Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate Pf1N1B4_3431 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3431 Length = 257 Score = 197 bits (501), Expect = 2e-55 Identities = 108/252 (42%), Positives = 153/252 (60%), Gaps = 4/252 (1%) Query: 7 LFAALLLPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLEVKC 66 L AL L + + + K ++ G+ YPPF S A DGS+ GFD ++GNA+C +++VKC Sbjct: 6 LLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEMKVKC 65 Query: 67 TWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGDT 126 WV EFDG+IPAL+ RK DAI+SSM++T R+K +DF+++ + +P ++ + + Sbjct: 66 VWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAGTAVSEN 125 Query: 127 PESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLEA 186 L GK +GV +GS+ E +AR LA LGA+IK Y SQ++ Y D+ GRLD T+ D Sbjct: 126 LAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGTVADATLL 185 Query: 187 QLNFLSKPEGSDFK-TGPAFKDPTLPLD-IAMGLRKNDQALRALINKGIAAVQADGTYAQ 244 FL G F GPAF D D + + +RK D AL+ IN IAA++ +G Y Q Sbjct: 186 DDGFLKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRKGD-ALKDKINTAIAAIRENGKYKQ 244 Query: 245 IQKKYFGDQDIY 256 IQ KYF DIY Sbjct: 245 IQDKYFA-FDIY 255 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: 192 Number of extensions: 11 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: 257 Length adjustment: 24 Effective length of query: 234 Effective length of database: 233 Effective search space: 54522 Effective search space used: 54522 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: 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