Align 3-oxoadipate CoA-transferase (EC 2.8.3.6) (characterized)
to candidate RR42_RS31950 RR42_RS31950 ketoacid CoA transferase
Query= reanno::pseudo3_N2E3:AO353_17200 (259 letters) >FitnessBrowser__Cup4G11:RR42_RS31950 Length = 267 Score = 90.1 bits (222), Expect = 4e-23 Identities = 85/256 (33%), Positives = 128/256 (50%), Gaps = 14/256 (5%) Query: 3 YSTNEMMTVAAARRLKN-GSVCFVGIGL-PSKAANLARLTSSPDVVLIYESGPIGAKPTV 60 ++ E+M AAAR ++ G V GIG P AA LARL +P ++L + +P Sbjct: 7 FTLAELMIAAAARAWRDDGEVMATGIGTGPRIAAGLARLLHNPGLMLTDGEAYLVEEP-- 64 Query: 61 LPLSIGDGELAETADTVVPTGEIFRYWLQGGRIDVGFLGAAQVDRFGNINTTVVGDYH-Q 119 +PL + A + +F L GGR + Q+DRFG N +++G H Q Sbjct: 65 VPLGRREPGFKVRASGWMGYARVFDC-LWGGRRHA-LVMPTQIDRFGQANISMLGGTHAQ 122 Query: 120 PKVRLPGAGGAPEIAGSAKSVLIILKQSARSFV-DKLDFITSVGHGEGGDSRKRLGLPGA 178 PK +L GA G P + + + S R+FV ++D + SVG+ +R+ G+ Sbjct: 123 PKKQLLGARGFPGNSIHHANSFFVPAHSPRAFVAGEVDMVCSVGYNP---ARQIEGMRSF 179 Query: 179 GPVGII-TDLCIMEPEAGTNEFVVTALHPGVTREQVIAATGWAVR--FADQLEHTAEPTA 235 + +I TDLC+M+ + V +LHPGV+ EQV AATG+A+ + L T PTA Sbjct: 180 VDLRVIVTDLCVMDFTGPDHAIRVRSLHPGVSLEQVRAATGFALANPSGEILPQTPAPTA 239 Query: 236 IELAALRDLEARTAAA 251 ELA + L+ A Sbjct: 240 DELAVIGRLDPHNLRA 255 Lambda K H 0.317 0.135 0.394 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: 214 Number of extensions: 9 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: 259 Length of database: 267 Length adjustment: 25 Effective length of query: 234 Effective length of database: 242 Effective search space: 56628 Effective search space used: 56628 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: 47 (22.7 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