Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate Echvi_4039 Echvi_4039 aconitate hydratase 1
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__Cola:Echvi_4039 Length = 925 Score = 687 bits (1774), Expect = 0.0 Identities = 373/897 (41%), Positives = 537/897 (59%), Gaps = 75/897 (8%) Query: 37 KLPYTSRVLAENLVRRCEPEMLTASLKQII----ESKQELDFPWFPARVVCHDILGQTAL 92 +LP++ R+L EN +R + +T + + + D P+ PARV+ D G A+ Sbjct: 36 ELPFSIRILLENALRNYDDFAITKEHTETLLNWKPEASDKDVPYKPARVLMQDFTGVPAV 95 Query: 93 VDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDR 152 VD+A LR KG DP ++NP++P L+VDHS+ V+Y G + ++ KN +E RN +R Sbjct: 96 VDIASLRAEAVRKGKDPQKINPLIPVDLVVDHSVQVDYFGTNY-SYKKNVDVEYERNGER 154 Query: 153 FHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVAFPDTLVGTDSHTPHVDA 212 + F+ W QK+F N V+P G GI HQ+NLE ++ + R+G FPDTLVGTDSHTP V+ Sbjct: 155 YEFLKWAQKSFDNFSVVPPGMGICHQVNLEYLAKGVIERDGNVFPDTLVGTDSHTPMVNG 214 Query: 213 LGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKV 272 +GV+ GVGG+EAE+ +LG+ Y +P ++G++LTG+ G TATD+VL +TE LR V Sbjct: 215 IGVVGWGVGGIEAEAALLGQPIYFIMPQVVGLKLTGELPLGTTATDMVLTITELLRKHGV 274 Query: 273 VSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLV 332 V ++E FG G + LT+ DRATISNM+PEFG T F ID +TLDY++ T R +Q+KLV Sbjct: 275 VGKFVEVFGPGLDTLTVPDRATISNMSPEFGCTVTYFPIDDRTLDYMSKTNRSKDQIKLV 334 Query: 333 ETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNP-------------------- 372 E YAK LW +D + Y + DL +V T++GP P Sbjct: 335 EDYAKANMLWREDEESVKYSSLVELDLGTVEPTVSGPKRPQDKILVRNFKEKFGELLEEV 394 Query: 373 HAR--VPTS--------------------------ELAARGISG------EVENEPGLMP 398 H R +P E+A + +G ++ NE + Sbjct: 395 HGREYIPIDKRDKSRWFSEGGGQPVDKPGDLPEDVEIATKTKNGLKTVEVKINNEEFALS 454 Query: 399 DGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEA 458 DG+++IAAITSCTNTSNP +I AGL+A+ A +GL KPWVKTSLAPGSK V YLE + Sbjct: 455 DGSIVIAAITSCTNTSNPSVMIGAGLVAQKARERGLDVKPWVKTSLAPGSKVVTDYLEAS 514 Query: 459 NLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPY 518 LL +LE+L F +VG+ CT+C G SG L I V + DL +VLSGNRNF+ R+HP Sbjct: 515 GLLDDLEALRFHVVGYGCTSCIGNSGPLPKHIAHAVEENDLVVASVLSGNRNFEARVHPQ 574 Query: 519 AKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVK 578 K +L SP LVVAYA+AG + D+ ++ LG D + +PV L +IWPS+ EI V+ + Sbjct: 575 VKMNYLMSPMLVVAYALAGRVDVDLNEEPLGFDPNLEPVYLKDIWPSNDEIFEVMGKVLS 634 Query: 579 PEQFRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRRPPYWEGALAGE----RTLKG 631 P F K Y +F+ + + + +P +Y+W +STYI+ P+++G L+ E + ++G Sbjct: 635 PGDFDKNYGEIFEGNEQWKNLQAPSDKVYNWSEKSTYIKEAPFFQG-LSNEVPEPQNIQG 693 Query: 632 MRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATF 691 R L LGD+ITTDH+SP+ A S AG+YL G+ ++DFNSY + RG+ R TF Sbjct: 694 ARVLLKLGDSITTDHISPAGAFAESSPAGQYLVGRGVEKKDFNSYGSRRGNDEVMVRGTF 753 Query: 692 ANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSS 751 AN ++KN++A ++G P G ++EA E Y PL+++AG +YG GSS Sbjct: 754 ANVRIKNQLA-----SREGGYTTHIPSGEEMTVFEASEKYQKDDTPLVVLAGKEYGSGSS 808 Query: 752 RDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG 811 RDWAAKG L G+ A++AE +ERIHR+NLVGMGVLPL+F G++ ++ G+DG E + G Sbjct: 809 RDWAAKGTTLLGIHAVIAESYERIHRSNLVGMGVLPLQFAEGQSASSLGLDGKEEITIEG 868 Query: 812 ---SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLESN 865 + P +L + G V V CRLD+ E++ Y+ GG+L ++FL+ + Sbjct: 869 ITEGLTPLKNLKATAKKDGGAVVNFDVVCRLDSEVEIAYYKNGGILHYVLREFLKQD 925 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: 1978 Number of extensions: 94 Number of successful extensions: 8 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: 925 Length adjustment: 43 Effective length of query: 824 Effective length of database: 882 Effective search space: 726768 Effective search space used: 726768 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