GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Desulfovibrio vulgaris Hildenborough

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 207786 DVU2299 glycine/betaine/L-proline ABC transporter, ATP binding protein

Query= uniprot:A8LLL2
         (373 letters)



>MicrobesOnline__882:207786
          Length = 397

 Score =  155 bits (392), Expect = 2e-42
 Identities = 85/249 (34%), Positives = 144/249 (57%), Gaps = 9/249 (3%)

Query: 23  NLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVNDVPP------AQRG 76
           + D+++GE++V +G SG GKSTL+R +  L + T GT+ +DG  V  +P        QR 
Sbjct: 47  SFDVEEGEIVVVMGLSGSGKSTLVRCLNRLIEPTAGTVTVDGRDVTSMPVDELRRLRQRS 106

Query: 77  IAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKALSG 136
             MVFQ++AL+PH TV +N +F L+     +AE +     + E++ L ++    P  LSG
Sbjct: 107 FGMVFQNFALFPHRTVLQNAAFGLEAMGVPRAERERQAMVSLERVGLAEWAASRPAQLSG 166

Query: 137 GQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVTHDQV 196
           G +QRV + R++  DP + L DE  S LD  +R   + E+ +L++ + + T+V+++HD  
Sbjct: 167 GMQQRVGLARALSLDPDILLMDEAFSALDPLIRRDMQDELLRLQDDL-QKTIVFISHDLD 225

Query: 197 EAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMN--LLPGKIIGTGAQT 254
           EA+ L  RIV++  G + Q+G+P ++   P +++VA+F+G   +   L  G ++      
Sbjct: 226 EALKLGDRIVLMRDGAVVQIGTPEDILTNPADDYVARFVGEADVTKVLTAGSVMKRSEAV 285

Query: 255 TVEMTDGGR 263
            V   DG R
Sbjct: 286 AVLGIDGPR 294


Lambda     K      H
   0.316    0.135    0.379 

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: 335
Number of extensions: 14
Number of successful extensions: 3
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: 373
Length of database: 397
Length adjustment: 30
Effective length of query: 343
Effective length of database: 367
Effective search space:   125881
Effective search space used:   125881
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: 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