Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Phaeo:GFF262 Length = 348 Score = 327 bits (838), Expect = 3e-94 Identities = 187/366 (51%), Positives = 234/366 (63%), Gaps = 23/366 (6%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA+V L + K YP E V + I+D EF V VGPSGCGK+T LRMIAGLEDITEG Sbjct: 1 MAQVTLNSVRKVYPNGVE-AVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEG 59 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 L IGDR VN+V P DRDIAMVFQNYALYPHMTV +N+A+GLK RK P+AEI ++V EAA Sbjct: 60 TLEIGDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQKVAEAA 119 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 K+L++ LDRKP LSGGQRQRVA+GRAIVR+P +FL DEPLSNLDAKLR QMR EI+ Sbjct: 120 KMLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKA 179 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 L +RL T IYVTHDQ EAMTM DRI+V+ G I+Q TP +Y P ++FVA F+G+P Sbjct: 180 LQRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPP 239 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEG-RYGVLKASGAIGKPVVLGVRPEDLHDEEVF 299 MN + I + LP+G G L S V LG+RPED+ Sbjct: 240 MNLLDATIANG-----------QVTLPDGVSMGALDTSAQ--GAVKLGIRPEDVQ----- 281 Query: 300 MTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIH 359 + L + VE++E +G+ LH +G V G+ ++++D I Sbjct: 282 --LVAEGGLAIDVELIEELGAHRLLHGKLGGQPFTIHVLKDIPVDPGTH-QISVDPAAIC 338 Query: 360 IFDAET 365 +FDAE+ Sbjct: 339 LFDAES 344 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: 377 Number of extensions: 15 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: 384 Length of database: 348 Length adjustment: 30 Effective length of query: 354 Effective length of database: 318 Effective search space: 112572 Effective search space used: 112572 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 17 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