GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Moritella dasanensis ArB 0140

Align 3-ketoacyl-CoA thiolase, mitochondrial; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; Acyl-CoA hydrolase, mitochondrial; Beta-ketothiolase; Mitochondrial 3-oxoacyl-CoA thiolase; EC 2.3.1.16; EC 2.3.1.9; EC 3.1.2.-; EC 3.1.2.1; EC 3.1.2.2 (characterized)
to candidate WP_017223546.1 A923_RS0120390 acetyl-CoA C-acetyltransferase

Query= SwissProt::P13437
         (397 letters)



>NCBI__GCF_000276805.1:WP_017223546.1
          Length = 426

 Score =  165 bits (417), Expect = 3e-45
 Identities = 127/433 (29%), Positives = 196/433 (45%), Gaps = 55/433 (12%)

Query: 4   LRGVFIVAAKRTPFGAYGGLLKDFTATDLTEFAARAALSAGKVPPETIDSVIVGNVMQSS 63
           +R V I+   R PF          +  D+     R  +    +  E +  V+ G V++ S
Sbjct: 6   IRRVAIIGGNRIPFARSNTAYSKLSNQDMLTETIRGLVVKYNLRGEQLGEVVAGAVIKHS 65

Query: 64  SDAAYLARHVGLRVGVPTETGALTLNRLCGSGFQSIVSGCQEICSKDAEVVLCGGTESMS 123
            D   L R   L  G+  ET    + + CG+G  + +    +I     E  + GG+++ S
Sbjct: 66  RDFN-LTREAVLSAGLAPETPCYDIQQACGTGLAAAIQVANKIALGQIEAGIAGGSDTTS 124

Query: 124 QSPYSV----RNV------------RFGTKFGLDLKLEDTLWAGLTDQHVKLPMGMTAEN 167
            +P +V    R+V            R      L LK    L     +   K+ MG   + 
Sbjct: 125 DAPIAVSEGMRSVLLELNRAKTGKQRLKALSRLRLKHFAPLTPANKEPRTKMAMGDHCQV 184

Query: 168 LAAKYNISREDCDRYALQSQQRWKAANEAGYFNEEMAPIEVKTKKGKQTMQVDEHARPQT 227
            A ++NISRE  D  A  S Q+  AA E G+F+  ++P+   TK        D   R  T
Sbjct: 185 TAKEWNISREAQDALACASHQKLAAAYEEGFFDTLVSPMAGLTK--------DNVLRADT 236

Query: 228 TLEQLQNLPPVFKK-EGTVTAGNASGMSDGAGVVIIASEDAVKKHNFTPLARVVGYFVSG 286
           T+E+L  L P F K  GT+TAGN++ ++DGA  V++ASE+    HN      V  Y   G
Sbjct: 237 TVEKLAKLKPCFDKVNGTMTAGNSTNLTDGASAVLLASEEWAAAHNLP----VQAYLTFG 292

Query: 287 CDPAI--------MGIGPVPAITGALKKAGLSLKDMDLIDVNEAFAPQFLAVQKSLD--- 335
              AI        + + P  A+   LK+AGL+L+D D  +++EAFA Q L+   + +   
Sbjct: 293 ETAAIDFVDKKEGLLMAPAYAVPKMLKRAGLTLQDFDYYEIHEAFAAQVLSTLAAWEDEK 352

Query: 336 --------------LDPSKTNVSGGAIALGHPLGGSGSRITAHLVHELRRRGGKYAVGSA 381
                         +D +K NV G ++A GHP   +G R+ A L   L ++G    + S 
Sbjct: 353 FCKEKLGLDAALGSIDMTKLNVKGSSLATGHPFAATGGRVVATLAQLLDQKGSGRGLISI 412

Query: 382 CIGGGQGISLIIQ 394
           C  GGQGI+ I++
Sbjct: 413 CAAGGQGITAILE 425


Lambda     K      H
   0.317    0.133    0.386 

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: 369
Number of extensions: 24
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: 397
Length of database: 426
Length adjustment: 31
Effective length of query: 366
Effective length of database: 395
Effective search space:   144570
Effective search space used:   144570
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