Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate CCNA_00572 CCNA_00572 PTS system, N-acetylglucosamine-specific IIBC component
Query= CharProtDB::CH_001857 (699 letters) >FitnessBrowser__Caulo:CCNA_00572 Length = 582 Score = 368 bits (945), Expect = e-106 Identities = 221/539 (41%), Positives = 321/539 (59%), Gaps = 35/539 (6%) Query: 8 VLQKIGRALMLPVAILPAAGILLAIG--NAMQNKDMIQVLHFLSNDNVQLVAGVMESAGQ 65 +LQ +GRALMLP+A+LP A +LL IG + + + H +S VA +AG Sbjct: 7 ILQPLGRALMLPIAVLPVAALLLRIGQPDLLGAPALAAATHGMSLS----VANTFGAAGG 62 Query: 66 IVFDNLPLLFAVGVAIGLANGD-GVAGIAAIIGYLVMNVSMSAVLLANGTIPSDSVERAK 124 +F +L L+FA+GVA+GLA + G AG+A ++ Y++ + A+L+A + + +VE AK Sbjct: 63 AIFASLGLIFAIGVAVGLARENHGAAGLAGVVCYVIATKGVEALLVAPPEVAAKAVEGAK 122 Query: 125 --FFTENHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRFVP 182 + L IP GI+ GV++ L+NR+ TI+LP+YL FF G+RFVP Sbjct: 123 DLAIAAWKAKEIGKLSIPV-------GILSGVISGALYNRYSTIQLPEYLAFFGGRRFVP 175 Query: 183 IVTSISALILGLIMLVIWPPIQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHHIF 242 IV ++ ++L L+ W ++ G++ S GLV A+ L ++G++ R LI GLHHI Sbjct: 176 IVAGLAGVVLALLFGAFWSTLEAGVDGLS-GLVTASGDLGLVVYGLLNRLLIVTGLHHIL 234 Query: 243 YSPFWYEFFSYKSAAGEIIRGDQRIFMAQIKDGVQLTAGTFMTGKYPFMMFGLPAAALAI 302 + W+ + G++ R F A K TAG FM+G +P MMFGLPAA LA+ Sbjct: 235 NNVVWFILGDFNGVTGDLNR-----FAAGDK-----TAGAFMSGFFPVMMFGLPAACLAM 284 Query: 303 YHEAKPQNKKLVAGIMGSAALTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSFMVMQL 362 H A+P+ +K VAG++GS ALTSFLTG+TEP+EF+F+F+APVLFAIH L GLS +M + Sbjct: 285 LHTARPERRKAVAGMLGSLALTSFLTGVTEPIEFTFMFLAPVLFAIHALLTGLSMALMNM 344 Query: 363 LNVKIGMTFSGGLIDYFLFGILPNRTAWWLVIPVGLGLAVIYYFGFRFAIRKFNLKTPGR 422 L+VK+G FS GL DY L T L+IPVGL +YY FRFAI +F+LKTPGR Sbjct: 345 LDVKLGFGFSAGLFDYVL--NFNKATRPLLLIPVGLVYGALYYGVFRFAILRFDLKTPGR 402 Query: 423 EDAAEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKVDKDRLKQ 482 ED A +A TG G ++L A+G N+ +DAC TRLR+ V DQ V++ LK Sbjct: 403 EDEAPPSAQAVTTG--GGRGADMLAALGGAANLVSVDACTTRLRLIVVDQGLVNEPALKA 460 Query: 483 LGASGVLEVGNN-IQAIFGPRSDGLKTQMQDIIAGRKPRPEPKTSAQEEVGQQVEEVIA 540 LGA GV+ + +Q + GP +D + +++ I+ P P + +V Q + ++A Sbjct: 461 LGARGVVRPSDKALQVVLGPIADTVAGEIRHAISA---PPAPAPAPAPDVSQAAKALLA 516 Score = 41.6 bits (96), Expect = 1e-07 Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 1/81 (1%) Query: 425 AAEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKVDKDRLKQLG 484 +A AP + +L A+G +N++ L +RLRV +ND ++VD+ L G Sbjct: 494 SAPPAPAPAPAPDVSQAAKALLAALGGADNLRDLSVHASRLRVVLNDPERVDQAALHTAG 553 Query: 485 ASGVLEVG-NNIQAIFGPRSD 504 G V + I GP ++ Sbjct: 554 VRGFAAVAPGAVHIIIGPHAE 574 Lambda K H 0.323 0.141 0.412 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: 1092 Number of extensions: 61 Number of successful extensions: 8 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: 699 Length of database: 582 Length adjustment: 38 Effective length of query: 661 Effective length of database: 544 Effective search space: 359584 Effective search space used: 359584 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 54 (25.4 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