GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SSS-glucose in Echinicola vietnamensis KMM 6221, DSM 17526

Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate Echvi_3497 Echvi_3497 transporter, SSS family

Query= SwissProt::P96169
         (543 letters)



>FitnessBrowser__Cola:Echvi_3497
          Length = 527

 Score =  258 bits (660), Expect = 3e-73
 Identities = 167/535 (31%), Positives = 280/535 (52%), Gaps = 49/535 (9%)

Query: 11  IDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISAEQF 70
           I I+ F  +  +++ V  W+ + +K    S + YFL G+SL    +  S+I  NIS E  
Sbjct: 3   ITILTFIAFT-LLVAVYAWL-KTRKENLDSEDGYFLGGRSLTGVVIAGSMIMTNISTEHL 60

Query: 71  IGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLKTIL 130
           +GM+GS Y  G  I ++E  SA+ LI+   YF+P +++ G+ T+P+++E RF+   ++++
Sbjct: 61  VGMNGSSYKNGFVIVAWEVTSALALIVAAVYFVPRYLKMGLTTVPQYLENRFDAGTRSLV 120

Query: 131 AVFWISLYIFVNLTSVLYLGGLALETILGIP----------LMYSILGLALFALVYSIYG 180
           A F +  +    L  VLY G + LE++  I           L Y++L +     +Y+I+G
Sbjct: 121 AFFLLISFAVTLLPIVLYTGAINLESLFNISDTLNISQEQGLWYTVLAVGGIGSIYAIFG 180

Query: 181 GLSAVVWTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQSN 240
           GL AV  +D I  + L+L G M   +A+  IG  +    G+ ++ + +P  F ++  + +
Sbjct: 181 GLKAVAVSDTINGYGLLLAGLMVPVIALFMIGDNNP-LLGLERVFENSPEKFNVVGGKDS 239

Query: 241 PQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFL 300
                LP  + L  GL +  LY+W  NQ IIQR L AK++ EAQKG+++   LKL+VPF+
Sbjct: 240 V----LP-FSTLFTGLIINQLYFWCMNQTIIQRALGAKNLKEAQKGLLYTGALKLLVPFI 294

Query: 301 VVLPGIAAYVITSDPQLMASLGDIAATNLPSAANADKAYPWLT-QFLPVGVKGVVFAALA 359
           +VLPG+  +    D                   N D  YP L  + LPVG+ GV  A + 
Sbjct: 295 IVLPGVIGFYFFGDRLY---------------ENQDMVYPELVKKVLPVGLTGVFAAVIM 339

Query: 360 AAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLGG 419
            A++S+  S+LNS +TIF++DIYK  I P +   +LV  G+ +A +  I + + APM+  
Sbjct: 340 GAVLSTFNSVLNSASTIFSIDIYKRLIRPGASAGQLVKAGKLSATILAITSMVAAPMVAN 399

Query: 420 IGQA-FQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFM-PLSM 477
             +  FQ +Q+  G+    I ++ L G F K  +   A + +V  + F +   F+  + +
Sbjct: 400 APEGLFQLLQQLNGIFFIPIASIMLAGFFTKWVSPLAAKVALVTGLTFYVLTTFVFDIGI 459

Query: 478 PF-----MDQMLYTLLFTMVVIAF--------TSLSTSINDDDPKGISVTSSMFV 519
            F     ++ +L  L+  +V +A+        T +S  IN D  K  S+ S + V
Sbjct: 460 HFVHIWGIEFVLNVLIMYVVSVAWPMAKPTEKTLISAKINTDKWKYASLVSIILV 514


Lambda     K      H
   0.326    0.141    0.421 

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: 816
Number of extensions: 48
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: 543
Length of database: 527
Length adjustment: 35
Effective length of query: 508
Effective length of database: 492
Effective search space:   249936
Effective search space used:   249936
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