Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate WP_085640555.1 MGEO_RS16995 ABC transporter permease subunit
Query= CharProtDB::CH_011913 (426 letters) >NCBI__GCF_002115805.1:WP_085640555.1 Length = 404 Score = 410 bits (1053), Expect = e-119 Identities = 221/428 (51%), Positives = 288/428 (67%), Gaps = 26/428 (6%) Query: 1 MALASDPPKAGFRLSMLIYDTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNF 60 M+ SDPP F+LSMLI DTR+RS T Q + L+L + +L +N NL+A G + ++ Sbjct: 1 MSTISDPPSGSFQLSMLINDTRYRSYTFQFIALILLILAFGYLGSNLLANLKAAGLNISY 60 Query: 61 SFLWTRAGYDLAQTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQ 120 FL AGYD+ QTLIPY++ TH++A + G+LNTLLV+ LGC++AT++G ++GVLRLS Sbjct: 61 QFLGEPAGYDINQTLIPYTSQSTHWQASLVGVLNTLLVAFLGCLMATVIGVVVGVLRLSD 120 Query: 121 NWLVARIMTVYVETFRNIPLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWF 180 NWLV ++M++YVE FRN+P+L+WIL++ + P P+DFR GE+ +ASM Sbjct: 121 NWLVRQLMSIYVEIFRNVPVLIWILIIMAVFIAVLPQPRDFR--------GEDAEASM-V 171 Query: 181 FDSVAVTNRGTNLPAPAFDHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKA 240 A T RG PAP F G V +AV AS G F AK Sbjct: 172 LGMFAFTGRGFYTPAPIFGVGSGFV---------------VAVFLASIAGIFAFRNYAKK 216 Query: 241 VQEATGTRPTTWWPSLLILFAP--ISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALL 298 G T+WPS+ I F P ++ + G L+YP++ F+F GG M +S AL Sbjct: 217 ALYERGRLIPTFWPSVAIFFIPSILAYFILGRPISLEYPELKGFNFQGGIFMRNSLIALW 276 Query: 299 IALTLYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQ 358 AL++YTAAFIAE VRAGI A+S+GQTEAA +LGLRPGR M+LV+LPQALRVI+PPLISQ Sbjct: 277 FALSIYTAAFIAENVRAGILAVSKGQTEAAASLGLRPGRIMNLVVLPQALRVIIPPLISQ 336 Query: 359 FLNLTKNSSLAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYN 418 +LNLTKNSSLAIAV YMDL GTLGGITLNQTGR +E + L+ML YL ISL IS++MN+YN Sbjct: 337 YLNLTKNSSLAIAVGYMDLTGTLGGITLNQTGRAIEAIFLLMLFYLAISLAISAIMNVYN 396 Query: 419 KSIKLKER 426 ++KLKER Sbjct: 397 NAVKLKER 404 Lambda K H 0.326 0.139 0.419 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: 457 Number of extensions: 20 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: 426 Length of database: 404 Length adjustment: 31 Effective length of query: 395 Effective length of database: 373 Effective search space: 147335 Effective search space used: 147335 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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