Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate BWI76_RS08220 BWI76_RS08220 PTS N-acetyl glucosamine transporter subunit IIABC
Query= SwissProt::P39816 (631 letters) >FitnessBrowser__Koxy:BWI76_RS08220 Length = 650 Score = 492 bits (1266), Expect = e-143 Identities = 280/642 (43%), Positives = 387/642 (60%), Gaps = 39/642 (6%) Query: 10 QQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAVGVAIGLA-G 68 Q+LGRAL P+AVLP A LLLRFG DLLNI I AGG +FDNL LIFA+GVA + Sbjct: 8 QRLGRALQLPIAVLPVAALLLRFGQPDLLNISFIAQAGGAIFDNLALIFAIGVASSWSKD 67 Query: 69 GEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIGLLAAYLYKR 128 G A LA +GY +LT + + I+MGV GII GL+ +Y R Sbjct: 68 SAGAAALAGAVGYFVLTKAMVTINPA-------------INMGVLAGIITGLVGGAVYNR 114 Query: 129 FSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAASS-LIADSTVGL 187 +S I+L L FF GKRFVPI T LV+ IF +VWP +QN I+A ++ +G Sbjct: 115 WSGIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQNAIHAGGEWIVGAGALGS 174 Query: 188 FFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDPTAGRFMMGD 247 + I RLLIP GLH + T +F +GE+T+ + G GD+ RF+AGD TAG FM G Sbjct: 175 GIFGFINRLLIPTGLHQVLNTIAWFQIGEFTN-AAGAVFHGDINRFYAGDGTAGMFMSGF 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 FPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAITAFLTGVTEPLEFLFMFLAPLLYL 293 Query: 308 INSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGL---STNGWVVIPVGIVFAFIYYY 364 +++IL G+ V + G++FS G IDYVL Y L S N W++I +G+VF IY+ Sbjct: 294 LHAILTGISLFVATALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLIVMGVVFFVIYFL 353 Query: 365 LFRFAILKWNLKTPGRE-------TDEDGQNEEKAPVAKDQLAFHVLQALGGQQNIANLD 417 LF I +NLKTPGRE T+E N E+ QLA + + A+GG N+ +D Sbjct: 354 LFSAVIRMFNLKTPGREDKVDDVVTEEANSNTEE---GLTQLATNYIAAVGGTDNLKAID 410 Query: 418 ACITRLRVTVHQPSQVCKDELKRLGAVGVLEVN-NNFQAIFGTKSDALKDDIKTIMAGGV 476 ACITRLR+TV + V KRLGA GV+++N Q I G K++++ D++K ++A G Sbjct: 411 ACITRLRLTVADSALVNDAACKRLGASGVVKLNKQTIQVIVGAKAESVGDEMKKVVARGP 470 Query: 477 PATAAALD---TVTDKPLKPD------SDETFIYPIKGETVSLGDVPDQVFSEKMMGEGF 527 A AAA V + +KP + E + PI G+ V+L VPD+ F+ K +G+G Sbjct: 471 VAAAAAASHSAPVAAQAVKPQAVANAKTVEALVSPITGDIVALEQVPDEAFASKAVGDGV 530 Query: 528 AIIPSEGKVVAPADGEIVSIFPTKHAIGFMSAGGTEILIHVGIDTVKLNGEGFEAHVTSG 587 A+ P++ VVAPA G +V IF T HA + G EI++H+GIDTV LNG+GF+ V G Sbjct: 531 AVKPTDKIVVAPAAGTVVKIFNTNHAFCLETENGAEIVVHMGIDTVALNGQGFKRLVEEG 590 Query: 588 QAVKQGELLLTFDLNYIKQHAASAITPVIFTNTSEEDLKHIQ 629 VK GE +L DL ++ +A S I+PV+ +N+ + IQ Sbjct: 591 AEVKAGEPILELDLEFLNANARSMISPVVCSNSDDYSALVIQ 632 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: 1052 Number of extensions: 55 Number of successful extensions: 8 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: 650 Length adjustment: 38 Effective length of query: 593 Effective length of database: 612 Effective search space: 362916 Effective search space used: 362916 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