Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate WP_002722555.1 RSPH17029_RS02005 ABC transporter permease subunit
Query= CharProtDB::CH_011913 (426 letters) >NCBI__GCF_000015985.1:WP_002722555.1 Length = 420 Score = 519 bits (1337), Expect = e-152 Identities = 261/426 (61%), Positives = 326/426 (76%), Gaps = 6/426 (1%) Query: 1 MALASDPPKAGFRLSMLIYDTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNF 60 MA +D PK FRLSML+YDTR+RS+TIQ+ V LF+AG WL++N NLEA GKDF+F Sbjct: 1 MANVADAPKDSFRLSMLLYDTRYRSLTIQVFVFFLFMAGAAWLVDNTMRNLEALGKDFDF 60 Query: 61 SFLWTRAGYDLAQTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQ 120 FLW RAGYD++Q L+ Y+ND TH RA++ GLLNTLL+++LGC+ AT++G ++GVLRLS+ Sbjct: 61 GFLWNRAGYDISQRLVDYTNDSTHGRAMLVGLLNTLLIALLGCMAATVIGVLVGVLRLSR 120 Query: 121 NWLVARIMTVYVETFRNIPLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWF 180 NW+V R+MTVYVE FRN+PLLLWILL+ + +E P P FR A F Sbjct: 121 NWIVGRLMTVYVEVFRNVPLLLWILLIYAVFSEATPAPNAFRPNPETGIADRS-----MF 175 Query: 181 FDSVAVTNRGTNLPAPAFDHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKA 240 D++AVTNR T LP P F LG +DLG V+++ LA++ + A ++ R ARA Sbjct: 176 LDAIAVTNRYTALPNPVFSRELGWLDLGL-FYVNMDVLAVIGAIIAGWFINRSVKARATR 234 Query: 241 VQEATGTRPTTWWPSLLILFAPISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIA 300 +QEATG RP TWW SLL+L A+L LGFHL++P++ F+F GG + +SF AL +A Sbjct: 235 IQEATGERPATWWSSLLLLVGLPVAVLLALGFHLEFPELRGFNFVGGLNVSNSFMALWLA 294 Query: 301 LTLYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFL 360 L+LYT AFIAEIVR GI A+SRGQ+EAA+ALGLRPGRTM+LVILPQALRVI+PPLISQ+L Sbjct: 295 LSLYTGAFIAEIVRGGILAVSRGQSEAAFALGLRPGRTMNLVILPQALRVIIPPLISQYL 354 Query: 361 NLTKNSSLAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKS 420 NLTKNSSLAIAV Y+DLRGTLGGITLNQTGRELEC+LLMMLIYL ISL IS +MN+YN + Sbjct: 355 NLTKNSSLAIAVGYLDLRGTLGGITLNQTGRELECVLLMMLIYLAISLVISGVMNVYNSA 414 Query: 421 IKLKER 426 +KLKER Sbjct: 415 VKLKER 420 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: 542 Number of extensions: 13 Number of successful extensions: 3 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: 420 Length adjustment: 32 Effective length of query: 394 Effective length of database: 388 Effective search space: 152872 Effective search space used: 152872 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 Apr 10 2024. 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