Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate PP_0282 PP_0282 L-arginine ABC transporter - periplasmic binding subunit
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >FitnessBrowser__Putida:PP_0282 Length = 250 Score = 116 bits (291), Expect = 4e-31 Identities = 72/247 (29%), Positives = 128/247 (51%), Gaps = 6/247 (2%) Query: 1 MNLRRNLLLASLAAAAFCTTGAQAQDNVLRVGTDATFPPMEFVE-NGKRTGFDIELVEAI 59 M+ + LLA+ A A+ LR+G +A +PP + +G GFD ++ +A+ Sbjct: 1 MHTYKKFLLAAAATLVMSANAMAAEK--LRMGIEAAYPPFNNKDASGNVVGFDKDIGDAL 58 Query: 60 AKTMGKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVK 119 M + V D+ G+IP L +K+FD VS++ ITDERK+ VDFT+ YY+ L + Sbjct: 59 CAKMKVECSVVTSDWDGIIPALNAKKFDFLVSSLSITDERKQAVDFTNPYYSNKLQFIAP 118 Query: 120 ADNKAINKLADLDGKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNLVDIGRADAAV 179 + L GK + Q T + +YL + +P V+ + + + + GR D + Sbjct: 119 KNVDFKTDKESLKGKVIGTQRATLAGTYLEDNYPDVEIKLYDTQENAYLDLVSGRIDGIL 178 Query: 180 TGKPAAFQYVRTRPGLRVL---DEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYA 236 K +++++++ G + + +++ G+A+RK +L +N A+ ++KADGTY Sbjct: 179 ADKYVQYEWLKSKDGSNFEFKGEPVMDSDKIGIAVRKGDTKLRDDLNKALAEIKADGTYK 238 Query: 237 AIVKKWF 243 I K+F Sbjct: 239 KINDKYF 245 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: 165 Number of extensions: 8 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: 250 Length adjustment: 24 Effective length of query: 225 Effective length of database: 226 Effective search space: 50850 Effective search space used: 50850 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