Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate CCNA_00572 CCNA_00572 PTS system, N-acetylglucosamine-specific IIBC component
Query= BRENDA::P69786 (477 letters) >FitnessBrowser__Caulo:CCNA_00572 Length = 582 Score = 324 bits (831), Expect = 4e-93 Identities = 194/488 (39%), Positives = 285/488 (58%), Gaps = 32/488 (6%) Query: 9 LQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAV----------VSHVMAEAGGSVFAN 58 LQ +G++LMLP++VLP+A +LL +G + PA+ V++ AGG++FA+ Sbjct: 8 LQPLGRALMLPIAVLPVAALLLRIGQPDLLGAPALAAATHGMSLSVANTFGAAGGAIFAS 67 Query: 59 MPLIFAIGVALGFTN-NDGVSALAAVVAYGIMVKTMA--VVAPLVLHLPAEEIA------ 109 + LIFAIGVA+G N G + LA VV Y I K + +VAP + A E A Sbjct: 68 LGLIFAIGVAVGLARENHGAAGLAGVVCYVIATKGVEALLVAPPEVAAKAVEGAKDLAIA 127 Query: 110 ---SKHLADTGVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGV 166 +K + + GI+SG I+ ++NR+ I+LPEYL FF G+RFVPI++GLA + + Sbjct: 128 AWKAKEIGKLSIPVGILSGVISGALYNRYSTIQLPEYLAFFGGRRFVPIVAGLAGVVLAL 187 Query: 167 VLSFIWPPIGSAIQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYT 226 + W + + + S + +YG + R L+ GLHHI N +G++ Sbjct: 188 LFGAFWSTLEAGVDGLSGLVTASGDL-GLVVYGLLNRLLIVTGLHHILNNVVWFILGDFN 246 Query: 227 NAAGQVFHGDIPRYMAGDPTAGK-LSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMI 285 G D+ R+ AGD TAG +SG F M+GLPAA +A+ H+A+PE R V G++ Sbjct: 247 GVTG-----DLNRFAAGDKTAGAFMSGFFPVMMFGLPAACLAMLHTARPERRKAVAGMLG 301 Query: 286 SAALTSFLTGITEPIEFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFI 345 S ALTSFLTG+TEPIEF+FMF+AP+L+ IHA+L GL+ + +L ++ G FS GL D++ Sbjct: 302 SLALTSFLTGVTEPIEFTFMFLAPVLFAIHALLTGLSMALMNMLDVKLGFGFSAGLFDYV 361 Query: 346 VLSGNSSKLWLFPIVGIGYAIVYYTIFRVLIKALDLKTPGRED-ATEDAKATGTSEMAPA 404 + +++ L VG+ Y +YY +FR I DLKTPGRED A A+A T A Sbjct: 362 LNFNKATRPLLLIPVGLVYGALYYGVFRFAILRFDLKTPGREDEAPPSAQAVTTGGGRGA 421 Query: 405 -LVAAFGGKENITNLDACITRLRVSVADVSKVDQAGLKKLGAAGVV-VAGSGVQAIFGTK 462 ++AA GG N+ ++DAC TRLR+ V D V++ LK LGA GVV + +Q + G Sbjct: 422 DMLAALGGAANLVSVDACTTRLRLIVVDQGLVNEPALKALGARGVVRPSDKALQVVLGPI 481 Query: 463 SDNLKTEM 470 +D + E+ Sbjct: 482 ADTVAGEI 489 Score = 48.9 bits (115), Expect = 5e-10 Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 1/79 (1%) Query: 389 ATEDAKATGTSEMAPALVAAFGGKENITNLDACITRLRVSVADVSKVDQAGLKKLGAAG- 447 A A A S+ A AL+AA GG +N+ +L +RLRV + D +VDQA L G G Sbjct: 498 APAPAPAPDVSQAAKALLAALGGADNLRDLSVHASRLRVVLNDPERVDQAALHTAGVRGF 557 Query: 448 VVVAGSGVQAIFGTKSDNL 466 VA V I G ++ + Sbjct: 558 AAVAPGAVHIIIGPHAERI 576 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: 807 Number of extensions: 55 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 477 Length of database: 582 Length adjustment: 35 Effective length of query: 442 Effective length of database: 547 Effective search space: 241774 Effective search space used: 241774 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 Apr 09 2024. 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