Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate YP_004144924.1 Mesci_5852 sodium:dicarboxylate symporter
Query= CharProtDB::CH_088342 (421 letters) >NCBI__GCF_000185905.1:YP_004144924.1 Length = 452 Score = 338 bits (868), Expect = 1e-97 Identities = 163/406 (40%), Positives = 265/406 (65%), Gaps = 9/406 (2%) Query: 9 QIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68 Q+ + LG+ VG ++ G + L+P+GD F++L+KMI+ P++ ++ G+A + DLK Sbjct: 43 QVLTAIALGVAVGYLYPGTGEA---LKPLGDAFIKLVKMIIAPVIFLTVTTGIAGMNDLK 99 Query: 69 KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMK--SLEKTDIQSYVDTTNEVQ 126 K+G++ GK +IYF +++A++VGL+ AN+ QPG+G+++ SL+ +Q YV +V Sbjct: 100 KVGRVAGKAMIYFLTFSSLALMVGLVVANVVQPGSGLDIDPASLDGQAVQGYVA---KVH 156 Query: 127 HHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAM 186 S+ +NI+P I + + G++L ++FFS++FG +A G+ GKPVL Q + Sbjct: 157 DQSVTGFLMNIIPSTIVGAFAEGNILQVLFFSILFGSALAMAGDTGKPVLSLLQALLAPV 216 Query: 187 FYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVAKLF 246 F + +M+ AP G F + T+ K+G+ S++ L+ LV Y T F+F +LG V + Sbjct: 217 FKLVGILMQAAPVGAFGAMAFTIGKYGIGSVVNLAMLVATFYFTAFVFVFGILGAVCRYN 276 Query: 247 GINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNLDGS 306 G +IF +++ +K+EL+L +T+SSE LP +M+KMEK G +++ VIPTGYSFNLDG+ Sbjct: 277 GFSIFSLVRYIKEELLLVLATSSSEAALPSLMEKMEKAGAKRSVVGLVIPTGYSFNLDGT 336 Query: 307 TLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTV-GIP 365 +Y LAA+FIAQ +SV+ QI LL+V M++SKG AG+ G FV L ATL + +P Sbjct: 337 NIYMTLAALFIAQATNTHLSVADQILLLVVAMLSSKGAAGITGAGFVTLAATLSVIPTVP 396 Query: 366 VEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEKGK 411 V G+A I G+DR + R NV+GN++AA+++++WEG+ +E + K Sbjct: 397 VAGMALILGVDRFMSECRALTNVVGNAVAALVVARWEGELDEARMK 442 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: 400 Number of extensions: 18 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: 452 Length adjustment: 32 Effective length of query: 389 Effective length of database: 420 Effective search space: 163380 Effective search space used: 163380 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 24 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