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_023432923.1 N177_RS13530 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_000496075.1:WP_023432923.1
          Length = 715

 Score =  326 bits (836), Expect = 2e-93
 Identities = 223/683 (32%), Positives = 345/683 (50%), Gaps = 36/683 (5%)

Query: 14  DNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFIAGADINM 73
           DN+A + ID  G   NTL A+  +++   ++++  ++  +G+V  SAK   FIAGADI  
Sbjct: 37  DNVAWLVIDKEGASANTLSADVLAELDRALEEIERDRP-KGLVIRSAKKSGFIAGADITE 95

Query: 74  IGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGRVCTDDPK 133
               +  +  E    +  +++  +  L I  +A +HG  LGGGLE+ALAC  R+    P+
Sbjct: 96  FRGIRDPKVVEEKISEANRVVDRLDRLDIPTVAIMHGYALGGGLEIALACDRRLAL--PE 153

Query: 134 TVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVDDVVPHSI 193
           T LG PEV LGL PG GGT R   L+    A+ M+LTGK   A++A ++GL+D+V+    
Sbjct: 154 TKLGFPEVLLGLHPGLGGTVRSTFLMDPVQAMTMMLTGKSHPARRAKRMGLIDEVIEERH 213

Query: 194 LLEAAVELAKKERPSSRPLPVRERILAGPLGRALLFKMVGKKTEHKTQG-NYPATERILE 252
           +L AAV+ A      SR    R+R L+   GR      +  +TE K    +YPA   ++ 
Sbjct: 214 VL-AAVKAAVSGGSKSRDRSFRDRALSSGPGRRFAAGRMRGETESKAPAEHYPAPHALIA 272

Query: 253 VVETGLAQGTSSGYDA----EARAFGELAMTPQSQALRSIFFASTDVKKDPGSDAPPAPL 308
           + E          YD     E ++F  L +T  +Q L  +FF    +K            
Sbjct: 273 LWEEH-----GGDYDQMKAEEIKSFARLLVTDTAQNLIRVFFLREHMK---AIGKGKTTF 324

Query: 309 NSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEGKVRRRHLKAS 368
             V ++G G MGG IA   A + G+ V + D+ P+ +  A++ +  +L  KV +   K  
Sbjct: 325 GHVHVVGAGAMGGEIAAWCALR-GLTVTLADMKPEVLGKAIRNA-HRLYEKVAKDGAKI- 381

Query: 369 ERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHTIFASNTSSLP 428
            RD    LI G   + G  H D++IEAV E +++K+++  +VE       I A+NTSS+ 
Sbjct: 382 -RDAMDRLIPGINGH-GIRHADIVIEAVPEKVDIKRKVYEQVEPLLKPGAILATNTSSIR 439

Query: 429 IGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAKKQGKTPIVVR 488
           + ++  H   P +  GLHFF+PV +M LVE++ H   S +T+    +      + P  V+
Sbjct: 440 LEELRGHLKDPSRFAGLHFFNPVSRMQLVEVVSHDQASEETLKKLERFTTSIDRLPAPVK 499

Query: 489 DKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDEVGIDTGTKII 548
              GF VNR L PY+ E + ML +G   E ID A  +FG P+GPI+L D+VG+D    + 
Sbjct: 500 SAPGFLVNRALMPYLMEGLLMLDEGTPKEVIDRAAEEFGMPMGPIELADQVGLDICLDVA 559

Query: 549 PVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQVDPAIYPLIGTQ 608
            +L A            +   + +   GRK G+G Y + + G+  K           G+ 
Sbjct: 560 DMLRANLDAELPQTPAWLREKVENGELGRKTGKGLYDW-KDGKVQKNDKG-------GSY 611

Query: 609 GQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPFLGGPFRYIDS 668
            +G      + +R ++ MLN  V C    VI  +   D   +FG GF PF GGP +Y   
Sbjct: 612 DRG------ITDRLILPMLNACVTCYRTGVIDDLDTLDGAMIFGTGFAPFRGGPIKYAHD 665

Query: 669 LGAGEVVAIMQRLATQYGSRFTP 691
               +V+A ++RL  Q+G+RF P
Sbjct: 666 RRITDVIASLKRLEKQHGARFAP 688


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: 1036
Number of extensions: 51
Number of successful extensions: 6
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: 714
Length of database: 715
Length adjustment: 39
Effective length of query: 675
Effective length of database: 676
Effective search space:   456300
Effective search space used:   456300
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