Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate PfGW456L13_2830 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2830 Length = 361 Score = 234 bits (596), Expect = 4e-66 Identities = 125/258 (48%), Positives = 172/258 (66%), Gaps = 7/258 (2%) Query: 4 IHCQALAKHYAGGP---PVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 I + ++K Y+ P P L + + I D EF LLGPSGCGK+T+LR IAG E +S G Sbjct: 7 IEVRNVSKRYSDDPGLAPALDNVSVDIADNEFFTLLGPSGCGKTTLLRTIAGFEHVSDGE 66 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 +R+ G VNDLP +R V VFQ+YAL+PHMSV NIAFGL I +RV E+ A Sbjct: 67 IRLAGEPVNDLPPFKRRVNTVFQSYALFPHMSVAQNIAFGLEMQGLDRKLIPQRVDEMLA 126 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 L+ ++ L +RKP +SGGQQQR A+ARA+ P V L DEPLS LD KLR +++ ++KR+ Sbjct: 127 LVQMQHLAKRKPAELSGGQQQRVALARALAPKPKVLLLDEPLSALDLKLRKEMQVELKRV 186 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 + T ++VTHDQ EA+TL+DR+ +M G+I+Q GSP E+Y P++ F A FIG + Sbjct: 187 QKEAGITFIFVTHDQEEALTLSDRIAVMSAGKILQIGSPNEIYERPQHQFVAQFIGD--I 244 Query: 241 NFLSGTVQR--QDGQLFI 256 NFL G ++R Q+ +LF+ Sbjct: 245 NFLPGHIKRGQQNEKLFV 262 Lambda K H 0.321 0.137 0.403 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: 390 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: 406 Length of database: 361 Length adjustment: 30 Effective length of query: 376 Effective length of database: 331 Effective search space: 124456 Effective search space used: 124456 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: 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