Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate BPHYT_RS02510 BPHYT_RS02510 C4-dicarboxylate ABC transporter
Query= SwissProt::P24943 (421 letters) >FitnessBrowser__BFirm:BPHYT_RS02510 Length = 426 Score = 329 bits (843), Expect = 1e-94 Identities = 153/404 (37%), Positives = 257/404 (63%), Gaps = 9/404 (2%) Query: 9 QIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68 Q+ + +I+GI +G + P +A ++P+GD F++LIKM++ PI+ ++V G+A + D+K Sbjct: 12 QVIVAIIIGIALGHFY---PNLAVDMKPLGDGFIKLIKMVIGPIIFCTVVTGIAGMEDMK 68 Query: 69 KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNMK--SLEKTDIQSYVDTTNEVQ 126 K+G++GGK ++YFEI++T A+V+GL+A ++ +PG G N+ +L+ + SY + Sbjct: 69 KVGRVGGKALLYFEIVSTFALVLGLIATHVLKPGVGFNIDPATLDGKAVASYAA---KAH 125 Query: 127 HHSMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAM 186 + V+ ++++P + + +G++L I+ +++FG +A GEKGK V F G + + Sbjct: 126 GQTTVDFLMHLIPDTLVSAFAQGEILQILLIALLFGAVLATAGEKGKVVTSFIDGLSHVL 185 Query: 187 FYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVAKLF 246 F + I K AP G F + T+ K+G+ SL+P+ KL+ Y T + F+ VVLG +A+ Sbjct: 186 FGIVRIITKLAPIGAFGAMAFTIGKYGIGSLLPMLKLIGTFYLTSIVFVVVVLGIIARAV 245 Query: 247 GINIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNLDGS 306 G NI + +K+E+++ T+SSE LP++M K+E GC +++ V+PTGYSFNLDG+ Sbjct: 246 GFNILRFVAYIKEEMLIVLGTSSSEAALPQLMLKLEKLGCSRSVVGLVVPTGYSFNLDGT 305 Query: 307 TLYQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTV-GIP 365 +Y +A +FIAQ D+ +QQ++LL V M+TSKG +GV G F+ L ATL V IP Sbjct: 306 NIYMTMAVLFIAQATNTDLTWTQQLTLLAVTMLTSKGASGVTGAGFITLAATLAVVPTIP 365 Query: 366 IEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409 + G+ I GIDR + R N++GN +A +++S WE + + K Sbjct: 366 LSGMVLILGIDRFMSECRALTNIVGNGVATVVVSAWEKELDRNK 409 Lambda K H 0.326 0.143 0.404 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: 429 Number of extensions: 22 Number of successful extensions: 3 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: 421 Length of database: 426 Length adjustment: 32 Effective length of query: 389 Effective length of database: 394 Effective search space: 153266 Effective search space used: 153266 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: 51 (24.3 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