GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SSS-glucose in Shewanella loihica PV-4

Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate 5210844 Shew_3270 SSS family solute/sodium (Na+) symporter (RefSeq)

Query= SwissProt::P96169
         (543 letters)



>FitnessBrowser__PV4:5210844
          Length = 474

 Score =  222 bits (565), Expect = 3e-62
 Identities = 147/486 (30%), Positives = 250/486 (51%), Gaps = 41/486 (8%)

Query: 11  IDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISAEQF 70
           I + +F     ++  +     R        + DYFLAG  L W  V  SL+  NISAEQ 
Sbjct: 5   IQVAIFVALTTLVALITYLKCRKVTRDANDSRDYFLAGGGLSWIVVAGSLMMTNISAEQI 64

Query: 71  IGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKK-LKTI 129
           +GM+G+     L +A +E  +AI LII+ K+ +PI+      T  E +E+++  K ++ +
Sbjct: 65  VGMNGAQT---LLVAWWEIAAAIGLIILAKWLIPIYYRYNCTTTTELLERKYQDKGIRAM 121

Query: 130 LAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGL--ALFALVYSIYGGLSAVVW 187
           +++ ++  Y F+ L  VLY G L ++++ G+ +  ++L +  A+   +Y+I+GGL A+  
Sbjct: 122 VSLLFMLGYAFILLPVVLYTGSLFMKSMFGLSISVTVLAIIFAVVGAIYAIFGGLRAIAI 181

Query: 188 TDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQSNPQYMNLP 247
           +D +    L+L G   +Y+A+  +   D   +G+            +I D  +    ++P
Sbjct: 182 SDTLNGLGLILMGLAVSYLAMHAV---DWDLSGIPLE------RLTLIGDSQS----DIP 228

Query: 248 GIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFLVVLPGIA 307
              +L G +++  ++YWG N  I QR LAAKSV EAQKG+  A  +KLI+P +VVLPGI 
Sbjct: 229 WSTLLTGMIFI-QIFYWGTNMVITQRALAAKSVKEAQKGLYAAVVMKLIIPVIVVLPGIV 287

Query: 308 AYVITSDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGVVFAALAAAIVSSLA 367
           A+      +L   +GD+A   L            +   LP  + G   A +A A++SS  
Sbjct: 288 AF------KLYGDVGDVAYGKL------------VGDLLPSWLSGAFAAVIAGAVLSSFN 329

Query: 368 SMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLGGIGQAFQYI 427
           S LNS A ++T DI++ YI+ D+   K   +G   A++  +I+  + P+          +
Sbjct: 330 SCLNSAAALYTCDIHQNYINADADVRK---IGSRVALLFTLISVALVPLFARSESIIALL 386

Query: 428 QEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMPLSMPFMDQMLYTL 487
           Q+  GL S  +LA F+  L +K  ++K    G+V  +       F+   + F+  M  TL
Sbjct: 387 QQLNGLYSMPVLAAFICALVFKNVSAKAIKWGLVFGVLLYALFTFIWSPLHFIHLMAITL 446

Query: 488 LFTMVV 493
           L T++V
Sbjct: 447 LATILV 452


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: 708
Number of extensions: 51
Number of successful extensions: 7
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: 474
Length adjustment: 34
Effective length of query: 509
Effective length of database: 440
Effective search space:   223960
Effective search space used:   223960
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