Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate BWI76_RS03120 BWI76_RS03120 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__Koxy:BWI76_RS03120 Length = 356 Score = 187 bits (476), Expect = 3e-52 Identities = 118/354 (33%), Positives = 193/354 (54%), Gaps = 6/354 (1%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 L+L +ISK+ + L +SL ++ G VL+G + GK++L+R++AGL+ + G + + Sbjct: 2 LSLQNISKQFDGKPALSALSLDIREGEFVVLVGPSGCGKSTLLRLLAGLEPVSEGEIWLH 61 Query: 63 GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKNID--ARVREIASRLHI 120 +++T M R+RN AM++Q + +P + V NI +K+R E+ RV ++A L + Sbjct: 62 DENITDMSPRERNFAMIFQNYALFPHLSVRDNITFGMKVRKEEKTSWQPRVDKVAQMLQL 121 Query: 121 DMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAG 180 D LDR PA+LSGGQ+QRVA+ARA+ + L L+DEPL NLD +LR E+R+ + L Sbjct: 122 DTLLDRKPAKLSGGQRQRVAMARAIVRNPRLFLMDEPLSNLDARLRSEVRDSIMDLHQQL 181 Query: 181 QSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMA 240 +++ VY T + EA+ + V++ G + Q G ++ P +L VA P MNL++ Sbjct: 182 RTSTVYVTHDQTEAMSMADRIVVMNGGHVQQVGRPEYLYANPANLFVAGFIGSPAMNLLS 241 Query: 241 ASATAQGVRLQGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGDVSVAGVVELAEIS 300 A G L G EL PLP + + +G+R + + + V E+ Sbjct: 242 LPC-ADGEVLLG--ELRYPLPPRYREESRVWLGIRPEHISDRVEENHLRLPATVLQRELM 298 Query: 301 GSDTFVHASTPWGDL-VAQLTGVHYFELGTAITLHLDPAQAYVFGADGRLAQAP 353 G+D +H STP G L ++ E G ++ L PA ++F A+ + AP Sbjct: 299 GADYLLHVSTPIGTLRFSRRHRGAVPEKGDSLILGFSPADVHLFHAEKQHNLAP 352 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: 271 Number of extensions: 18 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: 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