Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate AO353_24335 AO353_24335 L-asparagine permease
Query= TCDB::P40812 (497 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24335 Length = 494 Score = 665 bits (1715), Expect = 0.0 Identities = 311/451 (68%), Positives = 380/451 (84%) Query: 15 KRRWLNAHEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFS 74 + WL++HE GY K + R VQM+A+GGAIGTGLFLGAGARLQ+AGPALA++YL+CGIF+ Sbjct: 21 RSNWLDSHESGYSKHLKKRHVQMMALGGAIGTGLFLGAGARLQIAGPALAVIYLVCGIFA 80 Query: 75 FFILRALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMH 134 FFILRALGELV+HRPSSGSFVSY REF+GE+A++VAGWMYF+ WA+TG+VDITA+A+YM Sbjct: 81 FFILRALGELVMHRPSSGSFVSYTREFMGERASFVAGWMYFVVWALTGVVDITAIAIYMK 140 Query: 135 YWGAFGDVPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGT 194 YW F DVPQWVFAL AL +V MNM+GVKWF EMEFWFA+IKV AI IFLV+G+ F T Sbjct: 141 YWSVFSDVPQWVFALSALGVVTLMNMVGVKWFGEMEFWFAVIKVAAISIFLVIGSFFFAT 200 Query: 195 GQPLEGNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVP 254 G + G+ G HLITDNGG FPHGLLPA++++QGV+FA+ASIELVGTAAGE D +K++P Sbjct: 201 GHEVAGHIPGLHLITDNGGIFPHGLLPAIIIVQGVIFAYASIELVGTAAGETADARKVIP 260 Query: 255 KAINSVIWRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTA 314 KAIN VIWRI LFYVGSV LLV +LPW AY A SPFVTFF LGVP IGS+MNIVV+TA Sbjct: 261 KAINGVIWRISLFYVGSVFLLVTVLPWTAYSANVSPFVTFFEALGVPGIGSVMNIVVMTA 320 Query: 315 ALSSLNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVP 374 ALSSLNSGLY TGR+LRS++MGGSAPK +MS Q VPY GIL T+ + V GV LN+L+P Sbjct: 321 ALSSLNSGLYATGRVLRSLAMGGSAPKMFKRMSSQGVPYMGILVTMGINVFGVVLNFLIP 380 Query: 375 SRVFEIVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLL 434 +++FE++LN SLGII++WAFI++ Q+ R+A+K G+ VSF++PGAPFTSWLTL+FLL Sbjct: 381 AQLFELLLNLVSLGIISTWAFIVLSQINYRRAVKRGEVEMVSFRMPGAPFTSWLTLVFLL 440 Query: 435 SVLVLMAFDYPNGTYTIASLPLIAILLVAGW 465 VLVL+AFDYPNGTYT+ S+PL+A L+ GW Sbjct: 441 VVLVLLAFDYPNGTYTVLSIPLVAGALMLGW 471 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: 838 Number of extensions: 47 Number of successful extensions: 1 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: 494 Length adjustment: 34 Effective length of query: 463 Effective length of database: 460 Effective search space: 212980 Effective search space used: 212980 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