Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate GFF2241 PGA1_c22730 3-ketoacyl-CoA thiolase FadA
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Phaeo:GFF2241 Length = 394 Score = 456 bits (1174), Expect = e-133 Identities = 238/394 (60%), Positives = 288/394 (73%), Gaps = 2/394 (0%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M EAVIVSTARTPIG A++GALN + T++GHA++HAV+RAG+DP +EDVV+G+ + Sbjct: 1 MREAVIVSTARTPIGVAFKGALNNIKSPTMMGHAMQHAVERAGVDPGLIEDVVIGSVLTA 60 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G G N+AR + L AGLP T AG TIDRQC+SGL AIA AA+ ++ DG +AV GG E+I Sbjct: 61 GTAGMNVARLSALAAGLPNTVAGQTIDRQCSSGLMAIATAAKQIIVDGQNVAVAGGQENI 120 Query: 121 SLVQNDKMN-TFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179 S +QN + DP + A YM ML TAE VA+ YGISR+ QDEY+ SQ RTA Sbjct: 121 SALQNAYLKWAGDEKDPNVIAQSEHAYMPMLMTAENVARTYGISRDVQDEYAALSQGRTA 180 Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGE 239 AQ G F DEI PI+ V ++ TG + +++TLS+DEG RP TTAE L L V E Sbjct: 181 RAQAAGAFEDEIVPITAIKRVKNRETGEETVEEVTLSKDEGNRPGTTAETLGALNPVV-E 239 Query: 240 GFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVP 299 G ITAGNASQLSDGASA V+M K A +GL PLGI+RGM G P+EMG+GP+FA+P Sbjct: 240 GGLITAGNASQLSDGASACVLMEGKMAEQQGLTPLGIYRGMAVAGNAPEEMGVGPIFAIP 299 Query: 300 RLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARL 359 +LLK GL ++DIGLWELNEAFA QVLYCRD LGIDPE NVNGGAIS+GHPYGM+G R Sbjct: 300 KLLKNAGLRIEDIGLWELNEAFACQVLYCRDHLGIDPEIYNVNGGAISIGHPYGMTGVRQ 359 Query: 360 AGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEI 393 GHALIEGRRR KY V +MCVGGGMG+A LFE+ Sbjct: 360 VGHALIEGRRRGVKYVVTSMCVGGGMGAAALFEV 393 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: 521 Number of extensions: 18 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: 394 Length adjustment: 31 Effective length of query: 364 Effective length of database: 363 Effective search space: 132132 Effective search space used: 132132 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