Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate 209037 DVU0107 glutamine ABC transporter, periplasmic glutamine-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >MicrobesOnline__882:209037 Length = 249 Score = 138 bits (347), Expect = 1e-37 Identities = 89/249 (35%), Positives = 132/249 (53%), Gaps = 6/249 (2%) Query: 5 RNLLLASLAAAAFCTTGAQAQDNVLRVGTDATFPPMEFV-ENGKRTGFDIELVEAIAKTM 63 + L+ L A A A L V D F P EF E+GK TGFDIEL +AIAK Sbjct: 2 KRLVKLVLGLALVLGLAATASAKQLVVAHDTNFKPFEFKGEDGKYTGFDIELWQAIAKIA 61 Query: 64 GKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNK 123 G + +DF G+IPGL + D+ ++ I I ER VVDF+D YY GL+++V+ + Sbjct: 62 GVDYKLQPMDFNGIIPGLQTGNVDVGIAGITIKPERAAVVDFSDPYYDSGLMILVRENET 121 Query: 124 AINKLADLDGKKVSVQVGTKSVSYLTEKFPKVQRVEV-EKNQEMFNLVDIGRADAAVTGK 182 I + DL GK V+V+ T SV ++ + F K + +++ N MF + G ADA + Sbjct: 122 GIKAVEDLAGKIVAVKTATSSVDFM-KSFGKAKELKLFPNNDSMFFELMAGGADAVIFDM 180 Query: 183 PAAFQYVRT--RPGLRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAAIVK 240 P ++ T + ++V+ + YG+ K + EL VN A+ +LKADG+Y + Sbjct: 181 PVVKEFAMTAGKGKVKVVGPLYQGQSYGIGFPKGS-ELVGKVNDALKQLKADGSYDKLFV 239 Query: 241 KWFSNSAAK 249 KWF + K Sbjct: 240 KWFGYAPEK 248 Lambda K H 0.317 0.133 0.369 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: 157 Number of extensions: 10 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: 249 Length of database: 249 Length adjustment: 24 Effective length of query: 225 Effective length of database: 225 Effective search space: 50625 Effective search space used: 50625 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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