GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Sinorhizobium meliloti 1021

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate SMc00741 SMc00741 fatty-acid-CoA ligase

Query= SwissProt::P39062
         (572 letters)



>FitnessBrowser__Smeli:SMc00741
          Length = 548

 Score =  249 bits (636), Expect = 2e-70
 Identities = 181/551 (32%), Positives = 258/551 (46%), Gaps = 29/551 (5%)

Query: 15  LKNYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDEKY 74
           +++Y+E YR F W   E+          N      D  A    +     ++         
Sbjct: 5   IEDYDELYREFRWRIPER---------FNIGVAVSDAWAARDPERICLQHFSPDGAHLAL 55

Query: 75  TFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFM 134
           T+ +    S+     L  + +V  G+RV I +P+  E         K+GAIA PL   F 
Sbjct: 56  TYGDFAARSSAFAGGLAAH-DVSPGERVAILLPQGFEAAIAHAAIYKLGAIALPLALLFG 114

Query: 135 EGAVKDRLENSEAKVVVTTPELLERIPV--DKLPHLQHVFVVGGEAESGTNIINYDEAAK 192
             A+  RL+++ A  VVT     ER+     +LP L+ V +   + + GT  + + + A 
Sbjct: 115 VEALAYRLKDAGAAAVVTNRFGYERLAAIRGELPELRMVVLAEEDEKPGT--VRFRDIAA 172

Query: 193 QESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQ---YQTGKWVLDLKEEDI 249
            +  R D       D  L+ YTSG+TG PKG LH H  ++     +Q     L  +  D 
Sbjct: 173 GQG-RFDPAETKPDDPALMIYTSGTTGPPKGALHGHRVLLGHLPGFQFHHHFLP-QPGDR 230

Query: 250 YWCTADPGWVTGTVYGIFAPWLNGATNVIVGG-RFSPESWYGTIEQLGVNVWYSAPTAFR 308
            W  AD  W  G +  +      G   V     +F   + +  IE++ V   +  PTA R
Sbjct: 231 MWTPADWAWAGGLLNALLPSLFFGVPVVSSPAQKFDAHTAFRIIEEMEVRNAFIPPTALR 290

Query: 309 MLMGAG---DEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQL 365
           +L       D  A K     LR V S GE L  E   W        + + +  TE    +
Sbjct: 291 LLKSVERPRDRCALK-----LRTVGSAGEALGRETFEWARAALGVEVSEFYGQTECNIVI 345

Query: 366 ICNYPCMDIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTIWNNPEK 425
                    K GSMGK  PG + AI+D +G  LPP  +G +AI++  P M    W N E 
Sbjct: 346 SSATGLGVAKAGSMGKAAPGHQVAIIDGEGRVLPPGTVGQVAIRRPDPVMFLGYWRNEEA 405

Query: 426 YESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEA 485
            E+ F+ G W  +GD   MDEEGYF F GR DDVI +SG R+GP E+E  L  HP +  A
Sbjct: 406 TEAKFI-GDWMTTGDQGVMDEEGYFTFFGRDDDVITSSGYRIGPSEIEDCLAGHPDVQLA 464

Query: 486 GVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKT 545
             +GKPDP+R EI+KA++ L+ G    D+    IR +VK  L+ H  PREI F D LP T
Sbjct: 465 AAVGKPDPLRTEIVKAYVVLKPGVAAGDETAAGIRDWVKNRLSMHEYPREIAFVDSLPLT 524

Query: 546 RSGKIMRRVLK 556
            SGK++RR+L+
Sbjct: 525 TSGKVIRRLLR 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: 841
Number of extensions: 37
Number of successful extensions: 7
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: 548
Length adjustment: 36
Effective length of query: 536
Effective length of database: 512
Effective search space:   274432
Effective search space used:   274432
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