Align 2-isopropylmalate synthase / (R)-citramalate synthase; EC 2.3.1.182; EC 2.3.3.13 (characterized, see rationale)
to candidate 408370 DVUA0016 homocitrate synthase
Query= uniprot:D4GSQ2 (512 letters) >MicrobesOnline__882:408370 Length = 384 Score = 197 bits (501), Expect = 6e-55 Identities = 133/367 (36%), Positives = 199/367 (54%), Gaps = 18/367 (4%) Query: 17 VQLLDTTLRDGEQAPGVSLTPTQKADIARALDRAEVDYIEAGSACTGPGERE---TIKRV 73 V L+D+TLR+G QA GV + I + + + V EAG A G+ + T++ Sbjct: 22 VMLIDSTLREGAQAYGVYFDAADRESILQGVAASGVTEAEAGWA----GQDDLAATLRLG 77 Query: 74 TSLGLDATVTSFARGVKNDVDLALDCDVDGVTLVVPASDRHVESKVGTTREDVVETTDEL 133 + + + R D+D A + V + VP+SD H+ ++G R++V++ + Sbjct: 78 ARVAPSLRLAVWCRCCTADLDKAAEAGARRVHIGVPSSDAHMRLRLGMGRDEVLQRVTTV 137 Query: 134 VAYAKDHGLWVEVIG-EDGSRAAPEFLESLARASHDAGADRFCFADTVGHTSPEHTYEVV 192 + +A G +G ED RAAP+ LE+LAR + GA R +DTVG +P+ +V Sbjct: 138 LEHAAHLGFLHVTLGLEDAGRAAPDLLEALARTAARTGAHRLRCSDTVGLLTPDGMVRLV 197 Query: 193 --SRLSELGPTSTHTHDDLGLAMANVHASLAAGADLVHTTVNGIGERAGNVALEEVAIAL 250 +R + P + H H+DLGLA AN A+L AGAD ++ G+GERAG EE+A AL Sbjct: 198 LLARRASALPVAVHCHNDLGLATANALAALDAGADGADVSLLGLGERAGITRAEELAAAL 257 Query: 251 DHCYDVESVKLDELYALAQKVAQATGVSLPPNKAVVGQNAFTHESGIHTDGTLKDDAMYE 310 ES +LD L + +++A + + LPP+ AV G+N F ESG+H G +D A++E Sbjct: 258 VVLRG-ESYRLDMLRGVCRRLAASLEMRLPPHWAVAGENLFAVESGVHLHGVQRDPALFE 316 Query: 311 PYPPETVGRERRLVLGKHAGRAGVKAALDEHGV----DATDEEVAAVVERVKELGDRGKR 366 P+PP VG ERRL +G G AGV A HG+ DA V AV ++ L G+ Sbjct: 317 PFPPALVGAERRLGVGGKCGSAGVAAMAHSHGLTLQGDALRRHVRAVRDKACSL---GRP 373 Query: 367 VTDADLL 373 +TDA+ L Sbjct: 374 LTDAEFL 380 Lambda K H 0.312 0.129 0.361 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: 498 Number of extensions: 30 Number of successful extensions: 5 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: 512 Length of database: 384 Length adjustment: 32 Effective length of query: 480 Effective length of database: 352 Effective search space: 168960 Effective search space used: 168960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (24.3 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