Align Amino acid transporter (characterized, see rationale)
to candidate WP_036136365.1 N800_RS06840 amino acid permease
Query= uniprot:A0A0H3C3Q5 (483 letters) >NCBI__GCF_000768355.1:WP_036136365.1 Length = 474 Score = 293 bits (750), Expect = 9e-84 Identities = 171/467 (36%), Positives = 267/467 (57%), Gaps = 18/467 (3%) Query: 22 AGHADSH--QLKKTLSWPHLVALGVGAIVGTGIYTLTG-VGAGLAGPGVILSFLIAGAVC 78 A HAD+ L +TL L ALG+GA++G GI+ +TG A AGP ++LSF++A C Sbjct: 13 AAHADADGLSLHRTLGKWGLTALGIGAVIGGGIFVITGQAAADHAGPAIMLSFVLAAICC 72 Query: 79 ACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAVGWSAHAH 138 AL YAE ++M+P SGSAYTY+YA +GE AWF+GW L+LEY + +AVAV W+ + Sbjct: 73 TFCALAYAEFASMVPVSGSAYTYTYATLGELAAWFIGWMLVLEYGVSASAVAVSWTGYFL 132 Query: 139 GLFKM--IGFPDALLAGPHQ------GGLINMPAVFISMAVAGLLALGTRESATVNMVLV 190 L + I P AL+ P G + N+PA I + + + +G R+S+ +N +V Sbjct: 133 SLLEHFNIHLPAALVQAPLDSKLQPTGAIANLPAAAIVLLLTWVCYIGIRKSSGMNTAMV 192 Query: 191 FVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASLIFFAFY 250 +K +++ ++ + A++ PF+P EG + GV+ AS++FFA+ Sbjct: 193 LLKSGLIVLVIIAGWQYVDPANWEPFIPAN------EGPGKFGWE-GVLRGASMVFFAYI 245 Query: 251 GFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSEAPLVFI 310 GF+AVS AA+E+ NP++DL G++ S+A+CT +Y+ +AAV G + + E + + Sbjct: 246 GFEAVSVAAQESHNPQKDLPFGMLMSLAICTVLYIGMAAVMTGLTPYTLLGTDEPVVTAV 305 Query: 311 LESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKTGTPV 370 + +V + A+I L +V+L + GQ RIF +MARDGLLP ++++ K TP Sbjct: 306 AGHAELAWLRVVVEIGALIGLSSVVLVMIIGQPRIFMIMARDGLLPEVFTRIHPKHRTPH 365 Query: 371 MMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRVFSTPLW 430 + T++TG+ A+++ + L + EL + GTL AF AV A V++LR +P+ PR F Sbjct: 366 INTVITGIGIALLAAVFPLDILGELTSMGTLIAFGAVCAGVLILRRTQPDLPRPFRIRGV 425 Query: 431 PIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVL 477 V AGI CL L ++ + L +G +Y YG R S L Sbjct: 426 WFVCLAGIFSCLALLSAMTLHNWMLMLGWTTVGFAIYFLYGYRHSKL 472 Lambda K H 0.326 0.138 0.415 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: 674 Number of extensions: 40 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 483 Length of database: 474 Length adjustment: 34 Effective length of query: 449 Effective length of database: 440 Effective search space: 197560 Effective search space used: 197560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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