Align TM1746, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate BWI76_RS17240 BWI76_RS17240 oligopeptide ABC transporter substrate-binding protein OppA
Query= TCDB::Q9X268 (642 letters) >FitnessBrowser__Koxy:BWI76_RS17240 Length = 543 Score = 182 bits (462), Expect = 3e-50 Identities = 122/365 (33%), Positives = 196/365 (53%), Gaps = 23/365 (6%) Query: 49 IFEGLFGYVPDPKSLGGVKVVPAVCESYTVSEDGLTYTFYLRKDKRWSNGDPVTAYDFEF 108 +FEGL D + GV E + ++D +TF+LRKD +WS+G PVTA DF + Sbjct: 69 LFEGLLVSDLDGHPVAGV------AEKWD-NKDFKVWTFHLRKDAKWSDGTPVTAQDFVY 121 Query: 109 AWKRAASPETPTLPLWASPVQY--IKNVYDCKSGAKPLDELGVKALDDYTLQVTLSRPMP 166 +W+R A P+T + +AS +QY + N+ D +G KP +LGVKALDD+T +VTLS P+P Sbjct: 122 SWQRLADPKTASP--YASYLQYGHLANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVP 179 Query: 167 SFINMLVLGGAMPLHRKTVQEHPEDWWKPEYFVGNGPYVIESFTPNYEIVLVRNKYYVGD 226 F +LV P+ + +++ + W +P V NG Y ++ + N IVL RN Y + Sbjct: 180 YFYKLLVHPSVSPVPKSAIEKFGDKWTQPANIVSNGAYKLKDWVVNERIVLERNTNYWDN 239 Query: 227 FPGNVDRIV---LKAGGLGLQQYLAGEIDAVFITAVGDYVFALKNKQLSKELHEESGVQW 283 ++++ + + + +Y +GEID + + LK K++ KE+H + + Sbjct: 240 AKTVINQVTFLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLK-KEIPKEVHVDPYLCT 298 Query: 284 VGYEITRSLSPVFDDIRIRKALAMAIDKKVLTDIVLGGMAIPTHAYCSPDSEIAEAVKGI 343 YEI +P F D+R+R AL MA+D+ ++ + V +P ++Y P ++ + ++ Sbjct: 299 YYYEINNQKAP-FTDVRVRTALKMALDRDIIVNKVKNQGDLPAYSYTPPYTDGMKLIEPE 357 Query: 344 PYD------PEQAKKLLAEAGYPNGKGFPKVKFYITG-ASDPVAEALVDQWKKVLGITFE 396 + E+AKKLLAEAGY K Y T +A A+ WKK LG+ + Sbjct: 358 WFKWSQEKRNEEAKKLLAEAGYSADKPLTFNLLYNTSDLHKKLAIAVASIWKKNLGVNVK 417 Query: 397 IENIE 401 +EN E Sbjct: 418 LENQE 422 Lambda K H 0.319 0.138 0.431 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: 1005 Number of extensions: 48 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 642 Length of database: 543 Length adjustment: 37 Effective length of query: 605 Effective length of database: 506 Effective search space: 306130 Effective search space used: 306130 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 (21.7 bits) S2: 53 (25.0 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