GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Shewanella oneidensis MR-1

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate 201485 SO2341 alpha keto acid dehydrogenase complex, E2 component (NCBI ptt file)

Query= reanno::Marino:GFF1672
         (378 letters)



>FitnessBrowser__MR1:201485
          Length = 535

 Score =  378 bits (971), Expect = e-109
 Identities = 209/388 (53%), Positives = 264/388 (68%), Gaps = 11/388 (2%)

Query: 1   MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEPEEARTKPEPAAQLST 60
           MTDKA+V+I A KAG++ KL++++  +AKVHAPL+A        P  +  +    A  +T
Sbjct: 147 MTDKALVQIPAIKAGKIVKLHYRKGQLAKVHAPLYAIEVEGGVIPAVSAHETTNVAVANT 206

Query: 61  ATASPVAAASRQRIPA-------SPAVRRLVREHELNLSDIQGSGKDGRVLKADVLAYIE 113
           AT++  A AS  + PA       SPAVRR+ R  +++LS + GSGK GRV K D+  +  
Sbjct: 207 ATSAACATASVSQEPARQGKALASPAVRRMARALDIDLSRVPGSGKHGRVYKEDISRFQA 266

Query: 114 EGPKQ--AQNQAPADDAQTATTRSARRAPAADQEAR--VEPIRGIKAAMAKSMVKSATTI 169
           +G         A A   Q++ T+SA     A       VEPIRG+KA MAK MV+S +TI
Sbjct: 267 QGSATPVVAPVATASTQQSSVTQSAVPITVASAARADIVEPIRGVKAVMAKLMVESVSTI 326

Query: 170 PHFIYSEDIDVTDLLKLREQLKPEAEARGSRLTLMPFFMKAMALAVQEFPVLNSQLNDDV 229
           PHF Y E+ D+TDL+ LRE +K +  +   +LT+MPFFMKAM+LA+ +FPVLNSQ+N D 
Sbjct: 327 PHFTYCEEFDLTDLVALRESMKAKYSSDEVKLTMMPFFMKAMSLALTQFPVLNSQVNADC 386

Query: 230 TEIHYLPQCNIGMAVDGKAGLTVPNIKGVESLSLLGIADEVARLTEAARSGRVSQEDLKG 289
           TEI Y  + NIGMAVD K GL VPN+K V+  S+L +A E+ RLT AARSGRV+  DLK 
Sbjct: 387 TEITYKARHNIGMAVDSKVGLLVPNVKDVQDKSILEVAAEITRLTNAARSGRVAPADLKE 446

Query: 290 GTITISNIGALGGTYTAPIINAPEVAIVALGRTQKLPRFDANGQVVERAIMTVSWAGDHR 349
           GTI+ISNIGALGGT   PIIN PEVAIVALG+ Q LPRF+A G+V  R IM VSW+GDHR
Sbjct: 447 GTISISNIGALGGTVATPIINKPEVAIVALGKLQTLPRFNAKGEVEARQIMQVSWSGDHR 506

Query: 350 IIDGGTIARFCNRWKGYLESPQTMLLHM 377
           +IDGGTIARFCN WK YLE PQ MLL M
Sbjct: 507 VIDGGTIARFCNLWKQYLEQPQDMLLAM 534



 Score = 53.5 bits (127), Expect = 1e-11
 Identities = 32/70 (45%), Positives = 46/70 (65%), Gaps = 2/70 (2%)

Query: 1   MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEPEEARTKPEPAAQLST 60
           MTDKA+V+I AP AG VTKLY+ +  +AKVHAPL+A +  + EEP  ++  P+     + 
Sbjct: 40  MTDKALVQIPAPFAGVVTKLYYAKGDIAKVHAPLYA-VQIEAEEP-SSQVAPQTVEHSAP 97

Query: 61  ATASPVAAAS 70
             A+  AA+S
Sbjct: 98  NQAAISAASS 107


Lambda     K      H
   0.316    0.131    0.367 

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: 476
Number of extensions: 20
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 378
Length of database: 535
Length adjustment: 33
Effective length of query: 345
Effective length of database: 502
Effective search space:   173190
Effective search space used:   173190
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