Alignments for a candidate for acs in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_012408692.1 NPUN_RS10400 long-chain fatty acid--CoA ligase

Query= SwissProt::P39062
         (572 letters)



>NCBI__GCF_000020025.1:WP_012408692.1
          Length = 513

 Score =  232 bits (592), Expect = 2e-65
 Identities = 154/498 (30%), Positives = 250/498 (50%), Gaps = 19/498 (3%)

Query: 59  NKVALYYKDAKRDEKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLG 118
           NK A+ +++    E +T+K++ E  NR  N LR   ++ + DRV +F+P  PE     LG
Sbjct: 17  NKPAIIFEE----ESFTYKDLDEMVNRVANGLRSL-DIRRRDRVALFLPNIPEFVISYLG 71

Query: 119 AIKIGAIAGPLFEAFMEGAVKDRLENSEAKVVVTTPELLERIPVDKLPHLQHVFVVGGEA 178
            +KIGA+A  +        V+  L +  AK ++TT    E I    LP LQH+ +  G A
Sbjct: 72  ILKIGAVAVSINIMLKTDEVRYILNDCAAKAIITTESQTEYIQEPDLPQLQHILIAEGRA 131

Query: 179 ESGTNIINYDEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTG 238
             G ++      +  E+  ++   M + D   + YTSG+TG PKG    H  +I      
Sbjct: 132 NKGISLKQLMAKSSPEARAVE---MSRDDPASILYTSGTTGFPKGATLSHGNVIFNSYCA 188

Query: 239 KWVLDLKEEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVN 298
                +++ D            G    I    ++  T +I+  RF P+    TI    V 
Sbjct: 189 NCCYRIQKSDRLLLFLPLSHCFGQ-NAILNAGISACTTIILQRRFDPDQVLETITTHQVT 247

Query: 299 VWYSAPTAFRMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWM 358
           + +  PT F  L+       + Y+L ++R+  S   P+  +V    +K F   IH+ + +
Sbjct: 248 MLFGVPTVFIKLLNMD---TSNYNLENIRYYFSAAAPMPLQVAENWYKKFGFVIHEGYGL 304

Query: 359 TETGSQLICNYPCMDIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHT 418
           TET      N+  ++ K GS+G PI  VE  IVD  GN++    +G + IK    ++M  
Sbjct: 305 TETSPFAAYNHN-LNYKLGSVGTPIANVEMKIVDGDGNQVEIGELGEITIKGA--NVMLG 361

Query: 419 IWNNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVE 478
            WN P +  +  +  GW  +GD   MDE+G+F+   R  D+I+ SG +V P EVE+ + +
Sbjct: 362 YWNRPFE-TAEVIKNGWLHTGDIGRMDEDGFFYVIDRSKDMIVVSGFKVYPTEVENVIYQ 420

Query: 479 HPAIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEF 538
           HPA+AE  + G PDP++GEI+KA I L+         +++I  F  + +AA+  PR I F
Sbjct: 421 HPAVAEVAIYGVPDPLKGEIVKANIILKAS---QTITEQQIIDFCYERMAAYKVPRVINF 477

Query: 539 KDKLPKTRSGKIMRRVLK 556
            + +PK  +GK+++R L+
Sbjct: 478 VNSIPKNSTGKVLKRFLR 495


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: 626
Number of extensions: 40
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 572
Length of database: 513
Length adjustment: 35
Effective length of query: 537
Effective length of database: 478
Effective search space:   256686
Effective search space used:   256686
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources