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 AO353_05410 AO353_05410 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05410 Length = 323 Score = 239 bits (610), Expect = 7e-68 Identities = 121/299 (40%), Positives = 192/299 (64%), Gaps = 9/299 (3%) Query: 20 IVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLGKDLLKL 79 +V+A++G+S++L G++L +VGESG GKS +L R + G G+++ Sbjct: 26 LVRALNGVSFELEAGKTLAVVGESGCGKS----TLARALTLIEEPSSGSLKIAGQEVTGA 81 Query: 80 NKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNEEARERAIELLERV 139 NK E + +R KD+ ++FQ+P SLNP ++G Q+ EP++ + + E RE+ ++++V Sbjct: 82 NKAERKQLR-KDVQMVFQSPYASLNPRQKIGDQLAEPLLINTKLSAAERREKVQAMMKQV 140 Query: 140 GIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQIMELLQE 199 G+ P+ + YP FSGG RQR+ +A A+ PK+L+ADEPT+ALDV+IQAQ++ L + Sbjct: 141 GL--RPEHYQRYPHMFSGGQRQRIALARAMMLQPKVLVADEPTSALDVSIQAQVLNLFMD 198 Query: 200 LKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTKGLLNSTL 259 L++E+ + +FI+H+L+V + D+++ MY G+ VE P E+I PLHPYT+ LL++T Sbjct: 199 LQQEFNTAYVFISHNLAVVRHVADQVLVMYLGRPVEMGPKEDIYTRPLHPYTQALLSATP 258 Query: 260 EI-GSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEPPLVNISENHRVACH 317 I K + I G PNP PSGC FH RC +A E+C +EEP L + ++ +VACH Sbjct: 259 TIHPDPTKPKIKIVGELPNPLNPPSGCAFHKRCPYATELCSKEEPALRQL-DSRQVACH 316 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: 273 Number of extensions: 19 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: 323 Length adjustment: 28 Effective length of query: 296 Effective length of database: 295 Effective search space: 87320 Effective search space used: 87320 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