GapMind for catabolism of small carbon sources

 

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

Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate Pf6N2E2_883 Major myo-inositol transporter IolT

Query= SwissProt::P96710
         (464 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_883
          Length = 472

 Score =  280 bits (716), Expect = 7e-80
 Identities = 157/465 (33%), Positives = 257/465 (55%), Gaps = 11/465 (2%)

Query: 3   NTPTQLEPNVPVTRSHSMGFVILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFME 62
           NT       V   +  +  ++  I+  A  GGLL+G+DT VI+GA+ ++KD   L+PF E
Sbjct: 8   NTADTSAAYVSPEKHQAQRYLQKITWIATFGGLLFGFDTGVINGALLYMKDDLGLTPFTE 67

Query: 63  GLVISSIMIGGVVGVGISGFLSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARII 122
           GLV S+++IG ++G   SG LSD  GRR+I++  A++F + A+  AL+  +  ++ AR  
Sbjct: 68  GLVASALLIGAMMGALFSGRLSDLKGRRRIILFLAVVFFLGALACALAPTLDVMVAARFT 127

Query: 123 GGLGIGMGSSLSVTYITEAAPPAIRGSLSSLYQLFTILGISATYFINLAVQRSGTYEWGV 182
            GL +G  S +   Y++E AP +IRG + +  +L  + G    +  N  +    +   GV
Sbjct: 128 LGLAVGGASVVVPAYLSEMAPSSIRGRIITRNELMIVTGQFLAFTTNATLGNLFSDLDGV 187

Query: 183 HTGWRWMLAYGMVPSVIFFLVLLVVPESPRWLAKAGKTNEALKILTRINGETVAKEELKN 242
              WRWMLA   +P+V  +L +L +PESPRWLA  G+  E L++L  +  E  AK E++ 
Sbjct: 188 ---WRWMLALATLPAVALWLGMLYMPESPRWLATKGRFREGLEVLKLVREEYYAKAEMEA 244

Query: 243 IENSLKIEQM---GSLSQLFKPGLRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFG 299
           I   +  E+    G    L + G R+  +IGI +A+ +Q+ G+N+I Y+G +I    G  
Sbjct: 245 ITQQISNERFIKKGGWRDLSQKGARRIFLIGIGIAVTSQLTGVNSIMYFGTQILTEAGLE 304

Query: 300 QNAGFVTTCIVGVVEVIFTVIAVLLIDKVGRKKLMSIGSAFMAIFMILIGTSFYFELTSG 359
           Q +  +   + G++ +  T + + L+D+VGR+ +M +G     + ++LIG    F +   
Sbjct: 305 QRSALIANVVNGIISIGATFVGIALLDRVGRRPMMLLGFTGTTLSLLLIGLVSVF-VDPS 363

Query: 360 IMMIVLILGFVAAFCVS----VGPITWIMISEIFPNHLRARAAGIATIFLWGANWAIGQF 415
           +   +LILG +A F  S    +GP  W++++EIFP  +R    G+A    W  N  IG F
Sbjct: 364 VTRAMLILGAMAMFLASMQGLIGPAFWVLLAEIFPMRIRGGCMGMAIAAFWLTNVMIGMF 423

Query: 416 VPMMIDSFGLAYTFWIFAVINILCFLFVVTICPETKNKSLEEIEK 460
            P ++   G+  TF++F    +L   FV    PET+  +LEEIE+
Sbjct: 424 FPSLVAMIGIGQTFFVFVGAGLLSLTFVAVWVPETRGSTLEEIEQ 468


Lambda     K      H
   0.327    0.142    0.425 

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: 520
Number of extensions: 28
Number of successful extensions: 4
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: 464
Length of database: 472
Length adjustment: 33
Effective length of query: 431
Effective length of database: 439
Effective search space:   189209
Effective search space used:   189209
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: 51 (24.3 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