Align L-glutamine and L-histidine transporter (characterized)
to candidate H281DRAFT_02180 H281DRAFT_02180 amino acid/polyamine/organocation transporter, APC superfamily
Query= reanno::Korea:Ga0059261_1577 (470 letters) >FitnessBrowser__Burk376:H281DRAFT_02180 Length = 463 Score = 364 bits (934), Expect = e-105 Identities = 196/466 (42%), Positives = 280/466 (60%), Gaps = 17/466 (3%) Query: 5 LFRTKRVKDA-AEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGKAGPAVIMS 63 LFR K V+ A A L L L LGVGAI+GTGI L G GA +AGPA+++S Sbjct: 3 LFRKKSVEHMIATSAQNAGLKKALGALDLTFLGVGAIIGTGIFVLTGTGAVQAGPALMVS 62 Query: 64 FVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVA 123 F+IA C AALAYAE A+ +P +GS Y YSYA LGE+ AW++GW L+LEY L S V+ Sbjct: 63 FLIAAVACGFAALAYAEFASTIPVAGSIYTYSYATLGELAAWIIGWDLMLEYGLATSAVS 122 Query: 124 VGWSGYAAPLLHAW-TGMPLELMAGPHA----NGIVNLPAIFIIAVVAGLLCLGTKESAT 178 VGWSGY LL + +P+ L A P A + NLPA ++ + LL +G +ESA Sbjct: 123 VGWSGYLQSLLSGFGVSLPVALTAAPGALPGHETLFNLPAFLVMMAITALLSVGVRESAR 182 Query: 179 LNAALVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFA 238 +N +V +K++ + + +AV + + AN PF P G+ GV AAA++FFA Sbjct: 183 INNIMVAIKVVVVLLVIAVGVFHVTPANWHPFMPNGW----------NGVFGAAAVMFFA 232 Query: 239 FYGFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLA 298 F GFD++S+AAEE KNP RDL IGI+ S+ C +Y+ VA G P FAN P++ Sbjct: 233 FIGFDSVSSAAEEVKNPKRDLPIGIIASLGVCAVLYVAVAAVVTGIVPSAQFANISHPVS 292 Query: 299 LILRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKVSKR-GS 357 L+ G+ A F+ + A++ + TV+L +GQ+R+ F M+RDG+LP L++V R + Sbjct: 293 YALQVAGQKWVAGFIDLGAVLGMLTVILVMAYGQTRVIFAMSRDGLLPARLSRVHPRFAT 352 Query: 358 PVRITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTP 417 P T +I L+P++ +A L N GTLAAF+ V++ ++VLR P++PR FR P Sbjct: 353 PFFTTWLVGIFFGLIGALVPLNVLAELINIGTLAAFSMVSIAVLVLRKTHPELPRAFRCP 412 Query: 418 LWWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAYARPR 463 +V +AV C++L +L T + F+ W +G+VIYF Y+R R Sbjct: 413 GVPVVPVLAVASCVFLMANLQAVTWVAFVVWLLIGMVIYFGYSRRR 458 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: 37 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: 463 Length adjustment: 33 Effective length of query: 437 Effective length of database: 430 Effective search space: 187910 Effective search space used: 187910 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