Alignments for a candidate for acs in Sinorhizobium meliloti 1021

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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 paper from 2022 on GapMind for carbon sources, or view the source code.

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