Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_011423928.1 RHE_RS02825 FAD-dependent oxidoreductase
Query= metacyc::MONOMER-20678 (699 letters) >NCBI__GCF_000092045.1:WP_011423928.1 Length = 738 Score = 330 bits (847), Expect = 1e-94 Identities = 239/736 (32%), Positives = 358/736 (48%), Gaps = 58/736 (7%) Query: 11 DQVAIVTVDSP--PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADIT-- 66 D +A+VT D P +N +A V + ++A AD +V+ +V +F GAD++ Sbjct: 14 DGIALVTWDMPGKSMNVFTAEVMEELNAIIDATTADASVKGVVFTSGKSSFSGGADLSMI 73 Query: 67 ---------EFGKPPQPPA---------LNDVIAALENSPKPTIAAIHGTALGGGLEVAL 108 E K P+ ++ + LE S KP ++AI+GT +GG E++L Sbjct: 74 KSMFSSYQEEKAKSPEKAVQTLFGLVGRMSGLFRKLETSGKPWVSAINGTCMGGAFELSL 133 Query: 109 GCHFRVA--VKEAKLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALK 166 CH RVA K K+ LPEVK+G+ PGAGGTQR+PR + A+QM+ G + + A Sbjct: 134 ACHGRVASNAKSVKIALPEVKVGIFPGAGGTQRVPRLANAQDALQMMTTGQSLSGSRAKA 193 Query: 167 HGLVEEVVE--NLVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAA----KADRSIFTNAVA 220 LV +VVE L+ A K L +P+ + KL A ++ A A Sbjct: 194 MNLVHQVVEPDQLIPAAKQMIKDGL---KPVAPWDEKGFKLPGGGIWTPASAQLWPAAPA 250 Query: 221 AMTKKARG-LEAPFACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQ-RYAFFAER 278 + ++ G A A + + +PF+ GLK E+ F +++ + ++ + R F + + Sbjct: 251 ILRRETSGNYPAALAILKCVYEGLQVPFDTGLKIEQRYFTEVLQTREAFSMIRSLFISMQ 310 Query: 279 EAAKVDGVPDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIM 338 E K P G + V ++GAG MG IA A AGI VTLI+ E +G + Sbjct: 311 ELGKGARRPAGIPKTELKHVGVVGAGFMGASIAYVTAAAGISVTLIDRDMEAAAKGKAVS 370 Query: 339 QKNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDA 398 + + +G L D A ++ IT ++ + L+IEAVFE VKK V AV+A Sbjct: 371 EGLVKDAIGKGRLTQDEAAALLSRITPSGDYADLANVGLVIEAVFEDREVKKAVIDAVEA 430 Query: 399 HAKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLT 458 GA+ ASNTS L I +A +KRP D +G+HFFSP M L E++ G +T AL Sbjct: 431 VLPEGAIFASNTSTLPITGLARNSKRPADFIGIHFFSPVEKMMLTEVILGTETGDRALAV 490 Query: 459 AVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGP 518 A+ I K P+VV GF NR + +S +L EG P ++ GMP+GP Sbjct: 491 ALDYVAAIKKTPIVVNDTRGFFVNRCVLRYMSESYDMLIEGVPPAMIENAAKMAGMPVGP 550 Query: 519 FAMGDLAGLDIGWRSRK----DRGIKS------EIADALCE-AGRFGQKTGKGYYKYEQG 567 A+ D +D+ + K D G K+ E+ + E GRFG+K KG+Y Y Sbjct: 551 LALNDEVAIDLSLKILKAAVADLGEKAIDPRHMELISRMVEKEGRFGRKNSKGFYDYP-- 608 Query: 568 SRAPMPDPEVETLINDTLAKLGLKRRDITDEEIL-ERMVYPMINEGARILEEKIAARPSD 626 P P ++L D + K+ + D +L +R + + E AR +EE I P + Sbjct: 609 -----PKPAKKSLWPDLKSFYPQKKAEEVDVNVLKQRFLVTIALEAARTVEEGIVTDPRE 663 Query: 627 IDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGK 686 DV + G+G+ Y GG + Y D +G K + A+ D +P PLL LAA+G+ Sbjct: 664 ADVGSILGFGFAPYTGGALSYIDGMGAKAFVDLAERLAETYGD-HFKPTPLLRDLAAKGE 722 Query: 687 TFASLTQP---SKAAA 699 TF P +KAAA Sbjct: 723 TFYGRFDPYAGTKAAA 738 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: 1078 Number of extensions: 56 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: 738 Length adjustment: 40 Effective length of query: 659 Effective length of database: 698 Effective search space: 459982 Effective search space used: 459982 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 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