Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_068174326.1 HTA01S_RS19105 FAD-dependent oxidoreductase
Query= metacyc::MONOMER-20678 (699 letters) >NCBI__GCF_001592305.1:WP_068174326.1 Length = 684 Score = 545 bits (1404), Expect = e-159 Identities = 301/654 (46%), Positives = 418/654 (63%), Gaps = 16/654 (2%) Query: 13 VAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFGKPP 72 +A++ +D+PP+NA SAAVR+G++ + D ++ VL+ AG TFIAG+D+ EFG+P Sbjct: 13 IAVIVIDNPPINAGSAAVRQGLMAAIETLRNDDTLEGAVLIGAGNTFIAGSDLREFGQPL 72 Query: 73 QPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGLLP 132 P L VIAA+E KP +AA+HG A GGG E+ALGC RVA +GLPEV LG++P Sbjct: 73 TEPQLPAVIAAIEACGKPVVAALHGAAQGGGFELALGCDARVAAPGTVVGLPEVTLGIIP 132 Query: 133 GAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE-NLVAGAVAFAKKVLAE 191 GAGGTQRLPR VG A++MI G + AA AL+ GLV+ + NL + AVA A+++ + Sbjct: 133 GAGGTQRLPRIVGIPPAIRMICSGERVLAAAALEAGLVDLIATGNLRSAAVAHARQLKGQ 192 Query: 192 KRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLPFEEGL 251 KR +R D A+ AD + T A K+ ++A DAI A + F++GL Sbjct: 193 KRLVR----DRQVPPASSADVATATTAAPQAGKRRPAVQAAI---DAITATAQVGFDDGL 245 Query: 252 KKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGGGIA 311 ER F +L VS ++ A R+ FFAERE+AK + + T RPV RVA+IGAGTMG GIA Sbjct: 246 ADERAVFQRLRVSREAFALRHQFFAERESAKHPSLGEATA-RPVERVAVIGAGTMGSGIA 304 Query: 312 MSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVGLEN 371 ++ +AG V L+E L+RG G + ++ + G L A A A + + + Sbjct: 305 IAALDAGYRVLLLEQDAAALERGTGRIHAHYASRVQGGKLSASAAAACEARLQTSLDWAD 364 Query: 372 VKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDVLGM 431 + ADL+IEAVFE + VK++VF +DA A+PGAVLASNTSYL +D IAA T RP DV+G+ Sbjct: 365 LASADLVIEAVFEELGVKQQVFQRIDALARPGAVLASNTSYLDLDAIAAATSRPHDVIGL 424 Query: 432 HFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQ 491 HFFSPA+VMKL E+VRG +APDAL T +++ K++ K+PV+ G GF+GNR+ AA +Q Sbjct: 425 HFFSPAHVMKLMEVVRGQSSAPDALATGLAVGKRLKKMPVLTGNAFGFIGNRLYAAYRRQ 484 Query: 492 SEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIKSE-------IA 544 E ++ EGA P+QVDA + FG MGPFA+ DL+GLDI WR R+ + + I Sbjct: 485 CECMVEEGAWPEQVDAALRAFGFAMGPFAVADLSGLDIAWRMRQAQAATRDPQARYVHIP 544 Query: 545 DALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEILERM 604 D LCEAGR G+KTG GYY+Y +G + P D V LI A GL+ R++ D+EI+ R Sbjct: 545 DRLCEAGRLGRKTGAGYYRYPEGDQGPQVDEAVHALIAQARADKGLQPRELGDDEIVRRA 604 Query: 605 VYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAE 658 + ++NE A +L E +A R +D+DVV + GYG+P + GGP+ +A G + E Sbjct: 605 LLAIVNEAALLLAEGVAERATDVDVVLVNGYGFPRWEGGPVFWARERGAAALQE 658 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: 1115 Number of extensions: 57 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: 684 Length adjustment: 39 Effective length of query: 660 Effective length of database: 645 Effective search space: 425700 Effective search space used: 425700 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