Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate PP_4840 PP_4840 D-alanine, beta-alanine, D-serine, glycine permease
Query= TCDB::P40812 (497 letters) >FitnessBrowser__Putida:PP_4840 Length = 468 Score = 320 bits (820), Expect = 7e-92 Identities = 171/452 (37%), Positives = 270/452 (59%), Gaps = 7/452 (1%) Query: 23 EEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALG 82 E + + NR +Q+IAIGGAIGTGLF+G+G + +AGP++ VY+I G FF++RA+G Sbjct: 11 EPHLQRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMG 70 Query: 83 ELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDV 142 EL+L + SF+ ++ + LG A Y GW Y+ W +TGI D+ A+A Y +W F D+ Sbjct: 71 ELLLSNLNYKSFIDFSADLLGPWAGYFTGWTYWFCWVVTGIADVVAIAAYTQFW--FPDL 128 Query: 143 PQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTG-QPLEGN 201 PQW+ AL + ++ ++N++ VK F E+EFWFAL+K++AI+ + G + TG G Sbjct: 129 PQWIPALTCVGLLLSLNLVTVKMFGELEFWFALVKIVAILGLVATGLYMVITGFTSPSGR 188 Query: 202 ATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVI 261 + ++GG FPHGL+ Q VFAF IELVGT A E K+P++ +P+AINS+ Sbjct: 189 TAQLANLWNDGGMFPHGLMGFFAGFQIAVFAFVGIELVGTTAAEAKNPERTLPRAINSIP 248 Query: 262 WRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNS 321 RI +FYV +++ ++ + PW G+SPFV F G+P SI+N VVLT+A SS NS Sbjct: 249 IRIIVFYVLALIAIMAVTPWRDVVPGKSPFVELFVLAGLPAAASIINFVVLTSAASSANS 308 Query: 322 GLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRV--FE 379 G++ T R+L +S G APK K+S + VP G+ + ++G L YLVP+ V F Sbjct: 309 GVFSTSRMLYGLSQEGDAPKAFEKLSSRSVPANGLYFSCTCLLLGAVLIYLVPNVVEAFT 368 Query: 380 IVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVL 439 +V +++ + W I++ ++ R+ A ++K+PG F ++ L F +LVL Sbjct: 369 LVTTVSAVLFMFVWTLILLSYLKYRKDRAALHQAS-NYKMPGGRFMCYVCLSFFAFILVL 427 Query: 440 MAFDYPNGTYTIASLPLIAILLVAGWFGVRRR 471 ++ + + + + P+ ++L + VR R Sbjct: 428 LSLEADTRSALVVT-PIWFVVLAVTYQLVRSR 458 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: 664 Number of extensions: 34 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: 497 Length of database: 468 Length adjustment: 34 Effective length of query: 463 Effective length of database: 434 Effective search space: 200942 Effective search space used: 200942 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