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 Ga0059261_3874 Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Korea:Ga0059261_3874 Length = 243 Score = 97.8 bits (242), Expect = 2e-25 Identities = 77/218 (35%), Positives = 117/218 (53%), Gaps = 25/218 (11%) Query: 26 GISYKLNKGESLGIVGESGSGKS--VSVLSLLRLINRNGRIVDGEAIFLGKDLLKLNKEE 83 G+S + GE +VG SG GKS +++LS L L ++ GE LG + ++ Sbjct: 30 GVSVSVMPGELTLVVGPSGCGKSTLLAILSGLTLPDQ------GEVDALGNPICRMKAGA 83 Query: 84 LRNIRGKDISIIFQ-----NPMTSLNPIIRVGIQVMEPIIWHRLMKNEEARERAIELLER 138 R + +FQ N +T+ + V +Q M+ +K EAR+RA LE Sbjct: 84 RDAFRLANTGFVFQGFNLFNALTAEEQVAYV-LQCMK-------VKPAEARQRARAALEA 135 Query: 139 VGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQIMELLQ 198 VG+ P+ L PF+ SGG +QRV IA ALA P++L ADEPT+ALD ++ LL+ Sbjct: 136 VGL--GPRMRLR-PFELSGGEKQRVAIARALAKQPRILFADEPTSALDSHNGHAVIALLR 192 Query: 199 ELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEE 236 ++ G +V+ +THD + +F DRII M G+I+ + Sbjct: 193 DIAHNQGAAVLCVTHDPRL-LSFADRIIHMEDGRIIRD 229 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: 140 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: 243 Length adjustment: 26 Effective length of query: 298 Effective length of database: 217 Effective search space: 64666 Effective search space used: 64666 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 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