GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Magnetospirillum magneticum AMB-1

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_011383284.1 AMB_RS04295 acetyl-CoA C-acetyltransferase

Query= SwissProt::P50174
         (393 letters)



>NCBI__GCF_000009985.1:WP_011383284.1
          Length = 390

 Score =  513 bits (1321), Expect = e-150
 Identities = 260/387 (67%), Positives = 301/387 (77%)

Query: 6   IVIASAARTAVGSFNGAFGNTLAHELGAAAIKAVLERAGVEAGEVDEVILGQVLPAGEGQ 65
           IVIA+A RT VGSFNG+     A +LG   I+  L+RAGVEA  VDEV+LG +L AG GQ
Sbjct: 4   IVIAAATRTPVGSFNGSLAGLQAAQLGEIVIREALKRAGVEAEAVDEVLLGHILTAGCGQ 63

Query: 66  NPARQAAMKAGLPQEKTAWGMNQLCGSGLRAVALGMQQIATGDAKVIVAGGMESMSMAPH 125
           N ARQAA+KAG+P   TA  +NQLCGSGLRAVALG Q I  GDA +IVAGG ESMS A H
Sbjct: 64  NTARQAAIKAGVPNTATAMAINQLCGSGLRAVALGFQAIKLGDANIIVAGGQESMSNAQH 123

Query: 126 CAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGITAENVARKWQLTREEQDEFALASQN 185
             ++RGGVKMGD  ++DTMIKDGLTDAF   HMGITAEN+A K+Q+TREEQD FAL SQN
Sbjct: 124 AIYMRGGVKMGDASLVDTMIKDGLTDAFSPIHMGITAENLAEKFQITREEQDAFALGSQN 183

Query: 186 KAEAAQKAGRFADEIVPFVVKTRKGDVNVDQDEYIRHGATLDSIAKLRPAFDKEGTVTAG 245
           KAEAA KAGRF D+IVP  +  ++ +   D DE+IR G TLD IAK +PAF K+GTVTA 
Sbjct: 184 KAEAASKAGRFKDQIVPVTITVKREEKLFDTDEFIRMGCTLDQIAKPKPAFKKDGTVTAA 243

Query: 246 NASGLNDGAAAALLMTEAEAARRGIQPLARIVSWATAGVDPQIMGTGPIPASRKALEKAG 305
           NASG+NDG AA +LMT  EA +RGI+PLARI  WATAG DP  MG GP+PA++K L K G
Sbjct: 244 NASGINDGGAALVLMTAKEADKRGIKPLARIAGWATAGTDPNTMGYGPVPATQKLLAKLG 303

Query: 306 WSVADIELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLFE 365
           W   D++L+EANEAFAAQA AVNK +GWD S VNVNGGAIAIGHPIGASGAR+L  LL+E
Sbjct: 304 WKHEDLDLIEANEAFAAQAIAVNKGMGWDTSKVNVNGGAIAIGHPIGASGARILVDLLYE 363

Query: 366 MKRRGVSKGLATLCIGGGMGVAMCVER 392
           M RR   KGLATLCIGGGMG+A+CVER
Sbjct: 364 MGRRDAKKGLATLCIGGGMGIALCVER 390


Lambda     K      H
   0.317    0.132    0.381 

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: 441
Number of extensions: 18
Number of successful extensions: 1
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: 390
Length adjustment: 31
Effective length of query: 362
Effective length of database: 359
Effective search space:   129958
Effective search space used:   129958
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 17 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