Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 255 bits (651), Expect = 2e-72 Identities = 165/394 (41%), Positives = 221/394 (56%), Gaps = 57/394 (14%) Query: 1 MAKIQFSNIKKSF---------GSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAG 51 +A + F I+K F G VL GI+L+IA GEF+V+VGPSGCGKSTLLR LAG Sbjct: 23 VAGVVFEEIEKRFPEQARSPQKGEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAG 82 Query: 52 LESADSGTISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKN------- 104 LE+ G I + ++++ + + RDIAMVFQSYALYPH++V +N+ FGL+ + Sbjct: 83 LETPSRGLIKVGDRRVDRLPAKARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQ 142 Query: 105 ---LAA--------------AEITKRVNEISELLQIKHLLDRKPKELSGGQRQRVALGRA 147 LA A I +RV E++ +LQ+ LLDR+PK+LSGGQ+QRVALGRA Sbjct: 143 QLALATRSLPKSLQYEPEQEARIKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRA 202 Query: 148 LSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNSKSTMIYVTHDQMEATTLGDRIAVL 207 ++R V L DEPLSNLDA LR++ R +I L T +YVTHDQ EA T+GDRIAVL Sbjct: 203 IARNPQVFLMDEPLSNLDAKLRAETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVL 262 Query: 208 KDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFLEGAVLEKI-------------PW-P 253 G ++Q+ +P EIY RP N F+A FIGSP MN + V + W P Sbjct: 263 NRGHLQQVASPLEIYDRPANRFVAQFIGSPPMNLIPVTVRAPLQLTTENFRCTLPEAWEP 322 Query: 254 EARKAD---QILGIRPDAFALNQGPLGTQEVALGDFQIDISENLGGQQMLHGTL--AGNN 308 R D LGIRP+ L G ++ + + + E LG + G L +G Sbjct: 323 VLRLYDGQTVELGIRPE--HLEVGAAASKNLLI---TVTGVEALGSDTFIAGELKESGIA 377 Query: 309 VRILVDSMDNFSMKQTLPLKIDLTKAHLFDKKTG 342 V+ + + M L L + HLFD +TG Sbjct: 378 VQARLAPQQCWQMGDRLWLTFKPDQIHLFDLETG 411 Lambda K H 0.318 0.136 0.383 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: 361 Number of extensions: 10 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: 347 Length of database: 417 Length adjustment: 30 Effective length of query: 317 Effective length of database: 387 Effective search space: 122679 Effective search space used: 122679 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: 50 (23.9 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