Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate 351600 BT2072 aconitate hydratase (NCBI ptt file)
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__Btheta:351600 Length = 747 Score = 214 bits (544), Expect = 2e-59 Identities = 223/765 (29%), Positives = 331/765 (43%), Gaps = 116/765 (15%) Query: 78 PARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDA 137 P RV D Q AL+ + + VP+ + DH L Y G +D Sbjct: 61 PDRVAMQDATAQMALLQFM-----------NAGKEKVAVPSTVHCDH-LIQAYKGAKEDI 108 Query: 138 FAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVAFP 197 A + NE+ + F+ + I G GI+HQ+ LE AFP Sbjct: 109 -----ATATKTNEEVYDFLRDVSSRY-GIGFWKPGAGIIHQVVLENY----------AFP 152 Query: 198 D-TLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITA 256 +VGTDSHTP+ LG++AIGVGG +A VM G +++P IIGV LTGK + Sbjct: 153 GGMMVGTDSHTPNAGGLGMVAIGVGGADAVDVMTGMEWELKMPRIIGVRLTGKLSGWTSP 212 Query: 257 TDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTL 316 D++L L L + +S +E+FG G +L+ +ATI NM E GAT ++F D + Sbjct: 213 KDVILKLAGILTVKGGTNSIIEYFGPGTASLSATGKATICNMGAEVGATTSLFPFDGRMA 272 Query: 317 DYLTLTGRE--AEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHA 374 YL TGR+ E + V+ + +D+ + Y R + DLS++ I GP P A Sbjct: 273 TYLRATGRDRIVELAEAVDCELRADQQVTDE-PEKYYDRVIDIDLSTLEPYINGPFTPDA 331 Query: 375 RVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGL 434 P SE A + + + P M + I SCTN+S +++ A LAR K L Sbjct: 332 ATPISEFAEKVL---LNGYPRKME-----VGLIGSCTNSSY-QDLSRAASLARQVKEKNL 382 Query: 435 T-RKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQE 493 + P + + PGS+ ++ E ++ + +G I+ AC C G ++ Sbjct: 383 SVASPLI---INPGSEQIRATAERDGMMDDFMQIGAVIMANACGPCIGQ-------WKRH 432 Query: 494 VIDRDLYATAVLSGNRNF----DGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLG 549 D + V S NRNF DG + Y AF+ASP L +A IAG + F+ KD L Sbjct: 433 TDDPTRKNSIVTSFNRNFAKRADGNPNTY---AFVASPELTMALTIAGDLCFNPLKDRL- 488 Query: 550 LDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLYDWRPQ 609 ++ DG+ V+L P E+ R G K + + Q Sbjct: 489 MNHDGEKVKLAE--PVGDEL-----------PLRGFTSGNEGYITPGGTKTAINVNPASQ 535 Query: 610 STYIRRP-PYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGL 668 + P P W+G + + M L TTDH+ S AG +L G Sbjct: 536 RLQLLTPFPAWDG-----QDILNMPLLIKAQGKCTTDHI---------SMAGPWLRFRGH 581 Query: 669 PEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAI 728 E ++ + + N + N V G K + EGI Sbjct: 582 LENISDNMLMGAVNAFNGETNNVWN-RSTNTYGTVSGTAKM-----YKSEGI-------- 627 Query: 729 ETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPL 788 P I++A +YG+GSSR+ AA R V I+A+ F RIH TNL G+L L Sbjct: 628 --------PSIVVAEENYGEGSSREHAAMEPRFLNVRVILAKSFARIHETNLKKQGMLAL 679 Query: 789 EFKAGENRATYG-IDGTEVFDVIG--SIAPRADLTVIITRKNGER 830 F ++A Y I ++ VIG AP +LTV++ ++G + Sbjct: 680 TF---ADKADYDKIQEHDLLSVIGLPDFAPGRNLTVVLHHEDGTK 721 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: 1546 Number of extensions: 87 Number of successful extensions: 5 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: 747 Length adjustment: 41 Effective length of query: 826 Effective length of database: 706 Effective search space: 583156 Effective search space used: 583156 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 Apr 09 2024. 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