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) >lcl|FitnessBrowser__Putida:PP_4840 PP_4840 D-alanine, beta-alanine, D-serine, glycine permease 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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