Align sodium/glucose cotransporter 1 (characterized)
to candidate WP_079555937.1 CDL62_RS06475 sodium/solute symporter
Query= CharProtDB::CH_091086 (664 letters) >NCBI__GCF_002201795.1:WP_079555937.1 Length = 631 Score = 241 bits (616), Expect = 6e-68 Identities = 149/483 (30%), Positives = 253/483 (52%), Gaps = 21/483 (4%) Query: 28 DISIIVIYFVVVMAVGLWAMFSTNRGTVGG---FFLAGRSMVWWPIGASLFASNIGSGHF 84 D I Y ++M +GLW + T +G +FLAG ++ WW IGASL A+NI + HF Sbjct: 9 DYLIFGAYAALIMGIGLW-ISRTKKGEEKDSKDYFLAGGTLSWWAIGASLIAANISAEHF 67 Query: 85 VGLAGTGAASGIAIGGFEWNALVLVVVLGWLFVPIYIKAGVVTMPEYLRKRFGGQRIQVY 144 + ++G+G A G+ + +EW A ++++++ +P + + TMP++ R+R+ G + + Sbjct: 68 IAMSGSGYAIGLGMAAYEWIAAIVLILVAKYLLPQMLDKKIFTMPQFARERY-GSGVSFF 126 Query: 145 LSLLSLLLYIFTKISADIFSGAIFINLALGLNLYLAIFLLLAITALYTITGGLAAVIYTD 204 S LL+Y+F +++ + GA+ +N LG+ + + LL +Y+I GG+ +V +TD Sbjct: 127 FSFFWLLVYVFVNLTSVAWLGALAMNQILGVPILYGVPGLLIFAGVYSIYGGMKSVAWTD 186 Query: 205 TLQTVIMLVGSLILTGFAFHEVGGYDAFMEKYMKAIPTIVSDGNTTFQEKCYTPRADSFH 264 +Q ++ G LI FA V G + + + + T ++ Sbjct: 187 IVQVFFLIFGGLITAWFALDAVAGDGKSAFEGFRVVLNQIRASETDTHFNMIIGDSEG-- 244 Query: 265 IFRDPLTGDLPWPGFIFGMSILT-LWYWCTDQVIVQRCLSAKNMSHVKGGCILCGYLKLM 323 RD +LP IFG LT + YW +Q I+Q+ L+AKN+ K G + YLK++ Sbjct: 245 -TRDSFL-NLPGLAVIFGAMWLTNIGYWGFNQFIIQKGLAAKNLKEAKRGLLFAAYLKIL 302 Query: 324 PMFIMVMPGMISRILY-------TEKIACVVPSECEKYCGTKVGCTNIAYPTLVVELMPN 376 I+++PG+ + +++ +A + +V ++ AYP L+ P Sbjct: 303 IPIIVIIPGITAYVIHGMSVETADGSLAFINQMGDSTLLAGEVAISDDAYPWLLRNFAPV 362 Query: 377 GLRGLMLSVMLASLMSSLTSIFNSASTLFTMDIY-AKVRKRASEKELMIAGRLFILVLIG 435 G+RGL + ++A+++SSL S+ NS ST+FT+DIY + K ASE++L+ GR V + Sbjct: 363 GIRGLAFAALVAAVISSLASLLNSTSTIFTLDIYKTLINKSASERQLVRVGRFAAFVALA 422 Query: 436 ISI-AWVPIVQSAQSGQLFDYIQSITSYLGPPIAAVFLLAIFWKRVNEPGAFWGLILGLL 494 I+I A P++ Q F YIQ T ++ P + AVF + I WKR A W I + Sbjct: 423 IAIVAARPLLGGLD--QAFQYIQEYTGFIYPGVVAVFGMGILWKRATNRAALWTTIATIP 480 Query: 495 IGI 497 GI Sbjct: 481 TGI 483 Lambda K H 0.327 0.141 0.436 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: 859 Number of extensions: 37 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: 664 Length of database: 631 Length adjustment: 38 Effective length of query: 626 Effective length of database: 593 Effective search space: 371218 Effective search space used: 371218 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: 54 (25.4 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