Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate SMc01976 SMc01976 hypothetical protein
Query= BRENDA::Q7M844 (422 letters) >FitnessBrowser__Smeli:SMc01976 Length = 390 Score = 191 bits (485), Expect = 3e-53 Identities = 125/411 (30%), Positives = 201/411 (48%), Gaps = 45/411 (10%) Query: 12 YEKGKGEKSIAVPIYQTTAYKFDDTEHGANLFDLKELGNIYTRIMNPTTDVLEKRVALLE 71 +++ ++ PI QT+ + F D + + + + IYTR +NPT E+ +A LE Sbjct: 17 HDESNAFDAVVPPIVQTSLFTFKDYDEMVASYRGERVRPIYTRGLNPTVRHFEEMLAKLE 76 Query: 72 GGVAALASASGMASIFYAVANLAQSGENIIATTQLYGGTLNQFTHTLSRFGIEVRFFDGN 131 G A+ ASGM++I V + + G+ I+A +Y F L R +EV + DG Sbjct: 77 GAEDAIGFASGMSAISSTVLSFVEPGDRIVAVKHVYPDAFRLFGTHLKRMRVEVTYVDGR 136 Query: 132 HPQEARALIDSKSRALFFESLTNPSIDVPEIDTLAKIADEYGIVSIVDNTVATPAICRPI 191 +EA A ++ + ES T+ +D ++ LA +A GIV+++DN+ A+P +P+ Sbjct: 137 D-EEAVAKALPGAKLFYMESPTSWVMDTHDVAALAALARRQGIVTVIDNSWASPVFQQPV 195 Query: 192 EHGVDVVVHSASKYMGGQGLAIGGVLVESARVAEKLRGNPRYPHFNTPDPSYHGLVYASA 251 GVD+V+HSASKY+GG + GV+ S + ++R + YP+ Sbjct: 196 SLGVDLVIHSASKYLGGHSDVVAGVVAGSGELIGRIR-SEAYPY---------------- 238 Query: 252 PLPPFVLRARLALLRDIGATLSPFDSWLFIQGIETLSVRMREHSLSAMKIAHYLQNHPKV 311 +G LSPFD+WL I+G+ TL VRM+ H SA+ +A L HP V Sbjct: 239 ----------------LGGKLSPFDAWLLIRGMRTLPVRMKAHERSALAVARRLAEHPLV 282 Query: 312 QAVYYPGLESDKNHANAVKYFDEGM--FSGLLSFEVGDFELAQKIADSVKIFTLATNIGD 369 + V +PGL + + G+ SGL SF + ++ AD +K+F L + G Sbjct: 283 ETVCHPGLGN---------HLPPGLSGTSGLFSFIFREGVDVRRFADHLKLFKLGVSWGG 333 Query: 370 TKSIITHSASTTHRQVSAEGLKKAGVTPGLVRLSIGLEDYRDLIEDLAQAI 420 +S+I ++ G++P VRL +GLE L DL A+ Sbjct: 334 HESLIVPGEVVLAQKAEPNSAAAFGISPRSVRLHVGLEGTEALWSDLEAAM 384 Lambda K H 0.318 0.135 0.385 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: 344 Number of extensions: 14 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: 422 Length of database: 390 Length adjustment: 31 Effective length of query: 391 Effective length of database: 359 Effective search space: 140369 Effective search space used: 140369 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: 50 (23.9 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