GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized)
to candidate Pf1N1B4_772 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)

Query= reanno::pseudo3_N2E3:AO353_16280
         (223 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_772
          Length = 248

 Score =  124 bits (311), Expect = 2e-33
 Identities = 67/213 (31%), Positives = 124/213 (58%), Gaps = 6/213 (2%)

Query: 17  NGMVMTLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYVNYFRSIPLLLVITWFYL 76
           +G+  T+ + V   +  ++LG++L +MR   ++++S IA  YV  FR++PLL+ +  +Y 
Sbjct: 27  SGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWYF 86

Query: 77  AVPFVL-----RWITGEDTPI-GAFTSCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAK 130
            VP +L      W   +  P   AF S +V   +F  A  CE VR G+Q++P+GQ  AA+
Sbjct: 87  LVPDLLPADIQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTGIQALPRGQEAAAR 146

Query: 131 ALGMGYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNATRASGDIIG 190
           A+G    Q+   ++LPQA+R + P L  + + +F+++S+   +GL++ L  T+ + +   
Sbjct: 147 AMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSA 206

Query: 191 RANEFLIIAGLVYFTISFAASRLVKRLQKRFAV 223
              E   +A L+YFT++ +   L++ ++K+ AV
Sbjct: 207 NLFEAFTLATLIYFTLNMSLMLLMRSVEKKVAV 239


Lambda     K      H
   0.331    0.143    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: 140
Number of extensions: 5
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: 223
Length of database: 248
Length adjustment: 23
Effective length of query: 200
Effective length of database: 225
Effective search space:    45000
Effective search space used:    45000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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