Align PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized)
to candidate BWI76_RS08220 BWI76_RS08220 PTS N-acetyl glucosamine transporter subunit IIABC
Query= SwissProt::P37439 (477 letters) >FitnessBrowser__Koxy:BWI76_RS08220 Length = 650 Score = 382 bits (980), Expect = e-110 Identities = 204/485 (42%), Positives = 304/485 (62%), Gaps = 34/485 (7%) Query: 4 NAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMPLIF 63 N Q++G++L LP++VLP+A +LL G + + + A+AGG++F N+ LIF Sbjct: 2 NILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLNISFI-----AQAGGAIFDNLALIF 56 Query: 64 AIGVALGFTNND-GVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIAAKHLADTGVLGGI 122 AIGVA ++ + G +ALA V Y ++ K M + P + + GVL GI Sbjct: 57 AIGVASSWSKDSAGAAALAGAVGYFVLTKAMVTINPAI--------------NMGVLAGI 102 Query: 123 ISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFVWPPIGTAIQAF 182 I+G + ++NR+ IKLP++L FF GKRFVPI +G + + +VWPP+ AI A Sbjct: 103 ITGLVGGAVYNRWSGIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQNAIHAG 162 Query: 183 SQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYMA 242 +W + GI+GFI R L+P GLH + N QIGE+TNAAG VFHGDI R+ A Sbjct: 163 GEWIVGAG-ALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGAVFHGDINRFYA 221 Query: 243 GDPTAGM-LSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIE 301 GD TAGM +SG F M+GLP AA+A++ +A E R VGG+++S A+T+FLTG+TEP+E Sbjct: 222 GDGTAGMFMSGFFPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAITAFLTGVTEPLE 281 Query: 302 FSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIV---LSGNSSKLWLFP 358 F FMF+AP+LY++HAIL G++ + LG+ G SFS G ID+++ L S +W+ Sbjct: 282 FLFMFLAPLLYLLHAILTGISLFVATALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLI 341 Query: 359 IVGAGYAIVYYTVFRVLIKALDLKTPGREDTTDDA---KAGATSE-----MAPALVAAFG 410 ++G + ++Y+ +F +I+ +LKTPGRED DD +A + +E +A +AA G Sbjct: 342 VMGVVFFVIYFLLFSAVIRMFNLKTPGREDKVDDVVTEEANSNTEEGLTQLATNYIAAVG 401 Query: 411 GKENITNLDACITRLRVSVADVAKVDQAGLKKLGAAGVV-VAGSGVQAIFGTKSDNLKTE 469 G +N+ +DACITRLR++VAD A V+ A K+LGA+GVV + +Q I G K++++ E Sbjct: 402 GTDNLKAIDACITRLRLTVADSALVNDAACKRLGASGVVKLNKQTIQVIVGAKAESVGDE 461 Query: 470 MDEYI 474 M + + Sbjct: 462 MKKVV 466 Lambda K H 0.325 0.140 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: 851 Number of extensions: 50 Number of successful extensions: 9 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: 477 Length of database: 650 Length adjustment: 36 Effective length of query: 441 Effective length of database: 614 Effective search space: 270774 Effective search space used: 270774 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