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 351600 BT2072 aconitate hydratase (NCBI ptt file)
Query= SwissProt::Q937N8 (869 letters) >FitnessBrowser__Btheta:351600 Length = 747 Score = 207 bits (528), Expect = 1e-57 Identities = 233/838 (27%), Positives = 358/838 (42%), Gaps = 153/838 (18%) Query: 51 PATLTDSLL--------QLVGRKRDLDFPWF-PARVVCHDILGQTALVDLAGLRDAIADQ 101 P TL + +L L KR D+ F P RV D Q AL+ Sbjct: 29 PLTLAEKILYAHLFNEGDLKNYKRGEDYVNFRPDRVAMQDATAQMALLQFM--------- 79 Query: 102 GGDPAKVNPVVPVQLIVDHSLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKN 161 + K VP + DH + G + A A + NE+ + F+ + Sbjct: 80 --NAGKEKVAVPSTVHCDHLIQAYKGAKEDIATAT------KTNEEVYDFLRDVSSRY-G 130 Query: 162 VDVIPPGNGIMHQINLEKMSPVIHADNGVAYPD-TCVGTDSHTPHVDALGVIAIGVGGLE 220 + PG GI+HQ+ LE A+P VGTDSHTP+ LG++AIGVGG + Sbjct: 131 IGFWKPGAGIIHQVVLENY----------AFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD 180 Query: 221 AENVMLGRASWMRLPDIVGVELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGA 280 A +VM G +++P I+GV LTGK + D++L L L + + +E+ G G Sbjct: 181 AVDVMTGMEWELKMPRIIGVRLTGKLSGWTSPKDVILKLAGILTVKGGTNSIIEYFGPGT 240 Query: 281 SSLTLGDRATISNMAPEYGATAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWAD 340 +SL+ +ATI NM E GAT ++F D + YLR TGR D ++L E A L AD Sbjct: 241 ASLSATGKATICNMGAEVGATTSLFPFDGRMATYLRATGR-DRIVELAE--AVDCELRAD 297 Query: 341 SLKNAE----YERVLKFDLSSVVRNMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEG 396 E Y+RV+ DLS++ + GP P P S AE+ V L+ + G Sbjct: 298 QQVTDEPEKYYDRVIDIDLSTLEPYINGPFTPDAATPISEFAEK---VLLNGYPRKMEVG 354 Query: 397 LMPDGAVIIAAITSCTNTSNPRNVIAAALLARNANARGLA-RKPWVKSSLAPGSKAVELY 455 L I SCTN+S +++ AA LAR + L+ P + + PGS+ + Sbjct: 355 L----------IGSCTNSSY-QDLSRAASLARQVKEKNLSVASPLI---INPGSEQIRAT 400 Query: 456 LEEANLLPDLEKLGFGIVAFACTTCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNF--- 512 E ++ D ++G I+A AC C G + ++ D + V S NRNF Sbjct: 401 AERDGMMDDFMQIGAVIMANACGPCIG-------QWKRHTDDPTRKNSIVTSFNRNFAKR 453 Query: 513 -DGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEID 571 DG + Y AF+ASP L +A IAG + F+ KD L + DG+ V L + P +E+ Sbjct: 454 ADGNPNTY---AFVASPELTMALTIAGDLCFNPLKDRL-MNHDGEKVKLAE--PVGDEL- 506 Query: 572 AIVAKSVKPEQFRKVYEPMFAITAASGESVSP-----LYDWRPQSTYIRRP---PYWEGA 623 P+ T+ + ++P + P S ++ P W+G Sbjct: 507 -----------------PLRGFTSGNEGYITPGGTKTAINVNPASQRLQLLTPFPAWDG- 548 Query: 624 LAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAAGEYLARMGLPEEDFNSYATHRGD 683 + + + L TTDH+ S AG +L G E ++ + Sbjct: 549 ----QDILNMPLLIKAQGKCTTDHI---------SMAGPWLRFRGHLENISDNMLMGAVN 595 Query: 684 HLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEGKVVRMWEAIETYMDRKQPLIIIA 743 + N + N V G K Y P I++A Sbjct: 596 AFNGETNNVWNRS-TNTYGTVSGTAK---------------------MYKSEGIPSIVVA 633 Query: 744 GADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTNLIGMGVLPLEFKPGVNRLTLGLD 803 +YG+GSSR+ AA R V VI+A+ F RIH TNL G+L L F + D Sbjct: 634 EENYGEGSSREHAAMEPRFLNVRVILAKSFARIHETNLKKQGMLALTFADKAD-----YD 688 Query: 804 GTETYDVIG-----ERQPRATLTLVVNRKNGERVEVPVTCRLDSDEEVSIYEAGGVLH 856 + +D++ + P LT+V++ ++G + ++++++ + AG L+ Sbjct: 689 KIQEHDLLSVIGLPDFAPGRNLTVVLHHEDGTKESFEAQ-HTYNEQQIAWFRAGSALN 745 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: 1564 Number of extensions: 85 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: 747 Length adjustment: 41 Effective length of query: 828 Effective length of database: 706 Effective search space: 584568 Effective search space used: 584568 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