Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_102938052.1 B1812_RS04230 amino acid permease
Query= CharProtDB::CH_091324 (622 letters) >NCBI__GCF_002117405.1:WP_102938052.1 Length = 481 Score = 263 bits (671), Expect = 2e-74 Identities = 147/416 (35%), Positives = 226/416 (54%), Gaps = 25/416 (6%) Query: 18 VVDCSREESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALAS 77 + + EE+ L R L L+A+G+G +GAG++VL G A + AGP + ISFL++ LA Sbjct: 19 IAENDAEENGLKRALGWASLMAMGIGGIIGAGIFVLTGQAAADYAGPGVTISFLLSGLAC 78 Query: 78 VLAGLCYGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFD 137 LCY E A +P GS Y Y+YVT+GE++A+I GWNL+L Y G ++VA W+ F+ Sbjct: 79 TFVALCYAELAALIPAAGSTYTYTYVTLGEIFAWIIGWNLVLEYAAGAATVAVGWAGYFN 138 Query: 138 EL---IGKPIGE------FSRQHMALNAPGVLAQTPDIFAVIIIIILTGLLTLGVKESAM 188 + +G + E F+ H GV ++ A II++LT LL G ES+ Sbjct: 139 RVMQGLGIHLPEALTSAYFANAHSIGGTHGVF----NVPAAAIILLLTALLMRGTSESSF 194 Query: 189 VNKIFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGV 248 N I I V+V+ ++ G NW + F FG+SGV Sbjct: 195 FNNIIVVIKVMVVLVVIFVGAAHVDAANWTPL------------IPENTDHFGHFGWSGV 242 Query: 249 LSGAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYF 308 + GA+ F+A++GFD ++T +E PQ+ +P+GI+ SL+IC I Y V+A T ++ Y Sbjct: 243 VRGASVVFFAYIGFDGVSTAAQEAHTPQRDVPIGILGSLVICTILYVAVAAVATGVVSYK 302 Query: 309 CLDIDSPLPGAFKHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFL 368 L + P+ G + V +G++ L+T++L +F R+ YAMA+DGLL K Sbjct: 303 ELGVPDPMALVMDRTGVAWLSWVVKLGAIAGLTTAILLLLFGQTRIFYAMAQDGLLPKVF 362 Query: 369 AKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLR 424 A ++ +TP ++ G A+ A LF + L +++SIGTL A++LV VL LR Sbjct: 363 AAVHPVWRTPAVSQALVGVFVALAAGLFPINILDEMVSIGTLAAFALVCGAVLHLR 418 Score = 58.9 bits (141), Expect = 5e-13 Identities = 38/119 (31%), Positives = 59/119 (49%), Gaps = 17/119 (14%) Query: 486 GLIVNISAGLLAALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCMLVTGIIWRQPES 545 G+ V ++AGL I+ E ++ GTL A ++ G+VL R+ + Sbjct: 380 GVFVALAAGLFPINILD---------EMVSIGTLAAFALVCGAVLHL--------RRSQP 422 Query: 546 KTKLSFKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGIWHSEEA 604 F+ P +P +P+L I + LM+ L TW+R VW IG IYF YG+ H++ A Sbjct: 423 DMHRPFRAPGIPAMPLLGIASCLALMVALPLETWLRLIVWTAIGMAIYFFYGVKHAKRA 481 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: 709 Number of extensions: 36 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 622 Length of database: 481 Length adjustment: 36 Effective length of query: 586 Effective length of database: 445 Effective search space: 260770 Effective search space used: 260770 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: 52 (24.6 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