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 8501089 DvMF_1825 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Miya:8501089 Length = 339 Score = 300 bits (768), Expect = 3e-86 Identities = 148/302 (49%), Positives = 212/302 (70%), Gaps = 3/302 (0%) Query: 27 KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLND 86 + ++ AV+ +S +I GETL +VGESGCGKSTL RT++ L R GG+I + G+ I NL+D Sbjct: 39 RTVVHAVNDVSFDILPGETLSVVGESGCGKSTLARTVIGLYRATGGEILYRGERIDNLSD 98 Query: 87 KEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIG-TKKERRKRVEELLDMVGI 145 M PYR +MQ++FQDP SLNP+M V I+E+P+ H G + + R RV ++++ VG+ Sbjct: 99 NGMLPYRTRMQMVFQDPYASLNPRMKVREILEEPVRFHNPGISDADVRARVADVMEQVGV 158 Query: 146 GREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQK 205 + +PHEFSGGQ+QRI IARAL ++P+FIV DEP+SALDVSIQAQ+++L+ ++Q+K Sbjct: 159 NPLWGVRYPHEFSGGQRQRISIARALVVDPEFIVADEPISALDVSIQAQVLNLMMDMQEK 218 Query: 206 MGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPKIPW 265 ++YLFI+H+L+VVEHIS +VAVMYLG + E + +F NP HPYTRALL ++P+I Sbjct: 219 RNLTYLFISHDLSVVEHISTRVAVMYLGSLCELASAEDLFGNPRHPYTRALLSAIPRI-- 276 Query: 266 DGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVEKNHFVSCHLVRS 325 G+ L G++P+PI+LP GC F RC A C ++ P+ ++E V+CH V Sbjct: 277 GGKAAGHIKLSGDVPTPINLPTGCVFHGRCQHANARCMQEVPKARQLEGGAQVACHGVEE 336 Query: 326 YR 327 R Sbjct: 337 GR 338 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: 341 Number of extensions: 15 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: 339 Length adjustment: 28 Effective length of query: 300 Effective length of database: 311 Effective search space: 93300 Effective search space used: 93300 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