Align SSS sodium solute transporter (characterized, see rationale)
to candidate 3610525 Dshi_3906 SSS sodium solute transporter superfamily (RefSeq)
Query= uniprot:L0FZT5 (624 letters) >FitnessBrowser__Dino:3610525 Length = 533 Score = 264 bits (675), Expect = 6e-75 Identities = 163/474 (34%), Positives = 252/474 (53%), Gaps = 49/474 (10%) Query: 8 LDYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANISAEHF 67 +DY I ++Y + +++ G++VSR E+ A YFLA +SL W+ +G SL A+N+S F Sbjct: 11 IDYAIVVIYFIGVIAHGVYVSRKN---EEGADGYFLAGRSLPWYLIGFSLFASNMSGSSF 67 Query: 68 IGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGVSTAF 127 +G G +A G+ I YEW AA+ LI+ A + LP FLK + T+P+FL +R++ AF Sbjct: 68 VGLMGGAYANGIVIFNYEWTAALVLILFAIFVLPSFLKAKISTVPEFLEQRYDVRSRRAF 127 Query: 128 AVFWLLVYVFVNLTSVSYLGALALDKIMG-IPLQYGIIGLLIFSGIYSIYGGLEAVAWTD 186 ++F +L +F++ Y G L + + G + L + L + +GIY+I GGL AV TD Sbjct: 128 SIFTILAILFIDTAGALYAGGLVISNVTGYLNLWTAVAVLALVAGIYTILGGLSAVVVTD 187 Query: 187 VVQVIILVAGGLITTFLALDAVGMGDGIFAGMSNLYNDAKDHFVMIMPQGRVMVP-DGLG 245 VQ I+L+ G I +L LD +G + +F + + H +I+P +P GL Sbjct: 188 TVQAILLIIGAAILFWLGLDEIGGWEQLFVDI------PEGHDQLILPADDDFLPWTGLW 241 Query: 246 GSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAGYLKLLM 305 G V+L G + YW NQ+++Q+ L AK+++E + G LFAG+LKL Sbjct: 242 G------------VVLLGFY-----YWTINQFVVQRTLGAKNLKEGQIGALFAGFLKLPN 284 Query: 306 PIIVVIPGIAAYVLINDYSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPNGIRGLA 365 +++IPG+ A L PE ++ D A+P L +P G+RGL Sbjct: 285 IFLMIIPGVIALKLY----PE---------------LETPDLAFPTLAFELMPIGVRGLI 325 Query: 366 FAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAVVALAIAMIVA 425 AAL AAI+SSL S +NS ST+ D + ++ + + V GR+V + I A Sbjct: 326 MAALIAAIMSSLDSAMNSASTLVVKDFVEPIWE--VDEGKQVWIGRLVTGAVMVFGAIYA 383 Query: 426 PQLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIATIPAGI 479 P +A + +F Y Q YI P +VVV+ +GL + A WT I + GI Sbjct: 384 PSIAGFESLFSYFQSSLSYIIPTIVVVYIVGLFVPWLNGNGAFWTIILGLVVGI 437 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: 1094 Number of extensions: 76 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: 624 Length of database: 533 Length adjustment: 36 Effective length of query: 588 Effective length of database: 497 Effective search space: 292236 Effective search space used: 292236 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