GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1931
          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:

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