Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate GFF3696 PGA1_262p01000 dipeptide transport ATP-binding protein DppF
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Phaeo:GFF3696 Length = 344 Score = 291 bits (744), Expect = 2e-83 Identities = 148/319 (46%), Positives = 211/319 (66%), Gaps = 4/319 (1%) Query: 11 KPLLQTVDLKK-YFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRP 69 K L+T+ L+ + KR + AV+ +S+ GE L +VGESGCGKST+ R + LL P Sbjct: 25 KGFLETIKLRGGRITREKRAVHAVNNVSLSADRGEALCIVGESGCGKSTVARLVAGLLAP 84 Query: 70 DGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTK 129 GG+I ++G+ I + + EM P RKKMQ+IFQ+P SLNP+MT+ + +E+P+ H Sbjct: 85 SGGEIHYDGERIDDRSRGEMMPLRKKMQMIFQNPYASLNPRMTIQQALEEPVRHHNPSLS 144 Query: 130 K-ERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALD 188 + E R +V E++ VG+ + + +PHEFSGGQ+QRI IARAL ++P+FI+ DEP+SALD Sbjct: 145 RGEVRDKVSEVMRSVGVDPSWSSRYPHEFSGGQRQRIAIARALTVDPEFIIADEPISALD 204 Query: 189 VSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNP 248 VSIQAQ+++L+ E + + G++Y FI H+L+VVEH +VAV+YLG + E D +F NP Sbjct: 205 VSIQAQVLNLMLEAKDQRGLTYFFITHDLSVVEHFGTRVAVLYLGTLCELADTQTLFENP 264 Query: 249 IHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPE 308 HPYT+ALL +VP++ GQ L+GE+P+PI+LP+GC FQTRC A C E P Sbjct: 265 KHPYTKALLSAVPQLKDQGQNH--IRLQGEIPTPINLPQGCPFQTRCAFANARCRESRPR 322 Query: 309 LTEVEKNHFVSCHLVRSYR 327 V+CH V R Sbjct: 323 PLRQADGSTVACHAVEENR 341 Lambda K H 0.321 0.142 0.417 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: 357 Number of extensions: 8 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: 328 Length of database: 344 Length adjustment: 28 Effective length of query: 300 Effective length of database: 316 Effective search space: 94800 Effective search space used: 94800 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