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 BWI76_RS17220 BWI76_RS17220 oligopeptide ABC transporter ATP-binding protein OppF
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Koxy:BWI76_RS17220 Length = 334 Score = 310 bits (795), Expect = 2e-89 Identities = 161/305 (52%), Positives = 216/305 (70%), Gaps = 3/305 (0%) Query: 18 DLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFE 77 D K++F Q + LKAVDG+++ + EGETLG+VGESGCGKST R I+ L++ GK+ + Sbjct: 25 DGKQWFWQPSKTLKAVDGVTLRLYEGETLGVVGESGCGKSTFARAIIGLVKATDGKVAWL 84 Query: 78 GKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPL-IIHKIGTKKERRKRV 136 GKD+ + E + R +Q+IFQDPL SLNP+MT+G II +PL H ++E R RV Sbjct: 85 GKDLLGMKADEWRDVRSDIQMIFQDPLASLNPRMTIGEIIAEPLRTYHPKMPRQEVRDRV 144 Query: 137 EELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQII 196 + ++ VG+ IN +PHEFSGGQ QRIGIARAL L PK I+CDEPVSALDVSIQAQ++ Sbjct: 145 KAMMMKVGLLPNLINRYPHEFSGGQCQRIGIARALILEPKLIICDEPVSALDVSIQAQVV 204 Query: 197 DLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRAL 256 +LL+++Q++MG+S +FIAH+LAVV+HIS +V VMYLG VE G D+++ NP+HPYT+AL Sbjct: 205 NLLQQLQREMGLSLIFIAHDLAVVKHISDRVLVMYLGHAVELGTYDEVYHNPLHPYTKAL 264 Query: 257 LKSVPKIPWDGQKQR-FYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVEKN 315 + +VP D +K + L+GELPSPI+ P GC F+TRC C + P L E Sbjct: 265 MSAVPVPDPDKEKNKTIQLLEGELPSPINPPSGCVFRTRCPIAGPECAKTRPVL-EGSFR 323 Query: 316 HFVSC 320 H VSC Sbjct: 324 HAVSC 328 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: 348 Number of extensions: 19 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: 334 Length adjustment: 28 Effective length of query: 300 Effective length of database: 306 Effective search space: 91800 Effective search space used: 91800 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