Alignments for a candidate for fadB in Lysobacter daejeonensis GH1-9

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Lysobacter daejeonensis GH1-9

Align fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized)
to candidate WP_036135379.1 N800_RS04775 3-hydroxyacyl-CoA dehydrogenase

Query= metacyc::MONOMER-17591
         (715 letters)



>NCBI__GCF_000768355.1:WP_036135379.1
          Length = 689

 Score =  372 bits (955), Expect = e-107
 Identities = 247/679 (36%), Positives = 354/679 (52%), Gaps = 42/679 (6%)

Query: 11  KPLEGGIVELNFDLKGESVNKFNRLTLSELRAAVDAIKADASVKGVIVTSGKDV-FIVGA 69
           +P   G++ L FD  G  VN F +  L EL + ++ I  D   KG++V SGKD  FI GA
Sbjct: 22  EPRADGVLVLVFDRAGSPVNTFGQDVLIELDSLLERIAIDPP-KGLVVRSGKDKGFIAGA 80

Query: 70  DITEFVDNFQLPDEELMAGNL--EANKIFSDFEDLDVPTVAAINGIALGGGLEMCLAADF 127
           DI EF    Q  DE+ + G+      ++F    +L  PTVAAI+G  +GGG E+ LA  +
Sbjct: 81  DIKEF----QTFDEKGVVGDAISRGQRVFQRLAELPCPTVAAIHGFCMGGGTEIALACRY 136

Query: 128 RVMS--ATAKVGLPEVKLGIYPGFGGTVRLPRLIGCDNAVEWIASGKENKAEDALKVGAV 185
           RV S  A+ ++GLPEVKLGIYPG+GG+VRLPRL+G   A + + +G+   A  A  +G V
Sbjct: 137 RVASNDASTRIGLPEVKLGIYPGWGGSVRLPRLVGAPAAFDLMLTGRSLSASAARGMGLV 196

Query: 186 DAVVAPEQLQAAALDLAKRAVAGELDHKARRQPKLEKLKLNAIEQMMAFETAKGFVAGQA 245
           D VV P QL  AA  LA R        +A             +  M+A + A+       
Sbjct: 197 DKVVDPAQLIEAAATLALRGTQRPFKQRAMAWATNTLPARKLLAPMLAKQVARK----AR 252

Query: 246 GPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFVKLAKTSVAQSLIGLFLNDQELKKKAK 305
             +YPAP   I + ++A   G    L  E    VKLA T  A++LI +F   + LK +  
Sbjct: 253 KEHYPAPFALISTWERAGG-GIKSLLAAERKSVVKLASTPTARNLIRVFFLQERLKAQGG 311

Query: 306 KYDEVAKDVKLAAVLGAGIMGGGIAYQSALKGTPILMKDIREEGIQMGLNEAAKLLGKRV 365
           K   +        V+GAG+MGG IA  SA KG  + + D  +  I   L  A +L  K+V
Sbjct: 312 KEHRIQH----VHVVGAGVMGGDIAAWSAYKGFEVTLADREQRFIDGALARAGELFAKKV 367

Query: 366 EKGRLTPAKMAEALNGIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVEGAVKEDAII 425
           +     P   A     +R  +        D+V+EA++E P+ K+ +   VE  +K DA++
Sbjct: 368 KDEAKRPTVAAR----LRGDLEGDGVAKADLVIEAIIEKPEAKRDLYNAVEPRMKPDALL 423

Query: 426 ASNTSTISISLLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTGETAIATTVAYAKKM 485
            +NTS+I ++ L + ++RP  F G+H+FNPV +MPLVE+IR +           A+ K +
Sbjct: 424 TTNTSSIPLTELREHIQRPAQFAGLHYFNPVALMPLVEIIRHDGMAPETEQRLAAFCKAI 483

Query: 486 GKSPIVVNDCPGFLVNRVLFPYFGGFAKLLSFGVDFVRIDKVMEKFGWPMGPAYLSDVVG 545
            K P+ V   PGFLVNRVLFPY    A   + G+    IDK   KFG PMGP  L D VG
Sbjct: 484 DKLPVPVAGTPGFLVNRVLFPYMLEAATAFAEGIPGPAIDKAAVKFGMPMGPIELIDTVG 543

Query: 546 IDTGHHGRDVMAEGFPDRMAVEGKTAVDVMYEANRLGQKNGKGFYAYETDKRGKPKKVTD 605
           +D       V AE  P  + +    ++    EA + G+K+G+G Y +E  K  KP+   D
Sbjct: 544 LDV---AAGVGAELAP-FLGLPIPASLSTPPEAGKRGKKDGQGLYKWENGKAVKPELPKD 599

Query: 606 PQAYEVLKPIVVEQREVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEADMGLIYGIGFP 665
            QA                 D+ + +++PL  E V CL DG+V  A   D G+I+G GF 
Sbjct: 600 YQA---------------PSDLEDRLLLPLLNEAVACLHDGVVSDADLLDAGVIFGTGFA 644

Query: 666 PFRGGALRYIDSIGVAEFV 684
           PFRGG + ++ ++G  + V
Sbjct: 645 PFRGGPIAHVRAVGPDKLV 663


Lambda     K      H
   0.318    0.137    0.388 

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: 1107
Number of extensions: 57
Number of successful extensions: 7
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: 715
Length of database: 689
Length adjustment: 39
Effective length of query: 676
Effective length of database: 650
Effective search space:   439400
Effective search space used:   439400
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: 54 (25.4 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources