Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate GFF3618 Psest_3685 OAH/OAS sulfhydrylase
Query= SwissProt::Q9WZY4 (430 letters) >FitnessBrowser__psRCH2:GFF3618 Length = 425 Score = 479 bits (1232), Expect = e-140 Identities = 250/422 (59%), Positives = 309/422 (73%), Gaps = 5/422 (1%) Query: 10 TRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRIGNPTVSVL 69 T A+HAGY P + T + AVPIYQTTSY F D+ H A LF L+ PG IYTRI NPT VL Sbjct: 5 TLAIHAGYSP-DPTTRAVAVPIYQTTSYAFDDTQHGADLFDLKVPGNIYTRIMNPTTDVL 63 Query: 70 EERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFRHTLYKKSG 129 E+R+AALE GV ALAVASG AAITYAI IA GD IVS + LYGGTYNLF HTL + G Sbjct: 64 EQRVAALEGGVAALAVASGMAAITYAIQTIAEVGDNIVSVAKLYGGTYNLFAHTL-PRQG 122 Query: 130 IIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPLIVDNTV 189 I V+F D +E I E+TKAV+ E+IGNP V D A+AE AHRHGVPLIVDNTV Sbjct: 123 IEVRFAAHDDIAALESLIDERTKAVFCESIGNPAGNVIDLAALAEAAHRHGVPLIVDNTV 182 Query: 190 A-PYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWTNGK--FPELVEPDPSY 246 A P + RPFEHGADIVV+S TK++GGHGTSIGG++VDSGKF W K F L PD SY Sbjct: 183 ATPMLCRPFEHGADIVVHSLTKYMGGHGTSIGGIVVDSGKFPWAQHKKRFALLNTPDVSY 242 Query: 247 HGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCENALKIV 306 HGV+Y E F AA+I +CR LR++G+ +SPFN+FL + GLETL+LRM++HCENALK+ Sbjct: 243 HGVTYTEAFGPAAFIGRCRVVPLRNMGAAISPFNSFLILQGLETLALRMERHCENALKVA 302 Query: 307 EFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFIDSLTLIS 366 EFL++HP V+WV Y + E A +Y+ +I+ FG++GG EAG +FID+L L+ Sbjct: 303 EFLQAHPQVAWVKYAGLPDHPEHELARRYMGGTPASILCFGIEGGIEAGARFIDALKLVV 362 Query: 367 HLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADLDQALRK 426 L NIGDA++LA HPASTTH+QL +E + GV+ D+IRLS+GIE ++DI+ADL QAL Sbjct: 363 RLVNIGDAKSLACHPASTTHRQLNADELARAGVSQDLIRLSIGIEHIDDILADLAQALSA 422 Query: 427 SQ 428 S+ Sbjct: 423 SK 424 Lambda K H 0.317 0.136 0.398 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: 585 Number of extensions: 18 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: 430 Length of database: 425 Length adjustment: 32 Effective length of query: 398 Effective length of database: 393 Effective search space: 156414 Effective search space used: 156414 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 (21.6 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