Align ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS34470 BPHYT_RS34470 ABC transporter
Query= reanno::pseudo1_N1B4:Pf1N1B4_771 (304 letters) >FitnessBrowser__BFirm:BPHYT_RS34470 Length = 285 Score = 325 bits (834), Expect = 6e-94 Identities = 168/285 (58%), Positives = 205/285 (71%), Gaps = 3/285 (1%) Query: 17 ISTPVFAAEL--TGTLKKIKESGTITLGHRDASIPFSYIADASGKPVGYSHDIQLKIVEA 74 +S PV AA+ TGTLKKI++ +T+G+RDASIPFSY DA KP+GYS DI I++ Sbjct: 1 MSLPVIAADAAPTGTLKKIQDQHVVTIGYRDASIPFSYY-DAQQKPIGYSIDIANLIIDR 59 Query: 75 IKKDLDMPNLQVKYNLVTSQTRIPLVQNGTVDVECGSTTNNVERQQQVDFSVGIFEIGTK 134 IK L +LQV+ +TSQ RI L+QNGT+D EC STTNN R QQVDFS F+IGT+ Sbjct: 60 IKAQLKQGDLQVRLIPITSQNRISLLQNGTIDFECTSTTNNAARAQQVDFSNSFFDIGTR 119 Query: 135 LLSKKDSAYKDFADLKGKNVVTTAGTTSERILKSMNADKQMGMNVISAKDHGESFQMLET 194 LL +++S DFADLKGK VV AGTTSE+ +++MN +K MGMN+ISAKDH ESF ML T Sbjct: 120 LLVRQNSGIHDFADLKGKTVVVGAGTTSEKSIRNMNVEKSMGMNIISAKDHSESFLMLST 179 Query: 195 GRAVAFMMDDALLAGEMAKAKKPTDWAVTGTAQSNEIYGCMVRKGDAPFKKAVDDAIIAT 254 GRA A MMDDALLAGE AK +P D+A+ GT QS E YGCM+RK DA K +D AI Sbjct: 180 GRAKAMMMDDALLAGERAKTSRPEDYAIVGTPQSFEAYGCMLRKNDAQLKALMDAAIADA 239 Query: 255 YKSGEINKIYEKWFMQPIPPKGLNLMFPMSEELKALIANPTDKAA 299 +SG IY+KWFM PIPPKG+NL FPMS ++ L A+P DK A Sbjct: 240 ERSGVATAIYKKWFMAPIPPKGINLNFPMSTRMQTLFAHPNDKPA 284 Lambda K H 0.315 0.131 0.365 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: 278 Number of extensions: 9 Number of successful extensions: 2 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: 304 Length of database: 285 Length adjustment: 26 Effective length of query: 278 Effective length of database: 259 Effective search space: 72002 Effective search space used: 72002 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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