GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Thermoactinomyces daqus H-18

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_033100436.1 JG50_RS0107240 acetyl-CoA C-acetyltransferase

Query= SwissProt::P45855
         (393 letters)



>NCBI__GCF_000763315.1:WP_033100436.1
          Length = 393

 Score =  508 bits (1307), Expect = e-148
 Identities = 254/392 (64%), Positives = 313/392 (79%), Gaps = 1/392 (0%)

Query: 1   MRKTVIVSAARTPFGKFGGVLKEVKAAELGGIVMKEALQQAGVSGDDVEGNVMGMVVQAG 60
           M K VI+  ARTPFGKFGG LK+V A ELGG  ++ AL++AGV+ + V+  +MGMV+Q G
Sbjct: 1   MVKAVILGGARTPFGKFGGALKDVPAVELGGTAIRAALERAGVAAEMVDEVIMGMVLQGG 60

Query: 61  SGQIPSRQAARLAGMPWSVPSETLNKVCASGLRAVTLCDQMIRAQDADILVAGGMESMSN 120
           +GQIPSRQAARLAG+ W V +ET+NKVCASGLR+VTL DQ+IRA DA ++VAGGMESMSN
Sbjct: 61  AGQIPSRQAARLAGLGWEVGTETINKVCASGLRSVTLADQIIRAGDAGVVVAGGMESMSN 120

Query: 121 IPYAVPAGRWGARMGDGELRDLMVYDGLTCAFDEVHMAVHGNTAAKEYAISRREQDEWAL 180
            PY +P+GR+G RMGDG++ DLM++DGL CAF +VHM VHG+  AKEY ++R EQD WAL
Sbjct: 121 APYILPSGRFGQRMGDGKMVDLMIHDGLWCAFHDVHMIVHGSNTAKEYNVTREEQDAWAL 180

Query: 181 RSHARAAKAADEGKFQDEIVPVNWIGRKGKPNVVDKDEAIRRDTSLDQLAKLAPIYASDG 240
           RSH RA +A + G+F DEI PV  +  K +  VVD+DEA+R DT+L++L+ L P+Y  DG
Sbjct: 181 RSHQRALEAINHGRFADEITPVT-VKVKKQEIVVDRDEAVRADTTLEKLSGLKPVYLQDG 239

Query: 241 SITAGNAPGVNDGAGAFVLMSEEKAAELGKRPLATILGFSTTGMPAHELAAAPGFAINKL 300
           +ITAGNAPGVNDGA A V+ S EKA ELG +PLA+ILG +   M A +    P +AI KL
Sbjct: 240 TITAGNAPGVNDGAAALVVASSEKAQELGIKPLASILGHAAVAMEAKDFPITPAYAIKKL 299

Query: 301 LKKNGLTVQDIDLFEVNEAFASVVLTCEKIVGFDLEKVNVNGGAIALGHPIGASGARILM 360
           LKK+GLTV  IDLFE+NEAFA+V L   K++G D  K+NVNGGA+ALGHPIGASGARIL+
Sbjct: 300 LKKHGLTVAQIDLFEINEAFAAVALANSKLLGIDPGKLNVNGGAVALGHPIGASGARILL 359

Query: 361 TLVYELKRRGGGLGVAAICSGAAQGDAVLVQV 392
           TL+ ELKRRGGGLGVAAICSGAAQGDAVLV+V
Sbjct: 360 TLIMELKRRGGGLGVAAICSGAAQGDAVLVKV 391


Lambda     K      H
   0.317    0.134    0.387 

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: 541
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: 393
Length adjustment: 31
Effective length of query: 362
Effective length of database: 362
Effective search space:   131044
Effective search space used:   131044
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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