Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate Ga0059261_1647 Ga0059261_1647 PTS system, N-acetylglucosamine-specific IIBC component
Query= TCDB::Q8GBT6 (403 letters) >FitnessBrowser__Korea:Ga0059261_1647 Length = 560 Score = 381 bits (979), Expect = e-110 Identities = 200/407 (49%), Positives = 260/407 (63%), Gaps = 29/407 (7%) Query: 1 MAVLQRIGRSLMLPVAVLPAAALLVRLGNADMLGRPEFPAFVTKIAGFMAAGGNAILDNM 60 + LQ +GR+LMLP+AVLP A LL+R+G D+L F++A G AI N+ Sbjct: 5 LETLQPLGRALMLPIAVLPVAGLLLRIGQPDLLD-----------IAFVSAAGTAIFGNL 53 Query: 61 ALLFAVGIAIGFAKKSDGSTALAAVVGYLVFKNVLATF------TDKNLPQVAKAV---- 110 +LFA+G+A+GFA+ +G+ ALA V YLV TF LP A V Sbjct: 54 GILFAIGVAVGFARDGNGAAALAGVTCYLVSTTGAQTFLIAPPEVVAGLPDAAAKVVAQA 113 Query: 111 --DGKVVMVDAPVDAKVLGGVVMGLVVALLYQRFYRTKLPDWAGFFGGRRLVPILSAFAG 168 G++ ++ P+ G++ GL+ Y RF LP++ FFGGRR VPI + AG Sbjct: 114 WATGQIDRLEVPI------GIISGLIGGKFYNRFATIALPEYLAFFGGRRFVPIAAGIAG 167 Query: 169 LVIGIVFGYIWPVLGTGLHNFGEWLVGSGAVGAGIFGVANRALIPIGMHHLLNSFPWFQA 228 L++ V GY + + + L +V SG G ++GV NR L+ G+HHLLN+ WF Sbjct: 168 LLLAGVLGYGYAHISSALDAASHAVVESGGAGMFVYGVLNRLLLVTGLHHLLNNVAWFLV 227 Query: 229 GEYEGKSGDIARFLAGDPTAGQFMTGFFPIMMFALPAACLAIVHCARPERRKVVGGMMFS 288 G++ G +GD+ RF AGDP AG FM+GFFP+MMF LPAACLA+ H ARPERRK VGGM+FS Sbjct: 228 GDFGGATGDLGRFFAGDPNAGAFMSGFFPVMMFGLPAACLAMYHEARPERRKAVGGMLFS 287 Query: 289 LALTSFVTGVTEPIEFTFMFIAPVLYAIHAVLTGVSMALTWALGMKDGFGFSAGAVDFFL 348 LA TSF+TGVTEPIEFTFMF+APVLYAIHAVLTGV+M L LG+K GFGFSAG D+ L Sbjct: 288 LAFTSFLTGVTEPIEFTFMFLAPVLYAIHAVLTGVAMTLMDMLGIKLGFGFSAGLFDYVL 347 Query: 349 NLGIASNPWGLALVGVCFAALYYVVFRFAITKFNLPTPGRESDEELA 395 N +++ PW L VG +A +YY +FRF I K +L TPGRE E +A Sbjct: 348 NFKLSTRPWMLLPVGAAYAVIYYTLFRFFIRKLDLATPGREKGEAVA 394 Lambda K H 0.328 0.143 0.441 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: 728 Number of extensions: 39 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: 403 Length of database: 560 Length adjustment: 33 Effective length of query: 370 Effective length of database: 527 Effective search space: 194990 Effective search space used: 194990 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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