Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate GFF2274 Psest_2319 aconitate hydratase 1/2-methylisocitrate dehydratase, Fe/S-dependent
Query= BRENDA::Q8EJW3 (867 letters) >FitnessBrowser__psRCH2:GFF2274 Length = 867 Score = 1394 bits (3608), Expect = 0.0 Identities = 688/865 (79%), Positives = 761/865 (87%), Gaps = 8/865 (0%) Query: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64 MNT++RKPLPGT LDYFDTREAIEAI PG+Y KLPYTSRVLAE LVRRCEPE LT SLKQ Sbjct: 1 MNTEHRKPLPGTGLDYFDTREAIEAIQPGSYDKLPYTSRVLAEQLVRRCEPEALTDSLKQ 60 Query: 65 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124 IIE K++LDFPW+PARVVCHDILGQTALVDLAGLRDAIA +GGDPA+VNPVVPTQLIVDH Sbjct: 61 IIERKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEQGGDPAKVNPVVPTQLIVDH 120 Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184 SLAVE+ GFD DAF KNRA+E+RRNEDRFHFI WT+ AFKN+DVIP GNGIMHQINLE+M Sbjct: 121 SLAVEFAGFDPDAFEKNRAVEERRNEDRFHFIEWTKTAFKNVDVIPAGNGIMHQINLEKM 180 Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244 SPVI AR GVAFPDT VGTDSHTPHVDALGVIAIGVGGLEAE+VMLG S MRLPDI+GV Sbjct: 181 SPVIQARGGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAETVMLGLPSMMRLPDIVGV 240 Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304 LTGK QPGITATDIVLALTEFLR ++VV +++EFFGEGA++LT+GDRATISNM PE+GA Sbjct: 241 RLTGKRQPGITATDIVLALTEFLRKERVVGAWVEFFGEGADSLTIGDRATISNMCPEYGA 300 Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364 TA+MFYIDQQT+DYL LTGRE EQV LVE YAK GLW+ L+ A Y R L FDLSSVVR Sbjct: 301 TASMFYIDQQTIDYLKLTGREPEQVALVEQYAKETGLWATALEGAEYERVLEFDLSSVVR 360 Query: 365 TIAGPSNPHARVPTSELAARGISGE-------VENEPGLMPDGAVIIAAITSCTNTSNPR 417 +AGPSNPH R+PTS L RGI+ E E GL+PDGAVIIAAITSCTNTSNPR Sbjct: 361 NMAGPSNPHKRLPTSALHERGIADEDKLAAARAEEAEGLLPDGAVIIAAITSCTNTSNPR 420 Query: 418 NVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACT 477 NV+AAGLLA+ AN GL RKPWVKTS APGSK +LYLEEA LL ELE LGFGIV +ACT Sbjct: 421 NVVAAGLLAKKANELGLVRKPWVKTSFAPGSKVAKLYLEEAGLLSELEKLGFGIVAYACT 480 Query: 478 TCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 537 TCNGMSGALDPVIQQE+I+RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG Sbjct: 481 TCNGMSGALDPVIQQEIIERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 540 Query: 538 TIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYG 597 T+RFDIE+DVLG DK+G P+ L ++WPSD EIDA++A+SVKPEQF+++Y PMFDL Sbjct: 541 TVRFDIEQDVLGTDKNGNPITLKDLWPSDEEIDAIVASSVKPEQFKQIYIPMFDLGT-IE 599 Query: 598 DKVSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDS 657 + SPLYDWRP STYIRRPPYWEGALAGERTLKGMRPLA+L DNITTDHLSPSNAI++DS Sbjct: 600 EAKSPLYDWRPMSTYIRRPPYWEGALAGERTLKGMRPLAILPDNITTDHLSPSNAILLDS 659 Query: 658 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEP 717 AAGEYL KMGLPEEDFNSYATHRGDHLTAQRATFANP+L NEMA+VDGK ++GSLAR+EP Sbjct: 660 AAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPQLVNEMAVVDGKAQKGSLARVEP 719 Query: 718 EGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHR 777 EG V RMWEAIETYM+RKQ LII+AGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHR Sbjct: 720 EGKVMRMWEAIETYMNRKQNLIIVAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR 779 Query: 778 TNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTC 837 TNLVGMGVLP+EFK G R T G+DGTE FD+ G ++PR DLT++I +GE VPVTC Sbjct: 780 TNLVGMGVLPVEFKPGTTRLTLGLDGTETFDIEGELSPRCDLTLVIHHMSGEETRVPVTC 839 Query: 838 RLDTAEEVSIYEAGGVLQRFAQDFL 862 RLDTA EVS+Y+AGGVLQRFA+DFL Sbjct: 840 RLDTAAEVSVYQAGGVLQRFAKDFL 864 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: 2240 Number of extensions: 80 Number of successful extensions: 3 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: 867 Length adjustment: 42 Effective length of query: 825 Effective length of database: 825 Effective search space: 680625 Effective search space used: 680625 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