Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate RR42_RS28305 RR42_RS28305 proline-specific permease
Query= TCDB::P40812 (497 letters) >FitnessBrowser__Cup4G11:RR42_RS28305 Length = 472 Score = 409 bits (1050), Expect = e-118 Identities = 205/466 (43%), Positives = 305/466 (65%), Gaps = 8/466 (1%) Query: 16 RRWLN---AHEE-GYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICG 71 R+ LN HEE H+ + +R +QMIAIGGAIG GLFLGAG + +AGP L L Y I G Sbjct: 5 RKLLNEERVHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGG 64 Query: 72 IFSFFILRALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVAL 131 + FFI+RALGEL+L+RP SGSF +YA EF+G A + GW Y+ W +TG+ +ITAVA+ Sbjct: 65 VAIFFIMRALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAV 124 Query: 132 YMHYWGAFGDVPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIF 191 Y+HYW F DVPQW+ AL L ++ +N + V F E+EFWFALIKV+ IV +V+G Sbjct: 125 YVHYW--FPDVPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAI 182 Query: 192 LGTGQPLEGNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQK 251 + G G F + +GGF P G L ++ +Q V+FA+ +EL+G AGE ++P+K Sbjct: 183 IFFGVTPLGPTASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEK 242 Query: 252 MVPKAINSVIWRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVV 311 ++P A N V+WRI +FYVG++++++ L+PWN + G SPFV F ++GVP +I+N+VV Sbjct: 243 VLPHATNGVVWRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVV 302 Query: 312 LTAALSSLNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNY 371 +TAA SS NSG++ TGR+L +++ G AP+ ++S +HVP I + + +GV LNY Sbjct: 303 ITAAASSCNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNY 362 Query: 372 LVPSRVFEIVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLL 431 +VP +VF V + + +G + +W+ IM+ + R+AI G+ V+F++PGAP+ +WL + Sbjct: 363 IVPEQVFVWVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVA 422 Query: 432 FLLSVLVLMAFDYPNGTYTIASLPLIAILLVAGW-FGVRRRVAEIH 476 F+++V VL++ D P + P+ LL G+ F R + E H Sbjct: 423 FMIAVAVLLSLD-PGTRVALYVAPVWFALLGIGYRFTKSRALLEGH 467 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: 690 Number of extensions: 31 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