Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate 18063 b4035 fused maltose transport subunit, ATP-binding component of ABC superfamily/regulatory protein (NCBI)
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__Keio:18063 Length = 371 Score = 178 bits (452), Expect = 2e-49 Identities = 116/358 (32%), Positives = 184/358 (51%), Gaps = 19/358 (5%) Query: 5 LDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVDGK 64 L +++K G D++L + G V +G + GK++L+R++AGL+ T+G + + K Sbjct: 6 LQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFIGEK 65 Query: 65 DVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKN--IDARVREIASRLHIDM 122 + P +R V MV+Q + YP + VA N++ LKL G K I+ RV ++A L + Sbjct: 66 RMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEVLQLAH 125 Query: 123 FLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAGQS 182 LDR P LSGGQ+QRVA+ R L + LLDEPL NLD LR ++R E+++L Sbjct: 126 LLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLHKRLGR 185 Query: 183 TVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMAAS 242 T++Y T + EA+ L VLD G++ Q G E++H P VA P MN + Sbjct: 186 TMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMNFLPVK 245 Query: 243 ATAQGVRLQGGAELTLPLP-----------QGAATAAGLTVGVRASALRVHARPGDVSVA 291 TA + ++ LP+P + A +++G+R L + + DV + Sbjct: 246 VTATAI---DQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHL-LPSDIADVILE 301 Query: 292 GVVELAEISGSDTFVHASTP--WGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADG 347 G V++ E G++T +H P +LV + V E G + L P + ++F DG Sbjct: 302 GEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDG 359 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: 268 Number of extensions: 13 Number of successful extensions: 2 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: 371 Length adjustment: 30 Effective length of query: 333 Effective length of database: 341 Effective search space: 113553 Effective search space used: 113553 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