Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 8502075 DvMF_2788 ABC transporter related (RefSeq)
Query= TCDB::Q52666 (263 letters) >FitnessBrowser__Miya:8502075 Length = 243 Score = 320 bits (820), Expect = 2e-92 Identities = 157/242 (64%), Positives = 191/242 (78%), Gaps = 1/242 (0%) Query: 23 IQISQMNKWYGQ-FHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIV 81 I+ ++KWY HVL+DI L + +GE +VI GPSGSGKST+IRCIN+LE Q G I+V Sbjct: 2 IKFDHVHKWYASGLHVLQDITLEIKQGEVVVICGPSGSGKSTLIRCINKLEPIQKGHIVV 61 Query: 82 DGIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAMYY 141 DG+++ N+ +R+EVG VFQ FNL+PH+T+LEN+TLAP+ VR P+ EAE+TAM Sbjct: 62 DGVDINDPRTNLTMLRAEVGFVFQQFNLYPHMTVLENITLAPLLVRNTPRAEAEKTAMEL 121 Query: 142 LEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDTMI 201 LEKV IP++A YPGQLSGGQQQRVAIAR L MKP+IMLFDEPTSALDPEMI EVLD M Sbjct: 122 LEKVNIPDKAGAYPGQLSGGQQQRVAIARGLAMKPRIMLFDEPTSALDPEMINEVLDVMR 181 Query: 202 QLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQFLSQIL 261 QLA EGMTM+CVTHEMGFA+ VA+RVIFM G +VE+N P FF NP +RTK+FLS+IL Sbjct: 182 QLAREGMTMVCVTHEMGFAREVADRVIFMDQGVMVEENTPEAFFSNPVHDRTKEFLSKIL 241 Query: 262 GH 263 H Sbjct: 242 TH 243 Lambda K H 0.320 0.134 0.391 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: 233 Number of extensions: 5 Number of successful extensions: 1 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: 263 Length of database: 243 Length adjustment: 24 Effective length of query: 239 Effective length of database: 219 Effective search space: 52341 Effective search space used: 52341 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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