GapMind for catabolism of small carbon sources

 

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

Align polyol transporter 5 (characterized)
to candidate Pf6N2E2_883 Major myo-inositol transporter IolT

Query= CharProtDB::CH_091483
         (539 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_883
          Length = 472

 Score =  236 bits (602), Expect = 1e-66
 Identities = 144/461 (31%), Positives = 237/461 (51%), Gaps = 24/461 (5%)

Query: 42  LASMTSILLGYDIGVMSGAMIYIKRDLKINDLQIGILAGSLNIYSLIGSCAAGRTSDWIG 101
           +A+   +L G+D GV++GA++Y+K DL +     G++A +L I +++G+  +GR SD  G
Sbjct: 34  IATFGGLLFGFDTGVINGALLYMKDDLGLTPFTEGLVASALLIGAMMGALFSGRLSDLKG 93

Query: 102 RRYTIVLAGAIFFAGAILMGLSPNYAFLMFGRFIAGIGVGYALMIAPVYTAEVSPASSRG 161
           RR  I+    +FF GA+   L+P    ++  RF  G+ VG A ++ P Y +E++P+S RG
Sbjct: 94  RRRIILFLAVVFFLGALACALAPTLDVMVAARFTLGLAVGGASVVVPAYLSEMAPSSIRG 153

Query: 162 FLNSFPEVFINAGIMLGYVSNLAFSNL--PLKVGWRLMLGIGAVPSVILAIGVLAMPESP 219
            + +  E+ I  G  L + +N    NL   L   WR ML +  +P+V L +G+L MPESP
Sbjct: 154 RIITRNELMIVTGQFLAFTTNATLGNLFSDLDGVWRWMLALATLPAVALWLGMLYMPESP 213

Query: 220 RWLVMQGRLGDAKRVLDKTSDSPTEATLRLEDIKHAAGIPADCHDDVVQVSRRNSHGEGV 279
           RWL  +GR  +   VL K       A   +E I               Q+S      +G 
Sbjct: 214 RWLATKGRFREGLEVL-KLVREEYYAKAEMEAITQ-------------QISNERFIKKGG 259

Query: 280 WRELLIRPTPAVRRVMIAAIGIHFFQQASGIDAVVLFSPRIFKTAGLKTDHQQLLATVAV 339
           WR+L        RR+ +  IGI    Q +G+++++ F  +I   AGL+     L+A V  
Sbjct: 260 WRDL---SQKGARRIFLIGIGIAVTSQLTGVNSIMYFGTQILTEAGLE-QRSALIANVVN 315

Query: 340 GVVKTSFILVATFLLDRIGRRPLLLTSVGGMVLSLAALGTSLTIIDQSEKKVMWAVVVAI 399
           G++      V   LLDR+GRRP++L    G  LSL  +G     +D S  + M    + +
Sbjct: 316 GIISIGATFVGIALLDRVGRRPMMLLGFTGTTLSLLLIGLVSVFVDPSVTRAM----LIL 371

Query: 400 ATVMTYVATFSIGAGPITWVYSSEIFPLRLRSQGSSMGVVVNRVTSGVISISFLPMSKAM 459
             +  ++A+     GP  WV  +EIFP+R+R     M +    +T+ +I + F  +   +
Sbjct: 372 GAMAMFLASMQGLIGPAFWVLLAEIFPMRIRGGCMGMAIAAFWLTNVMIGMFFPSLVAMI 431

Query: 460 TTGGAFYLFGGIATVAWVFFYTFLPETQGRMLEDMDELFSG 500
             G  F++F G   ++  F   ++PET+G  LE++++   G
Sbjct: 432 GIGQTFFVFVGAGLLSLTFVAVWVPETRGSTLEEIEQRLYG 472


Lambda     K      H
   0.322    0.137    0.410 

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: 726
Number of extensions: 40
Number of successful extensions: 5
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: 539
Length of database: 472
Length adjustment: 34
Effective length of query: 505
Effective length of database: 438
Effective search space:   221190
Effective search space used:   221190
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 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