Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate WP_055445267.1 AMD28_RS16625 ABC transporter ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >NCBI__GCF_001418105.1:WP_055445267.1 Length = 228 Score = 140 bits (352), Expect = 5e-38 Identities = 80/200 (40%), Positives = 116/200 (58%), Gaps = 2/200 (1%) Query: 44 VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103 +K L IE G+ IMG SGSGKST++ LL L PT G L++G D++K+SD +L ++ Sbjct: 24 LKGIDLNIERGDYVAIMGPSGSGKSTLMNLLGCLDTPTSGSYLLNGQDVSKMSDDQLADI 83 Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPD 163 R K+I VFQ+F L+P T LDN A M AG + ER +A + L VGL + P+ Sbjct: 84 RNKEIGFVFQTFNLLPRTTALDNVALPMVYAGKSKSERHARAAEVLTDVGLADRMDHRPN 143 Query: 164 ELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISH 223 +LSGG RQRV + RAL NP I+L DE LD E+ ++ K T++ ++H Sbjct: 144 QLSGGQRQRVAVGRALVNNPSIILADEPTGNLDSKTGLEIMGLFDEIH-KAGNTVIMVTH 202 Query: 224 DLDEAMRIGDRIAIMQNGEV 243 + +E R+ +++G V Sbjct: 203 E-EEIAAHAHRVIRLRDGVV 221 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: 189 Number of extensions: 8 Number of successful extensions: 1 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: 228 Length adjustment: 27 Effective length of query: 373 Effective length of database: 201 Effective search space: 74973 Effective search space used: 74973 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: 48 (23.1 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