GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Phaeobacter inhibens BS107

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF1013 PGA1_c10300 acetyl-coenzyme A synthetase AcsA

Query= SwissProt::P39062
         (572 letters)



>FitnessBrowser__Phaeo:GFF1013
          Length = 516

 Score =  233 bits (593), Expect = 2e-65
 Identities = 166/529 (31%), Positives = 264/529 (49%), Gaps = 45/529 (8%)

Query: 36  WHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDEKYTFKEMKEESNRAGNVLRRYGN 95
           W     LN A +A+D   E      +      A+RD +Y   E+++  +     L +   
Sbjct: 19  WQFPSCLNMAAQALDHPDEQLALIDLTT---GARRDIRYG--ELRQMVDAVARDLMQ--R 71

Query: 96  VEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFMEGAVKDRLENSEAKVVVTTPE 155
           V+ GDRV + + +S +     L   KIGAI+ PLF+ F   A+  R+ ++  ++V+T   
Sbjct: 72  VQPGDRVGVLLSQSVDCAVAHLAIWKIGAISVPLFKLFQHDALASRIGDAGLELVLTDGG 131

Query: 156 LLERIPVDKLPHLQHVFVVGGEAESGTNIINYDEAAKQESTRLDIEWMDKKDGFLLHYTS 215
              ++     P L    +     +S  +++ Y E   +                +L YTS
Sbjct: 132 GTAQLGSLAQPLLVADILSASTGQSD-HLLPYAETTPETPA-------------VLIYTS 177

Query: 216 GSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEE--DIYWCTADPGWVTGTVYGIFAPWLNG 273
           G+TG+ KG LH H  +           D   +  D  W  AD  W+ G ++ +  P L  
Sbjct: 178 GTTGSAKGALHGHRVLSGHLPGVAISHDHLGQPGDCLWTPADWAWIGG-LFDVLMPGLAL 236

Query: 274 ATNVIVG--GRFSPESWYGTIEQLGVNVWYSAPTAFRMLMGAGDEMAAKYDLTSLRHVLS 331
              V+     +F+PE+    I Q  V   +  PTA R+L  AG        L  LR V S
Sbjct: 237 GVPVVAARLDKFTPEACAEIIRQGDVRNVFFPPTALRLLKAAGQ------GLDGLRSVAS 290

Query: 332 VGEPLNPEVIRWGHKVFNKRIHDTWWMTE---TGSQLICNYPCMDIKPGSMGKPIPGVEA 388
            GEPL  E++ WG +     I++ +  TE   T S  + ++P   ++PG +G+P+PG   
Sbjct: 291 GGEPLGAEMLAWGQRHLGVTINEFYGQTECNMTVSSCVADFP---VRPGCIGRPVPGCTV 347

Query: 389 AIVDNQGNELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFMPGGWYVSGDSAYMDEEG 448
            ++D+ G   P    G++A+++G  SMM   WN P+     F    W ++GD    + + 
Sbjct: 348 EVLDDTGT--PTKDEGDVAVRRGAASMMLEYWNRPDATAEKFH-ADWLITGDRGIWEGD- 403

Query: 449 YFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPDPVRGEIIKAFIALREG 508
           Y  F GR DDVI ++G R+GP E+E  L+ HPA+A  GV+GKPD +R EI+KA++ L+ G
Sbjct: 404 YLRFVGREDDVITSAGYRIGPAEIEDCLMTHPAVATVGVVGKPDELRTEIVKAYVVLKPG 463

Query: 509 FEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIMRRVLKA 557
             PS+    +++ +VK  LA ++ PRE+EF D LP T +GK++R+ LKA
Sbjct: 464 HSPSE---SDLQDYVKSRLAKYSYPREVEFLDALPMTVTGKVIRKELKA 509


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: 772
Number of extensions: 46
Number of successful extensions: 7
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: 516
Length adjustment: 35
Effective length of query: 537
Effective length of database: 481
Effective search space:   258297
Effective search space used:   258297
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 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