Align Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_090447771.1 BLS63_RS21120 acetyl-CoA C-acyltransferase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2411 (393 letters) >NCBI__GCF_900100495.1:WP_090447771.1 Length = 394 Score = 594 bits (1531), Expect = e-174 Identities = 301/394 (76%), Positives = 340/394 (86%), Gaps = 1/394 (0%) Query: 1 MNTPEIYVVSAARTAIGTFGGSLKDVPLADLATTAVKAALERAAVDPALVGHLVMGNVIP 60 M PE+Y+VSA RTAIG+FGG+LKD P +LATTAV AAL+R+ VGH+VMGNVIP Sbjct: 1 MPNPEVYIVSAVRTAIGSFGGTLKDTPPCELATTAVSAALQRSGCAAERVGHVVMGNVIP 60 Query: 61 TETRDAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAES 120 TETRDAYISRVAAMNAGIPKE PA+NVNRLCGSGLQAI++AAQ+L+LGD +I +GAGAES Sbjct: 61 TETRDAYISRVAAMNAGIPKEVPAFNVNRLCGSGLQAIVSAAQSLLLGDCEIAIGAGAES 120 Query: 121 MSRGPYLMPAARWGSRMGNAQVIDYMLGILHDPFHGIHMGITAENVAARNGITREMQDAL 180 MSRGPYL+P ARWG RMG+ Q +DYMLGILHDPF +HMGITAEN+A +GI+R QDAL Sbjct: 121 MSRGPYLLPGARWGGRMGDMQAVDYMLGILHDPFQRMHMGITAENIAELHGISRADQDAL 180 Query: 181 AFEDQQRAAHAIANGYFSEQIATVEIQDRKGVKLFSVDEHPRA-TSLEQLAAMKPAFKKD 239 A QQRAA AIA G F+ QI VEI+ RKG +LF VDEH R TSLEQLA M+ AFK+ Sbjct: 181 ALVSQQRAARAIAEGRFAGQIVPVEIKSRKGTQLFEVDEHVRGDTSLEQLAGMRTAFKQG 240 Query: 240 GSVTAGNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIPATRL 299 G+VTAGNASGLNDGAAA+V+A+G AVQA+NL+PLARLVSYAHAGVEPE MGLGPIPATRL Sbjct: 241 GTVTAGNASGLNDGAAAVVLATGAAVQADNLRPLARLVSYAHAGVEPELMGLGPIPATRL 300 Query: 300 ALKRAGLTVADLDVIEANIAFAAQACAVSQELDLDPAKVNPNGSGIALGHPVGATGAIIA 359 AL+RAGL V+DLDVIE+N AFAAQACAV++ LD DPAKVNPNGSGI+LGHPVGATGAII Sbjct: 301 ALQRAGLKVSDLDVIESNEAFAAQACAVARALDFDPAKVNPNGSGISLGHPVGATGAIIV 360 Query: 360 TKAIHELHRTGGRYALVTMCIGGGQGIAAIFERV 393 TKAIHEL RT GRYAL TMCIGGGQGIAAIFERV Sbjct: 361 TKAIHELQRTQGRYALATMCIGGGQGIAAIFERV 394 Lambda K H 0.318 0.133 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: 548 Number of extensions: 16 Number of successful extensions: 2 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: 393 Length of database: 394 Length adjustment: 31 Effective length of query: 362 Effective length of database: 363 Effective search space: 131406 Effective search space used: 131406 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 (21.7 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