Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate AO353_02800 AO353_02800 C4-dicarboxylate transporter
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__pseudo3_N2E3:AO353_02800 Length = 444 Score = 344 bits (883), Expect = 3e-99 Identities = 170/413 (41%), Positives = 272/413 (65%), Gaps = 9/413 (2%) Query: 6 LAWQIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVG 65 L +Q+ I + +GI +G + P+ A L+P+GD F++LIKM++ PI+ ++V G+A + Sbjct: 11 LYFQVIIAIAIGIALGHYY---PQTAVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQ 67 Query: 66 DLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAG--VNMKSLEKTDIQSYVDTTN 123 ++K +GK GG ++YFEI++TIA++VGL+ NI QPG G +++ +L+ + + +YV Sbjct: 68 NMKSVGKTGGYALLYFEIVSTIALLVGLVVVNIVQPGNGMHIDVSTLDASKVAAYVAAGA 127 Query: 124 EVQHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTA 183 + S+V +NI+P I + + GD+L ++ FSV+FG + +G GKP+L F A Sbjct: 128 D---QSVVGFLLNIIPATIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPILDFIDRFA 184 Query: 184 EAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVA 243 MF + N IMK AP G + T+ +GV SL+ L +L+ Y T + FI VLGG+A Sbjct: 185 HVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMACFYITCVVFILVVLGGIA 244 Query: 244 KLFGINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNL 303 + G ++ +I+ +++EL++ T+SSE+VLPR++ KME+ G K++ VIPTGYSFNL Sbjct: 245 RAHGFSVLKVIRYIREELLIVLGTSSSESVLPRMLIKMERLGAKKSVVGLVIPTGYSFNL 304 Query: 304 DGSTLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG 363 DG+ +Y +AA+FIAQ M ++ QI+LL+VL+++SKG AGV G F+VL ATL VG Sbjct: 305 DGTAIYLTMAAVFIAQATDTHMDITHQITLLVVLLLSSKGAAGVTGSGFIVLAATLSAVG 364 Query: 364 -IPVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEKGKQYLA 415 +PV GLA I GIDR + AR N++GN++A ++++KW + + ++ + LA Sbjct: 365 HLPVAGLALILGIDRFMSEARALTNLVGNAVATLVVAKWVKELDVDQMHEELA 417 Lambda K H 0.326 0.143 0.402 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: 373 Number of extensions: 14 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: 444 Length adjustment: 32 Effective length of query: 389 Effective length of database: 412 Effective search space: 160268 Effective search space used: 160268 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