GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Lutibaculum baratangense AMV1

Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate WP_023431067.1 N177_RS04545 enoyl-CoA hydratase

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_000496075.1:WP_023431067.1
          Length = 738

 Score =  392 bits (1007), Expect = e-113
 Identities = 242/724 (33%), Positives = 370/724 (51%), Gaps = 29/724 (4%)

Query: 7   FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66
           F + +  D IA++  D  G  MN +      ++  II ++   + ++G V  S K D F 
Sbjct: 6   FRIEIDADGIALVIWDTAGRSMNVIDLAVMDELETIIDRVSGEESIKGAVIASGK-DAFS 64

Query: 67  AGADINMIGNC----KTAQEAEALA---------RQGQQLMAEIHALPIQVIAAIHGACL 113
            GAD+ M+G       T +E +  A         R+  Q+   +       + AI+G  +
Sbjct: 65  GGADLKMLGGMLEAFHTERERDQTAATQRLFDESRRLSQIYRRLETSGKPWVCAINGTAM 124

Query: 114 GGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQ 173
           GG +ELALACH RV  ++PK   GLPEV++GL PG+GGTQR+ R++  + AL+ +L G+ 
Sbjct: 125 GGAVELALACHHRVAAENPKAKFGLPEVKVGLFPGAGGTQRVARMMPAADALQYLLQGRD 184

Query: 174 LRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRE-RILAGPLGRALLFKMV 232
           L    A K+GLVD++VP   L+EAA         + +P    + R+  GP+  A  F++ 
Sbjct: 185 LDFATARKMGLVDEIVPAERLVEAAKAWILGGGSAVKPWDEEKFRLPGGPVYSATGFQVF 244

Query: 233 GKKT---EHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQAL-RSI 288
                    +TQ NYP    I+  V  GL     +    E+R F  +  T ++ A+ RS+
Sbjct: 245 PAANAIYRRETQNNYPGARAIMSAVYEGLQLPMDAALRVESRYFAHVLQTKEAAAMIRSL 304

Query: 289 FFASTDVKK--DPGSDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGIN 346
           F +  ++ K     +D P +    VG+LG G MG  +AYV+A KAGI V + D + +   
Sbjct: 305 FVSMQELNKLARRPADVPASKARKVGVLGAGFMGAAVAYVSA-KAGIEVVLIDRDVESAE 363

Query: 347 HALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQM 406
               Y+   +   V R       +++ LA I  T DY+     DL+IEAVFE+ ++K  +
Sbjct: 364 RGKAYADTLVSKDVSRGKATHEAKEELLARIDATADYQRLEGCDLVIEAVFEDRDVKADV 423

Query: 407 VAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTS 466
           +   E       +  SNTS+ PI  +A  + RPE+ IG+HFFSPVEKM LVE+I    T 
Sbjct: 424 IQRAEAVVPETAVIGSNTSTFPISSLAKASVRPERFIGIHFFSPVEKMMLVEVIMGEATG 483

Query: 467 AQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKF 526
            + +A  +   +   KTPIVV D  GFY +R++  YI E   ML +G     I+      
Sbjct: 484 PEALAVALDYCRAIRKTPIVVNDSRGFYTSRVVGTYIREGHLMLAEGVPAAMIENVGRMA 543

Query: 527 GFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFSAPAN---VVSSILNDDRKGRKNGRGF 583
           G PVGP+ L DEV +D   KI+   +   GE    P     +   ++   R GRKNG+GF
Sbjct: 544 GMPVGPLALNDEVAVDLAWKILQATKKDLGESAVEPRQEHLLEEMVVKRGRLGRKNGQGF 603

Query: 584 YLYGQKGRKSKKQVDPAIYPLIGTQ-GQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSV 642
           Y Y   G   KK++ P +  L   +     +   ++  R +++   E  RC +E V+  V
Sbjct: 604 YDYPDAG---KKRLWPGLQDLQEIRLDPDTVDVGELKRRFLVMQALETARCFEEGVLTDV 660

Query: 643 RDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARG 702
           R+ D+G++ G GF PF GG   Y+D +G    V + + L  ++G RF P + L+ M   G
Sbjct: 661 READVGSILGFGFAPFTGGTLSYVDGMGTKAFVDLCRALEARHGPRFAPNDLLIAMAENG 720

Query: 703 ESFW 706
           E+F+
Sbjct: 721 ETFY 724


Lambda     K      H
   0.319    0.137    0.393 

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: 992
Number of extensions: 41
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 714
Length of database: 738
Length adjustment: 40
Effective length of query: 674
Effective length of database: 698
Effective search space:   470452
Effective search space used:   470452
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 (21.8 bits)
S2: 55 (25.8 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