Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate 3608990 Dshi_2380 ABC transporter related (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_00465 (263 letters) >FitnessBrowser__Dino:3608990 Length = 257 Score = 153 bits (387), Expect = 3e-42 Identities = 95/264 (35%), Positives = 150/264 (56%), Gaps = 19/264 (7%) Query: 1 MTDISTPSNTQPLLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVN 60 MTD ++P P++++RG+ K +GP EVL+GVDL + +G + +IG SG+GK+ +L+ V Sbjct: 1 MTDTTSPP---PMIELRGVSKAFGPKEVLRGVDLVIPKGESMVIIGGSGTGKSVMLKSVL 57 Query: 61 MLEEFQGGQIVLDGESIGYDDIDGKRVRHPEKLIARHRAMTGMAFQQFNLFPHLTALQNV 120 L GQI++DG+ + + D R GM FQ LF L QNV Sbjct: 58 GLISPDAGQILVDGKDVEKVERDAFLARF------------GMLFQGGALFDSLPVWQNV 105 Query: 121 TLGLLK-VKKLPKDEAVALAEKWLERVGLL-ERRDHFPGQLSGGQQQRVAIARAIAMNPS 178 + LL+ K P+ EA +A + L RVGL + D FP +LSGG Q+RV +ARAIA P Sbjct: 106 SFRLLRGALKRPRAEARDIAIEKLRRVGLTPDVADQFPAELSGGMQKRVGLARAIAAEPE 165 Query: 179 LMLFDEVTSALDPELVGEVLNVIKGL-AEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIE 237 ++ FDE T+ LDP + G + ++I+ + E G T + +TH+M ++D + ++ G+I Sbjct: 166 IIFFDEPTTGLDPIMSGVINDLIREIVVEMGATAMTITHDMTSVRAIADDVAMLHGGKIR 225 Query: 238 EQGPPKELFERPQSPRLAEFLKNT 261 GP ++ + P L +F+ + Sbjct: 226 WTGPVSDM-DHSGDPYLTQFISGS 248 Lambda K H 0.320 0.138 0.392 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: 179 Number of extensions: 9 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: 263 Length of database: 257 Length adjustment: 24 Effective length of query: 239 Effective length of database: 233 Effective search space: 55687 Effective search space used: 55687 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: 47 (22.7 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