Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_058929322.1 AU252_RS02190 aconitate hydratase AcnA
Query= BRENDA::Q8EJW3 (867 letters) >NCBI__GCF_001484605.1:WP_058929322.1 Length = 936 Score = 697 bits (1800), Expect = 0.0 Identities = 394/900 (43%), Positives = 539/900 (59%), Gaps = 88/900 (9%) Query: 38 LPYTSRVLAENLVRRCEPEMLTASLKQII-----ESKQELDFPWFPARVVCHDILGQTAL 92 LP++ +VL ENL+R + +TA + + +++ + + PARV+ D G + Sbjct: 34 LPFSLKVLLENLLRTEDGANITADHVRALAGWDPDAQPNTEIQFTPARVIMQDFTGVPCV 93 Query: 93 VDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDR 152 VDLA +R+A+ GGDP +VNP+ P ++++DHS+ ++ G + A +N IE +RN +R Sbjct: 94 VDLATMREAVKELGGDPKRVNPLAPAEMVIDHSVQIDAFG-NSGALERNMEIEYQRNGER 152 Query: 153 FHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHAR--NGV--AFPDTLVGTDSHTP 208 + F+ W Q AF + V+P G GI+HQ+N+E ++ + R +GV A+PDT VGTDSHT Sbjct: 153 YQFLRWGQTAFDDFKVVPPGTGIVHQVNIEYLARTVMTREIDGVLRAYPDTCVGTDSHTT 212 Query: 209 HVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLR 268 V+ LGV+ GVGG+EAE+ MLG+ M +P ++G +LTG G TATD+VL +TE LR Sbjct: 213 MVNGLGVLGWGVGGIEAEAAMLGQPVSMLIPRVVGFKLTGSIPAGATATDVVLTITEQLR 272 Query: 269 AQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQ 328 VV ++EF+GEG A+ L +RATI NM+PEFG+TAAMF ID TLDYL LTGR E Sbjct: 273 KHGVVGKFVEFYGEGVAAVPLANRATIGNMSPEFGSTAAMFPIDDVTLDYLRLTGRSDEN 332 Query: 329 VKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARV------------ 376 V LVE+YAK GLW D ++ + L DLS+VV +I+GP P R+ Sbjct: 333 VALVESYAKEQGLWHDASREIKFSEYLELDLSTVVPSISGPKRPQDRIELTDAKEQFRKD 392 Query: 377 --------------------PTSEL------------------AARGISGEVENEPGLMP 398 P S+ AA G G N + Sbjct: 393 IHNYVAIEDGSVDESLDESFPASDAPSFTHADSHTTETSRVVSAANGAHGRPSNPVHIKT 452 Query: 399 D---------GAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSK 449 + GAV IA+ITSCTNTSNP ++AA LLARNA KGLT KPWVKTS+APGSK Sbjct: 453 EDGREFELDHGAVSIASITSCTNTSNPSVMLAAALLARNAVDKGLTSKPWVKTSVAPGSK 512 Query: 450 AVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNR 509 V Y ++ L P LE LGF IVG+ C TC G SG LD I + + DL TAVLSGNR Sbjct: 513 VVTDYYNKSGLTPYLEKLGFYIVGYGCATCIGNSGPLDAEISEAIQANDLSVTAVLSGNR 572 Query: 510 NFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEI 569 NF+GRI+P K +LASPPLV+AYA+AG++ FD + D LG D+ G V L +IWP+ E+ Sbjct: 573 NFEGRINPDVKMNYLASPPLVIAYALAGSMDFDFDTDSLGKDEAGNDVFLKDIWPNPVEV 632 Query: 570 DAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLYD---WRPQSTYIRRPPYWEGALAGE 626 VI +S+ + F + YE +FD + +P D W P STY+R+PPY++G A Sbjct: 633 QQVIDSSIDKDMFARGYEGVFDGDARWKALDTPAGDTFAWDPNSTYVRKPPYFDGIKAQP 692 Query: 627 ---RTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDH 683 + + G R L LGD++TTDH+SP+ + D+ AG+YL G+ +DFNSY + RG+H Sbjct: 693 EPVQDISGARVLLKLGDSVTTDHISPAGSFKSDTPAGQYLLANGVERKDFNSYGSRRGNH 752 Query: 684 LTAQRATFANPKLKNEMAIVDGKVKQGSLAR--IEPEGIVTRMWEAIETYMDRKQPLIII 741 R TFAN ++KN+ I+DG +G R + +G +++A + Y PL+++ Sbjct: 753 EVMIRGTFANIRIKNQ--ILDG--VEGGFTRDFTQADGPQAYVYDAAQNYQAAGTPLVVL 808 Query: 742 AGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGI 801 AG +YG GSSRDWAAKG L GV+A+VAE +ERIHR+NL+GMGVLPL+F AGE+ AT G+ Sbjct: 809 AGKEYGSGSSRDWAAKGTALLGVKAVVAESYERIHRSNLIGMGVLPLQFPAGESAATLGL 868 Query: 802 DGTEVFDVIGSIA------PRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQ 855 GTE F V G A P+ L V T ++G R+DT E Y GG+LQ Sbjct: 869 TGTETFAVEGVTALNEGTTPKT-LKVTATAEDGSAKSFDAVLRIDTPGEADYYRNGGILQ 927 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: 2007 Number of extensions: 95 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: 936 Length adjustment: 43 Effective length of query: 824 Effective length of database: 893 Effective search space: 735832 Effective search space used: 735832 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 Apr 09 2024. 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