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

GapMind for catabolism of small carbon sources

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

Align Major myo-inositol transporter IolT (characterized)
to candidate Pf6N2E2_883 Major myo-inositol transporter IolT

Query= SwissProt::O34718
         (473 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_883
          Length = 472

 Score =  471 bits (1211), Expect = e-137
 Identities = 234/444 (52%), Positives = 315/444 (70%), Gaps = 2/444 (0%)

Query: 10  FLRTIILVSTFGGLLFGYDTGVLNGALPYMGEPDQLNLNAFTEGLVTSSLLFGAALGAVF 69
           +L+ I  ++TFGGLLFG+DTGV+NGAL YM   D L L  FTEGLV S+LL GA +GA+F
Sbjct: 27  YLQKITWIATFGGLLFGFDTGVINGALLYM--KDDLGLTPFTEGLVASALLIGAMMGALF 84

Query: 70  GGRMSDFNGRRKNILFLAVIFFISTIGCTFAPNVTVMIISRFVLGIAVGGASVTVPAYLA 129
            GR+SD  GRR+ ILFLAV+FF+  + C  AP + VM+ +RF LG+AVGGASV VPAYL+
Sbjct: 85  SGRLSDLKGRRRIILFLAVVFFLGALACALAPTLDVMVAARFTLGLAVGGASVVVPAYLS 144

Query: 130 EMSPVESRGRMVTQNELMIVSGQLLAFVFNAILGTTMGDNSHVWRFMLVIASLPALFLFF 189
           EM+P   RGR++T+NELMIV+GQ LAF  NA LG    D   VWR+ML +A+LPA+ L+ 
Sbjct: 145 EMAPSSIRGRIITRNELMIVTGQFLAFTTNATLGNLFSDLDGVWRWMLALATLPAVALWL 204

Query: 190 GMIRMPESPRWLVSKGRKEDALRVLKKIRDEKRAAAELQEIEFAFKKEDQLEKATFKDLS 249
           GM+ MPESPRWL +KGR  + L VLK +R+E  A AE++ I      E  ++K  ++DLS
Sbjct: 205 GMLYMPESPRWLATKGRFREGLEVLKLVREEYYAKAEMEAITQQISNERFIKKGGWRDLS 264

Query: 250 VPWVRRIVFIGLGIAIVQQITGVNSIMYYGTEILRNSGFQTEAALIGNIANGVISVLATF 309
               RRI  IG+GIA+  Q+TGVNSIMY+GT+IL  +G +  +ALI N+ NG+IS+ ATF
Sbjct: 265 QKGARRIFLIGIGIAVTSQLTGVNSIMYFGTQILTEAGLEQRSALIANVVNGIISIGATF 324

Query: 310 VGIWLLGRVGRRPMLMTGLIGTTTALLLIGIFSLVLEGSPALPYVVLSLTVTFLAFQQGA 369
           VGI LL RVGRRPM++ G  GTT +LLLIG+ S+ ++ S     ++L     FLA  QG 
Sbjct: 325 VGIALLDRVGRRPMMLLGFTGTTLSLLLIGLVSVFVDPSVTRAMLILGAMAMFLASMQGL 384

Query: 370 ISPVTWLMLSEIFPLRLRGLGMGVTVFCLWMVNFAVSFTFPILLAAIGLSTTFFIFVGLG 429
           I P  W++L+EIFP+R+RG  MG+ +   W+ N  +   FP L+A IG+  TFF+FVG G
Sbjct: 385 IGPAFWVLLAEIFPMRIRGGCMGMAIAAFWLTNVMIGMFFPSLVAMIGIGQTFFVFVGAG 444

Query: 430 ICSVLFVKRFLPETKGLSLEQLEE 453
           + S+ FV  ++PET+G +LE++E+
Sbjct: 445 LLSLTFVAVWVPETRGSTLEEIEQ 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: 706
Number of extensions: 23
Number of successful extensions: 2
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: 472
Length adjustment: 33
Effective length of query: 440
Effective length of database: 439
Effective search space:   193160
Effective search space used:   193160
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.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources