Align ABC transporter for L-Histidine, periplasmic substrate-binding component (characterized)
to candidate GFF2341 PS417_11935 ABC transporter substrate-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09620 (322 letters) >FitnessBrowser__WCS417:GFF2341 Length = 338 Score = 339 bits (869), Expect = 6e-98 Identities = 171/342 (50%), Positives = 227/342 (66%), Gaps = 25/342 (7%) Query: 1 MKSNKTLLT-TLLSMGLLASAGATQAAGWCESGKPVKFAGLNWESGMLLTDVLQVVLEKG 59 MK KTLL +L ++GL +A AA PV FA LNWESG L+T+VL+V++EKG Sbjct: 1 MKGLKTLLAASLTTLGLSVAALPVSAAE-----APVHFADLNWESGSLITEVLRVIVEKG 55 Query: 60 YDCKTDSLPGNSITMENALSSNDIQVFAEEWVGRSEVWNKAEKAGKVVGVGAPVVGAIEG 119 YD TD+LPG +IT+E AL+ NDIQV EEW GRS VW KAE GKVVG+G V GA EG Sbjct: 56 YDLPTDTLPGTTITLETALAKNDIQVIGEEWAGRSPVWVKAEAEGKVVGLGDTVKGATEG 115 Query: 120 WYVPRYVVEGDAKRKLEAKAPGLKNIADLGQYAAVFKDPEEPSKGRFYNCPAGWTCELDN 179 W+VP YVV+GD + ++ AP LK++ DL +Y VFKDPE P KGRF N P GWT E+ N Sbjct: 116 WWVPEYVVKGDPAKGIKPLAPELKSVKDLARYKDVFKDPESPGKGRFLNSPIGWTSEVVN 175 Query: 180 SEMLKSYGLEKTYTNFRPGTGPALDAAVLSSYKRGEPILFYYWSPTPLMGQVDLVKLEE- 238 + LK+YGL+ +Y NFR G+G ALDA + SS +RG+P+LFYYWSPTPLMG+ L++LEE Sbjct: 176 KQKLKAYGLDDSYVNFRSGSGAALDAEIASSIRRGKPVLFYYWSPTPLMGRYKLIQLEEP 235 Query: 239 ------------------KPGVDKSVSIKVGLSKTFHDEAPELVAVLEKVNLPIDILNQN 280 KP + + +G+S F E P++ EKV PI+ LN+ Sbjct: 236 PFDAEAWKTLTDADNPNPKPTRSLASKLSIGVSTPFQKEHPQIAQFFEKVEFPIEPLNKA 295 Query: 281 LGRMAKERIESPKLAKIFLKEHPEVWHAWVSEDAAKKIDAAL 322 L M++ ++A++FLKEHP+VW AW++ED A+K++A+L Sbjct: 296 LATMSENHTAPREVAQMFLKEHPQVWKAWLTEDVAQKVEASL 337 Lambda K H 0.314 0.133 0.398 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: 341 Number of extensions: 12 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: 322 Length of database: 338 Length adjustment: 28 Effective length of query: 294 Effective length of database: 310 Effective search space: 91140 Effective search space used: 91140 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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