Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_011842348.1 RSPH17029_RS17190 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_000015985.1:WP_011842348.1 Length = 359 Score = 338 bits (868), Expect = 1e-97 Identities = 188/359 (52%), Positives = 233/359 (64%), Gaps = 7/359 (1%) Query: 1 MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60 M + L+ I K YG ++ IHG+DL++++GEFV FVGPSGCGKST+LRMIAGLE+I+GG M Sbjct: 1 MARISLQKIVKRYGGMEAIHGVDLEVEDGEFVAFVGPSGCGKSTMLRMIAGLEDISGGHM 60 Query: 61 FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120 I VND+ P R +AMVFQ YALYPHMTV DN+ FG+++ E E I ++V AA + Sbjct: 61 RIGDRLVNDIEPKGRDVAMVFQDYALYPHMTVRDNIGFGLKMRGEPAETIRKKVEEAARI 120 Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180 LQL LDR P LSGGQRQRVA+GRAI R PKVFLFDEPLSNLDA LRV R +I +L Sbjct: 121 LQLEDLLDRRPGQLSGGQRQRVAMGRAIVRKPKVFLFDEPLSNLDAKLRVEMRTQIKRL- 179 Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240 RM TT IYVTHDQVEAMTLADR+VVL G I Q G PLELYERP+ FVA FIGSP M Sbjct: 180 HRMLRTTTIYVTHDQVEAMTLADRVVVLRKGSIIQHGRPLELYERPSCRFVAEFIGSPQM 239 Query: 241 NVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEG 300 N++P + ++ + T + + GG +P G + G+RPE L ++ F Sbjct: 240 NILPGRVASSDRGTVIEVGGGAIPLSHLPVPV---GTSLDVGLRPEHLEPCAPEEADFVA 296 Query: 301 TVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFD-TNGQ 358 V ++E LG TL L+ I ++P G G D+ LHLFD NGQ Sbjct: 297 EVDVLEELGSDTLAIC--LMGEREITVRVPADRARGLGRTQPLRFDRQNLHLFDAANGQ 353 Lambda K H 0.320 0.137 0.387 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: 397 Number of extensions: 14 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: 362 Length of database: 359 Length adjustment: 29 Effective length of query: 333 Effective length of database: 330 Effective search space: 109890 Effective search space used: 109890 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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