Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate PP_1059 PP_1059 Uncharacterized amino acid permease YtnA
Query= TCDB::P40812 (497 letters) >FitnessBrowser__Putida:PP_1059 Length = 472 Score = 357 bits (917), Expect = e-103 Identities = 172/415 (41%), Positives = 269/415 (64%), Gaps = 2/415 (0%) Query: 28 KAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGELVLH 87 + +G R ++++A+G IG GLFLG+ ++MAGPA+ L Y+I G+ I+RALGE+ +H Sbjct: 20 RELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMAVH 79 Query: 88 RPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWVF 147 P +GSF YA+++LG A ++ GW Y+ W +T + +ITAVA+YM W F DVP+W++ Sbjct: 80 NPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAIYMGIW--FPDVPRWIW 137 Query: 148 ALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTGQPLEGNATGFHL 207 AL AL +G +N++ VK F E EFWFALIK++ I+ ++ G + G +G A G Sbjct: 138 ALAALGSMGAVNLVAVKAFGEFEFWFALIKIVTIIAMVLGGIGIIAFGFGNDGVAVGISN 197 Query: 208 ITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWRIGLF 267 + NGGF P+G+ L+ +Q V+FA+ +E++G AGE ++PQK +P+AI SV WRI LF Sbjct: 198 LWSNGGFMPNGVTGVLMSLQMVMFAYLGVEMIGLTAGEARNPQKTIPQAIGSVFWRILLF 257 Query: 268 YVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGLYCTG 327 YVG++ +++ + PWN + SPFV F +LG+ I+N VV+TAALSS N G++ TG Sbjct: 258 YVGALFVILSIYPWNEIGSQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317 Query: 328 RILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLNFASL 387 R+L S++ G AP A+ S+ VP +L ++ ++GV NYLVP +VF V + A+ Sbjct: 318 RMLYSLAQNGQAPAAFARTSKNGVPRNALLLSIGALLLGVLANYLVPEKVFVWVTSIATF 377 Query: 388 GIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAF 442 G I +W I++ Q++ R + + + +++ P +S+L L FL+ V+ LMA+ Sbjct: 378 GAIWTWVMILLAQLKFRAGLTTAERKALKYRMWLWPLSSYLALAFLVLVVGLMAY 432 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: 696 Number of extensions: 43 Number of successful extensions: 2 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: 472 Length adjustment: 34 Effective length of query: 463 Effective length of database: 438 Effective search space: 202794 Effective search space used: 202794 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