Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate BWI76_RS11130 BWI76_RS11130 PTS glucose transporter subunit IIBC
Query= BRENDA::P45604 (651 letters) >FitnessBrowser__Koxy:BWI76_RS11130 Length = 477 Score = 381 bits (978), Expect = e-110 Identities = 204/485 (42%), Positives = 307/485 (63%), Gaps = 34/485 (7%) Query: 2 NILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLNVPFI-----AQAGGAIFDNLALIF 56 N Q++G++L LP++VLP+A +LL G + +P + A+AGG++F N+ LIF Sbjct: 4 NAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMPLIF 63 Query: 57 AIGVASSWSKDNAGSAALAGAVGYFVMTKAMVTINPEI--------------NMGVLAGI 102 AIGVA ++ +N G +ALA V Y +M K M + P + + GVL GI Sbjct: 64 AIGVALGFT-NNDGVSALASVVAYGIMVKTMSVVAPLVLHLPAEEIAAKHLADTGVLGGI 122 Query: 103 ITGLVAGAVYNRWAGIKLPDFLSFFGGKRFVPIATGFFCLILAAIFGYVWPPVQHAIHSG 162 I+G +A ++NR+ IKLP++L FF GKRFVPI +G + I ++WPP+ AI + Sbjct: 123 ISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVILSFIWPPIGTAIQTF 182 Query: 163 GEWIVSAG-ALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYA 221 +W + GI+GFI R L+P GLH + N QIGE+TNAAG VFHGDI R+ A Sbjct: 183 SQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYMA 242 Query: 222 GDGTAGMFMSGFFPIMMFGLPGAALAMYLAAPKARRPMVGGMLLSVAITAFLTGVTEPLE 281 GD TAG +SG F M+GLP AA+A++ +A R VGG+++S A+T+FLTG+TEP+E Sbjct: 243 GDPTAGK-LSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIE 301 Query: 282 FLFLFLAPLLYLLHAVLTGISLFIATALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLL 341 F F+F+AP+LY++HA+L G++ I LG+ G SFS G ID+++ L S +W+ Sbjct: 302 FSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIV---LSGNSSKLWLFP 358 Query: 342 VMGVVFFFVYFLLFSAVIRMFNLKTPGREDKAADVVTEEANSNTEEGLTQLATSYIAAVG 401 ++G+ + VY+++F +I+ +LKTPGRED TE++ + +++A + IAA G Sbjct: 359 IVGICYAIVYYVVFRVLIKALDLKTPGRED-----ATEDSKAG---ATSEMAPALIAAFG 410 Query: 402 GTDNLKAIDACITRLRLTVGDSAKVNDAACKRLGASGVVKLNKQTIQVIVGAKAESIGDE 461 G +N+ +DACITRLR++V D AKV+ A K+LGA+GVV + +Q I G K++++ E Sbjct: 411 GKENITNLDACITRLRVSVADVAKVDQAGLKKLGAAGVV-VAGSGVQAIFGTKSDNLKTE 469 Query: 462 MKKVV 466 M + + Sbjct: 470 MDEYI 474 Lambda K H 0.323 0.138 0.406 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: 747 Number of extensions: 42 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: 651 Length of database: 477 Length adjustment: 36 Effective length of query: 615 Effective length of database: 441 Effective search space: 271215 Effective search space used: 271215 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 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