Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate Dsui_2347 Dsui_2347 aconitate hydratase 1
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__PS:Dsui_2347 Length = 898 Score = 698 bits (1801), Expect = 0.0 Identities = 389/876 (44%), Positives = 533/876 (60%), Gaps = 50/876 (5%) Query: 21 FDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLT-------ASLKQIIESKQELD 73 F + A+EA G ++LP + R++ E L+R C+ +T A+ + E +E+ Sbjct: 22 FHSLPALEAAGIGPVSRLPVSLRIVLEALLRHCDGRRVTPRHVLQLANWQPRAERTEEI- 80 Query: 74 FPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAV-EYGG 132 P+ ARVV D G L DLA +RDA AA+G DP ++ P+VP L+VDHS+ V EYG Sbjct: 81 -PFVVARVVLQDFTGVPLLCDLAAMRDAAAAQGTDPKRIEPLVPVDLVVDHSVQVDEYG- 138 Query: 133 FDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARN 192 A +N +E +RN +R+ F+ W +AF V+P G GI+HQ+NLE + + + Sbjct: 139 -TPTALRRNMELEFQRNAERYQFMKWGMQAFDTFKVVPPGIGIVHQVNLEYLFRGVRRQG 197 Query: 193 GVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQP 252 + FPDTLVGTDSHT ++ +GV+ GVGG+EAE+ MLG+ Y PD++GVEL G+ Sbjct: 198 ELLFPDTLVGTDSHTTMINGVGVVGWGVGGIEAEAAMLGQPVYFLTPDVVGVELRGRLNE 257 Query: 253 GITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYID 312 G+TATD+VL +TE LR +KVV ++EFFG G+ +L+L DRATI+NM PE+GAT F +D Sbjct: 258 GVTATDLVLTVTELLRREKVVGKFVEFFGPGSTSLSLTDRATIANMAPEYGATLGFFPVD 317 Query: 313 QQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAV-YPRTLHFDLSSVVRTIAGPSN 371 ++T+DYL TGR +V+ E Y + GL+ + Y L DL+++V ++AGP Sbjct: 318 EKTVDYLRQTGRNEAEVEAFEAYFRAQGLFGAPRAGDIDYSTQLSLDLATIVPSLAGPKR 377 Query: 372 PHARVPTSEL------------AARGISGEVENEPGLMP---------DGAVIIAAITSC 410 P R+ S++ +A G E P P G V+IAAITSC Sbjct: 378 PQDRIDLSDMGRSFDTLFSQPTSANGFGKPAEQLPQRQPTARAGVDLGHGDVLIAAITSC 437 Query: 411 TNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFG 470 TNTSNP +IAAGLLA+ A KGL+ +P +KTSLAPGS+ V YLE+A LL L LGF Sbjct: 438 TNTSNPAVLIAAGLLAKKAVDKGLSVQPHIKTSLAPGSRVVTDYLEKAGLLAPLARLGFA 497 Query: 471 IVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLV 530 + G+ CTTC G +G L P Q + +RDL AVLSGNRNF+ RIHP + +LASPPLV Sbjct: 498 LAGYGCTTCIGNAGDLAPEFNQAIAERDLVVAAVLSGNRNFEARIHPAIRANYLASPPLV 557 Query: 531 VAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMF 590 VA+AIAG + D+ LG +DG+PV L IWPS EI V+ + P +R++Y F Sbjct: 558 VAFAIAGRVNVDLTTTPLGTGRDGQPVYLREIWPSSEEIATVLPFAQDPATYRRLYAD-F 616 Query: 591 DLSVDYGDKV----SPLYDWRPQSTYIRRPPYWEGALAGERTL---KGMRPLAVLGDNIT 643 D + V +YDW P STYI RPP+++G L G R L VLGD++T Sbjct: 617 TRDHDLWNAVPAPEGQIYDW-PPSTYIARPPFFDGFTVEPPPLAPINGARALLVLGDSVT 675 Query: 644 TDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEM--A 701 TDH+SP+ + + AG++L G+ DFNSY + RG H R TFAN ++KN M Sbjct: 676 TDHISPAGSFKAATPAGQWLTAQGVKSLDFNSYGSRRGHHEVMVRGTFANVRVKNLMLPP 735 Query: 702 IVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRL 761 DG +G ++ + + ++EA Y R P ++ AG +YG GSSRDWAAKG RL Sbjct: 736 KADGSPVEGGYTLLDGQQVT--VFEAASAYQQRGIPTLVFAGEEYGTGSSRDWAAKGTRL 793 Query: 762 AGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAP---RAD 818 GV A+VA FERIHR NLVGMGVLPL+FKAG + A+ G+DG+E FD+ G+ P + D Sbjct: 794 LGVRAVVARSFERIHRANLVGMGVLPLQFKAGTSAASLGLDGSEHFDLPGADGPLQAQQD 853 Query: 819 LTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854 L + ITR +G +VP+ CR+DT EV + GG+L Sbjct: 854 LMLRITRSDGRVEQVPLLCRIDTPIEVEYFRHGGIL 889 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: 2037 Number of extensions: 119 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 867 Length of database: 898 Length adjustment: 43 Effective length of query: 824 Effective length of database: 855 Effective search space: 704520 Effective search space used: 704520 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