Align high affinity cationic amino acid transporter 1 (characterized)
to candidate N515DRAFT_2924 N515DRAFT_2924 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= CharProtDB::CH_091324 (622 letters) >FitnessBrowser__Dyella79:N515DRAFT_2924 Length = 492 Score = 258 bits (659), Expect = 4e-73 Identities = 151/423 (35%), Positives = 232/423 (54%), Gaps = 33/423 (7%) Query: 25 ESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLCY 84 E+ L R L LV LG+G+ +GAG++V+ G A E+AGPAIV+SF+ A +A LA LCY Sbjct: 26 EATLKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALCY 85 Query: 85 GEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELIGKPI 144 EF A +P +GSAY YSY T+GE A+ GW+L+L Y+ ++VA WS F++L+ Sbjct: 86 AEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALIS 145 Query: 145 GEFSRQHMALNAPGVLAQTP---------------DIFAVIIIIILTGLLTLGVKESAMV 189 G ++ P LA P ++ AV II +TGL +G+ +SA V Sbjct: 146 GWIGHD---VSLPQTLAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFV 202 Query: 190 NKIFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVL 249 N I I V V+ + K + +N + EG +G++GV Sbjct: 203 NSIIVAIKVTVILLFIA------------FATKYINPDNWHPFIPASEGA-SKYGWAGVG 249 Query: 250 SGAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYFC 309 AA F++++GFD ++T E KNPQ+ +P+GI+ SL++C I Y V+ LT + + Sbjct: 250 RAAAIVFFSYIGFDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADFRL 309 Query: 310 LDIDSPLPGAF-KHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFL 368 L P+ A + + V IG++ LS+ +L + PR+ Y+MA DGL+ Sbjct: 310 LGTPEPVSTALDNYPSLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVF 369 Query: 369 AKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLRY-QP 427 +I+ + +TP + TV G +AA + LF + L +++++GTLLA++ V VLVLRY +P Sbjct: 370 GRIHQKFRTPHVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRP 429 Query: 428 EQP 430 E P Sbjct: 430 ELP 432 Score = 40.4 bits (93), Expect = 2e-07 Identities = 36/118 (30%), Positives = 55/118 (46%), Gaps = 9/118 (7%) Query: 491 ISAGLLAALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCMLVTGIIWRQPESKTKLS 550 + G+LAA + + + VLG E +A GTL A +C+ V + + +PE + Sbjct: 384 VVVGVLAAALGGLFNIGVLG-EMVAMGTLLAF------ATVCIGVLVLRYTRPELPR--A 434 Query: 551 FKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGIWHSEEASLAA 608 F+VP ++ L + L +Q W W+ IG IYF YG HS+ AA Sbjct: 435 FRVPVPWIVCPLGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSKLRKPAA 492 Score = 25.0 bits (53), Expect = 0.008 Identities = 29/134 (21%), Positives = 52/134 (38%), Gaps = 27/134 (20%) Query: 485 SGLIVNISAGLLAALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCMLVTGIIWRQPE 544 +G+ +N+ A + A I +C V + + A + A+ V +V+L + + P+ Sbjct: 173 TGMFINLPAVAIIAAITGLCYVGIT-QSAFVNSIIVAIKV---TVILLFIAFATKYINPD 228 Query: 545 SKTKLSFKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGIWHSEEA 604 + PF+P S + W I F Y G+ + Sbjct: 229 NWH------PFIPASEGASKY------------GWAGVGRAAAIVFFSYIGF-----DAV 265 Query: 605 SLAAGQAKTPDSNL 618 S AAG+AK P ++ Sbjct: 266 STAAGEAKNPQRDM 279 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: 773 Number of extensions: 49 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: 3 Length of query: 622 Length of database: 492 Length adjustment: 36 Effective length of query: 586 Effective length of database: 456 Effective search space: 267216 Effective search space used: 267216 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 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