Align SSS sodium solute transporter (characterized, see rationale)
to candidate 3610525 Dshi_3906 SSS sodium solute transporter superfamily (RefSeq)
Query= uniprot:L0FZF3 (547 letters) >FitnessBrowser__Dino:3610525 Length = 533 Score = 264 bits (675), Expect = 6e-75 Identities = 168/503 (33%), Positives = 255/503 (50%), Gaps = 47/503 (9%) Query: 6 LDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISAEQF 65 +D + V Y + +I G+ VSR+ + + + YFLA ++LPW+ +G SL ASN+S F Sbjct: 11 IDYAIVVIYFIGVIAHGVYVSRKNE---EGADGYFLAGRSLPWYLIGFSLFASNMSGSSF 67 Query: 66 IGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVRTVM 125 +G+ G +A G+ I YEW AA L++ AIF LP +LK I T+P+FL +RYD R R Sbjct: 68 VGLMGGAYANGIVIFNYEWTAALVLILFAIFVLPSFLKAKISTVPEFLEQRYDVRSRRAF 127 Query: 126 AIFWLLIYVFVNLTSVLYLGALSLETIMG-VPLTYGIIGLALFAMVYSIYGGLKAVAWTD 184 +IF +L +F++ LY G L + + G + L + LAL A +Y+I GGL AV TD Sbjct: 128 SIFTILAILFIDTAGALYAGGLVISNVTGYLNLWTAVAVLALVAGIYTILGGLSAVVVTD 187 Query: 185 VVQVVFLVAGGLATTYLALSLVGDGDVWEGIGILRKAAPSHFSMIIEKGEMMIPDGSGGS 244 VQ + L+ G +L L +G WE + + H +I+ + Sbjct: 188 TVQAILLIIGAAILFWLGLDEIGG---WEQLFV--DIPEGHDQLILP------------A 230 Query: 245 RDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLKLLMPL 304 D +L GL G+ ++ YW NQ++ QR L AK+L E Q G +FAGFLKL Sbjct: 231 DDDFLPWTGL----WGVVLLGFYYWTINQFVVQRTLGAKNLKEGQIGALFAGFLKLPNIF 286 Query: 305 IVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTL-LHLLPPGLKGLAFAALT 363 +++IPG+ A + + L D A+PTL L+P G++GL AAL Sbjct: 287 LMIIPGVIALKLYPE----------------LETPDLAFPTLAFELMPIGVRGLIMAALI 330 Query: 364 AAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIAAIVAPQLRQ 423 AAI+SSL S NS ST+ D + + V EGKQV IGR+ + AI AP + Sbjct: 331 AAIMSSLDSAMNSASTLVVKDFVEPIW--EVDEGKQVWIGRLVTGAVMVFGAIYAPSIAG 388 Query: 424 LDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLSAAFKVITPNLPF 483 + F Y Q ++ P + ++I G F N A +L + + ++ Sbjct: 389 FESLFSYFQSSLSYIIPTIVVVYIVGLFVPWLNGNGAFWTIILGLVVGIPLFIMKEVTGV 448 Query: 484 IDRMG---VVFLVLSVLIIAISL 503 MG + + ++S L++ + L Sbjct: 449 WAGMGLPEIHYTIMSTLMMCLGL 471 Lambda K H 0.326 0.140 0.414 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: 888 Number of extensions: 63 Number of successful extensions: 5 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: 547 Length of database: 533 Length adjustment: 35 Effective length of query: 512 Effective length of database: 498 Effective search space: 254976 Effective search space used: 254976 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 (21.6 bits) S2: 52 (24.6 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