Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_013402598.1 CALHY_RS03330 3-isopropylmalate dehydratase large subunit
Query= BRENDA::P19414 (778 letters) >NCBI__GCF_000166355.1:WP_013402598.1 Length = 429 Score = 179 bits (454), Expect = 3e-49 Identities = 140/450 (31%), Positives = 216/450 (48%), Gaps = 44/450 (9%) Query: 57 RPFTYAEKILYGHLDDPHGQDIQRGVSYLKLRPDRVACQDATAQMAILQFMSAGLPQV-- 114 +P T ++KIL H G++ + D V D T +AI +F G+ +V Sbjct: 3 KPMTMSQKILAYHA----GKEYVEPGDLIFANVDLVLGNDVTTPVAIKEFEKIGIDRVFD 58 Query: 115 AKPVTVHCDHLIQAQVGGEKDLKRAIDLNKEVYDFLASATAKYNM-GFWKPGS-GIIHQI 172 + + DH KD+K A K V +F KY + +++ G GI H + Sbjct: 59 KDKIAIVPDHFTP-----NKDIKSAQQC-KMVREF----AKKYEITNYFEVGEMGIEHAL 108 Query: 173 VLEN-YAFPGALIIGTDSHTPNAGGLGQLAIGVGGADAVDVMA-GRPWELKAPKILGVKL 230 + E PG L+IG DSHT G LG + G+G D MA G+ W K P+ + L Sbjct: 109 LPEKGLVVPGDLVIGADSHTCTYGALGAFSTGIGSTDMACAMATGKCW-FKVPEAIKFVL 167 Query: 231 TGKMNGWTSPKDIILKLAGITTVKGGTGKIVEYFGDGVDTFSATGMGTICNMGAEIGATT 290 GK GWTS KDIIL + G+ V G K +EY G+G+ + S TI NM E GA Sbjct: 168 YGKKTGWTSGKDIILHIIGMIGVDGALYKSMEYTGEGLKSLSMDDRFTIANMAIEAGAKN 227 Query: 291 SVFPFNKSMIEYLEATGRGKIADFAKLYHKDLLSADKDAEYDEVVEIDLNTLEPYINGPF 350 +F ++ IEY++ K Y + AD+DAEY EV EID++ ++P + P Sbjct: 228 GIFEVDEKTIEYVKHHS-------TKPY--KIFKADEDAEYSEVYEIDISKIKPTVAFPH 278 Query: 351 TPDLATPVSKMKEVAVANNWPLDVRVGLIGSCTNSSYEDMSRSASIVKDAAAHGLKSKTI 410 P+ + ++ E + + +IGSCTN ED+ +A I+K +K Sbjct: 279 LPENTKTIDEITE-------KIYIDQVVIGSCTNGRIEDLRIAAKILK---GRKVKKGLR 328 Query: 411 FTVTPGSEQIRATIERDGQLETFKEFGGIVLANACGPCIGQWDRRDIKKGDKNTIVSSYN 470 + P ++ I ++G +E F + G +V CGPC+G + G+K +++ N Sbjct: 329 CIIFPATQNIYKQALKEGLIEIFIDAGCVVSTPTCGPCLG-GHMGILADGEK--ALATTN 385 Query: 471 RNFTSRNDGNPQTHAFVASPELVTAFAIAG 500 RNF R G+P + +++SP + A A+ G Sbjct: 386 RNFVGRM-GHPNSEVYLSSPAIAAASAVLG 414 Lambda K H 0.317 0.136 0.405 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: 798 Number of extensions: 33 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: 778 Length of database: 429 Length adjustment: 36 Effective length of query: 742 Effective length of database: 393 Effective search space: 291606 Effective search space used: 291606 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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