Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_086510728.1 BZY95_RS15080 fatty acid oxidation complex subunit alpha FadB
Query= metacyc::MONOMER-20678 (699 letters) >NCBI__GCF_002151265.1:WP_086510728.1 Length = 725 Score = 348 bits (893), Expect = e-100 Identities = 240/709 (33%), Positives = 363/709 (51%), Gaps = 30/709 (4%) Query: 6 TRATQDQVAIVTVD--SPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGA 63 T+ D VA++T D +N LS+AV + E V A A+ ++ +V+ A +FI GA Sbjct: 14 TKNGGDDVAMLTFDLKDESINKLSSAVIAELDEAVQAIRAESGLKGLVIGSAKESFIVGA 73 Query: 64 DITEF----GKPPQ-----PPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRV 114 DITEF GK + ++D+ A+E+ P PT+ AI+G ALGGG EV L FRV Sbjct: 74 DITEFQTMFGKGAEFLESMLMKVHDIFNAIEDLPFPTVTAINGLALGGGCEVTLTTDFRV 133 Query: 115 AVKEAKLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV 174 +AK+GLPE KLG+LPG GG RLPR +G + AV+ I GG+ A ALK G V+ VV Sbjct: 134 MGDKAKIGLPETKLGILPGWGGCVRLPRMIGSDNAVEWIAGGTENRADAALKVGAVDAVV 193 Query: 175 EN--LVAGAVAFAKKVLAEKRPLRRLRDDDS---KLAAAKADRSIFTNAVAAMTKKARGL 229 N L A A+ + A + + R + + KL A + + T K Sbjct: 194 PNDQLEAAALDILARANAGELDYQARRAEKTGPLKLNAIEQMMAFETAKGYVAGKAGPHY 253 Query: 230 EAPFACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDG 289 AP AI E + F KL ++D + F ++ K G + Sbjct: 254 PAPIEAIKAIQKGAGEERARAQAIEAKAFAKLAMTDVAFNLVGLFMNDQVVKKKAGKFE- 312 Query: 290 TKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARG 349 + + V++ A++GAG MGGGIA A+ G P+ + + EE ++ GL +K + RG Sbjct: 313 KQAKAVNQTAVLGAGIMGGGIAYQSASKGTPILMKDIKEEAVELGLKESRKLFAKQVERG 372 Query: 350 GLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASN 409 L + A+++ LI + + DL++EAV E VK V T V+ +L SN Sbjct: 373 KLTTEQMAEKLTLIRPTLSYGDFGHVDLVVEAVVENPKVKDAVLTEVEGLVSEDTILTSN 432 Query: 410 TSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKV 469 TS +SI +A KRP++ GMHFF+P + M L E++RG KT A+ V+ A+ + K Sbjct: 433 TSTISITRLAQNLKRPENFCGMHFFNPVHRMPLVEVIRGEKTGDAAVAATVAYARAMGKT 492 Query: 470 PVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDI 529 P+VV C GF+ NR+L L+ +GA Q+VD V+ KFG PMGP + D+ G+D Sbjct: 493 PIVVNDCPGFLVNRVLFPYFGGFSLLVEQGADFQRVDKVMEKFGWPMGPAYLLDVVGMDT 552 Query: 530 ----------GWRSRKDRGIKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVET 579 G+ R R K+ I + E R GQK KG+Y YE+ + P + Sbjct: 553 AVHANEVMAEGFPERMARDGKTAI-QVMYENERLGQKNDKGFYAYEEDKKG-KPKKVSDD 610 Query: 580 LINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPI 639 + + ++ + ++ +DEEI+ RM+ P+ E R LE+ I P++ D+ +YG G+P Sbjct: 611 KAYELVKQVVVSEKEFSDEEIIARMMVPLCLETVRCLEDDIVETPAEADMALIYGIGFPP 670 Query: 640 YRGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688 +RGG + Y D++G+ + A+ P P L ++A G+ F Sbjct: 671 FRGGALRYIDAMGVAEFVKLADGLAEELG-PLYAPTDKLRKMAESGERF 718 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: 1060 Number of extensions: 51 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: 725 Length adjustment: 39 Effective length of query: 660 Effective length of database: 686 Effective search space: 452760 Effective search space used: 452760 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 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