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_084932255.1 HA51_RS04135 sugar porter family MFS transporter

Query= SwissProt::O34718
         (473 letters)



>NCBI__GCF_002095475.1:WP_084932255.1
          Length = 474

 Score =  571 bits (1471), Expect = e-167
 Identities = 272/456 (59%), Positives = 353/456 (77%), Gaps = 2/456 (0%)

Query: 1   MNKQGNQMSFLRTIILVSTFGGLLFGYDTGVLNGALPYMGEPDQLNLNAFTEGLVTSSLL 60
           M  Q     ++R II+++TFGGLLFGYD GV+NGALPYM +   L LN+ + GL+TS+LL
Sbjct: 1   MFDQAEHKRYMRKIIVIATFGGLLFGYDVGVINGALPYMAK--SLGLNSLSTGLITSALL 58

Query: 61  FGAALGAVFGGRMSDFNGRRKNILFLAVIFFISTIGCTFAPNVTVMIISRFVLGIAVGGA 120
            GA  GA+ GG++SD  GRRKNILFLA++FF+ST+GC+ AP++  M++ RFVLG AVGGA
Sbjct: 59  MGAVFGAILGGKLSDLVGRRKNILFLALLFFVSTLGCSIAPDIQTMMVCRFVLGFAVGGA 118

Query: 121 SVTVPAYLAEMSPVESRGRMVTQNELMIVSGQLLAFVFNAILGTTMGDNSHVWRFMLVIA 180
           SVTVP YLAEM+P +SRGRMVT NELMIV G L+AF+ NA+LG T+G+N HVWR+ML +A
Sbjct: 119 SVTVPTYLAEMAPAQSRGRMVTWNELMIVGGVLIAFISNAVLGITLGENEHVWRYMLALA 178

Query: 181 SLPALFLFFGMIRMPESPRWLVSKGRKEDALRVLKKIRDEKRAAAELQEIEFAFKKEDQL 240
            +PA+ LFFGM+ +PESPRWLV +GR+ +A  VL++IRDE  A  EL  I+ A   E QL
Sbjct: 179 MIPAVCLFFGMLTVPESPRWLVKQGREAEAKSVLERIRDEHTAGIELYNIKHAISHEQQL 238

Query: 241 EKATFKDLSVPWVRRIVFIGLGIAIVQQITGVNSIMYYGTEILRNSGFQTEAALIGNIAN 300
            K  F++L++PW+RRI+ IG+ +A+  Q TGVNSIMY+GTEILR++G +T AALIGN A 
Sbjct: 239 GKVKFRELNIPWIRRIMLIGIAVAVFSQTTGVNSIMYFGTEILRDAGLETSAALIGNTAF 298

Query: 301 GVISVLATFVGIWLLGRVGRRPMLMTGLIGTTTALLLIGIFSLVLEGSPALPYVVLSLTV 360
           G+ISVL+TF GIWLL R GRRPM++ GL GTT  LL+I I + +L G+PA+PYVVL+LTV
Sbjct: 299 GLISVLSTFAGIWLLDRAGRRPMMLVGLAGTTVILLVIAIATSMLAGNPAMPYVVLTLTV 358

Query: 361 TFLAFQQGAISPVTWLMLSEIFPLRLRGLGMGVTVFCLWMVNFAVSFTFPILLAAIGLST 420
            FLAF QGAI PV W+ LSEIFPLR+RG GMG++V  LW+ NF +  TFP++L   GLS 
Sbjct: 359 IFLAFMQGAIGPVLWVTLSEIFPLRIRGAGMGISVAFLWITNFFIGLTFPMMLEGFGLSG 418

Query: 421 TFFIFVGLGICSVLFVKRFLPETKGLSLEQLEENFR 456
           TFF F  +G+   + +K F PETKG SLE++EE+F+
Sbjct: 419 TFFAFAAIGVVGFIIMKMFFPETKGKSLEEIEESFK 454


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: 712
Number of extensions: 20
Number of successful extensions: 3
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: 474
Length adjustment: 33
Effective length of query: 440
Effective length of database: 441
Effective search space:   194040
Effective search space used:   194040
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.

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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