GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Sphingomonas koreensis DSMZ 15582

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate Ga0059261_0835 Ga0059261_0835 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II

Query= SwissProt::P39062
         (572 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_0835 Ga0059261_0835 Acyl-CoA
           synthetases (AMP-forming)/AMP-acid ligases II
          Length = 582

 Score =  169 bits (429), Expect = 2e-46
 Identities = 151/523 (28%), Positives = 233/523 (44%), Gaps = 60/523 (11%)

Query: 71  DEKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLF 130
           DE+ +F+       R    LR  G V KGDRV + M   PE   +   A+ IGAI  PL 
Sbjct: 74  DERVSFEANFRAVARLATQLREMG-VGKGDRVALAMRNLPEWPVVFFAAVSIGAILVPLN 132

Query: 131 EAFMEGAVKDRLENSEAKVVVTTPELLERIP--VDKLPHLQHVFVVGGEAESGTNIINYD 188
             +  G +   L +S + V+ T  E  +R+   +  LP L+H+ V       G  +   +
Sbjct: 133 AWWTSGELDYGLRDSGSVVLFTDGERYDRLADALPGLPDLKHIVVSRARGPLGEGVRQLE 192

Query: 189 EAAKQESTRLDIEWMDKKDGFL-------------LHYTSGSTGTPKGVLHVHEAMIQQY 235
           +   +       +W +  D  L             + YTSG+TG PKG L  H  +I   
Sbjct: 193 DLIGKPG-----DWAELPDAPLPAEPSLVPDDDATIFYTSGTTGHPKGALGTHRNLITNI 247

Query: 236 QTGKWV------------------LDLKEEDIYWCTADPGWVTGTVYGIFAPWLNGATNV 277
            +  +                   + L    ++  TA    + G V+        G T +
Sbjct: 248 LSSGYCGARPYLRRGEMPPDPTPRVGLMVIPLFHVTACSASLMGAVFA-------GHTTI 300

Query: 278 IVGGRFSPESWYGTIEQLGVNVWYSAPTAFRMLMGAGDEMAAKYDLTSLRHVLSVGEPLN 337
            +  ++  E     I++  VN+    PT    L+       AKYDL+SL  +   G P  
Sbjct: 301 FMR-KWDVEQAMEIIQREKVNLTGGVPTIAWQLLE--HPARAKYDLSSLEMIAYGGAPSA 357

Query: 338 PEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPCMDI--KPGSMGKPIPGVEAAIVDNQG 395
           PE+++  +  F     + W MTET +  +  +   D   +P S G P+P  E  I+D +G
Sbjct: 358 PELVKRIYTEFGALPGNGWGMTETMAT-VTQHSAEDYLNRPTSAGPPVPVAELKIMDAEG 416

Query: 396 -NELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQG 454
            +ELP   +G L  K   P ++   WN PE+    F  G W  +GD A +DEEG+ +   
Sbjct: 417 EHELPIGEVGELWAKG--PMIVKGYWNKPEETAESFRDG-WVRTGDLARVDEEGFLFIVD 473

Query: 455 RVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDK 514
           R  D+I+  GE +   EVE  L  HPA+ +A +IG P    GE   A + L  G + S+ 
Sbjct: 474 RAKDIIIRGGENIYSSEVEDVLYAHPAVTDAALIGIPHRTLGEEPVAVVHLAPGKQASE- 532

Query: 515 LKEEIRLFVKQGLAAHAAPREIEF-KDKLPKTRSGKIMRRVLK 556
              E++ +V+  LAA   P  I F +D LP+  +GKI+++ LK
Sbjct: 533 --AELQQWVRDRLAAFKVPVAIRFTRDTLPRNANGKILKKDLK 573


Lambda     K      H
   0.318    0.136    0.425 

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: 945
Number of extensions: 50
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: 572
Length of database: 582
Length adjustment: 36
Effective length of query: 536
Effective length of database: 546
Effective search space:   292656
Effective search space used:   292656
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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