Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate GFF1647 PGA1_c16700 binding protein-dependent transport system, inner membrane component
Query= reanno::Koxy:BWI76_RS01825 (514 letters) >FitnessBrowser__Phaeo:GFF1647 Length = 316 Score = 123 bits (308), Expect = 1e-32 Identities = 87/265 (32%), Positives = 138/265 (52%), Gaps = 28/265 (10%) Query: 249 EKLSPGYTVTIGWDNFTRVFQDE----GIQKPFFAIFVWTVVFSVLTVILTVAVGMVLAC 304 E L+P T +G++N+ +++ D ++ FF F W++ F +G+ LA Sbjct: 64 ELLNPFATGWVGFENYEKLWSDRKFWIALENTFFWTF-WSIFFQFF-------LGLGLAM 115 Query: 305 LVQWEALKGKAIYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALFGIKPAW--F 362 L+ + GK +++ L+ LP+AVP+F+S L + LFN G I L+AL + + Sbjct: 116 LLNTQFF-GKKLFQALVFLPWAVPTFLSALTWAWLFNPVIGPIPHWLAALGVLSEPYNIL 174 Query: 363 SDPTTARTMIIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGATPFQNFFKITLPLL 422 DP A I N W G P+ I + L++IP +LYEA+ +DGATP+Q+F KITLP L Sbjct: 175 GDPDLAIWGPITANIWFGVPFFAITLLAALQSIPGELYEAAEIDGATPWQSFTKITLPFL 234 Query: 423 IKPLTPLMIASFAFNFNNFV-LIQLLTNGGPDRLGTTTPAGYTDLLVSYTYRIAFEGGGG 481 P+ + + NF LI ++T GG PA T +L +Y + AF Sbjct: 235 -APMIAITVMLRTIWIANFADLIFVMTGGG--------PANSTQILSTYIFTTAFR---K 282 Query: 482 QDFGLAAAIATLIFLLVGLLAIVNL 506 DFG A+ IA + +++ A++ L Sbjct: 283 LDFGYASTIAVALLIILLAYAVILL 307 Lambda K H 0.325 0.140 0.426 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: 417 Number of extensions: 22 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: 514 Length of database: 316 Length adjustment: 31 Effective length of query: 483 Effective length of database: 285 Effective search space: 137655 Effective search space used: 137655 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 50 (23.9 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