GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadB in Acidovorax sp. GW101-3H11

Align Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate Ac3H11_1931 Enoyl-CoA hydratase [isoleucine degradation] (EC 4.2.1.17) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

Query= SwissProt::P28793
         (715 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1931 Enoyl-CoA hydratase
           [isoleucine degradation] (EC 4.2.1.17) /
           3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) /
           3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
          Length = 727

 Score =  335 bits (859), Expect = 5e-96
 Identities = 247/739 (33%), Positives = 363/739 (49%), Gaps = 52/739 (7%)

Query: 8   ITVTALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIKAD-----ASVKGVIVSSGK 62
           I     +  +  + FD     VN   R    EL +    + AD     A++KG++++S K
Sbjct: 9   IPAQGTDGEVAVITFDETNSPVNTMCRQWQQELGEVTARVAADRERLGAALKGIVLASAK 68

Query: 63  DVFIVGADITEFVENFKLPDAELIAGNLEA-NKIFSDFEDLNVPTVAAINGIALGGGLEM 121
             F  GAD+   +      DA    G +E   K F   E L +P VA +NG ALGGG E+
Sbjct: 69  TSFFAGADLKATMR-LTPADAPNAFGEIERMKKHFRTLETLGIPVVACLNGAALGGGWEV 127

Query: 122 CLAADFRVMADSAKI--GLPEVKLGIYPGFGGTVRLPRLIGVDNAVEWIASGKENRAEDA 179
            L A +R+     KI  GLPEV LG+ PG  G  ++ RL+G+  A  +I  GK     +A
Sbjct: 128 ALVAHYRIAVADPKIQFGLPEVTLGLMPGATGVTKMTRLLGLMGAQPYILEGKLFNPAEA 187

Query: 180 LKVSAV-DAVVTADKLGAAALDLIK---RAIS--GELDYK----AKRQPKLEKLKLNAIE 229
           L++  V + V T ++L  AAL  I     A+    + +YK        PK+       + 
Sbjct: 188 LELQLVHELVATREQLLPAALAHISTHPHAVQPWDDKNYKMPGGTPANPKIAGAL--TVA 245

Query: 230 QMMAFETAKGFVAGQAGPNYPAPVEAIKTIQKAANFGRDKALEVEAAGFAKLAKTSASNC 289
             M  +T +G         YPAP  A+  + + A    D AL +E+   A+L     +  
Sbjct: 246 PAMLKKTTRG--------RYPAPEAALAAMVEGAMVDYDTALRIESRYLARLMTGPVARN 297

Query: 290 LIGLFLNDQELKKKAK----VYDKIAKDVK--QAAVLGAGIMGGGIAYQSASKGTPILMK 343
           +I  F  D    K  K    V   +A   K  +  +LGAG+MG GIA+  AS+G   ++K
Sbjct: 298 MINTFFFDMNAIKSGKSRPAVNGAVAPRYKPQKVGILGAGMMGAGIAWAQASRGIATVLK 357

Query: 344 DINEHGIEQGLAEAAKLLVGRVDKGRMTPAKMAEVLNGIRPTLSYGDFGNVDLVVEAVVE 403
           D++    E G A +AKL   RVDKGRMT      +L+ I PT S  D    DL++EAV E
Sbjct: 358 DVSAEKAEAGKAYSAKLTQARVDKGRMTAEAQQALLSRITPTASAADLAGCDLIIEAVFE 417

Query: 404 NPKVKQAVLAEVENHVREDAILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVE 463
           +  +K  V  E E  +      ASNTST+ IS LA A  RPE FVG+HFF+PV  M LVE
Sbjct: 418 SRDLKAKVTQEAEPQLAPGGFFASNTSTLPISGLATASSRPEKFVGIHFFSPVDKMKLVE 477

Query: 464 VIRGEKSSDLAVATTVAYAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVR 523
           +IRG ++ D  VA    Y + +GK PIVVND  GF  +R    +    A ++  G+    
Sbjct: 478 IIRGNQTDDETVARAFDYVQALGKVPIVVNDSRGFYTSRTFGTFVMEGAAMLGEGIPAAA 537

Query: 524 IDKVMEKFGWPMGPAYLMDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAIDALY-----EA 578
           I+    + G P+GP  +MD   +    H  D     +    K    +  + L      E 
Sbjct: 538 IENAAMQAGLPVGPLAVMDETALTLSVHVLDQTRADYATEGKTYTATPGELLVERMVKEL 597

Query: 579 KRLGQKNGKGFYAYEADKKGKQKKLVDSSVLEVLKPIVYEQRDV--TDEDIINWMMIPLC 636
           KR G+  G GFY Y A   G +K L        LKP+ +E+  V  + ++I + ++    
Sbjct: 598 KRPGRAGGGGFYDYPA---GAKKHLWPE-----LKPL-FEKPGVEWSVQEIQDRLLYRQA 648

Query: 637 LETVRCLEDGIVETAAEADMGLVYGIGFPLFRGGALRYIDSIGVAEFVALADQY-AELGA 695
           +ET RCL +G++ +  +A++G ++GIGFP + GGA+++I   GV  F+  AD+  A+ G 
Sbjct: 649 IETARCLAEGVLTSVHDANIGSIFGIGFPAWTGGAMQFIYGTGVEAFLKRADELAAKYGT 708

Query: 696 LYHPTAKLREMAKNGQSFF 714
            +  TA+ R    N Q  +
Sbjct: 709 GFALTARARATVANFQPVY 727


Lambda     K      H
   0.318    0.137    0.386 

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: 1082
Number of extensions: 47
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: 715
Length of database: 727
Length adjustment: 40
Effective length of query: 675
Effective length of database: 687
Effective search space:   463725
Effective search space used:   463725
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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