Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_011385366.1 AMB_RS15050 multifunctional fatty acid oxidation complex subunit alpha
Query= metacyc::MONOMER-20678 (699 letters) >NCBI__GCF_000009985.1:WP_011385366.1 Length = 703 Score = 598 bits (1541), Expect = e-175 Identities = 323/697 (46%), Positives = 450/697 (64%), Gaps = 10/697 (1%) Query: 1 MSEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFI 60 MS+VVT + D++A VT+DSPPVNA VR G+ + A A++++CAGRTF+ Sbjct: 1 MSDVVTLSVSDRIATVTIDSPPVNAADHPVRAGLQKVFTDLAARSDYDAVLVLCAGRTFM 60 Query: 61 AGADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK 120 AGADI EF + P D+ +EN KP +AA+HGTALG G E+A+ CH+R+A K A+ Sbjct: 61 AGADIGEFDTGIKAPHHQDLFNLVENCAKPVVAALHGTALGAGTELAMACHYRIADKGAR 120 Query: 121 LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE-NLVA 179 +GLPE+ LG++PGAGGTQR PR +G + A+ +++ G P+ A +A + GLV+E+ +L A Sbjct: 121 IGLPELSLGIIPGAGGTQRAPRLIGLDAAMDLVLSGKPLPAPKAAELGLVDEIASGDLNA 180 Query: 180 GAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAI 239 A+AFAKK++AE + +RR D K AA A+ A A T K R +P +A+ Sbjct: 181 AALAFAKKLVAEGKGVRRTCDMAPKDAAKDAEIIAARQAQVAKTMKNR--TSPLKALEAM 238 Query: 240 GAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVA 299 A L F EGL+ E + +L + +++A R+ FFA+RE K+ G+ K RP+ +V Sbjct: 239 AATTTLSFAEGLRLEADISKQLEHAVEARAMRHLFFADREVRKIPGITKDIKARPIRKVG 298 Query: 300 IIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKR 359 IIGAGTMGGGIAM FAN GIPVT+I+ +E L+RGLG+++KN+E + +RG L + R Sbjct: 299 IIGAGTMGGGIAMCFANIGIPVTIIDVSDENLQRGLGVIRKNYERSVSRGSLTQEQLESR 358 Query: 360 MALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIA 419 M L++ +KDADL IEAVFE M +KK++F +DA GA+L +NTS L IDEIA Sbjct: 359 MGLLSASTDYAALKDADLAIEAVFEKMELKKDIFAKLDAVLPAGAILGTNTSTLDIDEIA 418 Query: 420 ATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGF 479 TTKRP DV+G+HFFSPANVM L EIV+G +TA D LLTA+ +AK I K VV VC GF Sbjct: 419 NTTKRPADVIGLHFFSPANVMPLLEIVQGKQTAMDVLLTALDMAKLIKKTGVVSKVCYGF 478 Query: 480 VGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR----- 534 +GNRM+ +++E+++ EGA P ++D + +GM MG A+ D+AG+++G +R Sbjct: 479 IGNRMMDPYGREAERMVLEGATPAEIDGALEGWGMAMGILAVYDMAGVEVGDNTRIANPH 538 Query: 535 --KDRGIKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKR 592 D + L GQK G+GYY+Y+ R DPEV +++ +L + Sbjct: 539 MVPDDPSFYRCSTLLVANKWLGQKVGRGYYRYDSPDRKRASDPEVIEMMHAEGKRLNVPA 598 Query: 593 RDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVG 652 R +EILER +Y MINEGA++LEE IA R SDIDVV+ GYG+P YRGGPM YAD++G Sbjct: 599 RKPGKDEILERCLYSMINEGAKLLEEGIALRASDIDVVYTAGYGFPRYRGGPMFYADTIG 658 Query: 653 LKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTFA 689 LK I +++ + K + PAPLL +LA G TFA Sbjct: 659 LKVIYDKIVEFQKTLDPRYWTPAPLLEKLAKAGSTFA 695 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: 1140 Number of extensions: 52 Number of successful extensions: 4 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: 703 Length adjustment: 39 Effective length of query: 660 Effective length of database: 664 Effective search space: 438240 Effective search space used: 438240 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: 54 (25.4 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