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; EC 2.3.1.168; Branched-chain alpha-keto acid dehydrogenase complex component E2; BCKAD-E2; BCKADE2; Dihydrolipoamide acetyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; Dihydrolipoamide branched chain transacylase; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (uncharacterized)
to candidate SMc01032 SMc01032 dihydrolipoamide S-acetyltransferase

Query= curated2:P37942
         (424 letters)



>FitnessBrowser__Smeli:SMc01032
          Length = 447

 Score =  206 bits (524), Expect = 1e-57
 Identities = 130/441 (29%), Positives = 221/441 (50%), Gaps = 34/441 (7%)

Query: 6   MTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEG 65
           +TMP L  ++ EG ++KWLV  GDKV   D IAE+ TDK   EV +   GT+ ++V   G
Sbjct: 5   ITMPALSPTMEEGNLAKWLVKEGDKVKSGDVIAEIETDKATMEVEAVDEGTVAKIVVPAG 64

Query: 66  -QTLQVGEMICKIETEG---------------ANPAEQKQEQ----------PAASEAAE 99
            + ++V  +I  +  EG               A PA + +E           PAA+ A +
Sbjct: 65  TEGVKVNALIAVLAAEGEDVATAAKGGNGAAGAVPAPKPKETAETAPAAAPAPAAAPAPQ 124

Query: 100 NPVAKSAGAADQPNKKRYS-PAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGV 158
                S   AD   K+ +S P   RLA E GIDL  + G+G  GR+ +KD++  +  G  
Sbjct: 125 AAAPASPAPADGEGKRIFSSPLARRLAKEAGIDLSAIAGSGPHGRVVKKDVETAVSGGAA 184

Query: 159 QEQNPEELKTAAPAPKSASKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIP 218
           +   P     AAPAP + +K   ++           + +P  G+RK IA  +  SK  IP
Sbjct: 185 K---PAGAPAAAPAPATLAKGMSEDAVLKLFEPGSYELVPHDGMRKTIAKRLVESKQTIP 241

Query: 219 HAWTMMEVDVTNMVAYRNSIKDSFKKTEG---FNLTFFAFFVKAVAQALKEFPQMNSMWA 275
           H +  ++ ++  ++A R  +  +  + +G   + L+     +KA+A AL++ P  N  W 
Sbjct: 242 HFYVSVDCELDALMALRAQLNAAAPEKDGKPVYKLSVNDMVIKALALALRDVPDANVSWT 301

Query: 276 GDKIIQKKDINISIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQ 335
              +++ K  ++ +AV+    L  P+++ A+ K++  I+ ++  L K+ ++ KL  ++ Q
Sbjct: 302 DQNMVKHKHADVGVAVSIPGGLITPIVRQAELKSLSAISNEMKDLGKRAKERKLKPEEYQ 361

Query: 336 GGTFTVNNTGSFGSVQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDH 395
           GGT  V+N G  G      ++N P A IL V +   R VV +  M+ + +++ + LS DH
Sbjct: 362 GGTTAVSNMGMMGVKDFAAVVNPPHATILAVGAGEDRVVVRNKEMV-IANVMTVTLSTDH 420

Query: 396 RVLDGLVCGRFLGRVKQILES 416
           R +DG +    L   K+ +E+
Sbjct: 421 RCVDGALGAELLAAFKRYIEN 441


Lambda     K      H
   0.312    0.129    0.359 

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: 448
Number of extensions: 34
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: 424
Length of database: 447
Length adjustment: 32
Effective length of query: 392
Effective length of database: 415
Effective search space:   162680
Effective search space used:   162680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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