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 WP_090275879.1 BLU11_RS18455 methionine ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >NCBI__GCF_900105005.1:WP_090275879.1 Length = 334 Score = 139 bits (350), Expect = 1e-37 Identities = 89/256 (34%), Positives = 135/256 (52%), Gaps = 15/256 (5%) Query: 1 MMELLNVNNLKVEFHRVEGI-VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLIN 59 M+E VN +RV G + A+ + G+ GI+G SG+GKS +LLRLIN Sbjct: 1 MIEFQQVNKA----YRVGGRDIPALHATDLTIEAGQVYGIIGHSGAGKS----TLLRLIN 52 Query: 60 RNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIW 119 R +G + G+D LN E LR R + + +IFQ+ +L V V P+ Sbjct: 53 RLEEPSNGRIMVAGEDTTALNAEGLRRFRQR-VGMIFQH--FNLLSSATVADNVALPLRL 109 Query: 120 HRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIAD 179 ++ R LL+RVG+ + + YP Q SGG +QRV IA ALA P +L+ D Sbjct: 110 AGSANRQQIAARVASLLDRVGLSDHASK---YPAQLSGGQKQRVGIARALATEPSILLCD 166 Query: 180 EPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPV 239 E T+ALD Q+++LL E+ E ++++ ITH++ V CD++ M G+IVE+ V Sbjct: 167 EATSALDPHTTGQVLQLLSEINRELNLTIVLITHEMDVIRRVCDQVAVMDGGRIVEQGTV 226 Query: 240 EEILKTPLHPYTKGLL 255 ++ P HP T+ + Sbjct: 227 ADVFLHPQHPTTRSFV 242 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: 232 Number of extensions: 6 Number of successful extensions: 2 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: 334 Length adjustment: 28 Effective length of query: 296 Effective length of database: 306 Effective search space: 90576 Effective search space used: 90576 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 24 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