GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07310 in Pseudomonas fluorescens FW300-N2C3

Align Inositol transport system permease protein (characterized)
to candidate AO356_00960 AO356_00960 ABC transporter permease

Query= reanno::Phaeo:GFF716
         (373 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_00960
          Length = 325

 Score =  142 bits (359), Expect = 1e-38
 Identities = 103/336 (30%), Positives = 153/336 (45%), Gaps = 43/336 (12%)

Query: 31  GIIGTITVFAMFLIFAGDSGMFNSQGVMNW--SQISAQFMIIAVGACLLMIAGEFDLSVG 88
           G+ G +   AM  +F+  S  F S    +   +QI    M++AVG   ++I G  DLSVG
Sbjct: 22  GLAGAL--LAMVALFSTLSSHFLSYDTFSTLANQIP-DLMVLAVGMTFILIIGGIDLSVG 78

Query: 89  SMIGFAGMLIAIFSVTLGWPVWLAILVTFAIATAIGALNGFIVVRTGLPSFIVTLAFLFI 148
           S++  A   +++  +  GW VW + L+  A+A   G + G I V   +PSFIV+L  L +
Sbjct: 79  SVLALAASTVSVAVLGWGWSVWPSALLGMAVAALAGTVTGSITVAWRIPSFIVSLGVLEM 138

Query: 149 LRGFAIYLPQTIERKTIIGGVADAAEGDWLAALFGGKILTGLFQWFGDNGWIAVFERGTR 208
            RG A  +  T  R   IG                       F W  +            
Sbjct: 139 ARGLAYQM--TGSRTAYIGDS---------------------FAWLSN------------ 163

Query: 209 KGQPVVEGLPMLIVWAILLVIIGHVILTKTRFGNWIFAAGGDAEAARNSGVPVNRVKILM 268
              P+  G+    + A+L++ I   +LT+T FG ++   G + EA R +G+     KIL+
Sbjct: 164 ---PIAFGISPSFIIALLVIFIAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILV 220

Query: 269 FMFTAFCATVFATCQVMEFGGAGSDRGLLKEFEAIIAVVIGGALLTGGYGSVLGAALGAL 328
           F      A V A  Q+     A  + G   E + I AVVIGG  L GG GSV+    G L
Sbjct: 221 FSLMGLLAGVAALFQISRLEAADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVL 280

Query: 329 IFGVVQQGLFFAGVESSLFRVFLGLILLFAVILNTY 364
           I  V+  GL   G      R+  G +++ AV+L+TY
Sbjct: 281 IISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTY 316


Lambda     K      H
   0.330    0.145    0.443 

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: 377
Number of extensions: 22
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 373
Length of database: 325
Length adjustment: 29
Effective length of query: 344
Effective length of database: 296
Effective search space:   101824
Effective search space used:   101824
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: 49 (23.5 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