Align Low-affinity (212 (characterized)
to candidate Ac3H11_3740 Gluconate permease
Query= TCDB::P0AC96 (446 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3740 Length = 456 Score = 293 bits (751), Expect = 6e-84 Identities = 163/459 (35%), Positives = 269/459 (58%), Gaps = 17/459 (3%) Query: 1 MTTLTLVLTAVGSVLLLLFLVMKARMHAFLALMVVSMGAGLFSGMPLDKIAATMEKGMGG 60 M+TL L+ GS+ LLL L+++ ++HAF+A+M+VS +GMP+ I +T+ GMGG Sbjct: 1 MSTLALLGIGAGSIALLLLLIIRWQVHAFVAMMLVSFLVAFATGMPIGDIISTLIAGMGG 60 Query: 61 TLGFLAVVVALGAMFGKILHETGAVDQIAVKMLKSFGHSRAHYAIGLAGLVCALPLFFEV 120 TLG +A++VALG+M G+++ +G +A + + G +R A+ A LV A+P+FF+V Sbjct: 61 TLGSVAILVALGSMLGRMIEVSGGAASLANRFTQLLGPTRVPMALTAAALVLAIPVFFDV 120 Query: 121 AIVLLISVAFSMARHTGTNLVKLVIPLFAGVAAAAAFLVPGPAPMLL--ASQMNADFGWM 178 ++L+ + + + G N +K +P+ AG+ AA +VP P P ++ A+ + D GW+ Sbjct: 121 GFIILVPIVYGFCKAAGVNPIKFGLPV-AGIMLAAHVVVP-PHPGIVGGAAIVKGDIGWI 178 Query: 179 ILIGLCAAIP----GMIIAG-------PLWGNFISRYVELHIPDDISEPHLGEGKMPSFG 227 +IGL IP ++AG P+ ++ +D + GK PS G Sbjct: 179 TIIGLAICIPLAALSQVVAGWLNRKGYPMLPTTAEQFAAFGNSEDSTASK--SGKAPSVG 236 Query: 228 FSLSLILLPLVLVGLKTIAARFVPEGSTAYEWFEFIGHPFTAILVACLVAIYGLAMRQGM 287 ++LI++PL L+ T A +P+G + FIG P A++VA +A++ L QG Sbjct: 237 TIMALIIIPLALIMAGTTGATLLPKGDSLRNVLGFIGSPIFALMVAVGLAMFLLGRNQGW 296 Query: 288 PKDKVMEICGHALQPAGIILLVIGAGGVFKQVLVDSGVGPALGEALTGMGLPIAITCFVL 347 +++ I AL PA ++LV GAGGVF +VL SG+G AL ++LT LP+ + F++ Sbjct: 297 NRERTNAIMESALPPAATVILVTGAGGVFAKVLTASGIGAALSQSLTATHLPLILLAFII 356 Query: 348 AAAVRIIQGSATVACLTAVGLVMPVIEQLNYSGAQMAALSICIAGGSIVVSHVNDAGFWL 407 + A+R QGSATVA +T GL+ + YS Q+A L++ I GS+ +SHVND+GFW+ Sbjct: 357 SLALRAAQGSATVAIITTCGLLADAMAGGGYSPLQVALLTVAIGFGSLGLSHVNDSGFWI 416 Query: 408 FGKFTGATEAETLKTWTMMETILGTVGAIVGMIAFQLLS 446 ++ G + + L+TWT++ T+LG G + + + L++ Sbjct: 417 VTRYLGLSVGDGLRTWTVLTTVLGIAGFAMTALLWVLVA 455 Lambda K H 0.328 0.142 0.423 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: 583 Number of extensions: 29 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: 446 Length of database: 456 Length adjustment: 33 Effective length of query: 413 Effective length of database: 423 Effective search space: 174699 Effective search space used: 174699 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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