Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein
Query= SwissProt::P17328 (400 letters) >NCBI__GCF_000009985.1:WP_011385004.1 Length = 379 Score = 171 bits (432), Expect = 4e-47 Identities = 95/241 (39%), Positives = 141/241 (58%), Gaps = 6/241 (2%) Query: 32 EQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVD 91 E I ++ G V+ LAI +GE F ++G SG GK+T++R+L PT G++LIDG D Sbjct: 26 EGISKRFGDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILIDGQD 85 Query: 92 IAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQ 151 + ++ E + + M+FQS+AL PHM+V DN AFG++ G+A ++K AL Sbjct: 86 VTEVPPYE------RPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALEL 139 Query: 152 VGLENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQ 211 V + ++ P +LSGG RQRV LAR LA P ++L+DE +ALD +R Q ELV +Q Sbjct: 140 VQMGRFSGRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQ 199 Query: 212 AKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDIS 271 + T V ++HD EAM + RI +M G + QVG+P +I P +V F ++ Sbjct: 200 DRVGITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIGAANMF 259 Query: 272 Q 272 Q Sbjct: 260 Q 260 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: 340 Number of extensions: 20 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: 379 Length adjustment: 30 Effective length of query: 370 Effective length of database: 349 Effective search space: 129130 Effective search space used: 129130 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