GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH 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:

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