Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_047092295.1 AAV99_RS02180 aconitate hydratase AcnA
Query= BRENDA::Q8EJW3 (867 letters) >NCBI__GCF_001013305.1:WP_047092295.1 Length = 890 Score = 686 bits (1769), Expect = 0.0 Identities = 381/887 (42%), Positives = 538/887 (60%), Gaps = 51/887 (5%) Query: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTAS--- 61 + T+ + G + Y+ A E G ++LP++ +VL EN++R E E T Sbjct: 9 LGTRKTLEVGGKSYAYYSLSAAEEKF--GDVSRLPHSMKVLLENMLR-FEDEGFTVGEEH 65 Query: 62 LKQIIESKQEL----DFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVP 117 ++ I++ ++ + + PARV+ D G +VDLA +RDAI GGD A++NP VP Sbjct: 66 VRAIVDWQKNPVTGNEIQYRPARVLLQDFTGVPCVVDLAAMRDAIGKLGGDTAKINPQVP 125 Query: 118 TQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMH 177 L++DHS+ V+ G K AF +N A+E RN +R+ F+ W + +N +P G GI H Sbjct: 126 VNLVIDHSVMVDEFGHPK-AFEQNMALEYERNAERYDFLKWGAVSLENFSAVPPGTGICH 184 Query: 178 QINLERMSPVIHA---RNG--VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGR 232 Q+NLE + + + +NG VA+PDT VGTDSHT ++ LGV+ GVGG+EAE+ MLG+ Sbjct: 185 QVNLEHIGKGVWSSEDQNGELVAYPDTCVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 244 Query: 233 ASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDR 292 M +P++ G L GK G+TATD+VL + LR VV ++EF+G G L+L DR Sbjct: 245 PISMLIPEVAGFRLDGKMAEGVTATDLVLTCVQMLREHGVVGRFVEFYGPGVANLSLADR 304 Query: 293 ATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYP 352 ATI+NM PE+GAT F ID +TL+YL LTGR E + LVE YAK G+W + V+ Sbjct: 305 ATIANMAPEYGATCGFFGIDDKTLEYLRLTGRPEETIALVEAYAKAQGMWFTPEAEPVFS 364 Query: 353 RTLHFDLSSVVRTIAGPSNPHARVPTSELAA------RGISGE-------VENEPGLMPD 399 TL D+++VV ++AGP P RV E+ + + G+ VE + + D Sbjct: 365 STLQLDMATVVPSLAGPKRPQDRVALPEVDELFNSDLKKVYGKDAPARVRVEGKDHDVGD 424 Query: 400 GAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEAN 459 G V+IAAITSCTNTSNP +IAAGL+A+ A KGL KPWVKTSLAPGS+ V YL ++ Sbjct: 425 GDVVIAAITSCTNTSNPDVLIAAGLVAKKAREKGLMPKPWVKTSLAPGSQVVTDYLVKSG 484 Query: 460 LLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYA 519 L +L+++GF +VG+ CTTC G SG L P I + + DL A +VLSGNRNF+GR+ P Sbjct: 485 LQEDLDAIGFDLVGYGCTTCIGNSGPLAPPISAAINNNDLVAASVLSGNRNFEGRVSPDV 544 Query: 520 KQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKP 579 + FLASPPLVVAYA+ GT+ DI +G D+DG V L ++WPS+ EI AA++ Sbjct: 545 RANFLASPPLVVAYALKGTVTQDITTTPIGQDQDGNDVMLADLWPSNLEIAENRAANIDR 604 Query: 580 EQFRKVYEPMFD-------LSVDYGDKVSPLYDWRPQSTYIRRPPYWEGALAGERTLK-- 630 F Y ++ + VD D Y+W P STY+ PPY++G +K Sbjct: 605 SMFEARYADVYKGDEHWQAIKVDASD----TYNWNPASTYVANPPYFDGMSMEPDAIKDI 660 Query: 631 -GMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRA 689 G +PLA+LGD++TTDH+SP+ +I DS AG YL +P++DFNSY + RG+H R Sbjct: 661 EGAKPLAILGDSVTTDHISPAGSIKEDSPAGSYLVNHQVPKKDFNSYGSRRGNHEVMMRG 720 Query: 690 TFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQG 749 TFAN ++KNEM V G V+ G G +++A + PL++I G +YG G Sbjct: 721 TFANIRIKNEM--VPG-VEGGETTY---NGEQMPIYDAAMKHKADGTPLVVIGGKEYGTG 774 Query: 750 SSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDV 809 SSRDWAAKG L GV A++ E +ERIHR+NL+GMGVLPL+F G+ R + G+ G F + Sbjct: 775 SSRDWAAKGTILLGVRAVIVESYERIHRSNLIGMGVLPLQFNDGDTRNSLGLTGDCTFSI 834 Query: 810 --IGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854 +G ++P D+ V +T+ +G + CR+DTA E+ Y GG+L Sbjct: 835 KGLGGLSPSQDVEVEVTKADGSTMSFMAKCRIDTANEMEYYRNGGIL 881 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: 1953 Number of extensions: 98 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: 890 Length adjustment: 43 Effective length of query: 824 Effective length of database: 847 Effective search space: 697928 Effective search space used: 697928 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