GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Rhizobium etli CFN 42

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011426974.1 RHE_RS19290 AMP-binding protein

Query= SwissProt::P39062
         (572 letters)



>NCBI__GCF_000092045.1:WP_011426974.1
          Length = 550

 Score =  261 bits (667), Expect = 5e-74
 Identities = 175/535 (32%), Positives = 263/535 (49%), Gaps = 13/535 (2%)

Query: 27  WAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDEKYTFKEMKEESNRA 86
           + +  + FSW      N      D  A    +     ++         T+ E+   S+  
Sbjct: 9   YGDLYRDFSWRIPEDFNIGRAVSDEWAARDPERVCLEHFSPNGDHLSLTYGELSAASSMF 68

Query: 87  GNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFMEGAVKDRLENSE 146
            N L   G +++GDRV + +P+S E     +   KIGAIA PL   F   A++ RL  S 
Sbjct: 69  ANALASLG-IKRGDRVALLVPQSFETVIAHVAIYKIGAIALPLALLFGVEALEYRLRISG 127

Query: 147 AKVVVTTPELLERIPV--DKLPHLQHVFVVGGEAESGTNIINYDEAAKQESTRLDIEWMD 204
           A  ++T    L+R+    D+LP L+HV  V   A++    +++ +     ++  + E   
Sbjct: 128 AAAIITNDFGLDRVRQIRDRLPELRHVISVSDAADA----LSFADLIASHASVFEGEKTT 183

Query: 205 KKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLD--LKEEDIYWCTADPGWVTGT 262
             D  L+ +TSG+TG PKG LH H  +       ++  +   K  D  W  +D  W  G 
Sbjct: 184 PDDAALMIFTSGTTGPPKGALHGHRVLPGHIPGMQFAHEGFPKVGDKVWTPSDWAWAGGL 243

Query: 263 VYGIFAPWLNGATNVIVGG-RFSPESWYGTIEQLGVNVWYSAPTAFRMLMGAGDEMAAKY 321
           +  +    L G   V     +F  ++ Y  + ++ V   +  PTA R++    D  + KY
Sbjct: 244 LNALLPSLLLGVPVVSSPAQKFDADTAYRIMAEMKVRNAFIPPTALRLMRSVSDPRS-KY 302

Query: 322 DLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPCMDIKPGSMGK 381
           DL  LR V S GE L  E   W  +     +++ +  TE    L  +      K G++G+
Sbjct: 303 DLV-LRTVGSAGEALGRETYDWARRTLGITVNEFYGQTECNFVLSSSAAFGVTKAGAIGR 361

Query: 382 PIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFMPGGWYVSGDS 441
            +PG   AIV   G+ELP    G +AI    P M    WN+    E  F+ G W ++GD 
Sbjct: 362 AVPGHRVAIVSEAGDELPAGESGQIAIASPDPVMFLGYWNDAAATERKFLHG-WLLTGDI 420

Query: 442 AYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPDPVRGEIIKA 501
              DE+GY  F+GR DDVI +SG R+GP E+E  L  HPA+  A  +GKPD VR EI+KA
Sbjct: 421 GRQDEDGYVTFEGRDDDVITSSGYRIGPAEIEDCLTGHPAVQLAAAVGKPDVVRTEIVKA 480

Query: 502 FIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIMRRVLK 556
           +I L  G  PS+ L  EIR +VK  L+ H  PRE+EF + LP T +GK++RR+L+
Sbjct: 481 YIVLSPGHSPSEALAAEIREWVKMRLSMHEYPREVEFVESLPLTTTGKVIRRLLR 535


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: 798
Number of extensions: 40
Number of successful extensions: 5
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: 550
Length adjustment: 36
Effective length of query: 536
Effective length of database: 514
Effective search space:   275504
Effective search space used:   275504
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 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