Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_092483642.1 BM299_RS10185 amino acid permease
Query= CharProtDB::CH_091324 (622 letters) >NCBI__GCF_900115975.1:WP_092483642.1 Length = 484 Score = 246 bits (629), Expect = 1e-69 Identities = 135/413 (32%), Positives = 221/413 (53%), Gaps = 35/413 (8%) Query: 18 VVDCSREESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALAS 77 + D + + L L DL ALGVG+ +G G++VL G A AGP +V SF+++ +A+ Sbjct: 13 LADKKKNKRGLVPTLGVADLTALGVGAVIGTGIFVLTGVAAANYAGPGVVFSFILSGIAA 72 Query: 78 VLAGLCYGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFD 137 LA + Y E GA +P GSAY +SYV++GE+ A++ GWNLIL Y++ +V+ WS+ Sbjct: 73 TLAAMVYAELGAAIPSAGSAYTFSYVSLGEIIAWLVGWNLILEYLVAAGAVSIGWSSYMG 132 Query: 138 ELIGKPIGEFSRQHMALNAPGVLAQTP------DIFAVIIIIILTGLLTLGVKESAMVNK 191 +L+ Q + + P +P ++ A +I++++TGL+ G + S NK Sbjct: 133 DLL---------QSVGITLPAAFTSSPFDGGIVNLPAALIVLVITGLIITGTQHSTTANK 183 Query: 192 IFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSG 251 I + + + G + NW+ +P+G SGV G Sbjct: 184 IIVVAKLAAIALFIALGVQHINPANWRPV--------------------LPYGISGVFHG 223 Query: 252 AATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYFCLD 311 AA F+A++GFD +AT EEVKNPQ+ +P GI+ +L+I + Y V+ LT M+ Y L+ Sbjct: 224 AAIVFFAYIGFDAVATASEEVKNPQRDLPRGIIWTLVISTLLYIVVAGILTGMVKYTNLN 283 Query: 312 IDSPLPGAFKHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKI 371 SP+ A G A V++G+L L++ LL +M+ R+ +AMA D LL + Sbjct: 284 TASPVATALLRAGIPWASALVSVGALAGLTSVLLVAMYGQSRIFFAMARDDLLPPIFDWL 343 Query: 372 NNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLR 424 + R +TPV ++ G + A++ + + +L +IGTL A+ V+ ++LR Sbjct: 344 HPRLRTPVWDSIIIGVLVALIGAFLPIGLVAELANIGTLTAFIAVSTGAIILR 396 Score = 57.8 bits (138), Expect = 1e-12 Identities = 39/116 (33%), Positives = 61/116 (52%), Gaps = 11/116 (9%) Query: 490 NISAGLLAALIITVCIVAVLGREALAEGTLWA-VFVMTGSVLLCMLVTGIIWRQPESKTK 548 +I G+L ALI + ++ E GTL A + V TG+++L R+ + Sbjct: 354 SIIIGVLVALIGAFLPIGLVA-ELANIGTLTAFIAVSTGAIIL---------RRTNPDLR 403 Query: 549 LSFKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGIWHSEEA 604 F++P++P +PVL+I YL + L TWVRF W+ IG +Y+ YG S+ A Sbjct: 404 RPFRLPWMPAIPVLTIISAGYLAINLPPLTWVRFIAWVAIGLVVYWLYGYRKSKLA 459 Lambda K H 0.324 0.138 0.417 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: 744 Number of extensions: 42 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 622 Length of database: 484 Length adjustment: 36 Effective length of query: 586 Effective length of database: 448 Effective search space: 262528 Effective search space used: 262528 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. 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