Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate GFF3855 PGA1_78p00190 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Phaeo:GFF3855 Length = 361 Score = 300 bits (767), Expect = 5e-86 Identities = 166/352 (47%), Positives = 216/352 (61%), Gaps = 16/352 (4%) Query: 4 IQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISID 63 ++ ++ FG VL ++LDI GEFLVL+G SGCGKSTLL +AGL G I I Sbjct: 8 VEIRDLDLHFGELQVLHQLNLDIEQGEFLVLLGSSGCGKSTLLNCIAGLLDISDGQIFIQ 67 Query: 64 GKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQI 123 G+ + EP R I MVFQSYALYP MTV N+ FGLK L AEI KRV +E+LQI Sbjct: 68 GQNVTWAEPSERGIGMVFQSYALYPQMTVEGNLSFGLKNARLPKAEIAKRVARAAEVLQI 127 Query: 124 KHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNS 183 + LL RKP LSGGQRQRVA+GRAL R V LFDEPLSNLDA LR+ +R+E+KRLH Sbjct: 128 EPLLKRKPAALSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRADLRVELKRLHQQL 187 Query: 184 KSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFLE 243 +TMIYVTHDQ+EA TL DRIA++K G I Q+ +P EIY+RP+N ++A FIGSP MN +E Sbjct: 188 ANTMIYVTHDQVEAMTLADRIAIMKGGRIMQLSSPDEIYNRPQNLYVAGFIGSPAMNLIE 247 Query: 244 GAVLE------KIPWPEAR--------KADQILGIRPDAFALNQGPLGTQEVALGDFQID 289 G +++ + P R ++GIRP+ + G T+ A + +D Sbjct: 248 GVLIDGVFHAGSLALPMQRYDYRNGPHHGAAVIGIRPE--HILTGEQITRADATAEVLVD 305 Query: 290 ISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFDKKT 341 + E LG +++ T N+R+ +D S L + D +A LFD T Sbjct: 306 LVEGLGSDTLVYATHGAQNLRLRMDGASRVSAGDRLRIGFDTGRASLFDPNT 357 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: 339 Number of extensions: 16 Number of successful extensions: 2 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: 361 Length adjustment: 29 Effective length of query: 318 Effective length of database: 332 Effective search space: 105576 Effective search space used: 105576 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 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