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.
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:
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