GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Moritella dasanensis ArB 0140

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_017222270.1 A923_RS0113825 long-chain-fatty-acid--CoA ligase

Query= metacyc::MONOMER-20125
         (556 letters)



>NCBI__GCF_000276805.1:WP_017222270.1
          Length = 556

 Score =  137 bits (346), Expect = 8e-37
 Identities = 117/361 (32%), Positives = 170/361 (47%), Gaps = 31/361 (8%)

Query: 185 DPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGVPKQPV----YLWTLPMFH--AN 238
           D   L YT GTT   KG +  HR I +  V  +     P+  +     +  LP++H  AN
Sbjct: 207 DIAYLQYTGGTTGIAKGAMLTHRNI-VANVLQVYGQFSPRTLLSKDHVVTPLPLYHIFAN 265

Query: 239 GWSYPWGMAAVGGTNICLRK-FDSEIIYDMIKRHGVTHMCGAPVVLN-MLSNAPGSEPLK 296
             S  + M  +GG N+ +    D +     +K +  T   G   + + ML N        
Sbjct: 266 SVSLMFIMM-IGGRNLLITNPRDMDGFIKELKGYPFTIFFGLNTLFSGMLKNEKFRALDF 324

Query: 297 TTVQIMTAGAPPPSAVLFRTESL--GFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERA 354
           +  +   AG       + +      G  V  GYGLTE + +V S    ++          
Sbjct: 325 SNARFTIAGGMSTQEDVAKEWQAVTGMPVVEGYGLTECSPVVCSGIHTQQ---------- 374

Query: 355 RLKSRQGVGTVM-QTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSM 413
             +   G+G  +  T++ VV+    A      + +GE+ +RG  VM GY K  + TA+S+
Sbjct: 375 --EYTAGIGVPLPSTEMRVVNDDHQAL---GVNVVGELQVRGPQVMSGYWKQAQATAESI 429

Query: 414 TADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVAR 473
            ADGWF TGD+  M  DG   I DR KD+I+  G N+ SVE+E +L  HPDI EAAVV  
Sbjct: 430 DADGWFSTGDMARMDQDGCFFIVDRKKDMILVSGFNVYSVEIEEVLRLHPDIEEAAVVGL 489

Query: 474 PDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQ 533
           P    GE   AF+       K  T KE+  +CR  L  Y VP+ + F+++LPK+  GKV 
Sbjct: 490 PHPVTGEQVKAFIC---SSNKALTSKEVQTHCRRYLTAYKVPRDIEFRDDLPKSPVGKVL 546

Query: 534 K 534
           K
Sbjct: 547 K 547


Lambda     K      H
   0.319    0.135    0.412 

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: 668
Number of extensions: 24
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: 556
Length of database: 556
Length adjustment: 36
Effective length of query: 520
Effective length of database: 520
Effective search space:   270400
Effective search space used:   270400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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