Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_013460368.1 SULKU_RS07600 homocitrate synthase
Query= BRENDA::P58637 (376 letters) >NCBI__GCF_000183725.1:WP_013460368.1 Length = 371 Score = 328 bits (842), Expect = 1e-94 Identities = 175/364 (48%), Positives = 235/364 (64%) Query: 5 LINDTTLRDGEQAAGVAFSVEEKIAIAKFLDAIGVHEIEVGIPAMGKAEQEAIANIVKLD 64 LINDTTLRDGEQA VAF+ EEK+ IA LDA G E+E+GI AMG E+E I ++ L Sbjct: 3 LINDTTLRDGEQAPYVAFNTEEKLRIATLLDACGADELEIGIAAMGAKEREDIKELLNLG 62 Query: 65 LSANLLGWNRAVIADIQASIACGLQRVHISIPVSAIQIAVKFHGQWQVVLQKLHDSISFA 124 L A ++ WNR + D+ AS++CG+Q V +SIP+S + I VKF G VL +L ++ A Sbjct: 63 LKARMMTWNRMKLEDLDASLSCGVQAVDLSIPISDLLIGVKFGGSKIKVLNELERVVTAA 122 Query: 125 VDQGLFVSIGGEDSSRAEESFLLDVVLAAQEWGASRFRFCDTVGILDPFTTHAKVKQLVA 184 +GLFV IGGEDSSR E SF+ DV+ +E GA RFR+CDT+G++ P T+ VK+L Sbjct: 123 TREGLFVCIGGEDSSRGELSFMRDVMELGRECGAGRFRYCDTIGVMTPTQTYQAVKELCD 182 Query: 185 SLTIPVEMHTHNDFGLATANALAGTKAGALSVNTTVNGLGERAGNAALEEVVMALKHLYH 244 +P+EMHTHNDFGLA ANAL+G AGA+S+NTTV GLGERAGNA+ E+++M+LKHLY Sbjct: 183 LNLLPIEMHTHNDFGLANANALSGIDAGAISMNTTVIGLGERAGNASFEQILMSLKHLYG 242 Query: 245 HDLGIDTRRLLEISQLVASASGHPVPPWKAIVGENTFAHESGIHAHGVLQNPQTYEPFAP 304 +D L + Q VA A+ + I+GE FAHESGIHA G++++ YEP+ Sbjct: 243 ESRAVDPLLLRSLVQSVADAANINLSANAPIIGERIFAHESGIHADGMMKDSHAYEPYEA 302 Query: 305 EEVGRERRLVVGKHSGRHLLSSILQQHDIILNHEETQFVLDAVRQESVEKKRSLTDQELL 364 +EVG +GKHSG + L + I ++ +L +R+ +KR L EL Sbjct: 303 KEVGLTSSFPIGKHSGSATIRYHLARMGISADNSILGDLLPKIREIVTSRKRVLEIGELK 362 Query: 365 HLVQ 368 L Q Sbjct: 363 SLYQ 366 Lambda K H 0.319 0.133 0.383 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: 340 Number of extensions: 11 Number of successful extensions: 1 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: 376 Length of database: 371 Length adjustment: 30 Effective length of query: 346 Effective length of database: 341 Effective search space: 117986 Effective search space used: 117986 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