Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate CCNA_00074 CCNA_00074 multifunctional fatty acid oxidation complex subunit alpha FadJ
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__Caulo:CCNA_00074 Length = 733 Score = 341 bits (874), Expect = 8e-98 Identities = 249/733 (33%), Positives = 357/733 (48%), Gaps = 54/733 (7%) Query: 11 DQVAIVTVDSP--PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRT-FIAGADITE 67 D VA+VT D P +N L+A+V + I E V +D ++ +V+ T F AGAD+ E Sbjct: 11 DGVALVTFDVPGRSMNTLTASVIKEIGEIVERIKSDAEIKGVVITSGKTTGFCAGADLGE 70 Query: 68 FGKPPQPP------------------ALNDVIAALENSPKPTIAAIHGTALGGGLEVALG 109 G ALN LE KP AAI+G A+GGGLE+AL Sbjct: 71 LGGGGGMAGGAAGGEAALKAAFDAGFALNKAFRGLETCGKPVAAAINGLAMGGGLEIALA 130 Query: 110 CHFRVAVKEAK--LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKH 167 CH+RV K L LPE K+GLLPGAGGTQRLPR +G A ++ G + AEAL + Sbjct: 131 CHYRVVADHPKIQLALPEAKVGLLPGAGGTQRLPRLMGVMAAAPYLLEGKSMKPAEALAN 190 Query: 168 GLVEEVV--ENLVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAA----KADRSIFTNAVAA 221 +V EVV + +V A + K + P+ D KL +F A Sbjct: 191 KVVHEVVPVDQVVEAAKTWVK---TKGDPVAPWDKKDFKLPGGGPYTPTGGQVFIMGNAM 247 Query: 222 MTKKARG-LEAPFACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQ-RYAFFAERE 279 + K+ G A A+ +PF+ ++ E F+K ++S Q+K R F + +E Sbjct: 248 LRKQTYGNYPAQLNILKAVYEGTQVPFDAAIRIETRYFLKTMMSPQAKGMIRTLFLSLQE 307 Query: 280 AAKVDGVPDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQ 339 K G P P +VA++GAG MG GIA A AGI LI+ +E ++G G + Sbjct: 308 LGKGSGRPADVPPSEAKKVAVLGAGMMGAGIAYVQAMAGIETVLIDQSQEAAEKGKGYAE 367 Query: 340 KNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAH 399 + +RG + D +ALIT +VK +DL+IEAVFE+ +K +V +A Sbjct: 368 NLLKKAVSRGKMTQDKADAVLALITPTTDYAHVKGSDLVIEAVFESREIKADVTQKAEAQ 427 Query: 400 AKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTA 459 A+ SNTS L I +A + RP++ +G+HFFSP + M L EI+ G +T+ +AL + Sbjct: 428 LAEDAIFGSNTSTLPITGLAKASVRPKNFIGIHFFSPVDKMGLVEIIMGEETSDEALAKS 487 Query: 460 VSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPF 519 + KI K P+VV GF +R ++ ++L +G P +D V GMP GP Sbjct: 488 IDYVLKIKKTPIVVNDSRGFYTSRCFGTFVQEGLEMLADGIAPAIIDNVGRATGMPRGPL 547 Query: 520 AMGDLAGLDIGWR----SRKDRGIKSE-------IADALCEAGRFGQKTGKGYYKYEQGS 568 M D LD+G++ ++KD G K E I + E RFG+K GKG+Y Y Sbjct: 548 EMNDDVALDLGYKVTQQTKKDLGDKFEDRPFAPIIEKMVVELQRFGRKNGKGFYDY---- 603 Query: 569 RAPMPDPEVETLINDTLAKLGLKRRD-ITDEEILERMVYPMINEGARILEEKIAARPSDI 627 P P+ LA + + D +EI R++Y E AR EE + P + Sbjct: 604 --PETGPKTLWKGLSELAPVTIAEADQALIQEIRTRLLYRQAVEAARCFEEGVITDPREA 661 Query: 628 DVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKT 687 DV + G+G+ + GGP+ D VG K E A+ PA LL +A +G+T Sbjct: 662 DVGAILGWGFAPWTGGPISLIDGVGAKAFVETCDQLAQKYGKRFAPPA-LLREMAEKGET 720 Query: 688 F-ASLTQPSKAAA 699 F +KAAA Sbjct: 721 FYGRFGAKAKAAA 733 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: 1122 Number of extensions: 56 Number of successful extensions: 7 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: 733 Length adjustment: 40 Effective length of query: 659 Effective length of database: 693 Effective search space: 456687 Effective search space used: 456687 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