Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate BWI76_RS16695 BWI76_RS16695 dipeptide/oligopeptide/nickel ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Koxy:BWI76_RS16695 Length = 326 Score = 273 bits (699), Expect = 3e-78 Identities = 143/314 (45%), Positives = 203/314 (64%), Gaps = 3/314 (0%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLIN-RNG 62 L+ N L V F + V+AV +S+ + G+++G+VGESG GKSV+ LSL+ L+ + Sbjct: 5 LITFNQLSVSFAADKSRVRAVQEVSFTIRAGQTVGVVGESGCGKSVTALSLMGLLPPQAA 64 Query: 63 RIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRL 122 RI GE +F G+DLL+L + ++RG +++IFQ PM++LNP++ VG Q+ EP+I HR Sbjct: 65 RIDGGEILFAGQDLLRLKNAHMADLRGNQLAMIFQEPMSALNPVLTVGEQLCEPLIRHRG 124 Query: 123 MKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPT 182 + A + AI+LL VG+ + +YP Q SGGM QRVMIAMAL+C PKLLIADEPT Sbjct: 125 ESPKLAWQHAIQLLADVGLARADSLMASYPHQLSGGMLQRVMIAMALSCQPKLLIADEPT 184 Query: 183 TALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEI 242 TALDVT+QAQI+ LL++ M+++ ITHDL V + ++ MYAG+IVE+ +I Sbjct: 185 TALDVTVQAQILRLLRDQARANRMAMMLITHDLGVIAQMAEHVVVMYAGRIVEQGATADI 244 Query: 243 LKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREE 302 L+ P HPYT+GL+ S G R ++L IPG P+ P GC F RC+ A C++ Sbjct: 245 LRNPQHPYTQGLIASRPVPGERRRRLYSIPGQVPDLAALPVGCAFAERCANATVRCRQGV 304 Query: 303 PPLVNISENHRVAC 316 PPLV + + AC Sbjct: 305 PPLV--GQTQQAAC 316 Lambda K H 0.320 0.139 0.401 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: 264 Number of extensions: 8 Number of successful extensions: 1 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: 324 Length of database: 326 Length adjustment: 28 Effective length of query: 296 Effective length of database: 298 Effective search space: 88208 Effective search space used: 88208 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