Align L-glutamine and L-histidine transporter (characterized)
to candidate N515DRAFT_0606 N515DRAFT_0606 basic amino acid/polyamine antiporter, APA family
Query= reanno::Korea:Ga0059261_1577 (470 letters) >FitnessBrowser__Dyella79:N515DRAFT_0606 Length = 477 Score = 315 bits (807), Expect = 2e-90 Identities = 180/438 (41%), Positives = 261/438 (59%), Gaps = 15/438 (3%) Query: 32 LVALGVGAIVGTGILTLIGVGAG-KAGPAVIMSFVIAGAICACAALAYAEMATMMPASGS 90 L A+G+G I+G G+ L G A AGPAV +SF+IAG A AAL YAE A ++P +GS Sbjct: 35 LTAIGIGGIIGVGVFVLAGQQAALNAGPAVAISFLIAGIASAAAALCYAEFAGLIPVTGS 94 Query: 91 AYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVAVGWSGYAAPLLHAWTGMPLELMA---- 146 AY Y YAVLGE+ AW++GW L+LEY+L+V+ VA+GWSGY L A G+ L + A Sbjct: 95 AYTYGYAVLGELAAWLIGWDLLLEYALIVAVVAIGWSGYVQSAL-ASIGVDLPVWAKGAI 153 Query: 147 GPHANGIVNLPAIFIIAVVAGLLCLGTKESATLNAALVVVKIIALAVFVAVALPYFNGAN 206 G + N+ A + V+ LL T+ A N +V +K+ A+A+ + V Y N Sbjct: 154 GTGEGHVFNVVAALVTLGVSALLIFRTEWGARFNTFVVAIKVAAVALVIGVGAFYVKPEN 213 Query: 207 LEPFAPFGFAKTISPDGVE----RGVMAAAAIIFFAFYGFDAISTAAEETKNPGRDLAIG 262 PF P + + DGV +GV AAA++FFA +G+D ++TAAEE+KNP RDL Sbjct: 214 WVPFIP---ERIVGSDGVGHFGFQGVATAAAVVFFAVFGYDTLTTAAEESKNPQRDLPRA 270 Query: 263 IVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLALILRDLGRPGFATFLAVSAIIALP 322 ++ S+ +A+Y+ V++ G +T + P+A + LG A ++VSA+ L Sbjct: 271 VLLSLGISMAMYLAVSMVLTGIAHYTTL-KTDAPVADAFKGLGLHWVALTVSVSAVFGLI 329 Query: 323 TVLLGFLFGQSRIFFTMARDGMLPIGLAKVSKR-GSPVRITLFTAAIVAVIAGLLPIDEI 381 +VL F+ G +RI+F +ARDG+LP AK R G+P R T+ A++AGLLPI+E+ Sbjct: 330 SVLFAFMLGATRIWFALARDGLLPGWFAKPHPRYGTPHRPTIVLGVFTALVAGLLPIEEV 389 Query: 382 AALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPLWWLVGAIAVLGCIYLFFSLPVKT 441 A L N G L+AF + +++LR R PD+ R FRTPL L+ + + I+L LP T Sbjct: 390 AKLVNIGVLSAFIVICSSVLILRKRKPDLYRAFRTPLVPLIPLVGIGFSIWLLAELPWVT 449 Query: 442 QLWFLAWNALGVVIYFAY 459 FL W ++G+V+YF Y Sbjct: 450 WEVFLIWVSIGLVVYFGY 467 Lambda K H 0.327 0.140 0.426 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: 715 Number of extensions: 49 Number of successful extensions: 5 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: 470 Length of database: 477 Length adjustment: 33 Effective length of query: 437 Effective length of database: 444 Effective search space: 194028 Effective search space used: 194028 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: 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