Align L-glutamine and L-histidine transporter (characterized)
to candidate WP_025765060.1 X939_RS0120010 amino acid permease
Query= reanno::Korea:Ga0059261_1577 (470 letters) >NCBI__GCF_000566685.1:WP_025765060.1 Length = 484 Score = 347 bits (889), Expect = e-100 Identities = 186/485 (38%), Positives = 290/485 (59%), Gaps = 34/485 (7%) Query: 1 MAGGLFRTKRVKDAAEQAP--EHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGK-AG 57 MA L+ K ++ +++ E++L +LS LVALG+GAI+G G+ +L G+ A + +G Sbjct: 1 MASQLWFKKPIEKLLQESTGEENQLKRSLSSLSLVALGIGAIIGAGLFSLTGIAAAEHSG 60 Query: 58 PAVIMSFVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSL 117 PAV +SF++A C A L YAE A+M+P +GSAY YSYA +GE +AW++GW L+LEY+L Sbjct: 61 PAVTISFIVAAVGCGFAGLCYAEFASMIPIAGSAYTYSYATMGEFVAWIIGWDLVLEYAL 120 Query: 118 VVSTVAVGWSGYAAPLLHAWT-GMPLELMAGPHA-----------NGIVNLPAIFIIAVV 165 +TV+V WS Y L + +P +L++ P NGI+NLPAI I+ ++ Sbjct: 121 GAATVSVSWSRYLLEFLSKFDIHLPTQLVSSPFEVLTLSDGTIIDNGIINLPAILIVWML 180 Query: 166 AGLLCLGTKESATLNAALVVVKIIALAVFVAVALPYFNGANLEPFAP--------FGFAK 217 + LL GT+ SA LN LV++K+ + +F+ + + N N P+ P FG++ Sbjct: 181 SLLLIRGTEGSAYLNNFLVILKVAVVLIFIGLGWSHINPENYVPYIPENTGNYENFGWS- 239 Query: 218 TISPDGVERGVMAAAAIIFFAFYGFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLV 277 G+ AA++FFAF GFDA+STAA+E KNP + + IGI+GS+I C +Y+L Sbjct: 240 ---------GIATGAAVVFFAFIGFDAVSTAAQEAKNPQKGMPIGILGSLIVCTILYVLF 290 Query: 278 AVAAVGATPFTHFANSPEPLALILRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFF 337 A G + FAN +P A G T L V+ + +V+L L GQSR+F+ Sbjct: 291 AHVMTGLVNYKEFANDAKPAATAFAATGYDSLQTGLIVAILAGYTSVMLVMLLGQSRVFY 350 Query: 338 TMARDGMLPIGLAKV-SKRGSPVRITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAV 396 +M++DG+LP +++ K +P + +F V++ AG +P+ ++ + + GTL AF+ V Sbjct: 351 SMSKDGLLPKFFSEIHPKFSTPWKTNIFFMLFVSIFAGFVPVSDLGHMVSIGTLFAFSLV 410 Query: 397 AVCMMVLRVRAPDMPRMFRTPLWWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIY 456 V + +LRV+ PD+PR FRTPL V + ++ C+YL +SLP+++ W ALG+ IY Sbjct: 411 CVGVWMLRVKRPDLPRSFRTPLVPFVPLMGIIVCVYLMYSLPIESWYRLAIWLALGLAIY 470 Query: 457 FAYAR 461 F Y + Sbjct: 471 FFYGK 475 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: 662 Number of extensions: 35 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: 484 Length adjustment: 33 Effective length of query: 437 Effective length of database: 451 Effective search space: 197087 Effective search space used: 197087 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 24 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