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 BPHYT_RS22030 BPHYT_RS22030 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__BFirm:BPHYT_RS22030 Length = 341 Score = 268 bits (686), Expect = 1e-76 Identities = 137/290 (47%), Positives = 202/290 (69%), Gaps = 4/290 (1%) Query: 23 FP-QGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKD- 80 FP GK L+AVDG+S ++ GET+GLVGESGCGKSTL R I+ L G + + G + Sbjct: 31 FPWSGKATLRAVDGVSFNVRRGETVGLVGESGCGKSTLARAIIGLAPVASGSVRWLGDET 90 Query: 81 ITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH-KIGTKKERRKRVEEL 139 + + R+ +Q+IFQDPL SL+P+MT+ +I+ +PL H + + + ++RV + Sbjct: 91 VLPGARRNTSRLRRDVQMIFQDPLASLDPRMTIEQIVSEPLTTHGQDVARADVQRRVLTM 150 Query: 140 LDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLL 199 L+ VG+ + + +PHEFSGGQ QR+GIARAL P+ ++CDEPVSALDVSIQAQI++LL Sbjct: 151 LERVGLNAQHLRRYPHEFSGGQCQRVGIARALIGEPQLVICDEPVSALDVSIQAQIVNLL 210 Query: 200 EEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKS 259 ++Q+++ +S LF+AH+LAVV+ ISH+V VMYLG+++E+GD +++ P HPYTRALL + Sbjct: 211 RDLQRELSLSLLFVAHDLAVVKAISHRVLVMYLGRVMEFGDKREVYGTPRHPYTRALLSA 270 Query: 260 VP-KIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPE 308 VP P + +R L+GE+ SP++ P GC F+TRC + C + P+ Sbjct: 271 VPVPDPVVERARRHLLLRGEIASPLNPPSGCAFRTRCPDAIDACAREIPQ 320 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: 320 Number of extensions: 9 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: 341 Length adjustment: 28 Effective length of query: 300 Effective length of database: 313 Effective search space: 93900 Effective search space used: 93900 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