GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_0835
          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:

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