Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate Ga0059261_1647 Ga0059261_1647 PTS system, N-acetylglucosamine-specific IIBC component
Query= SwissProt::P39816 (631 letters) >FitnessBrowser__Korea:Ga0059261_1647 Length = 560 Score = 366 bits (940), Expect = e-105 Identities = 211/500 (42%), Positives = 293/500 (58%), Gaps = 32/500 (6%) Query: 3 KKAFQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAVGV 62 +K + LQ LGRALM P+AVLP AGLLLR G DLL+I + AG +F NL ++FA+GV Sbjct: 2 RKILETLQPLGRALMLPIAVLPVAGLLLRIGQPDLLDIAFVSAAGTAIFGNLGILFAIGV 61 Query: 63 AIGLA-GGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLID------------ 109 A+G A G G A LA V YL+ T G L P E L D Sbjct: 62 AVGFARDGNGAAALAGVTCYLVSTT-----GAQTFLIAPPEVVAGLPDAAAKVVAQAWAT 116 Query: 110 -----MGVFGGIIIGLLAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSF 164 + V GII GL+ Y RF++I L L FF G+RFVPI ++ L++ + + Sbjct: 117 GQIDRLEVPIGIISGLIGGKFYNRFATIALPEYLAFFGGRRFVPIAAGIAGLLLAGVLGY 176 Query: 165 VWPLIQNGINAASSLIADST-VGLFFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTG 223 + I + ++AAS + +S G+F Y + RLL+ GLHH+ +F++G++ Sbjct: 177 GYAHISSALDAASHAVVESGGAGMFVYGVLNRLLLVTGLHHLLNNVAWFLVGDF------ 230 Query: 224 NTVTGDLTRFFAGDPTAGRFMMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVMISAAL 283 TGDL RFFAGDP AG FM G FP M+F LPA LA+ H ARPE++K + G++ S A Sbjct: 231 GGATGDLGRFFAGDPNAGAFMSGFFPVMMFGLPAACLAMYHEARPERRKAVGGMLFSLAF 290 Query: 284 TSMLTGITEPVEFSFLFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYG 343 TS LTG+TEP+EF+F+F+APVLY I+++L GV + D+ ++ G+ FS G DYVLN+ Sbjct: 291 TSFLTGVTEPIEFTFMFLAPVLYAIHAVLTGVAMTLMDMLGIKLGFGFSAGLFDYVLNFK 350 Query: 344 LSTNGWVVIPVGIVFAFIYYYLFRFAILKWNLKTPGRETDEDGQNEEKAPVAKDQLAFHV 403 LST W+++PVG +A IYY LFRF I K +L TPGRE E + ++ A V Sbjct: 351 LSTRPWMLLPVGAAYAVIYYTLFRFFIRKLDLATPGREKGEAVAAAGETAAGNERGAAFV 410 Query: 404 LQALGGQQNIANLDACITRLRVTVHQPSQVCKDELKRLGAVGVLEVN-NNFQAIFGTKSD 462 +ALGG N+ ++DAC TRLR+ V S V L LGA G++ + N Q + G +D Sbjct: 411 -KALGGAANLTSVDACTTRLRLIVADQSAVDDAALNALGARGIIRPSANATQVVLGPIAD 469 Query: 463 ALKDDIKTIMAGGVPATAAA 482 + ++I+ + GG A +AA Sbjct: 470 LVAEEIRGAIGGGAAAVSAA 489 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: 915 Number of extensions: 58 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 631 Length of database: 560 Length adjustment: 37 Effective length of query: 594 Effective length of database: 523 Effective search space: 310662 Effective search space used: 310662 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