Align high affinity cationic amino acid transporter 1 (characterized)
to candidate RR42_RS01585 RR42_RS01585 amino acid permease
Query= CharProtDB::CH_091324 (622 letters) >FitnessBrowser__Cup4G11:RR42_RS01585 Length = 464 Score = 251 bits (640), Expect = 6e-71 Identities = 143/408 (35%), Positives = 229/408 (56%), Gaps = 28/408 (6%) Query: 28 LSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLCYGEF 87 L + L DL+ +G+G+ +G G++VL G A AGPA+ +SF+IAALA A LCY EF Sbjct: 21 LKKVLGPVDLILMGIGAIIGTGIFVLTGTGAL-TAGPALTVSFVIAALACGFAALCYAEF 79 Query: 88 GARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELIGKPIGEF 147 + +P +GS Y YSY T+GE+ A++ GW+L+L Y + TS+V+ WS F L+ Sbjct: 80 ASAIPVSGSIYTYSYATLGEIVAWMIGWDLLLEYGLATSAVSVGWSGYFQSLMAG--FGI 137 Query: 148 SRQHMALNAPGVLAQTPDIF---AVIIIIILTGLLTLGVKESAMVNKIFTCINVLVLCFI 204 M APG + +F A +I++++T +++ GV+ESA +N + + + V+ Sbjct: 138 HLPAMLTAAPGAVPGVQTLFNLPAAVIMLLITWVVSYGVRESARLNNVMVAVKIAVVLLF 197 Query: 205 VVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSGAATCFYAFVGFDC 264 + G NW F PFG GV + AA F+AF+GFD Sbjct: 198 IGVGVWHVKPANWH--------------------PFAPFGLDGVFNAAALVFFAFIGFDA 237 Query: 265 IATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYF-CLDIDSPLPGAFKHQ 323 + + EEV+NP++ +P+GI+ SL +C + Y V+A +T ++P+ ID P+ A ++ Sbjct: 238 VTSAAEEVRNPRRDLPIGIIGSLAVCTVLYVTVAAIMTGIVPFAKFAGIDHPVSLALQYA 297 Query: 324 GWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKINNRTKTPVIATV 383 G V +G++ ++T +L F R+I+AM+ DGLL + L+ ++ TP AT Sbjct: 298 GENWVAGFVDLGAILGMTTVILVMTFGQTRIIFAMSRDGLLPERLSTVHPVHATPFFATW 357 Query: 384 TSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLR-YQPEQP 430 T G + A +A L L +L++IGTL A++L++ VLVLR +P+ P Sbjct: 358 TVGIVFAFIAAFVPLNVLAELINIGTLSAFTLISVAVLVLRKTRPDLP 405 Score = 54.3 bits (129), Expect = 1e-11 Identities = 37/118 (31%), Positives = 57/118 (48%), Gaps = 9/118 (7%) Query: 479 VEPSKFSGLIVNISAGLLAALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCMLVTGI 538 V P + + G++ A I + VL E + GTL A +++ +VL Sbjct: 345 VHPVHATPFFATWTVGIVFAFIAAFVPLNVLA-ELINIGTLSAFTLISVAVL-------- 395 Query: 539 IWRQPESKTKLSFKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGY 596 + R+ +F+ P VPV+P+LS+ ++LM L TWV F W+ IG IYF Y Sbjct: 396 VLRKTRPDLPRAFRCPGVPVVPLLSVGFCLFLMAHLQALTWVAFLAWLAIGLAIYFLY 453 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: 739 Number of extensions: 31 Number of successful extensions: 7 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: 464 Length adjustment: 35 Effective length of query: 587 Effective length of database: 429 Effective search space: 251823 Effective search space used: 251823 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 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