Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AO356_08485 AO356_08485 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_08485 Length = 290 Score = 274 bits (700), Expect = 2e-78 Identities = 142/290 (48%), Positives = 200/290 (68%), Gaps = 27/290 (9%) Query: 12 DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71 + +LKVE+L M+FGG+ A++D S + KR I ALIGPNGAGKTTVFNC+TGFYK T G I Sbjct: 3 EVVLKVENLMMQFGGIKALSDVSLQVKRNSIFALIGPNGAGKTTVFNCLTGFYKATGGKI 62 Query: 72 TFNQKSGKQYLLERLPD-FRIT-----------------------KEARVARTFQNIRLF 107 N + + +++ L + FR T A +ARTFQNIRLF Sbjct: 63 ELNVRGEQTNVIKLLGEAFRPTDFVSPKSFASRLYYKMFGGTHLVNRAGLARTFQNIRLF 122 Query: 108 SGLTVLENLLVAQHNKLMKASGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADD 167 ++VLENLLVAQH M + + G++ Y++ ++A++ A +WLE DL+D A+ Sbjct: 123 KEMSVLENLLVAQH---MWVNRSMVAGILNTKGYRKAESDALDHAFYWLEVVDLVDCANR 179 Query: 168 PAGDLPYGAQRRLEIARAMCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILL 227 AG+L YG QRRLEIARAMCT P+++CLDEPAAGLNP+E+ L+A+++ +R E +++L Sbjct: 180 LAGELSYGQQRRLEIARAMCTRPQIICLDEPAAGLNPQETEALSAMIRLLRDEHDLTVVL 239 Query: 228 IEHDMSVVMEISDHVVVLEYGQKISDGTPDHVKNDPRVIAAYLGVEDEEV 277 IEHDM +VM ISDH+VVL++G I++G P+ ++NDP+VIAAYLG ++EE+ Sbjct: 240 IEHDMGMVMSISDHIVVLDHGNVIAEGGPEAIRNDPKVIAAYLGADEEEL 289 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: 249 Number of extensions: 8 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: 292 Length of database: 290 Length adjustment: 26 Effective length of query: 266 Effective length of database: 264 Effective search space: 70224 Effective search space used: 70224 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 Apr 09 2024. 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