Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_064573369.1 M988_RS06580 histidine ABC transporter ATP-binding protein HisP
Query= TCDB::Q52666 (263 letters) >NCBI__GCF_001655005.1:WP_064573369.1 Length = 257 Score = 235 bits (599), Expect = 8e-67 Identities = 128/251 (50%), Positives = 171/251 (68%), Gaps = 12/251 (4%) Query: 23 IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVD 82 + + +++K YG VL+ ++LT G+ I I G SGSGKST +RCIN LE+ G I ++ Sbjct: 6 LNVIELHKRYGDHEVLKGVSLTAKAGDVISIIGSSGSGKSTFLRCINFLEKPSEGTIAIN 65 Query: 83 GIEL-----------TSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPK 131 G ++ D K + +R+ + MVFQHFNL+ H+T+LEN+ API V + K Sbjct: 66 GTDIGLVRDTDGQLKVGDKKQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSK 125 Query: 132 REAEETAMYYLEKVKIPEQAQ-KYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDP 190 EA E A+ YL+KV I E+A+ KYP LSGGQQQRV+IAR+L M+P+++LFDEPTSALDP Sbjct: 126 AEAHERAIRYLDKVGIDERARGKYPINLSGGQQQRVSIARALAMEPEVLLFDEPTSALDP 185 Query: 191 EMIKEVLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQS 250 E++ EVL M +LAEEG TM+ VTHEMGFA+ V+N VIF+ G I EQ P F NP+S Sbjct: 186 ELVGEVLRIMQKLAEEGKTMVVVTHEMGFARHVSNHVIFLHQGIIEEQGPPELVFGNPKS 245 Query: 251 ERTKQFLSQIL 261 R +QFLS L Sbjct: 246 VRLQQFLSGAL 256 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: 193 Number of extensions: 10 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: 263 Length of database: 257 Length adjustment: 24 Effective length of query: 239 Effective length of database: 233 Effective search space: 55687 Effective search space used: 55687 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: 47 (22.7 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