Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_012475142.1 CPHAMN1_RS08710 homocitrate synthase
Query= BRENDA::P58637 (376 letters) >NCBI__GCF_000020545.1:WP_012475142.1 Length = 383 Score = 257 bits (657), Expect = 3e-73 Identities = 149/362 (41%), Positives = 213/362 (58%), Gaps = 2/362 (0%) Query: 6 INDTTLRDGEQAAGVAFSVEEKIAIAKFLDAIGVHEIEVGIPAMGKAEQEAIANIVKLDL 65 I DTTLRDGEQA GV FS EEK IA + IG E+E+G PA+ EQ I IV + L Sbjct: 9 IIDTTLRDGEQAPGVVFSPEEKKDIAAMIADIGADELEIGYPAISVDEQRVIREIVAMKL 68 Query: 66 SANLLGWNRAVIADIQASIACGLQRVHISIPVSAIQIAVKFHGQWQVVLQKLHDSISFAV 125 L W+RA +DI+ + C + +HIS P+S + + + + V ++L I A Sbjct: 69 PKRLTCWSRAKRSDIECASRCETEGIHISFPISNLYLDL-MGKDYLWVREQLEILIPEAK 127 Query: 126 DQGLFVSIGGEDSSRAEESFLLDVVLAAQEWGASRFRFCDTVGILDPFTTHAKVKQLVAS 185 FVS G +D++R + + L A GA R R DTVGI P T ++QL +S Sbjct: 128 KHFSFVSAGAQDATRTDVTTLEAFARDASLCGADRVRIADTVGIATPLTLMRHIEQLKSS 187 Query: 186 LTIPVEMHTHNDFGLATANALAGTKAGALSVNTTVNGLGERAGNAALEEVVMALKHLYHH 245 +TIP+E H HND G+ATANA + +AG +V+ +VNGLGERAGNAALEE+ +ALK + Sbjct: 188 VTIPLEFHAHNDLGMATANAFSAIEAGCDAVSVSVNGLGERAGNAALEELSLALKLSGRY 247 Query: 246 DLGIDTRRLLEISQLVASASGHPVPPWKAIVGENTFAHESGIHAHGVLQNPQTYEPFAPE 305 I T RL + + VA AS + K + G F HESGIH + +L++P +Y+PF P Sbjct: 248 RNSIKTDRLHRLCEKVAKASNRIIQDQKPVTGSAVFQHESGIHCNALLKDPLSYQPFLPG 307 Query: 306 EVGRER-RLVVGKHSGRHLLSSILQQHDIILNHEETQFVLDAVRQESVEKKRSLTDQELL 364 ++G+E LV+GKHSG + ++ + I ++ EE +L +VR + KK L+ EL+ Sbjct: 308 DIGKEAYELVIGKHSGSASIQHAMEANGISIDREEAGKMLLSVRLAANRKKSGLSSAELM 367 Query: 365 HL 366 ++ Sbjct: 368 NI 369 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: 341 Number of extensions: 16 Number of successful extensions: 3 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: 383 Length adjustment: 30 Effective length of query: 346 Effective length of database: 353 Effective search space: 122138 Effective search space used: 122138 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