GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruG in Pseudomonas fluorescens FW300-N2E2

Align Fructose import permease protein FruG (characterized)
to candidate Pf6N2E2_163 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

Query= SwissProt::Q8G845
         (340 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_163
          Length = 325

 Score =  126 bits (316), Expect = 9e-34
 Identities = 88/297 (29%), Positives = 151/297 (50%), Gaps = 12/297 (4%)

Query: 33  ILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVGAIVAITA-V 91
           + M+ +  AL   ++     S+L      L++LAV MT  ++ GGIDLSVG+++A+ A  
Sbjct: 28  LAMVALFSALSSHFLSYDTFSTLANQIPDLMVLAVGMTFILIIGGIDLSVGSVLALAAST 87

Query: 92  VGLKLANAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLSTMFLARGLASIIS 151
           V + +   G   +   ++ + + A+ G + G++   + +  FI +L  + +ARGLA  + 
Sbjct: 88  VSVAVLGWGWSVWPSALLGMAVAALAGTVTGSITVAWRIPSFIVSLGVLEMARGLAYQM- 146

Query: 152 TDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVVFGYVFLHHTRTGRTI 211
           T S T   G+ F+++SN I    +P            IIAL+V+      L  T  GR +
Sbjct: 147 TGSRTAYIGDSFAWLSNPIAFGISPSF----------IIALLVIFIAQAVLTRTVFGRYL 196

Query: 212 YAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSAKNTVGVGWELDAVA 271
             IG +  +  L G+  K  + +++     LA +A++   + + +A    G G EL  +A
Sbjct: 197 IGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGVAALFQISRLEAADPNAGSGLELQVIA 256

Query: 272 SVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTSDFGVPAEWTTIVIGLMILVFVVL 328
           +VVIGGT + GG G V+ +  G L+ S+L    +  G       I+ G +I+V VVL
Sbjct: 257 AVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVL 313



 Score = 25.8 bits (55), Expect = 0.002
 Identities = 33/130 (25%), Positives = 58/130 (44%), Gaps = 10/130 (7%)

Query: 26  LAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVGAI 85
           +A +VIFI   ++ + +FG Y+ +G  ++   + A  +         IL   +   +  +
Sbjct: 175 IALLVIFIAQAVLTRTVFGRYL-IGIGTN---EEAVRLAGINPKPYKILVFSLMGLLAGV 230

Query: 86  VAITAVVGLKLA--NAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLSTMFLA 143
            A+  +  L+ A  NAG    L +I  ++IG    L+ G       +  F   L    LA
Sbjct: 231 AALFQISRLEAADPNAGSGLELQVIAAVVIGGT-SLMGG---RGSVISTFFGVLIISVLA 286

Query: 144 RGLASIISTD 153
            GLA I +T+
Sbjct: 287 AGLAQIGATE 296


Lambda     K      H
   0.327    0.142    0.400 

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: 267
Number of extensions: 17
Number of successful extensions: 4
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: 340
Length of database: 325
Length adjustment: 28
Effective length of query: 312
Effective length of database: 297
Effective search space:    92664
Effective search space used:    92664
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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