Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate GFF1489 PS417_07575 multifunctional fatty acid oxidation complex subunit alpha
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__WCS417:GFF1489 Length = 715 Score = 350 bits (898), Expect = e-100 Identities = 232/696 (33%), Positives = 356/696 (51%), Gaps = 41/696 (5%) Query: 23 VNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFGKPPQPP------- 75 VN + + + V+ AD +V+ +++ FI GADITEF + P Sbjct: 29 VNKFNRLTLNELRQAVDTIKADASVKGVIVSSGKDVFIVGADITEFVDNFKLPDAELVAG 88 Query: 76 --ALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGLLPG 133 N + + E+ PT+AAI+G ALGGGLE+ L FRV AK+GLPEVKLG+ PG Sbjct: 89 NLEANKIFSDFEDLNVPTVAAINGIALGGGLEMCLAADFRVMSATAKIGLPEVKLGIYPG 148 Query: 134 AGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE---------NLVAGAVAF 184 GGT RLPR +G + A++ I G A +ALK G V+ VV NL+ GA++ Sbjct: 149 FGGTVRLPRLIGADNAIEWIAAGKENKAEDALKVGAVDAVVAPDKLAEAALNLIKGAISG 208 Query: 185 AKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAID 244 A+++P + + KL A + S T + AP I A + Sbjct: 209 EFDYKAKRQP----KLEKLKLNAIEQMMSFETAKGFVAGQAGPNYPAPVEAIKTIQKAAN 264 Query: 245 LPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAG 304 ++ L+ E GF+KL + +++ F ++E K D + V + A++GAG Sbjct: 265 FGRDKALEVEAAGFVKLAKTSAAQSLIGLFLNDQELKKKAKAYDEIA-KDVKQAAVLGAG 323 Query: 305 TMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALIT 364 MGGGIA A+ G P+ + + E +++GL K +G + A+ + I Sbjct: 324 IMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKLLVGRVDKGRMTAAKMAEVLNGIR 383 Query: 365 GLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKR 424 + + DL++EAV E VK+ V V+A K +LASNTS +SI +A KR Sbjct: 384 PTLSYGDFGHVDLVVEAVVENPKVKQAVLAEVEAQVKDDTILASNTSTISISLLAKALKR 443 Query: 425 PQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRM 484 P++ +GMHFF+P ++M L E++RG K++ A+ T V+ AKK+ K P+VV C GF+ NR+ Sbjct: 444 PENFVGMHFFNPVHMMPLVEVIRGEKSSELAVATTVAYAKKMGKNPIVVNDCPGFLVNRV 503 Query: 485 LAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR---------K 535 L KL+ G ++D V+ KFG PMGP + D+ G+D G R + Sbjct: 504 LFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYLMDVVGIDTGHHGRDVMAEGFPDR 563 Query: 536 DRGIKSEIADALCEAGRFGQKTGKGYYKYE---QGSRAPMPDPEVETLINDTLAKLGLKR 592 + + DAL EA R GQK GKG+Y YE +G + + DP V ++ LA + ++ Sbjct: 564 MKDDRRSAIDALYEAKRLGQKNGKGFYAYEADKKGKQKKVADPSV----HEVLAPVIYEQ 619 Query: 593 RDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVG 652 R+++DE+I+ M+ + E R LE+ I ++ D+ +YG G+P +RGG + Y DS+G Sbjct: 620 REVSDEDIINWMMIALCLETVRCLEDGIVETAAEADMGLVYGIGFPPFRGGALRYIDSIG 679 Query: 653 LKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688 + YA P P L +A G++F Sbjct: 680 VAEFVALADKYADL--GPLYHPTAKLREMAKNGQSF 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: 1000 Number of extensions: 62 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