Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 7023651 Shewana3_0880 ABC transporter related (RefSeq)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__ANA3:7023651 Length = 241 Score = 125 bits (313), Expect = 2e-33 Identities = 81/241 (33%), Positives = 126/241 (52%), Gaps = 14/241 (5%) Query: 4 LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLET------- 56 + + N++K+YG LK I I GE + ++GPSG GKST + CI LE Sbjct: 2 INITNLHKSYGDNA--VLKGINEHIRQGEVVSVIGPSGSGKSTFLRCINLLEKPTQGDIE 59 Query: 57 ISGGAILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFG-LKIRKMPTAEIDEE 115 I G +I DA + + K + MVFQ++ L+P +V NI + ++ M AE D + Sbjct: 60 IEGQSITAKDACVDKLRQK---VGMVFQNFNLFPHKTVLQNITLAPVSLKLMTQAEADNK 116 Query: 116 VARVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMR 175 + + ++ + P LSGGQ+QRVA+ RALA P + LFDEP S LD ++ ++ Sbjct: 117 ALALLTQVGLQDKANAYPSSLSGGQKQRVAIARALAMEPDLMLFDEPTSALDPEMVGDVL 176 Query: 176 TEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASF 235 MK + Q+ T V VTH+ A + D+V M G + + P++++ P SF Sbjct: 177 DVMKDLAQK-GMTMVIVTHEMGFARDVSDRVIFMDGGYVVESNIPEELFTRPKEARTQSF 235 Query: 236 I 236 + Sbjct: 236 L 236 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: 220 Number of extensions: 11 Number of successful extensions: 4 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: 241 Length adjustment: 27 Effective length of query: 359 Effective length of database: 214 Effective search space: 76826 Effective search space used: 76826 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: 48 (23.1 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