Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate CCNA_03781 CCNA_03781 aconitate hydratase
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__Caulo:CCNA_03781 Length = 895 Score = 656 bits (1693), Expect = 0.0 Identities = 378/870 (43%), Positives = 523/870 (60%), Gaps = 42/870 (4%) Query: 20 YFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTAS-LKQII-----ESKQELD 73 Y+ R A EA + LP + +VL ENL+R + + LK + + E + Sbjct: 22 YYSLRAAEEA-GLADVSSLPVSMKVLLENLLRNEDGVSVNEDDLKAVAAWLNNKGSVEHE 80 Query: 74 FPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGF 133 + PARV+ D G A+VDLA +RDA+ A G DPA++NP+ P L++DHS+ V+ G Sbjct: 81 ISFRPARVLMQDFTGVPAVVDLAAMRDAMVALGADPAKINPLNPVDLVIDHSVMVDNFGN 140 Query: 134 DKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARN- 192 K A+ N E RN +R+ F+ W AF N V+P G GI HQ+NLE ++ + Sbjct: 141 PK-AYDDNVKREYERNIERYRFLRWGSSAFNNFRVVPPGTGICHQVNLEYLAQTVWTNTV 199 Query: 193 ---GVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGK 249 VA+PDT+VGTDSHT V+ L V+ GVGG+EAE+ MLG+ M +P++IG +LTG Sbjct: 200 DGAEVAYPDTVVGTDSHTTMVNGLAVLGWGVGGIEAEAAMLGQPIPMLIPEVIGFKLTGA 259 Query: 250 PQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMF 309 G TATD+VL +T+ LR + VV ++EF+G+ LTL D+ATI+NM PE+GAT F Sbjct: 260 MPEGATATDLVLTVTQMLRKKGVVGKFVEFYGDALANLTLEDQATIANMAPEYGATCGFF 319 Query: 310 YIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDD-LKQAVYPRTLHFDLSSVVRTIAG 368 I T+ YL TGR AE+V LVE YAK GLW + + + + TL DLS+V+ ++AG Sbjct: 320 PISAATIAYLKGTGRAAERVALVEAYAKEQGLWWEPGVAEPTFTDTLELDLSTVLPSLAG 379 Query: 369 PSNPHARVPTSELAAR---GISGE------------VENEPGLMPDGAVIIAAITSCTNT 413 P P RV S+ AA+ ++GE VE E + G V+IAAITSCTNT Sbjct: 380 PKRPQDRVLLSDAAAKFAESLAGEFGKAENPELRAPVEGEDFDVGHGDVVIAAITSCTNT 439 Query: 414 SNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVG 473 SNP +IAAGLLA+NA AKGL KPWVKTSLAPGS+ V YL +A L L++LGF +VG Sbjct: 440 SNPSVLIAAGLLAKNAVAKGLKAKPWVKTSLAPGSQVVTDYLAKAGLTKHLDALGFNLVG 499 Query: 474 FACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAY 533 + CTTC G SG L I + + D DL A +VLSGNRNF+GR++P + +LASPPLVVAY Sbjct: 500 YGCTTCIGNSGPLPEAISKTINDNDLVACSVLSGNRNFEGRVNPDVRANYLASPPLVVAY 559 Query: 534 AIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLS 593 A+AG+++ D+ +G DK G V L +IWPS+ +I A+ ++ + F Y +F Sbjct: 560 ALAGSLKIDLATQPIGQDKKGNDVFLKDIWPSNEDIAALQRKAINEKMFATRYGDVFKGD 619 Query: 594 VDY-GDKVS--PLYDWRPQSTYIRRPPYWEG---ALAGERTLKGMRPLAVLGDNITTDHL 647 ++ G KV+ Y W STY++ PPY+ A + R LAV GD+ITTDH+ Sbjct: 620 KNWQGIKVTGGQTYAWEADSTYVQNPPYFPNMSMTPAPVTDIVEARILAVFGDSITTDHI 679 Query: 648 SPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKV 707 SP+ +I S AG++L G+ DFN Y RG+H R TFAN +++N + Sbjct: 680 SPAGSIKASSPAGKFLIDNGVEPVDFNGYGARRGNHQVMMRGTFANIRIRNRIT----PD 735 Query: 708 KQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAI 767 +G + + P G V +++A Y + +P ++ G +YG GSSRDWAAKG +L GV A+ Sbjct: 736 IEGGVTKHFPTGEVMSIYDAAMKYQEEGRPAVVFGGKEYGTGSSRDWAAKGTKLLGVRAV 795 Query: 768 VAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG--SIAPRADLTVIITR 825 + E FERIHR+NLVGMGVLPL+F + + G E+ + G +APR L V + R Sbjct: 796 ICESFERIHRSNLVGMGVLPLQF-VQDGWQKLELTGEEIVSIRGLTDLAPRKQLIVELYR 854 Query: 826 KNGERV-EVPVTCRLDTAEEVSIYEAGGVL 854 R+ PV CR+DT E+ ++ GGVL Sbjct: 855 PTDGRIARFPVRCRIDTPTELEYFKNGGVL 884 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: 1916 Number of extensions: 90 Number of successful extensions: 11 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: 895 Length adjustment: 43 Effective length of query: 824 Effective length of database: 852 Effective search space: 702048 Effective search space used: 702048 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