Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_035240374.1 Q366_RS14810 acetyl-CoA C-acyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >NCBI__GCF_000745975.1:WP_035240374.1 Length = 416 Score = 253 bits (646), Expect = 7e-72 Identities = 164/422 (38%), Positives = 231/422 (54%), Gaps = 28/422 (6%) Query: 1 MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQA 60 M D I A RT IG +GG LKD+ L ++ ++ ++R +D +DDV YG + Sbjct: 1 MKDVVIVSACRTAIGAFGGTLKDLNGAHLASITMREAVKR-ANIDPAVIDDVRYGTCVEH 59 Query: 61 GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM 120 D N R++AL+AG+P P ATINR+C SGM+AV + I+AG A +++AGG E M Sbjct: 60 -HDTLNTTRVAALMAGIPDTVPAATINRVCISGMEAVLSGMAMIQAGMADVILAGGTEHM 118 Query: 121 TRAPFVMGKAASAFTRQ------AEIHDTTIGWRFVNPLMKRQYGVDS------------ 162 + P+ + A Q A IH G F+ PL + VD+ Sbjct: 119 SGVPYAVPNARWGCRLQDTGFVDAMIHALHCG-SFLLPLDETS-PVDTSQAPAADFLGQP 176 Query: 163 --MPETAENVAEQFGISRADQDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRV 220 M TAE VA+ ISRA+ D AL S A RA DG+ A+EIV VE+ Q+K D I Sbjct: 177 YIMGHTAEFVAQLLDISRAEMDEVALRSHNNAERATNDGSFAEEIVPVEVPQRKKDPIIF 236 Query: 221 TLDEHPRE-TSLESLARLKGVVRPD-GTVTAGNASGVNDGACALLIASQQAAEQYGLRRR 278 DEH R +LE LA L P G VTAGNASG+NDG+ ++I S + A++ GL Sbjct: 237 DKDEHFRPGMTLEKLAALPPAFVPKTGKVTAGNASGINDGSTGMVIMSAEKAKELGLTPI 296 Query: 279 ARVVGMATAGVEPRIMGIGPAPATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGL 338 A++ P +MG+ P PA + L+ + G+T++ +IE+NEAFA+Q L R LGL Sbjct: 297 AKIKATGMGACHPSVMGLSPVPAVKDLMAKSGITINDFHLIEVNEAFAAQYLGCERELGL 356 Query: 339 RDDDPRVNPNGGAIALGHPLGASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIE 398 + N NG I LGHP+G++GAR++TT ++ ++ L T+C G G +A IE Sbjct: 357 NRE--ITNVNGSGIGLGHPVGSTGARVMTTLMYAMKNKGKSLGLATLCGGGGVSMACAIE 414 Query: 399 RL 400 L Sbjct: 415 ML 416 Lambda K H 0.319 0.134 0.386 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: 407 Number of extensions: 15 Number of successful extensions: 5 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: 400 Length of database: 416 Length adjustment: 31 Effective length of query: 369 Effective length of database: 385 Effective search space: 142065 Effective search space used: 142065 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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