Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_900129305.1:WP_073038605.1 Length = 368 Score = 199 bits (506), Expect = 1e-55 Identities = 115/298 (38%), Positives = 178/298 (59%), Gaps = 20/298 (6%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M I+++ ++K FKK V + ++T+ ++GPSG GK+T LR+IAGLEE T Sbjct: 1 MAEIKLDQVNKRFKKNWV----VRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVT 56 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 SG I V+ + P+ R IAMVFQ++ALYP+M V+ N+AF L VP+D+I+ Sbjct: 57 SGEISIGGRVVNH-----VPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEID 111 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 +VK+ +E LG+S +L R P +LSGGQ QR A+ RA+V+DP+ L DEP SNLDA++R Sbjct: 112 RRVKQAAEILGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQ 171 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 RA + K+ + T + V+HD + +A++ V+ +GK Q+G P E+YE PA +A Sbjct: 172 MRAELAKLHERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVA 231 Query: 241 RLTG--EINLIQAKIIENNAII------ANLKVPLNNM-ELKGQSN--IVIGLRPDDL 287 G +N + +++E + LKVP + +G N ++ G+RP+D+ Sbjct: 232 GFIGSPSMNFLDVRLVEEAGDLWVDGESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDV 289 Lambda K H 0.317 0.136 0.374 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: 305 Number of extensions: 16 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: 371 Length of database: 368 Length adjustment: 30 Effective length of query: 341 Effective length of database: 338 Effective search space: 115258 Effective search space used: 115258 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 (21.6 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