Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_086508166.1 BZY95_RS01120 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_002151265.1:WP_086508166.1 Length = 371 Score = 357 bits (916), Expect = e-103 Identities = 200/361 (55%), Positives = 246/361 (68%), Gaps = 4/361 (1%) Query: 1 MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60 M L L I K Y V+V IDL I++GEFVVFVGPSGCGKSTLLRMIAGLE+I+ G+M Sbjct: 1 MGRLTLAGIGKDYAGVEVSRDIDLTIEDGEFVVFVGPSGCGKSTLLRMIAGLEDISHGEM 60 Query: 61 FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120 +DGER+N+VPP +R I MVFQSYALYPHMTV +NMAFG+++AR K EI RRV AA+M Sbjct: 61 RLDGERINEVPPQERDIGMVFQSYALYPHMTVAENMAFGLKLARTDKAEIRRRVEHAAEM 120 Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180 L L L+R PK LSGGQRQRVAIGR + + P VFLFDEPLSNLDAALRV R++IA+L Sbjct: 121 LHLGELLERKPKELSGGQRQRVAIGRTLVKEPAVFLFDEPLSNLDAALRVDMRVQIAELH 180 Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240 R+ TMIYVTHDQVEAMTLADRIV+L+ G I QVGAPL LY PA L VARFIGSP + Sbjct: 181 RRLG-ATMIYVTHDQVEAMTLADRIVLLAGGRIAQVGAPLSLYHFPATLEVARFIGSPRI 239 Query: 241 NVIPATITATG-QQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEAD-DFLF 298 NVIP + G Q+T+V L G ++ + V G A+ VR ED VT AD D Sbjct: 240 NVIPVEVLDPGRQRTSVRLPDGATLAVAVDGARLRAGDKATLAVRAEDF-VTPADADARL 298 Query: 299 EGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNGQ 358 + + E LG TL ++ +E + ++ G+ R+ G V + HLF +G+ Sbjct: 299 TARLMVAERLGYETLAHLRVEGVSETLTQRLDGLTRLEDGQAVELGLSGERCHLFAADGK 358 Query: 359 S 359 + Sbjct: 359 A 359 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: 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: 362 Length of database: 371 Length adjustment: 30 Effective length of query: 332 Effective length of database: 341 Effective search space: 113212 Effective search space used: 113212 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 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