Align SSS sodium solute transporter (characterized, see rationale)
to candidate 17739 b3679 predicted transporter (NCBI)
Query= uniprot:L0FZT5 (624 letters) >FitnessBrowser__Keio:17739 Length = 571 Score = 211 bits (537), Expect = 7e-59 Identities = 171/586 (29%), Positives = 277/586 (47%), Gaps = 57/586 (9%) Query: 6 STLDYVIFIVYALAIVSVGLW-VSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANISA 64 ++L + F+ + L + + W V +T G + Q YFLA +SL + ASL+ N+S Sbjct: 2 NSLQILSFVGFTLLVAVITWWKVRKTDTGSQ---QGYFLAGRSLKAPVIAASLMLTNLST 58 Query: 65 EHFIGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGVS 124 E +G SG + G+ + +E +A+ LI +A FLP +LK G+ T+P FL ER++K Sbjct: 59 EQLVGLSGQAYKSGMSVMGWEVTSAVTLIFLALIFLPRYLKRGIATIPDFLEERYDKTTR 118 Query: 125 TAFAVFWLLVYVFVNLTSVSYLGALALDKI--MGIPLQYG-------IIGLLIFSGI-YS 174 +L+ L V Y GALAL+ + +G LQ ++ LL +GI Y+ Sbjct: 119 IIIDFCFLIATGVCFLPIVLYSGALALNSLFHVGESLQISHGAAIWLLVILLGLAGILYA 178 Query: 175 IYGGLEAVAWTDVVQVIILVAGGLITTFLALDAVGMGDGIFAGMSNLYNDAKDHFVMIMP 234 + GGL A+A D + I LV GGL+ L A+G G G+ L + Sbjct: 179 VIGGLRAMAVADSINGIGLVIGGLMVPVFGLIAMGKG-SFMQGIEQLTTVHAEKL----- 232 Query: 235 QGRVMVPDGLGGSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKG 294 + +GG D LP + G+ L N YW NQ I+Q+ LA+KS+ E +KG Sbjct: 233 -------NSIGGPTD---PLP-IGAAFTGLILVNTFYWCTNQGIVQRTLASKSLAEGQKG 281 Query: 295 LLFAGYLKLLMPIIVVIPGIAAYVLINDYSPEQLAAILNMPVEHIGTIQKSDEAYPWLLR 354 L LK+L P+++V+PG+ A+ L D + K+D AYP L+ Sbjct: 282 ALLTAVLKMLDPLVLVLPGLIAFHLYQD-------------------LPKADMAYPTLVN 322 Query: 355 NFIPNGIRGLAFAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVA 414 N +P + G A L A++S+ +NS ST+F+M IY+ NA QLV GR Sbjct: 323 NVLPVPMVGFFGAVLFGAVISTFNGFLNSASTLFSMGIYRRIINQNAEPQQLVTVGRKFG 382 Query: 415 VVALAIAMIVAPQLASLDQ-VFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAA-LWTAI 472 ++++VAP +A+ Q ++ ++++ G +V + MG + + A AA + I Sbjct: 383 FFIAIVSVLVAPWIANAPQGLYSWMKQLNGIYNVPLVTIIIMGFFFPRIPALAAKVAMGI 442 Query: 473 ATIPAGIVFKIFYPEMPFLLRMGYVFIILCFIASLISFAEKK--KFANPD-YKTNKQAAK 529 I + + + FL + F I + +I F + + F D + + + K Sbjct: 443 GIISYITINYLVKFDFHFLYVLACTFCINVVVMLVIGFIKPRATPFTFKDAFAVDMKPWK 502 Query: 530 TVASSYFFIILGIICAVLGFALFNSY--EHVGIESIFMIAALFLML 573 V + I+ +I G A F Y + + S F+ A + + L Sbjct: 503 NVKIASIGILFAMIGVYAGLAEFGGYGTRWLAMISYFIAAVVIVYL 548 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: 1000 Number of extensions: 75 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: 571 Length adjustment: 37 Effective length of query: 587 Effective length of database: 534 Effective search space: 313458 Effective search space used: 313458 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