Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate Ac3H11_1956 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1956 Length = 252 Score = 90.5 bits (223), Expect = 5e-23 Identities = 68/216 (31%), Positives = 106/216 (49%), Gaps = 15/216 (6%) Query: 208 GWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSLLILFAPISALL 267 GW + VSL AL + V+ + R R V+ W L F I L+ Sbjct: 39 GWTVSVSLLALVLALVLGSLIGTLRTLQDRPMIVRLGNA------WVEL---FRNIPLLV 89 Query: 268 YGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAISRGQTEA 327 ++ P + F G + F +++AL +T+A IAE VR+GIQA+ RGQ A Sbjct: 90 QIFLWYHVIPSL--FPVMKG---VPGFALVVLALGFFTSARIAEQVRSGIQALPRGQRYA 144 Query: 328 AYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTLGGITLN 387 A+G +T V+LP A R+I+PPL S+ +N+ KNSS+A AVS +L Sbjct: 145 GMAVGFTTFQTYRYVLLPMAFRIIIPPLTSETMNIFKNSSVAFAVSVAELT-MFAMQAQE 203 Query: 388 QTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKL 423 +T R +E L + +Y+ + I+ +M K +++ Sbjct: 204 ETSRGIEVYLAVTSLYIISAFAINRIMAFIEKRVRI 239 Score = 51.6 bits (122), Expect = 3e-11 Identities = 31/91 (34%), Positives = 51/91 (56%), Gaps = 1/91 (1%) Query: 70 DLAQTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNW-LVARIM 128 ++ Q+ D T+ ++ T+ VS+L +LA +LG++IG LR Q+ ++ R+ Sbjct: 16 EVVQSCFGKGGDITYLDWMLSAWGWTVSVSLLALVLALVLGSLIGTLRTLQDRPMIVRLG 75 Query: 129 TVYVETFRNIPLLLWILLMGTILAETRPVPK 159 +VE FRNIPLL+ I L ++ PV K Sbjct: 76 NAWVELFRNIPLLVQIFLWYHVIPSLFPVMK 106 Lambda K H 0.326 0.139 0.419 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: 196 Number of extensions: 10 Number of successful extensions: 4 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: 426 Length of database: 252 Length adjustment: 28 Effective length of query: 398 Effective length of database: 224 Effective search space: 89152 Effective search space used: 89152 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 (21.7 bits) S2: 48 (23.1 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