Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)
Query= BRENDA::P69786 (477 letters) >FitnessBrowser__MR1:200788 Length = 499 Score = 424 bits (1091), Expect = e-123 Identities = 205/471 (43%), Positives = 307/471 (65%), Gaps = 8/471 (1%) Query: 6 FANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMPLIFAI 65 F Q++ ++L++P+++LP AG++LG+ + ++P V++ +M G +FA MP++FA+ Sbjct: 25 FKFAQRLSQALLIPIAILPAAGVMLGLTVSPIPFMPEVLNVLMLAVGKLIFAIMPILFAV 84 Query: 66 GVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVLGGIISG 125 VA+GF + G++A AV YG+M T+A +A L LP + + DTG+ GG++ G Sbjct: 85 AVAIGFCRDQGIAAFTAVFGYGVMTATLAALADLY-QLPTQLVLGMETLDTGIAGGMLIG 143 Query: 126 AIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQTFSQW 185 + + I+LP FF G+R ++ A+ G VL+ IWP + I+ S W Sbjct: 144 GVTCFAVRWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGYVLAHIWPSLSLLIERVSDW 203 Query: 186 AAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYMAGDP 245 A YQ P +AFG+YG +ER L+P GLHHIWN PF +++G+Y +V G++ RY+AGDP Sbjct: 204 AVYQKPAIAFGVYGALERLLIPLGLHHIWNAPFYLEVGQYQLQDAEVVRGEVARYLAGDP 263 Query: 246 TAGKLSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSFM 305 AG L+GG+L KM+GLPAAA+AIW A R +V GIM+SAA S+LTG+TEPIEF+FM Sbjct: 264 QAGNLAGGYLIKMWGLPAAALAIWRCADNSERNRVAGIMLSAAAASWLTGVTEPIEFAFM 323 Query: 306 FVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIVGIGYA 365 FVAP+L++IH +L+GLA+ +CI+L + FSHGL+DF +L S F ++G A Sbjct: 324 FVAPLLFLIHVMLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFAVLGPLTA 383 Query: 366 IVYYTIFRVLIKALDLKTPGR--EDATEDAKATGTSEMAPALVAAFGGKENITNLDACIT 423 ++YY +FR I A +LKTPGR D T+ G+ E A++AA GG++NI L+AC+T Sbjct: 384 VIYYILFRGSILAFNLKTPGRLQSDGTK-----GSKESLRAIIAALGGRDNIVELNACLT 438 Query: 424 RLRVSVADVSKVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYI 474 RLR+SV V++ L +LGA GV+V G GVQ ++GTK++ L+ + Y+ Sbjct: 439 RLRLSVHSPELVNKVRLSQLGAKGVIVMGKGVQIVYGTKAETLRKVLQRYL 489 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: 656 Number of extensions: 28 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: 499 Length adjustment: 34 Effective length of query: 443 Effective length of database: 465 Effective search space: 205995 Effective search space used: 205995 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: 52 (24.6 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