GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Halobacillus alkaliphilus FP5

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_089754212.1 BMZ06_RS17975 acetate--CoA ligase

Query= SwissProt::P39062
         (572 letters)



>NCBI__GCF_900113125.1:WP_089754212.1
          Length = 569

 Score =  859 bits (2219), Expect = 0.0
 Identities = 403/573 (70%), Positives = 480/573 (83%), Gaps = 5/573 (0%)

Query: 1   MNLKALPAIEGDHNLKNYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAES-FRKN 59
           M++K +PA  G+HN++NY+ETY  F+W + + +F+W +TG +N AYEAID+HAE   +KN
Sbjct: 1   MDMKPIPARSGNHNMENYKETYEQFNWEDVKTNFTWSKTGNVNIAYEAIDKHAEDPQKKN 60

Query: 60  KVALYYKDAKRDEKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGA 119
           + AL Y   +R+EK TF+++K +SN+  NVLR++ N+EKGDRVF+FM RSPE Y    G 
Sbjct: 61  QAALIYTSPEREEKLTFEDLKVKSNQFANVLRKH-NIEKGDRVFLFMHRSPEFYVAFFGI 119

Query: 120 IKIGAIAGPLFEAFMEGAVKDRLENSEAKVVVTTPELLERIPVDKLPHLQHVFVVGGEAE 179
           +KIGAIAGPLFEAFME AV+DRLE+SEA ++VTTPELL+R+P+D LP+L+ + +VGG+A 
Sbjct: 120 LKIGAIAGPLFEAFMEQAVRDRLEDSEATMLVTTPELLDRVPIDDLPNLKQIVLVGGDAP 179

Query: 180 SGTNIINYDEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGK 239
              N I+++E   Q S   DIEW+D +DG LLHYTSGSTG PKGV HVH AMIQ YQTGK
Sbjct: 180 G--NYISFEEEMDQASEEFDIEWVDLEDGMLLHYTSGSTGKPKGVYHVHNAMIQHYQTGK 237

Query: 240 WVLDLKEEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNV 299
           WVLDLKE D+YWCTADPGWVTGT YGIFAPWLNG TNVI GGRFSP+ WYGTI +  V+V
Sbjct: 238 WVLDLKEGDVYWCTADPGWVTGTSYGIFAPWLNGVTNVIRGGRFSPDDWYGTIAEQNVSV 297

Query: 300 WYSAPTAFRMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMT 359
           WYSAPTAFR L+ AG+E AAK+DL+SLRHVLSVGEPLNPEVI WG K F+ RIHDTWWMT
Sbjct: 298 WYSAPTAFRKLLSAGEEAAAKHDLSSLRHVLSVGEPLNPEVITWGLKAFDLRIHDTWWMT 357

Query: 360 ETGSQLICNYPCMDIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTI 419
           ETG+ LICNYP MDI+PGSMGKP PG+ AAIVDN+GNELPP +MGNLAIK+GWPSMM  I
Sbjct: 358 ETGAMLICNYPAMDIRPGSMGKPFPGIVAAIVDNEGNELPPNQMGNLAIKEGWPSMMRAI 417

Query: 420 WNNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEH 479
           WNNP K+ESYF+  GWYVSGDSAY DEEGYFWFQGR+DDVI TSGERVGPFEVESKL+EH
Sbjct: 418 WNNPGKFESYFL-NGWYVSGDSAYQDEEGYFWFQGRLDDVINTSGERVGPFEVESKLIEH 476

Query: 480 PAIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFK 539
            A+AEAGVIGKPDP RGEIIKAF+ LR+G+E SD L E+IR FVK+GL+AHAAPREIE K
Sbjct: 477 EAVAEAGVIGKPDPERGEIIKAFVTLRDGYEESDDLLEDIRQFVKKGLSAHAAPREIEIK 536

Query: 540 DKLPKTRSGKIMRRVLKAWELNLPAGDLSTMED 572
           D +PKTRSGKIMRR+LK+WEL LP GD ST+E+
Sbjct: 537 DTIPKTRSGKIMRRLLKSWELGLPTGDTSTLEE 569


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: 1232
Number of extensions: 51
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: 569
Length adjustment: 36
Effective length of query: 536
Effective length of database: 533
Effective search space:   285688
Effective search space used:   285688
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