Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate 14809 b0679 fused N-acetyl glucosamine specific PTS enzyme: IIC, IIB , and IIA components (NCBI)
Query= SwissProt::P39816 (631 letters) >FitnessBrowser__Keio:14809 Length = 648 Score = 480 bits (1235), Expect = e-140 Identities = 272/631 (43%), Positives = 385/631 (61%), Gaps = 32/631 (5%) Query: 10 QQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAVGVAIGLA-G 68 Q+LGRAL P+AVLP A LLLRFG DLLN+ I AGG +FDNL LIFA+GVA + Sbjct: 8 QRLGRALQLPIAVLPVAALLLRFGQPDLLNVAFIAQAGGAIFDNLALIFAIGVASSWSKD 67 Query: 69 GEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIGLLAAYLYKR 128 G A LA +GY +LT + + + P I+MGV GII GL+ Y R Sbjct: 68 SAGAAALAGAVGYFVLTKAM------VTINPE-------INMGVLAGIITGLVGGAAYNR 114 Query: 129 FSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAASS-LIADSTVGL 187 +S I+L L FF GKRFVPI T LV+ IF +VWP +Q+ I+A +++ +G Sbjct: 115 WSDIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWIVSAGALGS 174 Query: 188 FFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDPTAGRFMMGD 247 + I RLLIP GLH + T +F +GE+T+ + G GD+ RF+AGD TAG FM G Sbjct: 175 GIFGFINRLLIPTGLHQVLNTIAWFQIGEFTN-AAGTVFHGDINRFYAGDGTAGMFMSGF 233 Query: 248 FPYMIFCLPAVALAIIHTARPEKKKMISGVMISAALTSMLTGITEPVEFSFLFVAPVLYL 307 FP M+F LP ALA+ A E++ M+ G+++S A+T+ LTG+TEP+EF F+F+AP+LYL Sbjct: 234 FPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPLLYL 293 Query: 308 INSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGL---STNGWVVIPVGIVFAFIYYY 364 ++++L G+ V L + G++FS G IDY L Y L S N W+++ +G++F IY+ Sbjct: 294 LHALLTGISLFVATLLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLLVMGVIFFAIYFV 353 Query: 365 LFRFAILKWNLKTPGRETDEDGQNEEKAPVAKD----QLAFHVLQALGGQQNIANLDACI 420 +F I +NLKTPGRE ED E+A + QLA + + A+GG N+ +DACI Sbjct: 354 VFSLVIRMFNLKTPGREDKEDEIVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACI 413 Query: 421 TRLRVTVHQPSQVCKDELKRLGAVGVLEVN-NNFQAIFGTKSDALKDDIKTIMAGGVPAT 479 TRLR+TV ++V KRLGA GV+++N Q I G K++++ D +K ++A G A Sbjct: 414 TRLRLTVADSARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAESIGDAMKKVVARGPVAA 473 Query: 480 AAALDT-VTDKPL-KPD------SDETFIYPIKGETVSLGDVPDQVFSEKMMGEGFAIIP 531 A+A T T P+ KP S + PI G+ V+L VPD+ F+ K +G+G A+ P Sbjct: 474 ASAEATPATAAPVAKPQAVPNAVSIAELVSPITGDVVALDQVPDEAFASKAVGDGVAVKP 533 Query: 532 SEGKVVAPADGEIVSIFPTKHAIGFMSAGGTEILIHVGIDTVKLNGEGFEAHVTSGQAVK 591 ++ VV+PA G IV IF T HA + G EI++H+GIDTV L G+GF+ V G V Sbjct: 534 TDKIVVSPAAGTIVKIFNTNHAFCLETEKGAEIVVHMGIDTVALEGKGFKRLVEEGAQVS 593 Query: 592 QGELLLTFDLNYIKQHAASAITPVIFTNTSE 622 G+ +L DL+Y+ +A S I+PV+ +N + Sbjct: 594 AGQPILEMDLDYLNANARSMISPVVCSNIDD 624 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: 1076 Number of extensions: 54 Number of successful extensions: 7 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: 631 Length of database: 648 Length adjustment: 38 Effective length of query: 593 Effective length of database: 610 Effective search space: 361730 Effective search space used: 361730 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: 54 (25.4 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