Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate 8500851 DvMF_1589 ABC transporter related (RefSeq)
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Miya:8500851 Length = 354 Score = 171 bits (433), Expect = 3e-47 Identities = 96/260 (36%), Positives = 150/260 (57%), Gaps = 7/260 (2%) Query: 34 ILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIA 93 + ++ G V +L I GE F ++G SG GK+T +R++ + G++ + ++ Sbjct: 9 VTKRFGGVTAVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDGEIHVGDRLLS 68 Query: 94 KISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVG 153 + ++ MVFQ+FA+ PH++V +N AF + + ++A E + +AL Sbjct: 69 ARRNNYYLPPEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRRLSAAEIDRRTREALHHTS 128 Query: 154 LENYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAK 213 L + A PD+LSGG +QRV LARALAINPD++L+DE S+LDP +R EM+ E+ LQ Sbjct: 129 LADVAQKSPDDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEMRFEIKDLQRT 188 Query: 214 HQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDISQV 273 +I++++HD EAM + DRI +M+NG V QVGTP ++ NPAN +V F + +S Sbjct: 189 FGFSILYVTHDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFV---FGFIGLSNF 245 Query: 274 FSAKDIARRTPNGLIRKTPG 293 TP GL+R G Sbjct: 246 LD----VNLTPEGLVRVNGG 261 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: 327 Number of extensions: 16 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: 354 Length adjustment: 30 Effective length of query: 370 Effective length of database: 324 Effective search space: 119880 Effective search space used: 119880 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: 50 (23.9 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