Align L-glutamine and L-histidine transporter (characterized)
to candidate N515DRAFT_2925 N515DRAFT_2925 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= reanno::Korea:Ga0059261_1577 (470 letters) >FitnessBrowser__Dyella79:N515DRAFT_2925 Length = 480 Score = 308 bits (788), Expect = 3e-88 Identities = 169/450 (37%), Positives = 257/450 (57%), Gaps = 17/450 (3%) Query: 23 LAATLSWPHLVALGVGAIVGTGILTLIGVGAGK-AGPAVIMSFVIAGAICACAALAYAEM 81 L TL + ALG+GA++GTGI + G A + AGPAV++SF++A AL YAE Sbjct: 24 LRRTLGKWGITALGIGAVIGTGIFVVTGQAAAEHAGPAVLISFMLAAICSGFTALCYAEF 83 Query: 82 ATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVAVGWSGYAAPLL-HAWTGM 140 AT++P SGS+Y+Y+YA LGE++AW +GW+++LEY + S VA W+GY LL H + Sbjct: 84 ATLIPISGSSYSYAYATLGELVAWFIGWNMVLEYGISASAVAASWTGYFTSLLDHVGIHL 143 Query: 141 PLELMAGPHA---------NGIVNLPAIFIIAVVAGLLCLGTKESATLNAALVVVKIIAL 191 P+ L P A ++NLPA+ I+ + L +G +ES+ LN +V +K+ + Sbjct: 144 PVALTEAPLAFKDGHLVTTGHLLNLPAVAIVLALTWLCYVGIRESSGLNVLMVALKVGLI 203 Query: 192 AVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFAFYGFDAISTAAEE 251 V V Y + AN PF P A+ G+M AA++FFA+ GF+A STAA+E Sbjct: 204 IVVVVAGYRYVDPANWHPFIP---AEQEPGKYGWSGIMRGAAMVFFAYIGFEATSTAAQE 260 Query: 252 TKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLALILRDLGRPGFAT 311 KNP +DL G + S++ C +Y+ +A G P+T S EP+ +R+ G+ Sbjct: 261 CKNPQKDLPFGTLVSLVICTVLYLAMAAVLTGLIPYTELGTS-EPVVTAIRNHPELGWLR 319 Query: 312 FLA-VSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKV-SKRGSPVRITLFTAAIV 369 + + A+I L +V+L + Q RIF M+RDG+LP ++ K +P T+ T + Sbjct: 320 LVVEIGAMIGLSSVILVMIIAQPRIFMIMSRDGLLPPVFNRIHPKHRTPHLNTVITGIGI 379 Query: 370 AVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPLWWLVGAIAVLG 429 A++A + P+D +A L + GTL AF AV +++LR AP++PR+FR P W V V Sbjct: 380 AILAAVFPLDLLADLTSMGTLIAFVAVCAGVLILRYTAPELPRLFRVPAAWFVCTAGVFS 439 Query: 430 CIYLFFSLPVKTQLWFLAWNALGVVIYFAY 459 C+ L + + L + W A+G+ IYF Y Sbjct: 440 CLALLYFMAWFNWLLMIIWTAIGLAIYFGY 469 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: 628 Number of extensions: 35 Number of successful extensions: 7 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: 480 Length adjustment: 33 Effective length of query: 437 Effective length of database: 447 Effective search space: 195339 Effective search space used: 195339 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