Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate 5210267 Shew_2710 O-acetylhomoserine/O-acetylserine sulfhydrylase (RefSeq)
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__PV4:5210267 Length = 429 Score = 240 bits (613), Expect = 5e-68 Identities = 142/407 (34%), Positives = 221/407 (54%), Gaps = 28/407 (6%) Query: 30 PIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDKITKMEDGKSTICFATGM 89 PI+ + ++ ++D + A++F K G Y R NPT LE ++ +E G + A+GM Sbjct: 24 PIYQTTSYTFDDTQHGADLFDLKVAGNIYTRIMNPTTDVLEQRLAAIEGGIGALALASGM 83 Query: 90 AAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAKVSMVDATDVKNVEAAITAN 148 AAI +Q L + GD++VS++ L+G T +L+ T+ QG +V M D +EA I Sbjct: 84 AAITYAIQALTQVGDNIVSTSQLYGGTYNLFAHTLPRQGVEVRMAAFDDFDGLEAHIDDK 143 Query: 149 TRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPYLFRPKTVGAGLVVNSLT 208 T+ +F E+I NP + D+ R+ E+ G+ +VDNT+ +P L RP GA +V++SLT Sbjct: 144 TKALFCESIGNPAGNIVDIARLAEIAHRHGVPLIVDNTVATPVLCRPFEHGADIVIHSLT 203 Query: 209 KSIGGHGNALGGALTDTGEFDWTRYP------------HIAENYKKNPAPQWGMAQIRAK 256 K IGGHG +GG + D+G+FDW P + Y + P + + R Sbjct: 204 KYIGGHGTTIGGVIIDSGKFDWAAQPQRFALLNEPDPSYHGVVYTQAFGPAAFIGRCRVV 263 Query: 257 ALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYYPGLESHP 316 LR+ G +L P++A + G ET+ALR ER C NALALA L+ D RV+ V Y L++ P Sbjct: 264 PLRNTGAALSPQSAFLLLQGLETLALRMERHCDNALALANFLEQDPRVSWVNYGALDNSP 323 Query: 317 -QHALSKALFRSFGSLMSFELKDGIDCFD----------YLNRLRLAIPTSNLGDTRTLV 365 + K ++SF GI D +++ L++ + N+GD ++L Sbjct: 324 YRDNCEKITSGKASGIISF----GIKAEDSEAAKAAGGRFIDALQMILRLVNIGDAKSLA 379 Query: 366 IPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALD 412 A T ++ E A G++E LIR+SVG+E +D++AD QALD Sbjct: 380 CHPATTTHRQLNGEELAKAGVSEDLIRISVGIEHIEDIIADVSQALD 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: 488 Number of extensions: 31 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: 429 Length adjustment: 32 Effective length of query: 381 Effective length of database: 397 Effective search space: 151257 Effective search space used: 151257 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