GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Sinorhizobium meliloti 1021

Align Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial; Branched-chain alpha-keto acid dehydrogenase complex component E2; BCE2; BCKAD-E2; BCKADE2; Dihydrolipoamide acetyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; Dihydrolipoamide branched chain transacylase; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase; Protein DARK INDUCIBLE 3; EC 2.3.1.168 (characterized)
to candidate SM_b20019 SM_b20019 dihydrolipoamide succinyltransferase

Query= SwissProt::Q9M7Z1
         (483 letters)



>FitnessBrowser__Smeli:SM_b20019
          Length = 378

 Score =  137 bits (345), Expect = 6e-37
 Identities = 115/392 (29%), Positives = 185/392 (47%), Gaps = 42/392 (10%)

Query: 74  GLIDV--PLAQTGEGIAECELLKWFVKEGDSVEEFQPLCEVQSDKATIEITSRFKGKVAL 131
           G ID+  PL Q G    +  +  W  K GD V+   PL E+++DK T E+++   G +A 
Sbjct: 3   GFIDIQAPLEQEG---TKAVVRNWLRKIGDPVKSGDPLVELETDKVTQEVSAPADGVLAE 59

Query: 132 ISHSPGDIIKVGETLVRLAVEDSQDSLLTTDSSEIVTLGGSKQGTENLLGALSTPAVRNL 191
           I    GD    G  L R+              SE    G +            +PAVR+ 
Sbjct: 60  ILMRNGDDATPGAVLGRIG-------------SEAAGAGHAPH---------YSPAVRHA 97

Query: 192 AKDLGIDINVITGTGKDGRVLKEDVLRFSDQKGFVTDSVSSEHAVIGGDSVSTKASSNFE 251
           A++ G+D   +TGTG+ GRV + D+ R    +     SV++E     GD  +   S    
Sbjct: 98  AEEYGLDPATVTGTGRGGRVTRADMDRAFTARQEGPASVAAE----AGDRGAAPKS---- 149

Query: 252 DKTVPLRGFSRAMVKTM-TMATSVPHFHFVEEINCDSLVELKQFFKENNTDSTIKHTFLP 310
            + +P  G   A+ + M    T+ PH   V E +  +++  +    +       K ++  
Sbjct: 150 -RRIPHSGMRAAIAEHMLNSVTTAPHVTAVFEADFSAVMRHRDEHGKRLAADGTKLSYTA 208

Query: 311 TLIKSLSMALTKYPFVNSCFNAESLEIILKGSHNIGVAMATEHGLVVPNIKNVQSLSLLE 370
            ++ +   A+   P VNS ++ ++LE     +  +G+++  + GLVVP I   Q LSL E
Sbjct: 209 YVVSACVAAMRAVPEVNSRWHEDALETFDDINIGVGISLG-DKGLVVPVIHRAQDLSLAE 267

Query: 371 ITKELSRLQHLAANNKLNPEDVTGGTITLSNIGAIGGKFGSP-LLNLPEVAIIALGRIEK 429
           I   L  L   A +N L+  DVTGGT T+SN GA G    +P ++N P+ AI+ +G+++K
Sbjct: 268 IAARLQDLTTRARSNALSRADVTGGTFTISNHGASGSLLAAPIIINQPQSAILGVGKLDK 327

Query: 430 ---VPKFSKEGTVYPASIMMVNIAADHRVLDG 458
              V +     T+    +  V++  DHR LDG
Sbjct: 328 RVIVREVDGADTIQIRPMAYVSLTIDHRALDG 359


Lambda     K      H
   0.317    0.132    0.381 

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: 376
Number of extensions: 19
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: 483
Length of database: 378
Length adjustment: 32
Effective length of query: 451
Effective length of database: 346
Effective search space:   156046
Effective search space used:   156046
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 (21.6 bits)
S2: 51 (24.3 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