Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate Pf1N1B4_3888 Aconitate hydratase (EC 4.2.1.3)
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 Length = 913 Score = 723 bits (1865), Expect = 0.0 Identities = 404/901 (44%), Positives = 553/901 (61%), Gaps = 65/901 (7%) Query: 20 YFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLT-ASLKQII----ESKQELDF 74 YF EA +++ G KLP + +VL ENL+R + + +T A LK I E + + + Sbjct: 22 YFSLPEAAKSL--GDLDKLPMSLKVLLENLLRWEDEKTVTGADLKAIAAWLKERRSDREI 79 Query: 75 PWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFD 134 + PARV+ D G A+VDLA +R A+A GGDP ++NP+ P L++DHS+ V+ Sbjct: 80 QYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSPVDLVIDHSVMVDKYA-S 138 Query: 135 KDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNG- 193 AF +N IE +RN +R+ F+ W Q AF N V+P G GI HQ+NLE + + ++ Sbjct: 139 ASAFGQNVDIEMQRNHERYAFLRWGQSAFNNFSVVPPGTGICHQVNLEYLGRTVWTKDED 198 Query: 194 ---VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKP 250 AFPDTLVGTDSHT ++ LGV+ GVGG+EAE+ MLG+ M +P++IG +LTGK Sbjct: 199 GRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFKLTGKL 258 Query: 251 QPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFY 310 + GITATD+VL +T+ LR + VV ++EF+G+G L L DRATI+NM PE+GAT F Sbjct: 259 KEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADRATIANMAPEYGATCGFFP 318 Query: 311 IDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPS 370 +D+ TL+YL L+GR + VKLVE Y+KT GLW K+ V+ +L D+ SV ++AGP Sbjct: 319 VDEVTLEYLRLSGRTPQTVKLVEAYSKTQGLWRLPGKEPVFTDSLALDMGSVEASLAGPK 378 Query: 371 NPHARVPTSELA-------------ARGISGEVENEPG---------------------- 395 P RV +A + G +E+E G Sbjct: 379 RPQDRVSLPNVAQAFTDFLGLQFKPSSKEEGRLESEGGGGVAVGNADLIGEADYHHEGST 438 Query: 396 -LMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLY 454 + +GAV+IAAITSCTNTSNP ++AAGL+A+ A KGL RKPWVK+SLAPGSK V Y Sbjct: 439 YRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVEKGLKRKPWVKSSLAPGSKVVTDY 498 Query: 455 LEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGR 514 + A L L+ LGF +VG+ CTTC G SG L I++ + DL +VLSGNRNF+GR Sbjct: 499 YKAAGLTQYLDELGFALVGYGCTTCIGNSGPLPEPIEKAIQKADLTVASVLSGNRNFEGR 558 Query: 515 IHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEI-DAVI 573 +HP K +LASPPLVVAYA+AGT+R DI + LG DKDG PV L +IWPS EI DAV Sbjct: 559 VHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDKDGHPVYLRDIWPSTKEIADAV- 617 Query: 574 AASVKPEQFRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRRPPYWE---GALAGER 627 V F K Y +F + P Y W STYI+ PP+++ G + Sbjct: 618 -TQVNTAMFHKEYAEVFAGDEQWQAIEVPQAATYVWNNDSTYIQHPPFFDDIGGPAPVVK 676 Query: 628 TLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQ 687 ++G + LA+LGD++TTDH+SP+ I DS AG YL + G+ DFNSY + RG+H Sbjct: 677 DVEGAKVLALLGDSVTTDHISPAGNIKADSPAGHYLREQGVEPRDFNSYGSRRGNHQVMM 736 Query: 688 RATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYG 747 R TFAN +++NEM G + G+ I P G +++A Y PL++IAG +YG Sbjct: 737 RGTFANIRIRNEML---GGEEGGNTIYI-PTGEKLPIYDAAMRYQASGTPLVVIAGQEYG 792 Query: 748 QGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVF 807 GSSRDWAAKG L GV+A++AE FERIHR+NLVGMGVLPL+FK +NR + + G E Sbjct: 793 TGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTGKETL 852 Query: 808 DVIG----SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 863 D++G + PR +LT+++TR++G +V V CR+DT EV ++AGG+L + + Sbjct: 853 DILGLTGVELTPRMNLTLVVTREDGNTEKVEVLCRIDTLNEVEYFKAGGILHYVLRQLIA 912 Query: 864 S 864 S Sbjct: 913 S 913 Lambda K H 0.318 0.136 0.397 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: 2004 Number of extensions: 93 Number of successful extensions: 9 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: 867 Length of database: 913 Length adjustment: 43 Effective length of query: 824 Effective length of database: 870 Effective search space: 716880 Effective search space used: 716880 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