Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate Ac3H11_2058 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2058 Length = 360 Score = 238 bits (606), Expect = 3e-67 Identities = 137/306 (44%), Positives = 188/306 (61%), Gaps = 12/306 (3%) Query: 2 ATVTFDKATRIYPGSDKPA---VDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVN 58 A + F T+ Y G+D A V + + G ++GPSGCGK+T+LRM+AGLE Sbjct: 6 AGIVFRNITKRY-GTDSSAALAVKGISFEVPRGTLTTILGPSGCGKTTTLRMIAGLESPT 64 Query: 59 GGAIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEE 118 G I IG +DVT L P R+++M+FQ+YAL+PHM V +N+ + L+++G PK + R K E Sbjct: 65 SGEIFIGGKDVTTLGPAQRNVSMMFQSYALFPHMNVVENVMYGLRMSGQPKEQARAKAVE 124 Query: 119 AAKILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQI 178 A + + L + DR P LSGGQ+QRVA+ RA+V EP+V L DEPLSNLDA+LR R +I Sbjct: 125 ALRGVGLVGFDDRLPSELSGGQQQRVALARALVLEPEVLLFDEPLSNLDARLRREMREEI 184 Query: 179 ASLQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGS 238 +LQ+RL +T YVTHDQ EAM + D++ V+ GL+ Q SPR +Y+ P + FVAGF+G Sbjct: 185 RALQQRLSLTVAYVTHDQAEAMAVSDQIIVMNQGLIAQKGSPRALYETPHSEFVAGFMGE 244 Query: 239 PAMNLVEVPITDGGVKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELG-GAVAA 297 AM V DG V G P+ A G V V VRPE + + G G + A Sbjct: 245 -AMLFPAVADADGTVALG----PLVLRPRVAVKSG--PVKVAVRPEAWRITRQGEGLLPA 297 Query: 298 SLSKDS 303 L+K + Sbjct: 298 RLAKSA 303 Lambda K H 0.317 0.135 0.379 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: 345 Number of extensions: 21 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: 377 Length of database: 360 Length adjustment: 30 Effective length of query: 347 Effective length of database: 330 Effective search space: 114510 Effective search space used: 114510 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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