Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 214 bits (546), Expect = 2e-60 Identities = 122/291 (41%), Positives = 176/291 (60%), Gaps = 15/291 (5%) Query: 3 TLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLE-TISGGA 61 T+ LR+ KT+ G L+ ++L I GE ++L+GPSGCGK+T + IAGLE +GG Sbjct: 6 TITLRHCGKTFADGTL-ALQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGV 64 Query: 62 ILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSK 121 ++ D D++ + + R + MVFQSYAL+P M+V +NIA+GL++R++ A V + Sbjct: 65 VMFGDNDVTPLPIEQRGVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLA 124 Query: 122 LLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLM 181 ++ + R+ QLSGGQ+QRVA+ RA+A +P++ L DEPL+ LDAKLR +R ++ + Sbjct: 125 MMHLGPFAERRIDQLSGGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQL 184 Query: 182 HQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPM 241 + L T VYVTHDQ EAM LGD++ VM G I Q GTP+ IY PAN FVA FIG+ M Sbjct: 185 LRSLHITAVYVTHDQAEAMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGT--M 242 Query: 242 NFIPLRLQR-----------KDGRLLALLDSGQARCELPLGMQDAGLEDRE 281 N +P L+ + G +L + R EL +D L E Sbjct: 243 NRLPAVLEADAWRVPGGLVPRHGTAASLAAAPSPRAELLFRPEDVALAQAE 293 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: 340 Number of extensions: 16 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: 386 Length of database: 357 Length adjustment: 30 Effective length of query: 356 Effective length of database: 327 Effective search space: 116412 Effective search space used: 116412 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: 49 (23.5 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