GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpF in Pseudomonas putida KT2440

Align aquaglyceroporin (characterized)
to candidate PP_1076 PP_1076 aquaglyceroporin

Query= CharProtDB::CH_024677
         (281 letters)



>FitnessBrowser__Putida:PP_1076
          Length = 283

 Score =  387 bits (993), Expect = e-112
 Identities = 188/255 (73%), Positives = 221/255 (86%)

Query: 6   TLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIWGLGVAMAIYLTAGVSGA 65
           TL  QC+AEFLGT LLIFFG GCVAALKVAGASFG WEIS+IWG+GV+MAIYLTAG+SGA
Sbjct: 9   TLSSQCLAEFLGTALLIFFGTGCVAALKVAGASFGLWEISIIWGVGVSMAIYLTAGISGA 68

Query: 66  HLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIVRGS 125
           HLNPAV+IAL LFA FDKRK+  ++++QV GAFC AALVY LY NLFFDFEQ H ++RGS
Sbjct: 69  HLNPAVSIALTLFAGFDKRKLPFYMLAQVCGAFCGAALVYTLYSNLFFDFEQAHAMLRGS 128

Query: 126 VESVDLAGTFSTYPNPHINFVQAFAVEMVITAILMGLILALTDDGNGVPRGPLAPLLIGL 185
             S++LA  FSTYP+P ++  QAF VE+VITAILM +I+ALTDD NG+PRG +APLLIGL
Sbjct: 129 EGSLELASVFSTYPHPSLSTSQAFLVEVVITAILMAVIMALTDDNNGLPRGAMAPLLIGL 188

Query: 186 LIAVIGASMGPLTGFAMNPARDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGPIVGAI 245
           LIAVIG++MGPLTGFAMNPARDFGPK+  +LAGWG +AFTGGRDIPYFLVP+F PI+GA 
Sbjct: 189 LIAVIGSAMGPLTGFAMNPARDFGPKLMTFLAGWGEIAFTGGRDIPYFLVPVFAPILGAC 248

Query: 246 VGAFAYRKLIGRHLP 260
           +GA +YR LI R+LP
Sbjct: 249 LGAASYRGLIARNLP 263


Lambda     K      H
   0.327    0.143    0.451 

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: 307
Number of extensions: 8
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: 281
Length of database: 283
Length adjustment: 26
Effective length of query: 255
Effective length of database: 257
Effective search space:    65535
Effective search space used:    65535
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: 47 (22.7 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