GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Rhodococcus qingshengii djl-6-2

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_050655293.1 C1M55_RS02775 acetate--CoA ligase

Query= BRENDA::Q9Z3R3
         (650 letters)



>NCBI__GCF_002893965.1:WP_050655293.1
          Length = 643

 Score =  223 bits (567), Expect = 3e-62
 Identities = 187/628 (29%), Positives = 292/628 (46%), Gaps = 37/628 (5%)

Query: 36  ADYDAFHDWSVSERGAFWTAVWEHCKVIGESGEKALVDGDRMLDARFFPEARLNFAENLL 95
           AD D    W+       W   W             ++D      A++F   +LN A N +
Sbjct: 33  ADTDRLAFWANQAERLHWHEKWTD-----------VLDWTDAPVAKWFVGGKLNVAYNCV 81

Query: 96  RK---TGSGD--ALIFRGEDKVSYRLTWDELRALVSRLQQALRAQGIGAGDRVAAMMPNM 150
            +    G+GD  A+ F GE   S  LT+++L A VSR        G+ AGDRVA  MP +
Sbjct: 82  DRHVLAGNGDRIAIHFEGEPGDSRDLTYNDLLAEVSRAANTFTDLGLVAGDRVAIYMPMI 141

Query: 151 PETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQIAPKLFIVCDGYWYNGKRQDVDSKV 210
           PE I  MLA A +G   S     F    +  R      KL +  DG W  G    + + V
Sbjct: 142 PEAIVTMLACARLGLTHSVVFAGFSATALRSRIDDAQAKLVVTVDGQWRRGAAAPIKTAV 201

Query: 211 -RAVAKSLGAPTVIVPYAGDSAALAPTVEGGVTLADFIAGFQAGPLVFERLPFG--HPLY 267
             +VA +     V+V    +   +      G  L       QA P   E   F   HPL+
Sbjct: 202 DESVAGAESVQNVLVV---NRTGIDVDWTDGRDLWWHETVAQASP-EHEAQAFDAEHPLF 257

Query: 268 ILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGLRDGERLFYFTT-CGWMMWN-WLASG 325
           IL++SGTTG PK I+H++GG L Q    H      + G+ +++ T   GW+  + ++  G
Sbjct: 258 ILYTSGTTGKPKGIIHTSGGYLTQASYTHHNVFDHKAGQDVYWCTADIGWVTGHSYIVYG 317

Query: 326 -LAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTSAKYIDAVRKGGFTPARTHDLSS 384
            L+ G T  +Y+G+P  P+ +  FD       +++ T+   +    K G      HDLSS
Sbjct: 318 PLSNGVTQVVYEGTPNSPNEHRHFDIIEKYGVSIYYTAPTLVRTFMKWGREIPDAHDLSS 377

Query: 385 LRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDIVSCFVLGNPLKPVWR---GEIQ 441
           +RL+ S G P++PE + +  E I  + +   +       +  ++ +PL  +     G   
Sbjct: 378 IRLLGSVGEPINPEAWRWFREVIGGN-KAPIVDTWWQTETGAIMISPLPGITATKPGSAM 436

Query: 442 GPGLGLAVDVWNDEGKPVR-GEKGELVCTRAFPSMPVMFWNDPDGAKYRAAYFDRF--DN 498
            P  G++  + +D+ KP+  G  G LV    +P+M    W D D  +YR  Y+ R+  + 
Sbjct: 437 APLPGISAKIVDDDAKPLGPGGNGYLVLDEPWPAMLRGIWGDMD--RYRDTYWSRYAEEG 494

Query: 499 VWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQMDEVAEALCIGQ-DWE 557
            +  GD A++   G + + GR D  +N  G RI T+E+ + +     VAEA  +G  D  
Sbjct: 495 WYFAGDGAKYDDDGALWVLGRVDDVMNVSGHRISTSEVESALVNHHGVAEAAVVGAADET 554

Query: 558 DDVRVVLFVRLARGVELT-EALTREIKNRIRSGASPRHVPAKIIAVADIPRTKSGKIVEL 616
               +V FV L  GVE T + L  E+K ++ +  SP   P +I  V ++P+T+SGKI+  
Sbjct: 555 TGQGIVAFVILREGVENTGDVLIAELKAQVSTDISPIAKPRQITIVPELPKTRSGKIMRR 614

Query: 617 AVRDVVHGRPVKNKEALANPEALDLFAG 644
            +RDV  GR + +   L +P+  D   G
Sbjct: 615 LLRDVAEGRDLGDTSTLVDPKVFDAIRG 642


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: 1187
Number of extensions: 73
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 650
Length of database: 643
Length adjustment: 38
Effective length of query: 612
Effective length of database: 605
Effective search space:   370260
Effective search space used:   370260
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