Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate GFF4162 Psest_4235 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__psRCH2:GFF4162 Length = 701 Score = 701 bits (1809), Expect = 0.0 Identities = 365/696 (52%), Positives = 489/696 (70%), Gaps = 10/696 (1%) Query: 1 MSEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFI 60 M++VV Q ++A++TV++PPVNAL AVR G+ + +A ADP V+A+ LVC G TFI Sbjct: 1 MTDVVRLEVQGEIALITVNNPPVNALGQAVREGLQKAFQSAEADPQVRAVALVCEGNTFI 60 Query: 61 AGADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK 120 AGADI EFGKPPQ P+L +VI +E K ++A IHGTALGGGLEVALGCH+R+A K+AK Sbjct: 61 AGADIKEFGKPPQAPSLPEVIEIIEACNKSSVAVIHGTALGGGLEVALGCHYRIARKDAK 120 Query: 121 LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE-NLVA 179 +GLPEVKLGLLPGAGGTQRLPR G E A++MIV G PI AAEA++H +V+E+ E +LV Sbjct: 121 VGLPEVKLGLLPGAGGTQRLPRLAGVEKALEMIVSGQPISAAEAVEHNIVDELFEGDLVE 180 Query: 180 GAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAI 239 +A+ ++++ E R RR + L A + ++ A + K+ GL +P C A+ Sbjct: 181 AGLAYVRRMVEEGRTPRRTGEQTQGLEGAD-NEALIRAKHAEVAKRMPGLFSPLRCIAAV 239 Query: 240 GAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVA 299 AA LP EGLK+ERE F + + S Q A ++FFAER+A K++ +P TKPR ++ A Sbjct: 240 EAATKLPLAEGLKRERELFAECLNSPQRGALVHSFFAERQAGKINDLPSDTKPRSINSAA 299 Query: 300 IIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKR 359 +IG GTMG GIA+SFANAG+PV L+E EE L+RGL + + A+ RG L DA +R Sbjct: 300 VIGGGTMGVGIALSFANAGVPVKLLEINEEALQRGLQRARDTYAASVKRGSLTEDAMEQR 359 Query: 360 MALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIA 419 +ALI G+ + DAD+++EAVFE M VK++VF +DA KPGA+LASNTS L +D IA Sbjct: 360 LALIEGVTEYAALADADVVVEAVFEEMGVKQQVFEQLDAICKPGAILASNTSSLDLDAIA 419 Query: 420 ATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGF 479 A TKRP+DV+G+HFFSPANVM+L E+VRGAKT+ + L TA++I K++ KV VVVGVCDGF Sbjct: 420 AFTKRPEDVVGLHFFSPANVMRLLEVVRGAKTSDEVLATAMAIGKQLKKVSVVVGVCDGF 479 Query: 480 VGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGI 539 VGNRM+ +++E LL EGA PQQVDA + FGM MGPFAM DL+GLDIG RK + Sbjct: 480 VGNRMVFQYGREAEFLLEEGATPQQVDAALRNFGMAMGPFAMRDLSGLDIGQAIRKRQRA 539 Query: 540 K-------SEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKR 592 ++D LC AG GQKTG GYY+YE G+R P +P++ ++ + G++R Sbjct: 540 TLPAHLDFPTVSDKLCAAGMLGQKTGAGYYRYEPGNRTPQENPDLAPMLEAASLEKGIER 599 Query: 593 RDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVG 652 + + ++ I+ER ++ ++NEGA+ILEE IA R SDIDV++L GYG+P +RGGPM YADSVG Sbjct: 600 KALDEQYIVERCIFALVNEGAKILEEGIAQRSSDIDVIYLNGYGFPAFRGGPMFYADSVG 659 Query: 653 LKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688 L + R+ D +PAPLL +LAAEG+TF Sbjct: 660 LDRVLARVKELHARCGD-WWKPAPLLEKLAAEGRTF 694 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: 1208 Number of extensions: 62 Number of successful extensions: 3 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: 701 Length adjustment: 39 Effective length of query: 660 Effective length of database: 662 Effective search space: 436920 Effective search space used: 436920 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 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