Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate Pf1N1B4_4791 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4791 Length = 259 Score = 115 bits (287), Expect = 1e-30 Identities = 81/249 (32%), Positives = 122/249 (48%), Gaps = 11/249 (4%) Query: 7 LLLASLAAAAFCTTGAQAQD-NVLRVGTDATFPPMEFVE-NGKRTGFDIELVEAIAKTMG 64 L L +LA C+TGA A++ LR G + ++PP E +G GF ++L AI + Sbjct: 6 LTLPALALLC-CSTGASAKEWKELRFGVNPSYPPFESTTADGGVQGFGVDLGNAICAELK 64 Query: 65 KQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNKA 124 + WV DF GLIP L + +FD S++ +TD RKK +DFTD YAG ++ + D+ Sbjct: 65 LKCVWVSNDFDGLIPALKAGKFDAIESSMTVTDARKKQIDFTDRLYAGPTAIVTRKDSGL 124 Query: 125 INKLADLDGKKVSVQVGTKSVSYLTEKF-PKVQRVEVEKNQ-EMFNLVDIGRADAAVTGK 182 + L GK + GT +Y K P ++ +NQ +++ + GR DA++ K Sbjct: 125 LPTAESLRGKTIGYMQGTIQETYAKAKLGPGGVKLRAYQNQDQVYADLVFGRLDASIQDK 184 Query: 183 PAAFQYVRTRP------GLRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYA 236 A T P + + L E + +RKD EL +N AI L G YA Sbjct: 185 LQAQMSFLTSPQGADFQNSEGISDPLVPSEIAIGIRKDNEELKGMLNAAIKALHEKGIYA 244 Query: 237 AIVKKWFSN 245 I +K F + Sbjct: 245 QIQQKHFGD 253 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: 145 Number of extensions: 10 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: 249 Length of database: 259 Length adjustment: 24 Effective length of query: 225 Effective length of database: 235 Effective search space: 52875 Effective search space used: 52875 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: 47 (22.7 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