Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__Keio:17511 Length = 356 Score = 190 bits (483), Expect = 4e-53 Identities = 126/356 (35%), Positives = 193/356 (54%), Gaps = 12/356 (3%) Query: 3 LALDSISKKVGAQTWLYD-MSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTV 61 L L +++K +T + ++L + G V++G + GK++L+R++AGL+ T G + + Sbjct: 4 LKLQAVTKSWDGKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEGDIWI 63 Query: 62 DGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRG--EKNIDARVREIASRLH 119 + + VT M +DR +AMV+Q + YP M V N+A LK+RG ++ I RV+E A L Sbjct: 64 NDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAARILE 123 Query: 120 IDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAA 179 +D L R P ELSGGQ+QRVA+ RA+ + + L DEPL NLD KLR ++R EL QL Sbjct: 124 LDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQLHRR 183 Query: 180 GQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLM 239 ++T +Y T + EA+ L V++ G Q G EV+ P SL VA P MNL+ Sbjct: 184 LKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPAMNLL 243 Query: 240 AASATAQGVRLQGGAELTLPLPQGAATAAG--LTVGVRASALRVHARPGDVSVAGVVELA 297 +G + + LPL G AG +T+G+R + + ++ + V V++ Sbjct: 244 TGRVNNEGTHFELDGGIELPLNGGYRQYAGRKMTLGIRPEHIALSSQ-AEGGVPMVMDTL 302 Query: 298 EISGSDTFVHASTPWGD--LVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRLAQ 351 EI G+D H WG+ LV +L G+ + LHL Q ++F DG Q Sbjct: 303 EILGADNLAHGR--WGEQKLVVRLAHQERPTAGSTLWLHLAENQLHLF--DGETGQ 354 Lambda K H 0.318 0.133 0.375 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: 272 Number of extensions: 16 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: 363 Length of database: 356 Length adjustment: 29 Effective length of query: 334 Effective length of database: 327 Effective search space: 109218 Effective search space used: 109218 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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