Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate AO356_30295 AO356_30295 fatty-acid oxidation protein subunit alpha
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30295 Length = 703 Score = 550 bits (1416), Expect = e-160 Identities = 319/704 (45%), Positives = 439/704 (62%), Gaps = 22/704 (3%) Query: 2 SEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIA 61 S +V+ + VA++TV++PPVNAL+ +R I++ V A ADPAV AIVL+ G+ FIA Sbjct: 4 SLMVSYEVEGVVAVITVNNPPVNALTPEMRGSIIDAVTHANADPAVAAIVLMGGGQNFIA 63 Query: 62 GADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKL 121 GADI +FGK + + AAL+ S KPT+AAIHG ALGGGLE AL CH+R+A+ AKL Sbjct: 64 GADIRQFGKA-RTITTSMSAAALDASAKPTVAAIHGYALGGGLEHALACHYRIALPTAKL 122 Query: 122 GLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV-----EN 176 GLPEV LGL+PG GGTQRLPR VG +A ++V I A EAL+ GL+ ++V + Sbjct: 123 GLPEVALGLIPGGGGTQRLPRLVGAAVATDLLVSSRHIHAPEALQIGLISQIVPGTQNQE 182 Query: 177 LVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAM---TKKARGLEAPF 233 L AV +AK V A +P +R+RD LA D + AA KK+ +AP Sbjct: 183 LRDAAVRYAKAV-AHAQP-QRVRD----LALEPMDATTMDLLQAARREAAKKSPHNKAPQ 236 Query: 234 ACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPR 293 D I AA +LPF+E L+ E F +L SD +KA RYAFFAEREAAKV P G KP Sbjct: 237 YAIDCIEAAFNLPFDEALEVESRLFSELEGSDVAKALRYAFFAEREAAKVPDAPPGFKPA 296 Query: 294 PVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPP 353 V+ A+IGAGTMG GIA+ FA+AGI V L+E E L RGL ++ + RG + Sbjct: 297 GVTSAAVIGAGTMGAGIAICFADAGIVVKLLEASAEALDRGLQRIRDIYAVKVKRGRMTV 356 Query: 354 DAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYL 413 + + + E + D D+++EAVFE + +KK+VFT +DA KPGA+L +N+S + Sbjct: 357 QEMDACLQFVQPVSHYEEIGDCDVVVEAVFERIDLKKDVFTKLDAVMKPGALLLTNSSAI 416 Query: 414 SIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVV 473 I+ +A T RPQ V G HFF+PAN MKLCEIV+G +T+ + ++ A+ + + + KV V Sbjct: 417 DINVMANMTGRPQSVAGAHFFAPANAMKLCEIVKGDQTSIETVVRAMKMGRDLKKVCAVS 476 Query: 474 GVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRS 533 G CDGF NR A + LL EGA P+Q+D V+ +FG PMGPFA+ DL+GLD+ + + Sbjct: 477 GTCDGFAANRSRAPLVTEMMLLLEEGARPEQIDRVMVEFGYPMGPFAVSDLSGLDVSYDT 536 Query: 534 RKDRGI------KSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAK 587 RK R K + D + E GR GQK G G+Y+YE+G R P D EV +I + Sbjct: 537 RKRRAAADPQYRKLHVPDRMVELGRKGQKNGAGWYRYEEGDRTPRHDEEVMRIIATVAHE 596 Query: 588 LGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHY 647 LG +R TD EIL+R+++ INE +IL+E A R SDIDV+WLYG+G+P +RGG +++ Sbjct: 597 LGTPQRTFTDSEILKRLLFASINEACKILDEGKAYRASDIDVMWLYGFGFPRHRGGLLYW 656 Query: 648 ADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTFASL 691 AD++G I ++ + + P+PLL++ A EG + L Sbjct: 657 ADTIGATEIHLQVQQWHEQYG-RRWAPSPLLSKAANEGLSLREL 699 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: 1088 Number of extensions: 46 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 Apr 09 2024. 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