Aligments for a candidate for ech in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for ech in Dinoroseobacter shibae DFL-12

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 3607421 Dshi_0835 3-hydroxyacyl-CoA dehydrogenase NAD-binding (RefSeq)

Query= CharProtDB::CH_003230
         (714 letters)



>FitnessBrowser__Dino:3607421
          Length = 737

 Score =  410 bits (1053), Expect = e-118
 Identities = 260/729 (35%), Positives = 388/729 (53%), Gaps = 38/729 (5%)

Query: 7   FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66
           FT+    D +A+IT DV G+ MN +  +    + A++ +   +  ++G++  S K D+F 
Sbjct: 7   FTMKTDADGVAIITWDVQGKSMNVMNQQGFEDLDALVDKALADDTVKGIIITSGK-DSFA 65

Query: 67  AGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQ----------------VIAAIHG 110
            G D+N+I   +     +      + +MA +H +  +                V AA+ G
Sbjct: 66  GGMDLNVIAKMRDDAGDDPARGLFEGVMA-MHGILRKIERAGMDPKTNKGGKPVAAALPG 124

Query: 111 ACLGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILT 170
             LG GLE+ LACH     D+PK  +GLPE+ +G+ PG+GGT R+ R +G   A  ++L 
Sbjct: 125 TALGIGLEIPLACHRIFAADNPKAKIGLPEIMVGIFPGAGGTMRVSRKLGAMQAAPILLE 184

Query: 171 GKQLRAKQALKLGLVDDVVPHSILLEAAVE--LAKKERPSSRPLPVRERILAG--PLGRA 226
           GK    K+A   G+VD+VVP   LL+AA    L+ K+    +P  ++     G  P   A
Sbjct: 185 GKLFEPKKAKMAGIVDEVVPAEELLDAAKAWVLSAKDTDIVKPWDLKGYKFPGGAPYHPA 244

Query: 227 LLFKMVGKKT--EHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQA 284
                VG       KT G YPA + +L  V  G      +    EAR F  + M P S A
Sbjct: 245 GFMTFVGASAMIHSKTMGVYPAAKALLSAVYEGAMVPFDTALKIEARWFTNVLMNPSSSA 304

Query: 285 -LRSIFFASTDVKKDP-GSDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINP 342
            +RS+F     ++K     D P   +  VGILG G+MG GIAYV+A  AGI V + D   
Sbjct: 305 MIRSLFINKEALEKGAVRPDVPDQKVKKVGILGAGMMGAGIAYVSA-NAGIEVVLIDAAQ 363

Query: 343 QGINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLEL 402
           +  +    ++   L+  + R+ +   ++D+ LA I+ TTDY      DL++EAVFE+  +
Sbjct: 364 ESADRGKAHAAGILDKGIARKKVTPEKKDEVLARITATTDYAALEGCDLVVEAVFEDPGV 423

Query: 403 KQQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPH 462
           K ++ A+ E       IFA+NTS+LPI ++A  + RPEQ IG+HFFSPV+KM LVEII  
Sbjct: 424 KAEVTAKAEAVIPGDAIFATNTSTLPISELAKASARPEQFIGIHFFSPVDKMLLVEIIKG 483

Query: 463 AGTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAA 522
             T    +A  +   ++  KTPIVV D   FY NR + PYINE IRM+ +G     ++ A
Sbjct: 484 RQTGDVAVAKALDFVRQIRKTPIVVNDARFFYANRCIIPYINEGIRMVAEGVTPALVENA 543

Query: 523 LVKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFSAPANVVSSIL----NDDRKGRK 578
               G P+GP+QL+DE  ID G KI    +AA G+ +  P   V  +L    ++ R GRK
Sbjct: 544 AKLVGMPLGPLQLVDETSIDLGVKIAKATKAAMGDAY--PDGAVDEVLFWMADEGRLGRK 601

Query: 579 NGRGFYLYGQKGRKSKKQVDPA-IYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQ 637
           +  GFY Y + G++       A  YP    + Q  ++A  V  R +M  + EAVR +++ 
Sbjct: 602 SNAGFYTYDEAGKRGLLWEGLADRYP--AAKEQPELTA--VQHRLLMAQVLEAVRALEDG 657

Query: 638 VIRSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVE 697
           V+  +R+GD+GA+ G GF P+ GGP  ++D +GA   V I   L   +G+RFT    L E
Sbjct: 658 VLMDIREGDVGAILGWGFAPWSGGPLSWLDMIGAARAVEICDALTDTHGARFTTPALLRE 717

Query: 698 MGARGESFW 706
           M  +GE+F+
Sbjct: 718 MAEKGETFY 726


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: 1090
Number of extensions: 48
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: 737
Length adjustment: 40
Effective length of query: 674
Effective length of database: 697
Effective search space:   469778
Effective search space used:   469778
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 17 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 paper from 2022 on GapMind for carbon sources, or view the source code.

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