Align Homocitrate synthase 1; EC 2.3.3.14 (uncharacterized)
to candidate WP_012991460.1 THAL_RS02075 homocitrate synthase
Query= curated2:Q44290 (377 letters) >NCBI__GCF_000025605.1:WP_012991460.1 Length = 316 Score = 223 bits (569), Expect = 4e-63 Identities = 128/317 (40%), Positives = 190/317 (59%), Gaps = 2/317 (0%) Query: 3 KVLINDTTLRDGEQAAGVVFTLEEKVAIAKFLDTIGVPELEVGIPAMGEEEMRAICAISN 62 +V I DTTLR+G Q+ + +LEE+ A+ L ++ E+EVG+PA GEEE I ++ Sbjct: 2 RVYITDTTLREGIQSPSLELSLEERYALFNHLVSLNFYEIEVGVPAKGEEEREYIRKLTK 61 Query: 63 LGLKANLLAWNRAVISDIKASVACGMERVHIAIPVSGIQIAAKFHGQWRVSLQRLKDCIS 122 ++ WNRA I DI+ S++C +++V +A PVS I I K K+ + Sbjct: 62 GEHADRVIVWNRANIKDIEYSLSCNVKKVEVAFPVSDIMIEKKLRKSREYLKGLAKEIVP 121 Query: 123 FAVDQGLWVAVGGEDSSRADENFLLDVALYAQEWGASRFRFCDTVGVLDPFTTYGKVKLL 182 ++GL+++VG ED+SRAD NFLL+ + GA R R DTVGV++P + VK L Sbjct: 122 CCKEKGLYLSVGLEDASRADYNFLLEFVELVKTHGADRVRLSDTVGVMNPLSVAKVVKDL 181 Query: 183 VSALTIPVEVHTHNDFGMATANALAGIKAGASSVNTTVIGLGERAGNAALEEVVMAIKRI 242 S +T VEVH HNDFGMATANA+ + +GA VN++++GLGER G EEVV+ ++ I Sbjct: 182 -SNIT-DVEVHFHNDFGMATANAVVAVMSGAKFVNSSLLGLGERCGITPTEEVVIYLEVI 239 Query: 243 YGVDMGIDTPRLLELSQLVAAASGANVPPWKAIVGENTFAHESGIHAHGVLQNPDTYEPF 302 G++ GID +L E + +G V K I+G N F ++S IH G+ ++ DTY PF Sbjct: 240 LGINTGIDIRKLYEKIREFVNMTGIKVHDNKPIIGTNAFTNKSRIHIDGLSKSKDTYLPF 299 Query: 303 APEEVGWERRLVVGKHS 319 P+ +G ++ G +S Sbjct: 300 DPQLIGEMSKICKGYYS 316 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: 300 Number of extensions: 11 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: 377 Length of database: 316 Length adjustment: 29 Effective length of query: 348 Effective length of database: 287 Effective search space: 99876 Effective search space used: 99876 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: 49 (23.5 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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