Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate PfGW456L13_2830 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2830 Length = 361 Score = 222 bits (566), Expect = 1e-62 Identities = 133/297 (44%), Positives = 183/297 (61%), Gaps = 12/297 (4%) Query: 2 TSVSVRDLSLNF----GAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSD 57 T++ VR++S + G LD +++DI EF LLG SGCGK+TLL IAG VSD Sbjct: 5 TAIEVRNVSKRYSDDPGLAPALDNVSVDIADNEFFTLLGPSGCGKTTLLRTIAGFEHVSD 64 Query: 58 GQIFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRA 117 G+I + V P R + VFQSYAL+P M+V +N++FGL++ + I +RV Sbjct: 65 GEIRLAGEPVNDLPPFKRRVNTVFQSYALFPHMSVAQNIAFGLEMQGLDRKLIPQRVDEM 124 Query: 118 SEILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIK 177 ++Q+Q L KRKP+ELSGGQ+QRVA+ RAL V L DEPLS LD KLR E++VE+K Sbjct: 125 LALVQMQHLAKRKPAELSGGQQQRVALARALAPKPKVLLLDEPLSALDLKLRKEMQVELK 184 Query: 178 RLHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSP 237 R+ + T I+VTHDQ EALTL+DRIAVM +G I Q+ P IY P++ FVA FIG Sbjct: 185 RVQKEAGITFIFVTHDQEEALTLSDRIAVMSAGKILQIGSPNEIYERPQHQFVAQFIG-- 242 Query: 238 SMNFFRGEVE--PKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDE 292 +NF G ++ ++ + FV G+ ++ P + G KV L RPE ++ E Sbjct: 243 DINFLPGHIKRGQQNEKLFV-PNGMPVEI---PCPAQGFDGSKVQLAFRPERSQLVE 295 Lambda K H 0.320 0.137 0.392 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: 360 Number of extensions: 24 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: 361 Length of database: 361 Length adjustment: 29 Effective length of query: 332 Effective length of database: 332 Effective search space: 110224 Effective search space used: 110224 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: 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