Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate N515DRAFT_1821 N515DRAFT_1821 putative ABC transport system ATP-binding protein
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__Dyella79:N515DRAFT_1821 Length = 238 Score = 134 bits (336), Expect = 4e-36 Identities = 73/203 (35%), Positives = 124/203 (61%), Gaps = 2/203 (0%) Query: 44 VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103 ++D ++ ++EGE + G SGSGK+T + + L T G+ +DGV+++ ++D ++ Sbjct: 21 LRDFNIDVKEGEFVAVTGPSGSGKTTFLTIAGLLETFTGGEYHLDGVEVSNLNDNARSKI 80 Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQVGLENYAHAYPD 163 R +KI +FQ+F L+P + V DN + G+ A ER+++ +DAL +VGL + A YP Sbjct: 81 RNEKIGFIFQAFNLIPDLNVYDNVEVPLRYRGMKALERKQRIMDALERVGLASRAKHYPA 140 Query: 164 ELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISH 223 ELSGG +QRV +ARALA +P +LL DE LD + + + L ++ + TIV ++H Sbjct: 141 ELSGGQQQRVAIARALAGSPRLLLADEPTGNLDTQMARGVMELLEEIH-REGATIVMVTH 199 Query: 224 DLDEAMRIGDRIAIMQNGEVVQV 246 D + A R + ++ +G+VV + Sbjct: 200 DPELATRAQRNVHVI-DGQVVDL 221 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: 228 Number of extensions: 13 Number of successful extensions: 1 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: 238 Length adjustment: 27 Effective length of query: 373 Effective length of database: 211 Effective search space: 78703 Effective search space used: 78703 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