GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Thermoactinomyces daqus H-18

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_033100144.1 JG50_RS0105805 AMP-binding protein

Query= BRENDA::Q9Z3R3
         (650 letters)



>NCBI__GCF_000763315.1:WP_033100144.1
          Length = 646

 Score =  256 bits (655), Expect = 2e-72
 Identities = 199/659 (30%), Positives = 315/659 (47%), Gaps = 46/659 (6%)

Query: 5   RPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIG 64
           +P+W P +E +E++ +  F+   G      F DYD F++ S+     FW       +V+ 
Sbjct: 3   KPVWFPKQEQMEQTRLYRFMKRLG------FRDYDRFYEQSIKNIAWFWD------EVVN 50

Query: 65  ESGEKALVDGDRMLD-------ARFFPEARLNFAENLLRKTGSGDA------LIFRGEDK 111
           + G + ++   ++LD        R+F + ++N ++N L +     A      LI+ G+D 
Sbjct: 51  DLGLRWMMPYRQVLDMSDGIAWTRWFVDGKINISDNCLDRFVEEPAARHRLALIWEGDDG 110

Query: 112 VSYRLTWDELRALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCS 171
            + + T+ +L   V+RL   L+  G+ AGD VA  MP + E +  MLA A +GAI++ C 
Sbjct: 111 TTKKYTYRDLWLEVNRLACGLKKLGVAAGDCVAIYMPMIAENVIAMLAVARIGAIFTPCF 170

Query: 172 PDFGEQGVLDRFGQIAPKLFIVCDGYWYNGK----RQDVDSKVRAVAKSLGAP-TVIVPY 226
             +G + V  R      K  I  DGY   GK    +++ D   RA   S      V+V  
Sbjct: 171 SGYGAEAVATRIQGCQAKWLITADGYLRRGKVVAMKEEAD---RAADLSPSVEKVVVVSR 227

Query: 227 AGDSAALAPTVEGGVTLADFIAGFQA-GPLVFERLPFGHPLYILFSSGTTGVPKCIVHSA 285
            G      P  +  V      A  +   P V +      P  I+++SGTTG PK  VH  
Sbjct: 228 LGRDCPWNP--DRDVKWDQLTAEMKTLSPAVTDA---NDPFMIIYTSGTTGKPKGTVHVH 282

Query: 286 GGTLLQHLKEHRFHCGLRDGERLFYFTTCGWMMWNWLASG-LAVGATLCLYDGSPFCPDG 344
            G  L+   +  +   +  G+ LF+ T  GWMM  W+  G L +G+T+ +++G+P  P  
Sbjct: 283 SGFPLKAAFDAGYAFDVGPGDILFWVTDMGWMMGPWMVFGTLLLGSTMLVFEGTPDYPIP 342

Query: 345 NVLFDYAAAERFAVFGTSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVY 404
             L++          G S   I A+ K G +     DLSSLR+  STG P +PE + +++
Sbjct: 343 GRLWELTEKHGVTHLGISPTLIRALMKHGTSWFSQRDLSSLRVFGSTGEPWNPEPWHWLF 402

Query: 405 EGIKPD-VQLASISGGTDIVSCFVLGNPL-KPVWRGEIQGPGLGLAVDVWNDEGKPVRGE 462
           E +    V + + SGGT+I S  +LGN   KP+      GP  G+  +V++D+GK VRGE
Sbjct: 403 EQVGGKRVPIFNYSGGTEI-SGGILGNHFFKPIVPCGFAGPLPGMDAEVFDDQGKTVRGE 461

Query: 463 KGELVCTRAFPSMPVMFWNDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDA 522
            GELV  + +  M   FW   D  +Y   Y+ R+   W HGD+      G   I GRSD 
Sbjct: 462 VGELVLRQPWVGMTSGFWQ--DARRYEDTYWSRWPKTWLHGDWVIVDEGGQWFITGRSDD 519

Query: 523 TLNPGGVRIGTAEIYNQVEQMDEVAEALCIG-QDWEDDVRVVLFVRLARGVELTEALTRE 581
           TL   G R+G AE+ + +     V EA  IG  D +     V FV +    E  ++LT E
Sbjct: 520 TLKIAGKRLGPAEMESVLVDHPSVIEAATIGVPDADKGESAVCFVVVRGDGEEVQSLTEE 579

Query: 582 IKNRIRSGASPRHVPAKIIAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALD 640
           +   +         P ++  V ++P+T++GKI+   +R    G    +  +L N  A++
Sbjct: 580 LVRFVGERMGKALKPKRVHIVDELPKTRNGKILRRVIRAAYLGENAGDLSSLENAHAVE 638


Lambda     K      H
   0.322    0.139    0.441 

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: 1267
Number of extensions: 77
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 650
Length of database: 646
Length adjustment: 38
Effective length of query: 612
Effective length of database: 608
Effective search space:   372096
Effective search space used:   372096
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 (21.9 bits)
S2: 54 (25.4 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