Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate CA265_RS16400 CA265_RS16400 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683 (865 letters) >FitnessBrowser__Pedo557:CA265_RS16400 Length = 921 Score = 323 bits (829), Expect = 2e-92 Identities = 288/929 (31%), Positives = 446/929 (48%), Gaps = 118/929 (12%) Query: 4 EYRKHVAERAAEGIAPKPLD-ANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEAAY 62 +Y + + +R A+G+ PKP+D A ++ ++ +KN E ++ PG AA Sbjct: 6 DYIQEIEDRKAQGLHPKPIDGAELLSEIITQIKNVNNINREEAVNFFIYNTLPGTTAAAA 65 Query: 63 VKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDAL--DDAKLAPIAAKALS 120 VKA FL I E +TP+ A ELL M+GG +I L+D D+ A AA L Sbjct: 66 VKAQFLKEIILAEVIVAEITPDFAFELLSHMKGGPSIKVLLDIALADNGDKAKKAADVLK 125 Query: 121 HTLLMFDNFYD-VEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKV-TGETN 178 + ++D D +++ GNE AK++++S+A AE+F P +AE++ V F G+ + Sbjct: 126 TQVYLYDADTDRLKDAYNNGNEIAKEILESYAKAEFFTKLPEVAEEIKVVTFIAGIGDIS 185 Query: 179 TDDLSPAPDAWSRPDIPLHALAMLK-NAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVG 237 TD LSP A SR D LH M+ A+E I+ Q P K + + +KG Sbjct: 186 TDLLSPGNQAHSRSDRELHGKCMITPEAQEEIKALQ--AQHPDKSVMLVAEKG------- 236 Query: 238 DVVGTGSSRKSATNSV-LWFMGDDIPHVPNKRGGGLCLGGK-IAPIFFNTMEDAGALPIE 295 +G GSSR S N+V LW P+VP + G I+PIF T++ G + I+ Sbjct: 237 -TMGVGSSRMSGVNNVALWTGKRSSPYVPFVNIAPIVGGTNGISPIFLTTVDVTGGIGID 295 Query: 296 VD------------VSN------------LNMGDVIDVYPYKGEVRNHETGELLATFELK 331 + + N + G V+ + ++ N E EL+ + Sbjct: 296 LQNWVKKTDENGNVIRNEKDEPILEQRFSVETGTVLTINTKTKKLYNGEQ-ELIDISKAL 354 Query: 332 TDVLIDEVRAGGRIPLIIGRGLTTKAREALGLPHSDVFRQAKDVAESDRGFSLAQKMVGR 391 T ++ ++AGG +I G+ + T A + LG+ S VF AK+V+ +G + +K+ R Sbjct: 355 TPQKMEFMKAGGSYAIIFGKKIQTFAAKTLGIEASSVFAPAKEVSYEGQGLTAVEKIFNR 414 Query: 392 -ACGV---KGIRPGAYCEPKMTSVGSQDTTGPMTRDELKDLACLGFS--ADLVMQSFCHT 445 A G+ K + G+ ++ VGSQDTTG MT EL+ +A S D QS CHT Sbjct: 415 NAVGLTQGKVLHAGSDVRVEVNIVGSQDTTGLMTAQELEAMAATVISPIVDGAYQSGCHT 474 Query: 446 AA-YPKPVDVNTHHTLPDFIMNRGGVSLRPGDG-------VIHSWLNRMLLPD-TVGTGG 496 A+ + K N L F+ + G ++ R G VIH LN + + + + GG Sbjct: 475 ASVWDKKAQANIPK-LMKFMNDFGVITARDPKGEYHSMTDVIHKVLNDITIDEWAIIIGG 533 Query: 497 DSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVHAIPLY 556 DSHTR G++F A SG VA A ATG + +PESV V FKG M+ + RD+VHA L Sbjct: 534 DSHTRMSKGVAFGADSGTVALALATGEASMPIPESVKVTFKGLMKEHMDFRDVVHATQLQ 593 Query: 557 AIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASAERSAAGCTIKLNKEPI 616 ++Q +N+F GRI+E+ + L +QAF TD +AE A + + Sbjct: 594 MLQQ-------FDGENVFQGRIIEVH-IGTLLADQAFTFTDWTAEMKAKASICISQDDTL 645 Query: 617 IEYLNSNIVLLKWMIAEGYGDRRTL--------ERRIQGMEKWLANPELLEADADAEYAA 668 I+ L ++ MI +G + + +RI+ ++ + P L+ D +A+Y A Sbjct: 646 IQSLEIAKNRIQIMIDKGMDNHNQVLQGLINKANKRIEEIKTGI-KPALM-PDDNAKYYA 703 Query: 669 VIDIDLADIKEPILCAPN----------DPDDARPLSAVQGE-KIDEVFIGSCMTNIGHF 717 + IDL I+EP++ P+ D R L+ G+ K+D F+GSCM + Sbjct: 704 EVVIDLDLIEEPMIADPDVNNADVSKRYTHDTIRDLTFYGGDKKVDLGFVGSCMVHKDDL 763 Query: 718 RAAGKLL-----DAHKGQLPTRLWVAPPTRMDAAQLTEEG------------YYSVFGKS 760 + ++L K + L VA PT +L EG + KS Sbjct: 764 KIVSQMLKNVETQTGKVEFKAPLVVAAPTYNIIDELKAEGDWEYLQKYSGFEFSDALPKS 823 Query: 761 GAR--------IEIPGCSLCMGNQARVADGATVVSTSTRNFPNRL-----GTGANVFLAS 807 AR +E PGC+LCMGNQ + A G TV++TSTR F R+ G LAS Sbjct: 824 AARTEYENIMYLERPGCNLCMGNQEKAAKGDTVMATSTRLFQGRVVEDKDGKKGESLLAS 883 Query: 808 AELAAVAALIGKLPTPEEYQTYVAQVDKT 836 + ++A++G++P+ EEY+ V ++ T Sbjct: 884 TPVVVLSAILGRIPSIEEYKVAVEGINLT 912 Lambda K H 0.317 0.136 0.400 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: 1666 Number of extensions: 82 Number of successful extensions: 14 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: 865 Length of database: 921 Length adjustment: 43 Effective length of query: 822 Effective length of database: 878 Effective search space: 721716 Effective search space used: 721716 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