GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 7023651 Shewana3_0880 ABC transporter related (RefSeq)

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



>FitnessBrowser__ANA3:7023651
          Length = 241

 Score =  125 bits (313), Expect = 2e-33
 Identities = 81/241 (33%), Positives = 126/241 (52%), Gaps = 14/241 (5%)

Query: 4   LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLET------- 56
           + + N++K+YG      LK I   I  GE + ++GPSG GKST + CI  LE        
Sbjct: 2   INITNLHKSYGDNA--VLKGINEHIRQGEVVSVIGPSGSGKSTFLRCINLLEKPTQGDIE 59

Query: 57  ISGGAILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFG-LKIRKMPTAEIDEE 115
           I G +I   DA +  +  K   + MVFQ++ L+P  +V  NI    + ++ M  AE D +
Sbjct: 60  IEGQSITAKDACVDKLRQK---VGMVFQNFNLFPHKTVLQNITLAPVSLKLMTQAEADNK 116

Query: 116 VARVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMR 175
              +   + ++   +  P  LSGGQ+QRVA+ RALA  P + LFDEP S LD ++  ++ 
Sbjct: 117 ALALLTQVGLQDKANAYPSSLSGGQKQRVAIARALAMEPDLMLFDEPTSALDPEMVGDVL 176

Query: 176 TEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASF 235
             MK + Q+   T V VTH+   A  + D+V  M  G + +   P++++  P      SF
Sbjct: 177 DVMKDLAQK-GMTMVIVTHEMGFARDVSDRVIFMDGGYVVESNIPEELFTRPKEARTQSF 235

Query: 236 I 236
           +
Sbjct: 236 L 236


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: 220
Number of extensions: 11
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: 386
Length of database: 241
Length adjustment: 27
Effective length of query: 359
Effective length of database: 214
Effective search space:    76826
Effective search space used:    76826
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: 48 (23.1 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