Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_069331237.1 C8J29_RS14155 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_003046325.1:WP_069331237.1 Length = 349 Score = 332 bits (850), Expect = 1e-95 Identities = 179/366 (48%), Positives = 240/366 (65%), Gaps = 22/366 (6%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA + L + K+Y G + +L+I D EF V VGPSGCGK+T LRM+AGLE+IT G Sbjct: 1 MAEISLRDVRKSYSGLE--VIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEITAG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 + IG R VN + P++RDIAMVFQNYALYPHMTV +NMA+GL++ K+ KAEI+ RV +A Sbjct: 59 EIAIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAKLSKAEIEERVARSA 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 K+L++ LLDRKP+ LSGGQRQRVA+GRA+VR P FL+DEPLSNLDAKLRVQMR +I++ Sbjct: 119 KMLELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRLQIKE 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 L + ++TT IYVTHDQ EAMT+ DR+VVM GV +Q TP +Y +P FVAGFIGSPA Sbjct: 179 LQRTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFIGSPA 238 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFM 300 MN + + GDA +++ P GR ++LG+RPE LH Sbjct: 239 MNMLPARGL--GDALEVAGQRLAVPAPAGR------------DLILGIRPEHLHP----- 279 Query: 301 TTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNT-IVARVNPRHVYHVGSSVKLAIDLNKIH 359 + ++ V+ VE +G++ + H S+ T +V R + +K+A D +H Sbjct: 280 AGPEEPGFELHVQAVEWLGADAFAHGSLADGTDLVLRTPGKAPVRERDRLKVAPDAAALH 339 Query: 360 IFDAET 365 +FDA T Sbjct: 340 LFDAGT 345 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: 389 Number of extensions: 18 Number of successful extensions: 3 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: 349 Length adjustment: 30 Effective length of query: 354 Effective length of database: 319 Effective search space: 112926 Effective search space used: 112926 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