Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 287 bits (735), Expect = 3e-82 Identities = 171/374 (45%), Positives = 228/374 (60%), Gaps = 38/374 (10%) Query: 21 LKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVDDADISGMSPKDRDIA 80 L I L+I DGEF+++VGPSGCGKSTL+ +AGLET S G I V D + + K RDIA Sbjct: 50 LNGINLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDRLPAKARDIA 109 Query: 81 MVFQSYALYPTMSVRDNIAFGLK---------------IRKMPT---------AEIDEEV 116 MVFQSYALYP +SV DN+AFGL+ R +P A I V Sbjct: 110 MVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEARIKRRV 169 Query: 117 ARVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176 V+ +LQ++ LL R+P QLSGGQ+QRVA+GRA+AR P+++L DEPLSNLDAKLR E R Sbjct: 170 REVATMLQLDTLLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLRAETRA 229 Query: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFI 236 ++ + ++L TT+YVTHDQ EAMT+GD++AV+ G +QQ +P +IY+ PAN FVA FI Sbjct: 230 QIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANRFVAQFI 289 Query: 237 GSPPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDA-GLEDREVI-LGIRPEQI-IL 293 GSPPMN IP+ + R L + RC LP + L D + + LGIRPE + + Sbjct: 290 GSPPMNLIPVTV-----RAPLQLTTENFRCTLPEAWEPVLRLYDGQTVELGIRPEHLEVG 344 Query: 294 ANGEANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVC--CRLAPDVAPAVGETLTLQFDP 351 A N L T+ E G DT + L ++ + RLAP +G+ L L F P Sbjct: 345 AAASKNLLITVTG----VEALGSDTFIAGELKESGIAVQARLAPQQCWQMGDRLWLTFKP 400 Query: 352 AKVLLFDAKTGERL 365 ++ LFD +TG+ + Sbjct: 401 DQIHLFDLETGKAI 414 Lambda K H 0.319 0.138 0.393 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: 437 Number of extensions: 19 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: 386 Length of database: 417 Length adjustment: 31 Effective length of query: 355 Effective length of database: 386 Effective search space: 137030 Effective search space used: 137030 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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