Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate GFF4142 PS417_21215 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__WCS417:GFF4142 Length = 715 Score = 263 bits (673), Expect = 2e-74 Identities = 213/717 (29%), Positives = 333/717 (46%), Gaps = 51/717 (7%) Query: 10 QDQVAIVTVDSP--PVNALSAAVRRGI---LENVNAAVADPAVQAIVLVCAGRTFIAGAD 64 QD + ++T+D P N ++ A R + +E + A D A +V+ A +TF AG D Sbjct: 11 QDGIVVLTLDMPGQSANTMNGAYREAMAAMVERLEAQKDDLA--GVVITSAKKTFFAGGD 68 Query: 65 ITEFGKPPQPPA---------LNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVA 115 + E K + A L + LE KP +AAI+G ALGGG E+ L CH+RVA Sbjct: 69 LNELIKVDKAHAKDFYDSVRELKAQLRRLETLGKPVVAAINGAALGGGWEICLACHYRVA 128 Query: 116 V--KEAKLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEV 173 + K +LGLPEV LGLLPG GG R+ R +G E A+ ++ G + +AL+ GLV E+ Sbjct: 129 LDDKSVQLGLPEVTLGLLPGGGGVVRMVRMLGLEKALPYLLEGKKVRPQQALQAGLVNEL 188 Query: 174 V---ENLVAGAVAFAKKVLAEKRPL-RRLRDDDSKLAAAKADRSIFTNAVAAMTKKARG- 228 + L+A + A+ K+P + ++ + A + + K +G Sbjct: 189 AADRDELLAKSRAWILANPDAKQPWDNKGYQIPGGTPSSPKVAQMLAIAPSILRSKTQGC 248 Query: 229 LEAP--FACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAF-FAEREAAKVDG 285 AP CA GA +D F+ E F +LV +K F F E Sbjct: 249 FPAPEKILCAAVEGAQVD--FDTAHLIETRYFTELVTGQVAKNMIGTFWFQLNEINAGSS 306 Query: 286 VPDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEAT 345 P G P +V ++GAG MG GIA A+AGI V L + ++G + Sbjct: 307 RPQGFAPYVTRKVGVLGAGMMGAGIAYVSASAGIEVVLKDINLAAAEKGKAHSAALLDKK 366 Query: 346 AARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAV 405 +RG L + +A I E++ DLIIEAVFE +K +V A + AV Sbjct: 367 VSRGQLTAEQRETFLARIHPTATDEDLAGCDLIIEAVFEDRELKAKVSAAAQSVVGADAV 426 Query: 406 LASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKK 465 +ASNTS L I +A +G+HFFSP + M L EI++GA+T+ + L + Sbjct: 427 IASNTSTLPISGLATAVPDQTRFIGLHFFSPVDKMPLVEIIKGARTSDETLARGFDFVLQ 486 Query: 466 IAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLA 525 I K P+VV GF +R+ + + +L EG ++ K GMP+GP A+ D Sbjct: 487 IKKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGVAAPMIETEARKAGMPVGPLAVSDEV 546 Query: 526 GLD----IGWRSRKD-----RGIKSEIADALC-----EAGRFGQKTGKGYYKYEQGSRAP 571 L I ++ KD + + + A A+ E R G+ G G+Y Y G Sbjct: 547 SLSLMNHIRQQTAKDLQAEGKAVPTHPATAVIDLLVNEYQRMGKAAGGGFYDYPSGGH-- 604 Query: 572 MPDPEVETLINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVW 631 + L + ++ + I+ +++ +R+++ E R +EE + +D +V Sbjct: 605 ------KYLWPELKSRFERPDQRISPQDVRDRLLFIQAIETVRCVEEGVLMSTADANVGS 658 Query: 632 LYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688 ++G G+ + GG + + + GL R A+ + + PA LL + AA+G F Sbjct: 659 IFGIGFAPWSGGALQFINQYGLNDFIARARYLAEQYGERFMPPALLLEK-AAQGDVF 714 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: 1033 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: 715 Length adjustment: 39 Effective length of query: 660 Effective length of database: 676 Effective search space: 446160 Effective search space used: 446160 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