Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_900129305.1:WP_073038605.1 Length = 368 Score = 399 bits (1024), Expect = e-116 Identities = 201/369 (54%), Positives = 265/369 (71%), Gaps = 4/369 (1%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA + L+ + K + + V+DF L + DKEF V VGPSGCGK+TTLRMIAGLE++T G Sbjct: 1 MAEIKLDQVNKRF--KKNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 + IG R VN VPPKDRDIAMVFQ+YALYPHM VY+NMAFGL R VP+ EIDRRV++AA Sbjct: 59 EISIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAA 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 +IL I+ LL R+P LSGGQRQRVA+GRAIVR+PQ FL DEPLSNLDAKLRVQMRAE+ K Sbjct: 119 EILGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAK 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LH+RLQ+T++YVTHDQ EAMT+ DRIVVM+DG I Q P VY +P N FVAGFIGSP+ Sbjct: 179 LHERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPS 238 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFM 300 MNF+ +V++ + S L++P R + G + +PV+ G+RPED+ + Sbjct: 239 MNFLDVRLVEEAGDLWVDGESFRLKVPRHRAPAFR--GHVNRPVIFGIRPEDVKERPGDA 296 Query: 301 TTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIHI 360 L+ +V+V E +GSEV + ++G + AR++P V + LA+++NK+H+ Sbjct: 297 LPEGVEPLRAEVDVREPIGSEVIITATVGSHAFTARISPNVAVRVHDPIDLAVNMNKMHL 356 Query: 361 FDAETEESI 369 FD E+E+++ Sbjct: 357 FDPESEQAL 365 Lambda K H 0.321 0.138 0.395 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: 466 Number of extensions: 15 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: 384 Length of database: 368 Length adjustment: 30 Effective length of query: 354 Effective length of database: 338 Effective search space: 119652 Effective search space used: 119652 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: 50 (23.9 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