Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate GFF329 PGA1_c03400 acetyl-CoA acetyltransferase PhaA
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Phaeo:GFF329 Length = 391 Score = 257 bits (656), Expect = 5e-73 Identities = 155/397 (39%), Positives = 223/397 (56%), Gaps = 21/397 (5%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 MT VI S ART +G ++ GA T L ++ V+RAGID EV + ++G + Sbjct: 1 MTNVVIASAARTAVG-SFGGAFAKTPAHDLGAAVLQAVVERAGIDKSEVSETILGQVLT- 58 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 A G N AR+A + AGLP +A ++++ C SGL+A+ALAA+ + I GG E++ Sbjct: 59 AAQGQNPARQAHINAGLPQESAAWSLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENM 118 Query: 121 SLVQN-------DKMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYS 171 +L + KM +D + D + M TAE VA+++ ISRE QDE++ Sbjct: 119 TLSPHAANLRAGHKMGDMSYIDTMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFA 178 Query: 172 LESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLA 231 + SQ + AAQ+ GKF DEIA + K DI + QDE R T E + Sbjct: 179 VASQNKAEAAQKAGKFADEIAAFTVK----------TRKGDIIVDQDEYIRHGATIEAMQ 228 Query: 232 GLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMG 291 L+ + ++TA NAS L+DGA+AT++MS A +G++PL + G +P MG Sbjct: 229 KLRPAFAKDGSVTAANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMG 288 Query: 292 IGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHP 351 +GP++A + L++ G SVDD+ L E NEAFA Q +G DP +NVNGGAI++GHP Sbjct: 289 VGPIYASRKALEKAGWSVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHP 348 Query: 352 YGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 G SG R+ L E +RR AK + T+C+GGGMG A Sbjct: 349 IGASGCRVLNTLLFEMKRRDAKKGLATLCIGGGMGVA 385 Lambda K H 0.316 0.134 0.378 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: 414 Number of extensions: 11 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: 395 Length of database: 391 Length adjustment: 31 Effective length of query: 364 Effective length of database: 360 Effective search space: 131040 Effective search space used: 131040 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 (21.6 bits) S2: 50 (23.9 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