ++ E++ + G ++R+S+G+ED DD++AD Sbjct: 362 LEMFSHLANIGDTRSLVIHPASTTHRQLTPEQQVAAGAGPDVVRLSIGIEDVDDIIADLE 421 Query: 409 QAL 411 QAL Sbjct: 422 QAL 424 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: 487 Number of extensions: 20 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