Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115 Length = 381 Score = 189 bits (480), Expect = 1e-52 Identities = 126/362 (34%), Positives = 194/362 (53%), Gaps = 24/362 (6%) Query: 1 MQLALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVT 60 ++L LD+++K++G L D+SL + +G V +G + GK++L+R++AGLD+ G + Sbjct: 2 IKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLL 61 Query: 61 VDGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLR--GEKNIDARVREIASRL 118 +DG+ V + R+R V MV+Q + YP M V NI+ LKL + ++ RV + A L Sbjct: 62 IDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQIL 121 Query: 119 HIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFA 178 +D L R P ELSGGQ+QRVA+ RA+A+ ++L DEPL NLD LR ++R E+ +L Sbjct: 122 QLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHD 181 Query: 179 AGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNL 238 ST++Y T + EA+ L VL+ G++ Q G E++ P S VA P MN Sbjct: 182 RLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNF 241 Query: 239 MAASATAQGVRLQGGAELTL---------PLP---QGAATAAGLTVGVRASALRVHARPG 286 ++A RLQ E +L LP A L++G+R + + A G Sbjct: 242 LSA-------RLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADG 294 Query: 287 DVSVAGVVELAEISGSDTFVHASTPWGD-LVAQLTGVHYFELGTAITLHLDPAQAYVFGA 345 V VV E GS+T+VH T + L+ + ++ G + L LD ++F A Sbjct: 295 TAGV--VVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDA 352 Query: 346 DG 347 DG Sbjct: 353 DG 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: 300 Number of extensions: 13 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: 381 Length adjustment: 30 Effective length of query: 333 Effective length of database: 351 Effective search space: 116883 Effective search space used: 116883 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 Apr 09 2024. 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