Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >NCBI__GCF_000759345.1:WP_043527041.1 Length = 354 Score = 173 bits (439), Expect = 6e-48 Identities = 119/337 (35%), Positives = 181/337 (53%), Gaps = 15/337 (4%) Query: 21 MSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVDGKDVTGMPVRDRNVAMVY 80 + L + G VL+G + GK++L+R++AGL+ T G + +D + V + +R++AMV+ Sbjct: 23 IDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGTLKIDDRVVNDLEPAERDIAMVF 82 Query: 81 QQFINYPSMKVAANIASPLKLRGEKN--IDARVREIASRLHIDMFLDRYPAELSGGQQQR 138 Q + YP M V N+A LK RG K I+ RV + A+ L I+ FL+R P +LSGGQ+QR Sbjct: 83 QNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAAMLEIEPFLERKPRKLSGGQRQR 142 Query: 139 VALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAGQSTVVYATTEPGEALLLG 198 VA+ RAL + L DEPL NLD KLR ++R E+ QL ++T +Y T + EAL LG Sbjct: 143 VAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQLQRRLKTTSLYVTHDQLEALTLG 202 Query: 199 GYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMAASATAQGVRLQGGAELTL 258 VL+ G + Q G EV+ P S+ VA P MN++ + +R +G L Sbjct: 203 DRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAMNMLPVAY----LRERGANGLLD 258 Query: 259 PLPQGAATAAGLTVGVRASALRVHARPGD-VSVAGVVELAEISGSDTFVHASTPWGD--L 315 L A +G+R LR+ A D + V G VEL E +G+++ ++ S D Sbjct: 259 HL-----AADTDVIGIRPDDLRIEAPDEDHLVVTGTVELFEAAGAESHLYVSLEGSDQPT 313 Query: 316 VAQLTGVHYFELGTAITLHLDPAQAYVFG-ADGRLAQ 351 V + + G + H+ P+ + F A G+ Q Sbjct: 314 VIRTSARPPVAEGETMRFHVLPSALHPFNQASGKRTQ 350 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: 251 Number of extensions: 10 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: 354 Length adjustment: 29 Effective length of query: 334 Effective length of database: 325 Effective search space: 108550 Effective search space used: 108550 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 24 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