Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate PfGW456L13_4052 Aconitate hydratase (EC 4.2.1.3)
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 Length = 913 Score = 719 bits (1856), Expect = 0.0 Identities = 406/916 (44%), Positives = 561/916 (61%), Gaps = 65/916 (7%) Query: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLT-ASLK 63 +NT + YF EA +++ G KLP + +VL ENL+R + + +T A LK Sbjct: 7 LNTLKTLQVGNKTYHYFSLPEAAKSL--GDLNKLPMSLKVLLENLLRWEDEKTVTGADLK 64 Query: 64 QII----ESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQ 119 + E + + + + PARV+ D G A+VDLA +R A+A GG+P ++NP+ P Sbjct: 65 ALAAWLKERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGNPQRINPLSPVD 124 Query: 120 LIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQI 179 L++DHS+ V+ AF +N IE +RN +R+ F+ W Q AF N V+P G GI HQ+ Sbjct: 125 LVIDHSVMVDKFA-SSSAFEQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQV 183 Query: 180 NLERMSPVIHARNG----VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASY 235 NLE + + ++ AFPDTLVGTDSHT ++ LGV+ GVGG+EAE+ MLG+ Sbjct: 184 NLEYLGRTVWTKDEDGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVS 243 Query: 236 MRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATI 295 M +P++IG +LTGK + GITATD+VL +T+ LR + VV ++EF+G+G L L DRATI Sbjct: 244 MLIPEVIGFKLTGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADRATI 303 Query: 296 SNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTL 355 +NM PE+GAT F +D TLDYL L+GR E V+LVE Y+K GLW ++ V+ +L Sbjct: 304 ANMAPEYGATCGFFPVDDITLDYLRLSGRPLETVQLVEAYSKAQGLWRLPGQEPVFTDSL 363 Query: 356 HFDLSSVVRTIAGPSNPHARV------------------PTSELAAR------------- 384 D+ SV +AGP P RV PTS+ R Sbjct: 364 ALDMGSVEACLAGPKRPQDRVTLPNVAQAFSDFTDLQFKPTSKEEGRLESEGGGGVAVGN 423 Query: 385 -GISGEV----ENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPW 439 ++GE E + + +GAV+IAAITSCTNTSNP ++AAGL+A+ A KGL RKPW Sbjct: 424 ADMAGEADYDYEGQTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVEKGLKRKPW 483 Query: 440 VKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDL 499 VK+SLAPGSK V Y + A L L+ LGF +VG+ CTTC G SG L I++ + DL Sbjct: 484 VKSSLAPGSKVVTDYYKAAGLTQYLDELGFALVGYGCTTCIGNSGPLSEPIEKAIQQADL 543 Query: 500 YATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRL 559 +VLSGNRNF+GR+HP K +LASPPLVVAYA+AGT+R D+ ++ LG KDGKPV L Sbjct: 544 TVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRTDLSREPLGDGKDGKPVYL 603 Query: 560 INIWPSDAEI-DAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRR 615 +IWPS EI DAV V F K Y +F + P Y W+ STYI+ Sbjct: 604 RDIWPSSKEIADAV--NQVNTAMFHKEYAEVFAGDEQWQAIKVPQAATYVWQDDSTYIQH 661 Query: 616 PPYWE---GALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEED 672 PP+++ G + + G R LA+LGD++TTDH+SP+ I +DS AG+YL G+ D Sbjct: 662 PPFFDDIGGPAPVVKDVSGARILALLGDSVTTDHISPAGNIKVDSPAGQYLRDKGVEPRD 721 Query: 673 FNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYM 732 FNSY + RG+H R TFAN +++NEM + G ++G R P G +++A Y Sbjct: 722 FNSYGSRRGNHEVMMRGTFANIRIRNEM--LGG--EEGGNTRYIPTGEKMSIYDAAMRYQ 777 Query: 733 DRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKA 792 PL++IAG +YG GSSRDWAAKG L GV+A+VAE FERIHR+NLVGMGVLPL+FK Sbjct: 778 ASGTPLVVIAGQEYGTGSSRDWAAKGTILLGVKAVVAESFERIHRSNLVGMGVLPLQFKL 837 Query: 793 GENRATYGIDGTEVFDVIG----SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIY 848 +NR + + G+E D++G + PR +LT++ITR++G R ++ V CR+DT EV + Sbjct: 838 DQNRKSLKLGGSETLDILGLTGVELTPRMNLTLVITREDGSREKIEVLCRIDTLNEVEYF 897 Query: 849 EAGGVLQRFAQDFLES 864 ++GG+L + + S Sbjct: 898 KSGGILHYVLRQLIAS 913 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: 1991 Number of extensions: 95 Number of successful extensions: 9 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: 913 Length adjustment: 43 Effective length of query: 824 Effective length of database: 870 Effective search space: 716880 Effective search space used: 716880 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