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 N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 133 bits (334), Expect = 7e-36 Identities = 96/266 (36%), Positives = 141/266 (53%), Gaps = 21/266 (7%) Query: 15 HRVEGI-VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLG 73 +RV+G + A+ S + GE GI+G SG+GKS +L+RLIN R G + G Sbjct: 11 YRVDGKDIPALQPFSLDIADGEVFGIIGHSGAGKS----TLIRLINLLERPSGGSILIDG 66 Query: 74 KDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNEEA---RE 130 ++ L LR R + I +IFQ+ +L V + P+ RL +A + Sbjct: 67 TEMTALGDAALRAQRRR-IGMIFQH--FNLLSSQTVADNIAFPL---RLAGETDAGKIKA 120 Query: 131 RAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQ 190 R ELL RVG+ + YP Q SGG +QRV IA ALA P +L+ DE T+ALD Sbjct: 121 RVDELLRRVGLEAHASK---YPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTT 177 Query: 191 AQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPY 250 A ++ELL E+ E ++++ ITH++ V CDR+ + AG+IVE V ++ P HP Sbjct: 178 ASVLELLAEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPT 237 Query: 251 TKGLLNSTLEIGSRGKKLVP---IPG 273 T+ +N L + G +L P +PG Sbjct: 238 TRRFVNEALPEEAAG-ELAPYTHVPG 262 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: 249 Number of extensions: 6 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: 336 Length adjustment: 28 Effective length of query: 296 Effective length of database: 308 Effective search space: 91168 Effective search space used: 91168 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