Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate Pf6N2E2_5395 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5395 Length = 244 Score = 176 bits (446), Expect = 4e-49 Identities = 91/234 (38%), Positives = 141/234 (60%), Gaps = 4/234 (1%) Query: 25 KEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLEVKCTWVHNEFDGMIPALRARK 84 K +R G+ YPPF S ++G + GFD ++GNA+CA+++VKC W+ EFDG+IPAL+ +K Sbjct: 11 KTLRIGIEAAYPPFASKTSEGKIVGFDYDIGNALCAQMQVKCEWIEGEFDGLIPALKVKK 70 Query: 85 FDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGDTPESLMGKQVGVLQGSLQE 144 D +SSM +T R+K +DF+ + + + + ++ ++ A D +L GK VGV + + + Sbjct: 71 IDLALSSMTITEERKKSVDFTHKYYFTSSRLVMKEGAVVDDQYVNLKGKTVGVQRATTTD 130 Query: 145 AYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLEAQLNFLSKPEGSDFK-TGP 203 YA L G +K Y + ++ Y DL +GRLDA D + + +FLS P G + GP Sbjct: 131 RYATEVLEPKGVSVKRYSNNEEIYMDLASGRLDAIFADTIPLE-DFLSMPRGKGYAFVGP 189 Query: 204 AFKDPTLPLDIA-MGLRKNDQALRALINKGIAAVQADGTYAQIQKKYFGDQDIY 256 KDP + A + +RK + L A +NK I ++A+G Y +IQ KYF DIY Sbjct: 190 ELKDPKYVGEGAGIAVRKGNTQLVADLNKAIDGIRANGEYQKIQGKYF-KSDIY 242 Lambda K H 0.319 0.135 0.393 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: 161 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: 258 Length of database: 244 Length adjustment: 24 Effective length of query: 234 Effective length of database: 220 Effective search space: 51480 Effective search space used: 51480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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