Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate GFF3618 Psest_3685 OAH/OAS sulfhydrylase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__psRCH2:GFF3618 Length = 425 Score = 251 bits (641), Expect = 3e-71 Identities = 142/399 (35%), Positives = 228/399 (57%), Gaps = 15/399 (3%) Query: 30 PIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDKITKMEDGKSTICFATGM 89 PI+ + ++ ++D + A++F K PG Y R NPT LE ++ +E G + + A+GM Sbjct: 24 PIYQTTSYAFDDTQHGADLFDLKVPGNIYTRIMNPTTDVLEQRVAALEGGVAALAVASGM 83 Query: 90 AAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAKVSMVDATDVKNVEAAITAN 148 AAI +Q + GD++VS A L+G T +L+ T+ QG +V D+ +E+ I Sbjct: 84 AAITYAIQTIAEVGDNIVSVAKLYGGTYNLFAHTLPRQGIEVRFAAHDDIAALESLIDER 143 Query: 149 TRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPYLFRPKTVGAGLVVNSLT 208 T+ VF E+I NP V DL + E G+ +VDNT+ +P L RP GA +VV+SLT Sbjct: 144 TKAVFCESIGNPAGNVIDLAALAEAAHRHGVPLIVDNTVATPMLCRPFEHGADIVVHSLT 203 Query: 209 KSIGGHGNALGGALTDTGEFDWTRY---------PHIAEN---YKKNPAPQWGMAQIRAK 256 K +GGHG ++GG + D+G+F W ++ P ++ + Y + P + + R Sbjct: 204 KYMGGHGTSIGGIVVDSGKFPWAQHKKRFALLNTPDVSYHGVTYTEAFGPAAFIGRCRVV 263 Query: 257 ALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYYPGLESHP 316 LR+ G ++ P + I G ET+ALR ER C+NAL +A+ LQA +VA V Y GL HP Sbjct: 264 PLRNMGAAISPFNSFLILQGLETLALRMERHCENALKVAEFLQAHPQVAWVKYAGLPDHP 323 Query: 317 QHALSKALFRSF-GSLMSFELKDGIDC-FDYLNRLRLAIPTSNLGDTRTLVIPVAHTIFY 374 +H L++ S++ F ++ GI+ +++ L+L + N+GD ++L A T Sbjct: 324 EHELARRYMGGTPASILCFGIEGGIEAGARFIDALKLVVRLVNIGDAKSLACHPASTTHR 383 Query: 375 EMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 ++ A+ A G+++ LIR+S+G+E DD++AD QAL A Sbjct: 384 QLNADELARAGVSQDLIRLSIGIEHIDDILADLAQALSA 422 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: 471 Number of extensions: 26 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: 425 Length adjustment: 32 Effective length of query: 381 Effective length of database: 393 Effective search space: 149733 Effective search space used: 149733 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