GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5504 in Pseudomonas fluorescens FW300-N2E3

Align D-methionine ABC transporter membrane protein, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate AO353_22195 AO353_22195 metal ABC transporter permease

Query= TCDB::Q9HT69
         (225 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_22195
          Length = 223

 Score =  213 bits (541), Expect = 3e-60
 Identities = 111/213 (52%), Positives = 154/213 (72%), Gaps = 4/213 (1%)

Query: 11  NIDWYEIWL----ASVDTFWMLGGSLLFTVVLGLPLGVLLFLTGPRQMFEQKAVYTLLSL 66
           +IDW EI      A+ +T +M+  +  FT+++GLPLGVLLF++    ++    +   L  
Sbjct: 4   SIDWNEILQLVLNATGETLYMVLLAGFFTLLIGLPLGVLLFISRSGGLYPMPKLNKGLGG 63

Query: 67  VVNILRSLPFIILLIVMIPLTVLITGTSLGVAGAIPPLVVGATPFFARLVETALREVDKG 126
           +VN+ RSLPF+++LI +IPLT LI GT+LG   A+ P+ +GA PFFAR+VE AL EVDKG
Sbjct: 64  LVNLGRSLPFVVMLIALIPLTRLIVGTTLGSTAAVVPITIGAFPFFARIVENALDEVDKG 123

Query: 127 IIEATQAMGASTRQIIWNALLPEARPGIIAAITVTAITLVSYTAMAGVVGAGGLGDLAIR 186
            IEA  AMG   R +I+  LLPEA P ++A IT+T + L+ +++MAGV+G GGLGDLAIR
Sbjct: 124 RIEAILAMGGDIRHVIFKVLLPEALPALLAGITLTLVMLIGFSSMAGVIGGGGLGDLAIR 183

Query: 187 FGYQRFQTDVMVVTVVMLLILVQILQTVGDKLV 219
           +GYQRF   VMV TVV+L+ILVQ +Q++GD+LV
Sbjct: 184 YGYQRFNNQVMVATVVVLVILVQGVQSLGDRLV 216


Lambda     K      H
   0.329    0.143    0.419 

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: 123
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: 225
Length of database: 223
Length adjustment: 22
Effective length of query: 203
Effective length of database: 201
Effective search space:    40803
Effective search space used:    40803
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 (21.8 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