Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate 3608030 Dshi_1437 glycine betaine/L-proline ABC transporter, ATPase subunit (RefSeq)
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Dino:3608030 Length = 351 Score = 279 bits (714), Expect = 8e-80 Identities = 158/341 (46%), Positives = 219/341 (64%), Gaps = 13/341 (3%) Query: 5 LEIKNLYKIFGEHPQRAFKYI-EQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLS 63 +EI N++KIFG + Q A + + ++GLSK +IL + +GV D SL++ GEIF IMGLS Sbjct: 7 IEISNVWKIFGANAQAALEAVRDRGLSKAEILAEFNAVVGVADVSLSVRRGEIFCIMGLS 66 Query: 64 GSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTV 123 GSGKST+VR NRL+EPT G++ I+G D+ + EL+ R ++I MVFQ+FALMPH +V Sbjct: 67 GSGKSTLVRHFNRLLEPTAGRIEIEGTDVMALGTQELQRFRNRQIGMVFQNFALMPHRSV 126 Query: 124 LDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLARALAINP 183 LDN A +E+ + ER +A L V L + + EL GGM+QRVGLARALA NP Sbjct: 127 LDNVAMPLEIRKVPKNERMRQAAAILDIVELGAWGAKFAHELPGGMQQRVGLARALAANP 186 Query: 184 DILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEV 243 D+LLMDE FSALDPLIR ++QDE ++L ++T +FI+HDLDEA+RIGDRIAIM++G+V Sbjct: 187 DVLLMDEPFSALDPLIRRQLQDEFIRLSKILKKTTIFITHDLDEAVRIGDRIAIMRDGKV 246 Query: 244 VQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRTPNGLIRKTPGFGPRSALKLL 303 VQ+GT ++I+ +PA+DYV F G+ +V A + + P T G P + K+ Sbjct: 247 VQMGTAEDIVMHPADDYVADFVAGISRLKVVHAHAVMQ--PLEAYLATHGPLPAAVPKV- 303 Query: 304 QDEDREYGYVIERGNKFVGAVSIDSLKTALTQQQGLDAALI 344 DE +I ++ID L Q G D +I Sbjct: 304 -DEGETLSNLI--------TLAIDDENPILVQDAGRDVGII 335 Score = 24.6 bits (52), Expect = 0.005 Identities = 12/30 (40%), Positives = 16/30 (53%) Query: 355 PLSELLSHVGQAPCAVPVVDEDQQYVGIIS 384 PL L+ G P AVP VDE + +I+ Sbjct: 285 PLEAYLATHGPLPAAVPKVDEGETLSNLIT 314 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: 368 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 400 Length of database: 351 Length adjustment: 30 Effective length of query: 370 Effective length of database: 321 Effective search space: 118770 Effective search space used: 118770 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