GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Azospirillum brasilense Sp245

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate AZOBR_RS30610 AZOBR_RS30610 acetyl-CoA acetyltransferase

Query= SwissProt::P50174
         (393 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS30610 AZOBR_RS30610 acetyl-CoA
           acetyltransferase
          Length = 391

 Score =  564 bits (1454), Expect = e-165
 Identities = 282/387 (72%), Positives = 320/387 (82%)

Query: 6   IVIASAARTAVGSFNGAFGNTLAHELGAAAIKAVLERAGVEAGEVDEVILGQVLPAGEGQ 65
           +VIASAART +GSFNGA  +  AH LG  AI+  L RA  +A EV EVILGQ+L AG+GQ
Sbjct: 4   VVIASAARTPIGSFNGALSSVPAHYLGEIAIREALSRAKTDAAEVTEVILGQILTAGQGQ 63

Query: 66  NPARQAAMKAGLPQEKTAWGMNQLCGSGLRAVALGMQQIATGDAKVIVAGGMESMSMAPH 125
           NPARQAA+ AG+P   TA+G+NQLCGSGLR+VALG Q I  GDA+V+V GG ESMS APH
Sbjct: 64  NPARQAAVNAGIPASATAFGINQLCGSGLRSVALGYQAIRNGDAEVMVVGGQESMSQAPH 123

Query: 126 CAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGITAENVARKWQLTREEQDEFALASQN 185
             HLR GVKMG  +M+DTM+KDGL DAF GYHMG TAENVA+KWQLTREEQD FA ASQ 
Sbjct: 124 VMHLRNGVKMGAAEMLDTMLKDGLMDAFKGYHMGTTAENVAQKWQLTREEQDVFAAASQQ 183

Query: 186 KAEAAQKAGRFADEIVPFVVKTRKGDVNVDQDEYIRHGATLDSIAKLRPAFDKEGTVTAG 245
           KAEAAQK+GRF DEI+P  +K RKGD+ V  DEY +HG T +S+AKLRPAF KEGTVTAG
Sbjct: 184 KAEAAQKSGRFKDEIIPVTIKGRKGDIIVADDEYPKHGTTAESLAKLRPAFSKEGTVTAG 243

Query: 246 NASGLNDGAAAALLMTEAEAARRGIQPLARIVSWATAGVDPQIMGTGPIPASRKALEKAG 305
           NASG+NDGAAA +LMT   AARRG+ PLARIVSWATAGVDP IMGTGPIPASR ALEKAG
Sbjct: 244 NASGINDGAAALVLMTAENAARRGLTPLARIVSWATAGVDPAIMGTGPIPASRLALEKAG 303

Query: 306 WSVADIELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLFE 365
           W   D++L+EANEAFAAQA AVNKDLGWD S VNVNGGAIA+GHP+GASGARVL TLL+E
Sbjct: 304 WKHDDLDLIEANEAFAAQALAVNKDLGWDTSKVNVNGGAIALGHPVGASGARVLTTLLYE 363

Query: 366 MKRRGVSKGLATLCIGGGMGVAMCVER 392
           M++R   KGLATLCIGGGMG+A+ VER
Sbjct: 364 MQKRDAKKGLATLCIGGGMGIALTVER 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: 451
Number of extensions: 15
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: 391
Length adjustment: 31
Effective length of query: 362
Effective length of database: 360
Effective search space:   130320
Effective search space used:   130320
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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