GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 203725 SO4655 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>FitnessBrowser__MR1:203725
          Length = 354

 Score =  206 bits (523), Expect = 1e-57
 Identities = 114/293 (38%), Positives = 176/293 (60%), Gaps = 17/293 (5%)

Query: 3   TLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAI 62
           ++ ++ VNK +G  +   + ++ L+I  GE   L+GPSG GK+TL+  IAGLE    G +
Sbjct: 2   SIHIQQVNKHFGNFV--AVDSVNLEIKTGELTALLGPSGSGKTTLLRIIAGLEQADSGIV 59

Query: 63  LVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPT----AEIDEEVAR 118
             +  DI+     +R +  VFQ YAL+  M+V +N+A+GL +R   T    AEI E+V  
Sbjct: 60  KFNGEDITTQHVSERGVGFVFQHYALFKHMTVFENVAYGLTVRPRKTRPSKAEIAEKVHS 119

Query: 119 VSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEM 178
           + KL+Q++    R P QLSGGQ+QR+A+ RALA  PK+ L DEP   LDAK+R E+R  +
Sbjct: 120 LLKLVQLDWTADRYPSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRAELRRWL 179

Query: 179 KLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGS 238
           + +H  +  TTV+VTHDQ EA+ + DK+ VM  G I+Q GTP+++Y+ P+N FV  F+G+
Sbjct: 180 RRLHDEINVTTVFVTHDQEEALEVADKIVVMNKGRIEQQGTPEEVYDTPSNPFVYEFLGN 239

Query: 239 PPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQI 291
             +N    R++     +      G      P   + AG E+++ +  +RP +I
Sbjct: 240 --VNLFHARVKHGHSTI------GNIHIPSP---EHAGGEEQQGLAYVRPHEI 281


Lambda     K      H
   0.319    0.138    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: 322
Number of extensions: 17
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: 386
Length of database: 354
Length adjustment: 30
Effective length of query: 356
Effective length of database: 324
Effective search space:   115344
Effective search space used:   115344
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 (21.7 bits)
S2: 49 (23.5 bits)

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

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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