Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate 209035 DVU0105 glutamine ABC transporter, ATP-binding protein
Query= SwissProt::P17328 (400 letters) >MicrobesOnline__882:209035 Length = 244 Score = 171 bits (432), Expect = 3e-47 Identities = 98/265 (36%), Positives = 156/265 (58%), Gaps = 28/265 (10%) Query: 1 MAIKLEVKNLYKIFGEHPQRAFKYIEKGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIM 60 M +E++NL+K +G+H ++ +G+ L + GE+ V++ Sbjct: 1 MTPMIEIRNLHKSYGDH------HVLRGID------------------LTVRTGEVVVVI 36 Query: 61 GLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPH 120 G SGSGKST +R +NRL E T G +++DG D+ ++ VR + MVFQ F L PH Sbjct: 37 GPSGSGKSTALRCINRLEEITSGTIIVDGYDLYD-PKTDINHVRTEA-GMVFQQFNLFPH 94 Query: 121 MTVLDNTAFG-MELAGIAAQERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARAL 179 M+VL+N G +++ +A QE + L L +VGL + AHAYPD+LSGG +QRV +AR+L Sbjct: 95 MSVLENVTIGPVKVRRMARQEAQALGLALLEKVGLADKAHAYPDQLSGGQKQRVAIARSL 154 Query: 180 AINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQ 239 A+ P +LL DE SALDP + E+ E++K A+ T+V ++H++ A + DR+ + Sbjct: 155 AMQPKVLLFDEPTSALDPELVGEVL-EVMKQLAREGMTMVVVTHEMGFAREVADRVIFID 213 Query: 240 NGEVVQVGTPDEILNNPANDYVRTF 264 G++ + G P+E+ +P N +R F Sbjct: 214 YGKIQEEGPPNELFADPKNPRLREF 238 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: 246 Number of extensions: 17 Number of successful extensions: 5 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: 244 Length adjustment: 27 Effective length of query: 373 Effective length of database: 217 Effective search space: 80941 Effective search space used: 80941 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