Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate SMa1450 SMa1450 thiolase
Query= uniprot:A0A2Z5MFE9 (400 letters) >FitnessBrowser__Smeli:SMa1450 Length = 396 Score = 265 bits (677), Expect = 2e-75 Identities = 155/388 (39%), Positives = 232/388 (59%), Gaps = 8/388 (2%) Query: 11 RTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNRNVARM 70 RTP+G + G LKD+ A DLGA I ++R G+ AVD+V++GC AG+ + AR Sbjct: 14 RTPLGSFQGELKDLSAADLGAAAIVDALKR-AGLAPDAVDEVMFGCVLTAGQ-GQAPARQ 71 Query: 71 SALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPFVMGKA 130 +AL AGLP T+N++CGSGM A A IKA A +++AGG+ESMT AP+++ +A Sbjct: 72 AALGAGLPPGVGATTVNKMCGSGMKAAMLAHDLIKAESASIVVAGGMESMTNAPYLLDRA 131 Query: 131 ASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFALASQQ 190 + H + F++ L M AE+ AE + +R+ QD +A+AS + Sbjct: 132 RQGYRIG---HQKVLDHMFLDGLEDAYDKGRLMGSFAEDCAEAYQFTRSAQDEYAIASLE 188 Query: 191 KAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDGTVTAG 250 KA +A DG+ A+EIV + IA KG+ V LDE P++ L+ + LK R GT+TA Sbjct: 189 KAQKASADGSFAEEIVPLSIASGKGERT-VNLDEQPQKARLDKIPLLKPAFRDGGTITAA 247 Query: 251 NASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKLLRQLG 310 NAS ++DGA AL++ + AA++ G+ A + G AT P + P A + L R++G Sbjct: 248 NASSISDGAAALVLMRRSAADKQGIGPLAVICGHATHADAPSLFPTAPIGAIKALCRRIG 307 Query: 311 MTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARLVTTAL 370 + ++D+ E+NEAFA +A +R LGL D +VN +GGA ALGHP+GASGAR++ T + Sbjct: 308 WDIGEVDLFEINEAFAVVPMAAMRELGL--DAEKVNVHGGACALGHPIGASGARVIVTLV 365 Query: 371 HQLERSNGRFALCTMCIGVGQGIALVIE 398 + L R R + ++CIG G+ A+ +E Sbjct: 366 NALRRRGLRRGIASVCIGGGEATAVAVE 393 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: 399 Number of extensions: 26 Number of successful extensions: 6 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: 396 Length adjustment: 31 Effective length of query: 369 Effective length of database: 365 Effective search space: 134685 Effective search space used: 134685 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 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