Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate GFF2604 Psest_2654 fatty oxidation complex, alpha subunit FadB
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__psRCH2:GFF2604 Length = 715 Score = 352 bits (902), Expect = e-101 Identities = 226/689 (32%), Positives = 349/689 (50%), Gaps = 27/689 (3%) Query: 23 VNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFGKPPQPP------- 75 VN + + + V+A AD +V+ +++ FI GADITEF + Sbjct: 29 VNKFNRLTLNDLRQAVDAIKADASVKGVIVTSGKDVFIVGADITEFVDNFKMADEELVAG 88 Query: 76 --ALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGLLPG 133 N + + E+ PT+AAI+G ALGGG E+ + +RV AK+GLPEVKLG+ PG Sbjct: 89 NLEANKIFSDFEDLGVPTVAAINGIALGGGFEMCMAADYRVMSTTAKVGLPEVKLGIYPG 148 Query: 134 AGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV--ENLVAGAVAFAKKVLA- 190 GGT RLPR +G + AV+ I G A +ALK V+ VV + L A A+ K+ ++ Sbjct: 149 FGGTVRLPRLIGVDNAVEWIASGKENRAEDALKVHAVDAVVAPDKLQAAALDLVKRAISG 208 Query: 191 --EKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLPFE 248 + + R+ + D KL A + + T+ + AP I A + + Sbjct: 209 ELDYKAKRQPKLDKLKLNAIEQMMAFETSKAFVAGQAGPNYPAPVEAIKTIQKAANFTRD 268 Query: 249 EGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGG 308 + ++ E GF+KL + +++ F +++E K D + R V A++GAG MGG Sbjct: 269 KAIEVEAAGFVKLAKTSVAQSLVGLFLSDQELKKKAKAYD-KQARDVKLAAVLGAGIMGG 327 Query: 309 GIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVG 368 GIA A G P+ + + EE ++ GL K +G L D A+ + I + Sbjct: 328 GIAYQSAVKGTPILMKDIREEGIQMGLDEASKLLGKRVEKGRLTADKMAQALNAIRPTMS 387 Query: 369 LENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDV 428 + + D+++EAV E VK V V+ H + A++ASNTS +SI+ +A KRP++ Sbjct: 388 YGDFGNVDIVVEAVVENPKVKHAVLAEVEGHVREDAIIASNTSTISINYLAQALKRPENF 447 Query: 429 LGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAAR 488 GMHFF+P ++M L E++RG KT+ A+ T V+ AKK+ K PVVV C GF+ NR+L Sbjct: 448 CGMHFFNPVHMMPLVEVIRGEKTSEVAIATTVAYAKKMGKSPVVVNDCPGFLVNRVLFPY 507 Query: 489 SKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR---------KDRGI 539 + + G + D V+ KFG PMGP + D+ G+D G R + + Sbjct: 508 FGGFARAIAHGVDFVRADKVMEKFGWPMGPAYLMDVVGMDTGHHGRDVMAEGFPDRMKDD 567 Query: 540 KSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEE 599 D + EA R GQK GKG+Y YE + P V+ + L + + R+++DE+ Sbjct: 568 TRTAVDVMYEANRLGQKNGKGFYAYEMDKKG-KPKKVVDAQAYELLKPIVAETRELSDED 626 Query: 600 ILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAER 659 I+ M+ P+ E R LE+ I ++ D+ +YG G+P +RGG + Y DS+G+ Sbjct: 627 IINYMMIPLCLETVRCLEDGIVETAAEADMGLIYGIGFPPFRGGALRYIDSIGVAEFVAM 686 Query: 660 LSAYAKATNDPSLEPAPLLARLAAEGKTF 688 YA P P L +AA G+ F Sbjct: 687 ADKYADL--GPLYHPTAKLREMAANGQRF 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: 967 Number of extensions: 52 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