Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_085640004.1 MGEO_RS15835 FAD-dependent oxidoreductase
Query= metacyc::MONOMER-20678 (699 letters) >NCBI__GCF_002115805.1:WP_085640004.1 Length = 695 Score = 569 bits (1467), Expect = e-166 Identities = 322/706 (45%), Positives = 441/706 (62%), Gaps = 28/706 (3%) Query: 1 MSEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFI 60 M+ V+ +A++ +D+PPVNAL AVR+G++E V A AD A +A ++ GR+F Sbjct: 1 MTGVIRYNRDGDIAMIAIDNPPVNALGQAVRQGLVEAVEKAEADGA-RAALIYGEGRSFP 59 Query: 61 AGADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK 120 AGADI EFGKPP P L DV LE SP ++A+HGTALGGGLE+AL +R+A AK Sbjct: 60 AGADIREFGKPPLEPWLPDVCNRLETSPVLVVSALHGTALGGGLEIALASDYRIATPAAK 119 Query: 121 LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVENLVAG 180 +GLPEV +G++PGAGGTQRLPR VG E ++ +I G I A EA G+++ V + Sbjct: 120 VGLPEVLIGVMPGAGGTQRLPRLVGVETSIDVITSGRQISAGEAFDLGIIDRVEDGAPRD 179 Query: 181 -AVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSI-FTNAVAAMTKKARGLEAPFACADA 238 +++ + +LAE P R +R+ A + I F A + +KARG +P Sbjct: 180 IGLSYTRALLAENAPRRPIRE-------MPAPQPIDFDAAYDSALRKARGQISPAYAVRG 232 Query: 239 IGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRV 298 I AA +LPFEEGL +ERE F L+ +DQ + +AFFAER + + D T R V+ V Sbjct: 233 IQAACELPFEEGLTRERELFRALLETDQRQGLIHAFFAERAVGVLAELKD-TNARDVNSV 291 Query: 299 AIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDA--- 355 A+IG GTMG GIA SF AG PVTL+E E+ G + N RG + Sbjct: 292 AVIGGGTMGAGIATSFLLAGFPVTLLEMSEDAAHAARGRITGNLSGALKRGKIDQKTYDR 351 Query: 356 -PAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLS 414 +AL T +++++ADL+IEAVFE M VK++VF+ +DA KPGAVLA+NTSYL Sbjct: 352 LTGPALALTTSY---DDLREADLVIEAVFEDMNVKRDVFSRLDAICKPGAVLATNTSYLD 408 Query: 415 IDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVG 474 I++IA T+RP+DV+G+HFFSPA+VMKL E+V +TAPD + T ++AK++ K V G Sbjct: 409 INKIADATQRPEDVIGLHFFSPAHVMKLLEVVVADRTAPDTVATGFALAKRLKKTAVRAG 468 Query: 475 VCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR 534 VCDGF+GNR+LAA ++ ++ +GA P +DA + +FG MGPF + DLAGLDI W +R Sbjct: 469 VCDGFIGNRILAAYRAAADHMVLDGATPYDIDAAIREFGFAMGPFQVSDLAGLDIAWAAR 528 Query: 535 KDRGIKSE-------IADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAK 587 K R + +AD LCEAG FGQKTG+GYY Y + P P+PEV +I Sbjct: 529 KRRAATRDPRERVPLVADRLCEAGLFGQKTGQGYYLYNE--TPPKPNPEVAGIIESARET 586 Query: 588 LGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHY 647 LG+K R + EI R + M+NE A+++ + IA RP D+DVV L GYG+P YRGGP+ + Sbjct: 587 LGIKPRAFSRPEIQRRYLCAMVNEAAKVVGDGIARRPLDVDVVLLMGYGFPRYRGGPLKW 646 Query: 648 ADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTFASLTQ 693 AD GL I ++AYA+ + PAPLL +L AEG+TF L + Sbjct: 647 ADMDGLPKILSDITAYAQ-DDRYFWSPAPLLEQLVAEGRTFDDLNK 691 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: 1142 Number of extensions: 46 Number of successful extensions: 8 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: 695 Length adjustment: 39 Effective length of query: 660 Effective length of database: 656 Effective search space: 432960 Effective search space used: 432960 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 24 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