Align lysine-specific permease (characterized)
to candidate AO356_28340 AO356_28340 GABA permease
Query= CharProtDB::CH_003129 (489 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28340 Length = 466 Score = 273 bits (699), Expect = 7e-78 Identities = 158/450 (35%), Positives = 254/450 (56%), Gaps = 18/450 (4%) Query: 13 LRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTSLGEL 72 L + K RH+TM++I G IG GLFV SG I+ AGP +L+Y+ GL+V +M LGE+ Sbjct: 13 LAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPA-VMLAYLFSGLLVVLVMRMLGEM 71 Query: 73 AAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPDTPGWI 132 A P +GSF+TY + GF +GW YW+ W + I ++ +AA V++ WFP W+ Sbjct: 72 AVANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVLNQWFPAVDAWL 131 Query: 133 WSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIFKGAQPAGWSN 192 ++++ + ++ + N SV +GE E+WF++ KV +I FI +G +++G + +G S Sbjct: 132 FASVSIVLLAVTNLFSVSKYGEFEFWFAMAKVVAIIGFISLGFAVLMGWIPEREASGLSR 191 Query: 193 WTIGEAPFA-GGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFWRILL 251 FA G +A++G + + FSF GTE + IAA ES++PA+NI +A R V WRI + Sbjct: 192 LMEEHGGFAPNGLSAVVGAFITIMFSFIGTEAVTIAAAESDNPAQNIAKATRSVIWRIGV 251 Query: 252 FYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTAVLSA 311 FY+ +I ++ ++P+ DP L SV + + + A +++ V+L AV S Sbjct: 252 FYLLSIFVVISVVPWNDPLL-------ASVGSYQRALELMNIPHAKFLVDMVVLIAVASC 304 Query: 312 GNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSMFGNQTVY 371 NS +Y ++RMLY+L G AP+ S GVPR+A+ A+TV+ L S F ++ Sbjct: 305 MNSSIYIASRMLYSLGRRGDAPKALKVTSSAGVPRSAVIASTVLGAGVTLFSYFMPAGLF 364 Query: 372 LWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGPIFAFILCLII 431 +LL +SG + +L IAIS R RR ++Q +I +LP+R FP ++ L+I Sbjct: 365 QFLLASSGAIALLVYLVIAISQLRMRR--MMQRQNI-ELPFRMWLFP------WLTWLVI 415 Query: 432 TLGQNYEAFLKDTIDWGGVAATYIGIPLFL 461 A + T + +T +G+ L + Sbjct: 416 VFISAALAVMMITPEHRSEVSTTLGLALII 445 Lambda K H 0.327 0.142 0.451 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: 712 Number of extensions: 47 Number of successful extensions: 5 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: 489 Length of database: 466 Length adjustment: 34 Effective length of query: 455 Effective length of database: 432 Effective search space: 196560 Effective search space used: 196560 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