Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate GFF2490 PS417_12700 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__WCS417:GFF2490 Length = 367 Score = 201 bits (510), Expect = 3e-56 Identities = 126/367 (34%), Positives = 201/367 (54%), Gaps = 15/367 (4%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 L + ++ K + + + L + V +G + GK++L+R++AGL+ + G + +D Sbjct: 4 LKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIELD 63 Query: 63 GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRG--EKNIDARVREIASRLHI 120 G+D+T + R++AMV+Q + YP M V N++ L L G +K ++++V E A L + Sbjct: 64 GRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARILEL 123 Query: 121 DMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAG 180 L+R P +LSGGQ+QRVA+ RA+ + + L DEPL NLD LR ++R EL +L Sbjct: 124 GPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKEL 183 Query: 181 QSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMA 240 Q+T++Y T + EA+ L VL+ G++ Q G E++H P +L VA P M + Sbjct: 184 QATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMGFLK 243 Query: 241 ASAT-----AQGVRLQGGAELTLPLPQGAATAAG--LTVGVRASALRVHARPGDVSVAGV 293 T + V+L G + LPL GA + G +T+G+R L + A PG ++ Sbjct: 244 GKVTRVESQSCEVQLDAGTLINLPL-SGATLSVGSAVTLGIRPEHLEI-ASPGQTTLTVT 301 Query: 294 VELAEISGSDTFVHASTPWGD-LVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRLAQA 352 ++ E GSDTF H T G+ L ++ G + G + LHLDPA ++F DG A Sbjct: 302 ADVGERLGSDTFCHVITANGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFDTDG---VA 358 Query: 353 PARPVTA 359 ARP+ A Sbjct: 359 VARPLRA 365 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: 12 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: 367 Length adjustment: 30 Effective length of query: 333 Effective length of database: 337 Effective search space: 112221 Effective search space used: 112221 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