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_066329821.1 BLR17_RS09055 sodium/solute symporter

Query= SwissProt::P96169
         (543 letters)



>NCBI__GCF_900100165.1:WP_066329821.1
          Length = 545

 Score =  509 bits (1311), Expect = e-148
 Identities = 254/551 (46%), Positives = 367/551 (66%), Gaps = 20/551 (3%)

Query: 6   HGLSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANI 65
           + L   D +VF IY  I+   G+++ R KK    S+ DYFLA  SL WWA+GASLIA+NI
Sbjct: 2   NALQTADYIVFLIYFVIVTSYGMYIYRSKKNAVTSSNDYFLAEGSLTWWAIGASLIASNI 61

Query: 66  SAEQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKK 125
           SAE FIGMSGSG+++GLAI+SYEWMSA TLIIV  + LP++++  I+T+P+F+ KR+N  
Sbjct: 62  SAEHFIGMSGSGFALGLAISSYEWMSAATLIIVAMFILPVYLKNKIFTMPQFLAKRYNDT 121

Query: 126 LKTILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSIYGGLSAV 185
           +  I+AV W+ +YIFVNLTS++YLG LA+ +I  +   + ++GL+LF+++ ++ GG+  +
Sbjct: 122 VSAIMAVIWLLIYIFVNLTSIIYLGALAISSIAPVSFEFCVIGLSLFSVIVTL-GGMKVI 180

Query: 186 VWTDVIQVFFLVLGGFMTTYMAVSFIGGTDGW----FAGVSKMVDAAPGHFEMILDQSNP 241
            +TD+ QV  L+LGG +TTY+A++ +    G+    F G+S + D APGH +MI D+SNP
Sbjct: 181 GYTDMFQVIVLILGGLVTTYLALTLLSEQFGFGKDIFKGLSIIADKAPGHLQMIFDKSNP 240

Query: 242 QYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFLV 301
            Y  LPG++V++GG+ + NL YWG NQYI+QR L A  +  A+KGI+FAAFLKL+VP + 
Sbjct: 241 HYTELPGMSVIVGGMLINNLAYWGCNQYIVQRALGA-DLKTARKGILFAAFLKLLVPVIA 299

Query: 302 VLPGIAAYVITSDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGVVFAALAAA 361
           VLPGIA YV+  +      + D A    P     D+AYP L   LP G+KG+  AAL AA
Sbjct: 300 VLPGIAMYVMHQNGMFQHEMLDAAGVLKP-----DRAYPTLMNLLPAGLKGIALAALTAA 354

Query: 362 IVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLGGIG 421
           IV+SLA   NS +TIF++DIY++Y    + + KLV VGR A VVA+ I  ++AP L  + 
Sbjct: 355 IVASLAGKANSISTIFSLDIYRKYFDKTTSEKKLVRVGRLAVVVAMFIGAIVAPSLKSLD 414

Query: 422 QAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMPL------ 475
           QA+Q+IQEY G  SPG+LA+F+LG+FWKKTT+   + G + ++P A  LKF+P+      
Sbjct: 415 QAYQFIQEYVGFFSPGVLAIFMLGMFWKKTTANAGLAGALLTVPIATVLKFLPVWTNGAF 474

Query: 476 -SMPFMDQMLYTLLFTMVVIAFTSL--STSINDDDPKGISVTSSMFVTDRSFNIAAYGIM 532
              PF+D+M  T +  + ++   SL     + + +   I V ++MF     F I ++ I 
Sbjct: 475 PDFPFLDRMSITFVMIVAIMIGVSLLRPEPVLEHEKHKIEVDTTMFKVSSEFIIGSFIIC 534

Query: 533 IVLAVLYTLFW 543
            VL  LYT+FW
Sbjct: 535 SVLVALYTVFW 545


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: 918
Number of extensions: 46
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: 545
Length adjustment: 35
Effective length of query: 508
Effective length of database: 510
Effective search space:   259080
Effective search space used:   259080
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 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