GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Shewanella sp. ANA-3

Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate 7026373 Shewana3_3515 ABC transporter related (RefSeq)

Query= TCDB::O30494
         (367 letters)



>FitnessBrowser__ANA3:7026373
          Length = 349

 Score =  183 bits (464), Expect = 7e-51
 Identities = 110/319 (34%), Positives = 182/319 (57%), Gaps = 20/319 (6%)

Query: 2   ANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIE 61
           + L +  +   ++G  ++KG+DL +   E +  +GPSGCGK+TLLR +AGL+ +S+G I+
Sbjct: 3   STLNLHQVHSDYQGQQVLKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEIQ 62

Query: 62  LDGRDITE----VTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEA 117
           ++G+ ++     V   +R + M+FQ YAL+PH++V +N+ F +  A +     ++++++ 
Sbjct: 63  INGKTVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFGV--AKLTPAQRKARLDDM 120

Query: 118 ARILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELA 177
             +++L  L +R P +LSGGQ+QRV+I RA+   P++ L DEP SN+DA +R  M  E+ 
Sbjct: 121 LALVKLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAEIR 180

Query: 178 RLHKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTP 237
            + K+   + ++VTH + EA   AD + + N G I Q G    LY  P + +VA FLG+ 
Sbjct: 181 SILKQRNVSAVFVTHSKDEAFVFADTLAIFNQGVIVQHGRAENLYAAPNSRYVADFLGSG 240

Query: 238 KMGFLKGKVTRVDGQGCEVQLDAGTLISL-PLSGASLSVGSAVTLGIRPEHLEIASPGQT 296
              +L  +V  +DG    V    G L SL PLS +    G      +RP+ L +++    
Sbjct: 241 --NYLPAEV--IDGH--SVVTPIGELRSLTPLSQSHAFNGQVF---LRPQQLALSADDAG 291

Query: 297 TLTVTADVGERLGSDTFCH 315
             T+T    ER     FCH
Sbjct: 292 VGTIT----ERRFLGAFCH 306


Lambda     K      H
   0.319    0.137    0.387 

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: 267
Number of extensions: 7
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: 367
Length of database: 349
Length adjustment: 29
Effective length of query: 338
Effective length of database: 320
Effective search space:   108160
Effective search space used:   108160
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 (21.8 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