Align L-glutamine and L-histidine transporter (characterized)
to candidate N515DRAFT_0722 N515DRAFT_0722 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= reanno::Korea:Ga0059261_1577 (470 letters) >FitnessBrowser__Dyella79:N515DRAFT_0722 Length = 479 Score = 303 bits (775), Expect = 1e-86 Identities = 181/477 (37%), Positives = 262/477 (54%), Gaps = 37/477 (7%) Query: 5 LFRTKRVKDAAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGK-AGPAVIMS 63 LF K V+ A + L TL LV LGVGA++G GI + G A + AGPA+ +S Sbjct: 7 LFAVKPVE--ASLTADDSLRRTLGLKELVVLGVGAVIGAGIFVITGQAAAEHAGPALTLS 64 Query: 64 FVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVA 123 FV+AG A AAL+YAE A M+P SGSAY Y+YA GE++AW +GW+++ EY L VS+VA Sbjct: 65 FVLAGLAAALAALSYAEFAAMLPVSGSAYVYAYATFGELLAWFIGWNVVAEYLLAVSSVA 124 Query: 124 VGWSGYAAPLLH--------AWTGMPLELMAG--PHANGIVNLPAIFIIAVVAGLLCLGT 173 VGWSGY LL A PL G ++NLPA+ ++A + LL GT Sbjct: 125 VGWSGYGVGLLKSLGIEVPAALANAPLSFKDGHLELTGALLNLPALLVVAALTALLYRGT 184 Query: 174 KESATLNAALVVVKIIALAVFVAVALPYFNGANLEPFAP-------FGFAKTISPDGVER 226 ++S + +V +K+I + +FV L Y + + P+ P +G+A Sbjct: 185 RQSTMFASVVVALKVIVVVLFVVCGLQYVDPSLWHPYVPANQGGDHYGWA---------- 234 Query: 227 GVMAAAAIIFFAFYGFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATP 286 GV AA +F+A+ GFDA++TAA+ET+NP R++ GI+ S+ C +Y++VA G P Sbjct: 235 GVFRAATSVFYAYIGFDAVATAAQETRNPQRNVPAGILISLAICTVLYIIVAAVLTGLVP 294 Query: 287 FTHFANSPEPLALILRDLGRPGFA---TFLAVSAIIALPTVLLGFLFGQSRIFFTMARDG 343 + A + EP+A L P A V A+ L +V+L G SRI ++MA DG Sbjct: 295 YPQLATA-EPVATAL--AAHPPLAWLKLLTQVGAVAGLTSVILVMHLGLSRILYSMAGDG 351 Query: 344 MLPIGLAKVSKR-GSPVRITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMV 402 +LP V +R +P R TL A+ V+A + P+ + L + GTL AF V + ++V Sbjct: 352 LLPTFFGAVHERHRTPHRTTLLVGAVGGVLAAVFPLSLLGDLLSMGTLLAFATVCIGVLV 411 Query: 403 LRVRAPDMPRMFRTPLWWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAY 459 LR P++PR FR P V + VL C +L + + + AW LG++IY AY Sbjct: 412 LRRTHPNLPRGFRVPAAPAVCTLGVLVCAFLLAQMNLGNWILLAAWTTLGMLIYIAY 468 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: 583 Number of extensions: 28 Number of successful extensions: 6 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: 479 Length adjustment: 33 Effective length of query: 437 Effective length of database: 446 Effective search space: 194902 Effective search space used: 194902 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