Align N-Acetyl-D-glucosamine ABC transport system, permease component 1 (characterized)
to candidate HSERO_RS22740 HSERO_RS22740 ABC transporter permease
Query= reanno::Phaeo:GFF2751 (308 letters) >FitnessBrowser__HerbieS:HSERO_RS22740 Length = 304 Score = 366 bits (939), Expect = e-106 Identities = 175/301 (58%), Positives = 225/301 (74%), Gaps = 1/301 (0%) Query: 7 KPRRRWHIAVFLAPAVLVYTAIMIFPLFNTLRLALYSESDQ-IRQFVGLANFETLFGNPN 65 K R W +AV LAPAVL+Y PL +TLRL Y+ +D +R FVGL N+ T+ +P+ Sbjct: 2 KTIRAWQLAVLLAPAVLIYALFSALPLLDTLRLGFYTANDAGVRSFVGLDNYRTILFDPD 61 Query: 66 WSEQFWNALGNNFWFFFVHMLVQNPIGVALAAILSHPRLRFAALYRTAIFVPTILSFVIV 125 WS FWNA+ NN FF +HM +QNPIG+ LA + S LR A YRT IF+PT+LS VI+ Sbjct: 62 WSAAFWNAMWNNVKFFCIHMALQNPIGLLLATLFSLKGLRGARTYRTLIFLPTLLSVVII 121 Query: 126 GFAWKLILSPIWGITPDLLDAIGLKWLFAPWLGKEDYALTTLALISVWQFVGIPMMLIYA 185 GF W+LILSP+WG+ LL +GL FAPWLG+E AL TL+LISVWQ+VGIPMMLIYA Sbjct: 122 GFIWQLILSPLWGVGEKLLGTVGLADWFAPWLGQESTALLTLSLISVWQYVGIPMMLIYA 181 Query: 186 ALLSIPEEVIEAGEVDGITGMSAFWKIKLPLILPSIGIISILTFVGNFNAFDLIYTTQGA 245 ALL++PEEV+EA +G + M FW+IKLPLI P++G+++ILTFV NFNAFDLIY+ +GA Sbjct: 182 ALLAVPEEVLEAAHAEGASAMRIFWQIKLPLIYPTLGLVTILTFVANFNAFDLIYSVKGA 241 Query: 246 LAGPDFSTDILGTFMYRTFFGFQLQLGDPHMGSAIATAMFAIILIGVCIYLFGIQTRLRR 305 LAGP++++D+LGT+ YRTFFG+Q Q+G P MG+A+AT MF +IL GV Y +Q RL R Sbjct: 242 LAGPNYASDLLGTYFYRTFFGYQAQIGSPTMGAAVATLMFLVILGGVGAYFVLVQRRLTR 301 Query: 306 Y 306 Y Sbjct: 302 Y 302 Lambda K H 0.331 0.145 0.468 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: 389 Number of extensions: 18 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: 308 Length of database: 304 Length adjustment: 27 Effective length of query: 281 Effective length of database: 277 Effective search space: 77837 Effective search space used: 77837 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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