Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate 3608455 Dshi_1851 aconitate hydratase 1 (RefSeq)
Query= SwissProt::P70920 (906 letters) >FitnessBrowser__Dino:3608455 Length = 928 Score = 1109 bits (2868), Expect = 0.0 Identities = 568/928 (61%), Positives = 694/928 (74%), Gaps = 41/928 (4%) Query: 5 DSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDG-RSVKKAD 63 D+ K +KTL+VG ++ YYS+P AE GL SKLP ++KV+LEN+LR EDG R+V D Sbjct: 8 DTAKTRKTLRVGDQSLAYYSIPAAETAGLGDFSKLPAALKVVLENMLRFEDGGRTVSVDD 67 Query: 64 IVAVSKWLRKKSLE-HEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINPLV 122 I A + W K EIA+RPARVLMQDFTGVPAVVDLAAMR+ + LGGDAEKINPL Sbjct: 68 IRAFADWADKGGQNPREIAYRPARVLMQDFTGVPAVVDLAAMRDGIVGLGGDAEKINPLN 127 Query: 123 PVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGICH 182 PVDLVIDHSV+++ FG+ +AF NV EY++N ERY FLKWGQ+AF+NF VVPPGTGICH Sbjct: 128 PVDLVIDHSVMIDEFGNPRAFQMNVDREYERNIERYTFLKWGQSAFANFRVVPPGTGICH 187 Query: 183 QVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGIEA 242 QVNLEYL+Q VWT ++ EVAYPD+LVGTDSHTTMVNG+AVLGWGVGGIEA Sbjct: 188 QVNLEYLAQAVWTDTDQSGQ-------EVAYPDTLVGTDSHTTMVNGMAVLGWGVGGIEA 240 Query: 243 EACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGLD 302 EA MLGQP+SML+P VVGF+L G M EG T TDLVL V +MLR GVVGKFVEF+G GLD Sbjct: 241 EAAMLGQPISMLIPEVVGFELTGEMMEGTTGTDLVLKVVEMLRAKGVVGKFVEFYGAGLD 300 Query: 303 HLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFRTA 362 HL +AD+ATIANMAPEYGATCGFFP+D + Y++T+GR R+ALV+AYAK GL+R Sbjct: 301 HLPLADRATIANMAPEYGATCGFFPIDGETLRYMRTTGRDEARIALVEAYAKENGLWRGD 360 Query: 363 KSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVAL--------ANEYKKT 414 A PV+T+TL+LD+ +VP+++GPKRP+ +AL AE F + A+E K Sbjct: 361 DYA-PVYTDTLSLDMGTIVPAISGPKRPQDYVALDKAAETFRDYVTGQRPDWSADEEDKA 419 Query: 415 E-----------------EPAKRFAVEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGL 457 E KR V G Y I G +VIA+ITSCTNTSNP V+IGAGL Sbjct: 420 EWTDEGGAVAPRDIPGDRGKHKRARVRGADYTIHDGTIVIASITSCTNTSNPYVMIGAGL 479 Query: 458 LARNAAAKGLKAKPWVKTSLAPGSQVVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSG 517 +AR A A GL KPWVKTSLAPGSQVV+AYL +GLQ LD +GFNLVG+GCTTCIGNSG Sbjct: 480 VARKARALGLTRKPWVKTSLAPGSQVVSAYLEAAGLQEDLDAIGFNLVGYGCTTCIGNSG 539 Query: 518 PLPEEISKSINDNGIVAAAVLSGNRNFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLA 577 P+ EE+S++IND I+A +VLSGNRNFEGR+SPDV+ANYLASPPLVVA+ALAG + +L Sbjct: 540 PIQEELSEAINDGDIIATSVLSGNRNFEGRISPDVRANYLASPPLVVAYALAGDMNVDLT 599 Query: 578 VEPLGEGKDGKPVYLKDIWPTSKEINAFMKKFVTASIFKKKYADVFKGDTNWRKIKTVES 637 +PLG+ +DG VYLKDIWP++KEI +++ VT F+ KYADVFKGD W+ ++T +S Sbjct: 600 RDPLGQDRDGNDVYLKDIWPSTKEIAELVEQTVTREAFQAKYADVFKGDEKWQSVETTDS 659 Query: 638 ETYRWNMSSTYVQNPPYFEGMKKEPEPVTDIVEARILAMFGDKITTDHISPAGSIKLTSP 697 TY W SSTYVQNPPYF+GM EP +++I A+ILA+ GD ITTDHISPAGS K ++P Sbjct: 660 LTYDWPPSSTYVQNPPYFQGMSAEPGTISNIEGAKILAILGDMITTDHISPAGSFKESTP 719 Query: 698 AGKYLSEHQVRPADFNQYGTRRGNHEVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWP 757 AG+YL+E QV+P +FN YG+RRGNHEVMMRGTFANIRI+N ML G +G G P Sbjct: 720 AGRYLTERQVQPREFNSYGSRRGNHEVMMRGTFANIRIRNEMLDGVEGGYTLG------P 773 Query: 758 DGEQMSIYDAAMKYQQEQVPLVVFAGAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHR 817 DG+Q SI++AAM YQ+ PLV+F G +YG GSSRDWAAKGT LLGV+AVI +SFERIHR Sbjct: 774 DGQQTSIFEAAMAYQEMGTPLVIFGGEQYGAGSSRDWAAKGTSLLGVKAVIAESFERIHR 833 Query: 818 SNLVGMGVLPLTFEEGTSWSSLGLKGDEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVS 877 SNLVGMGV+P F G + +LGLKGDE V++ GL G + P ++ I GDG+ + ++ Sbjct: 834 SNLVGMGVIPFEFTGGDTRKTLGLKGDETVSITGLDGKIVPLSEMPCTITYGDGTTREIT 893 Query: 878 LLCRIDTLDELDYYRNGGILHYVLRKLA 905 L CRIDT E++Y NGG+LHYVLR LA Sbjct: 894 LKCRIDTEVEIEYIENGGVLHYVLRNLA 921 Lambda K H 0.317 0.134 0.393 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: 2226 Number of extensions: 111 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 906 Length of database: 928 Length adjustment: 43 Effective length of query: 863 Effective length of database: 885 Effective search space: 763755 Effective search space used: 763755 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: 57 (26.6 bits)
This GapMind analysis is from Sep 17 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