Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_036136365.1 N800_RS06840 amino acid permease
Query= CharProtDB::CH_091324 (622 letters) >NCBI__GCF_000768355.1:WP_036136365.1 Length = 474 Score = 247 bits (630), Expect = 9e-70 Identities = 144/417 (34%), Positives = 231/417 (55%), Gaps = 36/417 (8%) Query: 28 LSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLCYGEF 87 L R L + L ALG+G+ +G G++V+ G A ++AGPAI++SF++AA+ L Y EF Sbjct: 23 LHRTLGKWGLTALGIGAVIGGGIFVITGQAAADHAGPAIMLSFVLAAICCTFCALAYAEF 82 Query: 88 GARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELIGKPIGEF 147 + VP +GSAY Y+Y T+GEL A+ GW L+L Y + S+VA +W+ F L+ Sbjct: 83 ASMVPVSGSAYTYTYATLGELAAWFIGWMLVLEYGVSASAVAVSWTGYFLSLL------- 135 Query: 148 SRQHMALNAPGVLAQTP------------DIFAVIIIIILTGLLTLGVKESAMVNKIFTC 195 +H ++ P L Q P ++ A I+++LT + +G+++S+ +N Sbjct: 136 --EHFNIHLPAALVQAPLDSKLQPTGAIANLPAAAIVLLLTWVCYIGIRKSSGMNTAMVL 193 Query: 196 INVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSGAATC 255 + ++ ++++G+ NW E N G G FG+ GVL GA+ Sbjct: 194 LKSGLIVLVIIAGWQYVDPANW---EPFIPANE-------GPG---KFGWEGVLRGASMV 240 Query: 256 FYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYFCLDIDSP 315 F+A++GF+ ++ +E NPQK +P G++ SL IC + Y G++A +T + PY L D P Sbjct: 241 FFAYIGFEAVSVAAQESHNPQKDLPFGMLMSLAICTVLYIGMAAVMTGLTPYTLLGTDEP 300 Query: 316 LPGAFK-HQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKINNR 374 + A H + V IG+L LS+ +L + PR+ MA DGLL + +I+ + Sbjct: 301 VVTAVAGHAELAWLRVVVEIGALIGLSSVVLVMIIGQPRIFMIMARDGLLPEVFTRIHPK 360 Query: 375 TKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVL-RYQPEQP 430 +TP I TV +G A++A +F L L +L S+GTL+A+ V A VL+L R QP+ P Sbjct: 361 HRTPHINTVITGIGIALLAAVFPLDILGELTSMGTLIAFGAVCAGVLILRRTQPDLP 417 Score = 42.7 bits (99), Expect = 4e-08 Identities = 57/226 (25%), Positives = 88/226 (38%), Gaps = 44/226 (19%) Query: 377 TPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLRYQPEQPNLVYQM 436 TP T + +A EL L ++ IG L+ S V +++ QP + M Sbjct: 290 TPYTLLGTDEPVVTAVAGHAELAWLRVVVEIGALIGLSSVVLVMII-----GQPRIFMIM 344 Query: 437 ARTTEELDRVDQNELVSASESQTGFLPVAEKFSLKSILSPKNVEPSKFSGLIVNISAGLL 496 AR G LP E F+ + PK+ P I + G+ Sbjct: 345 ARD--------------------GLLP--EVFTR---IHPKHRTPH-----INTVITGIG 374 Query: 497 AALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCMLVTGIIWRQPESKTKLSFKVPFV 556 AL+ V + +LG E + GTL A + VL I R+ + F++ V Sbjct: 375 IALLAAVFPLDILG-ELTSMGTLIAFGAVCAGVL--------ILRRTQPDLPRPFRIRGV 425 Query: 557 PVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGIWHSE 602 + + IF + L+ + W+ W +GF IYF YG HS+ Sbjct: 426 WFVCLAGIFSCLALLSAMTLHNWMLMLGWTTVGFAIYFLYGYRHSK 471 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: 735 Number of extensions: 29 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: 474 Length adjustment: 35 Effective length of query: 587 Effective length of database: 439 Effective search space: 257693 Effective search space used: 257693 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