Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate H281DRAFT_01668 H281DRAFT_01668 gamma-aminobutyrate:proton symporter, AAT family
Query= TCDB::P40812 (497 letters) >FitnessBrowser__Burk376:H281DRAFT_01668 Length = 459 Score = 256 bits (654), Expect = 1e-72 Identities = 154/452 (34%), Positives = 244/452 (53%), Gaps = 5/452 (1%) Query: 28 KAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGELVLH 87 K++ R + MIA+GG IG GLF+G+G+ + AGPA L YLI G+ ++ LGE+ Sbjct: 8 KSLKQRHITMIALGGVIGAGLFVGSGSIIATAGPAAILSYLIGGVMVTLVMFMLGEMASR 67 Query: 88 RPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWVF 147 P SGSF +YA +LGE A + GW+Y+ +T V+ + +H + + VP Sbjct: 68 NPDSGSFSTYANSYLGEWAGFAVGWLYWFKSMITITVEAILLGAILHDFLPWLPVPAG-- 125 Query: 148 ALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTGQPLEGNATGFHL 207 AL L + N V+ F E E+W + KV I++F+V+G L QP A G Sbjct: 126 ALFMLIALMATNAYSVRAFGEAEYWLSFAKVATIIVFMVLGASILFGLQP-GIPAPGLLN 184 Query: 208 ITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWRIGLF 267 +TD+GGF P+G+ P + + V+F+ E+ AAGE ++P K V +AI SVI R+ +F Sbjct: 185 LTDHGGFMPNGISPVISGVMVVIFSLGGSEIAAVAAGESENPSKNVIRAIKSVILRVMVF 244 Query: 268 YVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGLYCTG 327 YVGSV +L+L +PW +SP+V+ FS G M IV+ + +S +NS L+ Sbjct: 245 YVGSVSILILCMPWTDKANLKSPYVSLFSMAGFTGAAVAMKIVLFVSFMSVMNSFLFSNS 304 Query: 328 RILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLNFASL 387 R+L S+S G AP + + + VP ++ LVV V + +++L +F ++ + Sbjct: 305 RMLFSLSQRGHAPAMFGRTNAKGVPMNALVLCLVVCVSILGIHFLSGGDLFLMLAKSSGA 364 Query: 388 GIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAFDYPNG 447 ++ W FI+V +R+ K + SF+ P ++W+ LL L++VL AF+ P Sbjct: 365 FVMIVWIFIIVAHFAMRRQTKHEQRDPASFRAWFYPVSNWVALLALVAVLGSQAFN-PES 423 Query: 448 TYTIASLPLIAILLVAGWFGVRRRVAEIHRTA 479 + A+ +VA W+ VRRR +T+ Sbjct: 424 RFQFWFAVSTALAIVA-WYYVRRRHPSFGQTS 454 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: 601 Number of extensions: 34 Number of successful extensions: 5 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: 459 Length adjustment: 34 Effective length of query: 463 Effective length of database: 425 Effective search space: 196775 Effective search space used: 196775 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 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