Alignments for a candidate for ech in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Dyella japonica UNC79MFTsu3.2

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 N515DRAFT_0416 N515DRAFT_0416 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase

Query= CharProtDB::CH_003230
         (714 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0416
          Length = 686

 Score =  377 bits (968), Expect = e-108
 Identities = 253/682 (37%), Positives = 362/682 (53%), Gaps = 35/682 (5%)

Query: 16  IAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFIAGADINMIG 75
           I  +T+D     +N L  E   ++  I+++L   K   GV+  SAKP  F  GADI    
Sbjct: 19  IVTLTLDRANSSVNALSREVLDELGQIVERLSIEKPA-GVLIHSAKPGGFAVGADIKEF- 76

Query: 76  NCKTAQEAEALAR--QGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGRVCTDDPK 133
             + A++   L     GQ++   +  LP   +AAIHGAC+GGG EL LAC  R+  DD K
Sbjct: 77  -VEYARDGTVLQNIENGQRVFESLARLPCPTVAAIHGACMGGGTELVLACRQRIAADDEK 135

Query: 134 TVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVDDVVPHSI 193
           T +GLPEV LG+ PG GGT RLPRLIG   AL ++LTGK L A++A  LG+VD + P + 
Sbjct: 136 TRIGLPEVMLGIHPGWGGTARLPRLIGALDALPVMLTGKALSARRAAALGVVDRLAPPNE 195

Query: 194 LLEAAVELAKKERPSSRPLPVRERILAGPL--GRALLFKMVGKKTEHKTQG-NYPATERI 250
           LL  A  L +  RP +RP   R +  A      R +L  MV K+T  K +  +YPA   +
Sbjct: 196 LLAEARALLR--RPHARPAARRLKAWATNTWPARQILAPMVLKQTAAKVRKEHYPAPFAL 253

Query: 251 LEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDPGSDAPPAPLNS 310
           + V + G           EAR+  +LA T  ++ L  IF     +K   GS      +  
Sbjct: 254 INVWQRG-GSSIQQRLKLEARSVAKLAETSTARNLIRIFLLQERLKGQ-GSGVEHG-IEH 310

Query: 311 VGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEGKVRRRHLKASER 370
           V ++G G+MGG IA   A K G  V ++D   + I  AL  +    E K     LK  E+
Sbjct: 311 VHVVGAGVMGGDIAAWAAFK-GFQVTLQDREMKFIQPALDRARALYEKK-----LKTPEK 364

Query: 371 DKQLAL-ISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHTIFASNTSSLPI 429
            ++ A  +    + +G A  DL IEA+FEN E KQ + A +E    A  I A+NTSS+P+
Sbjct: 365 VEETARRLRADVEGKGVAAADLAIEAIFENAEAKQALYASIEPQFQADEILATNTSSIPL 424

Query: 430 GDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAKKQGKTPIVVRD 489
            ++      P++ +GLHFF+PV +MPLVE++ H G   +     +   K  GK P+ V+ 
Sbjct: 425 DELRRGLKAPQRFLGLHFFNPVAQMPLVEVVRHDGLDPEVEKRALAFCKAIGKLPVAVKG 484

Query: 490 KAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDEVGIDTGTKIIP 549
             GF VNRIL PY+ EAIR+  +G     +D    KFG P+GPI+L D VG+D    +  
Sbjct: 485 TPGFLVNRILMPYLLEAIRLYNEGVPGPVLDKEAKKFGMPMGPIELADTVGLDVCASVGK 544

Query: 550 VLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQVDPAIYPLIGTQG 609
            L    G     P  +    L   ++G+K+G+GFY++ Q+G+  K +VDP          
Sbjct: 545 ELAPFLG--LELPPGIEDK-LAAGKRGKKDGQGFYVW-QEGKPQKPEVDP---------- 590

Query: 610 QGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPFLGGPFRYIDSL 669
                   + ER ++ M+NEAV C+ + V+      D G +FG GF PF GGP +Y+ S 
Sbjct: 591 -DYAVPADLQERMLLPMVNEAVACLADGVVDDADLLDAGVIFGTGFAPFRGGPIQYVRSE 649

Query: 670 GAGEVVAIMQRLATQYGSRFTP 691
           GA  +   ++RLA ++G RFTP
Sbjct: 650 GAAVIKGKLERLAQRHGERFTP 671


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: 1035
Number of extensions: 57
Number of successful extensions: 5
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: 686
Length adjustment: 39
Effective length of query: 675
Effective length of database: 647
Effective search space:   436725
Effective search space used:   436725
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 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