Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Synpcc7942_1893 Synpcc7942_1893 ATPase
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__SynE:Synpcc7942_1893 Length = 258 Score = 159 bits (402), Expect = 6e-44 Identities = 99/266 (37%), Positives = 150/266 (56%), Gaps = 14/266 (5%) Query: 10 SDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMG 69 ++ LL+ E LS +FGGL A+ D + G IT LIGPNGAGK+T+F ++ F K G Sbjct: 3 AESWLLEAEGLSKRFGGLQAVQDVRLQVAEGTITGLIGPNGAGKSTLFALLSNFLKADAG 62 Query: 70 MITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASG 129 + F ++ +E+L +++ + + RTFQ R S LTVLEN+L+ + + Sbjct: 63 KVRFRGRA-----IEKLQPYQLA-QLGLVRTFQVARSLSRLTVLENMLLGGQQQRGEKFW 116 Query: 130 YTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTG 189 L + +R+ E + A L L +A D AG L G ++ LE+ARA+ Sbjct: 117 QVWLHPQAI---RRQEQELRDRAFSLLSDVGLAAKAQDYAGSLSGGQRKLLEMARALMAQ 173 Query: 190 PELLCLDEPAAGLNPRESATLNALLKSIRA--ETGTSILLIEHDMSVVMEISDHVVVLEY 247 P+L+ LDEPAAG+NP A + + I+ + G S L+IEH+M V+M + D V VL Sbjct: 174 PQLVLLDEPAAGVNP---ALIEKICDHIQTWNQQGISFLIIEHNMDVIMSLCDRVWVLAE 230 Query: 248 GQKISDGTPDHVKNDPRVIAAYLGVE 273 G+ + DG P ++ D +V+AAYLG+E Sbjct: 231 GKNLVDGPPAQIQQDEQVLAAYLGLE 256 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: 191 Number of extensions: 11 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: 258 Length adjustment: 25 Effective length of query: 267 Effective length of database: 233 Effective search space: 62211 Effective search space used: 62211 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