Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF559 Psest_0564 urea ABC transporter, ATP-binding protein UrtD
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__psRCH2:GFF559 Length = 283 Score = 139 bits (350), Expect = 7e-38 Identities = 96/260 (36%), Positives = 138/260 (53%), Gaps = 19/260 (7%) Query: 13 TLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMIT 72 T+L +E +++ F G A+ D S G++ +IGPNGAGKTT+ + ITG +PT G Sbjct: 41 TILSLEDINVSFDGFKALTDLSLYIGVGELRCIIGPNGAGKTTMMDVITGKTRPTSGSAW 100 Query: 73 FNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQH-NKLMKASGYT 131 F G+ L R+ + I +A + R FQ +F L+V ENL +AQ +K + AS Sbjct: 101 F----GETLDLTRMSEVDIA-QAGIGRKFQKPTVFEALSVFENLELAQKTDKSVWASLRA 155 Query: 132 ILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPE 191 L G K E +E R L PAG L +G ++ LEI + P+ Sbjct: 156 KLS----GEQKDRIDEVLETIR-------LGQSRHRPAGLLSHGQKQFLEIGMLLMQSPQ 204 Query: 192 LLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKI 251 LL LDEP AG+ E+ L KS+ + S++++EHDM V I+DHV VL GQ + Sbjct: 205 LLLLDEPVAGMTDAETEFTAELFKSLARK--HSLMVVEHDMGFVETIADHVTVLHQGQVL 262 Query: 252 SDGTPDHVKNDPRVIAAYLG 271 ++G+ V+ D RVI YLG Sbjct: 263 AEGSLQQVQADERVIEVYLG 282 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: 176 Number of extensions: 8 Number of successful extensions: 4 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: 283 Length adjustment: 26 Effective length of query: 266 Effective length of database: 257 Effective search space: 68362 Effective search space used: 68362 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: 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