Align SSS sodium solute transporter (characterized, see rationale)
to candidate 5209833 Shew_2286 SSS family solute/sodium (Na+) symporter (RefSeq)
Query= uniprot:L0FZT5 (624 letters) >FitnessBrowser__PV4:5209833 Length = 519 Score = 489 bits (1258), Expect = e-142 Identities = 246/504 (48%), Positives = 348/504 (69%), Gaps = 33/504 (6%) Query: 7 TLDYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANISAEH 66 TLD I +VYAL ++ + LW+SR K E+ ++YFLA K+L WWA+GASL+A+NISAE Sbjct: 4 TLDIGILLVYALGLLGLALWISRQDKRHERDTKDYFLAGKALPWWAIGASLIASNISAEQ 63 Query: 67 FIGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGVSTA 126 IG SGSG+AIGL I++YEW+AAI LI+V KY LPIF+K+ +YTMPQ+L +RF+K V T Sbjct: 64 IIGMSGSGYAIGLAIASYEWMAAITLILVGKYMLPIFIKNEIYTMPQYLEQRFDKRVKTT 123 Query: 127 FAVFWLLVYVFVNLTSVSYLGALALDKIMGIPLQYGIIGLLIFSGIYSIYGGLEAVAWTD 186 A+FWL VY+ VNLT+V +LG LA++ + GI YG++ L +FS YS+YGGL+AVA+TD Sbjct: 124 LALFWLSVYILVNLTAVLWLGGLAIETVAGIDWLYGMVFLALFSLAYSLYGGLKAVAYTD 183 Query: 187 VVQVIILVAGGLITTFLALDAVGMGDGIFAGMSNLYNDAKDHFVMIMPQGRVMVPDGLGG 246 ++QV++L+ GGL+ ++LALD V G G+ AG L + +HF MI+ Q Sbjct: 184 IIQVVLLIFGGLLLSYLALDRVADGQGVLAGFDRLSSALPEHFEMILSQ----------- 232 Query: 247 SRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAGYLKLLMP 306 S + LPG++V++GG+W+ N+ YWGFNQYIIQ+ LAAKS+ EA+KG+ FA YLKLLMP Sbjct: 233 SNPHYMSLPGISVLVGGLWIMNISYWGFNQYIIQRALAAKSVAEAQKGIAFAAYLKLLMP 292 Query: 307 IIVVIPGIAAYVLINDYSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPNGIRGLAF 366 +IVV+PGIAA +L ++ D+AYP ++ +P G++GL F Sbjct: 293 LIVVLPGIAAVLLYPG-------------------LESPDQAYPSMMA-LMPAGVKGLVF 332 Query: 367 AALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAVVALAIAMIVA- 425 AAL AAIVSSLASM NS STIFTMDIY + +P + V GR+ ++++L IA+++A Sbjct: 333 AALVAAIVSSLASMTNSISTIFTMDIYAM-LRPAKSEGHYVLVGRLSSLISLLIALVMAQ 391 Query: 426 PQLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIATIPAGIVFKIFY 485 P L +Q FQYIQE+TG PG+VV+F G+ WR+AT+ AL A+ + + ++ Sbjct: 392 PLLGEFEQAFQYIQEFTGVFTPGIVVIFLTGMFWRRATSQGALAAALGSAIFSFGLRFYW 451 Query: 486 PEMPFLLRMGYVFIILCFIASLIS 509 PE+PF+ R+G VF++ ++ L+S Sbjct: 452 PELPFMDRIGLVFLLCLALSVLVS 475 Score = 32.0 bits (71), Expect = 7e-05 Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 7/89 (7%) Query: 541 GIICAVLGFALFNSY------EHVGIESIFMIAALFLMLGTILYTNVKMETADPKSFNTD 594 G + A LG A+F+ E ++ I ++ L L L ++L + + + S Sbjct: 432 GALAAALGSAIFSFGLRFYWPELPFMDRIGLVFLLCLAL-SVLVSLMGRSLEEGASVALG 490 Query: 595 PVLFNTTSSFNLGAAGIILIVGLLYYFFW 623 V F T +FN+ A G+++I+ LY +W Sbjct: 491 GVSFKTGRAFNVSALGVVVILNFLYVTWW 519 Lambda K H 0.327 0.142 0.427 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: 1084 Number of extensions: 56 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 624 Length of database: 519 Length adjustment: 36 Effective length of query: 588 Effective length of database: 483 Effective search space: 284004 Effective search space used: 284004 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 17 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