Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate 15248 b1126 putrescine/spermidine ABC transporter ATPase protein (NCBI)
Query= SwissProt::P17328 (400 letters) >FitnessBrowser__Keio:15248 Length = 378 Score = 174 bits (440), Expect = 5e-48 Identities = 99/238 (41%), Positives = 143/238 (60%), Gaps = 9/238 (3%) Query: 44 VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103 + L I GE ++G SG GK+T++RL+ L G++++D DI + AE R V Sbjct: 33 IPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLDNEDITHVP-AENRYV 91 Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQVGLENYAHAYPD 163 VFQS+AL PHMTV +N AFG+ + A E + ++ALR V LE +A P Sbjct: 92 NT-----VFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLETFAQRKPH 146 Query: 164 ELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISH 223 +LSGG +QRV +ARA+ P +LL+DE+ SALD +R +MQ+EL LQ K T VF++H Sbjct: 147 QLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLGITFVFVTH 206 Query: 224 DLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIAR 281 D +EA+ + DRI +M++G + Q GTP EI P N +V F ++ +F+A I R Sbjct: 207 DQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEIN---MFNATVIER 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: 330 Number of extensions: 13 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: 378 Length adjustment: 30 Effective length of query: 370 Effective length of database: 348 Effective search space: 128760 Effective search space used: 128760 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: 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