GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Rhizobium grahamii CCGE 502

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_016556399.1 RGCCGE502_RS21975 AMP-binding protein

Query= SwissProt::P39062
         (572 letters)



>NCBI__GCF_000298315.2:WP_016556399.1
          Length = 542

 Score =  263 bits (671), Expect = 2e-74
 Identities = 177/544 (32%), Positives = 265/544 (48%), Gaps = 21/544 (3%)

Query: 18  YEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDEKYTFK 77
           YE+ YR F W   E           N      D  AE         ++         T++
Sbjct: 9   YEDLYRDFAWDLPED---------FNIGRAVSDEWAERAPDRVCLEHFSPDGNHLSMTYR 59

Query: 78  EMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFMEGA 137
           ++ + S+   N L   G V++GDRV + +P+S E     +   KIGAIA PL   F   A
Sbjct: 60  QLADRSSSFANALMSLG-VKRGDRVALLLPQSFETVIAHVAIYKIGAIALPLALLFGVEA 118

Query: 138 VKDRLENSEAKVVVTTPELLERIPV--DKLPHLQHVFVVGGEAESGTNIINYDEAAKQES 195
           ++ RL  + A  V+T    L+RI    ++LP L  V  V G+      + ++    +   
Sbjct: 119 LEYRLRTAGASAVITNRFGLDRISHIRERLPDLAEVICVDGDRH---RVRSFAALVESHP 175

Query: 196 TRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLD--LKEEDIYWCT 253
              ++      D  L+ +TSG+TG PKG LH H+ +       ++  +   +  D  W  
Sbjct: 176 PVFEVAKTAPHDPALMIFTSGTTGPPKGALHGHQVLAGHIPGMQFAHEGFPQPGDKVWTP 235

Query: 254 ADPGWVTGTVYGIFAPWLNGATNVIVGG-RFSPESWYGTIEQLGVNVWYSAPTAFRMLMG 312
           +D  W  G +  +    L G   V     +F  +  Y  + ++ V   +  PTA R+L  
Sbjct: 236 SDWAWAGGLLNALLPSLLLGVPVVSSPAQKFDADMAYRIMAEMKVRNGFIPPTALRLLKS 295

Query: 313 AGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPCM 372
             D  + KYDL  LR + + GE L  E   W  +     +++ +  TE    L  N    
Sbjct: 296 VPDPRS-KYDLV-LRTIGAAGESLGAETQEWVKRTLGITVNEFYGQTECNFVLSSNAAMG 353

Query: 373 DIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFMP 432
             +PG++G+P+PG   AIV   G EL     G +AI++  P M    WN+    E  F+ 
Sbjct: 354 VSRPGAIGRPVPGHSVAIVSEAGEELAVGEAGQIAIRRPDPVMFLGYWNDAAATERKFL- 412

Query: 433 GGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPD 492
           G W ++GD    D +GY  F GR DDVI +SG R+GP E+E  L+ HPA+  A  +GKPD
Sbjct: 413 GDWLLTGDIGRQDADGYVTFFGRDDDVITSSGYRIGPAEIEDCLIGHPAVQLAATVGKPD 472

Query: 493 PVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIMR 552
           PVR EI+KA++ L  GFE SD+L  EI  +VK  L+ H  PRE+EF  +LP T +GK++R
Sbjct: 473 PVRTEIVKAYVVLAPGFEASDRLASEISDWVKLRLSMHEYPREVEFVTELPLTTTGKVIR 532

Query: 553 RVLK 556
           R+L+
Sbjct: 533 RLLR 536


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: 762
Number of extensions: 38
Number of successful extensions: 4
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: 542
Length adjustment: 36
Effective length of query: 536
Effective length of database: 506
Effective search space:   271216
Effective search space used:   271216
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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