Align Aconitate hydratase A; 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 CA265_RS16405 CA265_RS16405 aconitate hydratase
Query= SwissProt::Q937N8 (869 letters) >FitnessBrowser__Pedo557:CA265_RS16405 Length = 759 Score = 212 bits (539), Expect = 8e-59 Identities = 229/806 (28%), Positives = 345/806 (42%), Gaps = 123/806 (15%) Query: 65 KRDLDFPWF-PARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDHSLA 123 KR D+ F P RV D Q AL+ Q G P VP + DH + Sbjct: 51 KRGSDYVDFAPDRVAMQDATAQMALLQFM--------QAGRP---QVAVPSTVHCDHLIT 99 Query: 124 VECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKMSPV 183 + G AK + E F F+ + + PG GI+HQ+ LE Sbjct: 100 AKEGAAIDLPHAKTESAEV------FDFLSSVSNKY-GIGFWKPGAGIIHQVVLENY--- 149 Query: 184 IHADNGVAYPD-TCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGVEL 242 A+P +GTDSHT + LG++AIGVGG +A +VM G ++ P ++GV+L Sbjct: 150 -------AFPGGMMIGTDSHTVNAGGLGMVAIGVGGADACDVMAGLPWELKFPKLIGVKL 202 Query: 243 TGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGATA 302 TGK A D++L + L + GA +E+ G+GA+S++ + TI NM E GAT Sbjct: 203 TGKLNGWTAAKDVILKVAGILTVKGGTGAIVEYFGDGATSMSCTGKGTICNMGAEIGATT 262 Query: 303 AMFFIDEQTIDYLRLTGR---TDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVV 359 + F DE YLR TGR DE K+ A ++AD +++V++ DL ++ Sbjct: 263 STFGYDESMERYLRATGRNEVADEANKIAAYLTGDAEVYAD--PENYFDQVIEIDLDTLE 320 Query: 360 RNMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRN 419 + GP P P S + EAE V I SCTN+S + Sbjct: 321 PYLNGPFTPDLATPVSQM-------------KVEAEKNGWPLKVEWGLIGSCTNSSY-ED 366 Query: 420 VIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTT 479 + AA +A A A+GL K + PGS+ V + L E L I AC Sbjct: 367 LSRAASIANQAIAKGLVTK--ADFGINPGSEQVRYTADRDGFLKTFEDLNATIFTNACGP 424 Query: 480 CNGMSGALDPKIQQEIIDRDLYATAVLSGNRNF----DGRIHPYAKQAFLASPPLVVAYA 535 C GM + ++ T V S NRNF DG + + AF+ASP +V A A Sbjct: 425 CIGMWDRTGAEKAEK-------NTIVHSFNRNFAKRADGNPNTF---AFVASPEMVAAIA 474 Query: 536 IAGTIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITA 595 I+G + F+ D L T+ G+ V L P+ E+ P + V + + A Sbjct: 475 ISGNLGFNPLTDTL-TNDKGEQVKLDP--PTGFEL---------PTKGFAVEDAGYQAPA 522 Query: 596 ASGESVSPLYDWRPQSTYIRRP-PYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAI 654 A G SV L + P WEG L+ L+ L TTDH+ Sbjct: 523 ADGSSVQVLVSPTSHRLQLLDPFTPWEGT-----DLQGLKLLIKAKGKCTTDHI------ 571 Query: 655 MLNSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLA 714 S AG +L F + + +++ + N N + G+ G + Sbjct: 572 ---SMAGPWL--------KFRGHLDNISNNMLIGAVNYFNDKTDNVKNELTGEY--GPVP 618 Query: 715 RIEPEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFE 774 + + K + I++ +YG+GSSR+ AA R GV ++ + F Sbjct: 619 ATQRDYKAAGLGS------------IVVGDENYGEGSSREHAAMEPRHLGVRAVLVKSFA 666 Query: 775 RIHRTNLIGMGVLPLEF--KPGVNRLTLGLDGTETYDVIG--ERQPRATLTLVVNRKNGE 830 RIH TNL G+L L F K +++ +T D++G E P LTLV++ +G Sbjct: 667 RIHETNLKKQGMLGLTFADKDDYDKIL----EDDTIDILGLTEFTPDQPLTLVLHHADGT 722 Query: 831 RVEVPVTCRLDSDEEVSIYEAGGVLH 856 + PV ++ +++ ++AGG L+ Sbjct: 723 QESFPVNHSYNA-QQIDWFKAGGALN 747 Lambda K H 0.318 0.135 0.398 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: 1576 Number of extensions: 88 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 869 Length of database: 759 Length adjustment: 41 Effective length of query: 828 Effective length of database: 718 Effective search space: 594504 Effective search space used: 594504 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 (21.7 bits) S2: 56 (26.2 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