GapMind for catabolism of small carbon sources

 

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

Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate 200225 SO1042 amino acid ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q88NY5
         (256 letters)



>FitnessBrowser__MR1:200225
          Length = 241

 Score =  259 bits (663), Expect = 3e-74
 Identities = 137/243 (56%), Positives = 176/243 (72%), Gaps = 2/243 (0%)

Query: 13  MISIKNVNKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 72
           MI+I N++K YGD  VL   +  +++GEVV V GPSGSGKST ++C+N LE   +GDI +
Sbjct: 1   MINITNLHKSYGDNAVLKGINEHIRQGEVVSVIGPSGSGKSTFLRCINLLENPTQGDIEI 60

Query: 73  DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQRKVLGRSEAEATKKGLAL 132
           +G SI      + KLR +VGMVFQ+F LFPH T+ +N+T+A   +   ++AEA  K LAL
Sbjct: 61  EGQSITAKDACVDKLRQKVGMVFQNFNLFPHKTVLQNITLAPVSLKLMTQAEADNKALAL 120

Query: 133 LDRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVSEVLDVMV 192
           L +VGL   A  +P  LSGGQ+QRVAIARALAM+P +MLFDEPTSALDPEMV +VLDVM 
Sbjct: 121 LTQVGLQDKANAYPSSLSGGQKQRVAIARALAMEPDLMLFDEPTSALDPEMVGDVLDVMK 180

Query: 193 QLAQEGMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFFGDQSARDQRTQHLLSK 252
            LAQ+GMTM+ VTHEMGFAR V++RVIFMD G ++E    EE F     ++ RTQ  LSK
Sbjct: 181 DLAQKGMTMVIVTHEMGFARDVSDRVIFMDGGYVVESNIPEELF--TRPKEARTQSFLSK 238

Query: 253 ILQ 255
           +L+
Sbjct: 239 VLR 241


Lambda     K      H
   0.319    0.134    0.383 

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: 178
Number of extensions: 6
Number of successful extensions: 1
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: 256
Length of database: 241
Length adjustment: 24
Effective length of query: 232
Effective length of database: 217
Effective search space:    50344
Effective search space used:    50344
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: 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