GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaH in Dechlorosoma suillum PS

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 Dsui_0323 Dsui_0323 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>lcl|FitnessBrowser__PS:Dsui_0323 Dsui_0323 3-hydroxyacyl-CoA
           dehydrogenase
          Length = 645

 Score =  343 bits (881), Expect = 1e-98
 Identities = 224/660 (33%), Positives = 342/660 (51%), Gaps = 43/660 (6%)

Query: 14  DNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFIAGADINM 73
           D +A +++D  GE  N+L     +++  ++ +L + +  + ++  SAK   FIAGADI+ 
Sbjct: 21  DGLAWLSLDKAGESANSLSKAVMAELSGVLDEL-DRQPPKALIIRSAKSAGFIAGADISE 79

Query: 74  IGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGRVCTDDPK 133
                + + A+A+  +G +L   + A+P   +A + G CLGGGLELALAC   +  D+P 
Sbjct: 80  FDQLDSPEAAKAMVARGWELFNRLAAVPYPTLALVRGHCLGGGLELALACRTLLVVDEPG 139

Query: 134 TVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVDDVVPHSI 193
           T LGLPEV LG+ PG GG  RLPR +G + AL+++L GK + AK+A +LGL D+ VP  +
Sbjct: 140 TKLGLPEVMLGIFPGWGGMLRLPRRVGPAVALDLMLAGKTVDAKKAKRLGLADECVPPRV 199

Query: 194 LLEAAVELAKKERPSSRPLPVRERILAGPLGRALLFKMVGKKTEHKTQGNYPATERILEV 253
           +  AA +LA    PS +PLP+ +R+  GPL   +  +   +  +     +YPA   I+++
Sbjct: 200 MESAARQLALNP-PSRKPLPLLQRLFLGPLRGVVAGQARKQVAKRARPEHYPAPYAIIDL 258

Query: 254 VETGLAQGTSSGYDAEARAFGELA----MTPQSQALRSIFFASTDVKKDPGSDAPPAPLN 309
                     + YD  A A  E+      +  ++ L  +F     +K      A  A   
Sbjct: 259 W---------AKYDGNALAAPEITDRIVRSATARNLVRVFHLQERLKAFGKDSAFVA--K 307

Query: 310 SVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEGKVRRRHLKASE 369
            V ++G G+MGG IA   A + G+ V ++D N + I  A+K +      ++R +    + 
Sbjct: 308 RVHVVGAGVMGGDIAAWCAGR-GLTVTLQDQNVERIAPAIKRAHAGFARRIRDKLQLRAV 366

Query: 370 RDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHTIFASNTSSLPI 429
            D+ +    G     G AH D++IEA+FENLE K  ++  +E       + A+NTSSL +
Sbjct: 367 MDRLIPDPEG----HGAAHADVVIEAIFENLEAKHSLLKGLEARMKPDAVLATNTSSLKL 422

Query: 430 GDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAKKQGKTPIVVRD 489
            DI     RPE+++G+HFF+PV KMPLVE++  AG  A+         +   K P+ V+ 
Sbjct: 423 EDIRTVLQRPERLVGIHFFNPVAKMPLVEVVTAAGGDAEVTRQACAFVRGIDKLPLPVQS 482

Query: 490 KAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDEVGIDTGTKIIP 549
             GF VN +L PY+ EA+R + +G   E +D A + FG P+GPI+L D VG+D     + 
Sbjct: 483 APGFLVNAVLGPYLLEAMRCVDEGIAPETVDEAALAFGMPMGPIELADTVGLDIA---MA 539

Query: 550 VLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLY-GQKGRKSKKQVDPAIYPLIGTQ 608
             +A  G     P  +V      D  GRK+G+GFY Y   K +K      PA        
Sbjct: 540 AGKALAGNGTEPPKCLVQRFERGD-LGRKSGKGFYAYPAGKIQKGAAGAVPA-------- 590

Query: 609 GQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPFLGGPFRYIDS 668
                    +AER V  +L    + VD  V+      D G +FG GF PF GGP  Y  S
Sbjct: 591 --------GLAERLVQPLLQRTQQLVDAGVVADAELADAGVIFGTGFAPFTGGPLNYARS 642


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: 940
Number of extensions: 35
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: 714
Length of database: 645
Length adjustment: 39
Effective length of query: 675
Effective length of database: 606
Effective search space:   409050
Effective search space used:   409050
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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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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