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_057508907.1 ABB28_RS12160 methionine ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >NCBI__GCF_001431535.1:WP_057508907.1 Length = 335 Score = 131 bits (329), Expect = 3e-35 Identities = 84/243 (34%), Positives = 132/243 (54%), Gaps = 15/243 (6%) Query: 21 VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLGKDLLKLN 80 + A+ + + +GE GI+G SG+GKS +L+R+INR G + G+D+ L Sbjct: 18 ISALQPLDLTIQEGEVFGIIGHSGAGKS----TLIRMINRLEDPSGGRLLIAGEDVTALE 73 Query: 81 KEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNEEAR--ERAIELLER 138 LR +R + I +IFQ+ +L V V P+ L A+ R ELL+ Sbjct: 74 TAGLRTLRRR-IGMIFQH--FNLLSSRTVASNVAFPL---ELAGTPRAQIDARVAELLQT 127 Query: 139 VGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQIMELLQ 198 VG+ + YP Q SGG +QRV IA ALA P++L+ DE T+ALD A ++ LL Sbjct: 128 VGLQAHADK---YPAQLSGGQKQRVGIARALATGPQILLCDEATSALDPQTTASVLALLS 184 Query: 199 ELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTKGLLNST 258 ++ E G++++ ITH++ V CDR+ + AG++VE PV ++ P HP T+ ++ + Sbjct: 185 KINRELGLTIVLITHEMDVIRRVCDRVAVLDAGEMVEMGPVTDVFLHPQHPTTRRFVSES 244 Query: 259 LEI 261 I Sbjct: 245 EHI 247 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: 207 Number of extensions: 9 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 24 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