Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate CCNA_00572 CCNA_00572 PTS system, N-acetylglucosamine-specific IIBC component
Query= SwissProt::P39816 (631 letters) >FitnessBrowser__Caulo:CCNA_00572 Length = 582 Score = 364 bits (935), Expect = e-105 Identities = 215/517 (41%), Positives = 310/517 (59%), Gaps = 47/517 (9%) Query: 3 KKAFQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDA---------------G 47 + +ILQ LGRALM P+AVLP A LLLR G DLL P + A G Sbjct: 2 RSPLEILQPLGRALMLPIAVLPVAALLLRIGQPDLLGAPALAAATHGMSLSVANTFGAAG 61 Query: 48 GVVFDNLPLIFAVGVAIGLAG-GEGVAGLAAVIGYLILTVTLDNMGKLLGLQPP------ 100 G +F +L LIFA+GVA+GLA G AGLA V+ Y+I T ++ L + PP Sbjct: 62 GAIFASLGLIFAIGVAVGLARENHGAAGLAGVVCYVIATKGVE----ALLVAPPEVAAKA 117 Query: 101 YEGAEHLI----------DMGVFGGIIIGLLAAYLYKRFSSIELHPVLGFFSGKRFVPII 150 EGA+ L + + GI+ G+++ LY R+S+I+L L FF G+RFVPI+ Sbjct: 118 VEGAKDLAIAAWKAKEIGKLSIPVGILSGVISGALYNRYSTIQLPEYLAFFGGRRFVPIV 177 Query: 151 TSVSSLVIGVIFSFVWPLIQNGINAASSLI-ADSTVGLFFYATIYRLLIPFGLHHIFYTP 209 ++ +V+ ++F W ++ G++ S L+ A +GL Y + RLLI GLHHI Sbjct: 178 AGLAGVVLALLFGAFWSTLEAGVDGLSGLVTASGDLGLVVYGLLNRLLIVTGLHHILNNV 237 Query: 210 FYFMMGEYTDPSTGNTVTGDLTRFFAGDPTAGRFMMGDFPYMIFCLPAVALAIIHTARPE 269 +F++G++ N VTGDL RF AGD TAG FM G FP M+F LPA LA++HTARPE Sbjct: 238 VWFILGDF------NGVTGDLNRFAAGDKTAGAFMSGFFPVMMFGLPAACLAMLHTARPE 291 Query: 270 KKKMISGVMISAALTSMLTGITEPVEFSFLFVAPVLYLINSILAGVIFVVCDLFHVRHGY 329 ++K ++G++ S ALTS LTG+TEP+EF+F+F+APVL+ I+++L G+ + ++ V+ G+ Sbjct: 292 RRKAVAGMLGSLALTSFLTGVTEPIEFTFMFLAPVLFAIHALLTGLSMALMNMLDVKLGF 351 Query: 330 TFSGGGIDYVLNYGLSTNGWVVIPVGIVFAFIYYYLFRFAILKWNLKTPGRETDEDGQNE 389 FS G DYVLN+ +T ++IPVG+V+ +YY +FRFAIL+++LKTPGRE ++ Sbjct: 352 GFSAGLFDYVLNFNKATRPLLLIPVGLVYGALYYGVFRFAILRFDLKTPGRE--DEAPPS 409 Query: 390 EKAPVAKDQLAFHVLQALGGQQNIANLDACITRLRVTVHQPSQVCKDELKRLGAVGVLEV 449 +A +L ALGG N+ ++DAC TRLR+ V V + LK LGA GV+ Sbjct: 410 AQAVTTGGGRGADMLAALGGAANLVSVDACTTRLRLIVVDQGLVNEPALKALGARGVVRP 469 Query: 450 NNN-FQAIFGTKSDALKDDIK-TIMAGGVPATAAALD 484 ++ Q + G +D + +I+ I A PA A A D Sbjct: 470 SDKALQVVLGPIADTVAGEIRHAISAPPAPAPAPAPD 506 Score = 32.7 bits (73), Expect = 5e-05 Identities = 19/52 (36%), Positives = 27/52 (51%) Query: 398 QLAFHVLQALGGQQNIANLDACITRLRVTVHQPSQVCKDELKRLGAVGVLEV 449 Q A +L ALGG N+ +L +RLRV ++ P +V + L G G V Sbjct: 509 QAAKALLAALGGADNLRDLSVHASRLRVVLNDPERVDQAALHTAGVRGFAAV 560 Lambda K H 0.324 0.142 0.421 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: 943 Number of extensions: 54 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: 631 Length of database: 582 Length adjustment: 37 Effective length of query: 594 Effective length of database: 545 Effective search space: 323730 Effective search space used: 323730 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 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