Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_034526641.1 LOSG293_RS02350 amino acid permease
Query= CharProtDB::CH_091324 (622 letters) >NCBI__GCF_000740055.1:WP_034526641.1 Length = 470 Score = 247 bits (631), Expect = 7e-70 Identities = 140/412 (33%), Positives = 227/412 (55%), Gaps = 29/412 (7%) Query: 24 EESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLC 83 ++++L + +N DLV LGVG+ +G G+++L G VA +GPAIVISF++A + A +C Sbjct: 21 KDAQLEKTMNAKDLVMLGVGAVIGTGIFILPGTVAALYSGPAIVISFILATIVCTFAAMC 80 Query: 84 YGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELIGKP 143 Y EF + +P GSAY Y + GE+ ++ GW LIL Y++ +SV+ WSA F I Sbjct: 81 YAEFSSALPIAGSAYSYGNIVFGEVIGWVLGWALILEYMLAVASVSTGWSAYFLSFIK-- 138 Query: 144 IGEFSRQHMALNAPGVLAQTP--DIFAVIIIIILTGLLTLGVKESAMVNKIFTCINVLVL 201 G AL P A +IFA+II++++ +++ G K S MVN I + + ++ Sbjct: 139 -GFGISVPKALTGPFDPAHGTYINIFAIIIVLLIGLIISRGAKTSIMVNNIIVVVKIAII 197 Query: 202 CFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSGAATCFYAFVG 261 + G NW FMPFG G+++GA+ F+A++G Sbjct: 198 FLFLAVGLFYVKPTNWV--------------------PFMPFGVKGIMTGASLVFFAYLG 237 Query: 262 FDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYFCLDIDSPLPGAFK 321 FD ++ + EVKN +K +P+GI+ +LLIC I Y V+A LT M Y L++ P+ A Sbjct: 238 FDVVSASAAEVKNAKKNMPIGIIGTLLICTILYILVAAVLTGMTSYTKLNVSDPVSFALH 297 Query: 322 --HQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKINNRTKTPV 379 +Q W ++IG+L + T ++ +F R+IY++ DGLL K L KI + TP Sbjct: 298 LVNQNWVAG--IISIGALAGMFTMMVSMIFSSSRLIYSIGRDGLLPKALGKIEMKHHTPR 355 Query: 380 IATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLRYQPEQPN 431 ++ + I A++ L L L L++IGTL+A++ ++ ++ LR + + N Sbjct: 356 VSLIAVTIIIAILGGLVSLDRLTQLVNIGTLIAFTFISIGIIPLRRRKDIDN 407 Score = 60.5 bits (145), Expect = 2e-13 Identities = 37/106 (34%), Positives = 55/106 (51%), Gaps = 3/106 (2%) Query: 498 ALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCMLVTGII--WRQPESKTKLSFKVPF 555 +LI I+A+LG + V + T + + GII R+ + FKVP Sbjct: 357 SLIAVTIIIAILGGLVSLDRLTQLVNIGT-LIAFTFISIGIIPLRRRKDIDNAGGFKVPL 415 Query: 556 VPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGIWHS 601 PVLP++S + I+++ QL TW+ ++W LIG IYF YG HS Sbjct: 416 YPVLPIVSAALCIFMLAQLPLDTWIVSSIWFLIGLAIYFLYGAKHS 461 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: 753 Number of extensions: 34 Number of successful extensions: 5 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: 470 Length adjustment: 35 Effective length of query: 587 Effective length of database: 435 Effective search space: 255345 Effective search space used: 255345 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 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