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_1880 Echvi_1880 transporter, SSS family

Query= SwissProt::P96169
         (543 letters)



>FitnessBrowser__Cola:Echvi_1880
          Length = 624

 Score =  564 bits (1453), Expect = e-165
 Identities = 275/517 (53%), Positives = 377/517 (72%), Gaps = 17/517 (3%)

Query: 7   GLSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANIS 66
           G S +D ++F +Y   I+ VGLWVSR KKG +K+ ++YFLA KSL WWAVGASL+AANIS
Sbjct: 4   GFSTLDYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANIS 63

Query: 67  AEQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKL 126
           AE FIG SGSG++IGL I++YEW++AI LIIV KYFLPIF++ G+YT+P+F+ +RFNK +
Sbjct: 64  AEHFIGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGV 123

Query: 127 KTILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAVV 186
            T  AVFW+ +Y+FVNLTSV YLG LAL+ I+GIPL Y I+GL +F+ +YSIYGGL AV 
Sbjct: 124 STAFAVFWLLVYVFVNLTSVSYLGALALDKIMGIPLQYGIIGLLIFSGIYSIYGGLEAVA 183

Query: 187 WTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQ-------- 238
           WTDV+QV  LV GG +TT++A+  +G  DG FAG+S + + A  HF MI+ Q        
Sbjct: 184 WTDVVQVIILVAGGLITTFLALDAVGMGDGIFAGMSNLYNDAKDHFVMIMPQGRVMVPDG 243

Query: 239 ---SNPQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKL 295
              S   + +LPG+AV++GG+W+ NL YWGFNQYIIQ+ LAAKS+ EA+KG++FA +LKL
Sbjct: 244 LGGSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAGYLKL 303

Query: 296 IVPFLVVLPGIAAYVITSD--PQLMASLGDIAATNLPSAANADKAYPWLTQ-FLPVGVKG 352
           ++P +VV+PGIAAYV+ +D  P+ +A++ ++   ++ +   +D+AYPWL + F+P G++G
Sbjct: 304 LMPIIVVIPGIAAYVLINDYSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPNGIRG 363

Query: 353 VVFAALAAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACL 412
           + FAALAAAIVSSLASM+NST+TIFTMDIYK Y  P++ +H+LV  GR  AVVAL IA +
Sbjct: 364 LAFAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAVVALAIAMI 423

Query: 413 IAPMLGGIGQAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKF 472
           +AP L  + Q FQYIQEYTG + PG++ VF +GL W++ T+  A+   +A+IP  +  K 
Sbjct: 424 VAPQLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIATIPAGIVFKI 483

Query: 473 MPLSMPFMDQMLYT---LLFTMVVIAFTSLSTSINDD 506
               MPF+ +M Y    L F   +I+F       N D
Sbjct: 484 FYPEMPFLLRMGYVFIILCFIASLISFAEKKKFANPD 520



 Score = 44.3 bits (103), Expect = 1e-08
 Identities = 28/90 (31%), Positives = 50/90 (55%), Gaps = 8/90 (8%)

Query: 457 IIGVVASI-PFALFLKFMPLSMP--FMDQMLYTLLFTMVVIAFTSLSTSINDDDPKGISV 513
           I+G++ ++  FALF  +  + +   FM   L+ +L T   I +T++   +   DPK  + 
Sbjct: 539 ILGIICAVLGFALFNSYEHVGIESIFMIAALFLMLGT---ILYTNVK--METADPKSFNT 593

Query: 514 TSSMFVTDRSFNIAAYGIMIVLAVLYTLFW 543
              +F T  SFN+ A GI++++ +LY  FW
Sbjct: 594 DPVLFNTTSSFNLGAAGIILIVGLLYYFFW 623


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: 1171
Number of extensions: 53
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 543
Length of database: 624
Length adjustment: 36
Effective length of query: 507
Effective length of database: 588
Effective search space:   298116
Effective search space used:   298116
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: 53 (25.0 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