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 200964 SO1802 peptide ABC transporter, ATP-binding protein (NCBI ptt file)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__MR1:200964 Length = 335 Score = 212 bits (539), Expect = 1e-59 Identities = 118/326 (36%), Positives = 191/326 (58%), Gaps = 15/326 (4%) Query: 2 MELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN 61 M LL+V NL +E G V+A++ +S LN GE G+VGESGSG+S+ ++L + N Sbjct: 1 MPLLDVRNLTIELDTPHGKVRALEKVSLTLNAGEIHGLVGESGSGRSLLARAILGIPGPN 60 Query: 62 GRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPI---- 117 I ++ G +L+ ++ +E RN+ G D+++IFQ+P SL+P VG Q+M+ + Sbjct: 61 WTITADRMMWDGNNLMAMSSKERRNLMGSDMAMIFQDPSGSLDPSQTVGSQLMQAMPKNP 120 Query: 118 ---IWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPK 174 W K++ A+ A + L +VGI K +Y ++ S G Q+VMIAMA+A P+ Sbjct: 121 KAYFWQ---KHKHAKLTAQKWLHKVGIKNPQKVMSSYAWELSEGECQKVMIAMAIANQPR 177 Query: 175 LLIADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIV 234 LLIADEPT +++++ QAQI LL +L + +S++ I+H+L +CD + +Y G+++ Sbjct: 178 LLIADEPTNSMELSTQAQIFRLLSQLNQLQNVSILIISHELETLAQWCDHLSVLYCGQVM 237 Query: 235 EEAPVEEILKTPLHPYTKGLLNSTLEIG--SRGKKLVP-IPGNPPNPTKHPSGCKFHPRC 291 E P +E++ P HPYTK LL++ + K ++P +PG+ P P GC+ PRC Sbjct: 238 ESGPTDELINQPYHPYTKALLDNMPDYSGIEAHKAIMPTLPGSAPALQHLPIGCRLGPRC 297 Query: 292 SFAMEICQREEPPLVNISENHRVACH 317 A + C + P ++ S + ACH Sbjct: 298 PEAQKKCVNQ--PSLSHSRDRYFACH 321 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: 275 Number of extensions: 11 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: 324 Length of database: 335 Length adjustment: 28 Effective length of query: 296 Effective length of database: 307 Effective search space: 90872 Effective search space used: 90872 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