Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_004511499.1 GMET_RS07870 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000012925.1:WP_004511499.1 Length = 414 Score = 296 bits (759), Expect = 6e-85 Identities = 173/413 (41%), Positives = 248/413 (60%), Gaps = 6/413 (1%) Query: 5 KTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNP 64 + + T ++H + G G+ PI S +F +E A L ++F+G++ G+ Y R NP Sbjct: 3 RDFQLDTLLIHGGLEPG-PAGATTVPIVQSSSFAHETAEDLEDIFRGRKAGHVYTRINNP 61 Query: 65 TVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TV 123 T +LE ++ +E G S I ++GMAAI V ++R GD ++SSA LFG T SL+ T+ Sbjct: 62 TTESLERRLALLEGGISAIATSSGMAAITLAVLSIVRCGDEILSSASLFGGTFSLFRDTL 121 Query: 124 GAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVV 183 G VD +D+ + AA+T TRL+FVET+ NPR V DL + + RE G+ VV Sbjct: 122 SNYGIATRFVDPSDLAAMRAAVTERTRLIFVETMGNPRLDVPDLAALAAIAREAGVPLVV 181 Query: 184 DNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTR--YPHIAENYK 241 D T+T+P L R K +GA ++V+S +K I G G+A+GGA+ D G FDW R YPH E Y Sbjct: 182 DATVTTPVLGRVKELGADIIVHSTSKYINGTGSAIGGAIIDCGTFDWRRESYPHF-EPYV 240 Query: 242 KNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQAD 301 K A+ R +D G P ++ ++ G ET+ALR ER C NA LA+ L A Sbjct: 241 KKFRQFAFSARARKLIHKDLGACPAPMNSYLLSEGIETMALRMERNCANAQRLAEFLAAH 300 Query: 302 ERVAAVYYPGLESHPQHALSKALFRS-FGSLMSFELKDGIDCFDYLNRLRLAIPTSNLGD 360 +VA V YPGL S P H +KA F +G+L++F L D F ++ LRLA +N+GD Sbjct: 301 PKVAWVNYPGLTSSPWHETAKAQFGGRYGALLTFGLADKAAAFHCIDGLRLAKNLANIGD 360 Query: 361 TRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 T+TLVI A TI + G E +A MG++E +IRVSVG+E DD++ DF ++L+A Sbjct: 361 TKTLVIHPASTICADFGPEEKALMGVSEEMIRVSVGIEAIDDIIEDFAESLNA 413 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: 419 Number of extensions: 17 Number of successful extensions: 5 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: 414 Length adjustment: 31 Effective length of query: 382 Effective length of database: 383 Effective search space: 146306 Effective search space used: 146306 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