Alignments for a candidate for fadB in Nocardioides dokdonensis FR1436

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Nocardioides dokdonensis FR1436

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_068107229.1 I601_RS05525 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_001653335.1:WP_068107229.1
          Length = 734

 Score =  352 bits (903), Expect = e-101
 Identities = 258/733 (35%), Positives = 362/733 (49%), Gaps = 57/733 (7%)

Query: 14  DNIAVITIDVPGEKMNTLKAEFASQVRAIIKQL-----RENKELRGVVFVSAKPDNFIAG 68
           D I  +T+D P    NT+   + + + A + +L      + K + GVV  SAK   F  G
Sbjct: 16  DGIVTLTLDDPNASANTMNELYRTSMNACVDRLYDEIAADEKAVTGVVVASAKKTFFAGG 75

Query: 69  ADINMIGNCK-TAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGRV 127
              +M+      A E  A+A   +  +  +  LP  V+AAI+GA LGGGLE+ LAC+ RV
Sbjct: 76  NLKSMVTTTPGDAPEVFAMAEDVKASLRRLEKLPRPVVAAINGAALGGGLEITLACNHRV 135

Query: 128 CTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTAL-EMILTGKQLRAKQALKLGLVD 186
             DDPK  LGLPEV LGLLPG GG  R+ R++G+  AL  ++L GKQ +  QA ++GLVD
Sbjct: 136 VVDDPKVSLGLPEVTLGLLPGGGGVTRVVRMLGLQDALMSVLLEGKQFKPAQAKEVGLVD 195

Query: 187 DVVPHSILLEAAVELAKKERPSSRPLP------------VRERILAG--PLGRALLFKMV 232
           ++V     L  A +   +  P +   P             R   LAG  P+  ALL K  
Sbjct: 196 ELVATREELVPAAKAWIRANPDAHANPWDAPGYKMPGGSPRSPGLAGFLPVFPALLRK-- 253

Query: 233 GKKTEHKTQGN-YPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFA 291
                 +T+G  YPAT  IL     G ++   +    E+R    L +   S+ +   FF 
Sbjct: 254 ------QTKGAVYPATRAILSAAVEGASRDFDTASRIESRYLTNLVVNQGSKNMIQAFFL 307

Query: 292 STDV----KKDPGSDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINH 347
                   K  P     P     VG+LG G+MG GIAY  A +AG+ V +KD++ +    
Sbjct: 308 DLQAIGAGKLRP-QGIEPFKATKVGVLGAGMMGAGIAYSCA-RAGMQVVLKDVSAENAAQ 365

Query: 348 ALKYSWDQLEGK-VRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQM 406
              YS ++L  K V R  L   + D+ L  I+ T D    A  DL+IEAVFE+  LK ++
Sbjct: 366 GKAYS-EKLNAKAVERGKLTQEKSDELLGRITATADPADLAGCDLVIEAVFEDPALKAKV 424

Query: 407 VAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTS 466
            AEV        +  SNTS+LPI ++A    RP   IGLHFFSPV+KMPLVEII    TS
Sbjct: 425 FAEVAPYVNDDALLCSNTSTLPISELAGGVDRPADFIGLHFFSPVDKMPLVEIIKGEQTS 484

Query: 467 AQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKF 526
             T+A    + ++  KTPIVV D  GFY +R++   +NE + ML +G     I+ A  + 
Sbjct: 485 EVTLAKAYDVVQQIRKTPIVVNDSRGFYTSRVIGFMVNEGMAMLAEGVAPWTIERATSQA 544

Query: 527 GFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFSAPAN------VVSSILNDDRKGRKNG 580
           G+P   +QL DE+ ++   KI      A  ER            VVS +L   R GR  G
Sbjct: 545 GYPAPVLQLSDELNLELMGKIAKATREA-NERDGVQVEEHPGTAVVSRMLEAGRAGRLRG 603

Query: 581 RGFYLYGQKGRKSKKQVD-PAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVI 639
            GFY Y ++G+++        ++PL   Q           +R +     E  +C +E VI
Sbjct: 604 AGFYDYDEQGKRTTIWDGLSELFPLAEQQP----PIEDCKDRMLFAEALETAKCFEEGVI 659

Query: 640 RSVRDGDIGAVFGIGFPPFLGGPFRYI-------DSLGAGEVVAIMQRLATQYGSRFTPC 692
            S    +IG++ GIGFPP  GG  +++         +G    V     LA  YG RF P 
Sbjct: 660 TSAAAANIGSIMGIGFPPMTGGAAQFMTGYQHADGEVGLEAFVRRADELAETYGERFRPT 719

Query: 693 ERLVEMGARGESF 705
           + L +M A GE F
Sbjct: 720 QHLRDMAATGEGF 732


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: 1040
Number of extensions: 46
Number of successful extensions: 9
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: 734
Length adjustment: 40
Effective length of query: 674
Effective length of database: 694
Effective search space:   467756
Effective search space used:   467756
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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Protein sequences (fasta format)
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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 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