Align 2-isopropylmalate synthase / (R)-citramalate synthase; EC 2.3.1.182; EC 2.3.3.13 (characterized, see rationale)
to candidate WP_011767245.1 AZO_RS17695 2-isopropylmalate synthase
Query= uniprot:D4GSQ2 (512 letters) >NCBI__GCF_000061505.1:WP_011767245.1 Length = 572 Score = 107 bits (268), Expect = 9e-28 Identities = 100/315 (31%), Positives = 146/315 (46%), Gaps = 29/315 (9%) Query: 202 STHTHDDLGLAMANVHASLAAGADLVHTTVNGIGERAGNVALEEVAIALDHCYDVESVKL 261 S H H+D G A+A ++ AGAD V + G GER GNV L +A+ L + Sbjct: 250 SVHPHNDRGTAVAAAELAVMAGADRVEGCLFGNGERTGNVDLVTLALNLYSQGVHPGLDF 309 Query: 262 DELYALAQKVAQATGVSLPPNKAVVGQNAFTHESGIHTDGTLK------DDAMYE----P 311 + +A+ V T + + P VG FT SG H D K DA++E P Sbjct: 310 SRINEVARTVEHCTQLPIHPRHPYVGDLVFTAFSGSHQDAIKKGFAVQQPDAVWEVPYLP 369 Query: 312 YPPETVGR--ERRLVLGKHAGRAGVKAALD-EHGV---DATDEEVAAVVERVKELGDRGK 365 P +GR E + + +G+ G+ L+ E+G+ E +A ++R+ + +RG Sbjct: 370 VDPADLGRSYESIIRVNSQSGKGGIAYLLEAEYGLVMPRRLQVEFSAAIQRITD--ERGT 427 Query: 366 RVTDADL-LAFAEDVQGRERARQVELLDLTAASGGGTPTASVRLRVEGEERVASGTGSGP 424 ++ D+ AF E+ A ++ A GG S+ + G RV G G+GP Sbjct: 428 ELSAGDIWRAFEEEYLA--VAAPYAYVEHHLAEHGGQQGISLTVEEAGVRRVLRGVGNGP 485 Query: 425 VDAAVKAVREALGPDADAQLDEYHVDAITGGTD--AVVTVEVTMSLGDRSVSVAASHADI 482 +DAA+ A+ DA A L Y AI G D AV +E+ G S HA+I Sbjct: 486 IDAALHAL------DAGAVLLGYEERAIGQGGDARAVAYIELADGEGGGSTFGVGIHANI 539 Query: 483 TRASVQAMVDALDRL 497 ASV A+V ALDRL Sbjct: 540 VTASVLAIVSALDRL 554 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: 707 Number of extensions: 43 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: 512 Length of database: 572 Length adjustment: 35 Effective length of query: 477 Effective length of database: 537 Effective search space: 256149 Effective search space used: 256149 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: 52 (24.6 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