Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate AO353_00565 AO353_00565 aconitate hydratase
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__pseudo3_N2E3:AO353_00565 Length = 916 Score = 722 bits (1863), Expect = 0.0 Identities = 409/904 (45%), Positives = 556/904 (61%), Gaps = 68/904 (7%) Query: 20 YFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLT-ASLKQII----ESKQELDF 74 YF EA +++ G KLP + +VL ENL+R + + +T A LK + E + + + Sbjct: 22 YFSLPEAAKSL--GDLDKLPMSLKVLLENLLRWEDEKTVTGADLKALAAWLKERRSDREI 79 Query: 75 PWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFD 134 + PARV+ D G A+VDLA +R A+A GGDP ++NP+ P L++DHS+ V+ Sbjct: 80 QYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSPVDLVIDHSVMVDKFA-S 138 Query: 135 KDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNG- 193 AF +N IE +RN +R+ F+ W Q AF N V+P G GI HQ+NLE + + ++ Sbjct: 139 STAFTQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQVNLEYLGRTVWTKDED 198 Query: 194 ---VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKP 250 AFPDTLVGTDSHT ++ LGV+ GVGG+EAE+ MLG+ M +P++IG +LTGK Sbjct: 199 DRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFKLTGKL 258 Query: 251 QPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFY 310 + GITATD+VL +T+ LR + VV ++EF+G+G L L DRATI+NM PE+GAT F Sbjct: 259 KEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLAELPLADRATIANMAPEYGATCGFFP 318 Query: 311 IDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPS 370 +D+ TL+YL L+GR + VKLVE Y KT GLW ++ V+ +L D+SSV ++AGP Sbjct: 319 VDEVTLEYLRLSGRPSAVVKLVEAYCKTQGLWRLPGQEPVFTDSLALDMSSVEASLAGPK 378 Query: 371 NPHARV---------------------PTSE----LAARGISG--------------EVE 391 P RV PTS+ L + G G E E Sbjct: 379 RPQDRVSLPNVAQAFTDFLGLQVKPARPTSKEEGRLESEGGGGVAVGNADLVSEADYEYE 438 Query: 392 NEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAV 451 + + +GAV+IAAITSCTNTSNP ++AAGL+A+ A KGL RKPWVK+SLAPGSK V Sbjct: 439 GQTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVEKGLKRKPWVKSSLAPGSKVV 498 Query: 452 QLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNF 511 Y + A L L+ LGF +VG+ CTTC G SG L I++ + DL +VLSGNRNF Sbjct: 499 TDYYKAAGLTQYLDELGFSLVGYGCTTCIGNSGPLLEPIEKAIQSSDLAVASVLSGNRNF 558 Query: 512 DGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEI-D 570 +GR+HP K +LASPPLVVAYA+AG++R DI + LG KDGKPV L +IWPS EI D Sbjct: 559 EGRVHPLVKTNWLASPPLVVAYALAGSVRMDISSEPLGEGKDGKPVYLRDIWPSSKEIAD 618 Query: 571 AVIAASVKPEQFRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRRPPYWE---GALA 624 AV A V F K Y +F + P Y W+ STYI+ PP+++ G L Sbjct: 619 AV--AQVDTAMFHKEYAEVFAGDAQWQAIEVPQAATYVWQKDSTYIQHPPFFDDISGPLP 676 Query: 625 GERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHL 684 + + G R LA+LGD++TTDH+SP+ I DS AG YL + G+ DFNSY + RG+H Sbjct: 677 VIQDISGARILALLGDSVTTDHISPAGNIKADSPAGRYLREQGVEPRDFNSYGSRRGNHE 736 Query: 685 TAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGA 744 R TFAN +++NEM G + G+ I P G +++A Y PL++IAG Sbjct: 737 VMMRGTFANIRIRNEML---GGEEGGNTLYI-PTGEKLAIYDAAMRYQAAGTPLVVIAGQ 792 Query: 745 DYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGT 804 +YG GSSRDWAAKG L GV+A++AE FERIHR+NLVGMGVLPL+FK +NR + + G Sbjct: 793 EYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTGK 852 Query: 805 EVFDVIG----SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQD 860 E D+ G + PR +LT++ITR++G +V V CR+DT EV ++AGG+L + Sbjct: 853 ETLDIQGLTGVELTPRMNLTLVITREDGSSEKVEVLCRIDTLNEVEYFKAGGILHYVLRQ 912 Query: 861 FLES 864 + S Sbjct: 913 LIAS 916 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: 1961 Number of extensions: 94 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: 2 Length of query: 867 Length of database: 916 Length adjustment: 43 Effective length of query: 824 Effective length of database: 873 Effective search space: 719352 Effective search space used: 719352 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