Align SSS sodium solute transporter (characterized, see rationale)
to candidate 3610523 Dshi_3904 SSS sodium solute transporter superfamily (RefSeq)
Query= uniprot:L0FZT5 (624 letters) >FitnessBrowser__Dino:3610523 Length = 526 Score = 248 bits (634), Expect = 4e-70 Identities = 148/481 (30%), Positives = 247/481 (51%), Gaps = 45/481 (9%) Query: 1 MSAGFSTLDYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAA 60 + A + LDY + VY ++++G+WV+R + T ++ FLA +SL W A+G SL A+ Sbjct: 5 IDANLTMLDYGVIAVYLAIVIAIGVWVARKTR----TGEDLFLAGRSLGWAAIGFSLFAS 60 Query: 61 NISAEHFIGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFN 120 NIS +G +GS + GL +S+YEW+A I L+ +A F P+FLK + T P++L R++ Sbjct: 61 NISTSTLVGLTGSAYTGGLTVSSYEWMAGIPLLFMAFIFAPVFLKSRISTTPEYLENRYS 120 Query: 121 KGVSTAFAVFWLLVYVFVNLTSVSYLGALALDKIM-GIPLQYGIIGLLIFSGIYSIYGGL 179 + V F+ ++ V V+ Y GA+ L + + + + +F+GIY+ GGL Sbjct: 121 RRVRLYFSGLTIVFTVIVDTAGGLYAGAVVLKVFFPDLDIWMSCVAIGLFAGIYTATGGL 180 Query: 180 EAVAWTDVVQVIILVAGGLITTFLALDAVGMGDGIFAGMSNLYNDAKDHFVMIMPQGRVM 239 AV +TD++Q ++L+ G +T FL +V F+ S + H ++ P Sbjct: 181 RAVVYTDILQAVVLICGTGLTAFLMYQSVD-----FSWESVRSQVPEGHLSIVQPIDDDT 235 Query: 240 VPDGLGGSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAG 299 +P PGL G+WL YW NQYI+Q+ L AK + A+ G + G Sbjct: 236 LP------------WPGL---FTGVWLLGFWYWVTNQYIVQRVLGAKDLSNAQWGAILGG 280 Query: 300 YLKLLMPIIVVIPGIAAYVLINDYSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPN 359 LK+L +++PG+ A V + D IQ SD+ +P ++ +P+ Sbjct: 281 ILKILPTFFIILPGVMALVTLPD-------------------IQNSDQVFPIIITEVLPS 321 Query: 360 GIRGLAFAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAVVALA 419 G+ GL A L AAI+S++ S +NS+ST+ D + + + + G + + + Sbjct: 322 GLTGLVMAGLIAAIMSTVDSTLNSSSTLLIND-FLTRPEKEPDPETAKKWGMMATLGFMV 380 Query: 420 IAMIVAPQLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIATIPAGI 479 IA+ AP + ++ YIQ+ + P +VV F +G +W + T +AA WT I G+ Sbjct: 381 IAIAWAPLIQYFGGLWAYIQQAFSVLVPPLVVCFTLGALWSRGTENAAFWTLIIGHTLGL 440 Query: 480 V 480 V Sbjct: 441 V 441 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: 941 Number of extensions: 62 Number of successful extensions: 7 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: 526 Length adjustment: 36 Effective length of query: 588 Effective length of database: 490 Effective search space: 288120 Effective search space used: 288120 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