GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Brucella inopinata BO1

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_008507871.1 BIBO1_RS13010 long-chain fatty acid--CoA ligase

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>NCBI__GCF_000182725.1:WP_008507871.1
          Length = 581

 Score =  246 bits (629), Expect = 1e-69
 Identities = 169/522 (32%), Positives = 257/522 (49%), Gaps = 24/522 (4%)

Query: 54  GRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINP 113
           G+  +Y +L   +  LA+ L   GL  GDRV I   N  ++ +   A  + G V+VN+NP
Sbjct: 73  GKDISYKELDDHSRALAAWLQSRGLVKGDRVAIMMPNILQYPITFTAVLRAGFVVVNVNP 132

Query: 114 AYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTV 173
            Y   E+E+ LN  G K LV +  F T+    +     P       G +   K   +  V
Sbjct: 133 LYTPRELEHQLNDAGAKALVVLENFATTVEKALPSINVPNILVASMGDMLGFKGHIVNLV 192

Query: 174 VWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKG 233
           V    +     + PG +RF + +A+G A       V    Q  D   +Q+T GTTG  KG
Sbjct: 193 VRRVKKMVPAWNIPGHVRFKDALAQGRAKSFNPVPV----QGCDIAFLQYTGGTTGISKG 248

Query: 234 ATLTHRNILNNGFFIGECMKLT-------PADRLCIPVPLYHCFGMVLGNLACFTHGA-T 285
           A LTH NIL N   +   M +         A      +PLYH F + +  +     GA  
Sbjct: 249 AMLTHSNILANVEQMNLWMDVAFRNKGKPKALNFVCALPLYHIFALTVNAMIGMKLGARN 308

Query: 286 IVYPNDGFDPLTVLQTVQDERCTGLH---GVPTMFIAELDHPRFAEFNLSTLRTGIMAGS 342
           I+ PN    P  +   V++ +   +H   G+ T+F   +++P F   +   L   +  G 
Sbjct: 309 ILIPN----PRDIPSFVKELKKYPVHIFPGLNTLFNGLMNNPDFQTLDFKPLILTLGGGM 364

Query: 343 PCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIV 402
                V +R  + M    IT  YG++ETSPV+C ++ D   ++   T+G   P  +V I 
Sbjct: 365 AVQRPVAERW-QHMTGCHITEGYGLSETSPVACANALDA--TEFTGTIGLPMPSTDVVIR 421

Query: 403 DPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNI 462
           D D G+ +P+G+ GE C +G  VM GYW    +T  AI   G+  TGD+  MD  GY  I
Sbjct: 422 DDD-GSDLPLGKVGEICVRGPQVMKGYWNRPEETARAIMADGFFRTGDMGFMDERGYTKI 480

Query: 463 VGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPT 522
           V R KDM++  G N+YP EIEE    HP V +   VG+P++  GE +  +++ +   + T
Sbjct: 481 VDRKKDMILVSGFNVYPNEIEEVAAEHPGVLESAAVGIPNEHSGEVVKLYVVRR-DPELT 539

Query: 523 EDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
           ED+++AFC  ++ +YK PR + F  S P +  GKI + ++RD
Sbjct: 540 EDEVKAFCAERLTNYKRPREVEFRESLPKSNVGKILRRELRD 581


Lambda     K      H
   0.320    0.136    0.412 

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: 772
Number of extensions: 47
Number of successful extensions: 5
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: 578
Length of database: 581
Length adjustment: 36
Effective length of query: 542
Effective length of database: 545
Effective search space:   295390
Effective search space used:   295390
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 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