Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate 206100 DVU0676 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= CharProtDB::CH_011913 (426 letters) >MicrobesOnline__882:206100 Length = 295 Score = 86.3 bits (212), Expect = 1e-21 Identities = 49/124 (39%), Positives = 78/124 (62%), Gaps = 3/124 (2%) Query: 289 QMLHSFTALLIALTLYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQAL 348 + L +F + ++ L +Y A+I+EIVRAGI+++ RGQ +A+ + GL P + M VILPQAL Sbjct: 160 EQLSAFLSAVVTLAIYEGAYISEIVRAGIESVPRGQWDASSSFGLGPVQQMRHVILPQAL 219 Query: 349 RVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTLGGITL-NQTGRELECMLLMMLIYLTIS 407 R VPPL QF+++ K+S++ +S +L T G+ L T + E + L+YL ++ Sbjct: 220 RHAVPPLAGQFISIIKDSAIVSVISVPEL--TFQGMELMAATYQTFEIWTTIALLYLVLT 277 Query: 408 LTIS 411 L S Sbjct: 278 LGCS 281 Score = 45.8 bits (107), Expect = 2e-09 Identities = 35/141 (24%), Positives = 63/141 (44%), Gaps = 19/141 (13%) Query: 7 PPKAGFRLSMLIYDTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTR 66 P + G + L+ D F ++VL+ A VW +++ ++ + W R Sbjct: 2 PRRCGVSRAALMLDVAF------LLVLVGGAAWFVWRMDDV----------IHYRWHWGR 45 Query: 67 AGYDLAQTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVAR 126 L + + H L GL T+ +S+ + A +LGT+ G+LR + L Sbjct: 46 V---LEGLVYVTPQGEWHAGPLARGLAGTVRLSLWAMLAALLLGTVAGLLRTRRRLLARL 102 Query: 127 IMTVYVETFRNIPLLLWILLM 147 + YV++ RN+P L+ I +M Sbjct: 103 LAGTYVDSVRNLPALVLIFVM 123 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: 232 Number of extensions: 8 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 426 Length of database: 295 Length adjustment: 29 Effective length of query: 397 Effective length of database: 266 Effective search space: 105602 Effective search space used: 105602 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: 49 (23.5 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