GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Pseudarthrobacter sulfonivorans Ar51

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_058931641.1 AU252_RS16370 AMP-binding protein

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



>NCBI__GCF_001484605.1:WP_058931641.1
          Length = 558

 Score =  572 bits (1473), Expect = e-167
 Identities = 296/569 (52%), Positives = 378/569 (66%), Gaps = 25/569 (4%)

Query: 16  SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVH-----QGRRYTYAQLQTEAHRLA 70
           ++  G TDVPL+E+TIG  F  +VAR P  +AL+          RR++Y ++  +  RLA
Sbjct: 3   AYTAGDTDVPLLEETIGQNFERVVARFPFHDALIEAAPVPGADARRWSYTKMNDDVDRLA 62

Query: 71  SALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCK 130
            ALL  G+  GDRVGIWS N AEW L+Q ATA+ G +LVN+NPAYR+ E+E+ + + G +
Sbjct: 63  RALLASGVAKGDRVGIWSPNCAEWTLLQYATAKAGAILVNVNPAYRSHELEFVVKQNGMR 122

Query: 131 LLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGL- 189
           +LV+    + SDY+GM R+               A  P L+ +V++ D    G D  G  
Sbjct: 123 MLVAAPSDRNSDYVGMARQAL-------------AGCPDLRELVFLPDYGMDGLDAGGPQ 169

Query: 190 ----LRFTELIARGNAADPR-LAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNN 244
               L + EL+ R +A     L    A L   DPIN+Q+TSGTTGFPKGATLTH NILNN
Sbjct: 170 SDAELTYAELLKRADAVGHSGLKARMAELDPHDPINLQYTSGTTGFPKGATLTHHNILNN 229

Query: 245 GFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQD 304
           G+ IGE +  T  DR+ IPVP YHCFGMV+GNLA  +HGA  + P  GF P   L+ VQD
Sbjct: 230 GYSIGELLGYTEHDRVVIPVPFYHCFGMVIGNLAALSHGAATIIPGRGFTPAAALEAVQD 289

Query: 305 ERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIA 364
              T L+GVPTMFIAEL  P F+ ++L+TLRTG+MAGS CP +VM RV+ +M++ ++ I 
Sbjct: 290 FGGTSLYGVPTMFIAELALPDFSSYDLATLRTGVMAGSVCPIDVMNRVISEMHMVDVAIC 349

Query: 365 YGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYS 424
           YGMTETSPVS  +     L  R  TVG+  P LE +IVDP TG V+  G+ GE CT+GY+
Sbjct: 350 YGMTETSPVSTMTRNGDTLQHRTETVGRTMPRLENQIVDPGTGEVLERGEIGELCTRGYA 409

Query: 425 VMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEE 484
           VM GYW     T EAID   WMHTGDLA MD EGYV I GRIKD+VIRGGENIYPREIEE
Sbjct: 410 VMAGYWDQPETTAEAIDTDRWMHTGDLARMDDEGYVVIEGRIKDLVIRGGENIYPREIEE 469

Query: 485 FLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTE-DDIRAFCKGQIAHYKVPRYI 543
           FLY HP +QDVQV+GVPD +YGEEL A II   G +P +   +  FC+G++AHYK+PRY+
Sbjct: 470 FLYSHPSIQDVQVIGVPDARYGEELMACIILTAGAEPLDAAAVAEFCRGKLAHYKIPRYV 529

Query: 544 RFVTSFPMTVTGKIQKFKIRDEMKDQLGL 572
               SFPMTV+GKI+K ++R+E   +LGL
Sbjct: 530 DVRESFPMTVSGKIRKVEMREEAVARLGL 558


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: 874
Number of extensions: 39
Number of successful extensions: 4
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: 558
Length adjustment: 36
Effective length of query: 542
Effective length of database: 522
Effective search space:   282924
Effective search space used:   282924
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 Apr 09 2024. 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