Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 164 bits (414), Expect = 4e-45 Identities = 113/349 (32%), Positives = 190/349 (54%), Gaps = 40/349 (11%) Query: 6 VKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFD 65 V VSK + G + AL++ ++ ++ G ++G SG+GK++ +RIIAGL+V S G ++ Sbjct: 6 VSEVSKRYDAGSL-ALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGVVHLG 64 Query: 66 DRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVA 125 D+ + + + +VP D +I ++ Q + LYPN T ENIA PL + K ++R E+ Sbjct: 65 DQKILNPAQKLVPGYD-EIQLIHQEYKLYPNSTVEENIARPL--LLYDKAYQKERTAEIL 121 Query: 126 KILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKE 185 ++L + + PR+LSGGQQQ+VA+ RAL +P +LLLDEPFS+LDA + +KE Sbjct: 122 ELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEELKE 181 Query: 186 VQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEIN 245 + L VT++ V+HD D +++ + ++ KGKL+Q G +++ P S VA L G +N Sbjct: 182 IFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLFGYLN 241 Query: 246 ELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKL-SKDVIKDDSWILVGKGKVKVI 304 + G ++ A +RP +VK+ SK I K +V+ Sbjct: 242 LIPG-------------------AEEAY--VRPSEVKITSKTSI-----------KAEVV 269 Query: 305 GYQGGLFRITITPLDSEEEIFTYSDHP---IHSGEEVLVYVRKDKIKVF 350 Q + +T + E+F D P ++ G+EV + +K+++ F Sbjct: 270 KQQFLIHYNLLTVKLEDSELFWKVDDPSRSVNVGDEVFLDYQKEQLIQF 318 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: 248 Number of extensions: 16 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: 318 Length adjustment: 28 Effective length of query: 325 Effective length of database: 290 Effective search space: 94250 Effective search space used: 94250 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