GapMind for catabolism of small carbon sources

 

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

Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate 200226 SO1043 amino acid ABC transporter, permease protein (NCBI ptt file)

Query= TCDB::Q88NY3
         (248 letters)



>FitnessBrowser__MR1:200226
          Length = 226

 Score = 90.5 bits (223), Expect = 3e-23
 Identities = 67/213 (31%), Positives = 107/213 (50%), Gaps = 26/213 (12%)

Query: 33  IAIAITAWIIALLLGSLLGV----MRTVPNRLVSGIATAYVELFRNVPLLVQLFIWYFLV 88
           + + +     A+LLG++LGV    M+      +   A  YV + R  P++VQL I YF+V
Sbjct: 28  LKVTLIVTFFAMLLGAVLGVGTTLMKMSSKWYIRFPAELYVGVIRGTPVVVQLVILYFIV 87

Query: 89  PDLLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPKGQEAAARAM 148
              L          D++  T+A+I+     GL + A + E +R GIQA+ KGQ  AAR++
Sbjct: 88  LAAL----------DVDKITAAIIA----FGLNSGAYISEIIRAGIQAVDKGQTEAARSL 133

Query: 149 GFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQ----TKQTAEF 204
           G S       ++LPQA + I+P L +EF+ + K ++V   IG ++L+        +T E 
Sbjct: 134 GLSQAMTMKLIILPQAIKNILPALGNEFIVLLKETAVIGFIGGVDLMRAGEIIRSRTFED 193

Query: 205 SANLFEAFTLATLIYFTLNMGLMLLMRMVEKKV 237
           S  LF       LIY  L      ++   EK++
Sbjct: 194 SVPLF----TCALIYLFLTYSFTFMLSKFEKRL 222


Lambda     K      H
   0.325    0.139    0.425 

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: 118
Number of extensions: 6
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 248
Length of database: 226
Length adjustment: 23
Effective length of query: 225
Effective length of database: 203
Effective search space:    45675
Effective search space used:    45675
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 46 (22.3 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