Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate GFF1856 PGA1_c18830 aconitate hydratase AcnA
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__Phaeo:GFF1856 Length = 895 Score = 688 bits (1776), Expect = 0.0 Identities = 389/897 (43%), Positives = 536/897 (59%), Gaps = 48/897 (5%) Query: 6 NTQYRKPLP--GTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEP--EMLTAS 61 N + R+ L G ++ Y+ A EA G +AKLP +V+ EN++R + + T Sbjct: 9 NAKTRRKLSAGGKSISYYSIPAATEA-GLGDFAKLPAALKVVLENMLRFEDGGFSVSTDD 67 Query: 62 LKQIIE-----SKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVV 116 +K E K + + PARV+ D G A+VDLA +RD I A GGD ++NP+ Sbjct: 68 IKAFAEWGANGGKNPREIAYRPARVLMQDFTGVPAVVDLAAMRDGIKALGGDAQKINPLN 127 Query: 117 PTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIM 176 P L++DHS+ ++ G + AF N E RN +R+ F+ W Q AF N V+P G GI Sbjct: 128 PVDLVIDHSVMIDEFGNPR-AFQMNVDREYERNMERYQFLKWGQGAFNNFRVVPPGTGIC 186 Query: 177 HQINLERMSPVIHA---RNG--VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLG 231 HQ+NLE ++ I + +NG VA+PDTLVGTDSHT V+ V+ GVGG+EAE+ MLG Sbjct: 187 HQVNLEYLAQTIWSDEDQNGDMVAYPDTLVGTDSHTTMVNGAAVLGWGVGGIEAEAAMLG 246 Query: 232 RASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGD 291 + M +P++IG ELTG G T TD+VL + E LRA+ VV ++EF+G+G + L L D Sbjct: 247 QPISMLIPEVIGFELTGAMVEGTTGTDLVLKVVEMLRAKGVVGKFVEFYGKGLDTLPLAD 306 Query: 292 RATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVY 351 RATI+NM PE+GAT F ID +T+ YL TGR+ +++ LVE YAK G W D +Y Sbjct: 307 RATIANMAPEYGATCGFFPIDDETIRYLRNTGRDEDRIALVEAYAKENGFWRDADYAPIY 366 Query: 352 PRTLHFDLSSVVRTIAGPSNPHARVPTSELAAR-------------GISGEVENEPGLMP 398 TL D+ ++V I+GP P V + A G V+ E M Sbjct: 367 TDTLSLDMGTIVPAISGPKRPQDYVALTGAKAAFQKEMEETFKRPMGKEIAVKGEDYTME 426 Query: 399 DGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEA 458 G V+IA+ITSCTNTSNP +I AGL+AR A A GL RKPWVKTSLAPGS+ V YLE A Sbjct: 427 SGKVVIASITSCTNTSNPYVMIGAGLVARKAAALGLDRKPWVKTSLAPGSQVVSAYLEAA 486 Query: 459 NLLPELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPY 518 NL +L+ +GF +VG+ CTTC G SG + + + + DL AT+VLSGNRNF+GRI P Sbjct: 487 NLQEDLDKIGFNLVGYGCTTCIGNSGPIQQELSDAIAEGDLVATSVLSGNRNFEGRISPD 546 Query: 519 AKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVK 578 + +LASPPLVVAYA+AGT+ D+ D + DKDG V L +IWPS EI ++ A+V Sbjct: 547 VRANYLASPPLVVAYALAGTMDIDLATDPIAQDKDGNDVYLKDIWPSQKEIADLVEATVT 606 Query: 579 PEQFRKVYEPMFD-----LSVDYGDKVSPLYDWRPQSTYIRRPPYWEGALAGERT---LK 630 E F Y +F +V+ D + YDW STYI+ PPY++G T +K Sbjct: 607 REAFLSKYADVFKGDEKWQAVETTD--AETYDWPAASTYIQNPPYFQGMGTEPGTISNIK 664 Query: 631 GMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRAT 690 +PL +LGD +TTDH+SP+ + + AG+YL + +FNSY + RG+H R T Sbjct: 665 DAKPLLILGDMVTTDHISPAGSFATTTPAGQYLLDRQVQPREFNSYGSRRGNHEIMMRGT 724 Query: 691 FANPKLKNEMAI-VDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQG 749 FAN ++KNEM V+G +G P+G T ++EA Y ++ PL++ G YG G Sbjct: 725 FANIRIKNEMLDGVEGGYTKG------PDGEQTSVYEASMAYQEQGIPLVVFGGEQYGAG 778 Query: 750 SSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDV 809 SSRDWAAKG L GV+A++AE FERIHR+NLVGMGV+P EF G+ R + + G E + Sbjct: 779 SSRDWAAKGTALLGVKAVIAESFERIHRSNLVGMGVIPFEFTGGDTRKSLNLTGDETVSI 838 Query: 810 IG--SIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLES 864 G +I P+ +++ IT +G + + CR+DTA E+ E GGVL ++ +S Sbjct: 839 HGLDTIKPQEEVSCDITYGDGTTKTITLKCRIDTAPEIEYIEHGGVLHYVLRNLAKS 895 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: 1966 Number of extensions: 100 Number of successful extensions: 9 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