Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate PfGW456L13_4041 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 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__pseudo13_GW456_L13:PfGW456L13_4041 Length = 715 Score = 340 bits (871), Expect = 2e-97 Identities = 224/692 (32%), Positives = 352/692 (50%), Gaps = 33/692 (4%) Query: 23 VNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFGKPPQPP------- 75 VN + + + V+ AD +++ +++ FI GADITEF + P Sbjct: 29 VNKFNRLTLNELRQAVDTIKADASIKGVIVSSGKDVFIVGADITEFVDNFKLPDAELVAG 88 Query: 76 --ALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGLLPG 133 N + + E+ PT+AAI+G ALGGGLE+ L +RV +AK+GLPEVKLG+ PG Sbjct: 89 NLEANKIFSDFEDLNVPTVAAINGIALGGGLEMCLAADYRVMSTKAKIGLPEVKLGIYPG 148 Query: 134 AGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV--ENLVAGAVAFAKKVLA- 190 GGT RLPR +G + A++ I G +ALK G V+ VV E L A+ K+ ++ Sbjct: 149 FGGTVRLPRLIGADNAIEWIAAGKENRPEDALKVGAVDAVVAPEQLQDAALELIKRAISG 208 Query: 191 --EKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLPFE 248 + + R+ + + KL A + + T + AP I A + + Sbjct: 209 EFDYKAKRQPKLEKLKLNAIEQMMAFETAKGFVAGQAGPNYPAPVEAIKTIQKAANFGRD 268 Query: 249 EGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGG 308 + L+ E GF+KL + +++ F ++E K D + V + A++GAG MGG Sbjct: 269 KALEIEAAGFVKLAKTSAAQSLIGLFLNDQELKKKAKAYDEIA-KDVKQAAVLGAGIMGG 327 Query: 309 GIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVG 368 GIA A+ G P+ + + E +++GL K +G + A+ + I + Sbjct: 328 GIAYQSASKGTPILMKDINEHGIEQGLAEAAKLLVGRVDKGRMTAAKMAEVLNGIRPTLS 387 Query: 369 LENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDV 428 + DL++EAV E VK+ V V+ K +LASNTS +SI +A KRP++ Sbjct: 388 YGDFGHVDLVVEAVVENPKVKQAVLAEVEDKVKEDTILASNTSTISITLLAKALKRPENF 447 Query: 429 LGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAAR 488 +GMHFF+P ++M L E++RG K++ A+ T V+ AKK+ K P+VV C GF+ NR+L Sbjct: 448 VGMHFFNPVHMMPLVEVIRGEKSSELAVATTVAYAKKMGKNPIVVNDCPGFLVNRVLFPY 507 Query: 489 SKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR---------KDRGI 539 KL+ G ++D ++ KFG PMGP + D+ G+D G R + + Sbjct: 508 FGGFAKLVSAGVDFVRIDKIMEKFGWPMGPAYLMDVVGIDTGHHGRDVMAEGFPDRMKDD 567 Query: 540 KSEIADALCEAGRFGQKTGKGYYKYE---QGSRAPMPDPEVETLINDTLAKLGLKRRDIT 596 + D L EA R GQK GKG+Y YE +G + + DP V + L + ++R++T Sbjct: 568 RRSAVDVLYEAKRLGQKNGKGFYAYETDKKGKQKKVADPSV----LEVLKPIVYEQREVT 623 Query: 597 DEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHI 656 DE+I+ M+ P+ E R LE+ I ++ D+ +YG G+P +RGG + Y DS+G+ Sbjct: 624 DEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVYGIGFPPFRGGALRYIDSIGVAEF 683 Query: 657 AERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688 YA P L +A G++F Sbjct: 684 VALADQYADL--GALYHPTAKLREMAKNGQSF 713 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: 1006 Number of extensions: 64 Number of successful extensions: 6 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: 715 Length adjustment: 39 Effective length of query: 660 Effective length of database: 676 Effective search space: 446160 Effective search space used: 446160 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