Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_002115805.1:WP_085638943.1 Length = 350 Score = 320 bits (819), Expect = 5e-92 Identities = 187/373 (50%), Positives = 238/373 (63%), Gaps = 34/373 (9%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 M+ V LE + K Y GQT+ + +LD+QD EF VFVGPSGCGK+T LRM+AGLE+ TEG Sbjct: 1 MSGVTLESVIKRY-GQTQ-VIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 + IG R V + P DR ++MVFQ YALYPHMTV +NM FGLK+ +I +V EA+ Sbjct: 59 TIRIGGRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEAS 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 +IL + L RKPKALSGGQRQRVA+GRAIVR P+VFL DEPLSNLDA+LRV+MR EI + Sbjct: 119 RILKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIAR 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LH+ + T+IYVTHDQ EAMT+ D+IVV+R G I+Q P +Y P N FVAGFIGSP+ Sbjct: 179 LHKEIGATMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPS 238 Query: 241 MNFIR-----GEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHD 295 MNFIR GE+V DG S+S AS G+ V++G+RPE L Sbjct: 239 MNFIRGRVQGGEVVSDG-----LVHSVS----------KTASAQEGQEVLIGLRPEHLE- 282 Query: 296 EEVFMTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPN--TIVARVNPRHVYHVGSSVKLAI 353 P S +V++ E +G Y H IGP+ I+ H G V L + Sbjct: 283 ------LRPGS--SHRVDLTESLGGVSYAHL-IGPDGEKIIVEERGDHRSSDGDMVDLVV 333 Query: 354 DLNKIHIFDAETE 366 D + + +FDA+TE Sbjct: 334 DPDHMFLFDAKTE 346 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: 399 Number of extensions: 16 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: 350 Length adjustment: 30 Effective length of query: 354 Effective length of database: 320 Effective search space: 113280 Effective search space used: 113280 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