Align high affinity cationic amino acid transporter 1 (characterized)
to candidate CA265_RS17395 CA265_RS17395 amino acid transporter
Query= CharProtDB::CH_091324 (622 letters) >FitnessBrowser__Pedo557:CA265_RS17395 Length = 483 Score = 224 bits (570), Expect = 9e-63 Identities = 134/409 (32%), Positives = 219/409 (53%), Gaps = 22/409 (5%) Query: 25 ESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLCY 84 E L R L +L+ +GVG TLGAG++ + G A ++GPA+ +SF+IAAL A LCY Sbjct: 17 EGSLKRTLGPINLILIGVGLTLGAGLFSITGLAAANHSGPAVTLSFVIAALGCGFAALCY 76 Query: 85 GEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELIGK-- 142 EF + +P GSAY YSY T+GEL+A+I GW+L+L Y +G ++VA +WS + + Sbjct: 77 AEFASMIPVAGSAYTYSYATMGELFAWIIGWDLVLEYSVGCATVAISWSQYLTKFLASLH 136 Query: 143 ----PIGEFSRQHMALNAPG-VLAQTPDIFAVIIIIILTGLLTLGVKESAMVNKIFTCIN 197 P S A A G + +I A ++++++T +L G K SA+VN I + Sbjct: 137 IYLPPQLTLSPFETAKLADGSTVNGIINIPAALVVVLMTAILIRGTKGSAIVNGIIVFLK 196 Query: 198 V-LVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSGAATCF 256 V +VL FI + WQ + N + G F FG+SGVL GA F Sbjct: 197 VGVVLVFIAL---------GWQYIDP----ANYHPYIPENTGTFGQFGWSGVLRGAGLVF 243 Query: 257 YAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPY-FCLDIDSP 315 + F+GFD +A + +E KNP + +P+GI+ SLL+C + + +T + Y + +P Sbjct: 244 FVFIGFDAVAASAQETKNPARDLPIGIIGSLLVCTVLFGLFGHVMTGLANYKEFANSGAP 303 Query: 316 LPGAFKHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKINNRT 375 + A + + A+ + L ++ +L + R+ Y++++DGLL K + ++ + Sbjct: 304 VAIAIEKTPYAWLSQAIILAILIGYTSVILIDLMAQSRMFYSISKDGLLPKMFSDVHAKF 363 Query: 376 KTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLR 424 KTP + + + A + + ++ SIGTLLA+ +V +L+LR Sbjct: 364 KTPYKSNIILCVFIGLFAAFVPMNVVGEMTSIGTLLAFLMVCVGILILR 412 Score = 69.7 bits (169), Expect = 3e-16 Identities = 52/143 (36%), Positives = 75/143 (52%), Gaps = 19/143 (13%) Query: 455 SESQTGFLPVAEKFSLKSILSPKNVEPSKFSGLIVNISAGLLAALIITVCIVAVLGREAL 514 S S+ G LP + S + K P K S +I+ + GL AA + + V+G E Sbjct: 345 SISKDGLLP-----KMFSDVHAKFKTPYK-SNIILCVFIGLFAAFVP----MNVVG-EMT 393 Query: 515 AEGTLWAVFVMTGSVLLCMLVTGIIWRQPESKTKLSFKVPFVPVLPVLSIFVNIYLMMQL 574 + GTL A ++ +L I R+ + K FKVPFVP++P+L I I +M+ L Sbjct: 394 SIGTLLAFLMVCVGIL--------ILRKTNPEAKRPFKVPFVPLIPILGILTCIAMMVFL 445 Query: 575 DQGTWVRFAVWMLIGFTIYFGYG 597 TW+R AVW++IG IYF YG Sbjct: 446 PWETWLRLAVWLIIGLAIYFWYG 468 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: 769 Number of extensions: 35 Number of successful extensions: 4 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: 483 Length adjustment: 36 Effective length of query: 586 Effective length of database: 447 Effective search space: 261942 Effective search space used: 261942 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