Align Homocitrate synthase 1; EC 2.3.3.14 (uncharacterized)
to candidate WP_027177793.1 G496_RS0101950 pyruvate carboxyltransferase
Query= curated2:Q44290 (377 letters) >NCBI__GCF_000429985.1:WP_027177793.1 Length = 368 Score = 217 bits (553), Expect = 4e-61 Identities = 133/371 (35%), Positives = 207/371 (55%), Gaps = 5/371 (1%) Query: 5 LINDTTLRDGEQAAGVVFTLEEKVAIAKFLDTIGVPELEVGIPAMGEEEMRAICA-ISNL 63 ++ DTTLR+G Q G F L + IA L +G+ E+E+G +G++ + + I ++ Sbjct: 1 MLIDTTLREGAQLFGAYFNLSTRKKIAAGLAEVGIDEIELGW--IGQDNLGTLAEYIKDI 58 Query: 64 GLKANLLAWNRAVISDIKASVACGMERVHIAIPVSGIQIAAKFHGQWRVSLQRLKDCISF 123 L W +DI + ++RV+I +PVS + I + L RL I Sbjct: 59 SKDTYLSVWTPCREADIMKASKLPIDRVNIGVPVSDLHIEERLGLDRNGLLHRLSSAIRT 118 Query: 124 AVDQGL-WVAVGGEDSSRADENFLLDVALYAQEWGASRFRFCDTVGVLDPFTTYGKVKLL 182 A G+ +V+VG ED SRAD +F L VA +A+ GASR R D++G L P + ++ Sbjct: 119 AKAFGIEYVSVGMEDVSRADPDFALTVAAHAKNCGASRIRLSDSLGQLTPKSMEKLIETF 178 Query: 183 VSALTIPVEVHTHNDFGMATANALAGIKAGASSVNTTVIGLGERAGNAALEEVVMAIKRI 242 + + I VH H+DFGMATANA+ ++ GA + +V+G+GER+G AA EE+ + Sbjct: 179 RNHVKIDTAVHCHDDFGMATANAVTALECGADYADVSVLGIGERSGIAATEELAAYLALR 238 Query: 243 YGVDMGIDTPRLLELSQLVAAASGANVPPWKAIVGENTFAHESGIHAHGVLQNPDTYEPF 302 G T ++ L +VA +G VP KA+VGE+ FA ESG+H H + ++P+ +EP+ Sbjct: 239 CG-KKRYSTQKIKALCSMVALEAGVVVPRTKAVVGEDIFACESGLHTHALSKSPELFEPY 297 Query: 303 APEEVGWERRLVVGKHSGRHSVSNLLEQHGIFLNPEETQSVLDAVRQQSIKKKRSLTTEE 362 PE VG R+L VG SG+ +V + L+ G+ +P++ ++ AVRQ S + KR LT E Sbjct: 298 QPESVGISRKLAVGGKSGKAAVKSALKDCGVENDPKDITALTMAVRQLSSRLKRPLTRSE 357 Query: 363 LLNLVKEQRYS 373 + L + S Sbjct: 358 FIKLSSGEHLS 368 Lambda K H 0.318 0.133 0.388 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: 338 Number of extensions: 10 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: 377 Length of database: 368 Length adjustment: 30 Effective length of query: 347 Effective length of database: 338 Effective search space: 117286 Effective search space used: 117286 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 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