GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluD in Pseudomonas fluorescens GW456-L13

Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate PfGW456L13_4772 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)

Query= TCDB::P48245
         (273 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4772
          Length = 223

 Score =  109 bits (272), Expect = 6e-29
 Identities = 64/209 (30%), Positives = 111/209 (53%), Gaps = 8/209 (3%)

Query: 27  LPGLWG----TLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAIPVLILM 82
           LPGLW     TLK     VI  +++GT L L R+S  ++L       +  FR+IP+L+++
Sbjct: 12  LPGLWNGMIMTLKLMAMGVIGGIILGTILALMRLSHNKVLSNIAGAYVNYFRSIPLLLVI 71

Query: 83  IFAY---QMFAQYNIVPSSQL-AFAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAIA 138
            + Y       ++     + + AFA+ +    M+  +   EI+R+G+ S+PKGQ  AA A
Sbjct: 72  TWFYLAVPFVLRWITGEDTPIGAFASCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQA 131

Query: 139 LGMSSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQSASVNRN 198
           LGMS  Q    I+LPQA   M P L+ Q +I  +D++L Y +G ++ + +   S  +   
Sbjct: 132 LGMSYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLVDFLNASRASGDIIGR 191

Query: 199 YLAALFVVALIMIVLNFSLTALASRIERQ 227
               L    L+  +++F+ + L  R++++
Sbjct: 192 SNEFLIFAGLVYFIISFAASQLVKRLQKR 220


Lambda     K      H
   0.323    0.136    0.395 

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: 146
Number of extensions: 11
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: 273
Length of database: 223
Length adjustment: 24
Effective length of query: 249
Effective length of database: 199
Effective search space:    49551
Effective search space used:    49551
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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