Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family
Query= TCDB::P40812 (497 letters) >FitnessBrowser__Burk376:H281DRAFT_04042 Length = 506 Score = 333 bits (853), Expect = 1e-95 Identities = 171/467 (36%), Positives = 280/467 (59%), Gaps = 7/467 (1%) Query: 8 AAEQHAAKRRWLNA-HEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALV 66 A E H R NA ++G + + NR +Q+IA+GGAIGTGLFLG+ + LQ AGP++ L Sbjct: 36 AIEIHTLGRNLDNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILG 95 Query: 67 YLICGIFSFFILRALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDI 126 Y I G+ +F I+R LGE+V P +GSF +A ++ G+ +++GW Y++ + + + ++ Sbjct: 96 YAIGGVIAFMIMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAEL 155 Query: 127 TAVALYMHYWGAFGDVPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLV 186 TAV Y+HYW + VP WV AL + +N+ VK + E EFWFA+IKV+A++ ++ Sbjct: 156 TAVGTYVHYW--WPGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMIL 213 Query: 187 VGTIFLGTGQPLEGNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGEC 246 G L +G G + +GGFFPHG ++ ++F+F +EL+G A E Sbjct: 214 FGGYLLVSGHG--GPQASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEA 271 Query: 247 KDPQKMVPKAINSVIWRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSI 306 +PQK +PKA+N VI+RI +FY+ S+ +L+ L PWN AG SPFV FS++G ++ Sbjct: 272 DEPQKSIPKAVNQVIYRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANV 331 Query: 307 MNIVVLTAALSSLNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVG 366 +N+VVLTAALS NSG+Y R+L ++ G+AP+ + K+ R+ VPY I + + Sbjct: 332 LNVVVLTAALSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTC 391 Query: 367 VFLNYLVPSRVFEIVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTS 426 V +NYL+P+ +++ ++ +WA I + ++ R+A+ + FK P ++ Sbjct: 392 VIVNYLIPAEALGLLMALVVAALVLNWALISLTHLKSRRAM-VAAGETLVFKSFWFPVSN 450 Query: 427 WLTLLFLLSVLVLMAFDYPNGTYTIASLPLIAILLVAGWFGVRRRVA 473 W+ L F+ +LV++A P + ++ +P+ +++ AG+ RRR A Sbjct: 451 WICLAFMALILVILAMT-PGLSVSVLLVPVWLVVMWAGYAFKRRRAA 496 Lambda K H 0.328 0.140 0.434 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: 689 Number of extensions: 37 Number of successful extensions: 3 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: 497 Length of database: 506 Length adjustment: 34 Effective length of query: 463 Effective length of database: 472 Effective search space: 218536 Effective search space used: 218536 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: 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