Align L-asparagine permease; L-asparagine transport protein (characterized)
to candidate Pf6N2E2_4195 transport permease protein of gamma-aminobutyrate
Query= SwissProt::P77610 (499 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4195 Length = 464 Score = 265 bits (676), Expect = 3e-75 Identities = 154/454 (33%), Positives = 246/454 (54%), Gaps = 11/454 (2%) Query: 33 RQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGLFSFFILRALGELVLHRPSSG 92 R V M++I G IG GLF+G+G + AGPA+ L Y G ++R LGE+ + P +G Sbjct: 17 RHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGALVVLVMRMLGEMAVASPDTG 76 Query: 93 SFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGGVPQWVFALAAL 152 SF +YA +G A + GW+Y+ W + ++ A A +H W F V W F L Sbjct: 77 SFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAW--FPNVAIWAFTLVIT 134 Query: 153 TIVGTMNMIGVKWFAEMEFWFALIKVLAIVTFLVVGTVFLGSGQPLDGNTTGFHLITDNG 212 ++ N+ VK + E EFWFAL+KV+AI+ F+ +G + + P +G + D Sbjct: 135 LLLTVTNLFSVKNYGEFEFWFALVKVVAIIGFIGLGVMAIFGVLP-TSQVSGVSHLFDTQ 193 Query: 213 GFFPHGLLPALVLIQGVVFAFASIEMVGTAAGECKDPQTMVPKAINSVIWRIGLFYVGSV 272 GF P+G+ L I +F+F E+V AA E K+P + KA NSVIWRIGLFY+ S+ Sbjct: 194 GFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSVIWRIGLFYLVSI 253 Query: 273 VLLVMLLPWS-AYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGLYCTGRILR 331 ++V L+PW+ A + T ++G+P I++IVVL A S LNS LY R++ Sbjct: 254 FIVVALVPWNDPLLASVGSYQTVLERMGIPNAKLIVDIVVLVAVTSCLNSALYTASRMMF 313 Query: 332 SMAMGGSAPSFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLNFASLGIIA 391 S+ G AP+ + ++ PY ++ + + VF NY+ P+ VF+ +L AS G IA Sbjct: 314 SLGKRGDAPAVSQRTNKSGTPYWAVMLSTGAAFLAVFANYVAPAAVFDFLL--ASSGAIA 371 Query: 392 SWAFII--VCQMRLRKAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAFDYPNGTY 449 +++ V Q+R+RK + + V+F + P ++ ++F++ L +M F + Sbjct: 372 LLVYLVIAVSQLRMRKQ-RMARGEKVAFSMWLFPGLTYAVIVFIVGALTIMLFQEAH-RV 429 Query: 450 TIAALPIIGILLVI-GWFGVRKRVAEIHSTAPVV 482 I A ++ +L+VI G R+R+A+ P + Sbjct: 430 EILATGLLSVLVVISGVLVQRRRIAKTGRLVPTL 463 Lambda K H 0.327 0.141 0.435 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: 655 Number of extensions: 46 Number of successful extensions: 4 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: 499 Length of database: 464 Length adjustment: 34 Effective length of query: 465 Effective length of database: 430 Effective search space: 199950 Effective search space used: 199950 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