Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate 14985 b0860 arginine transporter subunit (NCBI)
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__Keio:14985 Length = 243 Score = 137 bits (345), Expect = 2e-37 Identities = 83/248 (33%), Positives = 135/248 (54%), Gaps = 15/248 (6%) Query: 7 LFAALLLPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLEVKC 66 + AALL A A E +I FGV YPPFES+ A+ + GFDI+L A+C +++ +C Sbjct: 5 VLAALLASFTFGASAAE--KINFGVSATYPPFESIGANNEIVGFDIDLAKALCKQMQAEC 62 Query: 67 TWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGDT 126 T+ ++ FD +IP+L+ RK+DA++S M +TP R K + F+ + + VI +K D T Sbjct: 63 TFTNHAFDSLIPSLKFRKYDAVISGMDITPERSKQVSFTTPYYENSAVVIAKK--DTYKT 120 Query: 127 PESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLEA 186 L GK++G+ G+ + Y + ++ + +Y S + DL+NGR+D D Sbjct: 121 FADLKGKRIGMENGTTHQKYIQDQHPEV--KTVSYDSYQNAFIDLKNGRIDGVFGDTAVV 178 Query: 187 QLNFLSKPEGSDFKTGPAFKDPTLPLDIAMGL----RKNDQALRALINKGIAAVQADGTY 242 + P+ G A + T P GL R +++AL +N +AA++ADGTY Sbjct: 179 NEWLKTNPQ-----LGVATEKVTDPQYFGTGLGIAVRPDNKALLEKLNNALAAIKADGTY 233 Query: 243 AQIQKKYF 250 +I ++F Sbjct: 234 QKISDQWF 241 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: 181 Number of extensions: 9 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: 258 Length of database: 243 Length adjustment: 24 Effective length of query: 234 Effective length of database: 219 Effective search space: 51246 Effective search space used: 51246 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