Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate YP_004141766.1 Mesci_2580 binding-protein-dependent transport system inner membrane protein
Query= CharProtDB::CH_011913 (426 letters) >NCBI__GCF_000185905.1:YP_004141766.1 Length = 387 Score = 176 bits (446), Expect = 1e-48 Identities = 127/417 (30%), Positives = 217/417 (52%), Gaps = 48/417 (11%) Query: 17 LIYDTRFRSITIQIV----VLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLA 72 L+ + + R+ +Q++ + + LAG+V A NL +G F FL+ G+D+ Sbjct: 4 LLRNQKVRNALLQVLYVGSIAAMVLAGIVI----ARRNLADQGITSGFDFLFKSTGWDVN 59 Query: 73 QTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYV 132 +L+P + +D ++ + G++NTL + +G ILATI+GTI+G+ R S N L + YV Sbjct: 60 FSLLPATANDPYWWYFLIGIINTLFLGSVGLILATIVGTIVGLARTSSNDLARLLGRTYV 119 Query: 133 ETFRNIPLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTN 192 + FRNIPL+L + I+ P P+ W F +T+RG Sbjct: 120 DIFRNIPLILQVFFWYAIITHL-PTPRSAH--------------EAWGF---LLTSRGLY 161 Query: 193 LPAPAFDHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTW 252 +P P N+ + A A +AV++A ++ R + + G R T Sbjct: 162 IPFP-------------NVGSAAFAAATVAVIAAIVLP--AWLGRTSLLAQPIGQRRTIQ 206 Query: 253 WPSLLILFAPISALLYGLGFH-----LDYPQITKFDFTGGFQMLHSFTALLIALTLYTAA 307 + + A + ++ LG LD+P + + GG ++ F L IA+ +Y + Sbjct: 207 FAAAAAALA-CATIILALGRLPDTPLLDFPALQGLNLRGGLRIPPEFATLAIAIAIYGGS 265 Query: 308 FIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSS 367 +IAEIVR G +++ GQ EAA +LGL P R +LV LP ALR ++P L +Q++ L K ++ Sbjct: 266 YIAEIVRGGFKSVGTGQVEAALSLGLSPWRVFTLVRLPLALRAMLPILANQYVWLMKATT 325 Query: 368 LAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLK 424 + IAV + D + +T+N +G+ LE + ++M +L I+L+++++ N NK+I LK Sbjct: 326 MGIAVGFTDF-FMIVALTINHSGQTLEAIGILMAGFLAINLSLAAVFNRINKAIALK 381 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: 337 Number of extensions: 17 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: 387 Length adjustment: 31 Effective length of query: 395 Effective length of database: 356 Effective search space: 140620 Effective search space used: 140620 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