Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate HSERO_RS01180 HSERO_RS01180 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__HerbieS:HSERO_RS01180 Length = 391 Score = 244 bits (623), Expect = 3e-69 Identities = 155/398 (38%), Positives = 222/398 (55%), Gaps = 22/398 (5%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M + VIV+ RT IGK + GAL+ A L I+ + + GI P+ + +V++G + Sbjct: 1 MDDVVIVAAQRTAIGK-FGGALSKIAAADLGAQVIKALLAKTGIKPEAISEVILGQVLTA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G G N AR++++++GLP + + C SGL+A+ LAA+++ +I + GG E++ Sbjct: 60 GL-GQNPARQSVIKSGLPDMVPAFVVGKVCGSGLKAVQLAAQAIRCGDAQIVIAGGQENM 118 Query: 121 SL---VQNDKMNTFHAVDPALE---AIKG--DVYMA--MLDTAETVAKRYGISRERQDEY 170 S V N+ + F D L + G DVY M TAE VAK++ ISRE QD + Sbjct: 119 SASPHVLNNSRDGFRMGDAKLTDTMIVDGLWDVYNQYHMGITAENVAKKFEISREEQDAF 178 Query: 171 SLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGL 230 + SQ + AAQ+ GKF DEI PI K + + DE + TAE L Sbjct: 179 AAASQNKAEAAQKAGKFKDEIVPIEIKG----------KKETVVFDTDEFVKHGVTAESL 228 Query: 231 AGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEM 290 A L+ + T+TAGNAS ++DGA+A V+ S K AA GL L + S G +P M Sbjct: 229 ATLRPAFDKAGTVTAGNASGINDGAAAVVVTSAKLAAELGLPVLAKIKAYSSAGLDPSIM 288 Query: 291 GIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGH 350 G+GPV A LK+ G + D+ L E+NEAFA Q + ++G D K+NVNGGAI++GH Sbjct: 289 GMGPVPASQLTLKKAGWTPQDLDLMEINEAFAAQAIAVNKQMGWDTSKINVNGGAIALGH 348 Query: 351 PYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 P G SG R+ L E RR AK + ++C+GGGMG A Sbjct: 349 PIGASGCRVLVTLLHEMVRRDAKKGLASLCIGGGMGVA 386 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: 408 Number of extensions: 13 Number of successful extensions: 4 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