Align 3-oxoadipate CoA-transferase (EC 2.8.3.6) (characterized)
to candidate WP_086508613.1 BZY95_RS03575 CoA-transferase subunit beta
Query= reanno::pseudo3_N2E3:AO353_17200 (259 letters) >NCBI__GCF_002151265.1:WP_086508613.1 Length = 262 Score = 330 bits (845), Expect = 2e-95 Identities = 163/253 (64%), Positives = 196/253 (77%) Query: 3 YSTNEMMTVAAARRLKNGSVCFVGIGLPSKAANLARLTSSPDVVLIYESGPIGAKPTVLP 62 Y++ EMMTV AAR L+NG CFVGIGLPS+AANLARLT +PDVVLIYESG + KP VLP Sbjct: 10 YTSAEMMTVTAARALENGMTCFVGIGLPSEAANLARLTHAPDVVLIYESGTLQTKPDVLP 69 Query: 63 LSIGDGELAETADTVVPTGEIFRYWLQGGRIDVGFLGAAQVDRFGNINTTVVGDYHQPKV 122 LSIGDGELAETA T V E+FRYWLQGG+IDVGFLG AQ+DR+ N+NTT++GDY +PKV Sbjct: 70 LSIGDGELAETALTTVSVPEMFRYWLQGGKIDVGFLGTAQIDRYCNLNTTLIGDYREPKV 129 Query: 123 RLPGAGGAPEIAGSAKSVLIILKQSARSFVDKLDFITSVGHGEGGDSRKRLGLPGAGPVG 182 RLPG GGAPEIA +A V I LK S R+FVD++DF+T++G G G R + G GP Sbjct: 130 RLPGGGGAPEIATNAGEVFITLKHSKRAFVDRVDFVTTLGFGRDGKGRDGVPNIGKGPTR 189 Query: 183 IITDLCIMEPEAGTNEFVVTALHPGVTREQVIAATGWAVRFADQLEHTAEPTAIELAALR 242 +ITDLC+M+P+ T E VV +LHPGV+RE VI ATGW +RFA+ LE T EP+A EL LR Sbjct: 190 VITDLCVMKPDPETKELVVVSLHPGVSREDVIEATGWEIRFAETLESTPEPSARELEVLR 249 Query: 243 DLEARTAAAHGQA 255 +L+ RTA AH A Sbjct: 250 ELKDRTARAHAGA 262 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: 296 Number of extensions: 11 Number of successful extensions: 1 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: 262 Length adjustment: 25 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 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 24 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