Align O-acetyl-L-homoserine sulfhydrylase 1; OAH-sulfhydrylase 1; EC 2.5.1.- (characterized)
to candidate WP_012505313.1 PAES_RS03655 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::Q5SK88 (421 letters) >NCBI__GCF_000020625.1:WP_012505313.1 Length = 430 Score = 535 bits (1377), Expect = e-156 Identities = 256/420 (60%), Positives = 320/420 (76%), Gaps = 1/420 (0%) Query: 2 RFETLQLHAGYEPEPTTLSRQVPIYPTTSYVFKSPEHAANLFALKEFGNIYSRIMNPTVD 61 RFETLQ+HAG EP+P T SR VPIY TTSYVF S EH A+LFALKEFGNIY+R+MNPT D Sbjct: 9 RFETLQVHAGQEPDPVTRSRAVPIYQTTSYVFDSAEHGADLFALKEFGNIYTRLMNPTTD 68 Query: 62 VLEKRLAALEGGKAALATASGHAAQFLALTTLAQAGDNIVSTPNLYGGTFNQFKVTLKRL 121 VLEKRLAALEGGKAALA ASGH+AQF+AL + +GD+IVS+P LYGG++NQFKV+ +RL Sbjct: 69 VLEKRLAALEGGKAALAVASGHSAQFIALGNICSSGDSIVSSPFLYGGSYNQFKVSFQRL 128 Query: 122 GIEVRFTSREERPEEFLALTDEKTRAWWVESIGNPALNIPDLEALAQAAREKGVALIVDN 181 GI VRF S + P+ A DE TRA ++ESIGNPA ++PD EA+A A E + LIVDN Sbjct: 129 GINVRF-SADLNPDNIRACIDETTRAIYLESIGNPAFHVPDFEAIAAIAHEFAIPLIVDN 187 Query: 182 TFGMGGYLLRPLAWGAALVTHSLTKWVGGHGAVIAGAIVDGGNFPWEGGRYPLLTEPQPG 241 TFG GGYL RPL GA +V S TKW+GGHG + G IVD G F W G++ +EP PG Sbjct: 188 TFGCGGYLCRPLDHGADIVVASATKWIGGHGTSMGGIIVDAGRFDWGSGKFAEFSEPSPG 247 Query: 242 YHGLRLTEAFGELAFIVKARVDGLRDQGQALGPFEAWVVLLGMETLSLRAERHVENTLHL 301 YHGL+ E FGELAFI++ RV+GLRD G A+ PF ++++L G+ETLSLR +RH +NT+ L Sbjct: 248 YHGLKFHETFGELAFIIRCRVEGLRDFGPAISPFNSFLLLQGLETLSLRVQRHADNTMAL 307 Query: 302 AHWLLEQPQVAWVNYPGLPHHPHHDRAQKYFKGKPGAVLTFGLKGGYEAAKRFISRLKLI 361 A WL+E P VAWVNYPGL +HP +D A +Y + G VL FGL GY+ A RFI ++L Sbjct: 308 ARWLVEHPAVAWVNYPGLSNHPTYDAASRYLRNGYGCVLAFGLNAGYDGAVRFIDSVRLA 367 Query: 362 SHLANVGDTRTLAIHPASTTHSQLSPEEQAQAGVSPEMVRLSVGLEHVEDLKAELKEALA 421 SHLANVGD +TL IHPASTTH QLS +EQ AGV +M+R+SVG+EH++D++ + ++A + Sbjct: 368 SHLANVGDAKTLVIHPASTTHQQLSADEQLSAGVKRDMIRVSVGIEHIDDIREDFEQAFS 427 Lambda K H 0.318 0.135 0.407 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: 526 Number of extensions: 19 Number of successful extensions: 2 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: 421 Length of database: 430 Length adjustment: 32 Effective length of query: 389 Effective length of database: 398 Effective search space: 154822 Effective search space used: 154822 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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