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 208073 DVU2576 oligopeptide ABC transporter, ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >MicrobesOnline__882:208073 Length = 321 Score = 196 bits (499), Expect = 5e-55 Identities = 118/318 (37%), Positives = 172/318 (54%), Gaps = 9/318 (2%) Query: 12 PLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG 71 PLL+ L F + AV +S + G TL +VGESGCGKS +L L+ G Sbjct: 4 PLLEVQGLDVVFDIEAGAIHAVRDVSFTLPHGRTLCIVGESGCGKSMTALALLGLVPAPG 63 Query: 72 G----KIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126 ++ F+G D+T L++ ++ R M ++FQDP+ SLNP VG + + L +H Sbjct: 64 RVTARRLQFDGHDLTALDENGLRALRGHHMAMVFQDPMTSLNPVFRVGDQVAEALRLHLR 123 Query: 127 GTKKERRKRVEELLDMVGIG--REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184 + R+ EL VGI + +PH+ SGG +QR+ IA AL+ P+ ++ DEP Sbjct: 124 LKGRAAREATIELFRQVGIPSPETRYDDYPHQLSGGMRQRVMIAMALSCGPRLLIADEPT 183 Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244 +ALDV+IQ QI+ LL +I S L I H+L VV + V VMY G IVE+ V ++ Sbjct: 184 TALDVTIQGQILGLLSDIAATGRASVLLITHDLGVVAETADDVIVMYAGAIVEHAPVQEL 243 Query: 245 FLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFE 304 F +P+HPYTR L++S P + + + R +++G +P DLP GC F+ RC C Sbjct: 244 FASPLHPYTRGLMRSAPPVHGE-RSPRLEAIRGNVPPLDDLPSGCAFRDRCEHAFERCAT 302 Query: 305 KEPELTEVEKNHFVSCHL 322 P L + K V C L Sbjct: 303 AAPPLFTLGK-QMVRCWL 319 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: 260 Number of extensions: 13 Number of successful extensions: 4 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: 321 Length adjustment: 28 Effective length of query: 300 Effective length of database: 293 Effective search space: 87900 Effective search space used: 87900 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: 48 (23.1 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