GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolT in Pantoea rwandensis LMG 26275

Align Major myo-inositol transporter IolT (characterized)
to candidate WP_084931685.1 HA51_RS02405 sugar porter family MFS transporter

Query= SwissProt::O34718
         (473 letters)



>NCBI__GCF_002095475.1:WP_084931685.1
          Length = 469

 Score =  402 bits (1034), Expect = e-116
 Identities = 216/459 (47%), Positives = 301/459 (65%), Gaps = 16/459 (3%)

Query: 11  LRTIILVSTFGGLLFGYDTGVLNGALPYMGEPDQLNLNAFTEGLVTSSLLFGAALGAVFG 70
           +R I +VST GGL FGYDTGV++GAL +M     LNL    EG +TS LLFGAALG++FG
Sbjct: 13  MRLITIVSTIGGLCFGYDTGVISGALIFMKY--DLNLTPTQEGFITSFLLFGAALGSLFG 70

Query: 71  GRMSDFNGRRKNILFLAVIFFISTIGCTFAPNVTVMIISRFVLGIAVGGASVTVPAYLAE 130
           G +SD  GRRKN+L++A IF    +G  FA +V  MI++RF+LG+AVG ASVTVP Y++E
Sbjct: 71  GYLSDKQGRRKNLLWVAAIFMFGALGTAFAWDVPSMIVARFILGLAVGCASVTVPIYISE 130

Query: 131 MSPVESRGRMVTQNELMIVSGQLLAFVFNAILGTTMGDNSHVWRFMLVIASLPALFLFFG 190
           ++  + R R+VT NELMIV+GQ LA+  NA +     +  H WR ML I +LP   L+FG
Sbjct: 131 LARADQRERLVTVNELMIVTGQFLAYSVNAAIVNLYPEMQHNWRIMLAIPALPGALLWFG 190

Query: 191 MIRMPESPRWLVSKGRKEDALRVLKKIRDEKRAAAELQEIEFAFKKEDQLEKATFKDLSV 250
           M+ MPESPR+ + +G  E A++VLK +R  +    E++EI+    K D+++   F +L  
Sbjct: 191 MLMMPESPRFFIRRGETEKAVKVLKTLRLPEEVDREVKEIQ-QIVKADEVKFNLFAELKN 249

Query: 251 PWVRRIVFIGLGIAIVQQITGVNSIMYYGTEILRNSGFQTEAALIGNIANGVISVLATFV 310
            WV ++V IGL I +  ++TGVN+IMYY   +L+ +G    AA+ G +ANG+ISVLAT +
Sbjct: 250 RWVIQLVLIGLMIVLATRVTGVNTIMYYAPTVLKATGLGDAAAVTGAVANGIISVLATLL 309

Query: 311 GIWLLGRVGRRPMLMTGLIGTTTALLLIGI-FSL-----VLEGSPAL-------PYVVLS 357
           G+ L+G+  RR M  TG  G T +L+LIG+ F L      + G   L       PYV+L 
Sbjct: 310 GMALIGKHSRRKMFFTGQAGVTVSLVLIGLAFKLFFHTETINGVDTLHANFANAPYVILG 369

Query: 358 LTVTFLAFQQGAISPVTWLMLSEIFPLRLRGLGMGVTVFCLWMVNFAVSFTFPILLAAIG 417
           L + FL F QG I+PV WLML+EI+PLR+RG+GMG  VF LW+ +F +   FP LL   G
Sbjct: 370 LMLVFLVFMQGWIAPVFWLMLAEIYPLRMRGVGMGFAVFGLWIFDFMIQSIFPYLLGHYG 429

Query: 418 LSTTFFIFVGLGICSVLFVKRFLPETKGLSLEQLEENFR 456
              TF  F    +  ++ + ++LPET+GL+LEQ+E+ FR
Sbjct: 430 GGMTFGFFGATNVIMLILLVKYLPETRGLTLEQIEKKFR 468


Lambda     K      H
   0.327    0.142    0.418 

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: 650
Number of extensions: 25
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: 473
Length of database: 469
Length adjustment: 33
Effective length of query: 440
Effective length of database: 436
Effective search space:   191840
Effective search space used:   191840
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 24 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