Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate 353365 BT3839 ABC transporter ATP-binding protein (NCBI ptt file)
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__Btheta:353365 Length = 256 Score = 131 bits (330), Expect = 2e-35 Identities = 75/236 (31%), Positives = 135/236 (57%), Gaps = 7/236 (2%) Query: 36 EKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKI 95 +KT LS + + + E G+ +I+G SGSGK+ +++ + L+ P +G+VL DG ++ + Sbjct: 13 DKTVLS----NINASFENGKTNLIIGQSGSGKTVLMKCIVGLLTPEKGEVLYDGRNLVLM 68 Query: 96 SDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMEL-AGIAAQERREKALDALRQVGL 154 E +++ RK++ M+FQS AL M+VLDN F + + + ++R ++A+ L +V L Sbjct: 69 GKKE-KKMLRKEMGMIFQSAALFDSMSVLDNVMFPLNMFSNDTLRDRTKRAMFCLERVNL 127 Query: 155 ENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKH 214 +P E+SGGM++RV +ARA+A+NP L DE S LDP + D + + ++ Sbjct: 128 TEAKDKFPGEISGGMQKRVAIARAIALNPQYLFCDEPNSGLDPKTSLVIDDLIHDITQEY 187 Query: 215 QRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDI 270 T + +HD++ + IG+++ + G GT D+I + N+ + F D+ Sbjct: 188 NMTTIINTHDMNSVLGIGEKVIYIYEGHKEWEGTKDDIFTS-TNERLNNFIFASDL 242 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: 208 Number of extensions: 11 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: 400 Length of database: 256 Length adjustment: 28 Effective length of query: 372 Effective length of database: 228 Effective search space: 84816 Effective search space used: 84816 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