Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_008343808.1 BA79_RS03665 aconitate hydratase AcnA
Query= BRENDA::Q8EJW3 (867 letters) >NCBI__GCF_000691145.1:WP_008343808.1 Length = 909 Score = 715 bits (1845), Expect = 0.0 Identities = 390/892 (43%), Positives = 558/892 (62%), Gaps = 55/892 (6%) Query: 20 YFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQIIESK--------QE 71 ++ + EA+E G +KLPY+ +VL E+++R+ + ++ K+ +E+ +E Sbjct: 27 HYYSLEALEKQGIGNVSKLPYSIKVLLESVLRQVDGRVIK---KEHVENLAKWGTAEVKE 83 Query: 72 LDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYG 131 +D P+ P+RV+ D G A+VDLA LR A+A GGDP ++NP +P L++DHS+ V+ Sbjct: 84 IDVPFKPSRVILQDFTGVPAVVDLASLRKAMADVGGDPDKINPEIPVDLVIDHSVQVDKA 143 Query: 132 GFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHA- 190 G + DA N +E RN +R++F++W +KAF N +P GI+HQ+NLE ++ V+HA Sbjct: 144 GTE-DALNINMDLEFERNAERYNFLSWAKKAFNNYQAVPPATGIVHQVNLEYLASVVHAI 202 Query: 191 -RNG--VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELT 247 +G + +PDTLVGTDSHT ++ +GV+ GVGG+EAE+ MLG+ SY +P++IG +L Sbjct: 203 EEDGEIITYPDTLVGTDSHTTMINGIGVLGWGVGGIEAEAGMLGQPSYFPVPEVIGAKLV 262 Query: 248 GKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAA 307 G+ G TATD+ L +T+ LR + VV+ ++EFFG G L L DRATI+NM PE+GAT Sbjct: 263 GELPNGTTATDLALKVTQVLREKGVVNKFVEFFGPGVAQLPLADRATIANMAPEYGATCG 322 Query: 308 MFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGL-WSDDLKQAVYPRTLHFDLSSVVRTI 366 F +D++ L YL LTGR+ EQ+ +VE Y++ GL ++ D ++ ++ + DLS + + Sbjct: 323 FFPVDEEALAYLRLTGRDEEQINIVEEYSRANGLFYTPDAEEPIFTDVVEIDLSQIESNL 382 Query: 367 AGPSNPHARVPTSELAA-----------------------RGISGEVEN-EPGLMPDGAV 402 +GP P +P S++ + I ++ N E +M GA+ Sbjct: 383 SGPKRPQDLIPLSQMKETFHKHIESPAGNQGFGLEKSELDKQIEFDLANGEKAVMKTGAI 442 Query: 403 IIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLP 462 IAAITSCTNTSNP +I AGL+A+ A+ G+ +VKTSLAPGSK V YL + LLP Sbjct: 443 AIAAITSCTNTSNPYVLIGAGLVAKKASELGMKVPNYVKTSLAPGSKVVTGYLVNSGLLP 502 Query: 463 ELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQA 522 L LGF IVG+ CTTC G SG L+ I+ V + DL T+VLSGNRNF+GRIHP K Sbjct: 503 YLRDLGFNIVGYGCTTCIGNSGPLEKEIEDAVSENDLLITSVLSGNRNFEGRIHPLVKGN 562 Query: 523 FLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQF 582 +LASPPLVVAYA+AGT+ D+ KD +G+DK+G+ V +IWPS EI++V+ ++V PE F Sbjct: 563 YLASPPLVVAYALAGTVNIDLTKDPIGVDKNGENVYFNDIWPSMDEINSVVKSTVTPELF 622 Query: 583 RKVYEPMFDLSVDYGD---KVSPLYDWRPQSTYIRRPPYWEGALAGE----RTLKGMRPL 635 R YE +FD + + + LY W STYI PP++E L+ E LKG+R + Sbjct: 623 RSEYETVFDNNDRWNEIKTTDDALYKWDENSTYIDNPPFFEN-LSVEPGKVEPLKGLRVV 681 Query: 636 AVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPK 695 A GD++TTDH+SP+ AI D+ AG+YL + G+ DFNSY + RG+H R TFAN + Sbjct: 682 AKFGDSVTTDHISPAGAIGKDTPAGKYLQERGVSPRDFNSYGSRRGNHHVMMRGTFANIR 741 Query: 696 LKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWA 755 +KN++A +G P G VT +++A Y + L I+AG DYG GSSRDWA Sbjct: 742 IKNQIA----PGTEGGYTTYWPTGEVTSIYDACMRYKEDGTGLAILAGKDYGMGSSRDWA 797 Query: 756 AKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVF--DVIGSI 813 AKG L G++ ++AE FERIHR+NLV MGVLPL+FK GE+ TYG+ GTE F DV ++ Sbjct: 798 AKGTNLLGIKFVLAESFERIHRSNLVFMGVLPLQFKDGESAETYGLTGTETFEVDVDETV 857 Query: 814 APRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLESN 865 PR +TV +G V R D+ E+ Y GG+LQ ++ L SN Sbjct: 858 RPRDLVTVKAIDTDGNEKTFEVIVRFDSEVEIDYYRHGGILQMVLREKLASN 909 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: 1899 Number of extensions: 101 Number of successful extensions: 10 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: 909 Length adjustment: 43 Effective length of query: 824 Effective length of database: 866 Effective search space: 713584 Effective search space used: 713584 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