GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Lentibacillus jeotgali Grbi

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_010531251.1 ON01_RS11790 acetate--CoA ligase

Query= SwissProt::P39062
         (572 letters)



>NCBI__GCF_000224785.1:WP_010531251.1
          Length = 571

 Score =  815 bits (2105), Expect = 0.0
 Identities = 376/573 (65%), Positives = 467/573 (81%), Gaps = 3/573 (0%)

Query: 1   MNLKALPAIEGDHNLKNYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAES-FRKN 59
           M+++ +PA +G +NL+NYE   + F W   +KHFSW++TGK+N AYEA+DRHAE   +K 
Sbjct: 1   MDMQRIPAQDGTYNLQNYENMRKTFSWDNVKKHFSWNDTGKVNMAYEAVDRHAEDPSKKV 60

Query: 60  KVALYYKDAKRDEKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGA 119
           K AL +    R+EK TF E++++SN+  NVL++ G VEKGDR+F+F+PRSPE Y    G 
Sbjct: 61  KAALLFSSPDREEKVTFDELRKQSNQFANVLKKNG-VEKGDRIFMFLPRSPEFYATFFGI 119

Query: 120 IKIGAIAGPLFEAFMEGAVKDRLENSEAKVVVTTPELLERIPVDKLPHLQHVFVVGGEAE 179
           +K GAIAGPLFEAFME AV+DRLE+SEA  ++TTP+LLER+P D LP L+ + +VG   E
Sbjct: 120 LKTGAIAGPLFEAFMEQAVRDRLEDSEASTLITTPDLLERVPQDDLPDLKKIVLVGENNE 179

Query: 180 SGTNIINYDEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGK 239
           +    I+Y +  K+ ST  DIEW+D +DG L+HYTSGSTG PKGV HVH AMIQ Y T +
Sbjct: 180 TSDKYIDYQQEMKEASTDFDIEWVDLEDGMLIHYTSGSTGKPKGVYHVHNAMIQHYATAE 239

Query: 240 WVLDLKEEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNV 299
           WVLDL+E+D+YWCTADPGWVTGT YGIFAPWL+G TNV+ GGRFSP++WYGTI++  V+V
Sbjct: 240 WVLDLREDDVYWCTADPGWVTGTSYGIFAPWLHGVTNVVRGGRFSPDAWYGTIDKYNVSV 299

Query: 300 WYSAPTAFRMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMT 359
           WY+APTA R L+ AG+++  K+D++SLRH++SVGEPLNPEVI WG + F+ RIHDTWWMT
Sbjct: 300 WYTAPTALRKLVSAGEDVVKKHDMSSLRHIMSVGEPLNPEVITWGLQAFDLRIHDTWWMT 359

Query: 360 ETGSQLICNYPCMDIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTI 419
           ETG+QLI N P  +I+PGSMGKPIPGVEA+IVDN+GNELP  +MGNLAIK  WP+MM  I
Sbjct: 360 ETGAQLIVNLPSQEIRPGSMGKPIPGVEASIVDNEGNELPANQMGNLAIKAPWPAMMRQI 419

Query: 420 WNNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEH 479
           W  PEKYESYF+  GWYVSGDSAY DE+GYFWFQGR+DDVI TSGERVGPFEVESKL+EH
Sbjct: 420 WKRPEKYESYFI-NGWYVSGDSAYKDEDGYFWFQGRLDDVINTSGERVGPFEVESKLIEH 478

Query: 480 PAIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFK 539
           PA+AEAGVIGKPDP RGEI+KAFI L +G+E S++L EE+R FVK GL+AHAAPRE+E K
Sbjct: 479 PAVAEAGVIGKPDPERGEIVKAFITLNDGYEDSEELLEEVRQFVKTGLSAHAAPRELEIK 538

Query: 540 DKLPKTRSGKIMRRVLKAWELNLPAGDLSTMED 572
           D +PKTRSGKIMRR+LK+WEL LP GD ST+E+
Sbjct: 539 DAIPKTRSGKIMRRLLKSWELGLPTGDTSTLEE 571


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: 1128
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: 571
Length adjustment: 36
Effective length of query: 536
Effective length of database: 535
Effective search space:   286760
Effective search space used:   286760
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.

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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