Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate 3608455 Dshi_1851 aconitate hydratase 1 (RefSeq)
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__Dino:3608455 Length = 928 Score = 683 bits (1762), Expect = 0.0 Identities = 383/893 (42%), Positives = 527/893 (59%), Gaps = 73/893 (8%) Query: 26 AIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQIIE--------SKQELDFPWF 77 A E G ++KLP +V+ EN++R E T S+ I + + + Sbjct: 30 AAETAGLGDFSKLPAALKVVLENMLR-FEDGGRTVSVDDIRAFADWADKGGQNPREIAYR 88 Query: 78 PARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDA 137 PARV+ D G A+VDLA +RD I GGD ++NP+ P L++DHS+ ++ G + A Sbjct: 89 PARVLMQDFTGVPAVVDLAAMRDGIVGLGGDAEKINPLNPVDLVIDHSVMIDEFGNPR-A 147 Query: 138 FAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVI-----HARN 192 F N E RN +R+ F+ W Q AF N V+P G GI HQ+NLE ++ + + Sbjct: 148 FQMNVDREYERNIERYTFLKWGQSAFANFRVVPPGTGICHQVNLEYLAQAVWTDTDQSGQ 207 Query: 193 GVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQP 252 VA+PDTLVGTDSHT V+ + V+ GVGG+EAE+ MLG+ M +P+++G ELTG+ Sbjct: 208 EVAYPDTLVGTDSHTTMVNGMAVLGWGVGGIEAEAAMLGQPISMLIPEVVGFELTGEMME 267 Query: 253 GITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYID 312 G T TD+VL + E LRA+ VV ++EF+G G + L L DRATI+NM PE+GAT F ID Sbjct: 268 GTTGTDLVLKVVEMLRAKGVVGKFVEFYGAGLDHLPLADRATIANMAPEYGATCGFFPID 327 Query: 313 QQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNP 372 +TL Y+ TGR+ ++ LVE YAK GLW D VY TL D+ ++V I+GP P Sbjct: 328 GETLRYMRTTGRDEARIALVEAYAKENGLWRGDDYAPVYTDTLSLDMGTIVPAISGPKRP 387 Query: 373 HARVPTSE--------------------------------LAARGISGE--------VEN 392 V + +A R I G+ V Sbjct: 388 QDYVALDKAAETFRDYVTGQRPDWSADEEDKAEWTDEGGAVAPRDIPGDRGKHKRARVRG 447 Query: 393 EPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQ 452 + DG ++IA+ITSCTNTSNP +I AGL+AR A A GLTRKPWVKTSLAPGS+ V Sbjct: 448 ADYTIHDGTIVIASITSCTNTSNPYVMIGAGLVARKARALGLTRKPWVKTSLAPGSQVVS 507 Query: 453 LYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFD 512 YLE A L +L+++GF +VG+ CTTC G SG + + + + D D+ AT+VLSGNRNF+ Sbjct: 508 AYLEAAGLQEDLDAIGFNLVGYGCTTCIGNSGPIQEELSEAINDGDIIATSVLSGNRNFE 567 Query: 513 GRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAV 572 GRI P + +LASPPLVVAYA+AG + D+ +D LG D+DG V L +IWPS EI + Sbjct: 568 GRISPDVRANYLASPPLVVAYALAGDMNVDLTRDPLGQDRDGNDVYLKDIWPSTKEIAEL 627 Query: 573 IAASVKPEQFRKVYEPMFD-----LSVDYGDKVSPLYDWRPQSTYIRRPPYWEGALAGER 627 + +V E F+ Y +F SV+ D ++ YDW P STY++ PPY++G A Sbjct: 628 VEQTVTREAFQAKYADVFKGDEKWQSVETTDSLT--YDWPPSSTYVQNPPYFQGMSAEPG 685 Query: 628 T---LKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHL 684 T ++G + LA+LGD ITTDH+SP+ + + AG YL + + +FNSY + RG+H Sbjct: 686 TISNIEGAKILAILGDMITTDHISPAGSFKESTPAGRYLTERQVQPREFNSYGSRRGNHE 745 Query: 685 TAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGA 744 R TFAN +++NEM +DG V+ G + P+G T ++EA Y + PL+I G Sbjct: 746 VMMRGTFANIRIRNEM--LDG-VEGG--YTLGPDGQQTSIFEAAMAYQEMGTPLVIFGGE 800 Query: 745 DYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGT 804 YG GSSRDWAAKG L GV+A++AE FERIHR+NLVGMGV+P EF G+ R T G+ G Sbjct: 801 QYGAGSSRDWAAKGTSLLGVKAVIAESFERIHRSNLVGMGVIPFEFTGGDTRKTLGLKGD 860 Query: 805 EVFDVI---GSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVL 854 E + G I P +++ IT +G E+ + CR+DT E+ E GGVL Sbjct: 861 ETVSITGLDGKIVPLSEMPCTITYGDGTTREITLKCRIDTEVEIEYIENGGVL 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: 2072 Number of extensions: 113 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: 928 Length adjustment: 43 Effective length of query: 824 Effective length of database: 885 Effective search space: 729240 Effective search space used: 729240 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