Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_012970751.1 ALVIN_RS07635 aminotransferase class V-fold PLP-dependent enzyme
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000025485.1:WP_012970751.1 Length = 425 Score = 230 bits (587), Expect = 5e-65 Identities = 136/419 (32%), Positives = 227/419 (54%), Gaps = 16/419 (3%) Query: 11 TTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALE 70 T +H+ + S+ PI+ + ++ ++D + A++F K G Y R NPT LE Sbjct: 5 TLAIHAGFEPDPATKSVATPIYQTTSYAFDDTQHGADLFDLKVAGNIYTRIMNPTSDVLE 64 Query: 71 DKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAK 129 +++ +E G + A+GMAA+ + L + GD++++ + L+G + +L+ T+ G + Sbjct: 65 KRVSALEGGVGALALASGMAAVTNSILTLAQAGDNIIAVSTLYGGSYNLFAHTLPRLGIQ 124 Query: 130 VSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTS 189 V D++ + A I A T+ VF E+I NP VAD+ + ++ G+ +VDNT+ + Sbjct: 125 VRFAAPNDIEGMAAQIDARTKAVFCESIGNPAGNVADIAPMADMAHAHGVPLIVDNTVPT 184 Query: 190 PYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTRY---------PHIAEN- 239 PYL RP GA +VV++LTK +GGHG +GGAL D+G F W + P I+ + Sbjct: 185 PYLCRPFEHGADIVVHALTKYMGGHGTTIGGALVDSGRFPWAEHAERFSLLNEPDISYHG 244 Query: 240 --YKKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQM 297 Y + +A+ R LR+ G ++ P + I G ET+ +R +R C+NA+A+A Sbjct: 245 VVYTETMGEAAYIARARVVPLRNMGAAISPFNSFLILQGIETLPVRMDRHCENAIAVANY 304 Query: 298 LQADERVAAVYYPGLESHPQHALSKALF--RSFGSLMSFELKDGIDCFD-YLNRLRLAIP 354 LQ +VA V Y GL P + L + S++SF +K G + +++ L+L + Sbjct: 305 LQDHPKVAWVRYAGLPDSPDYPLVQRYMDGARASSILSFGIKGGRETGGRFIDALKLTVR 364 Query: 355 TSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 N+GD +TL A T ++ E G++E LIR+S+G+E DD++ D QAL A Sbjct: 365 LVNIGDAKTLACHPATTTHRQLSPEELKRAGVSEDLIRLSIGIEHIDDIIEDLDQALAA 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: 451 Number of extensions: 19 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 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