Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_052665584.1 NITAL_RS08025 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_000969705.1:WP_052665584.1 Length = 399 Score = 343 bits (880), Expect = 5e-99 Identities = 197/399 (49%), Positives = 243/399 (60%), Gaps = 41/399 (10%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA V+ E + K YP + + D NL+I D EF + VGPSGCGK+T LRM+AGLE+IT G Sbjct: 1 MANVVFEDVNKVYPDGYQ-AIFDLNLEIADGEFVILVGPSGCGKSTALRMVAGLEEITSG 59 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 L IGDR VND+ PK+RDIAMVFQ+YALYPHM+V NM F LKL KV K EIDRRV+EA+ Sbjct: 60 KLSIGDRVVNDLTPKERDIAMVFQSYALYPHMSVADNMGFALKLAKVDKKEIDRRVKEAS 119 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 IL + LDRKPKALSGGQRQRVA+GRAIVR PQ FLMDEPLSNLDAKLRVQMRAEI Sbjct: 120 DILGLDEHLDRKPKALSGGQRQRVAMGRAIVRSPQAFLMDEPLSNLDAKLRVQMRAEIAA 179 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 L RL T +YVTHDQ EAMTMGDR+ V++ G + Q D PQV+Y +P N+FVAGF+GSP+ Sbjct: 180 LQDRLGVTTVYVTHDQVEAMTMGDRVAVLKKGYLMQVDAPQVLYDRPDNLFVAGFMGSPS 239 Query: 241 MNFIRGEIVQDGDAFYFRAP--SISLRLPEG---RYGVLKASGAIGKPVVLGVRPEDLHD 295 MN I ++ + L +P+ RY K + G V +G+RPE Sbjct: 240 MNLAEAVIRKEDGKVWIELDRGENRLHVPDAALDRYP--KVAERDGGKVAVGMRPEHFAP 297 Query: 296 EEVFMTTYPDSV-LQMQVEVVEHMGSEVYLHTSI-------------------------- 328 E PD V Q +V +VE +G+E+ +H S Sbjct: 298 AE---EVGPDQVWKQREVTLVELLGAEMLIHFSTTSAPIVTDDMKEAMDDEEAFEDLQRQ 354 Query: 329 ---GPNTIVARVNPRHVYHVGSSVKLAIDLNKIHIFDAE 364 G + AR P + +G + +H FDAE Sbjct: 355 AAEGGQSFTARFEPTYKAKLGDRKDVGFQTEHLHFFDAE 393 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: 500 Number of extensions: 17 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 384 Length of database: 399 Length adjustment: 31 Effective length of query: 353 Effective length of database: 368 Effective search space: 129904 Effective search space used: 129904 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 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