Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__HerbieS:HSERO_RS22750 Length = 377 Score = 189 bits (481), Expect = 8e-53 Identities = 121/340 (35%), Positives = 185/340 (54%), Gaps = 10/340 (2%) Query: 18 LYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVDGKDVTGMPVRDRNVA 77 L ++L ++ G VL+G + GK++L+R++ GL+ + G + + G+ V +P +R +A Sbjct: 20 LAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGGELAIGGQVVNHLPPAERGIA 79 Query: 78 MVYQQFINYPSMKVAANIASPLKLRG--EKNIDARVREIASRLHIDMFLDRYPAELSGGQ 135 MV+Q + YP M V N+A LK+ G + +IDAR+R A+ L ID L R P ELSGGQ Sbjct: 80 MVFQSYALYPHMNVYKNMAFGLKVAGNSKSDIDARIRHAAAILKIDHLLQRLPRELSGGQ 139 Query: 136 QQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAGQSTVVYATTEPGEAL 195 +QRVA+ RA+ + L L DEPL NLD LR + R E+ +L +T+VY T + EA+ Sbjct: 140 RQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAKLHRQLAATIVYVTHDQVEAM 199 Query: 196 LLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMAASATA---QGVRLQ- 251 LG V+ EG++ Q G E++ P +L VA P MN T GV+++ Sbjct: 200 TLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPKMNFFQGVVTRCDDSGVQVEI 259 Query: 252 -GGAELTLPL-PQGAATAAGLTVGVRASALRVHARPGDVSVAGVVELAEISGSDTFVHAS 309 GG L + P G A +T+G+RA +R G + GVV L E G F++ + Sbjct: 260 AGGLRLLADVDPLGVTPGAAVTLGLRAEQIREGLGDGQ-PLHGVVNLVEHLGEANFLYVT 318 Query: 310 TPWG-DLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGR 348 G D+V + G ++G I L + ++F A G+ Sbjct: 319 LDGGHDIVVRGDGNRNVDIGQPIALSVHSHAFHLFDAQGQ 358 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: 301 Number of extensions: 15 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: 377 Length adjustment: 30 Effective length of query: 333 Effective length of database: 347 Effective search space: 115551 Effective search space used: 115551 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