Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__PV4:5208462 Length = 378 Score = 216 bits (550), Expect = 8e-61 Identities = 122/323 (37%), Positives = 192/323 (59%), Gaps = 24/323 (7%) Query: 2 VRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61 V + ++ VSK+F V A+D+V++NI GE F +LG SG+GK+T +R++AG + P+ G Sbjct: 19 VLLKIERVSKLFDD--VRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGR 76 Query: 62 LYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRV 121 +Y D + + +PP +R I M+FQ++AL+P++T +NIAF L KM K EI +RV Sbjct: 77 IYLDGQDITD-----MPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDKMPKAEIEQRV 131 Query: 122 EEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARA 181 +E+ K++ + P +LSGGQ+QRVALAR+L K P LLLLDEP LD ++R + Sbjct: 132 KEMLKLVHMEPYAKRKPNQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQL 191 Query: 182 LVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLI 241 V ++ +GVT ++V+HD + +A+R+ ++ G + Q G P D+Y++P + VA I Sbjct: 192 EVVDILEAVGVTCVMVTHDQEEAMTMAERIAIMNDGWIAQTGSPMDIYESPANRMVAEFI 251 Query: 242 GEINELEGKVTN---EGVVIGSLRFP----------VSVSSDRAIIGIRPEDVKLSKDVI 288 G +N EG + + VVI P SV + + + IRPE +S++ Sbjct: 252 GSVNLFEGDIVEDEVDHVVINVANIPQPFYVGYGVSTSVDTTQVWVAIRPEKTHISREQP 311 Query: 289 KD-DSWILVGKGKVKVIGYQGGL 310 +D +W GKV+ I Y GG+ Sbjct: 312 EDARNWC---AGKVEDIAYLGGI 331 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: 316 Number of extensions: 14 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: 378 Length adjustment: 30 Effective length of query: 323 Effective length of database: 348 Effective search space: 112404 Effective search space used: 112404 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 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