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 RR42_RS21355 RR42_RS21355 ABC transporter permease
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__Cup4G11:RR42_RS21355 Length = 334 Score = 187 bits (474), Expect = 4e-52 Identities = 111/337 (32%), Positives = 182/337 (54%), Gaps = 28/337 (8%) Query: 22 MRFLKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQAT 81 M FL FLL RL + ++ V++I + L+ +APG+ +A D A+ Sbjct: 1 MNFLSFLLSRLWKALVVVLGVVIINFFLIRMAPGD------PATVLAGEAGAGDAAFVGQ 54 Query: 82 LKGFEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSI 141 L+ +++GL+ P+ Q+ +YLKG G S+ + + DLI ++ P T L + Sbjct: 55 LR---QQFGLDQPVLTQLGIYLKGVARLDLGYSYRNHLP-VLDLILDRLPATIVLMSGAF 110 Query: 142 LFALVVGVPLGILAAL----KKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWL 197 +F++V+GV LG+++A K WID M+ +++ A P + +++ I++FS+ LGWL Sbjct: 111 VFSIVLGVFLGVISARTRYENKRRWIDSAVMSAALLLYATPLFWLSLMAIILFSVVLGWL 170 Query: 198 PTSGWEGIRT--------------KILPTIALALGPLASVARFTRVSLLDTLNQDFIRTA 243 P G E I ILPTI+L +A R TR S+L+ + DF++TA Sbjct: 171 PAFGMETIGAGYTGLARIQDVALHMILPTISLGCFFMAVYVRLTRASMLEVMGMDFVKTA 230 Query: 244 YAKGGDDRTVIMKHALRPSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVT 303 AKG VI H LR +++P++T G Q+ + G V E +F PG+G+L +A + Sbjct: 231 RAKGVPAGRVIRVHVLRNALLPVITFAGIQLGQMAGGAVLTETVFSWPGIGRLMFDALLQ 290 Query: 304 RDYPLLVTSTFILALTVMIMNLIVDVLYAILDPRIKL 340 RDY LL+ F+ + V+ NL+ D++Y +DPRI + Sbjct: 291 RDYQLLLGIFFVTSALVVFFNLVTDIVYRFIDPRISV 327 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: 280 Number of extensions: 17 Number of successful extensions: 4 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: 341 Length of database: 334 Length adjustment: 28 Effective length of query: 313 Effective length of database: 306 Effective search space: 95778 Effective search space used: 95778 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: 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