Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= TCDB::G3LHY8 (358 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 179 bits (454), Expect = 1e-49 Identities = 111/327 (33%), Positives = 168/327 (51%), Gaps = 11/327 (3%) Query: 2 LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61 +E+R+ K G + +E G L V+LGP+ GKT+L+RL+AGL+ T G+IH Sbjct: 3 IEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIA 62 Query: 62 GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121 GTDVT +P KRN++MV+Q + +P L V NI +++ A I+R +++ +LL L Sbjct: 63 GTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLGL 122 Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181 + LD P LSGG QQR AL RA++ + LMDEPL+NLD KLR +R E+ + + Sbjct: 123 SGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRRL 182 Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241 G +Y T + EA+ + + G++ Q Y RP N A PP+N + Sbjct: 183 GITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIVP 242 Query: 242 VTKS-GNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQARTLVSE 300 + + G P G + + PD P +L LA ++G A + R E Sbjct: 243 LCPTQGGAALEPGGRLL----FPGMDPD-RYLFGIRPENLRLA-ESGQPAMVTGR----E 292 Query: 301 ITGSESFVHLEYDGVRWVMLAHGIHDI 327 GS++FV E G ++ G +I Sbjct: 293 YLGSDTFVSCEIHGQEVIVRTRGRRNI 319 Lambda K H 0.319 0.136 0.392 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: 322 Number of extensions: 13 Number of successful extensions: 1 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: 358 Length of database: 365 Length adjustment: 29 Effective length of query: 329 Effective length of database: 336 Effective search space: 110544 Effective search space used: 110544 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 (21.7 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