Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_043529276.1 JH15_RS08095 aconitate hydratase AcnA
Query= BRENDA::Q8EJW3 (867 letters) >NCBI__GCF_000759345.1:WP_043529276.1 Length = 914 Score = 721 bits (1862), Expect = 0.0 Identities = 400/896 (44%), Positives = 543/896 (60%), Gaps = 75/896 (8%) Query: 20 YFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQII-----ESKQELDF 74 Y+ +A EA+ G +LP T ++L EN +R + E ++ Q + E++ + Sbjct: 22 YYSLPKAAEAL--GDIQRLPVTLKILLENQLRFADDESVSREDMQALVDWQQEARSTREI 79 Query: 75 PWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFD 134 + PARV+ D G +VDLA +R A+ G DP+++NP+ P L++DHS+ V+ G D Sbjct: 80 GYRPARVLMQDFTGVPGVVDLASMRAAVEKLGEDPSRINPLSPVDLVIDHSVMVDKYG-D 138 Query: 135 KDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARN-- 192 AF N AIE RN +R+ F+ W Q AF N V+P G GI HQ+NLE + + + Sbjct: 139 PSAFRDNVAIEMDRNRERYEFLRWGQDAFDNFRVVPPGTGICHQVNLEYLGKTVWVKEED 198 Query: 193 --GVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKP 250 A+PDTLVGTDSHT ++ LGV+ GVGG+EAE+ MLG+ M +P+++G +LTGK Sbjct: 199 GKSFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVVGFKLTGKL 258 Query: 251 QPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFY 310 + GITATD+VL +T+ LR + VV ++EF+G+G + L L DRATI+NM PE+GAT F Sbjct: 259 REGITATDLVLTVTQMLRQKGVVGKFVEFYGDGLDDLPLADRATIANMAPEYGATCGFFP 318 Query: 311 IDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPS 370 +D +TL+YL LTGR E+V LVE Y K LW + V+ TL D+ V ++AGP Sbjct: 319 VDDETLNYLRLTGRSDEEVALVEAYCKEQDLWRKPGAEPVFSDTLQLDMGDVEASLAGPK 378 Query: 371 NPHARVPTSEL--------------AARGISGEVENEPGLMP------------------ 398 P RV S++ A+ G+ ++E G MP Sbjct: 379 RPQDRVALSDMKSTFENLMGDDAAEASATARGKFDSEGGQMPVGTHEHFEHHDSQDVDVE 438 Query: 399 -------DGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAV 451 GAV+IAAITSCTNTSNP ++AAGLLAR A KGL KPWVKTSLAPGSK V Sbjct: 439 GSTFKLNPGAVVIAAITSCTNTSNPSVMMAAGLLARKAVEKGLDTKPWVKTSLAPGSKVV 498 Query: 452 QLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNF 511 YL +L +LGF +VG+ CTTC G SG L P I++ + D DL +VLSGNRNF Sbjct: 499 TDYLAAGGFQDDLNALGFNLVGYGCTTCIGNSGPLLPPIEKAIEDGDLTVASVLSGNRNF 558 Query: 512 DGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDA 571 +GR+HP K +LASPPLVVAYA+AG +R DI K+ LG KDGKPV L +IWPS AEI A Sbjct: 559 EGRVHPLVKTNWLASPPLVVAYALAGNVRLDISKEPLGEGKDGKPVYLQDIWPSQAEI-A 617 Query: 572 VIAASVKPEQFRKVYEPMFDLSVDYGDKV--------SPLYDWRPQSTYIRRPPYWEGAL 623 V+ E +RK Y +F+ GD+V S +Y W STYI+ PP++EG Sbjct: 618 EAVEKVRTEMYRKEYAEVFE-----GDEVWKAIDVPQSQVYQWSEDSTYIQHPPFFEGMG 672 Query: 624 AGERTLKGM---RPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHR 680 L+ + R LA+LGD++TTDH+SP+ AI DS AG YL + G+ DFNSY + R Sbjct: 673 REPEPLQDVENARVLAMLGDSVTTDHISPAGAIKPDSPAGRYLQEHGVKPMDFNSYGSRR 732 Query: 681 GDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLII 740 G+H R TFAN +++NEM +DG +G R P +++A Y + +PL++ Sbjct: 733 GNHEVMMRGTFANVRIRNEM--LDG--VEGGYTRHVPSDEQMAIYDAAMKYAEEGRPLVV 788 Query: 741 IAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYG 800 IAG +YG GSSRDWAAKG RL GV A++AE +ERIHR+NL+GMGV+PL+F GE+R + G Sbjct: 789 IAGKEYGTGSSRDWAAKGTRLLGVRAVLAESYERIHRSNLIGMGVVPLQFPEGEDRKSLG 848 Query: 801 IDGTE--VFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854 + G E D I + P + V I GE+ ++ CR+DTA E+ Y GG+L Sbjct: 849 LTGDEEVSIDGIADLTPGGQVNVTIKSDKGEK-KIEALCRIDTANELEYYRHGGIL 903 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: 1994 Number of extensions: 91 Number of successful extensions: 8 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: 914 Length adjustment: 43 Effective length of query: 824 Effective length of database: 871 Effective search space: 717704 Effective search space used: 717704 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 24 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