Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate PfGW456L13_4635 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4635 Length = 260 Score = 275 bits (702), Expect = 9e-79 Identities = 136/253 (53%), Positives = 180/253 (71%) Query: 4 LRSLFAALLLPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLE 63 L +L A L +A A+E+KE+RFGV P Y PFES AADGSL GFDI+LGNAICA+L+ Sbjct: 5 LLTLSALALCMAAGSAMAKEYKELRFGVDPSYAPFESKAADGSLVGFDIDLGNAICAELK 64 Query: 64 VKCTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADF 123 VKC WV ++FDGMIP L+A KFD ++SSM VTPAREK+IDFS LF PT+ + +K + Sbjct: 65 VKCKWVESDFDGMIPGLKANKFDGVISSMTVTPAREKVIDFSSELFSGPTAYVFKKGSGL 124 Query: 124 GDTPESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDK 183 + SL GK VG QG++QEAYA+A L K G + +AYQ+QDQ Y+DL +GRLDA + D Sbjct: 125 TEDVASLKGKTVGYEQGTIQEAYAKAVLDKAGVKTQAYQNQDQVYSDLTSGRLDAAIQDM 184 Query: 184 LEAQLNFLSKPEGSDFKTGPAFKDPTLPLDIAMGLRKNDQALRALINKGIAAVQADGTYA 243 L+A+L FL P+G ++ LP A+G++K + L+AL++KGI A+ DGTYA Sbjct: 185 LQAELGFLKSPKGEGYEVSKPVDSELLPAKTAVGIKKGNTELKALLDKGIKALHDDGTYA 244 Query: 244 QIQKKYFGDQDIY 256 IQKK+FGD ++Y Sbjct: 245 TIQKKHFGDLNLY 257 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: 204 Number of extensions: 6 Number of successful extensions: 1 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: 260 Length adjustment: 24 Effective length of query: 234 Effective length of database: 236 Effective search space: 55224 Effective search space used: 55224 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