Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_013836024.1 THICY_RS07565 aminotransferase class V-fold PLP-dependent enzyme
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000214825.1:WP_013836024.1 Length = 426 Score = 233 bits (595), Expect = 6e-66 Identities = 143/420 (34%), Positives = 234/420 (55%), Gaps = 18/420 (4%) Query: 11 TTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALE 70 T LH + S+ PI+ + +F ++DA+ A++F K G Y R NPT A LE Sbjct: 5 TIALHGGYKPEDTTKSVAVPIYQTTSFAFDDAQHAADLFDLKVAGNIYSRIMNPTNAVLE 64 Query: 71 DKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAK 129 +I ME G + + ++GMAAI +Q L GD+++S+ L+G + +L+ T+ QG + Sbjct: 65 TRIAAMEGGIAGLAVSSGMAAITYTIQTLAEAGDNILSTGELYGGSYNLFAHTLPRQGLE 124 Query: 130 VSMV--DATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTM 187 V DA D +++ I ANT+L++ ET+ NP +AD++R+ +L + GI VVD+T+ Sbjct: 125 VRFFNKDAPD-QDIAQLIDANTKLLYCETVGNPSGGIADIERLAKLAHQHGIPLVVDSTV 183 Query: 188 TSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT----RYP--------H 235 +P L+RP GA +V++S TK IGGHG +GG + D+G+F W R+P + Sbjct: 184 ATPALWRPIEQGADIVIHSATKYIGGHGTTIGGVIVDSGKFPWAEHAERFPLLNTPDVSY 243 Query: 236 IAENYKKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALA 295 Y ++ +A+ R LR+ G +L P A + G ET+ALR ER C+NA +A Sbjct: 244 HGVTYTQDFGAAAFIARARVVPLRNMGAALSPMNAFQLMQGLETLALRMERVCENAHKVA 303 Query: 296 QMLQADERVAAVYYPGLESHPQHALSKALFRSFGS-LMSFELKDGID-CFDYLNRLRLAI 353 + L+ V+ V Y GL SH H L++ + S ++SF LK G + + + L++ + Sbjct: 304 EFLEEQPLVSWVNYAGLASHKDHQLAQKYMQGKASGILSFGLKSGREGTRKFYDALQMIL 363 Query: 354 PTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 N+GD ++ A T ++ + G++ ++R+S+G+E DD++AD QAL A Sbjct: 364 RLVNIGDAKSCASIPAETTHRQLNDVELKAAGVSPDMVRLSIGIEHIDDILADIDQALMA 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: 436 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: 426 Length adjustment: 32 Effective length of query: 381 Effective length of database: 394 Effective search space: 150114 Effective search space used: 150114 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