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 GFF4241 Psest_4314 ABC-type metal ion transport system, ATPase component
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__psRCH2:GFF4241 Length = 335 Score = 145 bits (367), Expect = 1e-39 Identities = 89/248 (35%), Positives = 135/248 (54%), Gaps = 17/248 (6%) Query: 12 VEFHRVEGI-------VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRI 64 +EFH+V V A+ ++ GE G++G SG+GKS +LLRLINR Sbjct: 2 IEFHQVHKTYRTGGRDVPALQPTQLEIASGEVFGLIGHSGAGKS----TLLRLINRLEEP 57 Query: 65 VDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMK 124 G + G+D+ L+ + LR R + + +IFQ+ ++ + + + P+ + Sbjct: 58 SGGRILVNGEDVTALDADGLRRFRQR-VGMIFQHFNLLMSKTVADNVAM--PLRLAGIRS 114 Query: 125 NEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTA 184 E R LLERVG+ E ++ YP Q SGG +QRV IA ALA P +L+ DE T+A Sbjct: 115 RREIDARVAALLERVGLKEHARK---YPAQLSGGQKQRVGIARALATEPSILLCDEATSA 171 Query: 185 LDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILK 244 LD A +++LL E+ E ++++ ITH++ V CDR+ M AG IVE+ PV E+ Sbjct: 172 LDPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDRVAVMDAGAIVEQGPVTEVFL 231 Query: 245 TPLHPYTK 252 P HP T+ Sbjct: 232 HPKHPTTQ 239 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: 246 Number of extensions: 10 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: 335 Length adjustment: 28 Effective length of query: 296 Effective length of database: 307 Effective search space: 90872 Effective search space used: 90872 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 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