GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SSS-glucose in Flavobacterium glycines Gm-149

Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate WP_066328313.1 BLR17_RS01540 sodium/solute symporter

Query= SwissProt::P96169
         (543 letters)



>NCBI__GCF_900100165.1:WP_066328313.1
          Length = 561

 Score =  423 bits (1087), Expect = e-122
 Identities = 233/575 (40%), Positives = 350/575 (60%), Gaps = 57/575 (9%)

Query: 8   LSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISA 67
           L F D  VF +Y   +   G  + R ++  +   + YFLA  +L WWA+GASLIA+NISA
Sbjct: 5   LEFADYAVFIVYFLAVSIYGYIIYRKREKNEHDAKAYFLAEGTLTWWAIGASLIASNISA 64

Query: 68  EQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLK 127
           EQFIGMSG G+ +G+A+A+YEW++AI LIIVG +F+P++++  IYT+P+F++ R+N    
Sbjct: 65  EQFIGMSGEGFFLGIAVAAYEWVAAIALIIVGIWFIPVYLKNKIYTMPQFLKTRYNDTTA 124

Query: 128 TILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSI-LGLALFALVYSIYGGLSAVV 186
            I+AVFW+ LY+FVNLTS+LYLG +A+  + G   ++ I LGLA+FAL+ S+ GG+  V 
Sbjct: 125 LIMAVFWLFLYVFVNLTSILYLGAVAINGLAGGDYLHVIMLGLAIFALIISL-GGMKVVA 183

Query: 187 WTDVIQVFFLVLGGFMTTYMAVSFIG-----GTDGWFAGVSKMVDAAPGHFEMILDQSN- 240
           +TDVIQV  L++GG +T+Y+A++ +G     G D   AG   +++ AP HF+MI+ +   
Sbjct: 184 YTDVIQVAVLIIGGLVTSYIALTTVGQYFGVGQDA-IAGFKVLMERAPEHFKMIIPRPTA 242

Query: 241 -------PQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFL 293
                   +Y+  PG+   + G+W+ NL YWG NQYI QR L A  ++ A+ G++FA  L
Sbjct: 243 SSTQLEIDKYLTFPGVLSYLAGIWIINLNYWGCNQYITQRALGA-DLTTARTGLLFAGML 301

Query: 294 KLIVPFLVVLPGIAAYVITSDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGV 353
           KL++P +V+LPGIAAYV+     L   +G             D AY  +  FLP G+KG+
Sbjct: 302 KLLMPVIVMLPGIAAYVLYEGGHLPQLVG-----------GKDGAYSAMLTFLPTGLKGL 350

Query: 354 VFAALAAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLI 413
             AAL AAIV+SLA  +NS +TI+T+D++K+YI  ++ D   VN+GR A   A+++A L 
Sbjct: 351 SVAALTAAIVASLAGKVNSISTIYTLDVHKKYIQKEASDRAQVNIGRYAVFAAMVLAVLF 410

Query: 414 A----PMLGGIGQAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFA-L 468
                  +GG+G  F YIQ+YTG +SPG+ A+F LG+FWK+TT   AI+GV+A    + L
Sbjct: 411 TWNDLLGIGGVG-GFTYIQKYTGFISPGVFAMFFLGMFWKRTTGTAAIVGVLAGFLLSVL 469

Query: 469 FLKFMP-------------------LSMPFMDQMLYTLLFTMV-VIAFTSLSTSINDDDP 508
           F ++ P                     +PF   M  + LFTM+ ++A +     +N   P
Sbjct: 470 FNEYAPAMFGNETFLYTAYANGKGAFEIPFHVCMGLSFLFTMILMVAVSYAGPKVN---P 526

Query: 509 KGISVTSSMFVTDRSFNIAAYGIMIVLAVLYTLFW 543
           K   + + MF       +     ++++A LY  FW
Sbjct: 527 KAFELDTEMFKVKPQTTVLIIITLLIIAALYVKFW 561


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: 1054
Number of extensions: 66
Number of successful extensions: 9
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: 561
Length adjustment: 36
Effective length of query: 507
Effective length of database: 525
Effective search space:   266175
Effective search space used:   266175
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 24 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