Align TM1747, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate BPHYT_RS22045 BPHYT_RS22045 peptide ABC transporter permease
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__BFirm:BPHYT_RS22045 Length = 312 Score = 201 bits (511), Expect = 2e-56 Identities = 111/323 (34%), Positives = 186/323 (57%), Gaps = 21/323 (6%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKG 84 L + L+R L +++ VI Y+L+ L PG F+ ++ A A L Sbjct: 2 LAYTLRRTLWAIPTILAVITACYLLLHLTPGGPFDTEKQLSA-------------AVLAN 48 Query: 85 FEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFA 144 +Y L+ PLW Q L YL + GPSF ++ DL+ + P++ + S+ A Sbjct: 49 LNAKYHLDEPLWLQYLHYLGSLLHGDLGPSFRYADWSVNDLVWKALPVSLGVGGVSVPIA 108 Query: 145 LVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYL------GWLP 198 LV+GV LG +AA++++ ++D+ M + +G +P +V+ L+ IF+I L GWLP Sbjct: 109 LVIGVALGTVAAVRRDRFVDHFVMVLGNLGNVVPPFVLGPVLVWIFAILLKTSEGHGWLP 168 Query: 199 TSGW-EGI-RTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMK 256 GW EG R ++LP + L + +A++AR R S+++ L+ +FIRTA AKG RT++++ Sbjct: 169 AGGWGEGEWRYRVLPIVLLTIINVAAIARVMRGSMIEVLSGNFIRTARAKGLPGRTIVLR 228 Query: 257 HALRPSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFIL 316 HA++P+++P+V+++G + V E++F +PGLGQL N A+ RDY L++ + Sbjct: 229 HAMKPALMPVVSLLGSICISSITAAVVTESVFALPGLGQLVVNGAINRDYTLVLGLVVLT 288 Query: 317 ALTVMIMNLIVDVLYAILDPRIK 339 ++ NL+VD+ YA LDPRI+ Sbjct: 289 TAVAVLFNLLVDLAYAWLDPRIR 311 Score = 24.3 bits (51), Expect = 0.004 Identities = 12/46 (26%), Positives = 24/46 (52%) Query: 9 PGLLLNMSNGVVDMRFLKFLLKRLLTIAISMVVVIVITYVLMWLAP 54 PGL + NG ++ + L +LT A++++ +++ WL P Sbjct: 263 PGLGQLVVNGAINRDYTLVLGLVVLTTAVAVLFNLLVDLAYAWLDP 308 Lambda K H 0.328 0.143 0.429 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: 308 Number of extensions: 13 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 341 Length of database: 312 Length adjustment: 28 Effective length of query: 313 Effective length of database: 284 Effective search space: 88892 Effective search space used: 88892 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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