GapMind for catabolism of small carbon sources

 

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

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 199928 SO0742 iron(III) ABC transporter, ATP-binding protein (NCBI ptt file)

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__MR1:199928
          Length = 349

 Score =  179 bits (454), Expect = 1e-49
 Identities = 101/256 (39%), Positives = 153/256 (59%), Gaps = 9/256 (3%)

Query: 4   LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63
           L L  V   Y   ++L  ++L + QGE++  +GPSGCGK+TLLR +AGL+ I+ G ++I+
Sbjct: 5   LNLHQVHSDYQGQQILKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEIQIN 64

Query: 64  GTVVND----VPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAE 119
           G  V+     VP  QRGI M+FQ YAL+PH+TV EN+ F   +AK + A+  A ++    
Sbjct: 65  GKTVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFG--VAKLTTAQRKARLDDMLA 122

Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179
            ++L     R P  LSGGQ+QRV+I R++  +P++ L DEP SN+DA +R +   EI  +
Sbjct: 123 LVKLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAEIRSI 182

Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPK 239
            +    S  V+VTH + EA   A  + + + G I Q G   +LY  P + +VA F+GS  
Sbjct: 183 LKQRNVSA-VFVTHSKDEAFVFADTLAIFSQGVIVQHGRAEDLYAAPNSRYVADFLGSG- 240

Query: 240 MNLLPGKIIGTGAQTT 255
            N LP +++   + TT
Sbjct: 241 -NYLPAEVVDGHSVTT 255


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: 324
Number of extensions: 19
Number of successful extensions: 4
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: 349
Length adjustment: 29
Effective length of query: 344
Effective length of database: 320
Effective search space:   110080
Effective search space used:   110080
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: 49 (23.5 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