Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate PfGW456L13_1967 Arginine/ornithine ABC transporter, ATP-binding protein AotP
Query= TCDB::Q52666 (263 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1967 Length = 254 Score = 241 bits (615), Expect = 1e-68 Identities = 121/247 (48%), Positives = 169/247 (68%), Gaps = 11/247 (4%) Query: 23 IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVD 82 +++ ++K YG VL+ ++L G+ I I G SGSGKST +RCIN LE+ +G+I+++ Sbjct: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGRILLN 63 Query: 83 GIEL-----------TSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPK 131 EL +D K + ++RS + MVFQHFNL+ H+T LEN+ AP+ V V K Sbjct: 64 NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTALENIMEAPVHVLGVSK 123 Query: 132 REAEETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPE 191 EA E A +YL KV + + YPG +SGG+QQRVAIAR+L M+P++MLFDEPTSALDPE Sbjct: 124 AEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183 Query: 192 MIKEVLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSE 251 ++ +VL M LA+EG TM+ VTHEMGFA+ V+N+++F+ G + E NP + NPQSE Sbjct: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243 Query: 252 RTKQFLS 258 R +QFLS Sbjct: 244 RLQQFLS 250 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: 188 Number of extensions: 8 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: 263 Length of database: 254 Length adjustment: 24 Effective length of query: 239 Effective length of database: 230 Effective search space: 54970 Effective search space used: 54970 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 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