GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Pseudomonas fluorescens FW300-N2E2

Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate Pf6N2E2_883 Major myo-inositol transporter IolT

Query= TCDB::Q8NTX0
         (491 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_883
          Length = 472

 Score =  427 bits (1097), Expect = e-124
 Identities = 219/442 (49%), Positives = 301/442 (68%), Gaps = 4/442 (0%)

Query: 32  VALVATFGGLLFGYDTGVINGALNPMTRELGLTAFTEGVVTSSLLFGAAAGAMFFGRISD 91
           +  +ATFGGLLFG+DTGVINGAL  M  +LGLT FTEG+V S+LL GA  GA+F GR+SD
Sbjct: 31  ITWIATFGGLLFGFDTGVINGALLYMKDDLGLTPFTEGLVASALLIGAMMGALFSGRLSD 90

Query: 92  NWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGLAVGGASTVVPVYLAELAPFE 151
             GRR+ I+ LAV FF+G + C  AP+  VMV  R  LGLAVGGAS VVP YL+E+AP  
Sbjct: 91  LKGRRRIILFLAVVFFLGALACALAPTLDVMVAARFTLGLAVGGASVVVPAYLSEMAPSS 150

Query: 152 IRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRYMLAIAAIPAIALFFGMLRVP 211
           IRG +  RNELMIV GQ  AF  NA +GN+F   DGVWR+MLA+A +PA+AL+ GML +P
Sbjct: 151 IRGRIITRNELMIVTGQFLAFTTNATLGNLFSDLDGVWRWMLALATLPAVALWLGMLYMP 210

Query: 212 ESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAREEHAVSEKSMGLREILSSKW 271
           ESPRWL  +GR  E   VL+ +R    A AE+  +      E  +  K  G R+ LS K 
Sbjct: 211 ESPRWLATKGRFREGLEVLKLVREEYYAKAEMEAITQQISNERFI--KKGGWRD-LSQKG 267

Query: 272 LVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENAALIANVAPGVIAVVGAFIAL 331
             RI L+GIG+ V  QLTG+NSIMY+G  +L EAG  + +ALIANV  G+I++   F+ +
Sbjct: 268 ARRIFLIGIGIAVTSQLTGVNSIMYFGTQILTEAGLEQRSALIANVVNGIISIGATFVGI 327

Query: 332 WMMDRINRRTTLITGYSLTTISHVLIGIASVAFPVGDPLRPYVILTLVVVFVGSMQTFLN 391
            ++DR+ RR  ++ G++ TT+S +LIG+ SV F      R  +IL  + +F+ SMQ  + 
Sbjct: 328 ALLDRVGRRPMMLLGFTGTTLSLLLIGLVSV-FVDPSVTRAMLILGAMAMFLASMQGLIG 386

Query: 392 VATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGLFFPTIMEAVGLTGTFFMFAGIGVV 451
            A WV+L+E+FP+ +RG  +G+++   W+ N  +G+FFP+++  +G+  TFF+F G G++
Sbjct: 387 PAFWVLLAEIFPMRIRGGCMGMAIAAFWLTNVMIGMFFPSLVAMIGIGQTFFVFVGAGLL 446

Query: 452 ALIFIYTQVPETRGRTLEEIDE 473
           +L F+   VPETRG TLEEI++
Sbjct: 447 SLTFVAVWVPETRGSTLEEIEQ 468


Lambda     K      H
   0.327    0.142    0.420 

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: 623
Number of extensions: 20
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: 491
Length of database: 472
Length adjustment: 34
Effective length of query: 457
Effective length of database: 438
Effective search space:   200166
Effective search space used:   200166
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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