GapMind for catabolism of small carbon sources

 

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

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate 199928 SO0742 iron(III) ABC transporter, ATP-binding protein (NCBI ptt file)

Query= uniprot:Q6MNM2
         (347 letters)



>FitnessBrowser__MR1:199928
          Length = 349

 Score =  192 bits (488), Expect = 1e-53
 Identities = 98/249 (39%), Positives = 154/249 (61%), Gaps = 8/249 (3%)

Query: 4   IQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISID 63
           +    +   +    +LKG+DL +A GE L L+GPSGCGK+TLLR +AGL++   G I I+
Sbjct: 5   LNLHQVHSDYQGQQILKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEIQIN 64

Query: 64  GKKIND----IEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISE 119
           GK ++     +  + R I M+FQ YAL+PH+TVAEN+ FG+    L  A+   R++++  
Sbjct: 65  GKTVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFGVA--KLTTAQRKARLDDMLA 122

Query: 120 LLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRL 179
           L++++ L  R P ELSGGQ+QRV++ RAL+ +  ++L DEP SN+DA +R  M  EI+ +
Sbjct: 123 LVKLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAEIRSI 182

Query: 180 HHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEM 239
                 + ++VTH + EA    D +A+   GVI Q G   ++Y  P + ++A F+GS   
Sbjct: 183 LKQRNVSAVFVTHSKDEAFVFADTLAIFSQGVIVQHGRAEDLYAAPNSRYVADFLGSG-- 240

Query: 240 NFLEGAVLE 248
           N+L   V++
Sbjct: 241 NYLPAEVVD 249


Lambda     K      H
   0.318    0.136    0.383 

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: 253
Number of extensions: 8
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: 347
Length of database: 349
Length adjustment: 29
Effective length of query: 318
Effective length of database: 320
Effective search space:   101760
Effective search space used:   101760
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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