Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_011023799.1 MA_RS20370 ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_000007345.1:WP_011023799.1 Length = 376 Score = 172 bits (437), Expect = 1e-47 Identities = 122/367 (33%), Positives = 197/367 (53%), Gaps = 39/367 (10%) Query: 14 KKGKVVALDNVNINIENGERFGIL-GPSGAGKTTFMRIIAGLDVPSTGEL------YFDD 66 KKG+ + ++N + + F +L G SG+GKTT +R IAGL+ P G + YFD Sbjct: 19 KKGENPSF-SMNCSFDANSDFVVLFGCSGSGKTTALRCIAGLENPDAGTIKINGTVYFDS 77 Query: 67 RLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAK 126 R K+ +PP+ RKIG +FQ AL+P++ +NI F L + S E RV E+ Sbjct: 78 RK-----KVNLPPQKRKIGYMFQENALFPHMNVRQNIEFGLKGL--SSMEKTDRVNEMLG 130 Query: 127 ILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEV 186 ++ I + +P ELSGGQ+Q+VALARAL +P +LLLDEPFS LD +R R ++++ Sbjct: 131 LVGIEELEFAYPDELSGGQKQKVALARALAPNPEVLLLDEPFSALDTVVRLKLRKELRDI 190 Query: 187 QSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINE 246 Q RL + ++ ++HDP + F +ADR+ V G++ Q+G PED++ +P + VA L+G N Sbjct: 191 QKRLKIPVIFITHDPVEAFTMADRMAVFEDGRVQQIGTPEDIFYHPKTRYVAELVGFSNL 250 Query: 247 LEGKVTN------EGVVIGSLRFPVSV------SSDRAIIGIRPEDVKL----SKDVIKD 290 + V E + SL ++ + DR GIRPE+++L + VI+ Sbjct: 251 FDNAVVGRHGNGAECTFLWSLGTEITAPYIERKAGDRVSWGIRPENIELVDRKNMHVIRQ 310 Query: 291 DSWILVGKGKVKVIGYQGGLFRITITPLDSEEEIF-------TYSDHPIHSGEEVLVYVR 343 + + G + + G R+ L + E++ + I +G+E +V +R Sbjct: 311 EDRKNLFDGIIMNV-VNKGTSRVMSLILKNSEDVLKVEVANHIFDSLKIGTGDECMVRLR 369 Query: 344 KDKIKVF 350 + +F Sbjct: 370 ASDMIIF 376 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: 317 Number of extensions: 16 Number of successful extensions: 4 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: 376 Length adjustment: 29 Effective length of query: 324 Effective length of database: 347 Effective search space: 112428 Effective search space used: 112428 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