Align L-glutamine and L-histidine transporter (characterized)
to candidate RR42_RS01585 RR42_RS01585 amino acid permease
Query= reanno::Korea:Ga0059261_1577 (470 letters) >FitnessBrowser__Cup4G11:RR42_RS01585 Length = 464 Score = 370 bits (950), Expect = e-107 Identities = 204/463 (44%), Positives = 278/463 (60%), Gaps = 16/463 (3%) Query: 5 LFRTKRVKDAAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGKAGPAVIMSF 64 LFRTK ++ A + L L L+ +G+GAI+GTGI L G GA AGPA+ +SF Sbjct: 3 LFRTKNIEAMLAAARDDGLKKVLGPVDLILMGIGAIIGTGIFVLTGTGALTAGPALTVSF 62 Query: 65 VIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVAV 124 VIA C AAL YAE A+ +P SGS Y YSYA LGEI+AW++GW L+LEY L S V+V Sbjct: 63 VIAALACGFAALCYAEFASAIPVSGSIYTYSYATLGEIVAWMIGWDLLLEYGLATSAVSV 122 Query: 125 GWSGYAAPLLHAW-TGMPLELMAGPHA----NGIVNLPAIFIIAVVAGLLCLGTKESATL 179 GWSGY L+ + +P L A P A + NLPA I+ ++ ++ G +ESA L Sbjct: 123 GWSGYFQSLMAGFGIHLPAMLTAAPGAVPGVQTLFNLPAAVIMLLITWVVSYGVRESARL 182 Query: 180 NAALVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFAF 239 N +V VKI + +F+ V + + AN PFAPFG GV AAA++FFAF Sbjct: 183 NNVMVAVKIAVVLLFIGVGVWHVKPANWHPFAPFGL----------DGVFNAAALVFFAF 232 Query: 240 YGFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLAL 299 GFDA+++AAEE +NP RDL IGI+GS+ C +Y+ VA G PF FA P++L Sbjct: 233 IGFDAVTSAAEEVRNPRRDLPIGIIGSLAVCTVLYVTVAAIMTGIVPFAKFAGIDHPVSL 292 Query: 300 ILRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKVSK-RGSP 358 L+ G A F+ + AI+ + TV+L FGQ+RI F M+RDG+LP L+ V +P Sbjct: 293 ALQYAGENWVAGFVDLGAILGMTTVILVMTFGQTRIIFAMSRDGLLPERLSTVHPVHATP 352 Query: 359 VRITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPL 418 T + A IA +P++ +A L N GTL+AFT ++V ++VLR PD+PR FR P Sbjct: 353 FFATWTVGIVFAFIAAFVPLNVLAELINIGTLSAFTLISVAVLVLRKTRPDLPRAFRCPG 412 Query: 419 WWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAYAR 461 +V ++V C++L L T + FLAW A+G+ IYF YAR Sbjct: 413 VPVVPLLSVGFCLFLMAHLQALTWVAFLAWLAIGLAIYFLYAR 455 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: 637 Number of extensions: 34 Number of successful extensions: 4 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: 464 Length adjustment: 33 Effective length of query: 437 Effective length of database: 431 Effective search space: 188347 Effective search space used: 188347 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