Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 6935814 Sama_0032 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= metacyc::MONOMER-20678 (699 letters) >FitnessBrowser__SB2B:6935814 Length = 716 Score = 340 bits (872), Expect = 1e-97 Identities = 245/685 (35%), Positives = 341/685 (49%), Gaps = 36/685 (5%) Query: 9 TQDQVAIVTVDSP-PVNALSAAVRRGILENVNAAV---ADPAVQAIVLVCAGRTFIAGAD 64 T D++A + ++P VN R L ++NAA+ D +A VL TFI GAD Sbjct: 13 TADKIARLCFNAPGSVNKFD----RETLASLNAALDVLKDSDAKAAVLTSGKDTFIVGAD 68 Query: 65 ITEF--------GKPPQPPA-LNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVA 115 ITEF K + A N V LE+ P PT++AI G ALGGG E L FRVA Sbjct: 69 ITEFLALFAEEDAKLMEWIAQANVVFNKLEDLPFPTVSAIKGFALGGGCEAILATDFRVA 128 Query: 116 VKEAKLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV- 174 AK+GLPE KLGL+PG GGT RLPR +G + A++ I G +ALK G ++ VV Sbjct: 129 DTSAKIGLPETKLGLIPGFGGTVRLPRLIGADNALEWITTGKDQRPEDALKVGAIDAVVA 188 Query: 175 -ENLVAGAVAFAKKVLAEKRP--LRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLE- 230 ENL A A+ LA K RR R + L K + + M G Sbjct: 189 PENLEAAAIQMLNDALAGKLDWQARRARKQ-APLTLPKLEAMMSFTTAKGMVYAVAGKHY 247 Query: 231 -APFACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDG 289 AP A + A + E L E F+KL +D + A F + K Sbjct: 248 PAPMAAVSVVEQAAGMSRAEALVVEHNAFIKLAKTDVATAL-IGIFLNDQLVKGKAKKAS 306 Query: 290 TKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARG 349 + + A++GAG MGGGIA A+ G P+ + + + L G+ K A ARG Sbjct: 307 KLAKDIKHAAVLGAGIMGGGIAYQSASKGTPIVMKDINQAALDLGVNEAAKLLSAQVARG 366 Query: 350 GLPPDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASN 409 PD AK + IT + +KD ++++EAV E VK V V+ A++ASN Sbjct: 367 RSTPDKMAKVLNNITPALDYAPLKDVNVVVEAVVENPKVKAMVLADVENVVADDAIIASN 426 Query: 410 TSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKV 469 TS +SID +A + K P GMHFF+P + M L E++RG T+ + + + V+ A K+ K Sbjct: 427 TSTISIDLLAKSLKNPARFCGMHFFNPVHKMPLVEVIRGKDTSEETVASVVAYASKMGKT 486 Query: 470 PVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTK-FGMPMGPFAMGDLAGLD 528 P+VV C GF NR+L LL +G +D V+ K FG PMGP + D+ GLD Sbjct: 487 PIVVNDCPGFFVNRVLFPYFAGFNGLLADGGDFAAIDKVMEKQFGWPMGPAYLLDVVGLD 546 Query: 529 IGWRSR-------KDRGIKS--EIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVET 579 G ++ DR KS + D + EAGR GQK GKG+Y+Y R P +V+ Sbjct: 547 TGHHAQAVMADGFPDRMGKSDKDAIDVMYEAGRLGQKNGKGFYQYSIDKRG-KPKKDVDP 605 Query: 580 LINDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPI 639 LA+ ++ +EI+ R + PMI E R LEE I A P++ D+ +YG G+P Sbjct: 606 ASYTMLAEAFGAQKAFEADEIIARTMIPMIIETVRCLEEGIVASPAEADMGLVYGLGFPP 665 Query: 640 YRGGPMHYADSVGLKHIAERLSAYA 664 +RGG Y D++G+ + YA Sbjct: 666 FRGGVFRYLDTMGVANFVALADKYA 690 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: 1079 Number of extensions: 60 Number of successful extensions: 7 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: 716 Length adjustment: 39 Effective length of query: 660 Effective length of database: 677 Effective search space: 446820 Effective search space used: 446820 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