Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate Ac3H11_2058 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2058 Length = 360 Score = 178 bits (451), Expect = 3e-49 Identities = 88/224 (39%), Positives = 138/224 (61%), Gaps = 6/224 (2%) Query: 41 SLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAEL 100 +L VK S + G + I+G SG GK+T +R++ L PT G++ I G D+ + A+ Sbjct: 24 ALAVKGISFEVPRGTLTTILGPSGCGKTTTLRMIAGLESPTSGEIFIGGKDVTTLGPAQ- 82 Query: 101 REVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLENYAHS 160 + ++M+FQS+AL PHM V++N +G+ ++G E+ R KA++ALR VGL + Sbjct: 83 -----RNVSMMFQSYALFPHMNVVENVMYGLRMSGQPKEQARAKAVEALRGVGLVGFDDR 137 Query: 161 YPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVF 220 P ELSGG +QRV LARAL + P++LL DE S LD +R EM++E+ LQ + T+ + Sbjct: 138 LPSELSGGQQQRVALARALVLEPEVLLFDEPLSNLDARLRREMREEIRALQQRLSLTVAY 197 Query: 221 ISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264 ++HD EAM + D+I +M G + Q G+P + P +++V F Sbjct: 198 VTHDQAEAMAVSDQIIVMNQGLIAQKGSPRALYETPHSEFVAGF 241 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: 332 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 400 Length of database: 360 Length adjustment: 30 Effective length of query: 370 Effective length of database: 330 Effective search space: 122100 Effective search space used: 122100 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 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