GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Nocardioides daejeonensis MJ31

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_110207571.1 DNK54_RS13705 thiolase family protein

Query= BRENDA::Q0KAI3
         (392 letters)



>NCBI__GCF_003194585.1:WP_110207571.1
          Length = 389

 Score =  516 bits (1328), Expect = e-151
 Identities = 257/389 (66%), Positives = 307/389 (78%), Gaps = 1/389 (0%)

Query: 5   VIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNK-LDPGLVDDVITGCVTQAGE 63
           +IVDA+R+P GR K G AF E+H  +LL+Q ++ L+ER+  +DPG VDDVI GCV+Q GE
Sbjct: 1   MIVDAVRTPSGRGKAGGAFAEVHPVDLLSQTVQTLLERSPAVDPGSVDDVIVGCVSQVGE 60

Query: 64  QSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIESMSR 123
           QSA PGR+AWL AG+P HVPATTIDRKCGSSQQAVHFAAQGI +G YD+V+A G+ESMSR
Sbjct: 61  QSATPGRLAWLGAGYPSHVPATTIDRKCGSSQQAVHFAAQGIRSGEYDVVVAGGVESMSR 120

Query: 124 VPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHELAATA 183
           V MGSAR+G +PYG  +  R+APGLVSQGVAAELV AK+ LSR  +D YSARSH+LAA A
Sbjct: 121 VVMGSARMGADPYGARIAERFAPGLVSQGVAAELVTAKWGLSRTQLDEYSARSHDLAAAA 180

Query: 184 RESGAFRREILGISTPNGLVEQDETIRPGTSVEKLGTLQASFRNDELSARFPQIGWNVTA 243
            +SGAF REI+ I  P G V  DETIR GT+ EKL  L+  F ND LSARFP++GW++TA
Sbjct: 181 SDSGAFAREIIAIEAPAGPVAVDETIRRGTTAEKLAGLKPVFENDALSARFPEVGWSITA 240

Query: 244 GNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMMLTAPIPASQRAIKKS 303
           GN+SQI+D ASA+L+MS      LGL PRAR  +  V GDDP++MLT PIPA+ + +++S
Sbjct: 241 GNSSQITDAASALLIMSRRRCDELGLTPRARIHSMAVVGDDPLLMLTGPIPATHKVLERS 300

Query: 304 GLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIALGHPLGASGVRLMTTMLH 363
           GL L  I H E+NEAFA VPLAW      DPA +NPRGGAIALGH LGASG RLMTTMLH
Sbjct: 301 GLALSDIGHVELNEAFAPVPLAWLAEFDVDPATVNPRGGAIALGHALGASGARLMTTMLH 360

Query: 364 ALEDSGQRYGLQSMCEAGGMANATIIERL 392
           ALED+ Q++GLQ MCEAGGMANATIIERL
Sbjct: 361 ALEDNDQQFGLQLMCEAGGMANATIIERL 389


Lambda     K      H
   0.318    0.132    0.384 

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: 13
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: 392
Length of database: 389
Length adjustment: 31
Effective length of query: 361
Effective length of database: 358
Effective search space:   129238
Effective search space used:   129238
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