Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate CCNA_00458 CCNA_00458 PTS system, N-acetylglucosamine-specific IIBC component
Query= BRENDA::P09323 (648 letters) >FitnessBrowser__Caulo:CCNA_00458 Length = 584 Score = 410 bits (1053), Expect = e-118 Identities = 236/538 (43%), Positives = 324/538 (60%), Gaps = 55/538 (10%) Query: 4 LGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLNVAFIAQA---------------GGAI 48 L Q LGRAL LPIAVLPVAALLLR GQPDLL +A A GGAI Sbjct: 5 LEILQPLGRALMLPIAVLPVAALLLRIGQPDLLGAPALAAATHGMSLSVANTFGAAGGAI 64 Query: 49 FDNLALIFAIGVASSWSKDSAGAAALAGAVGYFVLTK---AMVTINPEI----------- 94 F +L LIFAIGVA ++++ GAA LAG V Y + TK A++ PE+ Sbjct: 65 FASLGLIFAIGVAVGLARENHGAAGLAGVVCYVIATKGVEALLVAPPEVAAKAVEGAKDL 124 Query: 95 -----------NMGVLAGIITGLVGGAAYNRWSDIKLPDFLSFFGGKRFVPIATGFFCLV 143 + + GI++G++ GA YNR+S I+LP++L+FFGG+RFVPI G +V Sbjct: 125 AIAAWKAKEIGKLSIPVGILSGVISGALYNRYSTIQLPEYLAFFGGRRFVPIVAGLAGVV 184 Query: 144 LAAIFGYVWPPVQHAIHAGGEWIVSAGALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGE 203 LA +FG W ++ + + ++G LG ++G +NRLLI TGLH +LN + WF +G+ Sbjct: 185 LALLFGAFWSTLEAGVDGLSGLVTASGDLGLVVYGLLNRLLIVTGLHHILNNVVWFILGD 244 Query: 204 FTNAAGTVFHGDINRFYAGDGTAGMFMSGFFPIMMFGLPGAALAMYFAAPKERRPMVGGM 263 F G D+NRF AGD TAG FMSGFFP+MMFGLP A LAM A ERR V GM Sbjct: 245 FNGVTG-----DLNRFAAGDKTAGAFMSGFFPVMMFGLPAACLAMLHTARPERRKAVAGM 299 Query: 264 LLSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTGISLFVATLLGIHAGFSFSAGAID 323 L S+A+T+FLTGVTEP+EF FMFLAP+L+ +HALLTG+S+ + +L + GF FSAG D Sbjct: 300 LGSLALTSFLTGVTEPIEFTFMFLAPVLFAIHALLTGLSMALMNMLDVKLGFGFSAGLFD 359 Query: 324 YALMYNLPAASQNVWMLLVMGVIFFAIYFVVFSLVIRMFNLKTPGREDKEDEIVTEEANS 383 Y L +N + +L+ +G+++ A+Y+ VF I F+LKTPGRED+ A + Sbjct: 360 YVLNFN---KATRPLLLIPVGLVYGALYYGVFRFAILRFDLKTPGREDE----APPSAQA 412 Query: 384 NTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVADSARVNDTMCKRLGASGVVKLN 443 T G + +AA+GG NL ++DAC TRLRL V D VN+ K LGA GVV+ + Sbjct: 413 VTTGG--GRGADMLAALGGAANLVSVDACTTRLRLIVVDQGLVNEPALKALGARGVVRPS 470 Query: 444 KQTIQVIVGAKAESIGDAMKKVVARGPVAAASAEATPATAAPVAKPQAVPNAVSIAEL 501 + +QV++G A+++ ++ ++ P A A A A + A A A+ A ++ +L Sbjct: 471 DKALQVVLGPIADTVAGEIRHAIS-APPAPAPAPAPDVSQAAKALLAALGGADNLRDL 527 Score = 52.0 bits (123), Expect = 7e-11 Identities = 24/78 (30%), Positives = 45/78 (57%) Query: 389 LTQLATNYIAAVGGTDNLKAIDACITRLRLTVADSARVNDTMCKRLGASGVVKLNKQTIQ 448 ++Q A +AA+GG DNL+ + +RLR+ + D RV+ G G V++ + Sbjct: 507 VSQAAKALLAALGGADNLRDLSVHASRLRVVLNDPQRVDQAALHTAGVRGFVRVGEHAAH 566 Query: 449 VIVGAKAESIGDAMKKVV 466 V++G +A+ IG A++ ++ Sbjct: 567 VVLGPEAQRIGQAVRAMI 584 Lambda K H 0.324 0.139 0.408 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: 999 Number of extensions: 55 Number of successful extensions: 7 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: 648 Length of database: 584 Length adjustment: 37 Effective length of query: 611 Effective length of database: 547 Effective search space: 334217 Effective search space used: 334217 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: 41 (22.0 bits) S2: 53 (25.0 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