Align Sodium: solute symporter family protein (characterized, see rationale)
to candidate HSERO_RS03215 HSERO_RS03215 sodium:solute symporter
Query= uniprot:E4PHQ0 (588 letters) >FitnessBrowser__HerbieS:HSERO_RS03215 Length = 683 Score = 209 bits (531), Expect = 4e-58 Identities = 127/351 (36%), Positives = 192/351 (54%), Gaps = 38/351 (10%) Query: 233 GFNEYTADIDNKLNMVLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWALVFIALLY 292 G ++ ++DI N + LM+GTA LPH+++R++T P VA AR S W L FI L+Y Sbjct: 367 GRDQESSDIKRN-NFLALVFCLMLGTAALPHILMRYYTTPTVAGARTSVFWTLFFIMLIY 425 Query: 293 LTAPAVASMARLNLMTTIYPDGTSAEPIQYDERPNWIKEW----EITGLIQFTDKNEDGR 348 LT PA+ + + ++ T++ G+S Y P+W+ W ++ L+ TD N DG Sbjct: 426 LTVPALTVLVKYDIYTSLV--GSS-----YSHLPDWVYYWANMDKLNPLVSITDLNRDGL 478 Query: 349 IQLYNDSEAFAPTAEARGWNGNELVVNRDILVLANPEIANLPGWVIGLIAAGGLAAALST 408 +QL E+ ++ DI+VLA PEIA LP +V GL+AAGGLAAALST Sbjct: 479 VQL------------------GEISMDGDIIVLAMPEIAGLPYFVSGLVAAGGLAAALST 520 Query: 409 AAGLLLAISSAVSHDLIKGSINPAISEKGELLAARISMAVAIVVATYLGANPPGFAAQVV 468 A GLLL IS+A+SHD+ ++P+ S + + +++ + V ++A Y + PG +V Sbjct: 521 ADGLLLTISNALSHDVYYKVVDPSASTQKRVTISKLLLLVVALLAAYAASLKPGDILSMV 580 Query: 469 ALAFGIAAASLFPALMMGIFSKRVNNTGAIAGMLSGLTFTLVYIFVYKGWLFIPGTNNLP 528 AF +AA++LFPAL++G+F KR N GAIAG+L G + Y+ + + Sbjct: 581 GAAFSLAASTLFPALVLGVFWKRANQAGAIAGILCGFLMCVYYM--------LHTNPSFG 632 Query: 529 DTPDNWVLGISPLSIGAIGAIVNFAVAFIVSNATEEPPVEIQELVESVRYP 579 + I+P+S G G V A IVS T P L++ +R P Sbjct: 633 GSAAGQWFHIAPISAGIFGVPVGMAAMVIVSLLTPPPDEATIALIDHIRTP 683 Score = 175 bits (443), Expect = 6e-48 Identities = 87/233 (37%), Positives = 143/233 (61%), Gaps = 12/233 (5%) Query: 6 INIIFVGGSFLLYIAIAIWAKAGSTSDFYVAGGGVHPITNGAAIGADWMSAASFISMAGL 65 I +F+ + LY I + + ++YVAG V P+ NG A ADW+SAA+FIS+AG Sbjct: 42 IGYLFLFVTIGLYAGIGVVCRTSDVPEYYVAGRRVPPLFNGMATAADWISAATFISLAGG 101 Query: 66 IAAGGYANSTFLMGWTGGYVLLAMLLAPYLRKFGKFTVPEFIGDRFYSKNA-------RL 118 + G+ +++GWTGGY L+A+L+APYLRKFG++T+ +F+ R+ + R+ Sbjct: 102 LYLQGFDGLAYILGWTGGYCLVALLIAPYLRKFGQYTIADFLAARYPGRPGSQGVNVIRI 161 Query: 119 VAVICLIVASVTYVIGQMAGAGVAFSRFLEVDSTVGLMIAAVVVFVYAVMGGMKGITYTQ 178 +AV I+ S TYV+ Q+ G G+ SRF +D ++G+ + + V + +GGM+ IT+TQ Sbjct: 162 LAVAATILISFTYVVAQIYGVGLITSRFTGIDFSIGIFLGLASILVCSFLGGMRAITWTQ 221 Query: 179 VAQYCVLIVAYTIPAVFISLQLTGNPIPGLGLFSTHVDSGMPILSKLNQVITD 231 VAQY ++++AY IP +++S + T P+P + + +P LS + Q + D Sbjct: 222 VAQYIIILLAYLIPVIWLSAKHTTVPVPPVAYGAV-----LPKLSAIEQRLED 269 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: 988 Number of extensions: 44 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 588 Length of database: 683 Length adjustment: 38 Effective length of query: 550 Effective length of database: 645 Effective search space: 354750 Effective search space used: 354750 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: 54 (25.4 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