GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Dyella japonica UNC79MFTsu3.2

Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate N515DRAFT_1821 N515DRAFT_1821 putative ABC transport system ATP-binding protein

Query= TCDB::Q88NY5
         (256 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1821
          Length = 238

 Score =  147 bits (371), Expect = 2e-40
 Identities = 88/236 (37%), Positives = 140/236 (59%), Gaps = 9/236 (3%)

Query: 13  MISIKNVNKWYG----DFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKG 68
           M+ + +++K Y     +   L D + +VK+GE V V GPSGSGK+T +     LE F  G
Sbjct: 1   MLKMTHLSKVYRTEVVETYALRDFNIDVKEGEFVAVTGPSGSGKTTFLTIAGLLETFTGG 60

Query: 69  DIVVDGTSIADPKTNL-PKLRS-RVGMVFQHFELFPHLTITENLTIAQRKVLGRSEAEAT 126
           +  +DG  +++   N   K+R+ ++G +FQ F L P L + +N+ +  R   G    E  
Sbjct: 61  EYHLDGVEVSNLNDNARSKIRNEKIGFIFQAFNLIPDLNVYDNVEVPLR-YRGMKALERK 119

Query: 127 KKGLALLDRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVSE 186
           ++ +  L+RVGL++ AK +P +LSGGQQQRVAIARALA  P ++L DEPT  LD +M   
Sbjct: 120 QRIMDALERVGLASRAKHYPAELSGGQQQRVAIARALAGSPRLLLADEPTGNLDTQMARG 179

Query: 187 VLDVMVQLAQEGMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFFGDQSAR 242
           V++++ ++ +EG T++ VTH+   A +    V  +D G ++ D  ++  F  Q AR
Sbjct: 180 VMELLEEIHREGATIVMVTHDPELATRAQRNVHVID-GQVV-DLAEDPRFHQQQAR 233


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: 135
Number of extensions: 6
Number of successful extensions: 3
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: 238
Length adjustment: 24
Effective length of query: 232
Effective length of database: 214
Effective search space:    49648
Effective search space used:    49648
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