GapMind for catabolism of small carbon sources

 

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

Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate 203725 SO4655 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= BRENDA::P68187
         (371 letters)



>FitnessBrowser__MR1:203725
          Length = 354

 Score =  209 bits (532), Expect = 9e-59
 Identities = 125/331 (37%), Positives = 189/331 (57%), Gaps = 14/331 (4%)

Query: 3   SVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFI 62
           S+ +Q V K +G  V    +NL+I  GE    +GPSG GK+TLLR+IAGLE   SG +  
Sbjct: 2   SIHIQQVNKHFGNFVAVDSVNLEIKTGELTALLGPSGSGKTTLLRIIAGLEQADSGIVKF 61

Query: 63  GEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAK----KEVINQRVNQVA 118
             + +     +ERGVG VFQ YAL+ H++V EN+++GL +   K    K  I ++V+ + 
Sbjct: 62  NGEDITTQHVSERGVGFVFQHYALFKHMTVFENVAYGLTVRPRKTRPSKAEIAEKVHSLL 121

Query: 119 EVLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISR 178
           +++QL    DR P  LSGGQRQR+A+ R L  EP V LLDEP   LDA +R ++R  + R
Sbjct: 122 KLVQLDWTADRYPSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRAELRRWLRR 181

Query: 179 LHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPK 238
           LH  +  T ++VTHDQ EA+ +ADKIVV++ GR+ Q G P E+Y  P++ FV  F+G+  
Sbjct: 182 LHDEINVTTVFVTHDQEEALEVADKIVVMNKGRIEQQGTPEEVYDTPSNPFVYEFLGNVN 241

Query: 239 MNFLPVKVTATAIDQVQVELPM---PNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDI 295
           +    VK   + I  + +  P       QQ    V   +++V     L    E+ +  ++
Sbjct: 242 LFHARVKHGHSTIGNIHIPSPEHAGGEEQQGLAYVRPHEIEV-----LTQPTENAIKVNL 296

Query: 296 ADVILEGEVQVVEQLG--NETQIHIQIPSIR 324
             V + G V  +E L   +E  IH+++  ++
Sbjct: 297 DLVTIVGPVARLEVLTEIDEQLIHVELSKVQ 327


Lambda     K      H
   0.320    0.137    0.393 

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: 297
Number of extensions: 12
Number of successful extensions: 2
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: 371
Length of database: 354
Length adjustment: 29
Effective length of query: 342
Effective length of database: 325
Effective search space:   111150
Effective search space used:   111150
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