Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_017178050.1 A1QA_RS0106175 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:Q6MNM2 (347 letters) >NCBI__GCF_000295095.1:WP_017178050.1 Length = 375 Score = 275 bits (703), Expect = 1e-78 Identities = 153/326 (46%), Positives = 202/326 (61%), Gaps = 26/326 (7%) Query: 1 MAKIQFSNIKKSFGSAD--VLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSG 58 MA + F + + + D + ++L+IA GEFLVLVGPSGCGKST LR LAGLE +SG Sbjct: 1 MATVTFDHATRIYPGNDRPSVDQLNLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNSG 60 Query: 59 TISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEIS 118 I I + + D++P++RDIAMVFQ+YALYPHM+V +NMGF LK+ EI KRV E + Sbjct: 61 RILIGDRDVTDVQPKDRDIAMVFQNYALYPHMSVHDNMGFALKIAGTPKEEIDKRVREAA 120 Query: 119 ELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKR 178 ++L + LDRKPK LSGGQRQRVA+GRA+ R+ V L DEPLSNLDA LR Q R +I Sbjct: 121 KILGLTEYLDRKPKALSGGQRQRVAMGRAIVRKPKVFLMDEPLSNLDAKLRVQTRTQIAS 180 Query: 179 LHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPE 238 L + T +YVTHDQ EA T+GDRIAVLKDG+++Q+GTP E+Y +P N F+A FIGSP Sbjct: 181 LQRSLGVTTVYVTHDQTEALTMGDRIAVLKDGLLQQVGTPREMYDKPANEFVAGFIGSPA 240 Query: 239 MNF------------------LEGAVLEKIPWPEARKADQILGIRPDAFALNQGPLGTQE 280 MN L A L+ I + K +G RP++ + + + Sbjct: 241 MNLGHFTVSGDVASIGSAKIQLSRATLDAIKPEDGGKV--AIGFRPESLEV----VSASD 294 Query: 281 VALGDFQIDISENLGGQQMLHGTLAG 306 ++ E LG ++G L G Sbjct: 295 EHSIPVRVSFVEELGSDAYIYGELVG 320 Lambda K H 0.318 0.136 0.383 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: 335 Number of extensions: 7 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: 347 Length of database: 375 Length adjustment: 29 Effective length of query: 318 Effective length of database: 346 Effective search space: 110028 Effective search space used: 110028 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 (21.7 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