Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate SMc02227 SMc02227 fatty oxidation complex enoyl-COA hydratase/3-hydroxyacyl-COA dehydrogenase/3-hydroxybutyryl-COA epimerase
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__Smeli:SMc02227 Length = 737 Score = 312 bits (799), Expect = 4e-89 Identities = 230/731 (31%), Positives = 348/731 (47%), Gaps = 61/731 (8%) Query: 11 DQVAIVTVDSPP--VNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADIT-- 66 D +A+VT D P +N + V + + ++ ADPAV+ +V+ +F GAD++ Sbjct: 13 DGIALVTWDMPDKSMNVFTEEVMKELDAIIDQTTADPAVKGVVITSGKSSFSGGADLSMI 72 Query: 67 ---------EFGKPPQPPA---------LNDVIAALENSPKPTIAAIHGTALGGGLEVAL 108 E K P A + + LE S KP ++AI+GT +GG E++L Sbjct: 73 KSMFTFQAEERKKDPDNAARKLFDLVGRMTGLFRKLETSGKPWVSAINGTCMGGAFEMSL 132 Query: 109 GCHFRVA--VKEAKLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALK 166 CH RVA K K+ LPEVK+G+ PGAGGTQR+PR + A+QM+ GS + A A Sbjct: 133 ACHGRVASNAKSVKIALPEVKVGIFPGAGGTQRVPRLTNTQDALQMMTTGSSLTPARAKA 192 Query: 167 HGLVEEVVE--NLVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTK 224 GLV EVV+ L+ A A K L +P++ + KL I+T A A + Sbjct: 193 MGLVHEVVDPDKLIEAAKAMIKNGL---KPVQPWDEKGFKLPGG----GIWTPASAQLWP 245 Query: 225 KARGL---------EAPFACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQ-RYAF 274 A G+ A + + +PF+ LK E+ F +++ + ++ + R F Sbjct: 246 AASGILRRETYGNYPGAIAILKCVYEGLQVPFDTALKIEQRYFTEILQTTEAFSMIRSLF 305 Query: 275 FAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRG 334 + +E K P G + +V ++GAG MG IA A GIPVTLI+ E ++G Sbjct: 306 VSMQELGKGARRPAGVPKTELKKVGVVGAGFMGASIAYVTAAGGIPVTLIDRDMEAAEKG 365 Query: 335 LGIMQKNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFT 394 + + +G L + ++ IT +++DA L+IEAVFE VKK+V Sbjct: 366 KTHSEGLVKDAIGKGRLTKEEGEALLSRITPSADYGDLRDAGLVIEAVFEDRQVKKDVIE 425 Query: 395 AVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPD 454 V+A A+ ASNTS L I +A +KRP +G+HFFSP M L E++ G +T Sbjct: 426 KVEAVIAEDAIFASNTSTLPITGLARNSKRPDRFIGIHFFSPVEKMMLTEVILGKETGDR 485 Query: 455 ALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGM 514 AL A+ I K P+VV GF NR + ++ +L EG P ++ GM Sbjct: 486 ALAAALDYVAAIRKTPIVVNDTRGFYVNRCVFRYIHEAYDMLIEGVPPAMIENAAKMAGM 545 Query: 515 PMGPFAMGDLAGLDIGWRSRK----DRGIKSE-------IADALCEAGRFGQKTGKGYYK 563 P+GP ++ D +D+ + K D G K+ I + E R G+K GKG+Y+ Sbjct: 546 PVGPLSLNDEVAIDLSQKILKAAVADLGDKAVDLRHMALIDKMVDELDRRGRKNGKGFYE 605 Query: 564 YEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAAR 623 Y P ++ L A +I + +R++ + E AR +EE I Sbjct: 606 YPAKPARKYLWPGLKELYPQKDA------GEIEVGVLKQRLLVTIALEAARTIEEGIVTD 659 Query: 624 PSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAA 683 P + DV + G+G+ Y GG + Y D +G K E A A + P PLL +A Sbjct: 660 PREADVGSILGFGFAPYTGGTLSYIDGMGAKAFVELCEKLA-ADHGDHFRPTPLLKEMAE 718 Query: 684 EGKTFASLTQP 694 +G+TF P Sbjct: 719 KGETFYGRFDP 729 Lambda K H 0.317 0.134 0.383 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: 1127 Number of extensions: 68 Number of successful extensions: 7 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: 699 Length of database: 737 Length adjustment: 40 Effective length of query: 659 Effective length of database: 697 Effective search space: 459323 Effective search space used: 459323 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: 55 (25.8 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