Align ABC transporter for L-Histidine, periplasmic substrate-binding component (characterized)
to candidate PfGW456L13_3631 Histidine ABC transporter, histidine-binding protein (TC 3.A.1)
Query= reanno::pseudo5_N2C3_1:AO356_09620 (322 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3631 Length = 316 Score = 502 bits (1293), Expect = e-147 Identities = 232/316 (73%), Positives = 273/316 (86%) Query: 7 LLTTLLSMGLLASAGATQAAGWCESGKPVKFAGLNWESGMLLTDVLQVVLEKGYDCKTDS 66 LLT+LL++GLL + ++QA+GWCESGK VKFAGLNWESGMLLTD++ +VL+ GY C TD Sbjct: 1 LLTSLLTLGLLVGSASSQASGWCESGKSVKFAGLNWESGMLLTDIMMIVLKDGYGCTTDQ 60 Query: 67 LPGNSITMENALSSNDIQVFAEEWVGRSEVWNKAEKAGKVVGVGAPVVGAIEGWYVPRYV 126 L GN+I +E AL+ NDIQVF EEW+ RSEVW KA AGKVVGVGAP++GA +GWYVPRYV Sbjct: 61 LVGNTIILETALAGNDIQVFGEEWMERSEVWKKAVAAGKVVGVGAPIIGATQGWYVPRYV 120 Query: 127 VEGDAKRKLEAKAPGLKNIADLGQYAAVFKDPEEPSKGRFYNCPAGWTCELDNSEMLKSY 186 VEGDAKR A+AP L+ +ADL +YA+VF+D EEPSKGRFYNCPAGW CE DN+EMLK Y Sbjct: 121 VEGDAKRNRPAQAPDLRTVADLSKYASVFRDSEEPSKGRFYNCPAGWICEQDNTEMLKEY 180 Query: 187 GLEKTYTNFRPGTGPALDAAVLSSYKRGEPILFYYWSPTPLMGQVDLVKLEEKPGVDKSV 246 GLE T+TNFRPGTG ALDAAVLSSYKRGEP+LFYYWSPTPLMGQ+D ++LEEK G +K V Sbjct: 181 GLENTFTNFRPGTGAALDAAVLSSYKRGEPVLFYYWSPTPLMGQIDAIRLEEKTGANKDV 240 Query: 247 SIKVGLSKTFHDEAPELVAVLEKVNLPIDILNQNLGRMAKERIESPKLAKIFLKEHPEVW 306 VGLSK FH++APELVAVLEKVN+PID+LNQNL RM +ERIESPKLA++FLKEHPE+W Sbjct: 241 ITMVGLSKAFHEQAPELVAVLEKVNIPIDLLNQNLARMTRERIESPKLARMFLKEHPEIW 300 Query: 307 HAWVSEDAAKKIDAAL 322 HAWV E AAKKI+A+L Sbjct: 301 HAWVDEAAAKKIEASL 316 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: 373 Number of extensions: 10 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: 322 Length of database: 316 Length adjustment: 28 Effective length of query: 294 Effective length of database: 288 Effective search space: 84672 Effective search space used: 84672 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: 48 (23.1 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