Align PTS system mannose-specific EIIAB component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate WP_007668613.1 BN137_RS13775 PTS mannose transporter subunit IIAB
Query= CharProtDB::CH_088329 (323 letters) >NCBI__GCF_000319285.1:WP_007668613.1 Length = 320 Score = 583 bits (1502), Expect = e-171 Identities = 300/321 (93%), Positives = 309/321 (96%), Gaps = 3/321 (0%) Query: 1 MTIAIVIGTHGWAAEQLLKTAEMLLGEQENVGWIDFVPGENAETLIEKYNAQLAKLDTTK 60 MTIAIVIGTHGWAAEQLLKTAEMLLGEQENVGWIDFVPGENAETLIEKYNAQL KLDT+K Sbjct: 1 MTIAIVIGTHGWAAEQLLKTAEMLLGEQENVGWIDFVPGENAETLIEKYNAQLEKLDTSK 60 Query: 61 GVLFLVDTWGGSPFNAASRIVVDKEHYEVIAGVNIPMLVETLMARDDDPSFDELVALAVE 120 GV+FLVDTWGGSPFNAASRIVVDK +YEV+AGVNIPMLVET MARDDDPSFDELVALAVE Sbjct: 61 GVVFLVDTWGGSPFNAASRIVVDKPNYEVVAGVNIPMLVETFMARDDDPSFDELVALAVE 120 Query: 121 TGREGVKALKAKPVEKAAPAPAAAAPKAAPTPAKPMGPNDYMVIGLARIDDRLIHGQVAT 180 TGREGVKALKAKPVEKAAPA A APKAA AKPMGPNDYM IGLARIDDRLIHGQVAT Sbjct: 121 TGREGVKALKAKPVEKAAPA--APAPKAAAA-AKPMGPNDYMKIGLARIDDRLIHGQVAT 177 Query: 181 RWTKETNVSRIIVVSDEVAADTVRKTLLTQVAPPGVTAHVVDVAKMIRVYNNPKYAGERV 240 RWTKETNVSRIIVVSDEVAAD VRKTLLTQVAPPGVTAHVVDVAKMIRVYNNPKYAGERV Sbjct: 178 RWTKETNVSRIIVVSDEVAADNVRKTLLTQVAPPGVTAHVVDVAKMIRVYNNPKYAGERV 237 Query: 241 MLLFTNPTDVERLVEGGVKITSVNVGGMAFRQGKTQVNNAVSVDEKDIEAFKKLNARGIE 300 MLLFTNPTDVER+VEGGVKITSVN+GGMA+RQGKTQVNNAVSVDEKDIEAFKKLNARGIE Sbjct: 238 MLLFTNPTDVERIVEGGVKITSVNIGGMAYRQGKTQVNNAVSVDEKDIEAFKKLNARGIE 297 Query: 301 LEVRKVSTDPKLKMMDLISKI 321 LEVRKVS DP+LKMMDLISK+ Sbjct: 298 LEVRKVSNDPRLKMMDLISKV 318 Lambda K H 0.316 0.133 0.375 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: 441 Number of extensions: 11 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: 323 Length of database: 320 Length adjustment: 28 Effective length of query: 295 Effective length of database: 292 Effective search space: 86140 Effective search space used: 86140 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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