Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate Ac3H11_1931 Enoyl-CoA hydratase [isoleucine degradation] (EC 4.2.1.17) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1931 Length = 727 Score = 252 bits (644), Expect = 4e-71 Identities = 208/706 (29%), Positives = 329/706 (46%), Gaps = 56/706 (7%) Query: 4 VVTRATQDQVAIVTVD--SPPVNALSAAVRRGILENVNAAVAD-----PAVQAIVLVCAG 56 + + T +VA++T D + PVN + ++ + E AD A++ IVL A Sbjct: 9 IPAQGTDGEVAVITFDETNSPVNTMCRQWQQELGEVTARVAADRERLGAALKGIVLASAK 68 Query: 57 RTFIAGADIT---EFGKPPQPPALNDV------IAALENSPKPTIAAIHGTALGGGLEVA 107 +F AGAD+ P A ++ LE P +A ++G ALGGG EVA Sbjct: 69 TSFFAGADLKATMRLTPADAPNAFGEIERMKKHFRTLETLGIPVVACLNGAALGGGWEVA 128 Query: 108 LGCHFRVAVKEAKL--GLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEAL 165 L H+R+AV + K+ GLPEV LGL+PGA G ++ R +G A I+ G AEAL Sbjct: 129 LVAHYRIAVADPKIQFGLPEVTLGLMPGATGVTKMTRLLGLMGAQPYILEGKLFNPAEAL 188 Query: 166 KHGLVEEVV---ENLVAGAVAFAKKVLAEKRPLRRLRDDDSKL-AAAKADRSI---FTNA 218 + LV E+V E L+ A+A + ++ D + K+ A+ I T A Sbjct: 189 ELQLVHELVATREQLLPAALAH---ISTHPHAVQPWDDKNYKMPGGTPANPKIAGALTVA 245 Query: 219 VAAMTKKARG-LEAPFACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAE 277 A + K RG AP A A+ + ++ L+ E +L+ ++ FF + Sbjct: 246 PAMLKKTTRGRYPAPEAALAAMVEGAMVDYDTALRIESRYLARLMTGPVARNMINTFFFD 305 Query: 278 REAAKVD----GVPDGTKPR-PVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLK 332 A K V PR +V I+GAG MG GIA + A+ GI L + E+ + Sbjct: 306 MNAIKSGKSRPAVNGAVAPRYKPQKVGILGAGMMGAGIAWAQASRGIATVLKDVSAEKAE 365 Query: 333 RGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEV 392 G K +A +G + +A ++ IT ++ DLIIEAVFE+ +K +V Sbjct: 366 AGKAYSAKLTQARVDKGRMTAEAQQALLSRITPTASAADLAGCDLIIEAVFESRDLKAKV 425 Query: 393 FTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTA 452 + PG ASNTS L I +A + RP+ +G+HFFSP + MKL EI+RG +T Sbjct: 426 TQEAEPQLAPGGFFASNTSTLPISGLATASSRPEKFVGIHFFSPVDKMKLVEIIRGNQTD 485 Query: 453 PDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKF 512 + + A + + KVP+VV GF +R + +L EG ++ + Sbjct: 486 DETVARAFDYVQALGKVPIVVNDSRGFYTSRTFGTFVMEGAAMLGEGIPAAAIENAAMQA 545 Query: 513 GMPMGPFAMGDLAGLDIGW----RSRKDRGIKSEIADA----------LCEAGRFGQKTG 558 G+P+GP A+ D L + ++R D + + A + E R G+ G Sbjct: 546 GLPVGPLAVMDETALTLSVHVLDQTRADYATEGKTYTATPGELLVERMVKELKRPGRAGG 605 Query: 559 KGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEE 618 G+Y Y G++ + PE++ L K G+ + + +EI +R++Y E AR L E Sbjct: 606 GGFYDYPAGAKKHL-WPELKPLFE----KPGV---EWSVQEIQDRLLYRQAIETARCLAE 657 Query: 619 KIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYA 664 + D ++ ++G G+P + GG M + G++ +R A Sbjct: 658 GVLTSVHDANIGSIFGIGFPAWTGGAMQFIYGTGVEAFLKRADELA 703 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: 1052 Number of extensions: 44 Number of successful extensions: 5 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: 727 Length adjustment: 39 Effective length of query: 660 Effective length of database: 688 Effective search space: 454080 Effective search space used: 454080 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