Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate PfGW456L13_1569 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1569 Length = 372 Score = 202 bits (513), Expect = 1e-56 Identities = 107/255 (41%), Positives = 162/255 (63%), Gaps = 11/255 (4%) Query: 4 IIVKNVSKVFKKGKV--VALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61 + +++V KV+ K VAL +++++I + E F +LGPSG GKTT +R+IAG + P+ GE Sbjct: 12 VSIRSVRKVYGDPKTGPVALKSIDLDIRDNEFFTLLGPSGCGKTTLLRMIAGFEFPTEGE 71 Query: 62 LYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSK----EEI 117 + +A PP R + VFQ +AL+P++T EN+AF L + M K ++ Sbjct: 72 ILLYGENIADR-----PPFQRPVNTVFQHYALFPHMTIAENLAFGLESHPMGKVLHKTQL 126 Query: 118 RKRVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRD 177 +RV E+ ++ + N P +LSGGQQQRVALARAL P +LLLDEP S LD ++R Sbjct: 127 AERVREMLALVQMERFANRKPAQLSGGQQQRVALARALAPHPKVLLLDEPLSALDLKLRQ 186 Query: 178 SARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQV 237 + R +K +Q+R G+T + V+HD + ++DR+ VL +G++ QVG+PED+Y+ P + V Sbjct: 187 AMREELKTIQARTGITFIFVTHDQEEALTMSDRIAVLSEGEVQQVGRPEDIYERPRNRFV 246 Query: 238 ASLIGEINELEGKVT 252 A IGE N +EG VT Sbjct: 247 ADFIGETNFIEGTVT 261 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: 298 Number of extensions: 14 Number of successful extensions: 3 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: 372 Length adjustment: 29 Effective length of query: 324 Effective length of database: 343 Effective search space: 111132 Effective search space used: 111132 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