Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate GFF138 Psest_0138 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__psRCH2:GFF138 Length = 251 Score = 152 bits (385), Expect = 5e-42 Identities = 89/246 (36%), Positives = 137/246 (55%), Gaps = 10/246 (4%) Query: 7 LFAALLLPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLEVKC 66 L AA L + A A E ++R G YPPF + A G + GFD+++ +A+CAK++V+C Sbjct: 9 LTAAASLIIGTQAFAAE--KLRIGTEGAYPPFNLIDASGKVVGFDLDISHALCAKMKVEC 66 Query: 67 TWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGDT 126 V +++DG+IPAL A KFD + +SM+VT R+ +DF+D + + + K+ +F Sbjct: 67 EVVTSDWDGIIPALNAGKFDFLAASMSVTEERKNAVDFTDHYYTNKLQFVAPKNVEFQTD 126 Query: 127 PESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLEA 186 L GK +G + ++ + +L ++ IK Y +Q+ Y DL +GR+D L D Sbjct: 127 EGYLKGKVIGAQRATIAGTWLEDNLDRV-VDIKLYDTQENAYLDLASGRVDGILADTF-V 184 Query: 187 QLNFLSKPEGS--DFKTGPAFKDPTLPLDIAMGLRKNDQALRALINKGIAAVQADGTYAQ 244 Q +L G +FK P F D IA+ +RK + LR +NK +A + ADGTY Q Sbjct: 185 QWEWLKSDAGKNFEFKGEPVFDDD----KIAIAVRKGNDELRERLNKALAEIIADGTYKQ 240 Query: 245 IQKKYF 250 I KYF Sbjct: 241 INDKYF 246 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: 160 Number of extensions: 12 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: 251 Length adjustment: 24 Effective length of query: 234 Effective length of database: 227 Effective search space: 53118 Effective search space used: 53118 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 Apr 09 2024. 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