GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Rhodanobacter denitrificans 2APBS1

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_015446959.1 R2APBS1_RS03900 3-oxoadipyl-CoA thiolase

Query= SwissProt::P45369
         (394 letters)



>NCBI__GCF_000230695.2:WP_015446959.1
          Length = 400

 Score =  309 bits (791), Expect = 1e-88
 Identities = 172/395 (43%), Positives = 248/395 (62%), Gaps = 9/395 (2%)

Query: 7   IVDAGRSAIGTFSGSLSSLSATEIGTAVLKGLLAR-TGLAPEQIDEVILGQVLTAGV-GQ 64
           +VDA R+  G   G+L+ + A ++    +  L+AR   L    +DEVILG    AG   +
Sbjct: 6   LVDATRTPFGRLGGALAGVRADDLAALPIAALMARHPTLDWAALDEVILGCANQAGEDNR 65

Query: 65  NPARQTTLKAGLPHSVPAMTINKVCGSGLKAVHLAMQAIACGDADIVIAGGQESMSQSSH 124
           N AR  TL AGLP SVPA+T+N++C SGL+A+  A +AIACG+A++V+AGG ESMS++ +
Sbjct: 66  NVARMATLLAGLPQSVPAVTVNRLCASGLEAIGQAARAIACGEAELVVAGGVESMSRAPY 125

Query: 125 VLPRS----RDGQRMGDWSMKDTMIVDGLWDAFNNYHMGTTAENIAQKYGFTREQQDAFA 180
           VL ++      GQ++ D ++   ++   +   +    M  TAEN+A+++G  R+ QDA+A
Sbjct: 126 VLAKADVAYARGQQLEDTTLGWRLVNPRMQAGYGIDSMTQTAENLAREHGIDRDSQDAYA 185

Query: 181 AASQQKTEAAQKAGRFQDEIIPIEIPQRKGDPKVFDADEFPRHGTTAESLGKLRPAFSRD 240
             SQQ+T  AQ  G   +EI  +  P  K +  V   DE PR  TTA  L  L+P     
Sbjct: 186 LRSQQRTAHAQAQGWLAEEITAVHAPHGK-ESLVVQVDEHPRADTTAAKLAALKPLLGAG 244

Query: 241 GSVTAGNASGINDGAAMVVVMKESKAKELGLKPMARLVAFASAGVDPAIMGTGPIPASTK 300
            S+TAGNASG+NDGAA V++  E+     GL+P+AR+V  A+AGV P +MG GP+PA  K
Sbjct: 245 SSITAGNASGLNDGAAAVLLASEAALARYGLQPLARIVGMAAAGVAPRVMGIGPVPAIHK 304

Query: 301 CLEKAGWTPADLDLIEANEAFAAQAMSVNQDMGW--DLSKVNVNGGAIAIGHPIGASGAR 358
            L + G   +D D IE NEAFAAQ ++  + +G   D   VN NGGAIA+GHP+GASGAR
Sbjct: 305 LLARTGLGASDFDRIEINEAFAAQVLACTRSLGLPDDAEHVNANGGAIALGHPLGASGAR 364

Query: 359 VLVTLLYEMQKRDAKKGLATLCIGGGQGVALAVER 393
           + +T  + +++    + L +LC+G GQG+ALA+ER
Sbjct: 365 LALTAAFALRRHRQHRALVSLCVGVGQGLALALER 399


Lambda     K      H
   0.315    0.131    0.375 

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: 401
Number of extensions: 22
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: 394
Length of database: 400
Length adjustment: 31
Effective length of query: 363
Effective length of database: 369
Effective search space:   133947
Effective search space used:   133947
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 (21.6 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