Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_086511012.1 BZY95_RS16625 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Phaeo:GFF1302 (334 letters) >NCBI__GCF_002151265.1:WP_086511012.1 Length = 346 Score = 387 bits (994), Expect = e-112 Identities = 199/334 (59%), Positives = 242/334 (72%), Gaps = 2/334 (0%) Query: 1 MGQIKLESVTKNF-GPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGT 59 M + L + K F G VIP L+L IEDG FTV VGPSGCGKSTLLR+IAGLE +T G Sbjct: 1 MADVTLVDIEKTFRGKTTVIPNLNLRIEDGSFTVLVGPSGCGKSTLLRMIAGLETVTRGA 60 Query: 60 IRIDGEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAA 119 I I G D T P++R +AMVFQSYALYPHM+V +NI F M++A +P +E+ ++ AA Sbjct: 61 ISIGGRDVTTAEPSERNIAMVFQSYALYPHMTVARNIDFGMRLAKVPTEERMAKVAEAAR 120 Query: 120 ALNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISEL 179 LNL + L+R+P +LSGGQRQRVAIGRAIVR P FLFDEPLSNLDAALR MR+E++EL Sbjct: 121 LLNLEELLERKPAELSGGQRQRVAIGRAIVRNPGVFLFDEPLSNLDAALRNRMRVELAEL 180 Query: 180 HKRLATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKM 239 H+RL TMIYVTHDQVEAMT+AD IVV+ AG IEQVG+PM LY+ P +FVAGFIGSPKM Sbjct: 181 HQRLDATMIYVTHDQVEAMTLADCIVVMNAGQIEQVGTPMNLYQRPETLFVAGFIGSPKM 240 Query: 240 NLLTGPQAAQHNAATIGIRPEHLSISETEGMWAGTIGVSEHLGSDTFFHVQCDAFDDPLT 299 NL+ G A H A T+GIRPEHL +S G W + V E LG+D F +V DA PLT Sbjct: 241 NLIEGEVAKAHGATTLGIRPEHLEVSHEAGEWRTRVRVVEMLGADAFAYVDSDA-TGPLT 299 Query: 300 VRASGELDLGYGERVFLTPDMTHLHRFGSDGLRI 333 VR G+ ++ G+ ++LTP LH FG DG R+ Sbjct: 300 VRLPGDAEVRSGDILYLTPRYELLHAFGIDGRRL 333 Lambda K H 0.320 0.138 0.400 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: 350 Number of extensions: 9 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: 334 Length of database: 346 Length adjustment: 28 Effective length of query: 306 Effective length of database: 318 Effective search space: 97308 Effective search space used: 97308 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