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_RS31205 BPHYT_RS31205 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__BFirm:BPHYT_RS31205 Length = 347 Score = 270 bits (690), Expect = 4e-77 Identities = 144/308 (46%), Positives = 199/308 (64%), Gaps = 14/308 (4%) Query: 27 KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGK------- 79 ++I+ AVD +S+ I GE LGLVGESGCGKSTLGR + + P G I K Sbjct: 40 EQIVHAVDDVSLTIHRGEVLGLVGESGCGKSTLGRMLAGIGAPSSGSIRTLEKIAEQSAP 99 Query: 80 ----DITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKR 135 D T K +R Q+IFQDPL SLNP+ V II + ++H I +K+ Sbjct: 100 GSEHDGTRAG-KRTSRHRLATQMIFQDPLSSLNPRKRVRDIIGEAPLVHGIVERKQLDAY 158 Query: 136 VEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQI 195 V ++++ VG+ +F FPH+FSGGQ+QRIGI RALA+ P F++CDE ++ALDVSIQAQI Sbjct: 159 VVDVMERVGLNPDFRERFPHQFSGGQRQRIGIGRALAVKPDFLICDESIAALDVSIQAQI 218 Query: 196 IDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRA 255 I+L ++++ +G++YLFI+H+L VVEHIS +VA+MYLG+IVE ++F NP HPYT A Sbjct: 219 INLFMQLRRDLGLTYLFISHDLGVVEHISDRVAIMYLGRIVETAPTVELFANPQHPYTIA 278 Query: 256 LLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVEKN 315 LL VP++ +K++F S++GE+PSP+ P GC F RC C + P L + Sbjct: 279 LLAQVPRL--SNRKRQFESIQGEIPSPLAPPDGCHFHPRCPHATQRCRTERPLLRQSGAA 336 Query: 316 HFVSCHLV 323 H V+CHLV Sbjct: 337 HQVACHLV 344 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: 344 Number of extensions: 17 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: 347 Length adjustment: 28 Effective length of query: 300 Effective length of database: 319 Effective search space: 95700 Effective search space used: 95700 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