Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate 7025672 Shewana3_2822 PTS system, glucose-like IIB subunint (RefSeq)
Query= BRENDA::P69786 (477 letters) >FitnessBrowser__ANA3:7025672 Length = 452 Score = 417 bits (1072), Expect = e-121 Identities = 200/452 (44%), Positives = 293/452 (64%), Gaps = 4/452 (0%) Query: 23 LPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMPLIFAIGVALGFTNNDGVSALAA 82 +P AG++LG+ + ++P V++ +M G +FA MP++FA+ VA+GF + G++A A Sbjct: 1 MPAAGVMLGLTVSPIPFMPEVLTVLMLAVGKLIFAIMPILFAVAVAIGFCRDQGIAAFTA 60 Query: 83 VVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVLGGIISGAIAAYMFNRFYRIKLPE 142 V YG+M T+A +A L LP + + DTG+ GG++ G + + I+LP Sbjct: 61 VFGYGVMTATLAALADLY-QLPTQLLLGMETLDTGIAGGMLIGGVTCFAVRWSQYIRLPA 119 Query: 143 YLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQTFSQWAAYQNPVVAFGIYGFIE 202 FF G+R ++ A+ G +L+ +WPP+ I+ S WA YQ P +AFG+YG +E Sbjct: 120 IFSFFEGRRSASLLIIPLAMGLGYILAHVWPPLSLLIERVSDWAVYQKPAIAFGVYGALE 179 Query: 203 RCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYMAGDPTAGKLSGGFLFKMYGLP 262 R L+P GLHHIWN PF +++G+Y +V G++ RY+AGDP AG L+GG+L KM+GLP Sbjct: 180 RLLIPLGLHHIWNAPFYLEVGQYQLQNSEVVRGEVARYLAGDPQAGNLAGGYLIKMWGLP 239 Query: 263 AAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSFMFVAPILYIIHAILAGLA 322 AAA+AIW A+P R +V GIM+SAA S+LTG+TEPIEF+FMFVAP L++IH +L+GLA Sbjct: 240 AAALAIWRCAEPSERNRVAGIMLSAAAASWLTGVTEPIEFAFMFVAPFLFLIHVLLSGLA 299 Query: 323 FPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIVGIGYAIVYYTIFRVLIKALDLK 382 + +CI+L + FSHGL+DF +L S F +G A++YY +FR I A +LK Sbjct: 300 YFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFVFLGPLTAVIYYLLFRGSILAFNLK 359 Query: 383 TPGREDATEDAKATGTSEMAPALVAAFGGKENITNLDACITRLRVSVADVSKVDQAGLKK 442 TPGR E + G E A++AA GG+ENI L+AC+TRLR+SV V++ L + Sbjct: 360 TPGR---LEPDEPHGAKESLRAIIAALGGRENIVELNACLTRLRLSVHSPELVNKVRLSQ 416 Query: 443 LGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYI 474 LGA GV+V G GVQ ++GTK++ L+ + Y+ Sbjct: 417 LGAKGVIVMGKGVQVVYGTKAETLRKVLQRYL 448 Lambda K H 0.325 0.140 0.422 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: 621 Number of extensions: 23 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: 477 Length of database: 452 Length adjustment: 33 Effective length of query: 444 Effective length of database: 419 Effective search space: 186036 Effective search space used: 186036 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 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