Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate 15248 b1126 putrescine/spermidine ABC transporter ATPase protein (NCBI)
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Keio:15248 Length = 378 Score = 239 bits (609), Expect = 1e-67 Identities = 139/302 (46%), Positives = 185/302 (61%), Gaps = 6/302 (1%) Query: 6 LKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGE 65 L IRK + +VI +DL I GEF+ +GPSGCGK+T+LR+IAGLE + G + +D E Sbjct: 20 LAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLDNE 79 Query: 66 RVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTP 125 + VP R + VFQSYAL+PHMTV++N+AFG+R+ + EI RV A M+QL Sbjct: 80 DITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLET 139 Query: 126 YLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSD 185 + R P LSGGQ+QRVAI RA+ P++ L DE LS LD LR + E+ L ++ Sbjct: 140 FAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLG- 198 Query: 186 TTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPA 245 T ++VTHDQ EA+T++DRIVV+ G IEQ G P E+YE P NLFVA FIG +N+ A Sbjct: 199 ITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGE--INMFNA 256 Query: 246 T-ITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEA-DDFLFEGTVS 303 T I +Q + G+ + V A E G+ +RPEDLRV E DD EG + Sbjct: 257 TVIERLDEQRVRANVEGRECNIYV-NFAVEPGQKLHVLLRPEDLRVEEINDDNHAEGLIG 315 Query: 304 IV 305 V Sbjct: 316 YV 317 Lambda K H 0.320 0.137 0.387 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: 299 Number of extensions: 10 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: 362 Length of database: 378 Length adjustment: 30 Effective length of query: 332 Effective length of database: 348 Effective search space: 115536 Effective search space used: 115536 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: 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