GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SSS-glucose in Pedobacter sp. GW460-11-11-14-LB5

Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate CA265_RS06755 CA265_RS06755 sodium transporter

Query= SwissProt::P96169
         (543 letters)



>FitnessBrowser__Pedo557:CA265_RS06755
          Length = 542

 Score =  517 bits (1331), Expect = e-151
 Identities = 260/546 (47%), Positives = 365/546 (66%), Gaps = 17/546 (3%)

Query: 8   LSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISA 67
           LS  D  VF +Y  I+   G WV R KK  +  T+DYFLA  SL WWA+GAS+IA+NISA
Sbjct: 4   LSAFDYAVFLMYFVIVSAYGYWVYRSKKKKRTDTKDYFLAEGSLTWWAIGASIIASNISA 63

Query: 68  EQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLK 127
           E FIGMSGSG+++GLAIASYEWM+A TLIIV  +FLPI+I+  IYT+P+F+  R+N  + 
Sbjct: 64  EHFIGMSGSGFAMGLAIASYEWMAAATLIIVAIFFLPIYIKNKIYTMPQFLSNRYNNTVS 123

Query: 128 TILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAVVW 187
           T++AVFW+ +Y+FVNLTS+ +LG +A+ETI G+P    I+ LA+F+ + ++ GG+  + +
Sbjct: 124 TLMAVFWLLVYVFVNLTSIFFLGAIAIETITGVPFNICIIFLAIFSAIITL-GGMKVIGY 182

Query: 188 TDVIQVFFLVLGGFMTTYMAVSFIG---GTDGWFAGVSKMVDAAPGHFEMILDQSNPQYM 244
           TDVIQVF LV GG +T YMA+  +          A +  +   A  HF MI  + +  Y 
Sbjct: 183 TDVIQVFVLVAGGLITCYMALKLVSEKLDAPSVLASLPLLRSEASDHFHMIFSKGDKFYN 242

Query: 245 NLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFLVVLP 304
            LPGIAVL+GGLW+ NL YWG NQYI+QR L A  +   + G++FAAFLKL++P +VV+P
Sbjct: 243 ELPGIAVLVGGLWINNLNYWGCNQYIVQRALGA-DLKTGRNGLIFAAFLKLLIPVIVVIP 301

Query: 305 GIAAYVITSDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGVVFAALAAAIVS 364
           GIAAYV+       + + D A    P     D AYP L   LP G+KG+ FAAL AAIV+
Sbjct: 302 GIAAYVLYQRGYFHSEMLDAAGVVKP-----DHAYPVLMNLLPAGIKGLAFAALTAAIVA 356

Query: 365 SLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLGGIGQAF 424
           SLA   NS ATIFT+DIYK++I P++ + +LV+VGR + V+A +IA +IAP L    Q +
Sbjct: 357 SLAGKCNSIATIFTLDIYKKFIKPEASETRLVSVGRWSVVIASLIAIIIAPALRSFDQVY 416

Query: 425 QYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMP-------LSM 477
           Q+IQEY G +SPG+ A+FLLG FWKKTTS+ A+   + +IP +   KF+P         +
Sbjct: 417 QFIQEYVGFISPGVFAIFLLGFFWKKTTSRAALTAALLTIPLSTLFKFLPAVTNGAIAPI 476

Query: 478 PFMDQMLYTLLFTMVVIAFTSLSTSINDDDPKGISVTSSMFVTDRSFNIAAYGIMIVLAV 537
           PF+++M +  +  + ++   +L+   + D+P+G+ + SSMF    +F IA+  I  +LA 
Sbjct: 477 PFLNRMSWVFMIIIGLMIVVTLTDPKSKDNPQGLEIDSSMFKVTPAFTIASVMICGILAA 536

Query: 538 LYTLFW 543
           LYT+FW
Sbjct: 537 LYTVFW 542


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: 930
Number of extensions: 41
Number of successful extensions: 6
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: 542
Length adjustment: 35
Effective length of query: 508
Effective length of database: 507
Effective search space:   257556
Effective search space used:   257556
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