Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)
Query= TCDB::Q88P35 (384 letters) >FitnessBrowser__Miya:8501226 Length = 399 Score = 220 bits (560), Expect = 6e-62 Identities = 117/248 (47%), Positives = 167/248 (67%), Gaps = 10/248 (4%) Query: 4 LELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGGAIL 63 +ELR V KT+ + L I L+I++GEFL L+GPSGCGK+T++ ++G EQ T G + Sbjct: 8 IELRGVTKTFEDTV--ALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGEVR 65 Query: 64 IDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVAKLL 123 I+ Q V+ + P+ R + VFQ+YAL+P M+VR+N+ FGLK++ + A DE RV L Sbjct: 66 INGQVVNRVPPEQRQVNTVFQNYALFPHMTVRDNVAFGLKMQGV---AADETARRVLDAL 122 Query: 124 QIEHL---LARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++ HL RKP QLSGGQQQRVA+ RA+ P + L DEP S LD KLR +M+ E+K Sbjct: 123 RMVHLENFADRKPRQLSGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQLEIKH 182 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPP 240 + ++L T V+VTHDQ EA + D+V VM +G I+Q G P++IY +PAN +VA F+G Sbjct: 183 LQRQLGITFVFVTHDQEEAFAMSDRVVVMNEGRIEQIGAPKEIYEEPANMYVARFVGD-- 240 Query: 241 MNFIPVRL 248 +N +P R+ Sbjct: 241 INALPGRI 248 Lambda K H 0.320 0.137 0.391 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: 370 Number of extensions: 19 Number of successful extensions: 1 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: 384 Length of database: 399 Length adjustment: 31 Effective length of query: 353 Effective length of database: 368 Effective search space: 129904 Effective search space used: 129904 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