Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate Pf6N2E2_1850 Enoyl-CoA hydratase [isoleucine degradation] (EC 4.2.1.17) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1850 Length = 715 Score = 289 bits (740), Expect = 3e-82 Identities = 224/712 (31%), Positives = 338/712 (47%), Gaps = 46/712 (6%) Query: 11 DQVAIVTVDSP-PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFG 69 D + VT+D P PVNA++ R + VN + + +V+ A TF AG D+ E Sbjct: 11 DGIVTVTMDMPGPVNAMNQLYRETMAATVNRLEQENGLTGVVIASAKSTFFAGGDLNELT 70 Query: 70 --KPPQPPAL--------NDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKE- 118 KP ND + LE P P +AAI+G ALGGG E+AL C++RV + Sbjct: 71 DFKPGDEADFQAKIELTKND-LRRLERLPVPVVAAINGAALGGGFEIALACNYRVLLNSP 129 Query: 119 -AKLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVEN- 176 A +GLPEV LGLLPG GG RL +G E A+ +++ G + AEAL GLV E++E Sbjct: 130 AAVVGLPEVSLGLLPGGGGIVRLVHHLGLERALPLLLEGKRMKPAEALALGLVNELIEQA 189 Query: 177 --LVAGAVAFAKKVLAEKR-PLRRLRDDDSKLAAAKADR----SIFTNAVAAMTKKARGL 229 LV A A+ K + + L+ K+ A + + A A K RGL Sbjct: 190 DALVPAAKAWIKAQVGDDGVSLQPWDHKGHKIPGGTAQQPHVAQMIAGAQAMTAKNTRGL 249 Query: 230 -EAPFACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSK-AQRYAFFAEREAAKVDGVP 287 AP A L F+ L E G L S Q+K FF E P Sbjct: 250 LPAPERILAVAVEATLLDFDAALLVETRGLTHLAASVQAKNIINTMFFQMNEVNGGSSRP 309 Query: 288 DGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAA 347 G VS++ IIGAG MG GIA A GI V L++ E +RG ++K T + Sbjct: 310 TGFDKSKVSKLGIIGAGMMGNGIAHVSAKVGIEVMLLDVSLEAAERGKANVEKLLSKTVS 369 Query: 348 RGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLA 407 +G L + +ALI V +++ D ++EAVFE++ +K +V +A AV Sbjct: 370 QGRLSEAKKDEILALIKPTVDYADLQGVDFVVEAVFESVDLKGKVTQQAEAQLPESAVFG 429 Query: 408 SNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIA 467 +NTS L I +A +KRP + +G+HFFSP M L EI+ G +T+ AL A A++I Sbjct: 430 TNTSTLPISLLANASKRPANFIGIHFFSPVERMPLVEIICGEQTSDAALAKAFDFARQIG 489 Query: 468 KVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGL 527 K +VV GF +R + + KLL EG P +D + + GMP+GP + D L Sbjct: 490 KTAIVVNDSLGFFTSRTFGSYFDEGCKLLQEGVDPLLIDNLGKQIGMPVGPLTVLDEVSL 549 Query: 528 DIGWR---SRKDRGIKSEIAD----------ALCEAGRFGQKTGKGYYKYEQGSRAPMPD 574 ++ + ++K+ G+ + + D + E R G+ G G+Y Y +G + Sbjct: 550 ELMRKVNETQKEMGVFATVFDNSHSDAVGNILIKEYNRPGRHYGGGFYDYPEGGEKTIWP 609 Query: 575 PEVETLINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYG 634 E + + + E+I ER+++ + E + L+E + +D +V + G Sbjct: 610 GLYELFVRPEVV--------LPVEDIKERLLFRQVIEAVKCLQEGVLRSVADGNVGSILG 661 Query: 635 YGWPIYRGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGK 686 G P + GG + + + G++ +R A+ T P LL AA+G+ Sbjct: 662 IGAPTWTGGFLQFVNGYGVERFVQRARELAQ-TYGERFTPPVLLLEKAAKGE 712 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: 1016 Number of extensions: 51 Number of successful extensions: 5 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