Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate Ga0059261_1647 Ga0059261_1647 PTS system, N-acetylglucosamine-specific IIBC component
Query= reanno::BFirm:BPHYT_RS02745 (591 letters) >FitnessBrowser__Korea:Ga0059261_1647 Length = 560 Score = 532 bits (1371), Expect = e-155 Identities = 297/583 (50%), Positives = 371/583 (63%), Gaps = 59/583 (10%) Query: 9 IQRLGRALMLPIAVLPVAGLLLRLGQPDVFNIKMIADAGGAIFDNLPLLFAIGVAVGFAK 68 +Q LGRALMLPIAVLPVAGLLLR+GQPD+ +I ++ AG AIF NL +LFAIGVAVGFA+ Sbjct: 8 LQPLGRALMLPIAVLPVAGLLLRIGQPDLLDIAFVSAAGTAIFGNLGILFAIGVAVGFAR 67 Query: 69 DNNGVAGLAGAIGYLIE--------------VAVMKDINDKL-----------NMGVLSG 103 D NG A LAG YL+ VA + D K+ + V G Sbjct: 68 DGNGAAALAGVTCYLVSTTGAQTFLIAPPEVVAGLPDAAAKVVAQAWATGQIDRLEVPIG 127 Query: 104 IVAGIVAGLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDT 163 I++G++ G YNR+ I LP+YLAFFGG+RFVPI G+ L+L GY + + + +D Sbjct: 128 IISGLIGGKFYNRFATIALPEYLAFFGGRRFVPIAAGIAGLLLAGVLGYGYAHISSALDA 187 Query: 164 AGHWLTTAGALGAFVFGVLNRLLLVTGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFFA 223 A H + +G G FV+GVLNRLLLVTGLHH+LN++ WF+ G F GGA TGDL RFFA Sbjct: 188 ASHAVVESGGAGMFVYGVLNRLLLVTGLHHLLNNVAWFLVGDF---GGA--TGDLGRFFA 242 Query: 224 GDPTAGTFMTGFFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIE 283 GDP AG FM+GFFPVMMFGLPAACLAM+HEA ERR VGG+LFS+A TSFLTGVTEPIE Sbjct: 243 GDPNAGAFMSGFFPVMMFGLPAACLAMYHEARPERRKAVGGMLFSLAFTSFLTGVTEPIE 302 Query: 284 FSFMFLAPVLYVIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYGLSTRGWWAIPIG 343 F+FMFLAPVLY IHA+LTG+++ + LGI LGF FSAG DYVLN+ LSTR W +P+G Sbjct: 303 FTFMFLAPVLYAIHAVLTGVAMTLMDMLGIKLGFGFSAGLFDYVLNFKLSTRPWMLLPVG 362 Query: 344 LVYMVVYYGLFRFFIRKFNMATPGREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIAA 403 Y V+YY LFRFFIRK ++ATPGRE A AAG R ++ A Sbjct: 363 AAYAVIYYTLFRFFIRKLDLATPGREKGEAVAAAGETAAGN----------ERGAAFVKA 412 Query: 404 LGGASNLSVVDACTTRLRLSVVDSNKVSENELKTIGARGVLKRGSTNVQVIIGPEADIIA 463 LGGA+NL+ VDACTTRLRL V D + V + L +GARG+++ + QV++GP AD++A Sbjct: 413 LGGAANLTSVDACTTRLRLIVADQSAVDDAALNALGARGIIRPSANATQVVLGPIADLVA 472 Query: 464 DEIRTVIAQGGGDAVKPAAAAPAQVVAAAPVAASVAQGSGPLDPDPLRWLAVFGGAGNVL 523 +EIR I GGG A +AAPAQ +A V P LA GG N+ Sbjct: 473 EEIRGAI--GGGAAA--VSAAPAQALADEAVTL------------PAAILAALGGEANIR 516 Query: 524 SLDAIAATRLRIVVRDPSAVDRQRLATLDTAWISAD--TFHIV 564 +L A+ R R+ V D + D L +S +HI+ Sbjct: 517 ALQALHG-RFRVEVVDAARTDEASLLAAANGAVSPQPGVYHIL 558 Lambda K H 0.325 0.141 0.426 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: 1196 Number of extensions: 68 Number of successful extensions: 6 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: 591 Length of database: 560 Length adjustment: 36 Effective length of query: 555 Effective length of database: 524 Effective search space: 290820 Effective search space used: 290820 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: 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