Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_011613447.1 TERY_RS19750 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >NCBI__GCF_000014265.1:WP_011613447.1 Length = 407 Score = 178 bits (451), Expect = 3e-49 Identities = 96/240 (40%), Positives = 138/240 (57%), Gaps = 6/240 (2%) Query: 33 IPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLDNEDITHVPAEN---- 88 + + + I GE ++G SG GK+T++R I L SG I +D EDI H + Sbjct: 54 LADVSIDIGTGELFVVMGLSGSGKSTLVRCINRLVDPTSGHIYIDGEDIAHADEKRMRDI 113 Query: 89 --RYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLETFAQRKPH 146 V+ VFQ + LFPH TV ENV +GL+++ + +E L +V LE +A +P Sbjct: 114 RLNKVSMVFQRFGLFPHKTVAENVEYGLKVRGVSTTHRRQKALETLEVVGLEKWANYQPT 173 Query: 147 QLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLGITFVFVTH 206 LSGG QQRV +ARA+ +LL+DE+ SALD R +MQ+EL LQ++L T VF++H Sbjct: 174 SLSGGMQQRVGLARALATDADILLMDEAFSALDPLTRGEMQDELLRLQKELHKTIVFISH 233 Query: 207 DQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNATVIERLDEQR 266 D +E L + DRI VM+DG I Q GTP E+ PKN ++ F E+N + + +R Sbjct: 234 DMQEGLKLGDRIAVMKDGAIVQLGTPEELVTNPKNDYIKAFTEEVNSAQVITVGSIISKR 293 Lambda K H 0.319 0.136 0.385 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: 310 Number of extensions: 14 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: 378 Length of database: 407 Length adjustment: 31 Effective length of query: 347 Effective length of database: 376 Effective search space: 130472 Effective search space used: 130472 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 24 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