Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_041245581.1 GURA_RS20075 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000016745.1:WP_041245581.1 Length = 417 Score = 293 bits (749), Expect = 9e-84 Identities = 166/410 (40%), Positives = 242/410 (59%), Gaps = 6/410 (1%) Query: 7 YGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTV 66 Y F T ++H + G G+ PI S +F A +L ++F+G++ G Y R GNPT Sbjct: 8 YSFDTLLIHGGLEPG-PAGATTVPIVQSSSFAQATAEELEDIFRGRKVGQVYTRVGNPTT 66 Query: 67 AALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGA 125 +LE ++ +E G++ I A+GMAAI V ++R GD +++S+ LFG T SL+ T+ Sbjct: 67 ESLEKRLALLEGGQAAIATASGMAAITTAVMTIVRSGDEILASSSLFGGTFSLFRDTLSG 126 Query: 126 QGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDN 185 G + VD TD+ V I TRLVFVETI NP+ V D+ I + R GI +VD Sbjct: 127 YGISTTFVDPTDLAAVRNGINDRTRLVFVETIGNPKMDVPDIPAIALIARAAGIPLLVDA 186 Query: 186 TMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDW--TRYPHIAENYKKN 243 T+T+P L R +GA +V++S +K I G G+A+GG + D G FDW ++PH +KK Sbjct: 187 TVTTPCLARGSDLGADIVIHSTSKFINGTGSAIGGVIIDLGRFDWQSDKFPHFEPFHKKY 246 Query: 244 PAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADER 303 A + A+ R +DFG P + +A G ET++LR ER C NA LAQ L+A +R Sbjct: 247 RAFAF-TARARKLIHKDFGACAAPMNSFLLAEGVETLSLRMERHCANAQKLAQFLKAHDR 305 Query: 304 VAAVYYPGLESHPQHALSKALF-RSFGSLMSFELKDGIDCFDYLNRLRLAIPTSNLGDTR 362 V V YPGLE P H ++K L+ FG +++F L D F ++N +RLA +N+GD + Sbjct: 306 VRWVNYPGLEDSPHHQVAKKLYGDKFGGVLTFGLADKAAAFRFINGVRLAKNLANIGDAK 365 Query: 363 TLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALD 412 TLVI A TI + G E + MG+ E ++RVSVG+E +D++ DF AL+ Sbjct: 366 TLVIHPASTICCDYGPEEKGLMGVGEEMVRVSVGIEAINDIIEDFDSALN 415 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: 443 Number of extensions: 18 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: 417 Length adjustment: 31 Effective length of query: 382 Effective length of database: 386 Effective search space: 147452 Effective search space used: 147452 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