Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate Pf1N1B4_4352 Putrescine transport ATP-binding protein PotG (TC 3.A.1.11.2)
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4352 Length = 380 Score = 197 bits (502), Expect = 3e-55 Identities = 115/321 (35%), Positives = 181/321 (56%), Gaps = 22/321 (6%) Query: 3 RIIVKNVSKVFKK-GKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61 +++VK V +V KK + A+D+V++ I GE F +LG SG+GK+T +R++AG + P+ G Sbjct: 20 KVLVK-VDRVTKKFDETTAVDDVSLEIHQGEIFALLGGSGSGKSTLLRMLAGFERPTEGR 78 Query: 62 LYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRV 121 + D + +PP +R I M+FQ++AL+P++T +NIAF L ++ EI RV Sbjct: 79 ILLDGVDITD-----MPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDRLPASEIDARV 133 Query: 122 EEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARA 181 EE+ +++ + P +LSGGQ+QRVALAR+L K P LLLLDEP LD ++R + Sbjct: 134 EEMLRLVHMTQYARRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQL 193 Query: 182 LVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLI 241 + E+ R+GVT ++V+HD + +A+R+ ++ G + Q+G P D+Y+ PVS V I Sbjct: 194 ELVEIIERVGVTCVMVTHDQEEAMTMAERIAIMHLGWIAQIGSPVDIYEAPVSRMVCEFI 253 Query: 242 GEINELEGKVTNEGVVIGSLRFP-------------VSVSSDRAIIGIRPEDVKLSKDVI 288 G +N +G V + + P SV IRPE K+ + Sbjct: 254 GNVNAFDGTVVEDLEGHAIIHSPDLEQKIYVGHGVSTSVQDKSITYAIRPE--KMLVSTL 311 Query: 289 KDDSWILVGKGKVKVIGYQGG 309 K ++ +GKV I Y GG Sbjct: 312 KPETRYNWSEGKVHDIAYLGG 332 Lambda K H 0.319 0.139 0.390 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: 304 Number of extensions: 11 Number of successful extensions: 2 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: 353 Length of database: 380 Length adjustment: 30 Effective length of query: 323 Effective length of database: 350 Effective search space: 113050 Effective search space used: 113050 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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