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 7025500 Shewana3_2654 ABC transporter related (RefSeq)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__ANA3:7025500 Length = 261 Score = 160 bits (405), Expect = 3e-44 Identities = 92/234 (39%), Positives = 149/234 (63%), Gaps = 12/234 (5%) Query: 23 AVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLGKDLLKLN-K 81 A+ +S++LN+GE+L IVGE+GSGKS L+ R+G GE F G+ L N K Sbjct: 29 ALAPVSFELNRGETLAIVGEAGSGKSTLARILVGAEPRSG----GEIYFEGEALDSRNIK 84 Query: 82 EELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNEEARERAIELLERVGI 141 + R IR +IFQ+P TSLNP + +G + EP+ ++ + +E + I+ L +VG+ Sbjct: 85 QRCRLIR-----MIFQDPNTSLNPRLTIGQLLDEPLRFNTELSAKERSGQVIDTLRKVGL 139 Query: 142 PESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQIMELLQELK 201 F YP S G +QRV +A AL +PK++IADE TALD+++++QI+ LL +L+ Sbjct: 140 LPEHADF--YPHMISEGQKQRVAVARALMLNPKIIIADEALTALDLSVRSQILNLLLKLQ 197 Query: 202 EEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTKGLL 255 ++ G+S IF++H+L++ + D+I+ ++ G +VE+AP E+I +P H YT+ L+ Sbjct: 198 KDLGLSYIFVSHNLNIIRHVSDKIMVLHKGVMVEKAPTEQIFNSPQHEYTQRLI 251 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: 209 Number of extensions: 11 Number of successful extensions: 3 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: 261 Length adjustment: 26 Effective length of query: 298 Effective length of database: 235 Effective search space: 70030 Effective search space used: 70030 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: 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