Align LacK, component of Lactose porter (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= TCDB::Q01937 (363 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 265 bits (676), Expect = 2e-75 Identities = 155/379 (40%), Positives = 212/379 (55%), Gaps = 37/379 (9%) Query: 14 GSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGELTIGGTVMNDVDPS 73 G + V+ G+NLE++ GEF+V VGPSGCGKSTLLR++AGLE S G + +G ++ + Sbjct: 45 GEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDRLPAK 104 Query: 74 KRGIAMVFQTYALYPHMTVRENMGFALRFAG------------------------MAKDE 109 R IAMVFQ+YALYPH++V +N+ F LR G + Sbjct: 105 ARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEAR 164 Query: 110 IERRVNAAAKILELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELR 169 I+RRV A +L+LD L+DR+PK LSGGQ+QRVA+GRAI R P VFL DEPLSNLDA+LR Sbjct: 165 IKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLR 224 Query: 170 VHMRVEIARLHKELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMF 229 R +I L ++L T +YVTHDQ EAMT+ D+I V+ G ++QV +PL +YD P N F Sbjct: 225 AETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANRF 284 Query: 230 VAGFIGSPRMNFLPAVVIG----QAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGV 285 VA FIGSP MN +P V E + T+ P +L G V +G+ Sbjct: 285 VAQFIGSPPMNLIPVTVRAPLQLTTENFRCTLPEAWEPVLRL--------YDGQTVELGI 336 Query: 286 RPEHFLPAGSGDTQLTAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAV 345 RPEH + L V VE LG+ +++ + + + + GD + + Sbjct: 337 RPEHLEVGAAASKNLLITVTGVEALGSDTFIAGELKESGIAVQARLAPQQCWQMGDRLWL 396 Query: 346 GISAKTSFLFD-ASGRRIR 363 LFD +G+ IR Sbjct: 397 TFKPDQIHLFDLETGKAIR 415 Lambda K H 0.320 0.137 0.390 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: 393 Number of extensions: 12 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: 363 Length of database: 417 Length adjustment: 30 Effective length of query: 333 Effective length of database: 387 Effective search space: 128871 Effective search space used: 128871 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 (21.8 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