Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Caulo:CCNA_02751 Length = 332 Score = 191 bits (485), Expect = 3e-53 Identities = 99/219 (45%), Positives = 146/219 (66%), Gaps = 1/219 (0%) Query: 48 SLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKK 107 SL+++ GE+F ++G SG+GKST++RL+N L P+ GQV++DG D+A + A LR +RR+ Sbjct: 23 SLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQVIVDGDDVAALGVAGLRALRRR- 81 Query: 108 IAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSG 167 + M+FQ F L+ TV N AF ++LAG A E + + + L +VGL +A YP +LSG Sbjct: 82 VGMIFQHFNLLSGKTVAQNVAFPLKLAGRPAAEVKARTAELLERVGLSAHAGKYPAQLSG 141 Query: 168 GMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDE 227 G +QRVG+ARALA NP +LL DEA SALDP ++ D + L + TIV I+H++D Sbjct: 142 GQKQRVGIARALATNPKVLLCDEATSALDPETTEQILDLIAGLNRELGLTIVLITHEMDV 201 Query: 228 AMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFR 266 R+ DR+A++ G VV+ G +E+ +PA+D R F R Sbjct: 202 VRRVCDRVAVLDAGRVVEEGAVEEVFLHPASDTARRFVR 240 Lambda K H 0.319 0.137 0.378 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: 321 Number of extensions: 20 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: 400 Length of database: 332 Length adjustment: 29 Effective length of query: 371 Effective length of database: 303 Effective search space: 112413 Effective search space used: 112413 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 (21.7 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