Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Pf1N1B4_691 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_691 Length = 351 Score = 234 bits (598), Expect = 2e-66 Identities = 136/334 (40%), Positives = 197/334 (58%), Gaps = 16/334 (4%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 M + + + KHY G + ++LH+ +G+ V LGPSGCGK+T+LRMIAGLE ++GG Sbjct: 1 MTGLILENVEKHY-GSACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLTGGE 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 +R+ G + PA +RN MVFQ+ AL+PHM+V +NIA+ L+ A+ RV E+ Sbjct: 60 IRLDGEDIGHTPAHQRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKADQQARVVELLE 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 L+ L+ +++R +SGGQ+QR AIARAI P + L DEPLS LDAKLR ++ +I++L Sbjct: 120 LIQLQEMIDRPVAKLSGGQRQRVAIARAIASRPKILLLDEPLSALDAKLRESMQVEIRQL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGT--- 237 QRL TT+ VTHDQ EAMT+AD V+++ + R+ Q GSP E+YR+P N F A FIG+ Sbjct: 180 QQRLNITTIMVTHDQREAMTMADIVVVLGEHRVQQVGSPIEIYRHPANEFVADFIGSGNI 239 Query: 238 -PAMNFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREP 296 PA +G V G AL S + VK+ +RP+ ++++ + Sbjct: 240 FPATALGNGKVSLPGGD----------ALQVPICSSIVVGEKVKMLIRPEDLQLSQPQAT 289 Query: 297 AASLTCPVSVELVEILGADALLTTRCGDQTLTAL 330 A + V V +GA T C + TAL Sbjct: 290 AGNRLLG-KVTFVRDIGATIETTVECSGVSFTAL 322 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: 352 Number of extensions: 17 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: 351 Length adjustment: 30 Effective length of query: 376 Effective length of database: 321 Effective search space: 120696 Effective search space used: 120696 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