Align Sodium: solute symporter family protein (characterized, see rationale)
to candidate Echvi_1267 Echvi_1267 probable sodium:solute symporter, VC_2705 subfamily
Query= uniprot:E4PHQ0 (588 letters) >FitnessBrowser__Cola:Echvi_1267 Length = 567 Score = 677 bits (1747), Expect = 0.0 Identities = 351/580 (60%), Positives = 427/580 (73%), Gaps = 21/580 (3%) Query: 9 IFVGGSFLLYIAIAIWAKAGSTSDFYVAGGGVHPITNGAAIGADWMSAASFISMAGLIAA 68 I VG SF LYI IAIW++AGST +FYVAGGGV P+ NG A GADWMSAASFISMAGLI+ Sbjct: 9 ILVGLSFALYIGIAIWSRAGSTKEFYVAGGGVSPLANGMATGADWMSAASFISMAGLISF 68 Query: 69 GGYANSTFLMGWTGGYVLLAMLLAPYLRKFGKFTVPEFIGDRFYSKNARLVAVICLIVAS 128 GY S +LMGWTGGYVLLA+LLAPYLRKFGKFTVP+F+GDR+YS AR+VAV C I S Sbjct: 69 MGYDGSVYLMGWTGGYVLLALLLAPYLRKFGKFTVPDFVGDRYYSNKARVVAVFCAIFIS 128 Query: 129 VTYVIGQMAGAGVAFSRFLEVDSTVGLMIAAVVVFVYAVMGGMKGITYTQVAQYCVLIVA 188 TYV GQM G G+ FSR+LEVD G++I +VF YAV+GGMKGITYTQVAQYCVLI A Sbjct: 129 FTYVAGQMRGVGIVFSRYLEVDINTGVIIGMCIVFFYAVLGGMKGITYTQVAQYCVLIFA 188 Query: 189 YTIPAVFISLQLTGNPIPGLGLFSTHVDSGMPILSKLNQVITDLGFNEYTADIDNKLNMV 248 + +PA+FIS+QLT NPIP LGL T D G +L KL+ V+TDLGF+ YT+ + +M Sbjct: 189 FMVPAIFISMQLTSNPIPQLGLGGTVAD-GTYLLDKLDGVLTDLGFHAYTSGKKSMGDMF 247 Query: 249 LFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWALVFIALLYLTAPAVASMARLNLMT 308 TL+LM+GTAGLPHVI+RFFTVP+V DAR SAG+ALVFIA+LY TAPAV++ N + Sbjct: 248 AITLALMVGTAGLPHVIVRFFTVPRVKDARLSAGYALVFIAILYTTAPAVSAFGIYNAI- 306 Query: 309 TIYPDGTSAEPIQYDERPNWIKEWEITGLIQFTDKNEDGRIQLYNDSEAFAPTAEARGWN 368 D S +PI D+ P W+ W+ T LI+ DKN+DG +Q D E Sbjct: 307 ----DSVSEKPI--DDLPEWVTNWQQTQLIKINDKNQDGVVQYVADPER----------- 349 Query: 369 GNELVVNRDILVLANPEIANLPGWVIGLIAAGGLAAALSTAAGLLLAISSAVSHDLIKGS 428 NE +++DI+VLANPEIA LP WV+GL+AAGG+AAALSTAAGLLL IS++VS DL K + Sbjct: 350 -NEFTIDKDIMVLANPEIAQLPNWVVGLVAAGGMAAALSTAAGLLLVISTSVSRDLAK-N 407 Query: 429 INPAISEKGELLAARISMAVAIVVATYLGANPPGFAAQVVALAFGIAAASLFPALMMGIF 488 NP IS+K ELL AR++ AVA++VA Y G NPPGF A+VVA AFG+AAAS FP ++MGIF Sbjct: 408 FNPGISDKKELLIARVAAAVAVIVAGYFGVNPPGFVAEVVAFAFGLAAASFFPVIIMGIF 467 Query: 489 SKRVNNTGAIAGMLSGLTFTLVYIFVYKGWLFIPGTNNLPDTPDNWVLGISPLSIGAIGA 548 SKR+N GAI GML GL FTL YI +K + G T ++W GISP IG+IG Sbjct: 468 SKRMNKEGAIWGMLVGLVFTLSYIIYFKFGTDLFGIPAESLTAEHWWFGISPEGIGSIGM 527 Query: 549 IVNFAVAFIVSNATEEPPVEIQELVESVRYPRGAGQAQDH 588 ++NF V+F+VS T PP +QE+VE +R PRGAGQAQ H Sbjct: 528 VLNFLVSFVVSRVTPAPPEAVQEMVEDIRIPRGAGQAQGH 567 Lambda K H 0.323 0.138 0.413 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: 1063 Number of extensions: 50 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: 588 Length of database: 567 Length adjustment: 36 Effective length of query: 552 Effective length of database: 531 Effective search space: 293112 Effective search space used: 293112 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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