GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Rhodococcus qingshengii djl-6-2

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_050656999.1 C1M55_RS28700 acetyl-CoA C-acyltransferase

Query= BRENDA::Q0KAI3
         (392 letters)



>NCBI__GCF_002893965.1:WP_050656999.1
          Length = 397

 Score =  467 bits (1202), Expect = e-136
 Identities = 234/397 (58%), Positives = 297/397 (74%), Gaps = 5/397 (1%)

Query: 1   MQQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQ 60
           M +AVIVD +R   G+ KPG A +  H  EL+A V++ +  RN LDP LVDDVI GCV Q
Sbjct: 1   MTKAVIVDVVRIASGKGKPGGALSGTHPVELMAHVLRSITSRNGLDPALVDDVIGGCVGQ 60

Query: 61  AGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIES 120
           AGEQ+    R A L+AGFP+ VPATTIDR+CGSSQQA HFAAQG++AGAYDIVIA G+ES
Sbjct: 61  AGEQALNITRSAVLSAGFPESVPATTIDRQCGSSQQAAHFAAQGVIAGAYDIVIAAGVES 120

Query: 121 MSRVPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHELA 180
           MSRVPMG+  +G++  GP + ARY  GLV+QG++AEL+AAK++L R  +DS+SA+SH+ A
Sbjct: 121 MSRVPMGTTTMGKDASGPGVAARYPEGLVNQGISAELIAAKWKLDRDALDSFSAQSHQRA 180

Query: 181 ATARESGAFRREILGISTPNGLVEQ-----DETIRPGTSVEKLGTLQASFRNDELSARFP 235
           A A   G F +EIL IS  N   E      DET+R  T+ E L  L+ SF +++ + RFP
Sbjct: 181 AEAAAKGLFDKEILPISVTNAAGETVSHIVDETVRASTTAEGLAGLKPSFYSEKYAQRFP 240

Query: 236 QIGWNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMMLTAPIPA 295
           +  W++T GN+S ++DGASA L+MSE MA +LGL PRARF +F V GDDP+ MLTAPIPA
Sbjct: 241 EAQWSITPGNSSPLTDGASAALIMSEEMASKLGLTPRARFHSFSVAGDDPIFMLTAPIPA 300

Query: 296 SQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIALGHPLGASGV 355
           + + + ++GL +D ID YE+NEAFA VPLAW    GADPA+LNP GGAIALGH LG+SG 
Sbjct: 301 THKVLARAGLSIDDIDTYEVNEAFAPVPLAWAHEFGADPAKLNPWGGAIALGHALGSSGT 360

Query: 356 RLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392
           RL+TTM++ LE +G RYGLQ+MCE  GMANATIIER+
Sbjct: 361 RLLTTMVNHLEATGGRYGLQTMCEGAGMANATIIERI 397


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: 488
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: 392
Length of database: 397
Length adjustment: 31
Effective length of query: 361
Effective length of database: 366
Effective search space:   132126
Effective search space used:   132126
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