GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Bacteroides thetaiotaomicron VPI-5482

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate 353284 BT3758 acetylornithine aminotransferase (NCBI ptt file)

Query= reanno::Marino:GFF3099
         (404 letters)



>FitnessBrowser__Btheta:353284
          Length = 373

 Score =  227 bits (578), Expect = 5e-64
 Identities = 133/372 (35%), Positives = 208/372 (55%), Gaps = 18/372 (4%)

Query: 27  VRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMTNEPALR 86
           V+G+G ++WD+ G E++DL GG AV  +GH+HP  V  + +Q   +   SN + N+   +
Sbjct: 15  VKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGFYSNSVINKLQQQ 74

Query: 87  LAKTLCDLTFAE--RVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRTL 144
           +A+ L  ++  E   +F  NSGAEANE A KLA  Y    +G+ K  +ISF  +FHGRT 
Sbjct: 75  VAERLGKISGYEDYSLFLINSGAEANENALKLASFY----NGRTK--VISFSKAFHGRTS 128

Query: 145 FTVSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKLISKEKTCAIVVEPIQGEGGVMPGD 204
             V     P  +       G + +   ND+E++K+ ++K   CA+++E IQG GG+    
Sbjct: 129 LAVEATNNPTIIAPINNN-GHVTYLPLNDIEAMKQELAKGDVCAVIIEGIQGVGGIKIPT 187

Query: 205 QAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGVVPDILSSAKGLGGGFPVAA 264
             F+Q LR +C E   +L+ DE+QSG GRSG F+A+Q   + PDI++ AKG+G GFP+A 
Sbjct: 188 TEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKGIGNGFPMAG 247

Query: 265 MLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPEILKGVKARSDKLRKGMMDI 324
           +L +         G  G+T+GGN LAC+ A  V+D + Q  +++  KA  D L + +   
Sbjct: 248 VLISPMFKPV--YGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGDYLLEEL--- 302

Query: 325 GERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAGLEEGVMVLVAGANVIRLAPSLIIP 384
            +++    EVRG GL++G    E  +      +    +E V    +G NV+RL P L + 
Sbjct: 303 -KKFPQIKEVRGRGLMIGLEFEEPIKELRSRLI---YDEHVFTGASGTNVLRLLPPLCLS 358

Query: 385 EPDIELALERFE 396
             + +  L RF+
Sbjct: 359 MEEADEFLARFK 370


Lambda     K      H
   0.318    0.137    0.406 

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: 368
Number of extensions: 20
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: 404
Length of database: 373
Length adjustment: 30
Effective length of query: 374
Effective length of database: 343
Effective search space:   128282
Effective search space used:   128282
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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