Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__SB2B:6938538 Length = 378 Score = 219 bits (559), Expect = 8e-62 Identities = 128/309 (41%), Positives = 185/309 (59%), Gaps = 5/309 (1%) Query: 23 NIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVDDADISGMSPKDRDIAMV 82 ++ L I+ GE L+G SG GKSTL+ +AG E + G I +D DI+ + P +R I M+ Sbjct: 38 DVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYLDGQDITDLPPYERPINMM 97 Query: 83 FQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHLLSRKPGQLSGGQQQ 142 FQSYAL+P M+V NIAFGLK KM A+I + V + KL+ +E RKP QLSGGQ+Q Sbjct: 98 FQSYALFPHMTVEQNIAFGLKQDKMSKADISQRVQEMLKLVHMEQYAKRKPHQLSGGQRQ 157 Query: 143 RVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQIEAMTL 202 RVA+ R+LA+RPK+ L DEP+ LD KLR +M+ E+ + +R+ T V VTHDQ EAMT+ Sbjct: 158 RVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERVGVTCVMVTHDQEEAMTM 217 Query: 203 GDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNFIPLRLQRKDGRLLALLDSG 262 ++A+M DG I Q G+P DIY +P + +A FIG+ +N + +D A+L S Sbjct: 218 AGRIAIMSDGWIAQVGSPMDIYESPNSRMIAEFIGT--VNLFDCEI-IEDEADHAILKSP 274 Query: 263 QARCELPLGM-QDAGLEDREVILGIRPEQIILANGEANG-LPTIRAEVQVTEPTGPDTLV 320 +G LED+ V L +RPE+ ++ + G R +V G ++ Sbjct: 275 TLPQPFLIGHGVTTSLEDKHVWLAVRPEKTLITREQPEGEYNWARGKVHDIAYLGGLSVY 334 Query: 321 FVNLNDTKV 329 ++ L D K+ Sbjct: 335 YIKLEDDKI 343 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: 320 Number of extensions: 8 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: 378 Length adjustment: 30 Effective length of query: 356 Effective length of database: 348 Effective search space: 123888 Effective search space used: 123888 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