Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 7025598 Shewana3_2749 ABC transporter related (RefSeq)
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__ANA3:7025598 Length = 346 Score = 91.7 bits (226), Expect = 2e-23 Identities = 78/255 (30%), Positives = 114/255 (44%), Gaps = 30/255 (11%) Query: 6 TNTMSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYK 65 T++ + + ++ ++ FGG+ A+ D +G I +GPNG GK+T +TG Sbjct: 20 TSSATPEFAIETRGMTRAFGGINAVEDLDLAIPKGTIYGFLGPNGCGKSTSIRMLTGLLS 79 Query: 66 PTMGMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENL-LVAQHNKL 124 PT G I + L E LP R+ Q L+ L+V ENL VAQ Sbjct: 80 PTSGDI--------RVLGETLPGAEEKLRRRIGYMTQKFSLYDNLSVRENLEFVAQ---- 127 Query: 125 MKASGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIAR 184 I GL ++ A EL L DL R AG + G ++RL +A Sbjct: 128 -------IYGL----NRRQTKARLAEL----LSLYDLAGREKQMAGSMSGGQKQRLALAA 172 Query: 185 AMCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVV 244 A PELL LDEP + ++P L + A+ GT+IL+ H M E + + Sbjct: 173 ATLHHPELLFLDEPTSAVDPENRREFWERLFDLCAQ-GTTILVSTHYMDEA-ERCHGLAI 230 Query: 245 LEYGQKISDGTPDHV 259 LE G K +DG+P + Sbjct: 231 LERGIKRADGSPQQL 245 Lambda K H 0.318 0.136 0.386 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: 187 Number of extensions: 12 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: 292 Length of database: 346 Length adjustment: 27 Effective length of query: 265 Effective length of database: 319 Effective search space: 84535 Effective search space used: 84535 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 (21.7 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