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_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD
Query= TCDB::Q9X271 (324 letters) >NCBI__GCF_900141795.1:WP_074200832.1 Length = 227 Score = 116 bits (290), Expect = 6e-31 Identities = 75/212 (35%), Positives = 118/212 (55%), Gaps = 12/212 (5%) Query: 26 GISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLGKDLLKLNKEELR 85 G+S L++ E + IVG SGSGKS +LL L+ R DGE + LG+ KL + Sbjct: 27 GVSLILHRRERVAIVGSSGSGKS----TLLHLLGGLDRPTDGEVLLLGQPFSKLGEAARG 82 Query: 86 NIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNEEARERAIELLERVGIPESP 145 +R + + ++Q L P + VM P++ R AR++A+ LL+ VG+ Sbjct: 83 RLRNRHMGFVYQ--FHHLLPELTAEENVMMPLLIRR-ESEATARDKALALLDAVGLS--- 136 Query: 146 KRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQIMELLQELKEEYG 205 +R + P + SGG RQRV +A AL P ++ADEPT LD Q++ L+ +L + +G Sbjct: 137 RRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVLSLMDDLNQRFG 196 Query: 206 MSVIFITHDLSVATNFCDRIITMYAGKI-VEE 236 +++ +THD+++A DR +T+ G I VEE Sbjct: 197 TALLVVTHDVNIAARM-DRTLTLRDGMIRVEE 227 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: 148 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: 227 Length adjustment: 25 Effective length of query: 299 Effective length of database: 202 Effective search space: 60398 Effective search space used: 60398 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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