GapMind for catabolism of small carbon sources

 

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

Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate PfGW456L13_445 Cystine ABC transporter, permease protein

Query= TCDB::P48244
         (228 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_445
          Length = 221

 Score = 95.1 bits (235), Expect = 9e-25
 Identities = 66/207 (31%), Positives = 107/207 (51%), Gaps = 21/207 (10%)

Query: 7   DLGPSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTL 66
           D  P LL   + T+ L++      ++ G  L  MR+S  K++  ++  Y++  R TPL +
Sbjct: 10  DSAPFLLKGAYYTVILSLGGMFFGLVMGFGLALMRLSRFKLVSWIARIYVSFFRGTPLLV 69

Query: 67  VVLFCSFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINTVHFG 126
            +    +GL Q LGL L           +    A++GF L  + +  E LR+ I+++  G
Sbjct: 70  QLFVIYYGLPQ-LGLEL-----------DPLPAALIGFSLNMAAYACEILRAAISSIERG 117

Query: 127 QAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGE----ASL 182
           Q EAA S+G+    T R  I PQA+R A+ PLGN+ I+L K+T +A+ I V E    A L
Sbjct: 118 QWEAAASIGMTRAQTLRRAILPQAMRTALPPLGNSFISLVKDTALAATIQVPELFRQAQL 177

Query: 183 LMKATIENHANMLFVVFAIFAVGFMIL 209
           +   T E     +F ++   A+ + +L
Sbjct: 178 ITARTFE-----IFTMYLAAALIYWVL 199


Lambda     K      H
   0.327    0.139    0.397 

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: 108
Number of extensions: 7
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: 228
Length of database: 221
Length adjustment: 22
Effective length of query: 206
Effective length of database: 199
Effective search space:    40994
Effective search space used:    40994
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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