Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate AO353_24260 AO353_24260 hypothetical protein
Query= BRENDA::Q58595 (518 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24260 Length = 309 Score = 177 bits (450), Expect = 4e-49 Identities = 104/309 (33%), Positives = 171/309 (55%), Gaps = 6/309 (1%) Query: 24 VYIFDTTLRDGEQTPGVSLTPEEKIDIAIKLDDLGVDVIEAGFPVSSLGEQEAIKKICSL 83 + + D+TLR+G Q PGV LT + + IA L D G+D IEAG P +S E + + + Sbjct: 4 ITLVDSTLREGNQAPGVKLTTKSTLTIAYALADAGIDFIEAGHPYASKQEFDRVTALVKS 63 Query: 84 NLDAEICGLARAVKKDIDVAIDCGVDRIHTFIATSPLHRKYKLKKSKEEIIDIAVDAIEY 143 + I +RA + DID G + I F + +KY+++KSK +I D+ ++ Y Sbjct: 64 KIAKNILAHSRAHQDDIDAVAATGANWIGIFAGINETSQKYRIRKSKAQIQDLIKRSVLY 123 Query: 144 IKEHGIRVEFSAEDATRTEIDYLIEVYKKAVDAGADIINVPDTVGVMIPRAMYYLINELK 203 K G++V ++ EDA+RT D LIE +K A AGAD I D++GV P + I ++ Sbjct: 124 AKSLGLKVRYTIEDASRTPSDDLIETFKIAKAAGADRICYADSLGVCDPFKVQATIKLIR 183 Query: 204 KEIK-VPISVHCHNDFGLAVANSLAAVEAGAEQVHCTINGLGERGGNAALEEVVMSLMSI 262 + + + + VH H+D GLA+AN+LA++EAGA + CT+NG+GER G + E + + ++ Sbjct: 184 QSLSDIDLEVHFHDDRGLAMANTLASIEAGATFISCTVNGIGERCG---ITETCLLITNL 240 Query: 263 Y--GVKTNIKTQKLYEISQLVSKYTEIKVQPNKAIVGENAFAHESGIHAHGVLAHALTYE 320 + + + K K+ ++S +VSK + I+GE +F H + +H + Y Sbjct: 241 HFNSILCSGKASKVLKLSSIVSKELGDAFDRRRPIIGEYSFVHTAKLHVTANSRNKNCYH 300 Query: 321 PIPPELVGQ 329 I P + + Sbjct: 301 WIDPAYLSE 309 Lambda K H 0.316 0.135 0.368 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: 351 Number of extensions: 13 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: 518 Length of database: 309 Length adjustment: 31 Effective length of query: 487 Effective length of database: 278 Effective search space: 135386 Effective search space used: 135386 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 (21.6 bits) S2: 50 (23.9 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