GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Cronobacter universalis NCTC 9529

Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate WP_007700669.1 AFK65_RS04490 sugar porter family MFS transporter

Query= TCDB::Q8NTX0
         (491 letters)



>NCBI__GCF_001277175.1:WP_007700669.1
          Length = 501

 Score =  389 bits (998), Expect = e-112
 Identities = 208/459 (45%), Positives = 297/459 (64%), Gaps = 9/459 (1%)

Query: 19  PLTEGPYRKRLFYVALVATFGGLLFGYDTGVINGALNPMTRELGLTAFTEGVVTSSLLFG 78
           P ++ P    +  +A++AT GGLLFGYDTGVI+GAL  M  EL LT  T G+VTSSLLFG
Sbjct: 15  PNSDAPTAPFVKVIAIIATLGGLLFGYDTGVISGALLFMGSELHLTPLTTGLVTSSLLFG 74

Query: 79  AAAGAMFFGRISDNWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGLAVGGAST 138
           AA GA+  G +++  GR+K II LAV F +G +    AP  + M+  R++LG+AVGGA+ 
Sbjct: 75  AAFGALLAGHMANAAGRKKIIIYLAVIFAIGAIGTAMAPDVSWMIFFRLVLGVAVGGAAA 134

Query: 139 VVPVYLAELAPFEIRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRYMLAIAAI 198
            VPVY+AE+AP   RG L    ELMIV GQL A++ NA    ++G  +  WR+MLA+A +
Sbjct: 135 TVPVYIAEIAPANKRGQLVTLQELMIVSGQLLAYISNASFHELWG-GESTWRWMLAVATL 193

Query: 199 PAIALFFGMLRVPESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAREEHAVSE 258
           PA+ L+FGM+ +P++PRW   +GR+ EAR VL+  R  E    E+ ++E     + A  +
Sbjct: 194 PAVLLWFGMMFMPDTPRWYAMKGRLAEARRVLDRTRRPEDVEWELMEIEETLEAQRAQGK 253

Query: 259 KSMGLREILSSKWLVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENAALIANVA 318
               LRE+L + WL ++ ++GIG+ V QQ+TG+N+IMYY   VL   G S+NAAL+A VA
Sbjct: 254 PR--LRELL-TPWLFKLFMIGIGIAVIQQMTGVNTIMYYAPTVLTAVGMSDNAALVATVA 310

Query: 319 PGVIAVVGAFIALWMMDRINRRTTLITGYSLTTISHVLIGIASVAFP-----VGDPLRPY 373
            GV++V+  F+ +WM+ +I RRT  + G    T   V IG  S   P       D LR Y
Sbjct: 311 NGVVSVLMTFVGIWMLGKIGRRTMTMIGQFGCTACLVFIGAVSYLLPETVNGQPDALRGY 370

Query: 374 VILTLVVVFVGSMQTFLNVATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGLFFPTIM 433
           ++L  +++F+   Q  L+  TW++LSE+FP  +RG  +G +VF +WIAN  + LFFP ++
Sbjct: 371 MVLAGMLMFLCFQQGALSPVTWLLLSEIFPTRLRGIFMGGAVFSMWIANFLISLFFPILL 430

Query: 434 EAVGLTGTFFMFAGIGVVALIFIYTQVPETRGRTLEEID 472
             VGL+GTFF+FA  G+V   F+   VPETR R+LE+I+
Sbjct: 431 AWVGLSGTFFIFAAFGIVGATFVIKCVPETRNRSLEQIE 469


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: 645
Number of extensions: 24
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: 501
Length adjustment: 34
Effective length of query: 457
Effective length of database: 467
Effective search space:   213419
Effective search space used:   213419
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 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