GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Thermithiobacillus tepidarius DSM 3134

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_028989221.1 G579_RS0104490 acetate--CoA ligase

Query= BRENDA::Q9Z3R3
         (650 letters)



>NCBI__GCF_000423825.1:WP_028989221.1
          Length = 652

 Score =  205 bits (521), Expect = 6e-57
 Identities = 175/593 (29%), Positives = 272/593 (45%), Gaps = 34/593 (5%)

Query: 71  LVDGDRMLDARFFPEARLNFAENLLRK-----TGSGDALIFRGEDKVSYRLTWDELRALV 125
           ++D  R    R+F +  LN A N L +     T +  ALI+ GED      T+ +L   V
Sbjct: 65  VLDDSRAPFYRWFADGELNVAANCLDRHLSSPTRNKAALIWEGEDGEVRTFTYGQLHREV 124

Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
           SR    L+  GI  GDRVA  MP +PE    MLA A +GAI S     F  + + DR   
Sbjct: 125 SRFANVLKKLGITTGDRVAIYMPMVPEAAVAMLACARLGAIHSVVFGGFSAEALKDRIED 184

Query: 186 IAPKLFIVCDGYWYNGK----RQDVDSKVRAVAKSLGAPTVIVPYAGDSAALAPTVEGGV 241
              KL I  DG +  G+    +Q  D  +     S+    V++   G    +   ++G  
Sbjct: 185 TQAKLLITADGGFRAGRVVHLKQHADQALMRDGHSVDK-VVVLRRTGQEVDM---LDGRD 240

Query: 242 TLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCG 301
                +            +   HPL++L++SG+TG PK IVHS+GG LL      R+   
Sbjct: 241 LWWHELMQDAEPQCPAVSVNAEHPLFVLYTSGSTGKPKGIVHSSGGYLLWSALTMRWVFD 300

Query: 302 LRDGERLFYFTTCGWMMWNWLA--SGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVF 359
           ++  +  +     GW+  +  A    LAVGAT+ L++G P  PD    +        +VF
Sbjct: 301 IKPEDVYWCTADIGWVTGHTYALYGPLAVGATVLLFEGVPTYPDAGRFWAMIERHGVSVF 360

Query: 360 GTSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKP------DVQL 413
            T+   + A+ K G      +DLSSLRL+ + G P++PE + + Y  I        D   
Sbjct: 361 YTAPTAVRALMKLGEEWPGKYDLSSLRLLGTVGEPINPEAWMWYYRVIGKERCPVVDTWW 420

Query: 414 ASISGGTDIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEK--GELVCTRA 471
            + +GG  +++      PLKP   G    P  G+  D+ ++EG PV+G +  G LV  R 
Sbjct: 421 QTETGG-HLIAPLPGVTPLKP---GSCTRPLPGIFPDIVDEEGDPVQGTEAGGYLVVKRP 476

Query: 472 FPSMPVMFWNDPDGAKYRAAYFDRFDN-VWCHGDFAEWTPHGGIVIHGRSDATLNPGGVR 530
           +P M    W   + A+Y   Y+ +F N  +  GD A     G   I GR D  LN  G R
Sbjct: 477 WPGMLRTVWG--NDARYLETYWAKFQNRYYVAGDSAHRDADGYYWIMGRIDDVLNVSGHR 534

Query: 531 IGTAEIYNQVEQMDEVAEALCIGQDWE---DDVRVVLFVRLARGVELTEALTREIKNRIR 587
           +GT EI + +     VAEA  +G+  E   + +   + +R +   +  + LT  ++  + 
Sbjct: 535 LGTMEIESALVSHPAVAEAAVVGRPHEIKGEAITAFVILRQSHVQDDRDRLTEALRQHVS 594

Query: 588 SGASPRHVPAKIIAVADIPRTKSGKIVELAVRDVVHGRPV-KNKEALANPEAL 639
               P   P  I    ++P+T+SGKI+   +R +  G  + ++   L N E +
Sbjct: 595 EAIGPIAKPDDIRFTDNLPKTRSGKIMRRLLRAIARGEEITQDTSTLENEETV 647


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: 1243
Number of extensions: 85
Number of successful extensions: 6
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: 652
Length adjustment: 38
Effective length of query: 612
Effective length of database: 614
Effective search space:   375768
Effective search space used:   375768
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 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