Align SSS sodium solute transporter (characterized, see rationale)
to candidate Echvi_3497 Echvi_3497 transporter, SSS family
Query= uniprot:L0FZT5 (624 letters) >FitnessBrowser__Cola:Echvi_3497 Length = 527 Score = 244 bits (622), Expect = 9e-69 Identities = 162/554 (29%), Positives = 283/554 (51%), Gaps = 54/554 (9%) Query: 13 FIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANISAEHFIGTSG 72 FI + L +V+V W+ K+ L+ + YFL +SLT + S++ NIS EH +G +G Sbjct: 8 FIAFTL-LVAVYAWLKTRKENLD-SEDGYFLGGRSLTGVVIAGSMIMTNISTEHLVGMNG 65 Query: 73 SGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGVSTAFAVFWL 132 S + G I A+E +A+ALI+ A YF+P +LK G+ T+PQ+L RF+ G + A F L Sbjct: 66 SSYKNGFVIVAWEVTSALALIVAAVYFVPRYLKMGLTTVPQYLENRFDAGTRSLVAFFLL 125 Query: 133 LVYVFVNLTSVSYLGALALDKIMGIP----------LQYGIIGLLIFSGIYSIYGGLEAV 182 + + L V Y GA+ L+ + I L Y ++ + IY+I+GGL+AV Sbjct: 126 ISFAVTLLPIVLYTGAINLESLFNISDTLNISQEQGLWYTVLAVGGIGSIYAIFGGLKAV 185 Query: 183 AWTDVVQVIILVAGGLITTFLALDAVGMGDGIFAGMSNLYNDAKDHFVMIMPQGRVMVPD 242 A +D + L+ GL+ +AL +G + + G+ ++ ++ + F ++ Sbjct: 186 AVSDTINGYGLLLAGLMVPVIALFMIGDNNPLL-GLERVFENSPEKFNVV---------- 234 Query: 243 GLGGSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAGYLK 302 G +D+ LP + + G+ + L +W NQ IIQ+ L AK+++EA+KGLL+ G LK Sbjct: 235 ---GGKDSV--LP-FSTLFTGLIINQLYFWCMNQTIIQRALGAKNLKEAQKGLLYTGALK 288 Query: 303 LLMPIIVVIPGIAAYVLINDYSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPNGIR 362 LL+P I+V+PG+ + D + D YP L++ +P G+ Sbjct: 289 LLVPFIIVLPGVIGFYFFGD-----------------RLYENQDMVYPELVKKVLPVGLT 331 Query: 363 GLAFAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAVVALAIAM 422 G+ A + A++S+ S++NS STIF++DIYK +P A+ QLV+ G++ A + +M Sbjct: 332 GVFAAVIMGAVLSTFNSVLNSASTIFSIDIYKRLIRPGASAGQLVKAGKLSATILAITSM 391 Query: 423 IVAPQLASLDQ-VFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIATIPAGIVF 481 + AP +A+ + +FQ +Q+ G + + + G + + AA + + ++ Sbjct: 392 VAAPMVANAPEGLFQLLQQLNGIFFIPIASIMLAGFFTKWVSPLAAKVALVTGLTFYVLT 451 Query: 482 K-IFYPEMPFLLRMGYVFIILCFIASLISFA------EKKKFANPDYKTNKQAAKTVASS 534 +F + F+ G F++ I ++S A +K + T+K ++ S Sbjct: 452 TFVFDIGIHFVHIWGIEFVLNVLIMYVVSVAWPMAKPTEKTLISAKINTDKWKYASLVSI 511 Query: 535 YFFIILGIICAVLG 548 II +I +LG Sbjct: 512 ILVIITVVIYMLLG 525 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: 914 Number of extensions: 58 Number of successful extensions: 4 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: 527 Length adjustment: 36 Effective length of query: 588 Effective length of database: 491 Effective search space: 288708 Effective search space used: 288708 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