GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Chryseobacterium viscerum 687B-08

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_103234822.1 C1634_RS14760 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_002899945.2:WP_103234822.1
          Length = 416

 Score =  128 bits (321), Expect = 3e-34
 Identities = 69/223 (30%), Positives = 126/223 (56%), Gaps = 7/223 (3%)

Query: 19  LSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVND------VPP 72
           ++  + +I +GE  V +G SG GKSTLLR +  L + T G + I+   +        +  
Sbjct: 51  INKASFEIYEGEFFVIMGLSGSGKSTLLRCLNRLNEPTSGKVYINDDDITSKNNKELLEV 110

Query: 73  AQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPK 132
            +  ++MVFQ + L PH T+ +N  F L+I  + +A  +   + A + + L  + ++ P 
Sbjct: 111 RRTEMSMVFQKFGLLPHHTILDNAGFGLEIRGEDKASRNEKAQKALDIVGLNGFENQYPS 170

Query: 133 ALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVT 192
            LSGG +QRV + R++  DP+V L DE  S LD  ++   + ++ +L+  + + T+V++T
Sbjct: 171 QLSGGMQQRVGLARALANDPEVLLMDEAFSALDPLIKSEMQDQMLELQNTL-QKTIVFIT 229

Query: 193 HDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFI 235
           HD  EA+ +  RIV++  G I Q+G+  ++   P +++V  F+
Sbjct: 230 HDLDEAIKIGDRIVIMKDGVIEQIGTAEDILTNPASDYVKAFV 272


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: 329
Number of extensions: 18
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: 416
Length adjustment: 31
Effective length of query: 342
Effective length of database: 385
Effective search space:   131670
Effective search space used:   131670
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 24 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